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Azizoglu, A;Stelling, J | 10.1042/BST20190295 | null | 1ST FLR, 10 QUEEN STREET PLACE, LONDON, ENGLAND | 3034bk443e3q612p1s442q316z3m202t642527 | Controlling cell-to-cell variability with synthetic gene circuits | Swiss Fed Inst Technol | null | Stelling, J (corresponding author), Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland. | null | Azizoglu, Asli;Stelling, Jorg | Biochemistry & Molecular Biology | NCCR Molecular Systems Engineering - Swiss National Science Foundation | WOS | Stelling, J | Swiss Fed Inst Technol, Basel, Switzerland | 47 | cell-to-cell;circuits;controlling;gene;synthetic;variability;with | 1 | Azizoglu, Asli | PORTLAND PRESS LTD | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland;Swiss Fed Inst Technol, SIB Swiss Inst Bioinformat, CH-4058 Basel, Switzerland | Review | Swiss Fed Inst Technol | LONDON | null | null | Swiss Fed Inst Technol | NCCR Molecular Systems Engineering - Swiss National Science Foundation | Stelling, J (corresponding author), Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland. | 1804 | Azizoglu, Asli;Stelling, Jorg | 12 | 2 | 509,882,600,018 | NCCR Molecular Systems Engineering - Swiss National Science Foundation | Switzerland | BIOCHEMICAL SOCIETY TRANSACTIONS | Switzerland | null | null | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland | 0300-5127 | Azizoglu, A;Stelling, J | DEC | joerg.stelling@bsse.ethz.ch | controlling cell-to-cell variability;synthetic gene circuits | 2 | J | Biochemistry & Molecular Biology | BIOLOGICAL NOISE;BIOLOGY;broad synthetic toolset;cell-to-cell variability;closed-loop;combination;components;control;controlling cell-to-cell variability;DEGRADATION;DESIGN;designing synthetic gene;drawing;engineering;exploration;expression;extensions;gene expression;help understanding natural functions;HETEROGENEITY;independent regulation;individual genes;instrumental;intrinsic noise;intrinsic stochasticity;major conceptual advances will;mean expression;natural systems;networks;new synthetic functions;new theory;noise control;noise reduction;noise shaping;origins;perspective;presents challenges;reducing noise;REVEALS;robust operation;single genes;STOCHASTICITY;synthetic biology approaches;synthetic feedback circuits;synthetic gene circuits;systematic considerations;traditional engineering concepts;TRANSCRIPTION;translation mechanisms;uncovering mechanisms underlying variability;variability | Azizoglu, A | BIOLOGICAL NOISE;DEGRADATION;DESIGN;EXPRESSION;HETEROGENEITY;REVEALS;STOCHASTICITY | 1795 | [Azizoglu, Asli; Stelling, Jorg] Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland. [Azizoglu, Asli; Stelling, Jorg] Swiss Fed Inst Technol, SIB Swiss Inst Bioinformat, CH-4058 Basel, Switzerland. | We acknowledge financial support by the NCCR Molecular Systems Engineering funded by the Swiss National Science Foundation. | biology;broad synthetic toolset;cell-to-cell variability;closed-loop;combination;components;control;designing synthetic gene;drawing;engineering;exploration;extensions;gene expression;help understanding natural functions;independent regulation;individual genes;instrumental;intrinsic noise;intrinsic stochasticity;major conceptual advances will;mean expression;natural systems;networks;new synthetic functions;new theory;noise control;noise reduction;noise shaping;origins;perspective;presents challenges;reducing noise;robust operation;single genes;synthetic biology approaches;synthetic feedback circuits;systematic considerations;traditional engineering concepts;transcription;translation mechanisms;uncovering mechanisms underlying variability;variability | 10.1016/j.arcontrol.2018.04.007;10.1016/j.bpj.2010.01.018;10.1016/j.cell.2008.09.050;10.1016/j.cell.2011.01.030;10.1016/j.cell.2014.02.039;10.1016/j.celrep.2019.03.001;10.1016/j.cels.2015.10.011;10.1016/j.cels.2018.08.002;10.1016/j.jmb.2004.09.073;10.1016/j.jtbi.2016.02.004;10.1016/j.mib.2016.07.009;10.1016/j.plrev.2005.03.003;10.1016/j.synbio.2017.09.003;10.1016/j.tibtech.2019.03.016;10.1021/acssynbio.6b00014;10.1021/acssynbio.6b00189;10.1021/acssynbio.6b00251;10.1021/acssynbio.7b00087;10.1021/acssynbio.7b00122;10.1021/acssynbio.8b00029;10.1021/acssynbio.8b00279;10.1021/sb300116y;10.1038/35002125;10.1038/35014651;10.1038/nature01546;10.1038/nature03998;10.1038/nature04785;10.1038/nature14244;10.1038/nature19841;10.1038/ncomms2471;10.1038/ncomms5761;10.1038/ng869;10.1038/nrmicro3239;10.1038/nrmicro3491;10.1038/s41467-018-02898-6;10.1038/s41467-018-05882-2;10.1038/s41467-018-07391-8;10.1038/s41467-019-10330-w;10.1038/s41467-019-11116-w;10.1038/s41576-019-0130-6;10.1038/s41586-019-1321-1;10.1039/c7me00032d;10.1042/BST20180500;10.1073/pnas.0408507102;10.1073/pnas.0608451104;10.1073/pnas.0809901106;10.1073/pnas.1416533112;10.1073/pnas.151588598;10.1073/pnas.162041399;10.1088/0034-4885/77/2/026601;10.1093/nar/gkq091;10.1093/nar/gku126;10.1093/nar/gkw1194;10.1098/rsif.2016.0380;10.1098/rsif.2018.0079;10.1101/492207];10.1101/gr.168773.113;10.1101/gr.178426.114;10.1101/gr.191635.115;10.1103/PhysRevE.95.062418;10.1109/MCS.2018.2810459;10.1111/1567-1364.12188;10.1126/science.1070919;10.1126/science.1098641;10.1126/science.1188308;10.1126/science.aac7341;10.1146/annurev-biophys-070816-033903;10.1186/s13036-017-0068-1;10.1371/journal.pbio.0020137;10.1371/journal.pcbi.1002140;10.1371/journal.pcbi.1002644;10.1371/journal.pcbi.1003161;10.1371/journal.pgen.1005206;10.7554/eLife.37272;[10.1016/j.cels.2016.01.004, 10.1016/j.cels.2016.02.010] | Swiss Fed Inst Technol | Azizoglu, A;Stelling, J | Azizoglu, A: Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland | null | null | 75 | null | Switzerland | Swiss Fed Inst Technol | Azizoglu, Asli | Green Accepted | BIOLOGICAL NOISE;DEGRADATION;DESIGN;EXPRESSION;HETEROGENEITY;REVEALS;STOCHASTICITY | Azizoglu, Asli; Stelling, Jorg; | null | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland;Swiss Fed Inst Technol, SIB Swiss Inst Bioinformat, CH-4058 Basel, Switzerland | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland;Swiss Fed Inst Technol, SIB Swiss Inst Bioinformat, CH-4058 Basel, Switzerland | 1470-8752 | null | null | 2000;2001;2002;2003;2004;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017;2018;2019 | 3 | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland | Biochem. Soc. Trans. | Stelling, Jorg | PORTLAND PRESS LTD | ,;a;achieve;adapted;advances;also;an;and;approaches;are;argue;biology;broad;but;by;cell-to-cell;challenges;circuits;closed-loop;combination;components;concepts;conceptual;considerations;control;conversely;could;designing;drawing;either;engineering;establish;established;example;exploration;expression;extending;extensions;feedback;field;focus;for;from;functions;gene;genes;has;help;how;in;includes;independent;individual;individually;instead;instrumental;intrinsic;its;major;mean;mechanisms;more;natural;networks;new;noise;of;on;operation;or;originating;origins;other;perform;perspective;presents;reducing;reduction;regulation;require;robust;robustly;shaping;single;stochasticity;synthetic;systematic;systems;than;that;the;theory;these;this;to;toolset;traditional;transcription;translation;uncovering;underlying;understanding;use;variability;we;will;with | Swiss Fed Inst Technol | Cell-to-cell variability originating, for example, from the intrinsic stochasticity of gene expression, presents challenges for designing synthetic gene circuits that perform robustly. Conversely, synthetic biology approaches are instrumental in uncovering mechanisms underlying variability in natural systems. With a focus on reducing noise in individual genes, the field has established a broad synthetic toolset. This includes noise control by engineering of transcription and translation mechanisms either individually, or in combination to achieve independent regulation of mean expression and its variability. Synthetic feedback circuits use these components to establish more robust operation in closed-loop, either by drawing on, but also by extending traditional engineering concepts. In this perspective, we argue that major conceptual advances will require new theory of control adapted to biology, extensions from single genes to networks, more systematic considerations of origins of variability other than intrinsic noise, and an exploration of how noise shaping, instead of noise reduction, could establish new synthetic functions or help understanding natural functions. | null | BIOLOGICAL NOISE;DEGRADATION;DESIGN;EXPRESSION;HETEROGENEITY;REVEALS;STOCHASTICITY | 1 | null | null | 10 | BIOLOGICAL NOISE;DEGRADATION;DESIGN;EXPRESSION;HETEROGENEITY;REVEALS;STOCHASTICITY | WOS:000509882600018 | Swiss Fed Inst Technol, Basel, Switzerland | Switzerland | 2,019 | null | 0000-0002-2600-1322 | null | null | English | null | ACS SYNTH BIOL;ANNU REV BIOPHYS;ANNU REV CONTROL;BIOCHEM SOC T;BIOPHYS J;CELL;CELL REP;CELL SYST;CODON DEPENDENT NOIS;CURR OPIN MICROBIOL;ELIFE;FEMS YEAST RES;GENOME RES;IEEE CONTR SYST MAG;J Biol Eng;J MOL BIOL;J R SOC INTERFACE;J THEOR BIOL;MOL SYST DES ENG;NAT COMMUN;NAT GENET;NAT REV GENET;NAT REV MICROBIOL;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PHYS LIFE REV;PHYS REV E;PLOS BIOL;PLOS COMPUT BIOL;PLOS GENET;REP PROG PHYS;SCIENCE;SYN SYST BIOTECHNO;TRENDS BIOTECHNOL | Azizoglu, Asli;Stelling, Jorg | 2024-03-11
ER | Ackermann, M;Aoki, S K;Aranda-Díaz, A;Balleza E.;Balázsi, G;Bandiera, L;Bashor, C J;Baudrimont, A;Becskei, A;Benzinger, D;Blake, W J;Boada, Y;Borkowski, O;Briat, C;Butzin, N C;Cameron, D E;Caveney, P M;Cole, J A;Colman-Lerner, A;Csárdi, G;Darlington, A P S;Del Vecchio, D;Duveau, F;Eling, N;Elowitz, M B;Engl, C;Engstrom, M D;Farquhar, K S;Fraser, H B;Guantes, R;Guimaraes, J C;Hansen, M M K;Hausser, J;Hooshangi, S;Hsiao, V;Karamasioti, E;Keren, L;Li, J;Marquez-Lago, T T;Meng, X;Metzger, B P H;Mundt, M;Murphy, K F;Nevozhay, D;Newman, J R S;Nielsen, A A K;Ozbudak, E M;Paulsson, J;Potvin-Trottier, L;Raj, A;Raser, J M;Redden, H;Salari, R;Schmiedel, J M;Sharon, E;Sherman, M S;Shu, C C;Swain, P S;Taniguchi, Y;Thattai, M;Tsimring, L S;Vandemoortele, G;Way, J C;Weisse, A Y;Yamanishi, M;Yang, S;Zopf, C J | KG3ZR | Basel, Switzerland | 6 | null | 1 | 6 | 31,803,907 | Azizoglu, Asli;Stelling, Jorg | BIOCHEM SOC T | Basel, Switzerland |
Bagh, S;Bonnerjee, D;Mukhopadhyay, S | 10.1021/acs.bioconjchem.9b00517 | null | 1155 16TH ST, NW, WASHINGTON, DC 20036 USA | 545c2z6o1z191w37c51z571d2v4p1d4o1723f | Design, Fabrication, and Device Chemistry of a 3-Input-3-Output Synthetic Genetic Combinatorial Logic Circuit with a 3-Input AND Gate in a Single Bacterial Cell | Homi Bhabha Natl Inst HBNI | null | Bagh, S (corresponding author), Homi Bhabha Natl Inst, Biophys & Struct Genom Div, Saha Inst Nucl Phys, Block A-F,Sect 1, Kolkata 700064, India. | null | Bagh, Sangram;Bonnerjee, Deepro;Mukhopadhyay, Sayak | Biochemical Research Methods;Biochemistry & Molecular Biology;Chemistry, Multidisciplinary;Chemistry, Organic | SINP intramural funding (Department of Atomic Energy, Govt. of India); SERB [CRG/201B/001394]; Ramanujan Felowship (DST), Govt. of India | WOS | Bagh, S | Homi Bhabha Natl Inst, Kolkata, India | 30 | ,;3-Input;3-Input-3-Output;a;and;Bacterial;cell;chemistry;circuit;Combinatorial;design;device;Fabrication;gate;genetic;in;logic;of;Single;synthetic;with | 1 | Bagh, Sangram;Bonnerjee, Deepro;mukhopadhyay, sayak | AMER CHEMICAL SOC | Homi Bhabha Natl Inst, Biophys & Struct Genom Div, Saha Inst Nucl Phys, Block A-F,Sect 1, Kolkata 700064, India | Article | Homi Bhabha Natl Inst | WASHINGTON | null | null | Homi Bhabha Natl Inst | Ramanujan Felowship (DST), Govt. of India;SERB;SINP intramural funding (Department of Atomic Energy, Govt. of India) | Bagh, S (corresponding author), Homi Bhabha Natl Inst, Biophys & Struct Genom Div, Saha Inst Nucl Phys, Block A-F,Sect 1, Kolkata 700064, India. | 3020 | Bagh, Sangram;Bonnerjee, Deepro;Mukhopadhyay, Sayak | 25 | 1 | 503,917,900,004 | Ramanujan Felowship (DST), Govt. of India;SERB [CRG/201B/001394];SINP intramural funding (Department of Atomic Energy, Govt. of India) | India | BIOCONJUGATE CHEMISTRY | India | null | null | Homi Bhabha Natl Inst, Biophys & Struct Genom Div, Saha Inst Nucl Phys, Block A-F,Sect 1, Kolkata 700064, India | 1043-1802 | Bagh, S;Bonnerjee, D;Mukhopadhyay, S | DEC | sangram.bagh@saha.ac.in | 3-Input;3-Input-3-Output Synthetic Genetic Combinatorial Logic Circuit;Device Chemistry;Fabrication;Gate;Single Bacterial Cell | 3 | J | Biochemistry & Molecular Biology;Chemistry | 128 bp DNA scaffold;3-Input;3-input-3-output combinatorial logic circuit;3-input-3-output synthetic genetic circuit;3-Input-3-Output Synthetic Genetic Combinatorial Logic Circuit;advancement;BACTERIA;BINDING;BIOLOGY;biorobotics;circuit;circuit integrated three extracellular chemical signals;circuit minimization;complex systems level device chemistry;conjugated promoter engineering approach;cross-talk;Device Chemistry;digital-like;DNA;DNA nanotechnology;ESCHERICHIA-COLI;expression;Fabrication;few times;first;first 3-input-3-output logic function;first time;Gate;gate promoter reported;gates;higher number;hybrid promoter;in-cell molecular computation;increased physical size;inputs;integration;larger circuit;molecular computation;molecular interactions;multi-input-multi-output devices;multi-input-multi-output genetic logic devices;nature;new 2-input-2-output integrated circuit;noncascaded 1-gate-3-input synthetic;outputs;previous 3-input;principles;produced three different fluorescent proteins;protein-binding sites;realization;SCAFFOLD;SIGNIFICANCE;similar 3-input synthetic;Single Bacterial Cell;single piece;specificity;synthetic biology;truth table;two important characteristics | Bonnerjee, D | BINDING;BIOLOGY;ESCHERICHIA-COLI;EXPRESSION;PRINCIPLES;SPECIFICITY | 3013 | [Bonnerjee, Deepro; Mukhopadhyay, Sayak; Bagh, Sangram] Homi Bhabha Natl Inst, Biophys & Struct Genom Div, Saha Inst Nucl Phys, Block A-F,Sect 1, Kolkata 700064, India. | This work was financially supported by SINP intramural funding (Department of Atomic Energy, Govt. of India), SERB (CRG/201B/001394) and Ramanujan Felowship (DST), Govt. of India. | 128 bp DNA scaffold;3-input;3-input-3-output combinatorial logic circuit;3-input-3-output synthetic genetic circuit;advancement;bacteria;biorobotics;circuit;circuit integrated three extracellular chemical signals;circuit minimization;complex systems level device chemistry;conjugated promoter engineering approach;cross-talk;digital-like;DNA;DNA nanotechnology;few times;first;first 3-input-3-output logic function;first time;gate;gate promoter reported;gates;higher number;hybrid promoter;in-cell molecular computation;increased physical size;inputs;integration;larger circuit;molecular computation;molecular interactions;multi-input-multi-output devices;multi-input-multi-output genetic logic devices;nature;new 2-input-2-output integrated circuit;noncascaded 1-gate-3-input synthetic;outputs;previous 3-input;produced three different fluorescent proteins;protein-binding sites;realization;scaffold;SIGNIFICANCE;similar 3-input synthetic;single bacterial cell;single piece;synthetic biology;truth table;two important characteristics | 10.1002/biot.201300258;10.1007/s11047-018-9715-9;10.1016/j.bios.2012.08.011;10.1016/j.bpj.2009.08.050;10.1016/j.jmb.2015.10.004;10.1016/j.tibtech.2014.11.009;10.1016/S0092-8674(03)01077-8;10.1021/acs.nanolett.8b00526;10.1021/acssynbio.5b00124;10.1021/acssynbio.6b00057;10.1038/msb4100173;10.1038/nature11516;10.1038/nrm2698;10.1038/s41467-019-12021-y;10.1038/s41580-018-0024-z;10.1038/sj.gt.3302761;10.1073/pnas.0408507102;10.1073/pnas.1816591116;10.1093/nar/25.6.1203;10.1093/nar/gks973;10.1103/PhysRevE.77.021919;10.1103/PhysRevE.82.021911;10.1126/science.1232758;10.1128/JB.00427-09;10.1128/JB.186.3.631-637.2004;10.1186/s13036-019-0151-x;[10.1038/NMETH.2926, 10.1038/nmeth.2926];[10.1038/s41467-017-02473-5, 10.1038/s41467-018-05683-7] | Homi Bhabha Natl Inst | Bagh, S;Bonnerjee, D;Mukhopadhyay, S | Bonnerjee, D: Homi Bhabha Natl Inst, Biophys & Struct Genom Div, Saha Inst Nucl Phys, Block A-F,Sect 1, Kolkata 700064, India | mukhopadhyay, sayak | CRG/201B/001394 | 29 | null | India | Homi Bhabha Natl Inst | Bonnerjee, Deepro | null | BINDING;BIOLOGY;ESCHERICHIA-COLI;EXPRESSION;PRINCIPLES;SPECIFICITY | Bonnerjee, Deepro; Mukhopadhyay, Sayak; Bagh, Sangram; | null | Homi Bhabha Natl Inst, Biophys & Struct Genom Div, Saha Inst Nucl Phys, Block A-F,Sect 1, Kolkata 700064, India | Homi Bhabha Natl Inst, Biophys & Struct Genom Div, Saha Inst Nucl Phys, Block A-F,Sect 1, Kolkata 700064, India | 1520-4812 | null | 12 | 1997;2004;2005;2006;2007;2008;2009;2010;2012;2013;2014;2015;2016;2018;2019 | 8 | Homi Bhabha Natl Inst, Biophys & Struct Genom Div, Saha Inst Nucl Phys, Block A-F,Sect 1, Kolkata 700064, India | Bioconjugate Chem. | Bagh, Sangram | AMER CHEMICAL SOC | ,;1-gate-3-input;128;2-input-2-output;3-input;3-input-3-output;a;adapting;advancement;also;and;approach;as;bacteria;bacterial;biology;biorobotics;both;bp;by;cell;characteristics;chemical;chemistry;circuit;combinatorial;complex;computation;conjugated;consists;created;cross-talk;demonstrated;design;device;devices;different;digital;digital-like;DNA;engineering;extracellular;few;first;fluorescent;following;for;function;gate;gates;genetic;has;here;higher;however;hybrid;important;in;in-cell;increased;inputs;integrated;integrating;integration;interactions;larger;level;limited;logic;mathematically;minimization;molecular;multi-input-multi-output;nanotechnology;nature;new;noncascaded;not;number;of;our;outputs;physical;piece;predictable;predictive;previous;produced;promoter;protein-binding;proteins;realization;reported;requires;scaffold;showed;signals;SIGNIFICANCE;similar;single;sites;size;smaller;such;synthetic;systems;table;than;that;the;this;three;time;times;truth;two;various;was;we;were;which;with;work;worked | Homi Bhabha Natl Inst | Advancement of in-cell molecular computation requires multi-input-multi-output genetic logic devices. However, increased physical size, a higher number of molecular interactions, cross-talk, and complex systems level device chemistry limited the realization of such multi-input-multi-output devices in a single bacterial cell. Here, by adapting a circuit minimization and conjugated promoter engineering approach, we created the first 3-input-3-output logic function in a single bacterial cell. The circuit integrated three extracellular chemical signals as inputs and produced three different fluorescent proteins as outputs following the truth table of the circuit. First, we created a noncascaded 1-gate-3-input synthetic genetic AND gate in bacteria. We showed that the 3-input AND gate was digital in nature and mathematically predictable, two important characteristics, which were not reported for previous 3-input AND gates in bacteria. Our design consists of a 128 bp DNA scaffold, which conjugated various protein-binding sites in a single piece of DNA and worked as a hybrid promoter. The scaffold was a few times smaller than the similar 3-input synthetic genetic AND gate promoter reported. Integrating this AND gate with a new 2-input-2-output integrated circuit, which was also digital-like and predictive, we created a 3-input-3-output combinatorial logic circuit. This work demonstrated the integration of a 3-input AND gate in a larger circuit and a 3-input-3-output synthetic genetic circuit, both for the first time. The work has significance in molecular computation, biorobotics, DNA nanotechnology, and synthetic biology. | HJI-3440-2023 | BINDING;BIOLOGY;ESCHERICHIA-COLI;EXPRESSION;PRINCIPLES;SPECIFICITY | 0 | null | null | 8 | ESCHERICHIA-COLI;BINDING;BIOLOGY;EXPRESSION;PRINCIPLES;SPECIFICITY | WOS:000503917900004 | Homi Bhabha Natl Inst, Kolkata, India | India | 2,019 | null | 0000-0002-2172-6893;0000-0002-5736-0993;0000-0002-8565-0728 | null | null | English | null | ACS SYNTH BIOL;BIOPHYS J;BIOSENS BIOELECTRON;BIOTECHNOL J;CELL;ELECT C COMPUTATIONA;GENE THER;J BACTERIOL;J Biol Eng;J MOL BIOL;MOL SYST BIOL;NANO LETT;NAT COMMUN;NAT COMPUT;NAT METHODS;NAT REV MOL CELL BIO;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PHYS REV E;SCIENCE;TRENDS BIOTECHNOL | Bagh, Sangram;Bonnerjee, Deepro;Mukhopadhyay, Sayak | 2024-03-11
ER | Aleksandrov, A;Anderson, J C;Bagh, S;Bonnet, J;Bradley, R W;Brophy, J A N;Chen, Y;Del Vecchio, D;Fink, T L;Hirahara S.;Hooshangi, S;Iverson, S V;Lutz, R;Magaraci, M S;Mekler, V;Moon, T S;Müller, I E;Oehler, S;Pawson, T;Purnick, P E M;Roquet, N;Sarkar, K;Schwarz-Schilling, M;Swank, Z;Urbanowski, A L;Wang, B J;Xiang, Y Y;Xie, M Q | JX7NR | Kolkata, India | 8 | null | 1 | null | 31,596,072 | Bagh, Sangram;Bonnerjee, Deepro;Mukhopadhyay, Sayak | BIOCONJUGATE CHEM | Kolkata, India |
Bovenberg, R A L;Büttel, Z;Driessen, A J M;Mózsik, L;Nygård, Y | 10.1186/s12934-019-1253-3 | 203 | CAMPUS, 4 CRINAN ST, LONDON N1 9XW, ENGLAND | 9601h2m696ay6g5g5a6t146m5p2c664a56b3s | Synthetic control devices for gene regulation in <i>Penicillium chrysogenum</i> | Univ Groningen | null | Nygård, Y (corresponding author), Chalmers Univ Technol, Dept Biol & Biol Engn, Div Ind Biotechnol, Kemivagen 10, S-41296 Gothenburg, Sweden.;Nygård, Y (corresponding author), DSM Biotechnol Ctr, Alexander Fleminglaan 1, NL-2613 AX Delft, Netherlands.;Nygård, Y (corresponding author), Univ Groningen, Groningen Biomol Sci & Biotechnol Inst, Mol Microbiol, Nijenborgh 7, NL-9747 AG Groningen, Netherlands. | null | Bovenberg, Roel A L;Buttel, Zsofia;Driessen, Arnold J M;Mozsik, Laszlo;Nygard, Yvonne | Biotechnology & Applied Microbiology | People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme FP7/2007-2013/, under REA [607332]; European Union's Horizon 2020 Research and Innovation Programme under the Marie Sklodowska-Curie [713482] | WOS | Nygård, Y | Chalmers Univ Technol, Gothenburg, Sweden;DSM Biotechnol Ctr, Delft, Netherlands;Univ Groningen, Groningen, Netherlands | 18 | <i>Penicillium;chrysogenum</i>;control;devices;for;gene;in;regulation;synthetic | 2 | Buttel, Zsofia;Mozsik, Laszlo;Nygård, Yvonne | BMC | Chalmers Univ Technol, Dept Biol & Biol Engn, Div Ind Biotechnol, Kemivagen 10, S-41296 Gothenburg, Sweden;DSM Biotechnol Ctr, Alexander Fleminglaan 1, NL-2613 AX Delft, Netherlands;Univ Groningen, Groningen Biomol Sci & Biotechnol Inst, Mol Microbiol, Nijenborgh 7, NL-9747 AG Groningen, Netherlands;Univ Groningen, Groningen Biomol Sci & Biotechnol Inst, Mol Microbiol, Nijenborgh 7, NL-9747 AG Groningen, Netherlands.; Nygård, Y (corresponding author), DSM Biotechnol Ctr, Alexander Fleminglaan 1, NL-2613 AX Delft, Netherlands.; Nygård, Y (corresponding author), Chalmers Univ Technol, Dept Biol & Biol Engn, Div Ind Biotechnol, Kemivagen 10, S-41296 Gothenburg, Sweden;Univ Groningen, Groningen Biomol Sci & Biotechnol Inst, Synthet Biol & Cell Engn, Nijenborgh 7, NL-9747 AG Groningen, Netherlands | Article | Chalmers Univ Technol;DSM Biotechnol Ctr;Univ Groningen | LONDON | null | null | Chalmers Univ Technol;DSM Biotechnol Ctr;Univ Groningen | European Union's Horizon 2020 Research and Innovation Programme under the Marie Sklodowska-Curie;People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme FP7/2007-2013/, under REA | Nygård, Y (corresponding author), Univ Groningen, Groningen Biomol Sci & Biotechnol Inst, Mol Microbiol, Nijenborgh 7, NL-9747 AG Groningen, Netherlands.; Nygård, Y (corresponding author), DSM Biotechnol Ctr, Alexander Fleminglaan 1, NL-2613 AX Delft, Netherlands.; Nygård, Y (corresponding author), Chalmers Univ Technol, Dept Biol & Biol Engn, Div Ind Biotechnol, Kemivagen 10, S-41296 Gothenburg, Sweden. | null | Bovenberg, Roel A L;Buttel, Zsofia;Driessen, Arnold J M;Mozsik, Laszlo;Nygard, Yvonne | 7 | 4 | 511,651,300,003 | European Union's Horizon 2020 Research and Innovation Programme under the Marie Sklodowska-Curie [713482];People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme FP7/2007-2013/, under REA [607332] | Netherlands;Sweden | MICROBIAL CELL FACTORIES | Netherlands;Sweden | null | null | Univ Groningen, Groningen Biomol Sci & Biotechnol Inst, Mol Microbiol, Nijenborgh 7, NL-9747 AG Groningen, Netherlands | null | Bovenberg, R A L;Büttel, Z;Driessen, A J M;Mózsik, L;Nygård, Y | NOV 18 | yvonne.nygard@chalmers.se | <i>Penicillium chrysogenum</i>;gene regulation;synthetic control devices | 5 | J | Biotechnology & Applied Microbiology | <i>Penicillium chrysogenum</i>;affinity;application;background;binds;characterization;CLUSTER;compounds;conclusions;conditions;control device;control devices;CORE PROMOTERS;devices function;DNA binding domain;excellent indications;expression;EXPRESSION SYSTEM;filamentous fungi;fluorescent reporters;GENE;gene cluster;gene regulation;genes;great advantage;highest expressed native genes;Hybrid transcription factor;level;main components;microbioreactors;model filamentous fungus;Neurospora crassa;ORGANIZATION;PARTS;penicillin;Penicillium chrysogenum;performing control devices;production;production strains;PROTEIN;Q-SYSTEM;QF DNA-binding domain;quinic acid gene cluster;quinic acid upstream activating sequence (QUAS) elements;relevant cell factory;results;Secondary metabolite production;secondary metabolites;STRAIN;synthetic control devices;synthetic expression devices;Synthetic expression system;Synthetic gene cluster;synthetic promoter;synthetic transcription factor;synthetic transcription factors;SYSTEM;TET-ON;three;transcription factor;upstream activating domain;upstream activating sequences;versatility;VP16 activation domain;well-characterized | Mózsik, L | CLUSTER;CORE PROMOTERS;EXPRESSION SYSTEM;Gene regulation;Hybrid transcription factor;ORGANIZATION;PARTS;Penicillium chrysogenum;PROTEIN;Q-SYSTEM;Secondary metabolite production;STRAIN;Synthetic expression system;Synthetic gene cluster;TET-ON | null | [Mozsik, Laszlo; Buttel, Zsofia; Driessen, Arnold J. M.; Nygard, Yvonne] Univ Groningen, Groningen Biomol Sci & Biotechnol Inst, Mol Microbiol, Nijenborgh 7, NL-9747 AG Groningen, Netherlands. [Bovenberg, Roel A. L.; Nygard, Yvonne] DSM Biotechnol Ctr, Alexander Fleminglaan 1, NL-2613 AX Delft, Netherlands. [Bovenberg, Roel A. L.] Univ Groningen, Groningen Biomol Sci & Biotechnol Inst, Synthet Biol & Cell Engn, Nijenborgh 7, NL-9747 AG Groningen, Netherlands. [Nygard, Yvonne] Chalmers Univ Technol, Dept Biol & Biol Engn, Div Ind Biotechnol, Kemivagen 10, S-41296 Gothenburg, Sweden. | YN and ZB received funding the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme FP7/2007-2013/, under REA grant agreement [No 607332] (QuantFung) and LM received funding from the European Union's Horizon 2020 Research and Innovation Programme under the Marie Sklodowska-Curie grant agreement [No 713482] (ALERT). | affinity;application;background;binds;characterization;compounds;conclusions;conditions;control device;control devices;devices function;DNA binding domain;excellent indications;expression;filamentous fungi;fluorescent reporters;gene;gene cluster;genes;great advantage;highest expressed native genes;level;main components;microbioreactors;model filamentous fungus;Neurospora crassa;penicillin;Penicillium chrysogenum;performing control devices;production;production strains;QF DNA-binding domain;quinic acid gene cluster;quinic acid upstream activating sequence (QUAS) elements;relevant cell factory;results;secondary metabolites;synthetic control devices;synthetic expression devices;synthetic promoter;synthetic transcription factor;synthetic transcription factors;system;three;transcription factor;upstream activating domain;upstream activating sequences;versatility;VP16 activation domain;well-characterized | 10.1002/bit.24552;10.1007/978-1-4939-6371-3_3;10.1007/978-1-4939-7795-6_12;10.1007/978-1-61779-501-5_1;10.1007/s002530051509;10.1007/s10142-009-0110-6;10.1007/s12223-010-0019-4;10.1016/0022-2836(85)90183-4;10.1016/0092-8674(84)90457-4;10.1016/j.cell.2010.02.025;10.1016/j.fgb.2006.05.006;10.1016/j.fgb.2015.11.003;10.1016/j.fgb.2015.12.003;10.1016/j.ydbio.2009.08.009;10.1016/j.ymeth.2013.06.012;10.1016/S0003-2697(03)00166-0;10.1016/S0953-7562(09)80945-3;10.1021/acschembio.8b00679;10.1021/acssynbio.6b00082;10.1021/acssynbio.6b00178;10.1021/sb4001245;10.1021/sb500296p;10.1021/sb500366v;10.1038/335563a0;10.1038/nature07667;10.1038/nbt.1498;10.1038/ncomms13010;10.1038/nprot.2013.143;10.1039/c3np70034h;10.1042/BJ20081257;10.1073/pnas.1419028112;10.1080/07388550091144177;10.1093/nar/gkt1402;10.1093/nar/gkw553;10.1093/nar/gky558;10.1128/AEM.01529-12;10.1128/AEM.01702-10;10.1128/AEM.01742-17;10.1128/AEM.02740-10;10.1128/AEM.71.2.672-678.2005;10.1128/MCB.11.11.5746;10.1128/MMBR.49.3.338-358.1985;10.1186/1471-2164-10-75;10.1186/1471-2180-5-1;10.1186/1475-2859-13-53;10.1186/1475-2859-8-31;10.1186/s12864-015-2154-4;10.1186/s12934-016-0586-4;10.1186/s12934-019-1112-2;10.1186/s40694-016-0024-8;10.1371/journal.pone.0148320;10.1534/genetics.110.119917;10.3109/10408410903489576;10.3389/fmicb.2015.00184;[10.1038/nmeth.1929, 10.1038/NMETH.1929];[10.1038/nmeth.3250, 10.1038/NMETH.3250] | Univ Groningen | Bovenberg, R A L;Büttel, Z;Driessen, A J M;Mózsik, L;Nygård, Y | Mózsik, L: Univ Groningen, Groningen Biomol Sci & Biotechnol Inst, Mol Microbiol, Nijenborgh 7, NL-9747 AG Groningen, Netherlands | Driessen, Arnold J.M.;Nygård, Yvonne | 607332;713482 | 57 | null | Netherlands | Chalmers Univ Technol;DSM Biotechnol Ctr;Univ Groningen | Mozsik, Laszlo | Green Published, gold, Green Submitted | CLUSTER;CORE PROMOTERS;EXPRESSION SYSTEM;ORGANIZATION;PARTS;PROTEIN;Q-SYSTEM;STRAIN;TET-ON | Mozsik, Laszlo; Buttel, Zsofia; Bovenberg, Roel A. L.; Driessen, Arnold J. M.; Nygard, Yvonne; | null | Chalmers Univ Technol, Dept Biol & Biol Engn, Div Ind Biotechnol, Kemivagen 10, S-41296 Gothenburg, Sweden;DSM Biotechnol Ctr, Alexander Fleminglaan 1, NL-2613 AX Delft, Netherlands;Univ Groningen, Groningen Biomol Sci & Biotechnol Inst, Mol Microbiol, Nijenborgh 7, NL-9747 AG Groningen, Netherlands;Univ Groningen, Groningen Biomol Sci & Biotechnol Inst, Synthet Biol & Cell Engn, Nijenborgh 7, NL-9747 AG Groningen, Netherlands | Chalmers Univ Technol, Dept Biol & Biol Engn, Div Ind Biotechnol, Kemivagen 10, S-41296 Gothenburg, Sweden;DSM Biotechnol Ctr, Alexander Fleminglaan 1, NL-2613 AX Delft, Netherlands;Univ Groningen, Groningen Biomol Sci & Biotechnol Inst, Mol Microbiol, Nijenborgh 7, NL-9747 AG Groningen, Netherlands;Univ Groningen, Groningen Biomol Sci & Biotechnol Inst, Synthet Biol & Cell Engn, Nijenborgh 7, NL-9747 AG Groningen, Netherlands | 1475-2859 | Gene regulation;Hybrid transcription factor;Penicillium chrysogenum;Secondary metabolite production;Synthetic expression system;Synthetic gene cluster | 1 | 1984;1985;1988;1991;1992;1999;2000;2003;2005;2006;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017;2018;2019 | 13 | Chalmers Univ Technol, Dept Biol & Biol Engn, Div Ind Biotechnol, Kemivagen 10, S-41296 Gothenburg, Sweden;DSM Biotechnol Ctr, Alexander Fleminglaan 1, NL-2613 AX Delft, Netherlands;Univ Groningen, Groningen Biomol Sci & Biotechnol Inst, Mol Microbiol, Nijenborgh 7, NL-9747 AG Groningen, Netherlands | Microb. Cell. Fact. | Nygard, Yvonne | BMC | (QUAS);,;:;a;acid;activating;activation;advantage;affinity;an;and;anticipate;application;applied;background;be;binding;binds;by;can;cell;characterization;characterized;chrysogenum;cluster;components;compounds;conclusions;conditions;confirmed;containing;control;controlling;controls;crassa;demand;demonstrated;detectable;developed;device;devices;DNA;DNA-binding;domain;each;elements;excellent;expressed;expression;factor;factors;factory;filamentous;fluorescent;for;from;function;fungi;fungus;fused;gene;genes;give;great;hardly;highest;how;in;indications;individually;industrially;is;it;its;level;main;may;metabolites;microbioreactors;model;native;Neurospora;of;Orthogonal;other;penicillin;Penicillium;performing;production;promoter;proved;provided;QF;quinic;ranging;relevant;reporters;respect;resulted;results;robustly;secondary;sequence;sequences;similar;strains;synthetic;synthetically;system;that;the;their;these;this;three;to;transcription;tuned;under;upstream;versatility;VP16;was;we;well-characterized;were;where;which;widely;with | Chalmers Univ Technol;DSM Biotechnol Ctr;Univ Groningen | Background: Orthogonal, synthetic control devices were developed for Penicillium chrysogenum, a model filamentous fungus and industrially relevant cell factory. In the synthetic transcription factor, the QF DNA-binding domain of the transcription factor of the quinic acid gene cluster of Neurospora crassa is fused to the VP16 activation domain. This synthetic transcription factor controls the expression of genes under a synthetic promoter containing quinic acid upstream activating sequence (QUAS) elements, where it binds. A gene cluster may demand an expression tuned individually for each gene, which is a great advantage provided by this system. Results: The control devices were characterized with respect to three of their main components: expression of the synthetic transcription factors, upstream activating sequences, and the affinity of the DNA binding domain of the transcription factor to the upstream activating domain. This resulted in synthetic expression devices, with an expression ranging from hardly detectable to a level similar to that of highest expressed native genes. The versatility of the control device was demonstrated by fluorescent reporters and its application was confirmed by synthetically controlling the production of penicillin. Conclusions: The characterization of the control devices in microbioreactors, proved to give excellent indications for how the devices function in production strains and conditions. We anticipate that these well-characterized and robustly performing control devices can be widely applied for the production of secondary metabolites and other compounds in filamentous fungi. | AAV-4877-2020;D-1876-2012 | CLUSTER;CORE PROMOTERS;EXPRESSION SYSTEM;ORGANIZATION;PARTS;PROTEIN;Q-SYSTEM;STRAINS;TET-ON | 0 | null | Gene regulation;Hybrid transcription factor;Penicillium chrysogenum;Secondary metabolite production;Synthetic expression system;Synthetic gene cluster | 13 | CLUSTER;CORE PROMOTER;EXPRESSION SYSTEM;Gene regulation;Hybrid transcription factor;ORGANIZATION;PARTS;PENICILLIUM-CHRYSOGENUM;PROTEIN;Q-SYSTEM;Secondary metabolite production;STRAINS;Synthetic expression system;Synthetic gene cluster;TET-ON | WOS:000511651300003 | Chalmers Univ Technol, Gothenburg, Sweden;DSM Biotechnol Ctr, Delft, Netherlands;Univ Groningen, Groningen, Netherlands | Netherlands;Sweden | 2,019 | null | 0000-0001-5211-3873;0000-0001-6117-0343;0000-0003-0138-7553 | null | null | English | null | ACS CHEM BIOL;ACS SYNTH BIOL;ANAL BIOCHEM;APPL ENVIRON MICROB;APPL MICROBIOL BIOT;BIOCHEM J;BIOTECHNOL BIOENG;BMC GENOMICS;BMC MICROBIOL;CELL;CRIT REV BIOTECHNOL;CRIT REV MICROBIOL;DEV BIOL;FOLIA MICROBIOL;FRONT MICROBIOL;FUNCT INTEGR GENOMIC;Fungal Biol Biotechnol;FUNGAL GENET BIOL;GENETICS;J MOL BIOL;METHODS;METHODS MOL BIOL;MICROB CELL FACT;MICROBIOL REV;MOL CELL BIOL;MYCOL RES;NAT BIOTECHNOL;NAT COMMUN;NAT METHODS;NAT PROD REP;NAT PROTOC;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PLOS ONE;US patent | Bovenberg, Roel A L;Buttel, Zsofia;Driessen, Arnold J M;Mozsik, Laszlo;Nygard, Yvonne | 2024-03-11
ER | Blazeck, J;Bovenberg, R A L;Burger, G;Cai, P;Díez, B;Eidtmann, A;Ermak, G;Gibbs, P A;Giles, N H;Gorochowski, T E;Grau, M F;Gressler, M;Harris, D M;Juven-Gershon, T;Kakule, T B;Kalderon, D;Kaplan, N;Kensy, F;Kiel, J A K W;Kiesenhofer, D P;Koetsier, M J;Kovalchuk, A;Kunze, M;Lee, M E;Losson, R;Mcisaac, R S;Mclean, K J;Meyer Vera;Meyer, V;Nijland, J G;Ongley, S E;Pachlinger, R;Pfeiffer, B D;Pohl, C;Polli, F;Portela, R M C;Potter, C J;Rajkumar, A S;Ran, F A;Rantasalo, A;Riabinina, O;Ruiz, B;Sadowski, I;Salo, O V;Smidák, R;Sonderegger, C;Subedi, A;Van Den Berg, M A;Vogt, K;Wanka, F;Weber, S S;Wei, X;Zarnack, K | KI9BI | Delft, Netherlands.;Gothenburg, Sweden;Groningen, Netherlands. | 14 | null | 3 | null | 31,739,777 | Bovenberg, Roel A L;Buttel, Zsofia;Driessen, Arnold J M;Mozsik, Laszlo;Nygard, Yvonne | MICROB CELL FACT | Delft, Netherlands;Gothenburg, Sweden;Groningen, Netherlands |
Chang, M W;Foo, J L;Ling, H;Xia, P F | 10.1016/j.biotechadv.2019.04.015 | 107393 | THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND | 1s1f5j644g1t1r6l6f3p382v6n6d2p5f5g6e315p | Synthetic genetic circuits for programmable biological functionalities | Natl Univ Singapore | null | Foo, JL; Chang, MW (corresponding author), Ctr Life Sci, 28 Med Dr,02-07, Singapore 117456, Singapore. | null | Chang, Matthew Wook;Foo, Jee Loon;Ling, Hua;Xia, Peng-Fei | Biotechnology & Applied Microbiology | Synthetic Biology Initiative of the National University of Singapore [DPRT/943/09/14]; Ministry of Education, Singapore [MOE/2014/T2/2/128]; Synthetic Biology RD Programme [SBP-P2, SBP-P7]; Industry Alignment Fund Industry Collaboration Project [ICP1600012]; Investigatorship (NRFI) of the National Research Foundation, Singapore [ARO/2019/74459LS]; U.S. Army [ARO/2019/74459LS] | WOS | Chang, M W;Foo, J L | Natl Univ Singapore, Singapore, Singapore | 37 | biological;circuits;for;functionalities;genetic;programmable;synthetic | 1 | Ling, Hua;Xia, Pengfei | PERGAMON-ELSEVIER SCIENCE LTD | MW (corresponding author), Ctr Life Sci, 28 Med Dr,02-07, Singapore 117456, Singapore;Natl Univ Singapore, Dept Biochem, Yong Loo Lin Sch Med, 8 Med Dr, Singapore 117597, Singapore;Natl Univ Singapore, NUS Synthet Biol Clin & Technol Innovat SynCTI, 28 Med Dr, Singapore 117456, Singapore | Review | Ctr Life Sci | OXFORD | null | null | Natl Univ Singapore | Industry Alignment Fund Industry Collaboration Project;Investigatorship (NRFI) of the National Research Foundation, Singapore;Ministry of Education, Singapore;Synthetic Biology Initiative of the National University of Singapore;Synthetic Biology RD Programme;U.S. Army | Foo, JL; Chang, MW (corresponding author), Ctr Life Sci, 28 Med Dr,02-07, Singapore 117456, Singapore. | null | Chang, Matthew Wook;Foo, Jee Loon;Ling, Hua;Xia, Peng-Fei | 181 | 2 | 484,647,000,023 | Industry Alignment Fund Industry Collaboration Project [ICP1600012];Investigatorship (NRFI) of the National Research Foundation, Singapore [ARO/2019/74459LS];Ministry of Education, Singapore [MOE/2014/T2/2/128];Synthetic Biology Initiative of the National University of Singapore [DPRT/943/09/14];Synthetic Biology RD Programme [SBP-P2, SBP-P7];U.S. Army [ARO/2019/74459LS] | Singapore | BIOTECHNOLOGY ADVANCES | Singapore | null | null | Natl Univ Singapore, Dept Biochem, Yong Loo Lin Sch Med, 8 Med Dr, Singapore 117597, Singapore | 0734-9750 | Chang, M W;Foo, J L;Ling, H;Xia, P F | NOV 1 | bchcmw@nus.edu.sg;bchfjl@nus.edu.sg | programmable biological functionalities;synthetic genetic circuits | 4 | J | Biotechnology & Applied Microbiology | accomplishments;autonomous modulation;Bioengineering;biological containment methods;biological units;biotechnology;Boolean logic gates;building;capabilities;CARBON-DIOXIDE;challenges;circuit architecture;CIRCUITS;CLOSTRIDIUM-BEIJERINCKII;complex genetic machines;complex genetic networks;concepts;CRISPR-CAS SYSTEMS;DESIGN;diagnostics;different circuits;directed evolution;dynamic;DYNAMIC PATHWAY REGULATION;ENGINEERED BACTERIA;environment;expression;features;feedback loops;genetic circuit;Genetic circuits;genetic devices;genetic materials;guideline;LACTOCOCCUS-LACTIS;living organisms;metabolic networks;microorganisms;modularized building blocks;modularized genetic parts;networks;new chapter;novel applications;oscillators;principles;programmable biological functionalities;programmable decision-making;Programmable functionalities;rapid development;realistic applications;realization;recent advances;release;review gives new insights;STATE MACHINES;synthetic biology;synthetic genetic circuits;therapies;toggle switch;toggle switches;units;variety | Xia, P F | CARBON-DIOXIDE;CLOSTRIDIUM-BEIJERINCKII;CRISPR-CAS SYSTEMS;DESIGN;DYNAMIC PATHWAY REGULATION;ENGINEERED BACTERIA;EXPRESSION;Genetic circuits;Genetic devices;LACTOCOCCUS-LACTIS;Programmable functionalities;STATE MACHINES;toggle switch | null | [Xia, Peng-Fei; Ling, Hua; Foo, Jee Loon; Chang, Matthew Wook] Natl Univ Singapore, Dept Biochem, Yong Loo Lin Sch Med, 8 Med Dr, Singapore 117597, Singapore. [Xia, Peng-Fei; Ling, Hua; Foo, Jee Loon; Chang, Matthew Wook] Natl Univ Singapore, NUS Synthet Biol Clin & Technol Innovat SynCTI, 28 Med Dr, Singapore 117456, Singapore. | This work was supported by the Synthetic Biology Initiative of the National University of Singapore (DPRT/943/09/14), the Ministry of Education, Singapore (MOE/2014/T2/2/128), the Synthetic Biology R&D Programme (SBP-P2, SBP-P7), the Industry Alignment Fund Industry Collaboration Project (ICP1600012) and Investigatorship (NRFI) of the National Research Foundation, Singapore, and the U.S. Army (ARO/2019/74459LS). | accomplishments;autonomous modulation;bioengineering;biological containment methods;biological units;biotechnology;Boolean logic gates;building;capabilities;challenges;circuit architecture;circuits;complex genetic machines;complex genetic networks;concepts;diagnostics;different circuits;directed evolution;dynamic;environment;features;feedback loops;genetic circuit;genetic circuits;genetic materials;guideline;living organisms;metabolic networks;microorganisms;modularized building blocks;modularized genetic parts;networks;new chapter;novel applications;oscillators;principles;programmable decision-making;programmable functionalities;rapid development;realistic applications;realization;recent advances;release;review gives new insights;synthetic biology;synthetic genetic circuits;therapies;toggle switches;units;variety | 10.1002/biot.201300258;10.1002/biot.201600099;10.1002/biot.201700159;10.1002/biot.201700543;10.1002/bit.25722;10.1002/bit.25980;10.1002/bit.26020;10.1002/bit.26275;10.1002/bit.26279;10.1002/bit.26404;10.1007/s00018-018-2827-7;10.1007/s11047-018-9715-9;10.1016/j.bios.2012.08.011;10.1016/j.bios.2014.07.003;10.1016/j.biotechadv.2018.04.007;10.1016/j.biotechadv.2018.07.005;10.1016/j.cbpa.2013.10.003;10.1016/j.cbpa.2016.08.023;10.1016/j.cell.2009.12.029;10.1016/j.cell.2013.02.022;10.1016/j.cell.2016.05.003;10.1016/j.cels.2015.06.001;10.1016/j.cels.2016.07.012;10.1016/j.chembiol.2009.02.011;10.1016/j.copbio.2017.06.011;10.1016/j.copbio.2017.10.005;10.1016/j.copbio.2018.01.011;10.1016/j.drup.2016.06.002;10.1016/j.jmb.2015.10.004;10.1016/j.mib.2017.08.005;10.1016/j.mib.2017.12.011;10.1016/j.molcel.2011.08.023;10.1016/j.molcel.2016.06.006;10.1016/j.molcel.2017.10.033;10.1016/j.molcel.2018.01.003;10.1016/j.nbt.2014.12.009;10.1016/j.procbio.2017.02.013;10.1016/j.tibtech.2015.12.014;10.1016/j.tig.2005.05.008;10.1016/j.watres.2017.06.008;10.1016/j.ymben.2015.03.008;10.1016/j.ymben.2018.03.009;10.1016/j.ymben.2018.04.008;10.1016/j.ymben.2018.04.011;10.1016/j.ymben.2018.06.006;10.1016/S0092-8674(03)00346-5;10.1021/acssynbio.5b00264;10.1021/acssynbio.6b00044;10.1021/acssynbio.6b00060;10.1021/acssynbio.6b00167;10.1021/acssynbio.6b00201;10.1021/acssynbio.6b00257;10.1021/acssynbio.6b00374;10.1021/acssynbio.7b00163;10.1021/acssynbio.7b00203;10.1021/acssynbio.7b00322;10.1021/acssynbio.7b00328;10.1021/acssynbio.8b00213;10.1021/acssynbio.8b00488;10.1021/sb400077j;10.1021/sb4001799;10.1021/sb500090b;10.1038/35002131;10.1038/msb.2011.55;10.1038/msb.2013.58;10.1038/nature07389;10.1038/nature08187;10.1038/nature09565;10.1038/nature10213;10.1038/nature11516;10.1038/nature12148;10.1038/nature13314;10.1038/nature14121;10.1038/nature23017;10.1038/nature23271;10.1038/nbt.1586;10.1038/nbt.2510;10.1038/nbt.2689;10.1038/nbt.3471;10.1038/nbt.3796;10.1038/nbt.3805;10.1038/nbt.3879;10.1038/nbt740;10.1038/nbt840;10.1038/nbt986;10.1038/ncomms15028;10.1038/ncomms15336;10.1038/ncomms15459;10.1038/ncomms2404;10.1038/ncomms3580;10.1038/ncomms3595;10.1038/ncomms7989;10.1038/ncomms8832;10.1038/nprot.2014.089;10.1038/nrg3227;10.1038/nrm.2015.2;10.1038/nrmicro.2015.24;10.1038/nrmicro.2017.172;10.1038/nrmicro2730;10.1038/nrmicro3239;10.1038/s41467-017-00511-w;10.1038/s41467-017-01695-x;10.1038/s41467-018-04901-6;10.1038/s41467-018-05332-z;10.1038/s41467-018-05466-0;10.1038/s41580-018-0024-z;10.1038/s41589-018-0056-x;10.1038/s41589-018-0168-3;10.1038/s41598-018-21350-9;10.1039/c0cc05037g;10.1046/j.1365-2958.2003.03867.x;10.1073/pnas.1009747107;10.1073/pnas.1120788109;10.1073/pnas.120163297;10.1073/pnas.1202344109;10.1073/pnas.1321321111;10.1073/pnas.1406401111;10.1093/femsle/fny222;10.1093/nar/gkn991;10.1093/nar/gku1378;10.1093/nar/gku1388;10.1093/nar/gku593;10.1093/nar/gku971;10.1093/nar/gkw232;10.1093/nar/gkx1319;10.1093/nar/gky884;10.1101/gr.193433.115;10.1126/science.1100829;10.1126/science.1205527;10.1126/science.aac7341;10.1126/science.aad3317;10.1126/science.aad8559;10.1126/science.aao0958;10.1126/science.aap8992;10.1126/science.aat9249;10.1126/scitranslmed.aak9537;10.1128/mBio.00928-13;10.1146/annurev-genet-120215-034902;10.1146/annurev-micro-091014-104306;10.1186/s12915-015-0146-0;10.1186/s12934-016-0595-3;10.15252/msb.20156663;10.15252/msb.20188605;10.2337/db11-1019;10.2337/db13-1236;10.2337/db14-0635;10.3389/fmicb.2018.00154;10.3390/genes9070351;[10.1016/j.cophio.2018.01.002, 10.1016/j.copbio.2018.01.002];[10.1038/nchembio.1979, 10.1038/NCHEMBIO.1979];[10.1038/nchembio.2233, 10.1038/NCHEMBIO.2233];[10.1038/NCHEMBIO.919, 10.1038/nchembio.919];[10.1038/NMETH.1318, 10.1038/nmeth.1318];[10.1038/NMETH.2926, 10.1038/nmeth.2926];[10.1038/NNANO.2014.32, 10.1038/nnano.2014.32];[10.1039/c6ee01108j, 10.1039/C6EE01108J] | Natl Univ Singapore | Chang, M W;Foo, J L;Ling, H;Xia, P F | Xia, P F: Natl Univ Singapore, Dept Biochem, Yong Loo Lin Sch Med, 8 Med Dr, Singapore 117597, Singapore | Xia, Pengfei | ARO/2019/74459LS;DPRT/943/09/14;ICP1600012;MOE/2014/T2/2/128;SBP-P2;SBP-P7 | 158 | null | Singapore | Natl Univ Singapore | Xia, Peng-Fei | hybrid | CARBON-DIOXIDE;CLOSTRIDIUM-BEIJERINCKII;CRISPR-CAS SYSTEMS;DESIGN;DYNAMIC PATHWAY REGULATION;ENGINEERED BACTERIA;EXPRESSION;LACTOCOCCUS-LACTIS;STATE MACHINES;TOGGLE SWITCH | Xia, Peng-Fei; Ling, Hua; Foo, Jee Loon; Chang, Matthew Wook; | null | Natl Univ Singapore, Dept Biochem, Yong Loo Lin Sch Med, 8 Med Dr, Singapore 117597, Singapore;Natl Univ Singapore, NUS Synthet Biol Clin & Technol Innovat SynCTI, 28 Med Dr, Singapore 117456, Singapore | Natl Univ Singapore, Dept Biochem, Yong Loo Lin Sch Med, 8 Med Dr, Singapore 117597, Singapore;Natl Univ Singapore, NUS Synthet Biol Clin & Technol Innovat SynCTI, 28 Med Dr, Singapore 117456, Singapore | 1873-1899 | Genetic circuits;genetic device;Programmable functionalities | 6 | 1999;2000;2002;2003;2004;2005;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017;2018;2019 | 66 | Ctr Life Sci, 28 Med Dr,02-07, Singapore 117456, Singapore | Biotechnol. Adv. | Chang, Matthew Wook | PERGAMON-ELSEVIER SCIENCE LTD | ,;a;accomplishments;advances;and;applications;architecture;are;as;aspects;autonomous;be;been;bioengineering;biological;biology;biotechnology;blocks;Boolean;building;capabilities;challenges;chapter;circuit;circuits;complex;concepts;consequently;construct;containment;could;created;decision-making;design;development;diagnostics;different;directed;discussed;distinct;due;dynamic;employed;employing;engineered;environment;envision;evolution;evolve;facilitate;features;feedback;for;from;functionalities;furthermore;gates;genetic;gives;guideline;have;herein;highlighted;identified;impart;implementation;in;including;initiated;insights;interact;into;led;living;logic;loops;machines;materials;metabolic;methods;microorganisms;modularized;modulation;networks;new;novel;of;offers;on;organisms;oscillators;outline;parts;prevent;principles;programmable;rapid;realistic;realization;recent;release;remote;review;such;switches;synthetic;targeted;that;the;therapies;these;they;this;to;toggle;transforming;units;variety;various;we;well;with | Ctr Life Sci | Living organisms evolve complex genetic networks to interact with the environment. Due to the rapid development of synthetic biology, various modularized genetic parts and units have been identified from these networks. They have been employed to construct synthetic genetic circuits, including toggle switches, oscillators, feedback loops and Boolean logic gates. Building on these circuits, complex genetic machines with capabilities in programmable decision-making could be created. Consequently, these accomplishments have led to novel applications, such as dynamic and autonomous modulation of metabolic networks, directed evolution of biological units, remote and targeted diagnostics and therapies, as well as biological containment methods to prevent release of engineered microorganisms and genetic materials. Herein, we outline the principles in genetic circuit design that have initiated a new chapter in transforming concepts to realistic applications. The features of modularized building blocks and circuit architecture that facilitate realization of circuits for a variety of novel applications are discussed. Furthermore, recent advances and challenges in employing genetic circuits to impart microorganisms with distinct and programmable functionalities are highlighted. We envision that this review gives new insights into the design of synthetic genetic circuits and offers a guideline for the implementation of different circuits in various aspects of biotechnology and bioengineering. | Q-3174-2019 | CARBON-DIOXIDE;CLOSTRIDIUM-BEIJERINCKII;CRISPR-CAS SYSTEMS;DESIGN;DYNAMIC PATHWAY REGULATION;ENGINEERED BACTERIA;EXPRESSION;LACTOCOCCUS-LACTIS;STATE MACHINES;TOGGLE SWITCH | 8 | null | Genetic circuits;Genetic devices;Programmable functionalities | 12 | CARBON-DIOXIDE;CLOSTRIDIUM-BEIJERINCKII;CRISPR-CAS SYSTEMS;DESIGN;DYNAMIC PATHWAY REGULATION;ENGINEERED BACTERIA;EXPRESSION;Genetic circuits;genetic device;LACTOCOCCUS-LACTIS;Programmable functionalities;STATE MACHINES;toggle switch | WOS:000484647000023 | Natl Univ Singapore, Singapore, Singapore | Singapore | 2,019 | null | 0000-0001-5881-9834;0000-0002-0680-6422 | null | null | English | null | ACS SYNTH BIOL;ANNU REV GENET;ANNU REV MICROBIOL;APPL ENVIRON MICROB;BIOSENS BIOELECTRON;BIOTECHNOL ADV;BIOTECHNOL BIOENG;BIOTECHNOL J;BMC BIOL;CELL;CELL MOL LIFE SCI;CELL SYST;CHEM BIOL;CHEM COMMUN;CURR OPIN BIOTECH;CURR OPIN CHEM BIOL;CURR OPIN MICROBIOL;DIABETES;DRUG RESIST UPDATE;ENERG ENVIRON SCI;FEMS MICROBIOL LETT;FRONT MICROBIOL;GENES-BASEL;GENOME RES;J MOL BIOL;MBIO;METAB ENG;MICROB CELL FACT;MOL CELL;MOL MICROBIOL;MOL SYST BIOL;NAT BIOTECHNOL;NAT CHEM BIOL;NAT COMMUN;NAT COMPUT;NAT METHODS;NAT NANOTECHNOL;NAT PROTOC;NAT REV GENET;NAT REV MICROBIOL;NAT REV MOL CELL BIO;NATURE;NEW BIOTECHNOL;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PROCESS BIOCHEM;SCI REP-UK;SCI TRANSL MED;SCIENCE;TRENDS BIOTECHNOL;TRENDS GENET;WATER RES | Chang, Matthew Wook;Foo, Jee Loon;Ling, Hua;Xia, Peng-Fei | 2024-03-11
ER | Atkinson, M R;Atsumi, S;Bikard, D;Bonnet, J;Borrero, J;Bothfeld, W;Bradley, R W;Brophy, J A N;Caliando, B J;Callura, J M;Cameron, D E;Cao, Y X;Chan, C T Y;Chen, B B;Chou, H H;Dahl, R H;Daniel, R;Datsenko, K A;Deaner, M;Dominguez, A A;Dong, C;Dou, J;Duan, F F;Farzadfard, F;Foo, J L;Gallagher, R R;Gander, M W;Gardner, T S;Gibson, D G;Gomaa, A A;Gottesman, S;Green, A A;Groher, F;Gupta, A;Harms, A;Hayden, E C;Heaver, S L;Higashikuni, Y;Higo, A;Holkenbrink, C;Holtz, W J;Hoynes-O'Connor, A;Hsiao, V;Huang, C H;Huang, H;Hwang, I Y;Immethun, C M;Isaacs, F J;Jacobsen, C N;Jang, S;Joseph, R C;Jusiak, B;Kau, A L;Kim, S J;Kortmann, J;Kotula, J W;Kushwaha, M;Lee, H L;Lee, J W;Lee, Y J;Li, Z J;Lian, J Z;Liang, J C;Lim, H G;Liu, M M;Liu, Q J;Lo, T M;Luo, M L;Maier, J A H;Malyshev, D A;Mandal, M;Mandell, D J;Metzner, M;Meyer, A J;Mimee, M;Moon, T S;Moser, F;Mougiakos, L;Mutalik, V K;Nielsen, A A K;Oishi, K;Oliver, N J;Peters, J M;Pham, H L;Piraner, D I;Pontrelli, S;Qi, L S;Rebello, S;Rhodius, V A;Richter, H;Riglar, D T;Robert, S;Roquet, N;Rossmanith, J;Saeidi, N;Sakimoto, K K;Schwartz, C;Seok, J Y;Shao, Z Y;Shapiro, M G;Shen, Y;Sherwood, A V;Sheth, R U;Shipman, S L;Siuti, P;Slusarczyk, A L;Smanski, M J;Steidler, L;Stirling, F;Stricker, J;Sun, T;Szymanski, E;Tamsir, A;Tang, W X;Taton, A;Temme, K;Tolhurst, G;Wang, B J;Wang, H H;Wang, M M;Wang, Y;Webster, D P;Wei, N;Weinberg, B H;Williams, T C;Win, M N;Wong, A;Wong, A S L;Woolston, B M;Xia, P F;Xiang, Y Y;Xie, M Q;Xie, Z;Xu, P;Yang, J;Yang, Y P;Yao, L;Yin, H;Yu, B J;Zhang, S Y;Zheng, J H | IW0JA | Singapore, Singapore | 78 | null | 1 | null | 31,051,208 | Chang, Matthew Wook;Foo, Jee Loon;Ling, Hua;Xia, Peng-Fei | BIOTECHNOL ADV | Singapore, Singapore |
Dong, F;Gu, D C;Liao, Y Y;Wang, X W;Yang, Z Y;Zeng, L T | 10.1016/j.postharvbio.2019.110974 | 110974 | RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS | 2y4k4tm3l513w4x4k6w2r2c3c2i631b6d6g5q6k | Formation of and changes in phytohormone levels in response to stress during the manufacturing process of oolong tea (<i>Camellia sinensis</i>) | Chinese Acad Sci | null | Yang, ZY (corresponding author), Chinese Acad Sci, Guangdong Prov Key Lab Appl Bot, South China Bot Garden, 723 Xingke Rd, Guangzhou 510650, Guangdong, Peoples R China.;Yang, ZY (corresponding author), Chinese Acad Sci, Key Lab South China Agr Plant Mol Anal & Genet Im, 723 Xingke Rd, Guangzhou 510650, Guangdong, Peoples R China. | null | Dong, Fang;Gu, Dachuan;Liao, Yinyin;Wang, Xuewen;Yang, Ziyin;Zeng, Lanting | Agronomy;Food Science & Technology;Horticulture | National Natural Science Foundation of China [31870684]; National Key Research and Development Program of China [2018YFD1000601]; China Postdoctoral Science Foundation [2018M640837]; Guangdong Natural Science Foundation for Distinguished Young Scholar [2016A030306039] | WOS | Yang, Z Y | Chinese Acad Sci, Guangdong, Peoples R China;Guangdong Food & Drug Vocat Coll, Guangdong, Peoples R China;Univ Chinese Acad Sci, Beijing, Peoples R China | 157 | (<i>Camellia;and;changes;during;formation;in;levels;manufacturing;of;oolong;phytohormone;process;response;sinensis</i>);stress;tea;the;to | 1 | null | ELSEVIER | Chinese Acad Sci, Ctr Econ Bot, Core Bot Gardens, 723 Xingke Rd, Guangzhou 510650, Guangdong, Peoples R China;Chinese Acad Sci, Guangdong Prov Key Lab Appl Bot, South China Bot Garden, 723 Xingke Rd, Guangzhou 510650, Guangdong, Peoples R China;Chinese Acad Sci, Key Lab South China Agr Plant Mol Anal & Genet Im, 723 Xingke Rd, Guangzhou 510650, Guangdong, Peoples R China;Chinese Acad Sci, Key Lab South China Agr Plant Mol Anal & Genet Im, 723 Xingke Rd, Guangzhou 510650, Guangdong, Peoples R China.; Yang, ZY (corresponding author), Chinese Acad Sci, Guangdong Prov Key Lab Appl Bot, South China Bot Garden, 723 Xingke Rd, Guangzhou 510650, Guangdong, Peoples R China;Guangdong Food & Drug Vocat Coll, 321 Longdongbei Rd, Guangzhou 510520, Guangdong, Peoples R China;Univ Chinese Acad Sci, 19A Yuquan Rd, Beijing 100049, Peoples R China | Article | Chinese Acad Sci | AMSTERDAM | null | null | Chinese Acad Sci;Guangdong Food & Drug Vocat Coll;Univ Chinese Acad Sci | China Postdoctoral Science Foundation;Guangdong Natural Science Foundation for Distinguished Young Scholar;National Key Research and Development Program of China;National Natural Science Foundation of China | Yang, ZY (corresponding author), Chinese Acad Sci, Key Lab South China Agr Plant Mol Anal & Genet Im, 723 Xingke Rd, Guangzhou 510650, Guangdong, Peoples R China.; Yang, ZY (corresponding author), Chinese Acad Sci, Guangdong Prov Key Lab Appl Bot, South China Bot Garden, 723 Xingke Rd, Guangzhou 510650, Guangdong, Peoples R China. | null | Dong, Fang;Gu, Dachuan;Liao, Yinyin;Wang, Xuewen;Yang, Ziyin;Zeng, Lanting | 128 | 5 | 484,758,500,008 | China Postdoctoral Science Foundation [2018M640837];Guangdong Natural Science Foundation for Distinguished Young Scholar [2016A030306039];National Key Research and Development Program of China [2018YFD1000601];National Natural Science Foundation of China [31870684] | China | POSTHARVEST BIOLOGY AND TECHNOLOGY | China | null | null | Chinese Acad Sci, Key Lab South China Agr Plant Mol Anal & Genet Im, 723 Xingke Rd, Guangzhou 510650, Guangdong, Peoples R China | 0925-5214 | Dong, F;Gu, D C;Liao, Y Y;Wang, X W;Yang, Z Y;Zeng, L T | NOV | zyyang@scbg.ac.cn | formation;manufacturing process;oolong tea (<i>Camellia sinensis</i>);phytohormone levels;response | 6 | J | Agriculture;Food Science & Technology | 0.01);0.05);ABA;ABA (p;Abscisic acid;abscisic acid (ABA) levels;activated JA synthetic gene expression;Aroma;Camellia sinensis;characteristic aromas;continuous wounding;defense responses;dehydration stress;enhanced JA synthesis (p;formation;GENE-EXPRESSION;important upstream signals;increase;increased levels;JA;JA (p;Jasmonic acid;jasmonic acid (JA);key upstream signals;LEAF;LEAVES;manufacturing process;manufacturing processes (enzyme-active stage);oolong tea;oolong tea (<i>Camellia sinensis</i>);oolong tea (postharvest stage);phytohormone;phytohormone levels;phytohormones;plant volatiles' biosynthesis;response;SALICYLIC-ACID;Stress;stresses;study;Tea;tea leaves;turn;understanding;Volatile;VOLATILE COMPOUNDS;withering stage activated ABA synthetic gene expression;wounding | Zeng, L T | Abscisic acid;Aroma;Camellia sinensis;GENE-EXPRESSION;Jasmonic acid;LEAF;LEAVES;SALICYLIC-ACID;Tea;Volatile;VOLATILE COMPOUNDS | null | [Zeng, Lanting; Wang, Xuewen; Liao, Yinyin; Gu, Dachuan; Yang, Ziyin] Chinese Acad Sci, Key Lab South China Agr Plant Mol Anal & Genet Im, 723 Xingke Rd, Guangzhou 510650, Guangdong, Peoples R China. [Zeng, Lanting; Wang, Xuewen; Liao, Yinyin; Gu, Dachuan; Yang, Ziyin] Chinese Acad Sci, Guangdong Prov Key Lab Appl Bot, South China Bot Garden, 723 Xingke Rd, Guangzhou 510650, Guangdong, Peoples R China. [Zeng, Lanting; Yang, Ziyin] Chinese Acad Sci, Ctr Econ Bot, Core Bot Gardens, 723 Xingke Rd, Guangzhou 510650, Guangdong, Peoples R China. [Dong, Fang] Guangdong Food & Drug Vocat Coll, 321 Longdongbei Rd, Guangzhou 510520, Guangdong, Peoples R China. [Wang, Xuewen; Liao, Yinyin; Yang, Ziyin] Univ Chinese Acad Sci, 19A Yuquan Rd, Beijing 100049, Peoples R China. | This study was supported by the financial support from the National Natural Science Foundation of China (31870684), the National Key Research and Development Program of China (2018YFD1000601), the China Postdoctoral Science Foundation (2018M640837), and the Guangdong Natural Science Foundation for Distinguished Young Scholar (2016A030306039). | 0.01);0.05);ABA;ABA (p;abscisic acid (ABA) levels;activated JA synthetic gene expression;characteristic aromas;continuous wounding;defense responses;dehydration stress;enhanced JA synthesis (p;formation;important upstream signals;increase;increased levels;JA;JA (p;jasmonic acid (JA);key upstream signals;manufacturing process;manufacturing processes (enzyme-active stage);oolong tea;oolong tea (postharvest stage);phytohormone;phytohormones;plant volatiles' biosynthesis;response;stress;stresses;study;tea leaves;turn;understanding;withering stage activated ABA synthetic gene expression;wounding | 10.1007/s10886-007-9344-8;10.1016/j.foodchem.2012.12.048;10.1016/j.foodchem.2017.03.122;10.1016/j.foodchem.2017.05.137;10.1016/j.foodres.2013.02.011;10.1016/j.jplph.2010.01.003;10.1016/j.plantsci.2017.08.005;10.1016/j.postharvbio.2017.09.005;10.1016/j.tplants.2007.06.001;10.1016/j.tplants.2015.02.001;10.1016/S1360-1385(99)01497-1;10.1021/acs.jafc.5b02741;10.1021/acs.jafc.6b01742;10.1021/acs.jafc.8b00515;10.1021/jf010681x;10.1021/jf203396a;10.1038/224514a0;10.1038/hortres.2014.29;10.1038/nprot.2010.37;10.1039/c7ra03219f;10.1073/pnas.96.26.15354;10.1080/10408398.2018.1506907;10.1093/pcp/pcy091;10.1093/treephys/tpn049;10.1105/tpc.106.049353;10.1111/j.1399-3054.2005.00545.x;10.1126/science.250.4983.1002;10.1128/AEM.00694-08;10.1186/1471-2164-9-550;10.1271/bbb.60708;10.3389/fpls.2015.01248;10.3390/ijms151222155;10.3390/ijms19082440;10.3390/molecules21020124;10.4236/AJAC.2014.59070, 10.4236/ajac.2014.59070];10.7831/RAS.1.1] | Chinese Acad Sci | Dong, F;Gu, D C;Liao, Y Y;Wang, X W;Yang, Z Y;Zeng, L T | Zeng, L T: Chinese Acad Sci, Key Lab South China Agr Plant Mol Anal & Genet Im, 723 Xingke Rd, Guangzhou 510650, Guangdong, Peoples R China | Gu, Dachuan;Zeng, lanting | 2016A030306039;2018M640837;2018YFD1000601;31870684 | 41 | null | China | Chinese Acad Sci;Guangdong Food & Drug Vocat Coll;Univ Chinese Acad Sci | Zeng, Lanting | null | GENE-EXPRESSION;LEAF;LEAVES;SALICYLIC-ACID;VOLATILE COMPOUNDS | Zeng, Lanting; Wang, Xuewen; Liao, Yinyin; Gu, Dachuan; Dong, Fang; Yang, Ziyin; | null | Chinese Acad Sci, Ctr Econ Bot, Core Bot Gardens, 723 Xingke Rd, Guangzhou 510650, Guangdong, Peoples R China;Chinese Acad Sci, Guangdong Prov Key Lab Appl Bot, South China Bot Garden, 723 Xingke Rd, Guangzhou 510650, Guangdong, Peoples R China;Chinese Acad Sci, Key Lab South China Agr Plant Mol Anal & Genet Im, 723 Xingke Rd, Guangzhou 510650, Guangdong, Peoples R China;Guangdong Food & Drug Vocat Coll, 321 Longdongbei Rd, Guangzhou 510520, Guangdong, Peoples R China;Univ Chinese Acad Sci, 19A Yuquan Rd, Beijing 100049, Peoples R China | Chinese Acad Sci, Ctr Econ Bot, Core Bot Gardens, 723 Xingke Rd, Guangzhou 510650, Guangdong, Peoples R China;Chinese Acad Sci, Guangdong Prov Key Lab Appl Bot, South China Bot Garden, 723 Xingke Rd, Guangzhou 510650, Guangdong, Peoples R China;Chinese Acad Sci, Key Lab South China Agr Plant Mol Anal & Genet Im, 723 Xingke Rd, Guangzhou 510650, Guangdong, Peoples R China;Guangdong Food & Drug Vocat Coll, 321 Longdongbei Rd, Guangzhou 510520, Guangdong, Peoples R China;Univ Chinese Acad Sci, 19A Yuquan Rd, Beijing 100049, Peoples R China | 1873-2356 | Abscisic acid;Aroma;Camellia sinensis;Jasmonic acid;Tea;volatiles | null | 1969;1990;1999;2002;2003;2005;2007;2008;2009;2010;2011;2013;2014;2015;2016;2017;2018;2019 | 32 | Chinese Acad Sci, Guangdong Prov Key Lab Appl Bot, South China Bot Garden, 723 Xingke Rd, Guangzhou 510650, Guangdong, Peoples R China;Chinese Acad Sci, Key Lab South China Agr Plant Mol Anal & Genet Im, 723 Xingke Rd, Guangzhou 510650, Guangdong, Peoples R China | Postharvest Biol. Technol. | Yang, Ziyin | ELSEVIER | (ABA);(enzyme-active;(JA);(p;(postharvest;,;0.01);0.05);<;=;ABA;abscisic;acid;activated;advances;an;and;aromas;as;biosynthesis;characteristic;continuous;defense;dehydration;due;during;enhanced;expression;formation;from;further;gene;important;in;increase;increased;investigates;is;JA;jasmonic;key;leaves;levels;manufacturing;of;oolong;over;phytohormone;phytohormones;plant;plucking;process;processes;regulate;response;responses;resulting;signals;some;stage;stage);stress;stresses;study;synthesis;synthetic;tea;the;this;to;turn;under;understanding;upstream;various;volatiles';withering;wounding | Chinese Acad Sci | As important upstream signals, phytohormones regulate the plant volatiles' biosynthesis under various stresses. The formation of some characteristic aromas during the manufacturing process of oolong tea (postharvest stage) is due to the defense responses of tea leaves to stress. This study investigates the formation of phytohormone in response to stresses during the manufacturing process of oolong tea. Jasmonic acid (JA) and abscisic acid (ABA) levels enhanced during the manufacturing processes (enzyme-active stage) of oolong tea. Wounding from plucking activated JA synthetic gene expression, resulting in increased levels of JA (p <= 0.01), and continuous wounding from the turn over stage further enhanced JA synthesis (p <= 0.05). Dehydration stress during the withering stage activated ABA synthetic gene expression resulting in an increase of ABA (p <= 0.01). The study advances the understanding of key upstream signals, JA and ABA, during the manufacturing process of oolong tea. | AAH-5092-2021;JAA-9491-2023 | GENE-EXPRESSION;LEAF;LEAVES;SALICYLIC-ACID;VOLATILE COMPOUNDS | 3 | null | Abscisic acid;Aroma;Camellia sinensis;Jasmonic acid;Tea;Volatile | 8 | ABSCISIC-ACID;Aroma;Camellia sinensis;GENE-EXPRESSION;Jasmonic acid;LEAF;LEAVES;SALICYLIC-ACID;Tea;volatiles;VOLATILE COMPOUNDS | WOS:000484758500008 | Chinese Acad Sci, Guangdong, Peoples R China;Guangdong Food & Drug Vocat Coll, Guangdong, Peoples R China;Univ Chinese Acad Sci, Beijing, Peoples R China | China | 2,019 | null | null | null | null | English | null | AM J ANAL CHEM;APPL ENVIRON MICROB;BIOSCI BIOTECH BIOCH;BMC GENOMICS;CRIT REV FOOD SCI;FOOD CHEM;FOOD RES INT;FRONT PLANT SCI;HORTIC RES-ENGLAND;INT J MOL SCI;INT J PLANT PROD;J AGR FOOD CHEM;J CHEM ECOL;J PLANT PHYSIOL;MOLECULES;NAT PROTOC;NATURE;P NATL ACAD SCI USA;PHYSIOL PLANTARUM;PLANT CELL;PLANT CELL PHYSIOL;PLANT HORMONES BIOSY;PLANT SCI;POSTHARVEST BIOL TEC;READING AND DYSLEXIA IN DIFFERENT ORTHOGRAPHIES;RSC ADV;SCIENCE;STRESS PHYSL TEA FAC;Tea Biochemistry;TREE PHYSIOL;TRENDS PLANT SCI | Dong, Fang;Gu, Dachuan;Liao, Yinyin;Wang, Xuewen;Yang, Ziyin;Zeng, Lanting | 2024-03-11
ER | Baldermann S.;Barua, D N;Bömke, C;Cho, J Y;Constantinou, S;Cutler, A J;Dong, F;Ghanati, F;Gui, J D;Han, B Y;Hao, X Y;Huerta, L;Ishiwari, H;Kazan, K;Maffei, M E;Malamy, J;Mcdougall, S;Noguerol-Pato, R;Pan, X Q;Peng, Q Y;Pál, M;Qin, X Q;Schwartz S., H;Upadhyaya H.;Wan X.C.;Wang, D L;Wu, J Q;Xiao, Y H;Xue, T T;Yang, Z Y;Zeng, L T;Zhang L.;Zhou, L;Zhou, Y;Zhu, J Y | IW1VM | Guangdong, Peoples R China;Guangdong, Peoples R China. | 37 | null | 3 | null | null | Dong, Fang;Gu, Dachuan;Liao, Yinyin;Wang, Xuewen;Yang, Ziyin;Zeng, Lanting | POSTHARVEST BIOL TEC | Beijing, Peoples R China;Guangdong, Peoples R China |
Cao, Y B;Guo, Y K;Huang, H Y;Liao, W X;Liu, Q;Liu, Y Q;Lu, Y Y;Xie, Z | 10.1038/s41467-019-12794-2 | 4801 | MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND | 2ord1n1sg3w630r1224242oy6q6o2a1d6r | Oncolytic adenovirus programmed by synthetic gene circuit for cancer immunotherapy | Tsinghua Univ | null | Xie, Z (corresponding author), Tsinghua Univ, Bioinformat Div, Ctr Synthet & Syst Biol, Dept Automat,Beijing Natl Res Ctr Informat Sci &, Beijing 100084, Peoples R China.;Xie, Z (corresponding author), Tsinghua Univ, MOE Key Lab Bioinformat, Ctr Synthet & Syst Biol, Dept Automat,Beijing Natl Res Ctr Informat Sci &, Beijing 100084, Peoples R China. | null | Cao, Yubing;Guo, Yakun;Huang, Huiya;Liao, Weixi;Liu, Qiang;Liu, Yiqi;Lu, Yinying;Xie, Zhen | Multidisciplinary Sciences | Tsinghua National Laboratory for Information Science and Technology Bioinformatics Public Instrument Platform, Tsinghua Biomedical Sciences Public Instrument Platform, Tsinghua Animal Facility; National Natural Science Foundation of China [61721003]; Basic Research Program of Tsinghua National Lab for Information Science and Technology; Syngentech Inc. | WOS | Xie, Z | PLA Genaral Hosp, Beijing, Peoples R China;Syngentech Inc, Beijing, Peoples R China;Tsinghua Univ, Beijing, Peoples R China | 10 | adenovirus;by;cancer;circuit;for;gene;immunotherapy;oncolytic;programmed;synthetic | 1 | null | NATURE PUBLISHING GROUP | PLA Genaral Hosp, Comprehens Liver Canc Ctr, Med Ctr 5, 100 Xi Si Huan Middle Rd, Beijing 100039, Peoples R China;Syngentech Inc, Zhongguancun Life Sci Pk, Beijing 102206, Peoples R China;Tsinghua Univ, Bioinformat Div, Ctr Synthet & Syst Biol, Dept Automat,Beijing Natl Res Ctr Informat Sci &, Beijing 100084, Peoples R China;Tsinghua Univ, MOE Key Lab Bioinformat, Ctr Synthet & Syst Biol, Dept Automat,Beijing Natl Res Ctr Informat Sci &, Beijing 100084, Peoples R China;Tsinghua Univ, MOE Key Lab Bioinformat, Ctr Synthet & Syst Biol, Dept Automat,Beijing Natl Res Ctr Informat Sci &, Beijing 100084, Peoples R China.; Xie, Z (corresponding author), Tsinghua Univ, Bioinformat Div, Ctr Synthet & Syst Biol, Dept Automat,Beijing Natl Res Ctr Informat Sci &, Beijing 100084, Peoples R China | Article | Tsinghua Univ | LONDON | null | null | PLA Genaral Hosp;Syngentech Inc;Tsinghua Univ | Basic Research Program of Tsinghua National Lab for Information Science and Technology;National Natural Science Foundation of China;Syngentech Inc.;Tsinghua National Laboratory for Information Science and Technology Bioinformatics Public Instrument Platform, Tsinghua Biomedical Sciences Public Instrument Platform, Tsinghua Animal Facility | Xie, Z (corresponding author), Tsinghua Univ, MOE Key Lab Bioinformat, Ctr Synthet & Syst Biol, Dept Automat,Beijing Natl Res Ctr Informat Sci &, Beijing 100084, Peoples R China.; Xie, Z (corresponding author), Tsinghua Univ, Bioinformat Div, Ctr Synthet & Syst Biol, Dept Automat,Beijing Natl Res Ctr Informat Sci &, Beijing 100084, Peoples R China. | null | Cao, Yubing;Guo, Yakun;Huang, Huiya;Liao, Weixi;Liu, Qiang;Liu, Yiqi;Lu, Yinying;Xie, Zhen | 52 | 4 | 491,306,200,009 | Basic Research Program of Tsinghua National Lab for Information Science and Technology;National Natural Science Foundation of China [61721003];Syngentech Inc.;Tsinghua National Laboratory for Information Science and Technology Bioinformatics Public Instrument Platform, Tsinghua Biomedical Sciences Public Instrument Platform, Tsinghua Animal Facility | China | NATURE COMMUNICATIONS | China | null | null | Tsinghua Univ, MOE Key Lab Bioinformat, Ctr Synthet & Syst Biol, Dept Automat,Beijing Natl Res Ctr Informat Sci &, Beijing 100084, Peoples R China | 2041-1723 | Cao, Y B;Guo, Y K;Huang, H Y;Liao, W X;Liu, Q;Liu, Y Q;Lu, Y Y;Xie, Z | OCT 22 | zhenxie@tsinghua.edu.cn | cancer immunotherapy;oncolytic adenovirus;synthetic gene circuit | 8 | J | Science & Technology - Other Topics | adenoviral replication;ALPHA;ANTIBODY;CANCER;cancer immunotherapy;cancers;COLONY-STIMULATING FACTOR;combinatorial treatment;combining tumor lysis;computational simulations;DELIVERY;difficulty increasing specificity;effective strategy;hepatocellular carcinoma cells;HEPATOCELLULAR-CARCINOMA;IDENTIFICATION;immune effector;immune effectors;immune responses;immunocompetent mouse models;immunomodulators;improving efficacy;innovative immunotherapies;lead;limited understanding;LIVER;local lymphocyte cytotoxicity;microRNA inputs;modular synthetic gene circuits;multiple promoter;non-replicable adenovirus;oncolytic adenovirus;oncolytic virotherapy;oncolytic virus;performing mouse model experiments;population dynamics;programmable;release;replicable adenovirus;REPLICATIVE ADENOVIRUS;response;results;robust therapeutic efficacy;secretion;superior tumor-killing efficacy;synergistic effect;Synthetic gene circuit;systematic vaccination;variety;virus | Huang, H Y | ALPHA;ANTIBODY;COLONY-STIMULATING FACTOR;DELIVERY;HEPATOCELLULAR-CARCINOMA;IDENTIFICATION;LIVER;REPLICATIVE ADENOVIRUS;virus | null | [Huang, Huiya; Liao, Weixi; Xie, Zhen] Tsinghua Univ, MOE Key Lab Bioinformat, Ctr Synthet & Syst Biol, Dept Automat,Beijing Natl Res Ctr Informat Sci &, Beijing 100084, Peoples R China. [Huang, Huiya; Liao, Weixi; Xie, Zhen] Tsinghua Univ, Bioinformat Div, Ctr Synthet & Syst Biol, Dept Automat,Beijing Natl Res Ctr Informat Sci &, Beijing 100084, Peoples R China. [Liu, Yiqi; Cao, Yubing; Liu, Qiang; Guo, Yakun] Syngentech Inc, Zhongguancun Life Sci Pk, Beijing 102206, Peoples R China. [Lu, Yinying] PLA Genaral Hosp, Comprehens Liver Canc Ctr, Med Ctr 5, 100 Xi Si Huan Middle Rd, Beijing 100039, Peoples R China. | We thank members of Xie lab for helpful discussions. We thank Huixin Geng for technical support. The research was supported by Tsinghua National Laboratory for Information Science and Technology Bioinformatics Public Instrument Platform, Tsinghua Biomedical Sciences Public Instrument Platform, Tsinghua Animal Facility. The financial supports were provided by Syngentech Inc., National Natural Science Foundation of China (61721003) and the Basic Research Program of Tsinghua National Lab for Information Science and Technology. | adenoviral replication;cancer;cancers;combinatorial treatment;combining tumor lysis;computational simulations;difficulty increasing specificity;effective strategy;hepatocellular carcinoma cells;immune effector;immune effectors;immune responses;immunocompetent mouse models;immunomodulators;improving efficacy;innovative immunotherapies;lead;limited understanding;local lymphocyte cytotoxicity;microRNA inputs;modular synthetic gene circuits;multiple promoter;non-replicable adenovirus;oncolytic adenovirus;oncolytic virotherapy;oncolytic virus;performing mouse model experiments;population dynamics;programmable;release;replicable adenovirus;response;results;robust therapeutic efficacy;secretion;superior tumor-killing efficacy;synergistic effect;systematic vaccination;variety | 10.1006/mthe.2000.0130;10.1007/s002850050127;10.1016/j.canlet.2016.07.019;10.1016/j.ccr.2011.01.001;10.1016/j.cell.2007.04.040;10.1016/j.cell.2012.08.040;10.1016/j.cell.2017.08.027;10.1016/j.cell.2017.09.049;10.1016/j.celrep.2016.07.061;10.1016/j.ejca.2016.02.025;10.1016/j.omto.2016.12.004;10.1021/acssynbio.7b00134;10.1038/cgt.2011.67;10.1038/cgt.2014.34;10.1038/nature10358;10.1038/nature14011;10.1038/nature24649;10.1038/nbt.3301;10.1038/nbt957;10.1038/nchembio.1680;10.1038/nchembio.1736;10.1038/ncomms10456;10.1038/ncomms14754;10.1038/ncomms6293;10.1038/nm.1776;10.1038/nm.3089;10.1038/nm.4015;10.1038/nrclinonc.2016.58;10.1038/nrd.2016.254;10.1038/nrd4663;10.1038/sj.gt.3300870;10.1038/sj.gt.3302001;10.1056/NEJMoa1709684;10.1073/pnas.1604391113;10.1098/rsif.2017.0150;10.1101/gad.7.4.546;10.1126/science.1205527;10.1126/science.274.5286.373;10.1128/JVI.67.10.5911-5921.1993;10.1158/0008-5472.CAN-16-1708;10.1158/0008-5472.CAN-17-1662;10.1158/1078-0432.CCR-05-1059;10.1158/1535-7163.MCT-12-0157;10.1200/JCO.2014.58.3377;10.1200/JCO.2015.61.6870;10.1371/journal.pone.0005553;10.1371/journal.pone.0073964 | Tsinghua Univ | Cao, Y B;Guo, Y K;Huang, H Y;Liao, W X;Liu, Q;Liu, Y Q;Lu, Y Y;Xie, Z | Huang, H Y: Tsinghua Univ, MOE Key Lab Bioinformat, Ctr Synthet & Syst Biol, Dept Automat,Beijing Natl Res Ctr Informat Sci &, Beijing 100084, Peoples R China | Liu, Yiqi;Xie, Zhen | 61721003 | 48 | null | China | PLA Genaral Hosp;Syngentech Inc;Tsinghua Univ | Huang, Huiya | gold, Green Published | ALPHA;ANTIBODY;COLONY-STIMULATING FACTOR;DELIVERY;HEPATOCELLULAR-CARCINOMA;IDENTIFICATION;LIVER;REPLICATIVE ADENOVIRUS;VIRUS | Huang, Huiya; Liu, Yiqi; Liao, Weixi; Cao, Yubing; Liu, Qiang; Guo, Yakun; Lu, Yinying; Xie, Zhen; | null | PLA Genaral Hosp, Comprehens Liver Canc Ctr, Med Ctr 5, 100 Xi Si Huan Middle Rd, Beijing 100039, Peoples R China;Syngentech Inc, Zhongguancun Life Sci Pk, Beijing 102206, Peoples R China;Tsinghua Univ, Bioinformat Div, Ctr Synthet & Syst Biol, Dept Automat,Beijing Natl Res Ctr Informat Sci &, Beijing 100084, Peoples R China;Tsinghua Univ, MOE Key Lab Bioinformat, Ctr Synthet & Syst Biol, Dept Automat,Beijing Natl Res Ctr Informat Sci &, Beijing 100084, Peoples R China | PLA Genaral Hosp, Comprehens Liver Canc Ctr, Med Ctr 5, 100 Xi Si Huan Middle Rd, Beijing 100039, Peoples R China;Syngentech Inc, Zhongguancun Life Sci Pk, Beijing 102206, Peoples R China;Tsinghua Univ, Bioinformat Div, Ctr Synthet & Syst Biol, Dept Automat,Beijing Natl Res Ctr Informat Sci &, Beijing 100084, Peoples R China;Tsinghua Univ, MOE Key Lab Bioinformat, Ctr Synthet & Syst Biol, Dept Automat,Beijing Natl Res Ctr Informat Sci &, Beijing 100084, Peoples R China | null | null | null | 1993;1996;1998;1999;2000;2001;2003;2004;2006;2007;2008;2009;2011;2012;2013;2014;2015;2016;2017;2018 | 56 | Tsinghua Univ, Bioinformat Div, Ctr Synthet & Syst Biol, Dept Automat,Beijing Natl Res Ctr Informat Sci &, Beijing 100084, Peoples R China;Tsinghua Univ, MOE Key Lab Bioinformat, Ctr Synthet & Syst Biol, Dept Automat,Beijing Natl Res Ctr Informat Sci &, Beijing 100084, Peoples R China | Nat. Commun. | Xie, Zhen | NATURE PUBLISHING GROUP | ,;a;adenoviral;adenovirus;against;an;and;by;can;cancer;cancers;carcinoma;cells;challenging;circuits;combinatorial;combining;computational;construct;control;cytotoxicity;difficulty;due;dynamics;effect;effective;effector;effectors;efficacy;encodes;engineer;exert;experiments;find;for;furthermore;gene;has;hepatocellular;here;immune;immunocompetent;immunomodulators;immunotherapies;improving;in;increasing;innovative;inputs;its;lead;limited;local;lymphocyte;lysis;may;microRNA;model;models;modular;more;mouse;multiple;non-replicable;observe;of;on;oncolytic;our;performing;population;programmable;promoter;promoting;provide;release;remains;replicable;replication;response;responses;results;robust;secretion;selectively;show;simulations;specificity;strategy;superior;synergistic;synthetic;systematic;than;that;therapeutic;to;treatment;tumor;tumor-killing;understanding;vaccination;variety;virotherapy;virus;we;which;with | Tsinghua Univ | Improving efficacy of oncolytic virotherapy remains challenging due to difficulty increasing specificity and immune responses against cancer and limited understanding of its population dynamics. Here, we construct programmable and modular synthetic gene circuits to control adenoviral replication and release of immune effectors selectively in hepatocellular carcinoma cells in response to multiple promoter and microRNA inputs. By performing mouse model experiments and computational simulations, we find that replicable adenovirus has a superior tumor-killing efficacy than non-replicable adenovirus. We observe a synergistic effect on promoting local lymphocyte cytotoxicity and systematic vaccination in immunocompetent mouse models by combining tumor lysis and secretion of immunomodulators. Furthermore, our computational simulations show that oncolytic virus which encodes immunomodulators can exert a more robust therapeutic efficacy than combinatorial treatment with oncolytic virus and immune effector. Our results provide an effective strategy to engineer oncolytic adenovirus, which may lead to innovative immunotherapies for a variety of cancers. | AAK-1630-2020;GPW-5925-2022 | ALPHA;ANTIBODIES;COLONY-STIMULATING FACTOR;DELIVERY;HEPATOCELLULAR-CARCINOMA;IDENTIFICATION;LIVER;REPLICATING ADENOVIRUS;VIRUS | 1 | null | null | 15 | ALPHA;ANTIBODIES;COLONY-STIMULATING FACTOR;DELIVERY;HEPATOCELLULAR-CARCINOMA;IDENTIFICATION;LIVER;REPLICATING ADENOVIRUS;virus | WOS:000491306200009 | PLA Genaral Hosp, Beijing, Peoples R China;Syngentech Inc, Beijing, Peoples R China;Tsinghua Univ, Beijing, Peoples R China | China | 2,019 | null | null | null | null | English | null | ACS SYNTH BIOL;CANCER CELL;CANCER GENE THER;CANCER LETT;CANCER RES;CELL;CELL REP;CLIN CANCER RES;EUR J CANCER;GENE DEV;GENE THER;J CLIN ONCOL;J MATH BIOL;J R SOC INTERFACE;J VIROL;MOL CANCER THER;MOL THER;MOL THER-ONCOLYTICS;NAT BIOTECHNOL;NAT CHEM BIOL;NAT COMMUN;NAT MED;NAT REV CLIN ONCOL;NAT REV DRUG DISCOV;NATURE;NEW ENGL J MED;P NATL ACAD SCI USA;PLOS ONE;SCIENCE | Cao, Yubing;Guo, Yakun;Huang, Huiya;Liao, Weixi;Liu, Qiang;Liu, Yiqi;Lu, Yinying;Xie, Zhen | 2024-03-11
ER | Andtbacka, R H I;Angelici, B;Bett, A J;Bischoff, J R;Boutros, C;Breitbach, C J;Callegari, E;Chau, A H;Chiou, V L;Debbas, M;Dolgin, E;Du, T;Engler, C;Fajardo, C A;Guo, Y C;Havunen, R;Heo, J;Herbst, R S;Hofmann, L;Hou, J;Ishikawa, H;Kaufman, H L;Kelly, E J;Kirschner, D;Klebanoff, C A;Konstorum, A;Landgraf, P;Lapique, N;Li, Y Q;Liao, W X;Liu, X;Liu, Y H;Liu, Z Q;Ma, D;Morel, M;Nagayama, Y;Nissim, L;Ramesh, N;Ribas, A;Szymczak, A L;Toda, M;Wartewig, T;Wodarz, D;Wolchok, J D;Wroblewska, L;Xie, Z;Yuan, X F;Zhang, Z W | JF3SB | Beijing, Peoples R China;Beijing, Peoples R China. | 63 | null | 3 | null | 31,641,136 | Cao, Yubing;Guo, Yakun;Huang, Huiya;Liao, Weixi;Liu, Qiang;Liu, Yiqi;Lu, Yinying;Xie, Zhen | NAT COMMUN | Beijing, Peoples R China |
Dickinson, B C;Jones, K A;Zinkus-Boltz, J | 10.1088/2399-1984/ab4b78 | 042002 | TEMPLE CIRCUS, TEMPLE WAY, BRISTOL BS1 6BE, ENGLAND | 2y6601ymo634xq168f1q341j1w5461l4t | Recent advances in developing and applying biosensors for synthetic biology | Univ Chicago | null | Dickinson, BC (corresponding author), Univ Chicago, Dept Chem, Chicago, IL 60637 USA. | null | Dickinson, Bryan C;Jones, Krysten A;Zinkus-Boltz, Julia | Materials Science, Multidisciplinary;Nanoscience & Nanotechnology;Physics, Applied | University of Chicago; National Institute of Mental Health [RF1 MH114102]; National Cancer Institute of the National Institutes of Health [R21 CA217754] | WOS | Dickinson, B C | Univ Chicago, Chicago, IL USA | 3 | advances;and;applying;biology;biosensors;developing;for;in;recent;synthetic | 1 | Jones, Krysten;Zinkus-Boltz, Julia | IOP PUBLISHING LTD | Univ Chicago, Dept Chem, Chicago, IL 60637 USA | Review | Univ Chicago | BRISTOL | null | null | Univ Chicago | National Cancer Institute of the National Institutes of Health;National Institute of Mental Health;University of Chicago | Dickinson, BC (corresponding author), Univ Chicago, Dept Chem, Chicago, IL 60637 USA. | null | Dickinson, Bryan C;Jones, Krysten A;Zinkus-Boltz, Julia | 55 | 1 | 517,260,400,002 | National Cancer Institute of the National Institutes of Health [R21 CA217754];National Institute of Mental Health [RF1 MH114102];University of Chicago | USA | NANO FUTURES | USA | null | null | Univ Chicago, Dept Chem, Chicago, IL 60637 USA | null | Dickinson, B C;Jones, K A;Zinkus-Boltz, J | OCT | Dickinson@uchicago.edu | biosensors;developing;recent advances;synthetic biology | 3 | J | Materials Science;Physics;Science & Technology - Other Topics | advancements;applications;biological engineering efforts;BIOLOGY;biosensors;cellular signaling pathways;chemical biology;clinical applications;CONDITIONAL EXPRESSION;CRYSTAL-STRUCTURE;developing;directed evolution;ENZYME PRODRUG THERAPY;evolutionary methods;flexible biosensors;Gene circuits;host organisms;IN-VIVO;indispensable component;input signals;molecular protein scaffolds;naturally-occurring biological processes;PROTEIN-PROTEIN INTERACTIONS;rational design;recent advances;recent innovations;review;SPLIT-LUCIFERASE;STRUCTURAL BASIS;synthetic biologist's toolbox;synthetic biology;synthetic biology tools;synthetic gene circuits;T7 RNA-POLYMERASE;tractable outputs;utility across basic biological research;wide range | Jones, K A | biosensors;chemical biology;CONDITIONAL EXPRESSION;CRYSTAL-STRUCTURE;directed evolution;ENZYME PRODRUG THERAPY;Gene circuits;IN-VIVO;PROTEIN-PROTEIN INTERACTIONS;SPLIT-LUCIFERASE;STRUCTURAL BASIS;Synthetic biology;T7 RNA-POLYMERASE | null | [Jones, Krysten A.; Zinkus-Boltz, Julia; Dickinson, Bryan C.] Univ Chicago, Dept Chem, Chicago, IL 60637 USA. | This work was supported by the University of Chicago, the National Institute of Mental Health (RF1 MH114102) and the National Cancer Institute (R21 CA217754) of the National Institutes of Health. | advancements;applications;biological engineering efforts;biology;biosensors;cellular signaling pathways;clinical applications;evolutionary methods;flexible biosensors;host organisms;indispensable component;input signals;molecular protein scaffolds;naturally-occurring biological processes;rational design;recent innovations;review;synthetic biologist's toolbox;synthetic biology tools;synthetic gene circuits;tractable outputs;utility across basic biological research;wide range | 10.1002/1873-3468.12548;10.1002/biot.201700432;10.1002/biot.201700561;10.1002/biot.201700648;10.1002/bit.25676;10.1002/bit.26340;10.1002/cbic.200700713;10.1002/cbic.201000041;10.1002/cbic.201000642;10.1002/cbic.201800707;10.1007/978-1-4939-6940-1_14;10.1007/s00216-014-7980-8;10.1007/s00253-015-7090-3;10.1007/s11095-005-6156-9;10.1007/s13238-015-0153-5;10.1007/s13353-016-0341-x;10.1016/0022-2836(86)90385-2;10.1016/j.addr.2016.04.032;10.1016/j.biochi.2018.09.001;10.1016/j.biortech.2017.06.114;10.1016/j.biotechadv.2016.08.003;10.1016/j.biotechadv.2018.10.001;10.1016/j.bmcl.2008.12.057;10.1016/j.cbpa.2011.10.014;10.1016/j.cbpa.2013.09.012;10.1016/j.cbpa.2015.05.013;10.1016/j.ceca.2008.02.002;10.1016/j.cell.2010.07.014;10.1016/j.cell.2013.04.025;10.1016/j.cell.2013.06.044;10.1016/j.cell.2014.01.027;10.1016/j.cell.2014.02.001;10.1016/j.cell.2014.02.039;10.1016/j.cell.2015.08.007;10.1016/j.cell.2016.01.011;10.1016/j.cell.2016.01.012;10.1016/j.cell.2016.09.011;10.1016/j.cell.2016.11.017;10.1016/j.cell.2016.12.009;10.1016/j.cell.2017.03.041;10.1016/j.cell.2017.09.049;10.1016/j.cell.2018.02.033;10.1016/j.cell.2018.11.052;10.1016/j.cell.2019.04.009;10.1016/j.cell.2019.05.049;10.1016/j.celrep.2013.06.020;10.1016/j.cels.2015.06.001;10.1016/j.chembiol.2014.12.011;10.1016/j.copbio.2014.12.021;10.1016/j.copbio.2016.03.005;10.1016/j.jmb.2005.10.076;10.1016/j.jmb.2018.06.037;10.1016/j.molcel.2014.04.022;10.1016/j.molcel.2018.09.018;10.1016/j.sbi.2009.09.001;10.1016/j.sbi.2019.01.013;10.1016/j.tibtech.2010.10.004;10.1016/j.tibtech.2013.01.018;10.1016/j.tibtech.2015.12.014;10.1016/j.tig.2016.01.005;10.1016/S0076-6879(00)28399-7;10.1016/S0079-6603(03)01001-8;10.1016/S0092-8674(04)00059-5;10.1016/S0092-8674(04)00120-5;10.1016/S0959-440X(00)00235-9;10.1021/ac000617z;10.1021/ac0013296;10.1021/ac010717k;10.1021/acs.biochem.8b01202;10.1021/acs.molpharmaceut.5b00464;10.1021/acscentsci.7b00058;10.1021/acscentsci.7b00107;10.1021/acscentsci.9b00567;10.1021/acschembio.5b00753;10.1021/acschembio.5b01019;10.1021/acschembio.7b00532;10.1021/acschembio.8b00524;10.1021/acschembio.8b00919;10.1021/acssynbio.6b00248;10.1021/acssynbio.6b00279;10.1021/acssynbio.7b00059;10.1021/acssynbio.7b00136;10.1021/acssynbio.7b00169;10.1021/acssynbio.8b00242;10.1021/bi000365w;10.1021/bi00415a055;10.1021/cb800065s;10.1021/ja805203w;10.1021/ja994421w;10.1021/jacs.5b02774;10.1021/jacs.5b10290;10.1021/jacs.7b06152;10.1021/jacs.7b06555;10.1021/jacs.8b05012;10.1021/sb200016s;10.1021/sb400077j;10.1021/sb400081r;10.1021/sb400128g;10.1021/sb500299c;10.1038/19999;10.1038/228227a0;10.1038/346818a0;10.1038/364593a0;10.1038/cr.2013.122;10.1038/gt.2011.101;10.1038/mi.2009.116;10.1038/msb.2008.62;10.1038/mt.2011.256;10.1038/nature01129;10.1038/nature09929;10.1038/nature14592;10.1038/nature24049;10.1038/nature26155;10.1038/nbt.2501;10.1038/nbt.2510;10.1038/nbt.2623;10.1038/nbt.2689;10.1038/nbt.3245;10.1038/nbt.3404;10.1038/nbt.3563;10.1038/nbt.3879;10.1038/nbt.4222;10.1038/nbt0602-619;10.1038/nchembio.1753;10.1038/nchembio.2299;10.1038/nchembio.2390;10.1038/ncomms12009;10.1038/ncomms13056;10.1038/ncomms14370;10.1038/ncomms1516;10.1038/ncomms15690;10.1038/ncomms5240;10.1038/nmeth.2532;10.1038/nmeth.3993;10.1038/nmeth932;10.1038/nmeth967;10.1038/nprot.2009.239;10.1038/nprot.2017.119;10.1038/nrm3738;10.1038/nrmicro3239;10.1038/nsmb.3014;10.1038/s41467-018-03069-3;10.1038/s41467-018-04252-2;10.1038/s41467-018-05466-0;10.1038/s41467-018-05525-6;10.1038/s41467-018-07473-7;10.1038/s41467-018-07610-2;10.1038/s41557-018-0174-9;10.1038/s41564-017-0004-7;10.1038/s41564-018-0216-5;10.1038/s41589-018-0046-z;10.1038/s41589-018-0121-5;10.1038/s41589-018-0181-6;10.1038/s41592-018-0301-y;10.1038/sj.cgt.7700685;10.1038/sj.gt.3300569;10.1038/srep02854;10.1039/c1mb05070b;10.1039/c3cs35528d;10.1039/c3cs60141b;10.1039/c4an01418a;10.1042/EBC20150001;10.1049/ip-nbt:20050047;10.1053/j.gastro.2012.06.037;10.1073/pnas.0402940101;10.1073/pnas.0700293104;10.1073/pnas.0710487105;10.1073/pnas.1111943109;10.1073/pnas.1220157110;10.1073/pnas.1321321111;10.1073/pnas.1417910112;10.1073/pnas.1501698112;10.1073/pnas.1508521112;10.1073/pnas.1600375113;10.1073/pnas.77.5.2819;10.1073/pnas.81.7.2035;10.1073/pnas.95.1.352;10.1073/pnas.97.9.4826;10.1074/jbc.C200588200;10.1074/jbc.M400139200;10.1089/10430349950018968;10.1089/hum.2015.087;10.1093/hmg/ddv120;10.1093/nar/25.6.1203;10.1093/nar/gkh094;10.1093/nar/gkn924;10.1093/nar/gks597;10.1093/nar/gks636;10.1093/nar/gkt101;10.1093/nar/gkt135;10.1093/nar/gkt780;10.1093/nar/gku402;10.1093/nar/gku884;10.1093/nar/gkv1289;10.1093/nar/gkv601;10.1093/nar/gkv616;10.1093/nar/gkw117;10.1093/nar/gkw1267;10.1097/CJI.0b013e31819b7c8e;10.1101/cshperspect.a032532;10.1111/bph.13553;10.1126/science.1077464;10.1126/science.1138140;10.1126/science.1163433;10.1126/science.1179555;10.1126/science.1225829;10.1126/science.1247997;10.1126/science.1258096;10.1126/science.2200121;10.1126/science.273.5272.239;10.1126/science.286.5448.2305;10.1126/science.289.5483.1352;10.1126/science.aad1067;10.1126/science.aaf5573;10.1126/science.aaq0180;10.1126/science.aat0271;10.1126/science.aat5062;10.1126/scisignal.2001449;10.1126/scitranslmed.3005568;10.1128/AEM.01019-08;10.1128/jb.174.2.619-622.1992;10.1128/mBio.02321-18;10.1128/mSystems.00125-19;10.1136/gutjnl-2015-309990;10.1146/annurev-biochem-060614-034411;10.1146/annurev-immunol-051116-052302;10.1146/annurev-neuro-071013-014048;10.1146/annurev-virology-101416-041616;10.1152/physrev.00009.2017;10.1158/0008-5472.CAN-12-2649;10.1158/1078-0432.CCR-12-2422;10.1186/1471-2105-7-S2-S6;10.1186/s13104-018-3965-6;10.1210/en.2007-0235;10.1261/rna.2433111;10.1371/journal.pone.0131037;10.15252/msb.20145299;10.1534/genetics.113.152710;10.2116/analsci.30.539;10.2144/000112036;10.2174/1389200033489253;10.3389/fmicb.2015.00685;10.3390/foods7090141;10.3390/genes9070351;10.3390/genes9080375;10.3390/molecules23123178;10.3390/s17122918;10.7554/eLife.10606;10.7554/eLife.43826;[10.1038/NCHEMBIO.1453, 10.1038/nchembio.1453];[10.1038/NCHEMBIO.1793, 10.1038/nchembio.1793];[10.1038/NCHEMBIO.2253, 10.1038/nchembio.2253];[10.1038/NCHEMBIO.2565, 10.1038/nchembio.2565];[10.1038/NMETH.2205, 10.1038/nmeth.2205];[10.1038/nmeth.2598, 10.1038/NMETH.2598];[10.1038/nmeth.2600, 10.1038/NMETH.2600];[10.1038/NMETH.2969, 10.1038/nmeth.2969];[10.1038/NMETH.3486, 10.1038/nmeth.3486];[10.1038/NMETH.3580, 10.1038/nmeth.3580];[10.1038/NMETH.3994, 10.1038/nmeth.3994];[10.1038/NMETH.4042, 10.1038/nmeth.4042];[10.1038/NMETH.4430, 10.1038/nmeth.4430];[10.1038/NMICROBIOL.2016.85, 10.1038/nmicrobiol.2016.85];[10.1146/annurev.bioeng-071811-150118, 10.1146/annurev-bioeng-071811-150118];[10.2144/0000113943, 10.2144/000113943] | Univ Chicago | Dickinson, B C;Jones, K A;Zinkus-Boltz, J | Jones, K A: Univ Chicago, Dept Chem, Chicago, IL 60637 USA | null | R21 CA217754;RF1 MH114102 | 271 | null | USA | Univ Chicago | Jones, Krysten A | null | CONDITIONAL EXPRESSION;CRYSTAL-STRUCTURE;DIRECTED EVOLUTION;ENZYME PRODRUG THERAPY;GENE CIRCUITS;IN-VIVO;PROTEIN-PROTEIN INTERACTIONS;SPLIT-LUCIFERASE;STRUCTURAL BASIS;T7 RNA-POLYMERASE | Jones, Krysten A.; Zinkus-Boltz, Julia; Dickinson, Bryan C.; | null | Univ Chicago, Dept Chem, Chicago, IL 60637 USA | Univ Chicago, Dept Chem, Chicago, IL 60637 USA | 2399-1984 | Biosensor;chemical biology;directed evolution;Synthetic biology | 4 | 1970;1980;1984;1986;1987;1988;1990;1991;1992;1993;1996;1997;1998;1999;2000;2001;2002;2003;2004;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017;2018;2019 | 7 | Univ Chicago, Dept Chem, Chicago, IL 60637 USA | Nano Futures | Dickinson, Bryan C | IOP PUBLISHING LTD | ,;a;across;advancements;an;and;applications;are;basic;be;biological;biologist's;biology;biosensors;by;can;cellular;circuits;clinical;compiled;component;customized;design;efforts;engineering;evolutionary;flexible;for;gene;generation;harnessed;have;host;in;including;indispensable;informed;innovations;input;into;introduce;led;methods;molecular;naturally-occurring;of;organisms;outputs;pathways;processes;protein;range;rational;recent;reliable;research;review;robust;scaffolds;signaling;signals;synthetic;tailored;that;the;these;this;through;to;toolbox;tools;tractable;translate;using;utility;we;wide | Univ Chicago | Biosensors are an indispensable component of the synthetic biologist's toolbox. Informed by biology and customized through rational design and evolutionary methods, these molecular protein scaffolds translate input signals into tractable outputs. By using biosensors to introduce synthetic gene circuits and cellular signaling pathways into host organisms, naturally-occurring biological processes can be harnessed and tailored for a wide range of applications. In this review, we have compiled recent innovations and advancements that have led to the generation of robust, reliable, and flexible biosensors for utility across basic biological research and synthetic biology tools, including biological engineering efforts and clinical applications. | null | CONDITIONAL EXPRESSION;CRYSTAL-STRUCTURE;DIRECTED EVOLUTION;ENZYME PRODRUG THERAPY;GENE CIRCUITS;IN-VIVO;PROTEIN-PROTEIN INTERACTIONS;SPLIT-LUCIFERASE;STRUCTURAL BASIS;T7 RNA-POLYMERASE | 6 | null | biosensors;chemical biology;directed evolution;Synthetic biology | 21 | Biosensor;chemical biology;CONDITIONAL EXPRESSION;CRYSTAL-STRUCTURE;directed evolution;ENZYME PRODRUG THERAPY;Gene circuits;IN-VIVO;PROTEIN-PROTEIN INTERACTIONS;Split luciferase;STRUCTURAL BASIS;Synthetic biology;T7 RNA-POLYMERASE | WOS:000517260400002 | Univ Chicago, Chicago, IL USA | USA | 2,019 | null | 0000-0003-0028-5360;0000-0003-0711-5516 | null | null | English | null | ACS CENTRAL SCI;ACS CHEM BIOL;ACS SYNTH BIOL;ADV DRUG DELIVER REV;ANAL BIOANAL CHEM;ANAL CHEM;ANAL SCI;ANALYST;ANNU REV BIOCHEM;ANNU REV BIOMED ENG;ANNU REV IMMUNOL;ANNU REV NEUROSCI;ANNU REV VIROL;APPL ENVIRON MICROB;APPL MICROBIOL BIOT;BIOCHEMISTRY-US;BIOCHIMIE;BIOORG MED CHEM LETT;BIORESOURCE TECHNOL;BIOTECHNIQUES;BIOTECHNOL ADV;BIOTECHNOL BIOENG;BIOTECHNOL J;BMC BIOINFORMATICS;BMC Res Notes;BRIT J PHARMACOL;CANCER GENE THER;CANCER RES;CELL;CELL CALCIUM;CELL REP;CELL RES;CELL SYST;CHEM BIOL;CHEM SOC REV;CHEMBIOCHEM;CLIN CANCER RES;CSH PERSPECT BIOL;CURR DRUG METAB;CURR OPIN BIOTECH;CURR OPIN CHEM BIOL;CURR OPIN STRUC BIOL;ELIFE;ENDOCRINOLOGY;ESSAYS BIOCHEM;FEBS LETT;FOODS;FRONT MICROBIOL;GASTROENTEROLOGY;GENE THER;GENES-BASEL;GENETICS;GUT;HUM GENE THER;HUM MOL GENET;IEE P-NANOBIOTECHNOL;INHIBITION PROTEIN P;J AM CHEM SOC;J APPL GENET;J BACTERIOL;J BIOL CHEM;J IMMUNOTHER;J MOL BIOL;MBIO;METHOD ENZYMOL;METHODS MOL BIOL;MOL BIOSYST;MOL CELL;MOL PHARMACEUT;MOL SYST BIOL;MOL THER;MOLECULES;MSYSTEMS;MUCOSAL IMMUNOL;NAT BIOTECHNOL;NAT CHEM;NAT CHEM BIOL;NAT COMMUN;NAT METHODS;NAT MICROBIOL;NAT PROTOC;NAT REV MICROBIOL;NAT REV MOL CELL BIO;NAT STRUCT MOL BIOL;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;P NATL ACAD SCI-BIOL;PHARM RES-DORDR;PHYSIOL REV;PLOS ONE;PROG NUCLEIC ACID RE;PROTEIN CELL;RNA;SCI REP-UK;SCI SIGNAL;SCI TRANSL MED;SCIENCE;SENSORS-BASEL;TRENDS BIOTECHNOL;TRENDS GENET | Dickinson, Bryan C;Jones, Krysten A;Zinkus-Boltz, Julia | 2024-03-11
ER | Abil, Z;Abudayyeh, O O;Adli, M;Alam, K K;Anderson, J C;Arkin, A P;Armbruster, B N;Atasoy, D;Ausländer, S;Azad, T;Azzolini, M;Barnea, G;Barrangou, R;Bassett, A R;Baumschlager, A;Bayat, P;Beaumont, K;Beisel, C L;Bhalla, N;Bhaumik, S;Billerbeck, S;Boehm, C R;Borges, A L;Borujeni, A E;Brophy, J A N;Cabantous, S;Cameron, D E;Carlson, J C;Carpenter, A C;Carpenter, R O;Chamberl.M;Chandler, M;Chang, Z N L;Cheetham, G M T;Chen, T J;Chen, Y C;Cheng, A A;Cheng, A W;Cheng, F;Chew, W L;Chmielewski, M;Choi, J W;Chou, C J;Claeysen, S;Coward, P;Cox, D B T;Dahl, R H;Daringer, N M;Davanloo, P;Davis, K M;De Munter, S;Dicarlo, J E;Dixon, A S;Domin, G;Dong, S Y;Doudna, J A;Duan, F P;Dupin, A;Durniak, K J;Eggeling, L;Ellington, A D;Esvelt, K M;Farzadfard, F;Feng, J;Fernandez-Rodriguez, J;Fink, T;Fischbach, M A;Fowler, C C;Friedland, A E;Friedlos, F;Fu, Y F;Galarneau, A;Gangopadhyay, S A;Gao, X J;Gao, Y C;Gardner, T S;Ghosh, I;Gilbert, L A;Golynskiy, M V;Gratz, S J;Gray, D C;Green, O;Gruber, T D;Guntas, G;Han, T Y;Han, Y S;Hartfield, R M;Hattori, M;Hombach, A;Horvath, P;Hu, J H;Hwang, I Y;Hwang, W Y;Hynes, A P;Ikeda, R A;Imburgio, D;Iost, I;Isabella, V M;Jester, B W;Jiang, W Z;Jinek, M;Jones, K A;Jusiak, B;Justino, C I L;Juárez, J F;Kaczmarski, J A;Kenyon, C J;Kiani, S;Kim, C K;Kirsch, J;Kitada, T;Kleinstiver, B P;Kobayashi, H;Kodama, Y;Konermann, S;Kotula, J W;Kroeze, W K;Landowski, C P;Lanitis, E;Lavis, L D;Lee, H L;Lee, J;Lee, J F;Li, D T;Liang, F S;Liang, J C;Liang, P P;Lienert, F;Lin, Y N;Lippert, A R;Litcofsky, K D;Liu, Y C;Lutz, R;Lynch, S A;Ma, D C;Ma, Q Z;Machtel, P;Maeder, M L;Mahr, R;Maji, B;Marchesi, J R;Martell, J D;Mccormack, E;Mcguinness, R P;Meyer, A J;Michnick, S W;Mimee, M;Mishra, G K;Morsut, L;Muller, D K;Müller, S;Naydich, A D;Nguyen, D P;Niederholtmeyer, H;Nihongaki, Y;Nishimasu, H;Nissim, L;Niu, Y Y;Nolan, K F;Nuñez, J K;Oakes, B L;Ogawa, A;Ozawa, T;Pawluk, A;Peng, J;Perez-Pinera, P;Phelan, R M;Polstein, L R;Porterfield, W B;Pu, J Y;Puton, T;Raina, M;Rauch, B J;Rauch, S;Redfern, C H;Rehberg, M;Riglar, D T;Rogers, J K;Ronda, C;Roybal, K T;Schaerli, Y;Scheller, L;Schmelas, C;Schmidt, C M;Schopp, I M;Schwarz, K A;Segall-Shapiro, T H;Senturk, S;Sharma, V;Shaver Zachary, M;Shcherbakova, D M;Shekhawat, S S;Sheth, R U;Shi, S;Shin, J;Shis, D L;Shyu, Y J;Siuti, P;Slomovic, S;Sousa, R;Stano, N M;Steidler, L;Steitz, T A;Sternson, S M;Strader, C D;Studier, F W;Tahirov, T H;Temiakov, D;Temme, K;Terns, M P;Thodima, V;Tian, L;Toda, S;Townshend, B;Truong, D J J;Tuerk, C;Turner, A P F;Vandenbroucke, K;Varankovich, N V;Vorobyeva, A G;Wade, M;Wang, B J;Wang, D;Wang, H Y;Wang, J;Wang, M;Wang, T N;Wang, W Y;Way, J C;Wehr, M C;Westwood, J A;Whitaker, W R;Wierdl, M;Wintgens, J P;Wittmann, A;Wright, A V;Xie, H H;Xiu, Y;Xu, X S;Yang, Y P;Yin, Y W;Yoshimi, K;Yu, Y;Zhang, J | KQ9SA | Chicago, IL USA | 9 | null | 1 | null | null | Dickinson, Bryan C;Jones, Krysten A;Zinkus-Boltz, Julia | NANO FUTURES | Chicago, IL USA |
Nakanishi, H;Saito, H | 10.1016/j.cbpa.2019.04.013 | null | THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND | 4v1dh303h481x4h4d4182r5w60y3v4b105r45 | Mammalian gene circuits with biomolecule-responsive RNA devices | Kyoto Univ | null | Saito, H (corresponding author), Kyoto Univ, Ctr iPS Cell Res & Applicat CiRA, Sakyo Ku, 53 Kawahara Cho, Kyoto 6068507, Japan. | null | Nakanishi, Hideyuki;Saito, Hirohide | Biochemistry & Molecular Biology;Biophysics | Japan Society for the Promotion of Science (JSPS) KAKENHI [15H05722] | WOS | Saito, H | Kyoto Univ, Kyoto, Japan | 52 | biomolecule-responsive;circuits;devices;gene;mammalian;RNA;with | 1 | Nakanishi, Hideyuki | ELSEVIER SCI LTD | Kyoto Univ, Ctr iPS Cell Res & Applicat CiRA, Sakyo Ku, 53 Kawahara Cho, Kyoto 6068507, Japan | Review | Kyoto Univ | OXFORD | null | null | Kyoto Univ | Japan Society for the Promotion of Science (JSPS) KAKENHI | Saito, H (corresponding author), Kyoto Univ, Ctr iPS Cell Res & Applicat CiRA, Sakyo Ku, 53 Kawahara Cho, Kyoto 6068507, Japan. | 22 | Nakanishi, Hideyuki;Saito, Hirohide | 17 | 1 | 496,872,800,005 | Japan Society for the Promotion of Science (JSPS) KAKENHI [15H05722] | Japan | CURRENT OPINION IN CHEMICAL BIOLOGY | Japan | null | null | Kyoto Univ, Ctr iPS Cell Res & Applicat CiRA, Sakyo Ku, 53 Kawahara Cho, Kyoto 6068507, Japan | 1367-5931 | Nakanishi, H;Saito, H | OCT | hirohide.saito@cira.kyoto-u.ac.jp | biomolecule-responsive RNA devices;mammalian gene circuits | 2 | J | Biochemistry & Molecular Biology;Biophysics | another RNA device;autonomous cellular state-dependent regulation;biological studies;biomolecule-responsive mammalian gene circuits;biomolecule-responsive RNA devices;cell specific gene regulation;cells;CIRCUITS;components;input;insertional mutagenesis;killing;layered gene circuits;LIN28;low risk;mammalian gene circuits;mammalian synthetic gene circuits;one RNA device;output;recent advancements;review;RNA devices;sophisticated regulation;synthetic biologists;target cell population;therapeutic applications;tools | Nakanishi, H | CELLS;LIN28 | 16 | [Nakanishi, Hideyuki; Saito, Hirohide] Kyoto Univ, Ctr iPS Cell Res & Applicat CiRA, Sakyo Ku, 53 Kawahara Cho, Kyoto 6068507, Japan. | We thank Dr Peter Karagiannis (Kyoto University) for English proofreading. This work was supported by Japan Society for the Promotion of Science (JSPS) KAKENHI No. 15H05722. | another RNA device;autonomous cellular state-dependent regulation;biological studies;biomolecule-responsive mammalian gene circuits;biomolecule-responsive RNA devices;cell specific gene regulation;circuits;components;input;insertional mutagenesis;killing;layered gene circuits;low risk;mammalian synthetic gene circuits;one RNA device;output;recent advancements;review;RNA devices;sophisticated regulation;synthetic biologists;target cell population;therapeutic applications;tools | 10.1016/j.biomaterials.2017.02.033;10.1016/j.humpath.2010.09.007;10.1016/j.stem.2015.04.005;10.1016/j.ymthe.2018.02.021;10.1021/sb200005w;10.1038/nbt.3301;10.1038/ncomms1157;10.1038/ncomms3393;10.1038/s41467-017-00459-x;10.1038/s41467-018-06825-7;10.1038/s41467-018-07181-2;10.1038/s41589-018-0146-9;10.1038/sj.cgt.7700752;10.1038/sj.gt.3301602;10.1038/srep21991;10.1038/srep32532;10.1093/nar/gks668;10.1093/nar/gkx309;10.1096/fj.201600848R;10.1097/PAS.0b013e31802e708a;10.1128/JVI.79.12.7597-7608.2005;[10.1038/NCHEMBIO.273, 10.1038/nchembio.273] | Kyoto Univ | Nakanishi, H;Saito, H | Nakanishi, H: Kyoto Univ, Ctr iPS Cell Res & Applicat CiRA, Sakyo Ku, 53 Kawahara Cho, Kyoto 6068507, Japan | Nakanishi, Hideyuki | 15H05722 | 25 | null | Japan | Kyoto Univ | Nakanishi, Hideyuki | null | CELLS;LIN28 | Nakanishi, Hideyuki; Saito, Hirohide; | null | Kyoto Univ, Ctr iPS Cell Res & Applicat CiRA, Sakyo Ku, 53 Kawahara Cho, Kyoto 6068507, Japan | Kyoto Univ, Ctr iPS Cell Res & Applicat CiRA, Sakyo Ku, 53 Kawahara Cho, Kyoto 6068507, Japan | 1879-0402 | null | null | 2001;2004;2005;2007;2010;2011;2012;2013;2015;2016;2017;2018 | 8 | Kyoto Univ, Ctr iPS Cell Res & Applicat CiRA, Sakyo Ku, 53 Kawahara Cho, Kyoto 6068507, Japan | Curr. Opin. Chem. Biol. | Saito, Hirohide | ELSEVIER SCI LTD | ,;a;addition;advancements;and;another;applications;are;as;autonomous;based;be;because;biological;biologists;biomolecule-responsive;both;can;cell;cellular;circuits;components;construct;device;devices;enable;explain;for;gene;in;input;insertional;killing;layered;low;mammalian;more;mutagenesis;of;on;one;output;population;preferred;promising;recent;regulation;review;risk;RNA;sophisticated;specific;state-dependent;studies;such;synthetic;target;the;therapeutic;these;they;this;tools;we;with | Kyoto Univ | Mammalian synthetic gene circuits are promising tools for both biological studies and therapeutic applications. These circuits enable autonomous cellular state-dependent regulation such as the killing of a target cell population. Biomolecule-responsive RNA devices are preferred components of mammalian synthetic gene circuits, because they enable cell specific gene regulation with a low risk of insertional mutagenesis. In addition, because the output of one RNA device can be the input of another RNA device, synthetic biologists can construct layered gene circuits for more sophisticated regulation. In this review, we explain recent advancements of biomolecule-responsive mammalian gene circuits based on RNA devices. | Q-5855-2017 | CELLS;LIN28 | 1 | null | null | 7 | CELLS;LIN28 | WOS:000496872800005 | Kyoto Univ, Kyoto, Japan | Japan | 2,019 | null | 0000-0003-1159-3676 | null | null | English | null | ACS SYNTH BIOL;AM J SURG PATHOL;BIOMATERIALS;CANCER GENE THER;CELL STEM CELL;FASEB J;GENE THER;HUM PATHOL;J VIROL;MOL THER;NAT BIOTECHNOL;NAT CHEM BIOL;NAT COMMUN;NUCLEIC ACIDS RES;SCI REP;SCI REP-UK | Nakanishi, Hideyuki;Saito, Hirohide | 2024-03-11
ER | Cao, D F;Cella, F;Chen, J S;Endo, K;Hirosawa, M;Kashida, S;Kawasaki, S;Matsuura, S;Miki, K;Mou, H H;Nakanishi, H;Parisi, S;Parr, C J C;Petrakova, O;Saito, H;Sano, M;Santagata, S;Shibata, T;Stapleton, J A;Wagner, T E;Weeratna, R D;Wroblewska, L | JN4MH | Kyoto, Japan | 9 | null | 1 | null | 31,129,468 | Nakanishi, Hideyuki;Saito, Hirohide | CURR OPIN CHEM BIOL | Kyoto, Japan |
de Greef, T F A;Huck, W T S;Maerkl, S J;Pieters, P;Swank, Z;van der Linden, A J;Yelleswarapu, M | 10.3791/59655 | e59655 | 1 ALEWIFE CENTER, STE 200, CAMBRIDGE, MA 02140 USA | 3s1s1ym1o2t5g53x2m32k3u3i31175b3cdc | A Multilayer Microfluidic Platform for the Conduction of Prolonged Cell-Free Gene Expression | Eindhoven Univ Technol | null | de Greef, TFA (corresponding author), Eindhoven Univ Technol, Dept Biomed Engn, Computat Biol Grp, Inst Complex Mol Syst, Eindhoven, Netherlands.;de Greef, TFA (corresponding author), Radboud Univ Nijmegen, Inst Mol & Mat, Nijmegen, Netherlands.;Maerkl, SJ (corresponding author), Ecole Polytech Fed Lausanne, Sch Engn, Inst Bioengn, Lausanne, Switzerland. | null | de Greef, Tom F A;Huck, Wilhelm T S;Maerkl, Sebastian J;Pieters, Pascal;Swank, Zoe;van der Linden, Ardjan J;Yelleswarapu, Maaruthy | Multidisciplinary Sciences | European Research Council, ERC [677313 BioCircuit]; NWO-VIDI grant from the Netherlands Organization for Scientific Research (NWO) [723.016.003]; Ministry of Education, Culture and Science [024.001.035, 024.003.013]; Human Frontier Science Program [RGP0032/2015]; European Research Council under the European Union [723106]; Swiss National Science Foundation [200021_182019]; Swiss National Science Foundation (SNF) [200021_182019] Funding Source: Swiss National Science Foundation (SNF); European Research Council (ERC) [723106] Funding Source: European Research Council (ERC) | WOS | de Greef, T F A;Maerkl, S J | Ecole Polytech Fed Lausanne, Lausanne, Switzerland;Eindhoven Univ Technol, Eindhoven, Netherlands;Radboud Univ Nijmegen, Nijmegen, Netherlands | null | a;Cell-Free;Conduction;expression;for;gene;Microfluidic;Multilayer;of;Platform;Prolonged;the | 2 | Maerkl, Sebastian J. | JOURNAL OF VISUALIZED EXPERIMENTS | Ecole Polytech Fed Lausanne, Sch Engn, Inst Bioengn, Lausanne, Switzerland;Eindhoven Univ Technol, Dept Biomed Engn, Computat Biol Grp, Inst Complex Mol Syst, Eindhoven, Netherlands;Eindhoven Univ Technol, Dept Biomed Engn, Computat Biol Grp, Inst Complex Mol Syst, Eindhoven, Netherlands.; de Greef, TFA (corresponding author), Radboud Univ Nijmegen, Inst Mol & Mat, Nijmegen, Netherlands.; Maerkl, SJ (corresponding author), Ecole Polytech Fed Lausanne, Sch Engn, Inst Bioengn, Lausanne, Switzerland;Radboud Univ Nijmegen, Inst Mol & Mat, Nijmegen, Netherlands | Article | Ecole Polytech Fed Lausanne;Eindhoven Univ Technol;Radboud Univ Nijmegen | CAMBRIDGE | null | null | Ecole Polytech Fed Lausanne;Eindhoven Univ Technol;Radboud Univ Nijmegen | European Research Council (ERC);European Research Council under the European Union;European Research Council, ERC;Human Frontier Science Program;Ministry of Education, Culture and Science;NWO-VIDI grant from the Netherlands Organization for Scientific Research (NWO);Swiss National Science Foundation;Swiss National Science Foundation (SNF) | de Greef, TFA (corresponding author), Eindhoven Univ Technol, Dept Biomed Engn, Computat Biol Grp, Inst Complex Mol Syst, Eindhoven, Netherlands.; de Greef, TFA (corresponding author), Radboud Univ Nijmegen, Inst Mol & Mat, Nijmegen, Netherlands.; Maerkl, SJ (corresponding author), Ecole Polytech Fed Lausanne, Sch Engn, Inst Bioengn, Lausanne, Switzerland. | null | de Greef, Tom F A;Huck, Wilhelm T S;Maerkl, Sebastian J;Pieters, Pascal;Swank, Zoe;van der Linden, Ardjan J;Yelleswarapu, Maaruthy | 9 | 3 | 493,379,500,013 | European Research Council (ERC) [723106] Funding Source: European Research Council (ERC);European Research Council under the European Union [723106];European Research Council, ERC [677313 BioCircuit];Human Frontier Science Program [RGP0032/2015];Ministry of Education, Culture and Science [024.001.035, 024.003.013];NWO-VIDI grant from the Netherlands Organization for Scientific Research (NWO) [723.016.003];Swiss National Science Foundation (SNF) [200021_182019] Funding Source: Swiss National Science Foundation (SNF);Swiss National Science Foundation [200021_182019] | Netherlands;Switzerland | JOVE-JOURNAL OF VISUALIZED EXPERIMENTS | Netherlands;Switzerland | null | null | Eindhoven Univ Technol, Dept Biomed Engn, Computat Biol Grp, Inst Complex Mol Syst, Eindhoven, Netherlands | 1940-087X | de Greef, T F A;Huck, W T S;Maerkl, S J;Pieters, P;Swank, Z;van der Linden, A J;Yelleswarapu, M | OCT | sebastian.maerkl@epfl.ch;t.f.a.d.greef@tue.nl | Conduction;Multilayer Microfluidic Platform;Prolonged Cell-Free Gene Expression | 7 | J | Science & Technology - Other Topics | (by-) products;analysis;Bioengineering;cell-based synthetic biology;cell-free characterization;cellular environment;cellular processes;combining IVTT reactions;complex network behaviors;complex synthetic genetic regulatory circuits;Conduction;CONSTRUCTION;CONTEXT;contrast;dynamic behavior;environmental control;exogenous synthetic components;experimental environment;extended periods;Fabrication;FREE PROTEIN-SYNTHESIS;Gene circuits;hardware;host processes;in vitro transcription and translation;Issue 152;issues;IVTT reactions;lack;limitations;mechanisms;micro-reactors;microfluidic devices;microfluidic platform;MICROFLUIDICS;multilayer microfluidic device;Multilayer Microfluidic Platform;networks;novel circuitry;out-of-equilibrium environment;prevalent;Prolonged Cell-Free Gene Expression;prolonged durations;prolonged reactions;PROTEIN EXPRESSION;protocols;reaction products;reactions;regulation;removal;replenishment;researchers aim;resources;software;synthetic biology;synthetic genetic regulatory networks;time;translation (IVTT) mixtures;understanding;undesired behavior;unique system;use;vitro transcription;vivo | van der Linden, A J | Bioengineering;CONSTRUCTION;CONTEXT;FREE PROTEIN-SYNTHESIS;in vitro transcription and translation;Issue 152;micro-reactors;MICROFLUIDICS;NETWORKS;prolonged reactions;PROTEIN EXPRESSION;Synthetic biology | null | [van der Linden, Ardjan J.; Pieters, Pascal; de Greef, Tom F. A.] Eindhoven Univ Technol, Dept Biomed Engn, Computat Biol Grp, Inst Complex Mol Syst, Eindhoven, Netherlands. [Yelleswarapu, Maaruthy; Huck, Wilhelm T. S.; de Greef, Tom F. A.] Radboud Univ Nijmegen, Inst Mol & Mat, Nijmegen, Netherlands. [Swank, Zoe; Maerkl, Sebastian J.] Ecole Polytech Fed Lausanne, Sch Engn, Inst Bioengn, Lausanne, Switzerland. | This work was supported by the European Research Council, ERC (project n. 677313 BioCircuit) an NWO-VIDI grant from the Netherlands Organization for Scientific Research (NWO, 723.016.003), funding from the Ministry of Education, Culture and Science (Gravity programs, 024.001.035 & 024.003.013), the Human Frontier Science Program Grant RGP0032/2015, the European Research Council under the European Union's Horizon 2020 research and innovation program Grant 723106, and a Swiss National Science Foundation Grant 200021_182019. | (by-) products;analysis;cell-based synthetic biology;cell-free characterization;cellular environment;cellular processes;combining IVTT reactions;complex network behaviors;complex synthetic genetic regulatory circuits;contrast;dynamic behavior;environmental control;exogenous synthetic components;experimental environment;extended periods;fabrication;gene circuits;hardware;host processes;issues;IVTT reactions;lack;limitations;mechanisms;microfluidic devices;microfluidic platform;multilayer microfluidic device;novel circuitry;out-of-equilibrium environment;prevalent;prolonged durations;protocols;reaction products;reactions;regulation;removal;replenishment;researchers aim;resources;software;synthetic genetic regulatory networks;time;translation (IVTT) mixtures;understanding;undesired behavior;unique system;use;vitro transcription;vivo | 10.1002/biot.201200085;10.1002/smll.201502764;10.1006/bbrc.1999.0404;10.1016/j.biotechadv.2013.04.008;10.1016/j.cbpa.2012.05.179;10.1016/j.mib.2016.07.009;10.1016/j.molcel.2016.06.006;10.1016/j.ohx.2017.10.001;10.1016/j.ohx.2017.10.002;10.1016/j.tibtech.2014.11.009;10.1016/j.ymeth.2015.05.020;10.1021/acssynbio.5b00090;10.1021/acssynbio.5b00296;10.1021/sb200016s;10.1021/sb400131a;10.1038/35002125;10.1038/35002131;10.1038/90802;10.1038/nature04473;10.1038/ncomms15128;10.1038/nrg2775;10.1038/nrm2698;10.1039/b808034h;10.1039/c1lc20462a;10.1039/c2lc40649g;10.1039/c5cs00361j;10.1039/c5lc00700c;10.1039/c6lc00367b;10.1073/pnas.1212069109;10.1073/pnas.1311166110;10.1073/pnas.2135496100;10.1093/nar/gkr1191;10.1101/cshperspect.a023812;10.1109/ACC.2007.4282302;10.1126/science.1151721;10.1126/science.1192588;10.1126/science.1255550;10.1126/science.288.5463.113;10.1126/science.3055301;10.1371/journal.pone.0073015;10.7554/eLife.09771 | Eindhoven Univ Technol | de Greef, T F A;Huck, W T S;Maerkl, S J;Pieters, P;Swank, Z;van der Linden, A J;Yelleswarapu, M | van der Linden, A J: Eindhoven Univ Technol, Dept Biomed Engn, Computat Biol Grp, Inst Complex Mol Syst, Eindhoven, Netherlands | de Greef, Tom F. A.;Huck, Wilhelm T.S.;Maerkl, Sebastian J. J | 024.001.035;024.003.013;200021_182019;677313 BioCircuit;723.016.003;723106;RGP0032/2015 | 49 | null | Netherlands | Ecole Polytech Fed Lausanne;Eindhoven Univ Technol;Radboud Univ Nijmegen | van der Linden, Ardjan J | Green Published, Bronze, Green Submitted | CONSTRUCTION;CONTEXT;FREE PROTEIN-SYNTHESIS;NETWORKS;SYNTHETIC BIOLOGY | van der Linden, Ardjan J.; Yelleswarapu, Maaruthy; Pieters, Pascal; Swank, Zoe; Huck, Wilhelm T. S.; Maerkl, Sebastian J.; de Greef, Tom F. A.; | null | Ecole Polytech Fed Lausanne, Sch Engn, Inst Bioengn, Lausanne, Switzerland;Eindhoven Univ Technol, Dept Biomed Engn, Computat Biol Grp, Inst Complex Mol Syst, Eindhoven, Netherlands;Radboud Univ Nijmegen, Inst Mol & Mat, Nijmegen, Netherlands | Ecole Polytech Fed Lausanne, Sch Engn, Inst Bioengn, Lausanne, Switzerland;Eindhoven Univ Technol, Dept Biomed Engn, Computat Biol Grp, Inst Complex Mol Syst, Eindhoven, Netherlands;Radboud Univ Nijmegen, Inst Mol & Mat, Nijmegen, Netherlands | null | Bioengineering;in vitro transcription and translation;Issue 152;micro-reactors;Microfluidics;prolonged reactions;protein expression;Synthetic biology | 152 | 1988;1999;2000;2001;2003;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017;2018;2019 | 7 | Ecole Polytech Fed Lausanne, Sch Engn, Inst Bioengn, Lausanne, Switzerland;Eindhoven Univ Technol, Dept Biomed Engn, Computat Biol Grp, Inst Complex Mol Syst, Eindhoven, Netherlands;Radboud Univ Nijmegen, Inst Mol & Mat, Nijmegen, Netherlands | J. Vis. Exp. | de Greef, Tom F A | JOURNAL OF VISUALIZED EXPERIMENTS | (by-);(IVTT);,;a;accumulate;aim;allow;allows;an;analysis;analyze;and;apparent;are;as;automate;batch;be;becomes;becoming;been;behavior;behaviors;biology;by;can;cell-based;cell-free;cellular;characterization;circuitry;circuits;combining;complex;components;comprehensively;consuming;contrast;control;depleted;detail;develop;device;devices;durations;dynamic;each;emulated;environment;environmental;exogenous;experimental;exploit;extended;fabrication;for;from;fully;furthering;gene;genetic;hardware;have;here;host;in;increasingly;integrated;interacting;investigated;is;issues;it;IVTT;lack;larger;limitations;maintaining;manner;mechanisms;microfluidic;mixtures;more;multilayer;network;networks;novel;of;optimized;our;out-of-equilibrium;over;overcome;periods;platform;possible;presented;prevalent;processes;products;prolonged;protocols;reaction;reactions;regulate;regulation;regulatory;removal;replenishment;researchers;resources;resulting;software;suffers;sustain;synthetic;system;that;the;these;this;time;to;transcription;translation;understanding;undesired;unique;use;utilized;vitro;vivo;well;where;which;with | Ecole Polytech Fed Lausanne;Eindhoven Univ Technol;Radboud Univ Nijmegen | The limitations of cell-based synthetic biology are becoming increasingly apparent as researchers aim to develop larger and more complex synthetic genetic regulatory circuits. The analysis of synthetic genetic regulatory networks in vivo is time consuming and suffers from a lack of environmental control, with exogenous synthetic components interacting with host processes resulting in undesired behavior. To overcome these issues, cell-free characterization of novel circuitry is becoming more prevalent. In vitro transcription and translation (IVTT) mixtures allow the regulation of the experimental environment and can be optimized for each unique system. The protocols presented here detail the fabrication of a multilayer microfluidic device that can be utilized to sustain IVTT reactions for prolonged durations. In contrast to batch reactions, where resources are depleted over time and (by-) products accumulate, the use of microfluidic devices allows the replenishment of resources as well as the removal of reaction products. In this manner, the cellular environment is emulated by maintaining an out-of-equilibrium environment in which the dynamic behavior of gene circuits can be investigated over extended periods of time. To fully exploit the multilayer microfluidic device, hardware and software have been integrated to automate the IVTT reactions. By combining IVTT reactions with the microfluidic platform presented here, it becomes possible to comprehensively analyze complex network behaviors, furthering our understanding of the mechanisms that regulate cellular processes. | B-1471-2012;C-5438-2008;I-8124-2014 | CONSTRUCTION;CONTEXT;FREE PROTEIN-SYNTHESIS;NETWORKS;SYNTHETIC BIOLOGY | 0 | null | Bioengineering;in vitro transcription and translation;Issue 152;micro-reactors;Microfluidics;prolonged reactions;protein expression;Synthetic biology | 14 | Bioengineering;CONSTRUCTION;CONTEXT;FREE PROTEIN-SYNTHESIS;in vitro transcription and translation;Issue 152;micro-reactors;MICROFLUIDICS;NETWORKS;prolonged reactions;PROTEIN EXPRESSION;Synthetic biology | WOS:000493379500013 | Ecole Polytech Fed Lausanne, Lausanne, Switzerland;Eindhoven Univ Technol, Eindhoven, Netherlands;Radboud Univ Nijmegen, Nijmegen, Netherlands | Netherlands;Switzerland | 2,019 | null | 0000-0003-1917-5268 | null | null | English | null | 2007 American Control Conference;ACS SYNTH BIOL;ACSYNTHETIC BIOL;BIOCHEM BIOPH RES CO;BIOTECHNOL ADV;BIOTECHNOL J;BIOTECHNOLOGY BIOENG;CHEM SOC REV;CSH PERSPECT BIOL;CURR OPIN CHEM BIOL;CURR OPIN MICROBIOL;ELIFE;HARDWAREX;J VAC SCI TECHNOL B;LAB CHIP;METHODS;MOL CELL;MOL SYSTEMS BIOL;NAT BIOTECHNOL;NAT COMMUN;NAT REV GENET;NAT REV MOL CELL BIO;NATURE;NATURE MICROBIOLOGY;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PLOS ONE;SCI REPORTS;SCIENCE;SMALL;TRENDS BIOTECHNOL | de Greef, Tom F A;Huck, Wilhelm T S;Maerkl, Sebastian J;Pieters, Pascal;Swank, Zoe;van der Linden, Ardjan J;Yelleswarapu, Maaruthy | 2024-03-11
ER | Borkowski, O;Brower, K;Cardinale, S;De Los Santos, E L C;Del Vecchio D.;Del Vecchio, D;Doktycz M. J.;Dunlop M., J;Elowitz, M B;Galas, J C;Garamella, J;Gardner, T S;Genot, A J;Georgi, V;Gibson, D G;Guido, N J;Guo, S;Hockenberry, A J;Hughes, R A;Iyer, S;Kaminski, T S;Kantak C.;Karig, D K;Karzbrun, E;Khalil, A S;Khnouf, R;Lee, J W;Liao C.;Montagne K.;Niederholtmeyer, H;Noireaux, V;Oberholzer, T;Padirac, A;Purnick, P E M;Scott, M;Shimizu, Y;Shin, J;Siuti, P;Spirin, A S;Sun, Z Z;Takahashi, M K;Timm, A C;Unger, M A;Van Roekel, H W H;Venturelli, O S;White, J A;Yelleswarapu, M;Yoshiyama T. | JI3PV | Eindhoven, Netherlands.;Lausanne, Switzerland;Nijmegen, Netherlands. | 8 | null | 3 | null | 31,633,684 | de Greef, Tom F A;Huck, Wilhelm T S;Maerkl, Sebastian J;Pieters, Pascal;Swank, Zoe;van der Linden, Ardjan J;Yelleswarapu, Maaruthy | JOVE-J VIS EXP | Eindhoven, Netherlands;Lausanne, Switzerland;Nijmegen, Netherlands |
Graham, D;Jun, T;Lu, T K;Müller, I E;Rubens, J R;Xavier, R | 10.1038/s41467-019-12021-y | 4028 | MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND | 5s640a1k66m5n3z6kg2gf6h395p5f6x5do | Gene networks that compensate for crosstalk with crosstalk | MIT | null | Lu, TK (corresponding author), MIT, Dept Elect Engn & Comp Sci, Elect Res Lab, Synthet Biol Grp,Synthet Biol Ctr, Cambridge, MA 02139 USA.;Lu, TK (corresponding author), MIT, Microbiol Program, Cambridge, MA 02139 USA. | null | Graham, Daniel;Jun, Tomi;Lu, Timothy K;Mueller, Isaak E;Rubens, Jacob R;Xavier, Ramnik | Multidisciplinary Sciences | NSF Graduate Research Fellowship; National Science Foundation [1350625, 1124247]; Office of Naval Research [N000141310424]; NIH New Innovator Award [1DP2OD008435]; NIH National Centers for Systems Biology [1P50GM098792]; Direct For Biological Sciences; Div Of Molecular and Cellular Bioscience [1350625] Funding Source: National Science Foundation; Division of Computing and Communication Foundations; Direct For Computer & Info Scie & Enginr [1124247] Funding Source: National Science Foundation | WOS | Lu, T K | Broad Inst, Cambridge, MA USA;Harvard MIT Hlth Sci & Technol Program, Cambridge, MA USA;Massachusetts Gen Hosp, Boston, MA USA;MIT, Cambridge, MA USA;Mt Sinai Hosp, New York, NY USA | 10 | compensate;crosstalk;for;gene;networks;that;with | 1 | Jun, Tomi | NATURE PUBLISHING GROUP | Broad Inst, Program Med & Populat Genet, Cambridge, MA 02142 USA;Harvard MIT Hlth Sci & Technol Program, Cambridge, MA 02139 USA;Massachusetts Gen Hosp, Ctr Computat & Integrat Biol, Boston, MA 02114 USA;Massachusetts Gen Hosp, Ctr Study Inflammatory Bowel Dis, Boston, MA 02114 USA;Massachusetts Gen Hosp, Gastrointestinal Unit, Boston, MA 02114 USA;MIT, Dept Elect Engn & Comp Sci, Elect Res Lab, Synthet Biol Grp,Synthet Biol Ctr, Cambridge, MA 02139 USA;MIT, Dept Elect Engn & Comp Sci, Elect Res Lab, Synthet Biol Grp,Synthet Biol Ctr, Cambridge, MA 02139 USA.; Lu, TK (corresponding author), MIT, Microbiol Program, Cambridge, MA 02139 USA;MIT, Microbiol Program, Cambridge, MA 02139 USA;Mt Sinai Hosp, Div Hematol & Med Oncol, New York, NY 10029 USA | Article | MIT | LONDON | null | null | Broad Inst;Dept Elect Engn & Comp Sci;Harvard MIT Hlth Sci & Technol Program;Massachusetts Gen Hosp;MIT;Mt Sinai Hosp | Direct For Biological Sciences;Direct For Computer & Info Scie & Enginr;Div Of Molecular and Cellular Bioscience;Division of Computing and Communication Foundations;National Science Foundation;NIH National Centers for Systems Biology;NIH New Innovator Award;NSF Graduate Research Fellowship;Office of Naval Research | Lu, TK (corresponding author), MIT, Dept Elect Engn & Comp Sci, Elect Res Lab, Synthet Biol Grp,Synthet Biol Ctr, Cambridge, MA 02139 USA.; Lu, TK (corresponding author), MIT, Microbiol Program, Cambridge, MA 02139 USA. | null | Graham, Daniel;Jun, Tomi;Lu, Timothy K;Mueller, Isaak E;Rubens, Jacob R;Xavier, Ramnik | 21 | 8 | 484,596,900,008 | Direct For Biological Sciences;Direct For Computer & Info Scie & Enginr [1124247] Funding Source: National Science Foundation;Div Of Molecular and Cellular Bioscience [1350625] Funding Source: National Science Foundation;Division of Computing and Communication Foundations;National Science Foundation [1350625, 1124247];NIH National Centers for Systems Biology [1P50GM098792];NIH New Innovator Award [1DP2OD008435];NSF Graduate Research Fellowship;Office of Naval Research [N000141310424] | USA | NATURE COMMUNICATIONS | USA;USA.; | null | null | MIT, Dept Elect Engn & Comp Sci, Elect Res Lab, Synthet Biol Grp,Synthet Biol Ctr, Cambridge, MA 02139 USA | 2041-1723 | Graham, D;Jun, T;Lu, T K;Müller, I E;Rubens, J R;Xavier, R | SEP 6 | timlu@mit.edu | crosstalk;gene | 6 | J | Science & Technology - Other Topics | biological networks;COMBINATORIAL;common approach;compensatory crosstalk;crosstalk;degree;DESIGN;design gene;engineering sophisticated synthetic gene networks;environmental signals;Escherichia coli;ESCHERICHIA-COLI;evolution;exhibit concentration-dependent crosstalk;GENE;gene network level;HYDROGEN-PEROXIDE;integrating pathway signals;major challenge;molecular-level crosstalk;natural gene networks;non-cognate ROS;pathway crosstalk;pathway insulation;principle;reactive oxygen species (ROS)-responsive gene circuits;regulatory networks;resulting gene network exhibits reduced crosstalk;results;sensing;signal-transduction pathways;simple network motifs;SOXR PROTEIN;specificity;strategy;synthetic gene networks;synthetic genetic components;TALK;two different ROS;unknown interactions;yeast | Müller, I E | COMBINATORIAL;DESIGN;ESCHERICHIA-COLI;EVOLUTION;HYDROGEN-PEROXIDE;REGULATORY NETWORKS;SOXR PROTEIN;SPECIFICITY;TALK;YEAST | null | [Mueller, Isaak E.; Rubens, Jacob R.; Jun, Tomi; Lu, Timothy K.] MIT, Dept Elect Engn & Comp Sci, Elect Res Lab, Synthet Biol Grp,Synthet Biol Ctr, Cambridge, MA 02139 USA. [Mueller, Isaak E.; Rubens, Jacob R.; Lu, Timothy K.] MIT, Microbiol Program, Cambridge, MA 02139 USA. [Jun, Tomi] Harvard MIT Hlth Sci & Technol Program, Cambridge, MA 02139 USA. [Graham, Daniel; Xavier, Ramnik] Broad Inst, Program Med & Populat Genet, Cambridge, MA 02142 USA. [Graham, Daniel; Xavier, Ramnik] Massachusetts Gen Hosp, Gastrointestinal Unit, Boston, MA 02114 USA. [Graham, Daniel; Xavier, Ramnik] Massachusetts Gen Hosp, Ctr Study Inflammatory Bowel Dis, Boston, MA 02114 USA. [Xavier, Ramnik] Massachusetts Gen Hosp, Ctr Computat & Integrat Biol, Boston, MA 02114 USA. [Jun, Tomi] Mt Sinai Hosp, Div Hematol & Med Oncol, New York, NY 10029 USA. | We would like to thank members of the Lu Lab, the MIT Microbiology Program, and the MIT Synthetic Biology Center for their feedback. We thank the staff at the Koch Institute Flow Cytometry Core for their assistance in flow cytometry. J.R.R. was supported by an NSF Graduate Research Fellowship. This work was supported by the National Science Foundation (#1350625 and #1124247) and the Office of Naval Research (#N000141310424), an NIH New Innovator Award (#1DP2OD008435), and the NIH National Centers for Systems Biology (#1P50GM098792). | biological networks;common approach;compensatory crosstalk;crosstalk;degree;design gene;engineering sophisticated synthetic gene networks;environmental signals;Escherichia coli;exhibit concentration-dependent crosstalk;gene network level;integrating pathway signals;major challenge;molecular-level crosstalk;natural gene networks;non-cognate ROS;pathway crosstalk;pathway insulation;principle;reactive oxygen species (ROS)-responsive gene circuits;resulting gene network exhibits reduced crosstalk;results;sensing;signal-transduction pathways;simple network motifs;strategy;synthetic gene networks;synthetic genetic components;two different ROS;unknown interactions | 10.1002/biot.201100487;10.1016/j.cell.2009.01.055;10.1016/j.cell.2012.05.033;10.1016/j.cell.2014.02.033;10.1016/j.cell.2014.04.047;10.1016/j.chembiol.2014.10.008;10.1016/j.cub.2008.07.050;10.1016/j.devcel.2011.11.006;10.1016/j.mib.2010.09.001;10.1016/j.tibs.2011.03.006;10.1021/sb300030d;10.1021/sb300084h;10.1038/463288a;10.1038/cr.2008.302;10.1038/msb.2013.58;10.1038/msb4100050;10.1038/msb4100135;10.1038/msb4100187;10.1038/nature02178;10.1038/nature06347;10.1038/nature11149;10.1038/nature11259;10.1038/nature11516;10.1038/nature12148;10.1038/nature13582;10.1038/nbt.1536;10.1038/nbt.1617;10.1038/nbt1209;10.1038/nbt731;10.1038/ncomms11658;10.1038/ncomms2471;10.1038/ng881;10.1038/nmeth.2884;10.1038/nrg3227;10.1038/nrmicro3032;10.1038/nrmicro3238;10.1073/pnas.0403350102;10.1073/pnas.0608451104;10.1073/pnas.1312414110;10.1073/pnas.1317178111;10.1073/pnas.1418058112;10.1074/jbc.M110715200;10.1074/jbc.M112.395079;10.1093/emboj/17.9.2629;10.1093/nar/25.6.1203;10.1093/nar/gkq810;10.1093/nar/gkt452;10.1101/gad.1700308;10.1111/j.1365-2958.2008.06426.x;10.1111/j.1365-2958.2010.07520.x;10.1126/science.1075090;10.1126/science.1192588;10.1126/science.1207084;10.1126/science.1256272;10.1126/science.271.5251.990;10.1126/scitranslmed.3005568;10.1128/AEM.00791-07;10.1128/AEM.62.7.2252-2256.1996;10.1146/annurev-micro-092611-150039;10.1146/annurev.genet.41.042007.170548;10.1186/1752-0509-5-111;10.1186/1754-1611-5-12;10.1186/1754-1611-8-2;10.1371/journal.pbio.0030334;10.1371/journal.pone.0011909;10.1371/journal.pone.0016136;10.7554/eLife.00669 | MIT | Graham, D;Jun, T;Lu, T K;Müller, I E;Rubens, J R;Xavier, R | Müller, I E: MIT, Dept Elect Engn & Comp Sci, Elect Res Lab, Synthet Biol Grp,Synthet Biol Ctr, Cambridge, MA 02139 USA | Jun, Tomi;Lu, Timothy K | 1124247;1350625;1DP2OD008435;1P50GM098792;N000141310424 | 69 | null | USA | Broad Inst;Harvard MIT Hlth Sci & Technol Program;Massachusetts Gen Hosp;MIT;Mt Sinai Hosp | Mueller, Isaak E | Green Published, gold | COMBINATORIAL;DESIGN;ESCHERICHIA-COLI;EVOLUTION;HYDROGEN-PEROXIDE;REGULATORY NETWORKS;SOXR PROTEIN;SPECIFICITY;TALK;YEAST | Mueller, Isaak E.; Rubens, Jacob R.; Jun, Tomi; Graham, Daniel; Xavier, Ramnik; Lu, Timothy K.; | null | Broad Inst, Program Med & Populat Genet, Cambridge, MA 02142 USA;Harvard MIT Hlth Sci & Technol Program, Cambridge, MA 02139 USA;Massachusetts Gen Hosp, Ctr Computat & Integrat Biol, Boston, MA 02114 USA;Massachusetts Gen Hosp, Ctr Study Inflammatory Bowel Dis, Boston, MA 02114 USA;Massachusetts Gen Hosp, Gastrointestinal Unit, Boston, MA 02114 USA;MIT, Dept Elect Engn & Comp Sci, Elect Res Lab, Synthet Biol Grp,Synthet Biol Ctr, Cambridge, MA 02139 USA;MIT, Microbiol Program, Cambridge, MA 02139 USA;Mt Sinai Hosp, Div Hematol & Med Oncol, New York, NY 10029 USA | Broad Inst, Program Med & Populat Genet, Cambridge, MA 02142 USA;Harvard MIT Hlth Sci & Technol Program, Cambridge, MA 02139 USA;Massachusetts Gen Hosp, Ctr Computat & Integrat Biol, Boston, MA 02114 USA;Massachusetts Gen Hosp, Ctr Study Inflammatory Bowel Dis, Boston, MA 02114 USA;Massachusetts Gen Hosp, Gastrointestinal Unit, Boston, MA 02114 USA;MIT, Dept Elect Engn & Comp Sci, Elect Res Lab, Synthet Biol Grp,Synthet Biol Ctr, Cambridge, MA 02139 USA;MIT, Microbiol Program, Cambridge, MA 02139 USA;Mt Sinai Hosp, Div Hematol & Med Oncol, New York, NY 10029 USA | null | null | null | 1991;1996;1997;1998;1999;2002;2003;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016 | 21 | MIT, Dept Elect Engn & Comp Sci, Elect Res Lab, Synthet Biol Grp,Synthet Biol Ctr, Cambridge, MA 02139 USA;MIT, Microbiol Program, Cambridge, MA 02139 USA | Nat. Commun. | Lu, Timothy K | NATURE PUBLISHING GROUP | (ROS)-responsive;,;a;accurately;and;apply;approach;at;be;between;biological;but;by;can;challenge;circuits;coli;common;compensate;compensatory;complex;components;concentration-dependent;context;crosstalk;degree;demonstrate;design;different;difficult;endogenous;engineered;engineering;environmental;Escherichia;exhibit;exhibits;for;gene;genetic;here;in;insulate;insulation;integrating;interactions;interpret;introduce;is;level;major;map;minimizing;molecular-level;motifs;natural;network;networks;non-cognate;of;our;oxygen;pathway;pathways;principle;quantitatively;rather;reactive;reduced;resulting;results;ROS;sensing;show;signal-transduction;signals;simple;sophisticated;species;strategy;suggest;synthetic;than;that;the;this;to;two;unknown;used;using;we;with | MIT | Crosstalk is a major challenge to engineering sophisticated synthetic gene networks. A common approach is to insulate signal-transduction pathways by minimizing molecular-level crosstalk between endogenous and synthetic genetic components, but this strategy can be difficult to apply in the context of complex, natural gene networks and unknown interactions. Here, we show that synthetic gene networks can be engineered to compensate for crosstalk by integrating pathway signals, rather than by pathway insulation. We demonstrate this principle using reactive oxygen species (ROS)-responsive gene circuits in Escherichia coli that exhibit concentration-dependent crosstalk with non-cognate ROS. We quantitatively map the degree of crosstalk and design gene circuits that introduce compensatory crosstalk at the gene network level. The resulting gene network exhibits reduced crosstalk in the sensing of the two different ROS. Our results suggest that simple network motifs that compensate for pathway crosstalk can be used by biological networks to accurately interpret environmental signals. | AAJ-4152-2020;G-4267-2012 | COMBINATORIAL;DESIGN;ESCHERICHIA-COLI;EVOLUTION;HYDROGEN-PEROXIDE;REGULATORY NETWORKS;SOXR PROTEIN;SPECIFICITY;TALK;YEAST | 0 | null | null | 8 | ESCHERICHIA-COLI;YEAST;COMBINATORIAL;DESIGN;EVOLUTION;HYDROGEN-PEROXIDE;REGULATORY NETWORKS;SOXR PROTEIN;SPECIFICITY;TALK | WOS:000484596900008 | Broad Inst, Cambridge, MA USA;Harvard MIT Hlth Sci & Technol Program, Cambridge, MA USA;Massachusetts Gen Hosp, Boston, MA USA;MIT, Cambridge, MA USA;Mt Sinai Hosp, New York, NY USA | USA | 2,019 | null | 0000-0002-2120-1704 | null | null | English | null | ACS SYNTH BIOL;ANNU REV GENET;ANNU REV MICROBIOL;APPL ENVIRON MICROB;BIOTECHNOL J;BMC SYST BIOL;CELL;CELL RES;CHEM BIOL;CURR BIOL;CURR OPIN MICROBIOL;DEV CELL;ELIFE;EMBO J;GENE DEV;J BACTERIOL;J BIOCHEM-TOKYO;J BIOL CHEM;J Biol Eng;MOL MICROBIOL;MOL SYST BIOL;NAT BIOTECHNOL;NAT COMMUN;NAT GENET;NAT METHODS;NAT REV GENET;NAT REV MICROBIOL;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PLOS BIOL;PLOS ONE;SCI TRANSL MED;SCIENCE;TRENDS BIOCHEM SCI | Graham, Daniel;Jun, Tomi;Lu, Timothy K;Mueller, Isaak E;Rubens, Jacob R;Xavier, Ramnik | 2024-03-11
ER | Ausländer, S;Baba, T;Beal, J;Belkin, S;Cai, S J;Cantone, I;Capra, E J;Chubukov, V;Collins, C H;Cox, R S;Daniel, R;Davis, J H;Dessaud, E;Dwyer, D J;Ellis, T;Escalante-Chong, R;Farzadfard, F;Fischbach, M A;Fujikawa, M;González-Flecha, B;Gu, M Z;Guo, X;Hidalgo, E;Imlay, J A;Keiler, K C;Kemmer, C;Keung, A J;Kiviet, D J;Kogenaru, M;Kostallas, G;Kwok, R;Laub, M T;Lee, S K;Lee, T I;Lee, T S;Li, G W;Lutz, R;Madar, D;Marguet, P;Mendoza, M C;Mitrophanov, A Y;Moon, T S;Morey, K J;Murphy, K F;Nandagopal, N;Nevozhay, D;Olson, E J;Rhodius, V A;Rodrigo, G;Rowland, M A;Rubens, J R;Rössger, K;Saito, H;Scialdone, A;Scott, M;Shen-Orr, S S;Shibata, T;Siryaporn, A;Skerker, J M;Slusarczyk, A L;Takahashi, M K;Takahashi, S;Tao, K;Vert, G;Weber, W;Wei, P;Wu, F Q;Zarrinpar, A | IV9PW | Cambridge, MA USA;Cambridge, MA USA. | 26 | null | 5 | null | 31,492,904 | Graham, Daniel;Jun, Tomi;Lu, Timothy K;Mueller, Isaak E;Rubens, Jacob R;Xavier, Ramnik | NAT COMMUN | Boston, MA USA;Cambridge, MA USA;New York, NY USA |
Hamada, H;Hanai, T;Honjo, H;Iwasaki, K;Soma, Y;Tsuruno, K | 10.1016/j.ymben.2019.08.007 | null | 525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA | 5v605b585f1z2i62rd4076h241de4iu3w47 | Synthetic microbial consortium with specific roles designated by genetic circuits for cooperative chemical production | Kyushu Univ | null | Hanai, T (corresponding author), Kyushu Univ, Grad Sch Syst Lifesci, Lab Bioinformat, Nishi Ku, 729 West Bldg 5,744 Motooka, Fukuoka, Fukuoka 8190395, Japan. | null | Hamada, Hiroyuki;Hanai, Taizo;Honjo, Hiroshi;Iwasaki, Kenshiro;Soma, Yuki;Tsuruno, Keigo | Biotechnology & Applied Microbiology | JSPS KAKENHI [JP23119002, JP18K14065]; Chemical Innovation Encouragement Prize from Japan Association for Chemical Innovation; Sumitomo Foundation | WOS | Hanai, T | Kyushu Univ, Fukuoka, Japan | 55 | by;chemical;circuits;consortium;cooperative;designated;for;genetic;microbial;production;roles;specific;synthetic;with | 1 | Soma, Yuki | ACADEMIC PRESS INC ELSEVIER SCIENCE | Kyushu Univ, Grad Sch Syst Lifesci, Lab Bioinformat, Nishi Ku, 729 West Bldg 5,744 Motooka, Fukuoka, Fukuoka 8190395, Japan;Kyushu Univ, Med Inst Bioregulat, Res Ctr Trans Med, Div Metabol,Higashi Ku, 3-1-1 Maidashi, Fukuoka, Fukuoka 8128582, Japan | Article | Kyushu Univ | SAN DIEGO | null | null | Kyushu Univ | Chemical Innovation Encouragement Prize from Japan Association for Chemical Innovation;JSPS KAKENHI;Sumitomo Foundation | Hanai, T (corresponding author), Kyushu Univ, Grad Sch Syst Lifesci, Lab Bioinformat, Nishi Ku, 729 West Bldg 5,744 Motooka, Fukuoka, Fukuoka 8190395, Japan. | 275 | Hamada, Hiroyuki;Hanai, Taizo;Honjo, Hiroshi;Iwasaki, Kenshiro;Soma, Yuki;Tsuruno, Keigo | 63 | 2 | 482,582,100,028 | Chemical Innovation Encouragement Prize from Japan Association for Chemical Innovation;JSPS KAKENHI [JP23119002, JP18K14065];Sumitomo Foundation | Japan | METABOLIC ENGINEERING | Japan | null | null | Kyushu Univ, Grad Sch Syst Lifesci, Lab Bioinformat, Nishi Ku, 729 West Bldg 5,744 Motooka, Fukuoka, Fukuoka 8190395, Japan | 1096-7176 | Hamada, H;Hanai, T;Honjo, H;Iwasaki, K;Soma, Y;Tsuruno, K | SEP | taizo@brs.kyushu-u.ac.jp | cooperative chemical production;genetic circuits;specific roles;synthetic microbial consortium | 6 | J | Biotechnology & Applied Microbiology | beta-glucosidase;biomass;capacities;CELLOBIOSE;chemical production;converts cellobiose;cooperative chemical production;desired cell density;developed;different synthetic genetic circuits;distributed tasks;divided synthetic metabolic pathway components;effective chemical production;efficient saccharification;enzyme;enzyme-producing strain;enzymes;Escherichia coli;ESCHERICHIA-COLI;expression;few consortia;FLUX;Genetic circuits;glucose;ISOPROPANOL PRODUCTION;LYSIS;lytic genes;metabolic pathway;microorganisms;release;results;sensor;single microorganisms;specific roles;synthetic genetic circuit;synthetic metabolic pathway;synthetic microbial consortia;synthetic microbial consortium;target chemical-producing strain;via | Honjo, H | CELLOBIOSE;ESCHERICHIA-COLI;EXPRESSION;FLUX;ISOPROPANOL PRODUCTION;LYSIS;metabolic pathway;SENSOR | 268 | [Honjo, Hiroshi; Iwasaki, Kenshiro; Soma, Yuki; Tsuruno, Keigo; Hamada, Hiroyuki; Hanai, Taizo] Kyushu Univ, Grad Sch Syst Lifesci, Lab Bioinformat, Nishi Ku, 729 West Bldg 5,744 Motooka, Fukuoka, Fukuoka 8190395, Japan. [Soma, Yuki] Kyushu Univ, Med Inst Bioregulat, Res Ctr Trans Med, Div Metabol,Higashi Ku, 3-1-1 Maidashi, Fukuoka, Fukuoka 8128582, Japan. | This work was supported by JSPS KAKENHI Grant Numbers JP23119002, JP18K14065, Chemical Innovation Encouragement Prize from Japan Association for Chemical Innovation, and a Grant for a Basic Science Research Project from the Sumitomo Foundation. | beta-glucosidase;biomass;capacities;chemical production;converts cellobiose;desired cell density;developed;different synthetic genetic circuits;distributed tasks;divided synthetic metabolic pathway components;effective chemical production;efficient saccharification;enzyme;enzyme-producing strain;enzymes;Escherichia coli;few consortia;glucose;isopropanol production;lytic genes;microorganisms;release;results;single microorganisms;synthetic genetic circuit;synthetic metabolic pathway;synthetic microbial consortia;synthetic microbial consortium;target chemical-producing strain;via | 10.1002/biot.201400422;10.1006/RWGN.2001.0106];10.1007/s00253-013-5504-7;10.1016/B978-0-12-385120-8.00002-4;10.1016/j.cell.2009.12.029;10.1016/j.ces.2013.03.021;10.1016/j.copbio.2008.07.009;10.1016/j.copbio.2014.12.022;10.1016/j.jbiosc.2012.02.019;10.1016/j.tibtech.2005.12.003;10.1016/j.tibtech.2008.05.004;10.1016/j.ymben.2012.08.006;10.1016/j.ymben.2014.02.008;10.1016/j.ymben.2015.04.005;10.1021/bp010018t;10.1021/sb400002n;10.1038/35002131;10.1038/msb.2008.24;10.1038/msb.2011.16;10.1038/msb4100187;10.1038/nature07389;10.1038/nature09565;10.1038/nature18930;10.1038/nbt.1937;10.1038/nbt.2149;10.1038/nbt.2899;10.1038/nbt.3095;10.1038/nbt.3796;10.1038/ncomms13858;10.1038/nrmicro3239;10.1038/s41589-018-0091-7;10.1073/pnas.0702609104;10.1073/pnas.93.18.9505;10.1128/AEM.01140-07;10.1128/AEM.01688-07;10.1186/1752-0509-8-S5-S7;10.1186/1754-1611-5-8;10.1371/journal.pone.0011909;[10.1038/NCHEMBIO.970, 10.1038/nchembio.970];[10.1038/NMETH.3727, 10.1038/nmeth.3727] | Kyushu Univ | Hamada, H;Hanai, T;Honjo, H;Iwasaki, K;Soma, Y;Tsuruno, K | Honjo, H: Kyushu Univ, Grad Sch Syst Lifesci, Lab Bioinformat, Nishi Ku, 729 West Bldg 5,744 Motooka, Fukuoka, Fukuoka 8190395, Japan | Soma, Yuki | JP18K14065;JP23119002 | 41 | null | Japan | Kyushu Univ | Honjo, Hiroshi | null | CELLOBIOSE;ESCHERICHIA-COLI;EXPRESSION;FLUX;ISOPROPANOL PRODUCTION;LYSIS;METABOLIC PATHWAY;SENSOR | Honjo, Hiroshi; Iwasaki, Kenshiro; Soma, Yuki; Tsuruno, Keigo; Hamada, Hiroyuki; Hanai, Taizo; | null | Kyushu Univ, Grad Sch Syst Lifesci, Lab Bioinformat, Nishi Ku, 729 West Bldg 5,744 Motooka, Fukuoka, Fukuoka 8190395, Japan;Kyushu Univ, Med Inst Bioregulat, Res Ctr Trans Med, Div Metabol,Higashi Ku, 3-1-1 Maidashi, Fukuoka, Fukuoka 8128582, Japan | Kyushu Univ, Grad Sch Syst Lifesci, Lab Bioinformat, Nishi Ku, 729 West Bldg 5,744 Motooka, Fukuoka, Fukuoka 8190395, Japan;Kyushu Univ, Med Inst Bioregulat, Res Ctr Trans Med, Div Metabol,Higashi Ku, 3-1-1 Maidashi, Fukuoka, Fukuoka 8128582, Japan | 1096-7184 | null | null | 1988;1996;2000;2001;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017;2018 | 36 | Kyushu Univ, Grad Sch Syst Lifesci, Lab Bioinformat, Nishi Ku, 729 West Bldg 5,744 Motooka, Fukuoka, Fukuoka 8190395, Japan | Metab. Eng. | Hanai, Taizo | ACADEMIC PRESS INC ELSEVIER SCIENCE | ,;a;an;and;are;been;benefits;beta-glucosidase;beyond;biomass;by;can;capacities;cell;cellobiose;chemical;chemical-producing;circuit;circuits;coli;components;composed;consisting;consortia;consortium;constructed;converts;demonstrate;density;designed;desired;destroys;developed;different;distributed;divided;effective;efficient;enzyme;enzyme-producing;enzymes;Escherichia;exert;express;few;for;from;functions;genes;genetic;glucose;grows;harbored;have;however;in;is;isopropanol;itself;lytic;metabolic;microbial;microorganisms;of;or;our;pathway;produce;production;programmed;reached;release;results;saccharification;single;strain;synthetic;target;tasks;that;the;to;until;using;via;was;we;when;which;with | Kyushu Univ | Synthetic microbial consortia consisting of microorganisms with different synthetic genetic circuits or divided synthetic metabolic pathway components can exert functions that are beyond the capacities of single microorganisms. However, few consortia of microorganisms with different synthetic genetic circuits have been developed. We designed and constructed a synthetic microbial consortium composed of an enzyme-producing strain and a target chemical-producing strain using Escherichia coli for chemical production with efficient saccharification. The enzyme-producing strain harbored a synthetic genetic circuit to produce beta-glucosidase, which converts cellobiose to glucose, destroys itself via the lytic genes, and release the enzyme when the desired cell density is reached. The target chemical-producing strain was programmed by a synthetic genetic circuit to express enzymes in the synthetic metabolic pathway for isopropanol production when the enzyme-producing strain grows until release of the enzyme. Our results demonstrate the benefits of synthetic microbial consortia with distributed tasks for effective chemical production from biomass. | ABI-7016-2020 | CELLOBIOSE;ESCHERICHIA-COLI;EXPRESSION;FLUX;ISOPROPANOL PRODUCTION;LYSIS;METABOLIC PATHWAYS;SENSOR | 9 | null | null | 8 | ESCHERICHIA-COLI;CELLOBIOSE;EXPRESSION;FLUX;ISOPROPANOL PRODUCTION;LYSIS;METABOLIC PATHWAYS;SENSOR | WOS:000482582100028 | Kyushu Univ, Fukuoka, Japan | Japan | 2,019 | null | 0000-0003-1083-6824 | null | null | English | null | ACS SYNTH BIOL;APPL ENVIRON MICROB;APPL MICROBIOL BIOT;BACTERIOPHAGES;BIOTECHNOL J;BIOTECHNOL PROGR;BMC SYST BIOL;CELL;CHEM ENG SCI;CURR OPIN BIOTECH;J Biol Eng;J BIOSCI BIOENG;METAB ENG;METHOD ENZYMOL;MOL SYST BIOL;NAT BIOTECHNOL;NAT CHEM BIOL;NAT COMMUN;NAT METHODS;NAT REV MICROBIOL;NATURE;P NATL ACAD SCI USA;PLOS ONE;TRENDS BIOTECHNOL | Hamada, Hiroyuki;Hanai, Taizo;Honjo, Hiroshi;Iwasaki, Kenshiro;Soma, Yuki;Tsuruno, Keigo | 2024-03-11
ER | Balagadde, F K;Bonde, M T;Brenner, K;Brockman, I M;Brödel, A K;Calendar R.;Cameron, D E;Cox, R S;Desai, S H;Din, M O;Gardner, T S;Gupta, A;Hammer, K;Hanai, T;Haseltine, E L;Holtz, W J;Hsu, C Y;Kong, W T;Lee, J W;Levin-Karp, A;Lo, T M;Marguet, P;Morita, M;Nielsen, J;Park, J H;Pasotti, L;Prather, K L J;Salis, H M;Schaefer, A L;Smolke C. D.;Solomon, K V;Soma, Y;Stricker, J;Tamsir, A;Venayak, N;Vilanova, C;Xavier, J B;Zhang, F Z;Zhou, K | IT1BX | Fukuoka, Japan | 43 | null | 1 | null | 31,401,244 | Hamada, Hiroyuki;Hanai, Taizo;Honjo, Hiroshi;Iwasaki, Kenshiro;Soma, Yuki;Tsuruno, Keigo | METAB ENG | Fukuoka, Japan |
Fan, K L;Li, H J;Li, K;Liu, H W;Wang, Q D;Xia, Y Z;Xun, L Y;Yang, Y Y | 10.1021/acssynbio.9b00210 | null | 1155 16TH ST, NW, WASHINGTON, DC 20036 USA | 1i1l186v3l542b276a553v1c1d385t134x6q56g | Synthetic Gene Circuits Enable <i>Escherichia coli</i> To Use Endogenous H<sub>2</sub>S as a Signaling Molecule for Quorum Sensing | Shandong Univ | null | Xia, YZ; Xun, LY (corresponding author), Shandong Univ, State Key Lab Microbial Technol, Qingdao 266237, Shandong, Peoples R China.;Xun, LY (corresponding author), Washington State Univ, Sch Mol Biosci, Pullman, WA 99164 USA. | null | Fan, Kaili;Li, Huanjie;Li, Kai;Liu, Huaiwei;Wang, Qingda;Xia, Yongzhen;Xun, Luying;Yang, Yunyun | Biochemical Research Methods | National Key R&D Program of China [2018YFA0901200]; National Natural Science Foundation of China [31770093, 91751207]; Natural Science Foudation of Shandong Province [ZR2016CM03] | WOS | Xia, Y Z;Xun, L Y | Shandong Univ, Shandong, Peoples R China;Washington State Univ, Pullman, WA USA | 8 | <i>Escherichia;a;as;circuits;coli</i>;Enable;Endogenous;for;gene;H<sub>2</sub>S;Molecule;Quorum;Sensing;Signaling;synthetic;to;Use | 2 | Fan, Kaili;Li, Huanjie;Liu, Huaiwei;Xia, Yongzhen | AMER CHEMICAL SOC | LY (corresponding author), Shandong Univ, State Key Lab Microbial Technol, Qingdao 266237, Shandong, Peoples R China.; Xun, LY (corresponding author), Washington State Univ, Sch Mol Biosci, Pullman, WA 99164 USA;Shandong Univ, State Key Lab Microbial Technol, Qingdao 266237, Shandong, Peoples R China;Washington State Univ, Sch Mol Biosci, Pullman, WA 99164 USA | Article | Shandong Univ;Washington State Univ | WASHINGTON | null | null | Shandong Univ;Washington State Univ | National Key R&D Program of China;National Natural Science Foundation of China;Natural Science Foudation of Shandong Province | Xia, YZ; Xun, LY (corresponding author), Shandong Univ, State Key Lab Microbial Technol, Qingdao 266237, Shandong, Peoples R China.; Xun, LY (corresponding author), Washington State Univ, Sch Mol Biosci, Pullman, WA 99164 USA. | 2120 | Fan, Kaili;Li, Huanjie;Li, Kai;Liu, Huaiwei;Wang, Qingda;Xia, Yongzhen;Xun, Luying;Yang, Yunyun | 69 | 2 | 487,577,300,017 | National Key R&D Program of China [2018YFA0901200];National Natural Science Foundation of China [31770093, 91751207];Natural Science Foudation of Shandong Province [ZR2016CM03] | China;USA | ACS SYNTHETIC BIOLOGY | China;USA | null | null | Shandong Univ, State Key Lab Microbial Technol, Qingdao 266237, Shandong, Peoples R China | 2161-5063 | Fan, K L;Li, H J;Li, K;Liu, H W;Wang, Q D;Xia, Y Z;Xun, L Y;Yang, Y Y | SEP | luying_xun@vetmed.wsu.edu;xiayongzhen2002@sdu.edu.cn | <i>Escherichia coli</i>;Endogenous H<sub>2</sub>S;Quorum Sensing;Signaling Molecule;synthetic gene circuits | 8 | J | Biochemistry & Molecular Biology | 2);24 different circuits;<i>Escherichia coli</i>;ACIDS;adjustable sensitivity;autoinducer;autonomous switch;cell density;cell factories;CHEMISTRY;CIRCUITS;common metabolites;concentrations;designed synthetic gene;dynamic metabolic engineering;Endogenous H<sub>2</sub>S;Escherichia coli;Escherichia coli produced sulfide (H2S;gene expression;gene regulator CstR;growth phase;H2S-mediated gene circuits endowed E. coli cells;HS-;hydrogen sulfide;HYDROGEN-SULFIDE;indiffusible hydrogen polysulfide (HSnH;metabolic engineering;METABOLIC FLUX;microcolony;microorganisms;n;new tool-kit;OXIDOREDUCTASE;PATHWAY;production phase;quorum sensing;quorum sensing (QS);S2-);same batch;Signaling Molecule;sulfide/quinone oxidoreductase converted diffusible H2S;Sulfur;synchronous behaviors;synthetic biology;Synthetic gene circuit;synthetic gene circuits;THIOSULFATE;three element libraries;turn;use specific autoinducers;used H2S | Liu, H W | ACIDS;CHEMISTRY;dynamic metabolic engineering;Escherichia coli;hydrogen sulfide;HYDROGEN-SULFIDE;METABOLIC FLUX;OXIDOREDUCTASE;PATHWAY;quorum sensing;Sulfur;Synthetic gene circuit;THIOSULFATE | 2113 | [Liu, Huaiwei; Fan, Kaili; Li, Huanjie; Wang, Qingda; Yang, Yunyun; Li, Kai; Xia, Yongzhen; Xun, Luying] Shandong Univ, State Key Lab Microbial Technol, Qingdao 266237, Shandong, Peoples R China. [Xun, Luying] Washington State Univ, Sch Mol Biosci, Pullman, WA 99164 USA. | The work was financially supported by grants of the National Key R&D Program of China (2018YFA0901200), the National Natural Science Foundation of China (31770093, 91751207), and the Natural Science Foudation of Shandong Province (ZR2016CM03). | 2);24 different circuits;adjustable sensitivity;autoinducer;autonomous switch;cell density;cell factories;circuits;common metabolites;concentrations;designed synthetic gene;Escherichia coli produced sulfide (H2S;gene expression;gene regulator CstR;growth phase;H2S-mediated gene circuits endowed E. coli cells;HS-;indiffusible hydrogen polysulfide (HSnH;metabolic engineering;microcolony;microorganisms;n;new tool-kit;production phase;quorum sensing;quorum sensing (QS);S2-);same batch;sulfide/quinone oxidoreductase converted diffusible H2S;synchronous behaviors;synthetic biology;three element libraries;turn;use specific autoinducers;used H2S | 10.1002/biot.201400422;10.1002/bit.20954;10.1002/prot.22665;10.1016/j.ab.2011.01.044;10.1016/j.biortech.2011.08.065;10.1016/j.copbio.2017.10.009;10.1016/j.copbio.2018.02.007;10.1016/j.freeradbiomed.2014.09.007;10.1016/j.redox.2017.02.021;10.1016/j.tim.2006.08.003;10.1016/j.ymben.2008.06.004;10.1016/j.ymben.2014.02.008;10.1016/j.ymben.2015.03.009;10.1021/ac60152a035;10.1021/ac60276a029;10.1021/sb300129j;10.1038/75398;10.1038/msb4100110;10.1038/nature24624;10.1038/nbt.3796;10.1038/nrmicro.2016.89;10.1038/s41564-017-0044-z;10.1038/s41589-018-0091-7;10.1038/srep14774;10.1073/pnas.1406401111;10.1073/pnas.1720770115;10.1093/nar/gky1169;10.1111/1462-2920.13511;10.1111/j.1751-908X.2009.00907.x;10.1111/mmi.13726;10.1126/science.1216379;10.1128/AEM.28.2.303-305.1974;10.1128/MMBR.69.1.12-50.2005;10.3390/molecules190812789 | Shandong Univ | Fan, K L;Li, H J;Li, K;Liu, H W;Wang, Q D;Xia, Y Z;Xun, L Y;Yang, Y Y | Liu, H W: Shandong Univ, State Key Lab Microbial Technol, Qingdao 266237, Shandong, Peoples R China | Li, Huanjie;Liu, Huaiwei | 2018YFA0901200;31770093;91751207;ZR2016CM03 | 35 | null | China | Shandong Univ;Washington State Univ | Liu, Huaiwei | null | ACIDS;CHEMISTRY;HYDROGEN-SULFIDE;METABOLIC FLUX;OXIDOREDUCTASE;PATHWAY;SULFUR;THIOSULFATE | Liu, Huaiwei; Fan, Kaili; Li, Huanjie; Wang, Qingda; Yang, Yunyun; Li, Kai; Xia, Yongzhen; Xun, Luying; | null | Shandong Univ, State Key Lab Microbial Technol, Qingdao 266237, Shandong, Peoples R China;Washington State Univ, Sch Mol Biosci, Pullman, WA 99164 USA | Shandong Univ, State Key Lab Microbial Technol, Qingdao 266237, Shandong, Peoples R China;Washington State Univ, Sch Mol Biosci, Pullman, WA 99164 USA | null | Escherichia coli;dynamic metabolic engineering;hydrogen sulfide;quorum sensing;Synthetic gene circuit | 9 | 1959;1969;1974;2000;2005;2006;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017;2018;2019 | 15 | Shandong Univ, State Key Lab Microbial Technol, Qingdao 266237, Shandong, Peoples R China;Washington State Univ, Sch Mol Biosci, Pullman, WA 99164 USA | ACS Synth. Biol. | Xun, Luying | AMER CHEMICAL SOC | (H2S;(HSnH;(QS);,;2);24;=;>;a;adjustable;an;and;as;assembled;autoinducer;autoinducers;autonomous;batch;be;behaviors;biology;capable;cell;cells;circuits;coli;common;concentrations;constructed;converted;correlated;could;CstR;demonstrated;density;designed;different;diffusible;E.;element;endowed;engineering;Escherichia;expression;factories;for;from;gene;growth;H2S;H2S-mediated;herein;highly;HS-;hydrogen;indiffusible;its;latter;libraries;metabolic;metabolites;microcolony;microorganisms;n;new;of;often;on;or;other;oxidoreductase;phase;polysulfide;produced;production;proportionally;provide;quorum;regulator;S2-);same;sensed;sensing;sensitivity;specific;successfully;sulfide;sulfide/quinone;switch;synchronous;synthetic;than;that;the;them;then;these;three;thus;to;tool-kit;turn;use;used;using;we;which;with;within | Shandong Univ;Washington State Univ | Microorganisms often use specific autoinducers other than common metabolites for quorum sensing (QS). Herein, we demonstrated that Escherichia coli produced sulfide (H2S, HS-, and S2-) with the concentrations proportionally correlated to its cell density. We then designed synthetic gene circuits that used H2S as an autoinducer for quorum sensing. A sulfide/quinone oxidoreductase converted diffusible H2S to indiffusible hydrogen polysulfide (HSnH, n >= 2), and a gene regulator CstR sensed the latter to turn on the gene expression. We constructed three element libraries, with which 24 different circuits could be assembled for adjustable sensitivity to cell density. The H2S-mediated gene circuits endowed E. coli cells within the same batch or microcolony with highly synchronous behaviors. Using them we successfully constructed cell factories capable of an autonomous switch from growth phase to production phase. Thus, these circuits provide a new tool-kit for metabolic engineering and synthetic biology. | ABE-2328-2021;GOG-9430-2022 | ACID;CHEMISTRY;HYDROGEN-SULFIDE;METABOLIC FLUX;OXIDOREDUCTASE;PATHWAY;SULFUR;THIOSULFATE | 3 | null | dynamic metabolic engineering;Escherichia coli;hydrogen sulfide;quorum sensing;Synthetic gene circuit | 15 | ESCHERICHIA-COLI;ACID;CHEMISTRY;dynamic metabolic engineering;hydrogen sulfide;METABOLIC FLUX;OXIDOREDUCTASE;PATHWAY;quorum sensing;Sulfur;synthetic gene circuits;THIOSULFATE | WOS:000487577300017 | Shandong Univ, Shandong, Peoples R China;Washington State Univ, Pullman, WA USA | China;USA | 2,019 | null | 0000-0001-9950-1910;0000-0002-0483-5318;0000-0002-4611-771X;0000-0002-4997-0927 | null | null | English | null | ACS SYNTH BIOL;ANAL BIOCHEM;ANAL CHEM;APPL MICROBIOL;BIORESOUR BIOPROCESS;BIORESOURCE TECHNOL;BIOTECHNOL BIOENG;BIOTECHNOL J;CURR OPIN BIOTECH;ENVIRON MICROBIOL;FREE RADICAL BIO MED;GEOSTAND GEOANAL RES;METAB ENG;MICROBIOL MOL BIOL R;MOL MICROBIOL;MOL SYST BIOL;MOLECULES;NAT BIOTECHNOL;NAT CHEM BIOL;NAT MICROBIOL;NAT REV MICROBIOL;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PROTEINS;REDOX BIOL;SCI REP-UK;SCIENCE;TRENDS MICROBIOL | Fan, Kaili;Li, Huanjie;Li, Kai;Liu, Huaiwei;Wang, Qingda;Xia, Yongzhen;Xun, Luying;Yang, Yunyun | 2024-03-11
ER | Anesiadis, N;Bareia, T;Brockman, I M;Farmer, W R;Giedroc, D P;Gupta, A;Kamyshny, A;Karig, D;Kelly, D P;Kimura, Y;Kong, W;Kong, W T;Lalwani, M A;Lara, A R;Lien, O G;Liu, H;Liu, H W;Lloyd, D;Longo, D;Maker, M D;Marcia, M;Munsky, B;Olson, K R;Ono, K;Papenfort, K;Soma, Y;Toohey, J I;Whiteley, M;Wolfe, A J;Xia, Y Z;Xin, Y F;Xu, P | JA1LA | Pullman, WA USA;Shandong, Peoples R China. | 18 | null | 2 | null | 31,386,360 | Fan, Kaili;Li, Huanjie;Li, Kai;Liu, Huaiwei;Wang, Qingda;Xia, Yongzhen;Xun, Luying;Yang, Yunyun | ACS SYNTH BIOL | Pullman, WA USA;Shandong, Peoples R China |
Isilak, M E;Kehribar, E S;Lu, T K;Olmez, T T;Seker, U O S | 10.1021/acssynbio.9b00235 | null | 1155 16TH ST, NW, WASHINGTON, DC 20036 USA | 6z695s392z1r4f6r181d2y1c5v29v2e5n2j5in | Synthetic Genetic Circuits for Self-Actuated Cellular Nanomaterial Fabrication Devices | Bilkent Univ | null | Seker, UOS (corresponding author), Bilkent Univ, UNAM Inst Mat & Nanotechnol, Ankara, Turkey. | null | Isilak, Musa Efe;Kehribar, Ebru Sahin;Lu, Timothy K;Olmez, Tolga Tarkan;Seker, Urartu Ozgur Safak | Biochemical Research Methods | TUBITAK [114M163, 115Z217]; TUBAGEBIP Award | WOS | Seker, U O S | Bilkent Univ, Ankara, Turkey;MIT, Cambridge, MA USA | 8 | Cellular;circuits;devices;Fabrication;for;genetic;Nanomaterial;Self-Actuated;synthetic | 2 | Seker, Urartu;Ölmez, Tolga Tarkan | AMER CHEMICAL SOC | Bilkent Univ, UNAM Inst Mat & Nanotechnol, Ankara, Turkey;MIT, Dept Biol Engn, Synthet Biol Ctr, 77 Massachusetts Ave, Cambridge, MA 02139 USA | Article | Bilkent Univ | WASHINGTON | null | null | Bilkent Univ;MIT | TUBAGEBIP Award;TUBITAK | Seker, UOS (corresponding author), Bilkent Univ, UNAM Inst Mat & Nanotechnol, Ankara, Turkey. | 2162 | Isilak, Musa Efe;Kehribar, Ebru Sahin;Lu, Timothy K;Olmez, Tolga Tarkan;Seker, Urartu Ozgur Safak | 39 | 2 | 487,577,300,021 | TUBAGEBIP Award;TUBITAK [114M163, 115Z217] | Turkey;USA | ACS SYNTHETIC BIOLOGY | Turkey | null | null | Bilkent Univ, UNAM Inst Mat & Nanotechnol, Ankara, Turkey | 2161-5063 | Isilak, M E;Kehribar, E S;Lu, T K;Olmez, T T;Seker, U O S | SEP | urartu@bilkent.edu.tr | Self-Actuated Cellular Nanomaterial Fabrication Devices;synthetic genetic circuits | 5 | J | Biochemistry & Molecular Biology | autonomous living material;BACTERIAL SENSORS;biofilms;biomaterials;BIOMINERALIZATION;biosilica;biosystems;cadmium;cells;CIRCUITS;controlled synthetic biosystems;corresponding extracellular matrix;CURLI BIOGENESIS;detection;ESCHERICHIA-COLI;Genetic circuits;gold;green approach;hard tissues;IN-VITRO;iron ions;living cells;materials;materials synthesis module;METALLOTHIONEINS;NANOCRYSTALS;nanomagnets;nanomaterial precursor-sensing module (sensor);nanomaterial synthesis;nanomaterials;nanoscale materials;natural ability;ORGANISMS;PEPTIDE-SYNTHESIS;potential;precursor ion;proof-of-concept study;PROTEIN;proteins;PSEUDOMONAS-AERUGINOSA;related nanomaterial-nucleating extracellular matrix;Self-Actuated Cellular Nanomaterial Fabrication Devices;sensor;solid materials;synthesis;synthetic biology;synthetic genetic circuits;SYSTEM;variety;whole-cell biosensors;wide range | Olmez, T T | BACTERIAL SENSORS;biofilms;BIOMINERALIZATION;CURLI BIOGENESIS;ESCHERICHIA-COLI;Genetic circuits;IN-VITRO;METALLOTHIONEINS;NANOCRYSTALS;nanomaterials;PEPTIDE-SYNTHESIS;PROTEIN;PSEUDOMONAS-AERUGINOSA;Synthetic biology;whole-cell biosensors | 2152 | [Olmez, Tolga Tarkan; Kehribar, Ebru Sahin; Isilak, Musa Efe; Seker, Urartu Ozgur Safak] Bilkent Univ, UNAM Inst Mat & Nanotechnol, Ankara, Turkey. [Lu, Timothy K.] MIT, Dept Biol Engn, Synthet Biol Ctr, 77 Massachusetts Ave, Cambridge, MA 02139 USA. | This study was supported by TUBITAK (Grant Nos. 114M163 and 115Z217). U.O.S.S. acknowledges the TUBAGEBIP Award. | autonomous living material;biomaterials;biosilica;biosystems;cadmium;cells;circuits;controlled synthetic biosystems;corresponding extracellular matrix;detection;gold;green approach;hard tissues;iron ions;living cells;materials;materials synthesis module;nanomagnets;nanomaterial precursor-sensing module (sensor);nanomaterial synthesis;nanomaterials;nanoscale materials;natural ability;organisms;potential;precursor ion;proof-of-concept study;proteins;related nanomaterial-nucleating extracellular matrix;sensor;solid materials;synthesis;synthetic genetic circuits;system;variety;wide range | 10.1002/anie.200903572;10.1002/bit.260191010;10.1006/jmbi.2000.3682;10.1007/BF02738153;10.1007/s00253-006-0718-6;10.1007/s11051-012-1218-5;10.1016/j.bbamcr.2013.09.010;10.1016/j.biomaterials.2007.05.040;10.1016/j.bpj.2016.12.036;10.1016/j.copbio.2016.11.023;10.1016/j.jcis.2018.03.016;10.1016/j.str.2011.05.015;10.1016/S0006-291X(03)01366-4;10.1016/S0168-6445(03)00051-2;10.1021/acssensors.7b00728;10.1021/acssynbio.6b00166;10.1021/ar300321e;10.1021/cr8002328;10.1021/cr990115p;10.1021/es702688c;10.1021/ja907454f;10.1021/ja909406n;10.1021/jz2016473;10.1021/la047428m;10.1021/la104942t;10.1021/la500160p;10.1021/nn202566n;10.1021/nn900720g;10.1038/35015043;10.1038/35101627;10.1038/ncomms5945;10.1038/ncomms9747;10.1038/nmat758;10.1038/nmat964;10.1038/nrmicro3253;10.1038/s41598-017-01442-8;10.1038/s41598-017-13613-8;10.1039/c2sc01119k;10.1039/c7ra06289c;10.1073/pnas.0703310104;10.1073/pnas.0832310100;10.1073/pnas.2433456100;10.1073/pnas.90.14.6385;10.1074/jbc.270.45.26723;10.1093/nar/gkm631;10.1099/00221287-144-5-1407;10.1104/pp.123.3.825;10.1111/mmi.12515;10.1126/science.1082387;10.1128/AEM.02343-17;10.1128/JB.00122-16;10.1128/JB.180.9.2280-2284.1998;10.1128/JB.180.9.2442-2449.1998;10.1128/JB.185.23.6826-6840.2003;10.1146/annurev.arplant.53.100301.135154;10.1146/annurev.micro.60.080805.142106;10.2976/1.2896331;10.3762/bjoc.10.118;[10.1038/NCHEM.1025, 10.1038/nchem.1025];[10.1038/NMETH.1318, 10.1038/nmeth.1318] | Bilkent Univ | Isilak, M E;Kehribar, E S;Lu, T K;Olmez, T T;Seker, U O S | Olmez, T T: Bilkent Univ, UNAM Inst Mat & Nanotechnol, Ankara, Turkey | Lu, Timothy K;Seker, Urartu;Ölmez, Tolga Tarkan;Ölmez, Tolga Tarkan T | 114M163;115Z217 | 61 | null | Turkey | Bilkent Univ;MIT | Olmez, Tolga Tarkan | null | BACTERIAL SENSORS;BIOMINERALIZATION;CURLI BIOGENESIS;ESCHERICHIA-COLI;IN-VITRO;METALLOTHIONEINS;NANOCRYSTALS;PEPTIDE-SYNTHESIS;PROTEIN;PSEUDOMONAS-AERUGINOSA | Olmez, Tolga Tarkan; Kehribar, Ebru Sahin; Isilak, Musa Efe; Lu, Timothy K.; Seker, Urartu Ozgur Safak; | null | Bilkent Univ, UNAM Inst Mat & Nanotechnol, Ankara, Turkey;MIT, Dept Biol Engn, Synthet Biol Ctr, 77 Massachusetts Ave, Cambridge, MA 02139 USA | Bilkent Univ, UNAM Inst Mat & Nanotechnol, Ankara, Turkey;MIT, Dept Biol Engn, Synthet Biol Ctr, 77 Massachusetts Ave, Cambridge, MA 02139 USA | null | biofilm;Genetic circuits;nanomaterials;Synthetic biology;whole-cell biosensor | 9 | 1977;1993;1995;1998;1999;2000;2001;2002;2003;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017;2018 | 10 | Bilkent Univ, UNAM Inst Mat & Nanotechnol, Ankara, Turkey | ACS Synth. Biol. | Seker, Urartu Ozgur Safak | AMER CHEMICAL SOC | (sensor);,;:;a;ability;an;and;approach;are;as;autonomous;availability;be;being;biomaterials;biosilica;biosystems;cadmium;cells;circuits;consisting;controlled;corresponding;coupled;create;dedicated;demonstrate;designed;detection;detects;developed;enables;encode;endowing;engineered;express;extended;extracellular;form;genetic;genetically;gold;green;hard;has;have;ion;ions;iron;living;many;material;materials;matrix;modeled;module;nanomagnets;nanomaterial;nanomaterial-nucleating;nanomaterials;nanoscale;natural;of;on;or;organisms;potential;precursor;precursor-sensing;presence;proof-of-concept;proteins;range;related;sense;sensor;shows;solid;study;such;synthesis;synthesize;synthesizing;synthetic;system;that;the;these;they;this;tissues;to;triggers;using;variety;we;when;wide;with | Bilkent Univ | Genetically controlled synthetic biosystems are being developed to create nanoscale materials. These biosystems are modeled on the natural ability of living cells to synthesize materials: many organisms have dedicated proteins that synthesize a wide range of hard tissues and solid materials, such as nanomagnets and biosilica. We designed an autonomous living material synthesizing system consisting of engineered cells with genetic circuits that synthesize nanomaterials. The circuits encode a nanomaterial precursor-sensing module (sensor) coupled with a materials synthesis module. The sensor detects the presence of cadmium, gold, or iron ions, and this detection triggers the synthesis of the related nanomaterial-nucleating extracellular matrix. We demonstrate that when engineered cells sense the availability of a precursor ion, they express the corresponding extracellular matrix to form the nanomaterials. This proof-of-concept study shows that endowing cells with synthetic genetic circuits enables nanomaterial synthesis and has the potential to be extended to the synthesis of a variety of nanomaterials and biomaterials using a green approach. | AAF-7261-2020;C-8309-2012;F-4299-2010;G-4267-2012 | BACTERIAL SENSORS;BIOMINERALIZATION;CURLI BIOGENESIS;ESCHERICHIA-COLI;IN-VITRO;METALLOTHIONEIN;NANOCRYSTALS;PEPTIDE-SYNTHESIS;PROTEIN;PSEUDOMONAS-AERUGINOSA | 3 | null | biofilms;Genetic circuits;nanomaterials;Synthetic biology;whole-cell biosensors | 21 | ESCHERICHIA-COLI;PSEUDOMONAS-AERUGINOSA;BACTERIAL SENSORS;biofilms;BIOMINERALIZATION;CURLI BIOGENESIS;Genetic circuits;IN-VITRO;Metallothionein;NANOCRYSTALS;nanomaterials;PEPTIDE-SYNTHESIS;PROTEIN;Synthetic biology;WHOLE-CELL BIOSENSOR | WOS:000487577300021 | Bilkent Univ, Ankara, Turkey;MIT, Cambridge, MA USA | Turkey;USA | 2,019 | null | 0000-0002-5272-1876;0000-0002-8818-4507 | null | null | English | null | ACCOUNTS CHEM RES;ACS NANO;ACS SENSORS;ACS SYNTH BIOL;ANGEW CHEM INT EDIT;ANNU REV MICROBIOL;ANNU REV PLANT BIOL;APPL ENVIRON MICROB;APPL MICROBIOL BIOT;BBA-MOL CELL RES;BEILSTEIN J ORG CHEM;BIOCHEM BIOPH RES CO;BIOMATERIALS;BIOPHYS J;BIOTECHNOL BIOENG;CELL BIOCHEM BIOPHYS;CHEM REV;CHEM SCI;CURR OPIN BIOTECH;ENVIRON SCI TECHNOL;FEMS MICROBIOL REV;HFSP J;J AM CHEM SOC;J BACTERIOL;J BIOL CHEM;J COLLOID INTERF SCI;J MOL BIOL;J NANOPART RES;J PHYS CHEM LETT;LANGMUIR;MICROBIOL-UK;MOL MICROBIOL;NAT CHEM;NAT COMMUN;NAT MATER;NAT METHODS;NAT REV MICROBIOL;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PLANT PHYSIOL;RSC ADV;SCI REP-UK;SCIENCE;STRUCTURE;WHOLE CELL SENSING S | Isilak, Musa Efe;Kehribar, Ebru Sahin;Lu, Timothy K;Olmez, Tolga Tarkan;Seker, Urartu Ozgur Safak | 2024-03-11
ER | Banerjee, I A;Barbas, C F;Barnhart, M M;Briggs, B D;Brocklehurst, K R;Brown, N L;Brown, S;Chen, C L;Chen, Z;Chiu, C Y;Cobbett, C;Cobbett, C S;Cui, Y Y;Daunert, S;Dickerson, M B;Evans, M L;Gibson, D G;Golec, P;Hammer, N D;Jungmann, R;Kalyoncu, E;Karube, I;Kunkle, C A;Kwon, S;Lamour, G;Lee, J Y;Lower, B H;Mao, C B;Mäde, V;Naik, R R;Neilands, J B;Nguyen, P Q;Nikel, P I;Onur, T;Rauser, W E;Reches, M;Roehrich, A;Roggo, C;Sakaguchi, T;Saltepe, B;Sano, K I;Sarikaya, M;Seker, U O S;Shimomura-Shimizu M.;Sousa, C;Taglialegna, A;Tamerler, C;Tan, Y N;Taylor, J D;Tesson, B;Van Gerven, N;Vidal, O;Wang, L Y;Wei, W;Whaley, S R;White, C;Whiteley, M;Yagi, K;Zhou, W | JA1LA | Ankara, Turkey | 12 | null | 2 | null | 31,419,103 | Isilak, Musa Efe;Kehribar, Ebru Sahin;Lu, Timothy K;Olmez, Tolga Tarkan;Seker, Urartu Ozgur Safak | ACS SYNTH BIOL | Ankara, Turkey;Cambridge, MA USA |
Chang, T H;Chiang, V L;Hsu, T S;Hung, E T;Jiang, J;Kao, C T;Kuan, C Y;Li, W;Lin, C C;Lin, Y C J;Liu, G F;Ma, H Y;Miao, F;Qu, G Z;Tsai, N C;Wang, J P;Wang, Z F;Yeh, C S;Yu, J H;Zhou, C G | 10.1101/gr.245951.118 | null | 1 BUNGTOWN RD, COLD SPRING HARBOR, NY 11724 USA | 4e6t4t3d1z712m5u6o5w6n505bka2dp13x3 | A novel synthetic-genetic-array-based yeast one-hybrid system for high discovery rate and short processing time | Acad Sinica | null | Chang, TH (corresponding author), Acad Sinica, Genom Res Ctr, Taipei 11529, Taiwan.;Chiang, VL; Lin, YCJ (corresponding author), North Carolina State Univ, Dept Forestry & Environm Resources, Forest Biotechnol Grp, Raleigh, NC 27695 USA.;Li, W; Chiang, VL; Lin, YCJ (corresponding author), Northeast Forestry Univ, State Key Lab Tree Genet & Breeding, Harbin 150040, Peoples R China.;Lin, YCJ (corresponding author), Natl Taiwan Univ, Coll Life Sci, Dept Life Sci, Taipei 10617, Taiwan.;Lin, YCJ (corresponding author), Natl Taiwan Univ, Coll Life Sci, Inst Plant Biol, Taipei 10617, Taiwan. | null | Chang, Tien-Hsien;Chiang, Vincent L;Hsu, Tzu-Shu;Hung, Er-Tsi;Jiang, Jing;Kao, Chung-Ting;Kuan, Chen-Yu;Li, Wei;Lin, Chia-Chang;Lin, Ying-Chung Jimmy;Liu, Guifeng;Ma, Hongyan;Miao, Fang;Qu, Guan-Zheng;Tsai, Ni-Chiao;Wang, Jack P;Wang, Zhifeng;Yeh, Chung-Shu;Yu, Jhong-He;Zhou, Chenguang | Biochemistry & Molecular Biology;Biotechnology & Applied Microbiology;Genetics & Heredity | National Natural Science Foundation of China (NSFC) [31522014]; China 1000-Talents Plan for young researchers; Taiwan Ministry of Science and Technology [MOST 105-2311-B-001-059]; Academia Sinica (Taiwan); MOST [106-0210-01-15-02, 107-0210-01-19-01]; Academia Sinica Thematic Project [AS-103-TP-B12]; Taiwan MOST [106-2311-B-002-001-MY2, 107-2636-B-002-003]; MOST Young Scholar Fellowship Columbus Program; Academia Sinica Postdoctoral Fellowship; NSFC [31430093]; U.S. National Science Foundation [DBI-0922391]; U.S. Office of Science (Biological and Environmental Research), Department of Energy [DE-SC000691]; North Carolina State University Jordan Family Distinguished Professor Endowment; North Carolina State University Forest Biotechnology Industrial Research Consortium | WOS | Chang, T H;Chiang, V L;Li, W;Lin, Y C J | Acad Sinica, Taipei, Taiwan;Natl Taiwan Univ, Taipei, Taiwan;Natl Yang Ming Univ, Taipei, Taiwan;North Carolina State Univ, Raleigh, NC USA;Northeast Forestry Univ, Harbin, Peoples R China | 29 | a;and;discovery;for;high;novel;one-hybrid;processing;rate;short;synthetic-genetic-array-based;system;time;yeast | 3 | KAO, CHUNG-TING;Kuan, chen-yu;Li, Wei;Wang, Jack P. | COLD SPRING HARBOR LAB PRESS | Acad Sinica, Genom Res Ctr, Taipei 11529, Taiwan;Acad Sinica, Genom Res Ctr, Taipei 11529, Taiwan.; Li, W; Chiang, VL; Lin, YCJ (corresponding author), Northeast Forestry Univ, State Key Lab Tree Genet & Breeding, Harbin 150040, Peoples R China.; Lin, YCJ (corresponding author), Natl Taiwan Univ, Coll Life Sci, Dept Life Sci, Taipei 10617, Taiwan.; Lin, YCJ (corresponding author), Natl Taiwan Univ, Coll Life Sci, Inst Plant Biol, Taipei 10617, Taiwan.; Chiang, VL; Lin, YCJ (corresponding author), North Carolina State Univ, Dept Forestry & Environm Resources, Forest Biotechnol Grp, Raleigh, NC 27695 USA;Natl Taiwan Univ, Coll Life Sci, Dept Life Sci, Taipei 10617, Taiwan;Natl Taiwan Univ, Coll Life Sci, Inst Plant Biol, Taipei 10617, Taiwan;Natl Yang Ming Univ, Ctr Syst & Synthet Biol, Taipei 11221, Taiwan;Natl Yang Ming Univ, Inst Biomed Informat, Taipei 11221, Taiwan;North Carolina State Univ, Dept Forestry & Environm Resources, Forest Biotechnol Grp, Raleigh, NC 27695 USA;Northeast Forestry Univ, State Key Lab Tree Genet & Breeding, Harbin 150040, Peoples R China | Article | Acad Sinica;North Carolina State Univ;Natl Taiwan Univ;Northeast Forestry Univ | COLD SPRING HARBOR | null | null | Acad Sinica;Natl Taiwan Univ;Natl Yang Ming Univ;North Carolina State Univ;Northeast Forestry Univ | Academia Sinica (Taiwan);Academia Sinica Postdoctoral Fellowship;Academia Sinica Thematic Project;China 1000-Talents Plan for young researchers;MOST;MOST Young Scholar Fellowship Columbus Program;National Natural Science Foundation of China (NSFC);North Carolina State University Forest Biotechnology Industrial Research Consortium;North Carolina State University Jordan Family Distinguished Professor Endowment;NSFC;Taiwan Ministry of Science and Technology;Taiwan MOST;U.S. National Science Foundation;U.S. Office of Science (Biological and Environmental Research), Department of Energy | Chang, TH (corresponding author), Acad Sinica, Genom Res Ctr, Taipei 11529, Taiwan.; Li, W; Chiang, VL; Lin, YCJ (corresponding author), Northeast Forestry Univ, State Key Lab Tree Genet & Breeding, Harbin 150040, Peoples R China.; Lin, YCJ (corresponding author), Natl Taiwan Univ, Coll Life Sci, Dept Life Sci, Taipei 10617, Taiwan.; Lin, YCJ (corresponding author), Natl Taiwan Univ, Coll Life Sci, Inst Plant Biol, Taipei 10617, Taiwan.; Chiang, VL; Lin, YCJ (corresponding author), North Carolina State Univ, Dept Forestry & Environm Resources, Forest Biotechnol Grp, Raleigh, NC 27695 USA. | 1351 | Chang, Tien-Hsien;Chiang, Vincent L;Hsu, Tzu-Shu;Hung, Er-Tsi;Jiang, Jing;Kao, Chung-Ting;Kuan, Chen-Yu;Li, Wei;Lin, Chia-Chang;Lin, Ying-Chung Jimmy;Liu, Guifeng;Ma, Hongyan;Miao, Fang;Qu, Guan-Zheng;Tsai, Ni-Chiao;Wang, Jack P;Wang, Zhifeng;Yeh, Chung-Shu;Yu, Jhong-He;Zhou, Chenguang | 41 | 7 | 482,830,700,012 | Academia Sinica (Taiwan);Academia Sinica Postdoctoral Fellowship;Academia Sinica Thematic Project [AS-103-TP-B12];China 1000-Talents Plan for young researchers;MOST [106-0210-01-15-02, 107-0210-01-19-01];MOST Young Scholar Fellowship Columbus Program;National Natural Science Foundation of China (NSFC) [31522014];North Carolina State University Forest Biotechnology Industrial Research Consortium;North Carolina State University Jordan Family Distinguished Professor Endowment;NSFC [31430093];Taiwan Ministry of Science and Technology [MOST 105-2311-B-001-059];Taiwan MOST [106-2311-B-002-001-MY2, 107-2636-B-002-003];U.S. National Science Foundation [DBI-0922391];U.S. Office of Science (Biological and Environmental Research), Department of Energy [DE-SC000691] | China;Taiwan;USA | GENOME RESEARCH | China;Taiwan.;;USA | null | null | Acad Sinica, Genom Res Ctr, Taipei 11529, Taiwan | 1088-9051 | Chang, T H;Chiang, V L;Hsu, T S;Hung, E T;Jiang, J;Kao, C T;Kuan, C Y;Li, W;Lin, C C;Lin, Y C J;Liu, G F;Ma, H Y;Miao, F;Qu, G Z;Tsai, N C;Wang, J P;Wang, Z F;Yeh, C S;Yu, J H;Zhou, C G | AUG | chang108@gate.sinica.edu.tw;vchiang@ncsu.edu;weili2015@nefu.edu.cn;ycjimmylin@ntu.edu.tw | high discovery rate;novel synthetic-genetic-array-based yeast one-hybrid system;short processing time | 20 | J | Biochemistry & Molecular Biology;Biotechnology & Applied Microbiology;Genetics & Heredity | ASSAYS;chromatin immunoprecipitation;comprehensive genome-scale gene regulatory networks;conventional diploid-mating approach;deletion;DNA cis targets;DNA INTERACTIONS;eukaryotic gene expression;FAMILIES;haploid-transformation method;high;high discovery rate;high-throughput;high-throughput meiosis-directed yeast one-hybrid system;highest accuracy;identifying TF-DNA interactions;interactions;LIGNIN;Magic Markers;meiosis-directed YIH system;novel;novel synthetic-genetic-array-based yeast one-hybrid system;one;one-tenth;ORGANISMS;processing time;PROTEIN;REGULATORY NETWORK;short processing time;SND1 TRANSCRIPTION FACTOR;synthetic genetic array analysis;SYSTEM;transcription factor-DNA interaction discovery rate;transcription factors (TFs);unique features;used methods;vivo;WOOD FORMATION;yeast one-hybrid (YIH) | Yeh, C S | ASSAYS;DELETION;DNA INTERACTIONS;FAMILIES;HIGH-THROUGHPUT;LIGNIN;PROTEIN;REGULATORY NETWORK;SND1 TRANSCRIPTION FACTOR;WOOD FORMATION | 1343 | [Yeh, Chung-Shu; Chang, Tien-Hsien] Acad Sinica, Genom Res Ctr, Taipei 11529, Taiwan. [Wang, Zhifeng; Ma, Hongyan; Zhou, Chenguang; Qu, Guan-Zheng; Jiang, Jing; Liu, Guifeng; Wang, Jack P.; Li, Wei; Chiang, Vincent L.; Lin, Ying-Chung Jimmy] Northeast Forestry Univ, State Key Lab Tree Genet & Breeding, Harbin 150040, Peoples R China. [Miao, Fang; Kao, Chung-Ting; Hsu, Tzu-Shu; Yu, Jhong-He; Hung, Er-Tsi; Lin, Chia-Chang; Kuan, Chen-Yu; Tsai, Ni-Chiao; Lin, Ying-Chung Jimmy] Natl Taiwan Univ, Coll Life Sci, Dept Life Sci, Taipei 10617, Taiwan. [Miao, Fang; Kao, Chung-Ting; Hsu, Tzu-Shu; Yu, Jhong-He; Hung, Er-Tsi; Lin, Chia-Chang; Kuan, Chen-Yu; Tsai, Ni-Chiao; Lin, Ying-Chung Jimmy] Natl Taiwan Univ, Coll Life Sci, Inst Plant Biol, Taipei 10617, Taiwan. [Hsu, Tzu-Shu] Natl Yang Ming Univ, Inst Biomed Informat, Taipei 11221, Taiwan. [Hsu, Tzu-Shu] Natl Yang Ming Univ, Ctr Syst & Synthet Biol, Taipei 11221, Taiwan. [Wang, Jack P.; Chiang, Vincent L.; Lin, Ying-Chung Jimmy] North Carolina State Univ, Dept Forestry & Environm Resources, Forest Biotechnol Grp, Raleigh, NC 27695 USA. | W.L. is supported by the National Natural Science Foundation of China (NSFC 31522014) and China 1000-Talents Plan for young researchers. T.-H.C. is supported by the Taiwan Ministry of Science and Technology (MOST 105-2311-B-001-059), Academia Sinica (Taiwan) and MOST (106-0210-01-15-02 and 107-0210-01-19-01), and Academia Sinica Thematic Project (AS-103-TP-B12). Y.-C.J.L. is supported by Taiwan MOST (106-2311-B-002-001-MY2 and 107-2636-B-002-003) and MOST Young Scholar Fellowship Columbus Program. C.-S.Y. is supported by an Academia Sinica Postdoctoral Fellowship. V.L.C. is supported by the NSFC Grant (31430093), U.S. National Science Foundation, Plant Genome Research Program Grant DBI-0922391, U.S. Office of Science (Biological and Environmental Research), Department of Energy Grant DE-SC000691, North Carolina State University Jordan Family Distinguished Professor Endowment, and North Carolina State University Forest Biotechnology Industrial Research Consortium. | chromatin immunoprecipitation;comprehensive genome-scale gene regulatory networks;conventional diploid-mating approach;DNA cis targets;eukaryotic gene expression;haploid-transformation method;high;high-throughput meiosis-directed yeast one-hybrid system;highest accuracy;identifying TF-DNA interactions;interactions;Magic Markers;meiosis-directed YIH system;novel;one;one-tenth;organisms;processing time;synthetic genetic array analysis;system;transcription factor-DNA interaction discovery rate;transcription factors (TFs);unique features;used methods;vivo;yeast one-hybrid (YIH) | 10.1007/s00425-016-2640-1;10.1016/j.cell.2006.04.038;10.1016/j.cell.2015.03.003;10.1016/j.cell.2016.04.038;10.1016/j.molp.2016.10.020;10.1016/j.ymeth.2012.07.027;10.1016/S0092-8674(88)90469-2;10.1016/S0580-9517(06)36016-3;10.1038/nature14099;10.1038/NMETH.1240;10.1038/NMETH1063;10.1038/nprot.2014.146;10.1038/nprot.2014.147;10.1038/s41586-018-0656-3;10.1073/pnas.1212977109;10.1073/pnas.1714422114;10.1091/mbc.E15-08-0573;10.1093/nar/gkx608;10.1093/treephys/tpx093;10.1093/treephys/tpx121;10.1101/pdb.prot4590;10.1104/pp.106.086678;10.1105/tpc.113.117697;10.1105/tpc.113.120881;10.1111/j.1469-8137.2012.04201.x;10.1111/nph.15505;10.1111/tpj.12162;10.1126/science.1065810;10.1126/science.1182213;10.1126/science.8266075;10.1177/1087057103256465;10.1177/1087057114534298;[10.1038/NMETH.1748, 10.1038/nmeth.1748];[10.1038/NMETH.1750, 10.1038/nmeth.1750];[10.1038/NMETH.1763, 10.1038/nmeth.1763] | Acad Sinica | Chang, T H;Chiang, V L;Hsu, T S;Hung, E T;Jiang, J;Kao, C T;Kuan, C Y;Li, W;Lin, C C;Lin, Y C J;Liu, G F;Ma, H Y;Miao, F;Qu, G Z;Tsai, N C;Wang, J P;Wang, Z F;Yeh, C S;Yu, J H;Zhou, C G | Yeh, C S: Acad Sinica, Genom Res Ctr, Taipei 11529, Taiwan | wang, jack;Zhou, Chenguang | 106-0210-01-15-02;106-2311-B-002-001-MY2;107-0210-01-19-01;107-2636-B-002-003;31430093;31522014;AS-103-TP-B12;DBI-0922391;DE-SC000691;MOST 105-2311-B-001-059 | 37 | null | Taiwan | Acad Sinica;Natl Taiwan Univ;Natl Yang Ming Univ;North Carolina State Univ;Northeast Forestry Univ | Yeh, Chung-Shu | Green Published, hybrid, Green Submitted | ASSAYS;DELETION;DNA INTERACTIONS;FAMILIES;HIGH-THROUGHPUT;LIGNIN;PROTEIN;REGULATORY NETWORK;SND1 TRANSCRIPTION FACTOR;WOOD FORMATION | Yeh, Chung-Shu; Wang, Zhifeng; Miao, Fang; Ma, Hongyan; Kao, Chung-Ting; Hsu, Tzu-Shu; Yu, Jhong-He; Hung, Er-Tsi; Lin, Chia-Chang; Kuan, Chen-Yu; Tsai, Ni-Chiao; Zhou, Chenguang; Qu, Guan-Zheng; Jiang, Jing; Liu, Guifeng; Wang, Jack P.; Li, Wei; Chiang, Vincent L.; Chang, Tien-Hsien; Lin, Ying-Chung Jimmy; | null | Acad Sinica, Genom Res Ctr, Taipei 11529, Taiwan;Natl Taiwan Univ, Coll Life Sci, Dept Life Sci, Taipei 10617, Taiwan;Natl Taiwan Univ, Coll Life Sci, Inst Plant Biol, Taipei 10617, Taiwan;Natl Yang Ming Univ, Ctr Syst & Synthet Biol, Taipei 11221, Taiwan;Natl Yang Ming Univ, Inst Biomed Informat, Taipei 11221, Taiwan;North Carolina State Univ, Dept Forestry & Environm Resources, Forest Biotechnol Grp, Raleigh, NC 27695 USA;Northeast Forestry Univ, State Key Lab Tree Genet & Breeding, Harbin 150040, Peoples R China | Acad Sinica, Genom Res Ctr, Taipei 11529, Taiwan;Natl Taiwan Univ, Coll Life Sci, Dept Life Sci, Taipei 10617, Taiwan;Natl Taiwan Univ, Coll Life Sci, Inst Plant Biol, Taipei 10617, Taiwan;Natl Yang Ming Univ, Ctr Syst & Synthet Biol, Taipei 11221, Taiwan;Natl Yang Ming Univ, Inst Biomed Informat, Taipei 11221, Taiwan;North Carolina State Univ, Dept Forestry & Environm Resources, Forest Biotechnol Grp, Raleigh, NC 27695 USA;Northeast Forestry Univ, State Key Lab Tree Genet & Breeding, Harbin 150040, Peoples R China | 1549-5469 | null | 8 | 1988;1993;1998;2001;2003;2006;2007;2008;2010;2011;2012;2013;2014;2015;2016;2017;2018;2019 | 17 | Acad Sinica, Genom Res Ctr, Taipei 11529, Taiwan;Natl Taiwan Univ, Coll Life Sci, Dept Life Sci, Taipei 10617, Taiwan;Natl Taiwan Univ, Coll Life Sci, Inst Plant Biol, Taipei 10617, Taiwan;North Carolina State Univ, Dept Forestry & Environm Resources, Forest Biotechnol Grp, Raleigh, NC 27695 USA;Northeast Forestry Univ, State Key Lab Tree Genet & Breeding, Harbin 150040, Peoples R China | Genome Res. | Lin, Ying-Chung Jimmy | COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT | (TFs);(YIH);,;a;accuracy;also;analysis;and;approach;array;as;authenticated;be;between;by;can;chromatin;cis;comprehensive;constructing;conventional;developed;diploid-mating;discover;discovery;DNA;eukaryotic;expression;extensively;factor-DNA;factors;features;for;gene;genetic;genome-scale;haploid-transformation;has;high;high-throughput;highest;identifying;immunoprecipitation;in;interaction;interactions;is;Magic;Markers;meiosis-directed;method;methods;most;nearly;networks;novel;of;offers;often;one;one-hybrid;one-tenth;organisms;particularly;processing;rate;regulated;regulatory;suited;synthetic;system;targets;TF-DNA;that;the;their;these;this;tightly;time;to;transcription;twice;unique;used;using;various;vivo;we;with;yeast;YIH | Acad Sinica;Natl Taiwan Univ;North Carolina State Univ;Northeast Forestry Univ | Eukaryotic gene expression is often tightly regulated by interactions between transcription factors (TFs) and their DNA cis targets. Yeast one-hybrid (YIH) is one of the most extensively used methods to discover these interactions. We developed a high-throughput meiosis-directed yeast one-hybrid system using the Magic Markers of the synthetic genetic array analysis. The system has a transcription factor-DNA interaction discovery rate twice as high as the conventional diploid-mating approach and a processing time nearly one-tenth of the haploid-transformation method. The system also offers the highest accuracy in identifying TF-DNA interactions that can be authenticated in vivo by chromatin immunoprecipitation. With these unique features, this meiosis-directed YIH system is particularly suited for constructing novel and comprehensive genome-scale gene regulatory networks for various organisms. | E-7931-2010;JLL-8637-2023 | ASSAY;DELETION;DNA INTERACTION;FAMILY;HIGH-THROUGHPUT;LIGNIN;PROTEIN;REGULATORY NETWORKS;SND1 TRANSCRIPTION FACTOR;WOOD FORMATION | 4 | null | null | 9 | ASSAY;DELETION;DNA INTERACTION;FAMILY;HIGH-THROUGHPUT;LIGNIN;PROTEIN;REGULATORY NETWORKS;SND1 TRANSCRIPTION FACTOR;WOOD FORMATION | WOS:000482830700012 | Acad Sinica, Taipei, Taiwan;Natl Taiwan Univ, Taipei, Taiwan;Natl Yang Ming Univ, Taipei, Taiwan;North Carolina State Univ, Raleigh, NC USA;Northeast Forestry Univ, Harbin, Peoples R China | China;Taiwan;USA | 2,019 | null | 0000-0002-1176-4802;0000-0002-4407-9334;0000-0002-5392-0076;0000-0002-8232-963X | null | null | English | null | CELL;CSH Protoc;J BIOMOL SCREEN;METHOD MICROBIOL;METHODS;METHODS MOL BIOL;MOL BIOL CELL;MOL PLANT;NAT METHODS;NAT PROTOC;NATURE;NEW PHYTOL;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PLANT CELL;PLANT J;PLANT PHYSIOL;PLANTA;SCIENCE;TREE PHYSIOL;YEAST | Chang, Tien-Hsien;Chiang, Vincent L;Hsu, Tzu-Shu;Hung, Er-Tsi;Jiang, Jing;Kao, Chung-Ting;Kuan, Chen-Yu;Li, Wei;Lin, Chia-Chang;Lin, Ying-Chung Jimmy;Liu, Guifeng;Ma, Hongyan;Miao, Fang;Qu, Guan-Zheng;Tsai, Ni-Chiao;Wang, Jack P;Wang, Zhifeng;Yeh, Chung-Shu;Yu, Jhong-He;Zhou, Chenguang | 2024-03-11
ER | Bass, J I F;Brachmann, C B;Chan, Y F;Deplancke Bart;Deplancke, B;French, S;Gaudinier, A;Hens, K;Iglesias-Fernández, R;Li, J J;Li, Q Z;Li, W;Lin, Y C;Lin, Y C J;Lundholt, B K;Mangat, C S;O'Malley, R C;Petzold, H E;Reece-Hoyes, J S;Romano, J M;Shi, R;Solomon, M J;Suzuki, S;Taylor-Teeples, M;Tong Amy Hin Yan;Tong, A H Y;Typas, A;Vermeirssen, V;Wang, J P;Xu, C Z;Yan, X J;Yang, F;Yeh, C S | IT4KV | Harbin, Peoples R China.;Raleigh, NC USA;Taipei, Taiwan. | 17 | null | 5 | null | 31,186,303 | Chang, Tien-Hsien;Chiang, Vincent L;Hsu, Tzu-Shu;Hung, Er-Tsi;Jiang, Jing;Kao, Chung-Ting;Kuan, Chen-Yu;Li, Wei;Lin, Chia-Chang;Lin, Ying-Chung Jimmy;Liu, Guifeng;Ma, Hongyan;Miao, Fang;Qu, Guan-Zheng;Tsai, Ni-Chiao;Wang, Jack P;Wang, Zhifeng;Yeh, Chung-Shu;Yu, Jhong-He;Zhou, Chenguang | GENOME RES | Harbin, Peoples R China;Raleigh, NC USA;Taipei, Taiwan |
Arbulu, S;Cintas, L M;Feito, J;Gútiez, L;Hernández, P E;Herranz, C;Jiménez, J J | 10.1016/j.foodres.2019.01.015 | null | RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS | 4y3p4i1axp644tp4l116f2h3b5806lk1t | Cloning and expression of synthetic genes encoding native, hybrid- and bacteriocin-derived chimeras from mature class IIa bacteriocins, by <i>Pichia pastoris</i> (syn. <i>Komagataella</i> spp.) | UCM | null | Hernández, PE (corresponding author), UCM, Secc Dept Nutr & Ciencia Alimentos, Nutr Bromatol Higene & Seguridad Alimentaria, Fac Vet, Ave Puerta Hierro S-N, Madrid 28040, Spain. | null | Arbulu, Sara;Cintas, Luis M;Feito, Javier;Gutiez, Loreto;Hernandez, Pablo E;Herranz, Carmen;Jimenez, Juan J | Food Science & Technology | Ministerio de Economia y Competitividad (MINECO) [AGL2012-34829]; Comunidad de Madrid (CAM) [S2013/ABI-2747]; Universidad Complutense of Madrid (UCM), Spain [FEI 16/54]; MINECO; Ministerio de Ciencia e Innovacion (MICINN); Ministerio de Education y Ciencia (MEC), Spain | WOS | Hernández, P E | ACD Pharmaceut AS, Leknes, Norway;CESAG Univ Pontificia Comillas, Palma De Mallorca, Spain;TEAGASC, Cork, Ireland;UCM, Madrid, Spain;Univ Coll Cork, Cork, Ireland | 121 | (syn;,;<i>Pichia;and;bacteriocin-derived;bacteriocins;by;chimeras;class;cloning;encoding;expression;From;genes;hybrid-;i>Komagataella</i>;IIa;mature;native;of;pastoris</i>;spp;synthetic | 3 | Arbulu, Sara;Cintas, Luis M.;Feito, Javier;Hernandez, Pablo E. | ELSEVIER | ACD Pharmaceut AS, Leknes, Norway;CESAG Univ Pontificia Comillas, Palma De Mallorca, Spain;TEAGASC, Food Res Ctr, Fermoy, Cork, Ireland;UCM, Secc Dept Nutr & Ciencia Alimentos, Nutr Bromatol Higene & Seguridad Alimentaria, Fac Vet, Ave Puerta Hierro S-N, Madrid 28040, Spain;Univ Coll Cork, APC Microbiome Ireland, Cork, Ireland | Article | UCM | AMSTERDAM | null | null | ACD Pharmaceut AS;CESAG Univ Pontificia Comillas;Secc Dept Nutr & Ciencia Alimentos;TEAGASC;UCM;Univ Coll Cork | Comunidad de Madrid (CAM);MINECO;Ministerio de Ciencia e Innovacion (MICINN);Ministerio de Economia y Competitividad (MINECO);Ministerio de Education y Ciencia (MEC), Spain;Universidad Complutense of Madrid (UCM), Spain | Hernández, PE (corresponding author), UCM, Secc Dept Nutr & Ciencia Alimentos, Nutr Bromatol Higene & Seguridad Alimentaria, Fac Vet, Ave Puerta Hierro S-N, Madrid 28040, Spain. | 899 | Arbulu, Sara;Cintas, Luis M;Feito, Javier;Gutiez, Loreto;Hernandez, Pablo E;Herranz, Carmen;Jimenez, Juan J | 43 | 5 | 470,048,200,096 | Comunidad de Madrid (CAM) [S2013/ABI-2747];MINECO;Ministerio de Ciencia e Innovacion (MICINN);Ministerio de Economia y Competitividad (MINECO) [AGL2012-34829];Ministerio de Education y Ciencia (MEC), Spain;Universidad Complutense of Madrid (UCM), Spain [FEI 16/54] | Ireland;Norway;Spain | FOOD RESEARCH INTERNATIONAL | Spain | null | null | UCM, Secc Dept Nutr & Ciencia Alimentos, Nutr Bromatol Higene & Seguridad Alimentaria, Fac Vet, Ave Puerta Hierro S-N, Madrid 28040, Spain | 0963-9969 | Arbulu, S;Cintas, L M;Feito, J;Gútiez, L;Hernández, P E;Herranz, C;Jiménez, J J | JUL | cherranz@vet.ucm.es;ehernan@vet.ucm.es;j.feito@ucm.es;jjjm@vet.ucm.es;lcintas@vet.ucm.es;lgutiez@vet.ucm.es;sara.arbulu@pdi.ucm.es | <i>Pichia pastoris</i> (syn;bacteriocin-derived chimeras;expression;hybrid-;i>Komagataella</i> spp;mature class IIa bacteriocins;synthetic genes encoding native | 7 | J | Food Science & Technology | (a);(b);(c);(EntA);<i>Pichia pastoris</i> (syn;antimicrobial activity;ANTIMICROBIAL PEPTIDE;bacteriocin-derived chimeras;bacteriocins produced;biologically-produced bacteriocin-derived chimera;C-terminal end;class IIa bacteriocins enterocin HF (EntHF);different Listeria strains;direct antimicrobial activity;EntA;EntCRL35;enterocin;enterocin CRL35 (EntCRL35);enterocin P (EntP);ENTEROCOCCUS-FAECIUM T136;EntHF;EntHF chimera;EntHF peptide;EntP;expected molecular mass;expression;FUNCTIONAL EXPRESSION;fusion;Heterologous bacteriocin production;higher specific antimicrobial activity;highest antimicrobial activity;hSUMO3-fused bacteriocins;hybrid bacteriocins;hybrid-;Hybrid- and bacteriocin-derived chimeras;i>Komagataella</i> spp;IMMUNITY;L. monocytogenes;LACTIC-ACID BACTERIA;MALDI-TOF MS analysis;mature class IIa bacteriocins;MRM-ESI-LC-MS/MS (QTRAP) analysis;multi-step chromatographic purified fractions;N-terminal region;native amino acid sequence;Native bacteriocins;optimization;P. pastoris;P. pastoris producers;P. pastoris X-33;P13;peptides;permitted detection;Pichia pastoris;plasmid pP-alpha hSUMO3;plasmid pPICZ alpha;processing;producer;production;purified fractions;recognition;recombinant P. pastoris;SAMPLES;SEC-DEPENDENT BACTERIOCIN;secretion;supernatants;synthetic counterpart;synthetic EntP;synthetic genes;synthetic genes encoding EntHF;synthetic genes encoding native;tri-glycine peptide linker | Arbulu, S | ANTIMICROBIAL PEPTIDE;ENTEROCOCCUS-FAECIUM T136;FUNCTIONAL EXPRESSION;Heterologous bacteriocin production;Hybrid- and bacteriocin-derived chimeras;IMMUNITY;LACTIC-ACID BACTERIA;MALDI-TOF MS analysis;MRM-ESI-LC-MS/MS (QTRAP) analysis;Native bacteriocins;OPTIMIZATION;P13;Pichia pastoris;RECOGNITION;SEC-DEPENDENT BACTERIOCIN;Synthetic genes | 888 | [Arbulu, Sara; Jimenez, Juan J.; Gutiez, Loreto; Feito, Javier; Cintas, Luis M.; Herranz, Carmen; Hernandez, Pablo E.] UCM, Secc Dept Nutr & Ciencia Alimentos, Nutr Bromatol Higene & Seguridad Alimentaria, Fac Vet, Ave Puerta Hierro S-N, Madrid 28040, Spain. [Arbulu, Sara] Univ Coll Cork, APC Microbiome Ireland, Cork, Ireland. [Arbulu, Sara] TEAGASC, Food Res Ctr, Fermoy, Cork, Ireland. [Jimenez, Juan J.] ACD Pharmaceut AS, Leknes, Norway. [Gutiez, Loreto] CESAG Univ Pontificia Comillas, Palma De Mallorca, Spain. | Financial support was provided by project AGL2012-34829 from the Ministerio de Economia y Competitividad (MINECO), by grant S2013/ABI-2747 from the Comunidad de Madrid (CAM) and by Fund FEI 16/54 from the Universidad Complutense of Madrid (UCM), Spain. S. Arbulu held a fellowship (FPI) from the MINECO. J.J. Jimenez held a fellowship (FPI) from the Ministerio de Ciencia e Innovacion (MICINN) and L. Gutiez held a fellowship (FPU) from the Ministerio de Education y Ciencia (MEC), Spain. | (a);(b);(c);(EntA);antimicrobial activity;bacteriocin-derived chimeras;bacteriocins produced;biologically-produced bacteriocin-derived chimera;C-terminal end;class IIa bacteriocins enterocin HF (EntHF);different Listeria strains;direct antimicrobial activity;EntA;EntCRL35;enterocin;enterocin CRL35 (EntCRL35);enterocin P (EntP);EntHF;EntHF chimera;EntHF peptide;EntP;expected molecular mass;expression;fusion;higher specific antimicrobial activity;highest antimicrobial activity;hSUMO3-fused bacteriocins;hybrid bacteriocins;hybrid-;L. monocytogenes;MRM-ESI-LC-MS/MS (QTRAP) analysis;multi-step chromatographic purified fractions;N-terminal region;native amino acid sequence;P. pastoris;P. pastoris producers;P. pastoris X-33;peptides;permitted detection;plasmid pP-alpha hSUMO3;plasmid pPICZ alpha;processing;producer;production;purified fractions;recombinant P. pastoris;samples;secretion;supernatants;synthetic counterpart;synthetic EntP;synthetic genes;synthetic genes encoding EntHF;tri-glycine peptide linker | 10.1002/pmic.200900398;10.1002/yea.1542;10.1007/978-1-4419-7692-5_8;10.1007/s00253-012-4257-z;10.1007/s00253-015-6470-z;10.1007/s00253-016-7343-9;10.1007/s10295-013-1302-6;10.1007/s11947-010-0465-7;10.1007/s12033-014-9731-7;10.1016/j.copbio.2007.07.005;10.1016/j.copbio.2017.07.011;10.1016/j.fob.2012.01.002;10.1016/j.jbiotec.2011.07.038;10.1016/j.jbiotec.2016.04.024;10.1016/j.pep.2015.09.022;10.1021/acs.biochem.5b01306;10.1021/acs.jafc.5b03882;10.1021/bi991351x;10.1021/ja3089229;10.1038/nmeth.3213;10.1038/nrmicro1273;10.1038/nrmicro2937;10.1038/s41598-017-09102-7;10.1073/pnas.0608775104;10.1074/jbc.M204928200;10.1074/jbc.M412712200;10.1093/bioinformatics/btq054;10.1099/00221287-143-7-2287;10.1099/mic.0.052571-0;10.1111/j.1365-2958.2008.06279.x;10.1111/lam.12246;10.1128/AAC.48.7.2778-2781.2004;10.1128/AAC.49.7.3004-3008.2005;10.1128/AEM.00530-12;10.1128/AEM.01173-10;10.1128/AEM.02528-17;10.1128/AEM.02559-07;10.1128/AEM.03477-14;10.1128/AEM.63.11.4321-4330.1997;10.1128/JB.00777-10;10.1155/2015/767183;10.1186/1471-2164-9-S2-S27;10.1186/s12866-016-0840-2;10.1371/journal.pone.0037915;10.1371/journal.pone.0075347;10.1371/journal.pone.0103456;10.2174/138920109787048661;10.3109/09687688.2011.602219 | UCM | Arbulu, S;Cintas, L M;Feito, J;Gútiez, L;Hernández, P E;Herranz, C;Jiménez, J J | Arbulu, S: UCM, Secc Dept Nutr & Ciencia Alimentos, Nutr Bromatol Higene & Seguridad Alimentaria, Fac Vet, Ave Puerta Hierro S-N, Madrid 28040, Spain | Arbulu, Sara;Cintas, Luis M;Feito, Javier;Hernandez, Pablo E.;Herranz, Carmen | AGL2012-34829;FEI 16/54;S2013/ABI-2747 | 50 | null | Spain | ACD Pharmaceut AS;CESAG Univ Pontificia Comillas;TEAGASC;UCM;Univ Coll Cork | Arbulu, Sara | null | ANTIMICROBIAL PEPTIDE;ENTEROCOCCUS-FAECIUM T136;FUNCTIONAL EXPRESSION;IMMUNITY;LACTIC-ACID BACTERIA;OPTIMIZATION;P13;RECOGNITION;SEC-DEPENDENT BACTERIOCIN | Arbulu, Sara; Jimenez, Juan J.; Gutiez, Loreto; Feito, Javier; Cintas, Luis M.; Herranz, Carmen; Hernandez, Pablo E.; | null | ACD Pharmaceut AS, Leknes, Norway;CESAG Univ Pontificia Comillas, Palma De Mallorca, Spain;TEAGASC, Food Res Ctr, Fermoy, Cork, Ireland;UCM, Secc Dept Nutr & Ciencia Alimentos, Nutr Bromatol Higene & Seguridad Alimentaria, Fac Vet, Ave Puerta Hierro S-N, Madrid 28040, Spain;Univ Coll Cork, APC Microbiome Ireland, Cork, Ireland | ACD Pharmaceut AS, Leknes, Norway;CESAG Univ Pontificia Comillas, Palma De Mallorca, Spain;TEAGASC, Food Res Ctr, Fermoy, Cork, Ireland;UCM, Secc Dept Nutr & Ciencia Alimentos, Nutr Bromatol Higene & Seguridad Alimentaria, Fac Vet, Ave Puerta Hierro S-N, Madrid 28040, Spain;Univ Coll Cork, APC Microbiome Ireland, Cork, Ireland | 1873-7145 | Heterologous bacteriocin production;Hybrid- and bacteriocin-derived chimeras;MALDI-TOF MS analysis;MRM-ESI-LC-MS/MS (QTRAP) analysis;Native bacteriocins;Pichia pastoris;Synthetic gene | null | 1997;1999;2002;2004;2005;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017;2018 | 14 | UCM, Secc Dept Nutr & Ciencia Alimentos, Nutr Bromatol Higene & Seguridad Alimentaria, Fac Vet, Ave Puerta Hierro S-N, Madrid 28040, Spain | Food Res. Int. | Hernandez, Pablo E | ELSEVIER | (a);(b);(c);(EntA);(EntCRL35);(EntHF);(EntP);(QTRAP);,;:;a;acid;activity;against;alpha;also;amino;analysis;and;antimicrobial;bacteriocin-derived;bacteriocins;biologically-produced;by;C-terminal;chimera;chimeras;chromatographic;class;cloned;compared;counterpart;CRL35;derived;designed;detection;devised;different;direct;displayed;drive;encoding;end;EntA;EntCRL35;enterocin;EntHF;EntP;expected;expressing;expression;for;fractions;from;fusion;genes;HF;higher;highest;hSUMO3;hSUMO3-fused;hybrid;hybrid-;IIa;important;in;including;its;itself;L.;linker;Listeria;mass;molecular;monocytogenes;more;MRM-ESI-LC-MS/MS;multi-step;N-terminal;native;of;only;P;P.;pastoris;peptide;peptides;permitted;plasmid;pP-alpha;pPICZ;processing;produced;producer;producers;production;purified;recombinant;region;samples;secretion;seems;sequence;showed;shows;specific;strains;suggest;supernatants;synthetic;than;that;the;their;this;through;to;tri-glycine;were;whereas;with;work;X-33 | UCM | In this work, synthetic genes designed from (a), the native amino acid sequence of the class IIa bacteriocins enterocin HF (EntHF) and enterocin CRL35 (EntCRL35), (b) from hybrid bacteriocins derived from fusion of enterocin A (EntA) to itself and to EntHF and EntCRL35 through a tri-glycine peptide linker, and (c) from bacteriocin-derived chimeras devised from fusion of the N-terminal region of EntA and enterocin P (EntP) to the C-terminal end of EntHF and EntCRL35, were cloned in plasmid pPICZ alpha A for expression by P. pastoris X-33. Synthetic genes encoding EntHF and EntCRL35 were also cloned in plasmid pP-alpha hSUMO3 for expression of the hSUMO3-fused bacteriocins by P. pastoris. Only recombinant P. pastoris expressing the bacteriocin-derived chimeras displayed a direct antimicrobial activity whereas P. pastoris X-33, producer of EntP::EntHF, showed the highest antimicrobial activity in their supernatants and in the multi-step chromatographic purified fractions. The MRM-ESI-LC-MS/MS (QTRAP) analysis of purified fractions from P. pastoris producers of hybrid- and bacteriocin-derived chimeras, permitted detection in the samples of peptides with the expected molecular mass of the bacteriocins produced. The antimicrobial activity of the EntP::EntHF chimera compared to that of the synthetic EntP::EntHF peptide, suggest that the biologically-produced bacteriocin-derived chimera shows a higher specific antimicrobial activity than its synthetic counterpart against different Listeria strains, including L. monocytogenes. More important, the N-terminal region of EntA and EntP seems to drive the production, processing and secretion of hybrid- and bacteriocin-derived chimeras, by P. pastoris X-33. | AAN-7273-2020;C-7030-2017;H-1694-2017;P-8701-2014;Z-6308-2019 | ANTIMICROBIAL PEPTIDES;ENTEROCOCCUS-FAECIUM T136;FUNCTIONAL EXPRESSION;IMMUNIZATION;LACTIC-ACID BACTERIA;OPTIMIZATION;P13;RECOGNITION;SEC-DEPENDENT BACTERIOCIN | 4 | null | Heterologous bacteriocin production;Hybrid- and bacteriocin-derived chimeras;MALDI-TOF MS analysis;MRM-ESI-LC-MS/MS (QTRAP) analysis;Native bacteriocins;Pichia pastoris;Synthetic genes | 12 | Antimicrobial peptides;ENTEROCOCCUS-FAECIUM T136;FUNCTIONAL EXPRESSION;Heterologous bacteriocin production;Hybrid- and bacteriocin-derived chimeras;IMMUNIZATION;LACTIC-ACID BACTERIA;MALDI-TOF MS analysis;MRM-ESI-LC-MS/MS (QTRAP) analysis;Native bacteriocins;OPTIMIZATION;P13;Pichia pastoris;RECOGNITION;SEC-DEPENDENT BACTERIOCIN;Synthetic gene | WOS:000470048200096 | ACD Pharmaceut AS, Leknes, Norway;CESAG Univ Pontificia Comillas, Palma De Mallorca, Spain;TEAGASC, Cork, Ireland;UCM, Madrid, Spain;Univ Coll Cork, Cork, Ireland | Ireland;Norway;Spain | 2,019 | null | 0000-0001-6259-8456;0000-0001-9889-3692;0000-0003-1774-3372;0000-0003-4161-0385 | null | null | English | null | ANTIMICROB AGENTS CH;APPL ENVIRON MICROB;APPL MICROBIOL BIOT;BIOCHEMISTRY-US;BIOINFORMATICS;BIOMED RES INT;BMC GENOMICS;BMC MICROBIOL;CURR OPIN BIOTECH;CURR OPIN FOOD SCI;CURR PHARM BIOTECHNO;FEBS OPEN BIO;FOOD BIOPROCESS TECH;J AGR FOOD CHEM;J AM CHEM SOC;J BACTERIOL;J BIOL CHEM;J BIOTECHNOL;J IND MICROBIOL BIOT;LETT APPL MICROBIOL;MICROBIOL-SGM;MOL BIOTECHNOL;MOL MICROBIOL;NAT METHODS;NAT REV MICROBIOL;P NATL ACAD SCI USA;PLOS ONE;PROTEIN EXPRES PURIF;PROTEOMICS;PYMOL MOL GRAPH SYST;SCI REP-UK;YEAST | Arbulu, Sara;Cintas, Luis M;Feito, Javier;Gutiez, Loreto;Hernandez, Pablo E;Herranz, Carmen;Jimenez, Juan J | 2024-03-11
ER | Acedo, J Z;Acuña, L;Alvarez-Sieiro, P;Arbulu, S;Borrero, J;Casaus, P;Chikindas, M L;Cintas, L M;Cotter, P D;De La Cruz, S;Delano W. L.;Diep, D B;Field, D;Geng M.;Gutiérrez, J;Jiménez, J J;Johnsen, L;Kjos, M;Lohans, C T;Love, K R;Maclean, B;Malmström, J;Ni, Z H;Nissen-Meyer, J;O'Connor, P M;Papo, N;Puxbaum, V;Saavedra, L;Sanchez, J;Tileva, M;Tiwari, S K;Tymoszewska, A;Wang, X J;Wang, Y J;Yang, J Y;Yang, S;Zhang, C;Zhang, M J;Zhang, Y;Zhao, Y M | IB1TQ | Madrid, Spain | 15 | null | 5 | null | 31,108,822 | Arbulu, Sara;Cintas, Luis M;Feito, Javier;Gutiez, Loreto;Hernandez, Pablo E;Herranz, Carmen;Jimenez, Juan J | FOOD RES INT | Cork, Ireland;Leknes, Norway;Madrid, Spain;Palma De Mallorca, Spain |
He, X L;Liang, F Y;Lin, R S;Shi, C Y;Wang, B;Xiao, Y L;Yao, Y Q;Zhang, M S;Zhou, B | 10.1094/PHYTO-07-18-0266-R | null | 3340 PILOT KNOB ROAD, ST PAUL, MN 55121 USA | 74986od301u5l10f666z6e3o2z5u1q1a1q21 | Systematic Identification of Pathogenic <i>Streptomyces</i> sp. AMCC400023 That Causes Common Scab and Genomic Analysis of Its Pathogenicity Island | Shandong Agr Univ | null | Zhou, B (corresponding author), Natl Engn Lab Efficient Utilizat Soil & Fertilize, Tai An 271018, Shandong, Peoples R China.;Zhou, B; Wang, B (corresponding author), Shandong Agr Univ, Coll Life Sci, Dept Microbiol, Tai An 271018, Shandong, Peoples R China. | null | He, Xiaoli;Liang, Feiyang;Lin, Rongshan;Shi, Chunyu;Wang, Bing;Xiao, Yunli;Yao, Yaqian;Zhang, Mingshuo;Zhou, Bo | Plant Sciences | National Key RD Program [2017YFD0201100, 2017YFD0800200]; Shandong Province Potato Industry Innovation Team Chief Expert Project [SDAIT-16-01] | WOS | Wang, B;Zhou, B | Natl Engn Lab Efficient Utilizat Soil & Fertilize, Shandong, Peoples R China;Shandong Agr Univ, Shandong, Peoples R China;Shandong Plant Protect Stn, Shandong, Peoples R China | 109 | <i>Streptomyces</i>;AMCC400023;Analysis;and;Causes;Common;Genomic;Identification;Island;its;of;Pathogenic;Pathogenicity;Scab;sp;systematic;that | 1 | Liang, Feiyang;Zhou, Bo | AMER PHYTOPATHOLOGICAL SOC | B (corresponding author), Shandong Agr Univ, Coll Life Sci, Dept Microbiol, Tai An 271018, Shandong, Peoples R China.; Zhou, B (corresponding author), Natl Engn Lab Efficient Utilizat Soil & Fertilize, Tai An 271018, Shandong, Peoples R China;Natl Engn Lab Efficient Utilizat Soil & Fertilize, Tai An 271018, Shandong, Peoples R China;Shandong Agr Univ, Agr Coll, Tai An 271018, Shandong, Peoples R China;Shandong Agr Univ, Coll Life Sci, Dept Microbiol, Tai An 271018, Shandong, Peoples R China;Shandong Plant Protect Stn, Linyi, Shandong, Peoples R China | Article | Natl Engn Lab Efficient Utilizat Soil & Fertilize;Shandong Agr Univ | ST PAUL | null | null | Natl Engn Lab Efficient Utilizat Soil & Fertilize;Shandong Agr Univ;Shandong Plant Protect Stn | National Key RD Program;Shandong Province Potato Industry Innovation Team Chief Expert Project | Zhou, B; Wang, B (corresponding author), Shandong Agr Univ, Coll Life Sci, Dept Microbiol, Tai An 271018, Shandong, Peoples R China.; Zhou, B (corresponding author), Natl Engn Lab Efficient Utilizat Soil & Fertilize, Tai An 271018, Shandong, Peoples R China. | 1128 | He, Xiaoli;Liang, Feiyang;Lin, Rongshan;Shi, Chunyu;Wang, Bing;Xiao, Yunli;Yao, Yaqian;Zhang, Mingshuo;Zhou, Bo | 39 | 4 | 473,667,800,003 | National Key RD Program [2017YFD0201100, 2017YFD0800200];Shandong Province Potato Industry Innovation Team Chief Expert Project [SDAIT-16-01] | China | PHYTOPATHOLOGY | China | null | null | Shandong Agr Univ, Coll Life Sci, Dept Microbiol, Tai An 271018, Shandong, Peoples R China | 0031-949X | He, X L;Liang, F Y;Lin, R S;Shi, C Y;Wang, B;Xiao, Y L;Yao, Y Q;Zhang, M S;Zhou, B | JUL | bwang@sdau.edu.cn;zhoubo2798@163.com | AMCC400023;Common Scab;Genomic Analysis;Pathogenic <i>Streptomyces</i> sp;Pathogenicity Island;systematic Identification | 9 | J | Plant Sciences | 16S ribosomal RNA analyses;31 Streptomyces genomes;31 Streptomyces species;accurate taxonomic status;AMCC400023;analyses;ANI;average nucleotide identity (ANI);biochemical characteristics;China;close homologous relationship;close relationship;collinearity analysis;colonization region;Common Scab;complete pathogenicity island (PAI) composition;data;detection;distinct phytopathogen;DNA-DNA HYBRIDIZATION;formed;genome level;Genomic Analysis;Hebei Province;horizontal gene transfer;isDDH analyses;least;member;PAI;PAI structure mapping;pathogen strain;Pathogenic <i>Streptomyces</i> sp;pathogenicity;Pathogenicity Island;PHYLOGENETIC ANALYSIS;phylogenetic relationships;phylogenetic tree;phytotoxin thaxtomin A.;PHYTOTOXINS;PLANT PATHOGENICITY;POTATO;potato common scab;potato scab;potato scabs;potato tuber slice assay;potato-growing areas;potted back experiment;radish seedling test;results;RIBOSOMAL-RNA GENE;S. scabiei;S. scabiei 87-22;same time;sequence;serious soilborne disease;severe economic losses;silico DNADNA hybridization (isDDH);SP-NOV;species level;Streptomyces scabiei;Streptomyces sp;Streptomyces spp.;Streptomyces strain AMCC400023;synthetic gene cluster tree construction;systematic Identification;taxonomic status;test strain Streptomyces sp;thaxtomin;THAXTOMIN BIOSYNTHESIS;toxicity-related genes;toxin region;two pathogens;VIRULENCE;whole genome;whole-genome level | Liang, F Y | DNA-DNA HYBRIDIZATION;PHYLOGENETIC ANALYSIS;PHYTOTOXINS;PLANT PATHOGENICITY;POTATO;RIBOSOMAL-RNA GENE;SEQUENCE;SP-NOV;THAXTOMIN BIOSYNTHESIS;VIRULENCE | 1115 | [Liang, Feiyang; Lin, Rongshan; Yao, Yaqian; Zhang, Mingshuo; He, Xiaoli; Zhou, Bo; Wang, Bing] Shandong Agr Univ, Coll Life Sci, Dept Microbiol, Tai An 271018, Shandong, Peoples R China. [Xiao, Yunli] Shandong Plant Protect Stn, Linyi, Shandong, Peoples R China. [Shi, Chunyu] Shandong Agr Univ, Agr Coll, Tai An 271018, Shandong, Peoples R China. [Zhou, Bo] Natl Engn Lab Efficient Utilizat Soil & Fertilize, Tai An 271018, Shandong, Peoples R China. | This work was partially supported by National Key R&D Program grants 2017YFD0201100 and 2017YFD0800200 and funding from Shandong Province Potato Industry Innovation Team Chief Expert Project grant SDAIT-16-01. | 16S ribosomal RNA analyses;31 Streptomyces genomes;31 Streptomyces species;accurate taxonomic status;AMCC400023;analyses;ANI;average nucleotide identity (ANI);biochemical characteristics;China;close homologous relationship;close relationship;collinearity analysis;colonization region;complete pathogenicity island (PAI) composition;data;detection;distinct phytopathogen;formed;genome level;Hebei Province;horizontal gene transfer;isDDH analyses;least;member;PAI;PAI structure mapping;pathogen strain;pathogenicity;phylogenetic relationships;phylogenetic tree;phytotoxin thaxtomin A.;potato common scab;potato scab;potato scabs;potato tuber slice assay;potato-growing areas;potted back experiment;radish seedling test;results;S. scabiei;S. scabiei 87-22;same time;serious soilborne disease;severe economic losses;silico DNADNA hybridization (isDDH);species level;Streptomyces scabiei;Streptomyces sp;Streptomyces spp.;Streptomyces strain AMCC400023;synthetic gene cluster tree construction;taxonomic status;test strain Streptomyces sp;thaxtomin;toxicity-related genes;toxin region;two pathogens;whole genome;whole-genome level | 10.1007/s00203-007-0225-x;10.1007/s10482-008-9240-4;10.1007/s10482-010-9429-1;10.1007/s10482-011-9656-0;10.1007/s10482-015-0556-6;10.1007/s10482-015-0610-4;10.1007/s12230-017-9575-3;10.1016/j.plasmid.2010.11.002;10.1016/j.pmpp.2007.09.003;10.1016/j.syapm.2016.04.001;10.1016/S0065-2911(00)42003-5;10.1021/jf00044a042;10.1038/417141a;10.1038/ja.2005.1;10.1039/c39890000849;10.1046/j.1365-2958.2000.02170.x;10.1073/pnas.0906412106;10.1074/jbc.M112.420182;10.1093/bioinformatics/btu033;10.1093/femspd/ftw107;10.1093/nar/17.19.7843;10.1093/nar/30.11.2478;10.1093/nar/gkh340;10.1093/nar/gkr1293;10.1094/MPMI-04-16-0068-R;10.1094/MPMI-09-16-0190-R;10.1094/MPMI-20-6-0599;10.1094/MPMI-20-7-0751;10.1094/MPMI-23-2-0161;10.1094/MPMI-23-9-1164;10.1094/PDIS-93-12-1329;10.1094/PDIS.1997.81.8.836;10.1094/Phyto-80-606;10.1094/Phyto-85-537;10.1094/Phyto-86-709;10.1094/PHYTO-96-1363;10.1094/PHYTO.1999.89.6.462;10.1099/00207713-39-4-387;10.1099/00207713-39-4-393;10.1099/00207713-46-3-635;10.1099/00207713-48-2-495;10.1099/00207713-50-1-91;10.1099/ijs.0.02624-0;10.1099/ijs.0.02629-0;10.1099/ijs.0.64483-0;10.1099/ijs.0.65224-0;10.1101/gr.1224503;10.1111/j.1365-2958.2004.04461.x;10.1111/j.1365-2958.2007.05942.x;10.1111/j.1365-3059.2012.02619.x;10.1111/j.1365-3059.2012.02659.x;10.1111/j.1574-6968.2006.00368.x;10.1111/j.1574-6976.2007.00072.x;10.1111/jam.12369;10.1111/mpp.12296;10.1128/AEM.68.2.738-744.2002;10.1128/JB.01010-08;10.1128/JB.186.5.1362-1373.2004;10.1128/MMBR.63.2.266-292.1999;10.1146/annurev.phyto.44.032905.091147;10.1186/1471-2105-14-60;10.1186/1471-2105-5-113;10.1186/1471-2164-9-75;10.1371/journal.pone.0099345;10.1371/journal.ppat.1006811;10.4056/sigs.531120;[10.1111/J.1364-3703.2009.00561.X, 10.1111/j.1364-3703.2009.00561.x] | Shandong Agr Univ | He, X L;Liang, F Y;Lin, R S;Shi, C Y;Wang, B;Xiao, Y L;Yao, Y Q;Zhang, M S;Zhou, B | Liang, F Y: Shandong Agr Univ, Coll Life Sci, Dept Microbiol, Tai An 271018, Shandong, Peoples R China | li, zhang;Zhang, Lijun;Zhou, Bo | 2017YFD0201100;2017YFD0800200;SDAIT-16-01 | 73 | null | China | Natl Engn Lab Efficient Utilizat Soil & Fertilize;Shandong Agr Univ;Shandong Plant Protect Stn | Liang, Feiyang | hybrid | DNA-DNA HYBRIDIZATION;PHYLOGENETIC ANALYSIS;PHYTOTOXINS;PLANT PATHOGENICITY;POTATO;RIBOSOMAL-RNA GENE;SEQUENCE;SP-NOV;THAXTOMIN BIOSYNTHESIS;VIRULENCE | Liang, Feiyang; Lin, Rongshan; Yao, Yaqian; Xiao, Yunli; Zhang, Mingshuo; Shi, Chunyu; He, Xiaoli; Zhou, Bo; Wang, Bing; | null | Natl Engn Lab Efficient Utilizat Soil & Fertilize, Tai An 271018, Shandong, Peoples R China;Shandong Agr Univ, Agr Coll, Tai An 271018, Shandong, Peoples R China;Shandong Agr Univ, Coll Life Sci, Dept Microbiol, Tai An 271018, Shandong, Peoples R China;Shandong Plant Protect Stn, Linyi, Shandong, Peoples R China | Natl Engn Lab Efficient Utilizat Soil & Fertilize, Tai An 271018, Shandong, Peoples R China;Shandong Agr Univ, Agr Coll, Tai An 271018, Shandong, Peoples R China;Shandong Agr Univ, Coll Life Sci, Dept Microbiol, Tai An 271018, Shandong, Peoples R China;Shandong Plant Protect Stn, Linyi, Shandong, Peoples R China | 1943-7684 | null | 7 | 1966;1989;1990;1994;1995;1996;1997;1998;1999;2000;2002;2003;2004;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017;2018 | 8 | Natl Engn Lab Efficient Utilizat Soil & Fertilize, Tai An 271018, Shandong, Peoples R China;Shandong Agr Univ, Coll Life Sci, Dept Microbiol, Tai An 271018, Shandong, Peoples R China | Phytopathology | Wang, Bing | AMER PHYTOPATHOLOGICAL SOC | (ANI);(isDDH);(PAI);,;16S;31;87-22;a;A.;accurate;acquired;all;AMCC400023;among;analyses;analysis;analyzed;and;ANI;areas;as;assay;at;average;back;based;be;between;biochemical;by;carried;caused;characteristics;China;clearly;close;cluster;collinearity;colonization;common;compared;complete;composition;conjectured;construction;contained;data;detection;determined;directly;disease;distinct;DNADNA;economic;experiment;formed;from;gene;genes;genome;genomes;had;Hebei;homologous;horizontal;hybridization;identified;identity;important;in;indicated;indirectly;instead;isDDH;island;isolated;it;least;level;losses;mapping;member;might;Morphological;most;nucleotide;obtain;occurs;of;on;or;out;PAI;paper;pathogen;pathogenicity;pathogens;phylogenetic;physiological;phytopathogen;phytotoxin;potato;potato-growing;potted;Province;radish;region;relationship;relationships;relatively;results;ribosomal;RNA;S.;same;scab;scabiei;scabs;seedling;separating;sequenced;series;serious;severe;silico;slice;soilborne;sp;species;spp.;status;strain;Streptomyces;structure;such;supported;synthetic;systematically;taxonomic;test;that;thaxtomin;the;there;this;time;to;toxicity-related;toxin;transfer;tree;tuber;two;verified;very;was;were;which;while;whole;whole-genome;with;worldwide | Natl Engn Lab Efficient Utilizat Soil & Fertilize;Shandong Agr Univ | Potato scab, a serious soilborne disease caused by Streptomyces spp., occurs in potato-growing areas worldwide and results in severe economic losses. In this paper, the pathogenicity of Streptomyces strain AMCC400023, isolated from potato scabs in Hebei Province, China, was verified systematically by the radish seedling test, the potato tuber slice assay, the potted back experiment, and the detection of phytotoxin thaxtomin A. Morphological, physiological, and biochemical characteristics were determined, and the 16S ribosomal RNA analyses of Streptomyces sp. AMCC400023 were carried out. To obtain the accurate taxonomic status of the pathogen strain, the whole genome was sequenced, and the phylogenetic tree among 31 Streptomyces genomes was formed. The average nucleotide identity (ANI) and in silico DNADNA hybridization (isDDH) were analyzed, and at the same time, the toxicity-related genes between Streptomyces sp. AMCC400023 and Streptomyces scabiei were compared, all based on the whole-genome level. All of the data supported that, instead of a member of S. scabiei, test strain Streptomyces sp. AMCC400023 was a distinct phytopathogen of potato common scab, which had a relatively close relationship with S. scabiei while separating clearly from S. scabiei at least in the species level of taxonomic status. The complete pathogenicity island (PAI) composition of Streptomyces sp. AMCC400023 was identified, which contained a toxin region and a colonization region. It was conjectured that the PAI of Streptomyces sp. AMCC400023 might be directly or indirectly acquired from S. scabiei 87-22 by horizontal gene transfer, or at the very least, there was a very close homologous relationship between the two pathogens as indicated by a series of analyses, such as phylogenetic relationships among 31 Streptomyces species, ANI and isDDH analyses, PAI structure mapping, thaxtomin A synthetic gene cluster tree construction, and most important, the collinearity analysis at the genome level. | JEZ-7925-2023;JHV-1750-2023;T-9297-2019 | DNA-DNA HYBRIDIZATION;PHYLOGENETIC ANALYSIS;PHYTOTOXIN;PLANT PATHOGEN;POTATO;RIBOSOMAL-RNA GENES;SEQUENCE;SP-NOV;THAXTOMIN BIOSYNTHESIS;VIRULENCE | 3 | null | null | 14 | DNA-DNA HYBRIDIZATION;PHYLOGENETIC ANALYSIS;PHYTOTOXIN;plant pathogen;POTATO;RIBOSOMAL-RNA GENES;SEQUENCE;SP-NOV;THAXTOMIN BIOSYNTHESIS;VIRULENCE | WOS:000473667800003 | Natl Engn Lab Efficient Utilizat Soil & Fertilize, Shandong, Peoples R China;Shandong Agr Univ, Shandong, Peoples R China;Shandong Plant Protect Stn, Shandong, Peoples R China | China | 2,019 | null | 0000-0002-9771-0919;0000-0003-2746-350X | null | null | English | null | ADV MICROB PHYSIOL;AM J POTATO RES;ANNU REV PHYTOPATHOL;ANTON LEEUW INT J G;APPL ENVIRON MICROB;ARCH MICROBIOL;BIOINFORMATICS;BMC BIOINFORMATICS;BMC GENOMICS;FEMS MICROBIOL LETT;FEMS MICROBIOL REV;GENOME RES;INT J CURR MICROBIOL;INT J SYST BACTERIOL;INT J SYST EVOL MICR;J AGR FOOD CHEM;J ANTIBIOT;J APPL MICROBIOL;J BACTERIOL;J BIOL CHEM;J CHEM SOC CHEM COMM;J FOOD AGRIC ENVIRON;MICROBIOL MOL BIOL R;Mob Genet Elements;MOL MICROBIOL;MOL PLANT MICROBE IN;MOL PLANT PATHOL;NATURE;NUCL ACIDS;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PATHOG DIS;PHYSIOL MOL PLANT P;PHYTOPATHOLOGY;PLANT DIS;PLANT PATHOL;PLASMID;PLOS ONE;PLOS PATHOG;STAND GENOMIC SCI;SYST APPL MICROBIOL | He, Xiaoli;Liang, Feiyang;Lin, Rongshan;Shi, Chunyu;Wang, Bing;Xiao, Yunli;Yao, Yaqian;Zhang, Mingshuo;Zhou, Bo | 2024-03-11
ER | [Anonymous];Abdel-Rahman, T M A;Auch, A F;Aziz, R K;Bender, C L;Bentley, S D;Bertram, R;Bignell, D R D;Bordeleau Eric;Bouchek-Mechiche, K;Braun, S;Bukhalid, R A;Bérdy, J;Chapleau, M;Dees, M W;Delcher, A L;Edgar, R C;Edwards, U;Eggers, C H;Goris, J;Goyer, C;Guo, Y P;Hao, J J;Healy, F G;Herbst, D A;Hodgson, D A;Huguet-Tapia, J C;Johnson, E G;Joshi, M;Joshi, M V;Kers, J A;King, R R;Kreuze, J F;Labeda, D P;Lambert, D H;Lawrence, C H;Leiminger, J;Leiner, R H;Lerat, S;Li, L;Loria, R;Mcclerklin, S A;Meier-Kolthoff, J P;Miyajima, K;Park, D H;Pertry, I;Punta M.;Richter, M;Seipke, R F;Shirling E. B.;Song, J;Spaepen, S;Stamatakis, A;Stegmann, E;Wach, M J;Wang, Y P;Wanner, L A;Zhang, Y C | IG2YY | Shandong, Peoples R China;Shandong, Peoples R China. | 8 | null | 3 | null | 30,829,555 | He, Xiaoli;Liang, Feiyang;Lin, Rongshan;Shi, Chunyu;Wang, Bing;Xiao, Yunli;Yao, Yaqian;Zhang, Mingshuo;Zhou, Bo | PHYTOPATHOLOGY | Shandong, Peoples R China |
Santos-Moreno, J;Schaerli, Y | 10.1021/acssynbio.9b00174 | null | 1155 16TH ST, NW, WASHINGTON, DC 20036 USA | 3w1cx6b4p6i3f6o5q4i5i3b44n3lzmp2z | A Framework for the Modular and Combinatorial Assembly of Synthetic Gene Circuits | Univ Lausanne | null | Santos-Moreno, J; Schaerli, Y (corresponding author), Univ Lausanne, Dept Fundamental Microbiol, Biophore Bldg, CH-1015 Lausanne, Switzerland. | null | Santos-Moreno, Javier;Schaerli, Yolanda | Biochemical Research Methods | Swiss National Science Foundation [31003A_175608]; Swiss National Science Foundation (SNF) [31003A_175608] Funding Source: Swiss National Science Foundation (SNF) | WOS | Santos-Moreno, J;Schaerli, Y | Univ Lausanne, Lausanne, Switzerland | 8 | a;and;Assembly;circuits;Combinatorial;for;Framework;gene;Modular;of;synthetic;the | 1 | Moreno, Javier Santos;Schaerli, Yolanda | AMER CHEMICAL SOC | Univ Lausanne, Dept Fundamental Microbiol, Biophore Bldg, CH-1015 Lausanne, Switzerland;Y (corresponding author), Univ Lausanne, Dept Fundamental Microbiol, Biophore Bldg, CH-1015 Lausanne, Switzerland | Article | Univ Lausanne | WASHINGTON | null | null | Univ Lausanne | Swiss National Science Foundation;Swiss National Science Foundation (SNF) | Santos-Moreno, J; Schaerli, Y (corresponding author), Univ Lausanne, Dept Fundamental Microbiol, Biophore Bldg, CH-1015 Lausanne, Switzerland. | 1697 | Santos-Moreno, Javier;Schaerli, Yolanda | 36 | 1 | 476,957,300,025 | Swiss National Science Foundation (SNF) [31003A_175608] Funding Source: Swiss National Science Foundation (SNF);Swiss National Science Foundation [31003A_175608] | Switzerland | ACS SYNTHETIC BIOLOGY | Switzerland | null | null | Univ Lausanne, Dept Fundamental Microbiol, Biophore Bldg, CH-1015 Lausanne, Switzerland | 2161-5063 | Santos-Moreno, J;Schaerli, Y | JUL | javier.santosmoreno@unil.ch;yolanda.schaerli@unil.ch | Combinatorial Assembly;synthetic gene circuits | 2 | J | Biochemistry & Molecular Biology | 3-node networks;accurate assembly;approach;available;circuit construction process;CIRCUITS;cloning;Combinatorial Assembly;combinatorial circuit libraries;combinatorial library;constituent parts;CONSTRUCTION;costs;CRISPR;CRISPR-based double-inverter circuit;DNA;DNA assembly;Escherichia coli;fast;final circuit;first step;gene circuit;gene circuit construction;Gene circuits;Gibson assembly;individual intermediate plasmids;iterative design-build-test cycles;LIBRARIES;plasmids;regions;restriction enzymes;scheme;second Gibson assembly;second step;simple;single plasmid;specific sets;synthetic biology;synthetic gene circuits;TAGS;time;time-limiting step;transcriptional units;two-step;usefulness;widespread Gibson assembly method | Santos-Moreno, J | cloning;CONSTRUCTION;CRISPR;DNA;DNA assembly;gene circuit;Gibson assembly;LIBRARIES;Synthetic biology;TAGS | 1691 | [Santos-Moreno, Javier; Schaerli, Yolanda] Univ Lausanne, Dept Fundamental Microbiol, Biophore Bldg, CH-1015 Lausanne, Switzerland. | We thank Marc Garcia-Garcera for help with R language, and Florence Gauye and Leo Moser for excellent technical assistance. We also thank all Schaerli lab members for useful discussions, and Lance E. Keller for critical reading of the manuscript. This work was funded by Swiss National Science Foundation Grant 31003A_175608. | 3-node networks;accurate assembly;approach;available;circuit construction process;circuits;combinatorial assembly;combinatorial circuit libraries;combinatorial library;constituent parts;costs;CRISPR-based double-inverter circuit;Escherichia coli;fast;final circuit;first step;gene circuit construction;gene circuits;Gibson assembly;individual intermediate plasmids;iterative design-build-test cycles;plasmids;regions;restriction enzymes;scheme;second Gibson assembly;second step;simple;single plasmid;specific sets;synthetic gene circuits;time;time-limiting step;transcriptional units;two-step;usefulness;widespread Gibson assembly method | 10.1002/mbo3.753;10.1016/j.cell.2007.12.033;10.1016/j.cell.2013.02.022;10.1021/acssynbio.5b00147;10.1021/acssynbio.7b00111;10.1021/acssynbio.7b00122;10.1021/acssynbio.8b00060;10.1021/sb4001323;10.1038/nature19841;10.1038/nbt.2355;10.1038/nbt1172;10.1038/ncomms5905;10.1038/NMETH1010;10.1039/c2mb25483b;10.1042/BJ20081949;10.1093/nar/gkr1288;10.1093/nar/gkt605;10.1093/nar/gkt860;10.1093/nar/gkt915;10.1093/nar/gky1182;10.1101/cshperspect.a023812;10.1111/nph.15625;10.1126/science.1192272;10.1186/1754-1611-2-5;10.1186/1754-1611-7-13;10.1186/1754-1611-8-2;10.1371/journal.pone.0003647;10.1371/journal.pone.0006441;10.1371/journal.pone.0016765;10.15252/msb.20167449;[10.1038/NMETH.1318, 10.1038/nmeth.1318] | Univ Lausanne | Santos-Moreno, J;Schaerli, Y | Santos-Moreno, J: Univ Lausanne, Dept Fundamental Microbiol, Biophore Bldg, CH-1015 Lausanne, Switzerland | Moreno, Javier Santos;Schaerli, Yolanda | 31003A_175608 | 31 | null | Switzerland | Univ Lausanne | Santos-Moreno, Javier | Green Submitted, Green Accepted | CONSTRUCTION;CRISPR;DNA;LIBRARIES;TAGS | Santos-Moreno, Javier; Schaerli, Yolanda; | null | Univ Lausanne, Dept Fundamental Microbiol, Biophore Bldg, CH-1015 Lausanne, Switzerland | Univ Lausanne, Dept Fundamental Microbiol, Biophore Bldg, CH-1015 Lausanne, Switzerland | null | cloning;DNA assembly;Gene circuits;Gibson assembly;Synthetic biology | 7 | 2006;2007;2008;2009;2010;2011;2012;2013;2014;2016;2017;2018;2019 | 11 | Univ Lausanne, Dept Fundamental Microbiol, Biophore Bldg, CH-1015 Lausanne, Switzerland | ACS Synth. Biol. | Schaerli, Yolanda | AMER CHEMICAL SOC | ,;3-node;a;accurate;allows;and;approach;are;assembling;assembly;associated;available;based;by;circuit;circuits;cloning;coli;combinatorial;commonly;constituent;constructed;construction;costs;CRISPR-based;cycles;demonstrate;design-build-test;digested;double-inverter;drive;efficient;emerge;enzymes;Escherichia;fast;final;first;flanking;for;framework;freely;from;gene;Gibson;have;here;hierarchical;in;individual;intermediate;into;involves;is;iterative;libraries;library;make;method;modular;most;networks;of;on;our;overlaps;parts;plasmid;plasmids;present;process;reduces;regions;restriction;resulting;scheme;second;sequencing;set;sets;simple;single;specific;step;substantially;synthetic;that;the;these;this;time;time-limiting;to;transcriptional;two-step;units;usefulness;we;widespread;with;yield | Univ Lausanne | Synthetic gene circuits emerge from iterative design-build-test cycles. Most commonly, the time-limiting step is the circuit construction process. Here, we present a hierarchical cloning scheme based on the widespread Gibson assembly method and make the set of constructed plasmids freely available. Our two-step modular cloning scheme allows for simple, fast, efficient, and accurate assembly of gene circuits and combinatorial circuit libraries in Escherichia coli. The first step involves Gibson assembly of transcriptional units from constituent parts into individual intermediate plasmids. In the second step, these plasmids are digested with specific sets of restriction enzymes. The resulting flanking regions have overlaps that drive a second Gibson assembly into a single plasmid to yield the final circuit. This approach substantially reduces time and sequencing costs associated with gene circuit construction and allows for modular and combinatorial assembly of circuits. We demonstrate the usefulness of our framework by assembling a CRISPR-based double-inverter circuit and a combinatorial library of 3-node networks. | AAH-9318-2019;T-8864-2017 | CONSTRUCTION;CRISPR;DNA;LIBRARIES;TAG | 3 | null | cloning;DNA assembly;gene circuit;Gibson assembly;Synthetic biology | 13 | cloning;CONSTRUCTION;CRISPR;DNA;DNA assembly;Gene circuits;Gibson assembly;LIBRARIES;Synthetic biology;TAG | WOS:000476957300025 | Univ Lausanne, Lausanne, Switzerland | Switzerland | 2,019 | null | 0000-0001-6268-2623;0000-0002-9083-7343 | null | null | English | null | ACS SYNTH BIOL;BIOCHEM J;CELL;CSH PERSPECT BIOL;J Biol Eng;MICROBIOLOGYOPEN;MOL BIOSYST;MOL SYST BIOL;NAT BIOTECHNOL;NAT COMMUN;NAT METHODS;NATURE;NEW PHYTOL;NUCLEIC ACIDS RES;PLOS ONE;SCIENCE | Santos-Moreno, Javier;Schaerli, Yolanda | 2024-03-11
ER | Butzin, N C;Casini, A;Didovyk, A;Duarte, J M;Engler, C;Gibson, D G;Guye, P;Halleran, A D;Haurwitz, R E;Hughes, R A;Kahl, L J;Kogenaru, M;Li, M Z;Liu, X;Pereira, S B;Pollak, B;Potvin-Trottier, L;Pédelacq, J D;Qi, L;Qi, L S;Quan, J Y;Sakaue-Sawano, A;Schaerli, Y;Shcherbo, D;Shetty Reshma, P;Taylor, G M;Torella, J P;Weber, E;Zhang, Y W | IL0AB | Lausanne, Switzerland | 13 | null | 1 | null | 31,185,158 | Santos-Moreno, Javier;Schaerli, Yolanda | ACS SYNTH BIOL | Lausanne, Switzerland |
Burley, G A;Padroni, G;Parkinson, J A;Reichenbach, L F;Taladriz-Sender, A;Withers, J M | 10.1021/jacs.8b12444 | null | 1155 16TH ST, NW, WASHINGTON, DC 20036 USA | 3k383o6d1u2j29501t6lvk1o1s363166j5dq | Sequence-Selective Minor Groove Recognition of a DNA Duplex Containing Synthetic Genetic Components | Univ Strathclyde | null | Burley, GA (corresponding author), Univ Strathclyde, Dept Pure & Appl Chem, Thomas Graham Bldg,295 Cathedral St, Glasgow G1 1XL, Lanark, Scotland. | null | Burley, Glenn A;Padroni, Giacomo;Parkinson, John A;Reichenbach, Linus F;Taladriz-Sender, Andrea;Withers, Jamie M | Chemistry, Multidisciplinary | University of Strathclyde studentship scheme; STFC [ST/M000125/1]; BBSRC [BB/R006857/1]; Leverhulme Trust [RPG-2018-149]; BBSRC [BB/R006857/1] Funding Source: UKRI; STFC [ST/M000125/1] Funding Source: UKRI | WOS | Burley, G A | Univ Strathclyde, Lanark, Scotland | 141 | a;Components;Containing;DNA;Duplex;genetic;Groove;Minor;of;recognition;sequence-Selective;synthetic | 1 | Burley, Glenn;Padroni, Giacomo;Parkinson, John Andrew;Taladriz-Sender, Andrea;Withers, Jamie | AMER CHEMICAL SOC | Univ Strathclyde, Dept Pure & Appl Chem, Thomas Graham Bldg,295 Cathedral St, Glasgow G1 1XL, Lanark, Scotland | Article | Univ Strathclyde | WASHINGTON | null | null | Univ Strathclyde | BBSRC;Leverhulme Trust;STFC;University of Strathclyde studentship scheme | Burley, GA (corresponding author), Univ Strathclyde, Dept Pure & Appl Chem, Thomas Graham Bldg,295 Cathedral St, Glasgow G1 1XL, Lanark, Scotland. | 9563 | Burley, Glenn A;Padroni, Giacomo;Parkinson, John A;Reichenbach, Linus F;Taladriz-Sender, Andrea;Withers, Jamie M | 27 | 1 | 471,835,600,023 | BBSRC [BB/R006857/1];BBSRC [BB/R006857/1] Funding Source: UKRI;Leverhulme Trust [RPG-2018-149];STFC [ST/M000125/1];STFC [ST/M000125/1] Funding Source: UKRI;University of Strathclyde studentship scheme | UK | JOURNAL OF THE AMERICAN CHEMICAL SOCIETY | UK | null | null | Univ Strathclyde, Dept Pure & Appl Chem, Thomas Graham Bldg,295 Cathedral St, Glasgow G1 1XL, Lanark, Scotland | 0002-7863 | Burley, G A;Padroni, G;Parkinson, J A;Reichenbach, L F;Taladriz-Sender, A;Withers, J M | JUN 19 | glenn.burley@strath.ac.uk | DNA Duplex;sequence-Selective Minor Groove Recognition;Synthetic Genetic Components | 6 | J | Chemistry | allosteric distortion;basis;BINDING;described;DNA;DNA Duplex;evolution;G.C pair;HAIRPIN POLYAMIDE;hairpin polyamides;hairpin pyrrole-imidazole polyamides;higher melting stabilization;imidazole unit;incorporation;influence minor groove recognition;major groove;minor groove;minor groove recognition;molecular determinants;NMR CHARACTERIZATION;NMR structural study;P nucleotide;P-Z-containing DNA duplex;P.Z pair;polyamide;PYRROLE-IMIDAZOLE POLYAMIDES;pyrrole-imidazole polyamides bind;reduced level;relative;RNA;sequence-Selective Minor Groove Recognition;site;stable complex;STRUCTURAL BASIS;structural hallmark;synthetic biology applications;synthetic genetic components;synthetic genetic information;SYSTEM;TRANSCRIPTION;two isolated P.Z pairs;UNNATURAL BASE-PAIR;unnatural base-pairs;unnatural P.Z base-pair;Watson-Crick base-pairs | Padroni, G | BINDING;EVOLUTION;HAIRPIN POLYAMIDE;NMR CHARACTERIZATION;PYRROLE-IMIDAZOLE POLYAMIDES;RNA;STRUCTURAL BASIS;SYSTEM;TRANSCRIPTION;UNNATURAL BASE-PAIR | 9555 | [Padroni, Giacomo; Withers, Jamie M.; Taladriz-Sender, Andrea; Reichenbach, Linus F.; Parkinson, John A.; Burley, Glenn A.] Univ Strathclyde, Dept Pure & Appl Chem, Thomas Graham Bldg,295 Cathedral St, Glasgow G1 1XL, Lanark, Scotland. | This work was supported by the University of Strathclyde studentship scheme [G.P.], the STFC [ST/M000125/1], BBSRC [BB/R006857/1], and Leverhulme Trust [RPG-2018-149]. | allosteric distortion;basis;binding;described;DNA;DNA duplex;G.C pair;hairpin polyamides;hairpin pyrrole-imidazole polyamides;higher melting stabilization;imidazole unit;incorporation;influence minor groove recognition;major groove;minor groove;minor groove recognition;molecular determinants;NMR structural study;P nucleotide;P-Z-containing DNA duplex;P.Z pair;polyamide;pyrrole-imidazole polyamides bind;reduced level;relative;site;stable complex;structural basis;structural hallmark;synthetic biology applications;synthetic genetic components;synthetic genetic information;two isolated P.Z pairs;unnatural base-pairs;unnatural P.Z base-pair;Watson-Crick base-pairs | 10.1002/anie.200905173;10.1002/anie.201006735;10.1007/978-3-642-23394-4_33;10.1016/B978-0-12-409547-2.12561-2];10.1016/j.bmc.2018.01.026;10.1016/j.bpc.2004.06.001;10.1016/j.chempr.2016.11.009;10.1016/j.tet.2007.03.041;10.1016/j.tibs.2014.07.002;10.1016/S0079-6565(97)00023-X;10.1016/S0959-440X(03)00081-2;10.1021/acs.accounts.7b00403;10.1021/acs.biochem.6b00533;10.1021/acs.jpcb.6b00125;10.1021/acs.jpcb.7b00345;10.1021/acschembio.5b00952;10.1021/acssynbio.6b00224;10.1021/ar030287f;10.1021/ar200257x;10.1021/bi301327v;10.1021/bi400558c;10.1021/bi982628g;10.1021/ja00259a030;10.1021/ja0373622;10.1021/ja0744899;10.1021/ja105068b;10.1021/ja1072383;10.1021/ja204910n;10.1021/ja207907d;10.1021/ja3014924;10.1021/ja308888c;10.1021/ja408814g;10.1021/ja800888d;10.1021/ja901309z;10.1021/ja964314r;10.1021/ja971569b;10.1021/ja983671u;10.1021/jacs.5b02251;10.1021/jacs.5b03482;10.1021/jacs.7b03540;10.1021/jacs.8b05042;10.1021/sb500268n;10.1038/382559a0;10.1038/nbt.2556;10.1038/ncomms7706;10.1038/nmeth915;10.1038/srep01883;10.1039/c2cc36293g;10.1073/pnas.0509843102;10.1073/pnas.0704217104;10.1073/pnas.0906532106;10.1073/pnas.1222035110;10.1073/pnas.1311778111;10.1093/nar/29.3.693;10.1093/nar/gkl633;10.1093/nar/gkv638;10.1093/nar/gkw890;10.1093/nar/gkx1211;10.1093/nar/gkx144;10.1101/cshperspect.a023770;10.1126/science.7939719;10.1126/science.aan6414;10.1126/science.aat0971;10.1146/annurev-biochem-060408-091030;10.1186/s13637-016-0055-8;10.1358/dof.2001.026.01.858702;10.2174/1568011054222346 | Univ Strathclyde | Burley, G A;Padroni, G;Parkinson, J A;Reichenbach, L F;Taladriz-Sender, A;Withers, J M | Padroni, G: Univ Strathclyde, Dept Pure & Appl Chem, Thomas Graham Bldg,295 Cathedral St, Glasgow G1 1XL, Lanark, Scotland | Burley, Glenn;Padroni, Giacomo;Taladriz-Sender, Andrea | BB/R006857/1;RPG-2018-149;ST/M000125/1 | 67 | null | UK | Univ Strathclyde | Padroni, Giacomo | Green Accepted, hybrid | BINDING;EVOLUTION;HAIRPIN POLYAMIDE;NMR CHARACTERIZATION;PYRROLE-IMIDAZOLE POLYAMIDES;RNA;STRUCTURAL BASIS;SYSTEM;TRANSCRIPTION;UNNATURAL BASE-PAIR | Padroni, Giacomo; Withers, Jamie M.; Taladriz-Sender, Andrea; Reichenbach, Linus F.; Parkinson, John A.; Burley, Glenn A.; | null | Univ Strathclyde, Dept Pure & Appl Chem, Thomas Graham Bldg,295 Cathedral St, Glasgow G1 1XL, Lanark, Scotland | Univ Strathclyde, Dept Pure & Appl Chem, Thomas Graham Bldg,295 Cathedral St, Glasgow G1 1XL, Lanark, Scotland | null | null | 24 | 1987;1994;1996;1997;1998;1999;2001;2003;2004;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017;2018;2019 | 11 | Univ Strathclyde, Dept Pure & Appl Chem, Thomas Graham Bldg,295 Cathedral St, Glasgow G1 1XL, Lanark, Scotland | J. Am. Chem. Soc. | Burley, Glenn A | AMER CHEMICAL SOC | ,;a;aligned;allosteric;an;and;applications;at;base-pair;base-pairs;basis;bind;binding;biology;by;complex;components;consisting;containing;described;determinants;develop;distortion;DNA;duplex;effectively;enlarges;entirely;for;form;further;G.C;genetic;groove;hairpin;hallmark;higher;imidazole;incorporation;induce;induced;influence;information;is;isolated;level;major;melting;mimicking;minor;molecular;narrows;NMR;nucleotide;of;P;P-Z-containing;P.Z;pair;pairs;polyamide;polyamides;provides;pyrrole-imidazole;recognition;reduced;relative;showed;site;slightly;stabilization;stable;structural;study;synthetic;that;the;this;to;two;understanding;unit;unnatural;Watson-Crick;when;with | Univ Strathclyde | The structural basis of minor groove recognition of a DNA duplex containing synthetic genetic information by hairpin pyrrole-imidazole polyamides is described. Hairpin polyamides induce a higher melting stabilization of a DNA duplex containing the unnatural P.Z base-pair when an imidazole unit is aligned with a P nucleotide. An NMR structural study showed that the incorporation of two isolated P.Z pairs enlarges the minor groove and slightly narrows the major groove at the site of this synthetic genetic information, relative to a DNA duplex consisting entirely of Watson-Crick base-pairs. Pyrrole-imidazole polyamides bind to a P-Z-containing DNA duplex to form a stable complex, effectively mimicking a G.C pair. A structural hallmark of minor groove recognition of a P.Z pair by a polyamide is the reduced level of allosteric distortion induced by binding of a polyamide to a DNA duplex. Understanding the molecular determinants that influence minor groove recognition of DNA containing synthetic genetic components provides the basis to further develop unnatural base-pairs for synthetic biology applications. | AAV-8541-2021;ABC-2701-2021;HJY-7356-2023 | BINDING;EVOLUTION;HAIRPIN POLYAMIDES;NMR CHARACTERIZATION;PYRROLE-IMIDAZOLE POLYAMIDES;RNA;STRUCTURAL BASIS;SYSTEM;TRANSCRIPTION;UNNATURAL BASE-PAIR | 1 | null | null | 9 | BINDING;EVOLUTION;HAIRPIN POLYAMIDES;NMR CHARACTERIZATION;PYRROLE-IMIDAZOLE POLYAMIDES;RNA;STRUCTURAL BASIS;SYSTEM;TRANSCRIPTION;UNNATURAL BASE-PAIR | WOS:000471835600023 | Univ Strathclyde, Lanark, Scotland | UK | 2,019 | null | 0000-0002-1406-4449;0000-0002-4896-113X;0000-0002-8274-4761;0000-0002-9746-9467;0000-0003-4270-6135 | null | null | English | null | ACCOUNTS CHEM RES;ACS CHEM BIOL;ACS SYNTH BIOL;ANGEW CHEM INT EDIT;ANNU REV BIOCHEM;BIOCHEMISTRY-US;BIOORGAN MED CHEM;BIOPHYS CHEM;CHEM COMMUN;CHEM-US;CSH PERSPECT BIOL;CURR OPIN STRUC BIOL;Current Medicinal Chemistry - Anti-Cancer Agents;DRUG FUTURE;ENERGY AND ENVIRONMENTAL PERSPECTIVES;EURASIP J BIOINFORM;J AM CHEM SOC;J PHYS CHEM B;NAT BIOTECHNOL;NAT COMMUN;NAT METHODS;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PROG NUCL MAG RES SP;SCI REP-UK;SCIENCE;TETRAHEDRON;TRENDS BIOCHEM SCI | Burley, Glenn A;Padroni, Giacomo;Parkinson, John A;Reichenbach, Linus F;Taladriz-Sender, Andrea;Withers, Jamie M | 2024-03-11
ER | Bando, T;Benner, S A;Biondi, E;Bostock-Smith, C E;Chawla, M;Chenoweth, D M;De Clairac, R P L;Declairac, R P L;Dervan Peter B.;Dervan, P B;Dose, C;Erwin, G S;Feldman, A W;Feldmann, A W;Geierstanger, B H;Georgiadis, M M;Hirao, I;Hiraoka, K;Hoshika, S;Hsu, C F;Ishizuka, T;James, P L;Kawamoto, Y;Kimoto, M;Krpetic, Z;Laos, R;Lavergne, T;Leal, N A;Li, L J;Meier, J L;Molt, R W;Nickols, N G;Ogundijo, O E;Padroni, G;Pandav, K;Panunto, T W;Pilch, D S;Puckett, J W;Ramakers, L A I;Reichenbach, L F;Rohs, R;Sefah, K;Seo, Y J;Sharma, S K;Slattery, M;Someya, T;Su, W;Trauger, J W;Wang, S;Wang, X Y;Warren, C L;White, S;Wijmenga, S S;Winiger, C B;Withers J.M.;Yang, F;Yang, Z Y;Zhang, L Q;Zhang, Q | ID7BB | Lanark, Scotland | 14 | null | 1 | null | 31,117,639 | Burley, Glenn A;Padroni, Giacomo;Parkinson, John A;Reichenbach, Linus F;Taladriz-Sender, Andrea;Withers, Jamie M | J AM CHEM SOC | Lanark, Scotland |
Cho, G;Kwak, Y S | 10.25387/g3.8030795 | null | 9650 ROCKVILLE AVE, BETHESDA, MD 20814 USA | 6s3d4y6t3h1q3231725y2os2e6565lx3i2s | Evolution of Antibiotic Synthesis Gene Clusters in the <i>Streptomyces globisporus</i> TFH56, Isolated from Tomato Flower | Gyeongsang Natl Univ | null | Kwak, YS (corresponding author), Gyeongsang Natl Univ, 501 Jinju Daero, Jinju 52828, South Korea. | null | Cho, Gyeongjun;Kwak, Youn-Sig | Genetics & Heredity | Next-Generation BioGreen 21 Program [PJ013250]; Technology Development Program for Agriculture and Forestry, Ministry for Food, Agriculture, Forestry, and Fisheries, Republic of Korea [315004-5] | WOS | Kwak, Y S | Gyeongsang Natl Univ, Jinju, South Korea | 9 | ,;<i>Streptomyces;Antibiotic;Clusters;evolution;Flower;From;gene;globisporus</i>;in;Isolated;of;synthesis;TFH56;the;Tomato | 1 | null | GENETICS SOCIETY AMERICA | Gyeongsang Natl Univ, 501 Jinju Daero, Jinju 52828, South Korea;Gyeongsang Natl Univ, Dept Plant Med, Inst Agr & Life Sci, Jinju 52828, South Korea;Gyeongsang Natl Univ, Div Appl Life Sci BK21Plus, Jinju 52828, South Korea | Article | Gyeongsang Natl Univ | BETHESDA | null | null | Gyeongsang Natl Univ | Next-Generation BioGreen 21 Program;Technology Development Program for Agriculture and Forestry, Ministry for Food, Agriculture, Forestry, and Fisheries, Republic of Korea | Kwak, YS (corresponding author), Gyeongsang Natl Univ, 501 Jinju Daero, Jinju 52828, South Korea. | 1813 | Cho, Gyeongjun;Kwak, Youn-Sig | 5 | 2 | 535,489,600,003 | Next-Generation BioGreen 21 Program [PJ013250];Technology Development Program for Agriculture and Forestry, Ministry for Food, Agriculture, Forestry, and Fisheries, Republic of Korea [315004-5] | South Korea | G3-GENES GENOMES GENETICS | South Korea | null | null | Gyeongsang Natl Univ, Div Appl Life Sci BK21Plus, Jinju 52828, South Korea | 2160-1836 | Cho, G;Kwak, Y S | JUN | kwak@gnu.ac.kr | <i>Streptomyces globisporus</i> TFH56;Antibiotic Synthesis Gene Clusters;evolution;Tomato Flower | 2 | J | Genetics & Heredity | <i>Streptomyces globisporus</i> TFH56;Antibiotic Synthesis Gene Clusters;average nucleotide identity;bioactive compound;bioactive metabolites;Botrytis cinerea;C-1027;caryolan-1-ol synthase gene;COMPLETE GENOME SEQUENCE;conprimycin synthetic gene cluster;evolution;genome;genome sequence;gray mold pathogen;lidamycin synthetic gene cluster;linear chromosome;linear plasmids;Pacific Biosciences RS II platform;plant diseases;S. globisporus;strain TFH56;Streptomyces complete genome;Streptomyces globisporus;streptomyces species;Streptomyces strain TFH56;study;three linear sequences (7.67 Mbp;Tomato Flower;total) | Cho, G | bioactive compound;C-1027;COMPLETE GENOME SEQUENCE;linear chromosome;Streptomyces complete genome | 1807 | [Cho, Gyeongjun; Kwak, Youn-Sig] Gyeongsang Natl Univ, Div Appl Life Sci BK21Plus, Jinju 52828, South Korea. [Kwak, Youn-Sig] Gyeongsang Natl Univ, Dept Plant Med, Inst Agr & Life Sci, Jinju 52828, South Korea. | This research was supported by the Next-Generation BioGreen 21 Program (PJ013250) and by the Technology Development Program for Agriculture and Forestry, Ministry for Food, Agriculture, Forestry, and Fisheries, Republic of Korea (project no. 315004-5). | average nucleotide identity;bioactive metabolites;Botrytis cinerea;caryolan-1-ol synthase gene;conprimycin synthetic gene cluster;genome;genome sequence;gray mold pathogen;lidamycin synthetic gene cluster;linear chromosome;linear plasmids;Pacific Biosciences RS II platform;plant diseases;S. globisporus;strain TFH56;Streptomyces globisporus;streptomyces species;Streptomyces strain TFH56;study;three linear sequences (7.67 Mbp;tomato flower;total) | 10.1007/s10482-016-0824-0;10.1007/s41348-017-0090-z;10.1016/j.jbiotec.2016.02.004;10.1038/417141a;10.1038/ismej.2015.95;10.1038/nbt820;10.1038/srep08365;10.1098/rsob.170075;10.1099/mic.0.27758-0;10.1111/1574-6968.12128;10.1126/science.1072110;10.7164/antibiotics.41.1575;[10.1038/ja.2012.54, 10.1038/ja.2012.27];[10.1094/MPMI-05-18-0129-R, 10.1094/mpmi-05-18-0129-r] | Gyeongsang Natl Univ | Cho, G;Kwak, Y S | Cho, G: Gyeongsang Natl Univ, Div Appl Life Sci BK21Plus, Jinju 52828, South Korea | null | 315004-5;PJ013250 | 15 | null | South Korea | Gyeongsang Natl Univ | Cho, Gyeongjun | null | C-1027;COMPLETE GENOME SEQUENCE | Cho, Gyeongjun; Kwak, Youn-Sig; | null | Gyeongsang Natl Univ, Dept Plant Med, Inst Agr & Life Sci, Jinju 52828, South Korea;Gyeongsang Natl Univ, Div Appl Life Sci BK21Plus, Jinju 52828, South Korea | Gyeongsang Natl Univ, Dept Plant Med, Inst Agr & Life Sci, Jinju 52828, South Korea;Gyeongsang Natl Univ, Div Appl Life Sci BK21Plus, Jinju 52828, South Korea | null | Bioactive compounds;linear chromosome;Streptomyces complete genome | 6 | 1988;2002;2003;2005;2008;2012;2013;2015;2016;2017;2018;2019 | 6 | Gyeongsang Natl Univ, 501 Jinju Daero, Jinju 52828, South Korea | G3-Genes Genomes Genet. | Kwak, Youn-Sig | GENETICS SOCIETY AMERICA | (7.67;,;a;acquired;and;are;as;average;based;bioactive;Biosciences;Botrytis;can;caryolan-1-ol;chromosome;cinerea;classified;cluster;conprimycin;consistent;diseases;examples;flower;found;gene;genome;globisporus;gray;identity;II;in;included;inhibit;is;known;lidamycin;linear;Mbp;metabolites;mold;moreover;nucleotide;obtained;of;on;other;Pacific;pathogen;plant;plasmids;platform;presence;prevent;previously;produce;RS;S.;sequence;sequences;species;strain;Streptomyces;study;synthase;synthetic;TFH56;that;the;this;three;to;tomato;total);using;various;was;were;which;with | Gyeongsang Natl Univ | Streptomyces species are known to produce various bioactive metabolites that can prevent plant diseases. Previously, the Streptomyces strain TFH56 was found to inhibit the gray mold pathogen, Botrytis cinerea, in tomato flower. In this study, the genome sequence of strain TFH56 was acquired using the Pacific Biosciences RS II platform. Three linear sequences (7.67 Mbp in total) were obtained. Based on average nucleotide identity, strain TFH56 was classified as Streptomyces globisporus, which is consistent with the presence of a linear chromosome and linear plasmids. Moreover, as with other examples of S. globisporus, the genome of strain TFH56 included a caryolan-1-ol synthase gene, a conprimycin synthetic gene cluster, and a lidamycin synthetic gene cluster | null | C-1027;COMPLETE GENOME SEQUENCE | 0 | null | bioactive compound;linear chromosome;Streptomyces complete genome | 7 | BIOACTIVE COMPOUNDS;C-1027;COMPLETE GENOME SEQUENCE;linear chromosome;Streptomyces complete genome | WOS:000535489600003 | Gyeongsang Natl Univ, Jinju, South Korea | South Korea | 2,019 | null | null | null | null | English | null | ANTON LEEUW INT J G;FEMS MICROBIOL LETT;Genus Streptomyces;ISME J;J ANTIBIOT;J BIOTECHNOL;J PLANT DIS PROTECT;MICROBIOL-SGM;MOL PLANT MICROBE IN;NAT BIOTECHNOL;NATURE;OPEN BIOL;SCI REP-UK;SCIENCE | Cho, Gyeongjun;Kwak, Youn-Sig | 2024-03-11
ER | Bentley, S D;Brettin, T;Bérdy, J;Cha, J Y;Cho, G;Euzeby J. P.;Hu, J;Ikeda, H;Kim, D R;Kwon, Y;Labeda, D P;Li, X X;Liu, W;Taechowisan, T;Yagüe, P | LR1XG | Jinju, South Korea | 6 | null | 1 | null | 31,018,944 | Cho, Gyeongjun;Kwak, Youn-Sig | G3-GENES GENOM GENET | Jinju, South Korea |
Ceroni, F;Nikolados, E M;Oyarzún, D A;Weiss, A Y | 10.1021/acssynbio.8b00531 | null | 1155 16TH ST, NW, WASHINGTON, DC 20036 USA | 205j511e2m3h4h6c2g1g3m1v496j3m4n5d252f6b | Growth Defects and Loss-of-Function in Synthetic Gene Circuits | Univ Edinburgh | null | Oyarzún, DA (corresponding author), Univ Edinburgh, Sch Biol Sci, Edinburgh EH9 3BF, Midlothian, Scotland.;Oyarzún, DA (corresponding author), Univ Edinburgh, Sch Informat, Edinburgh EH8 9AB, Midlothian, Scotland.;Oyarzún, DA (corresponding author), Univ Edinburgh, SynthSys Ctr Synthet & Syst Biol, Edinburgh EH9 3BF, Midlothian, Scotland. | null | Ceroni, Francesca;Nikolados, Evangelos-Marios;Oyarzun, Diego A;Weiss, Andrea Y | Biochemical Research Methods | null | WOS | Oyarzún, D A | Imperial Coll London, London, England;Univ Edinburgh, Midlothian, Scotland | 8 | and;circuits;Defects;gene;growth;in;Loss-of-Function;synthetic | 1 | Ceroni, Francesca;Nikolados, Evangelos-Marios | AMER CHEMICAL SOC | Imperial Coll London, Dept Chem Engn, London SW7 2AZ, England;Imperial Coll London, Hammersmith Hosp, Dept Med, London W12 0NN, England;Imperial Coll London, Imperial Coll Ctr Synthet Biol, London SW7 2AZ, England;Univ Edinburgh, Sch Biol Sci, Edinburgh EH9 3BF, Midlothian, Scotland;Univ Edinburgh, Sch Biol Sci, Edinburgh EH9 3BF, Midlothian, Scotland.; Oyarzún, DA (corresponding author), Univ Edinburgh, Sch Informat, Edinburgh EH8 9AB, Midlothian, Scotland.; Oyarzún, DA (corresponding author), Univ Edinburgh, SynthSys Ctr Synthet & Syst Biol, Edinburgh EH9 3BF, Midlothian, Scotland;Univ Edinburgh, Sch Informat, Edinburgh EH8 9AB, Midlothian, Scotland;Univ Edinburgh, SynthSys Ctr Synthet & Syst Biol, Edinburgh EH9 3BF, Midlothian, Scotland | Article | Univ Edinburgh | WASHINGTON | null | null | Imperial Coll London;Univ Edinburgh | null | Oyarzún, DA (corresponding author), Univ Edinburgh, Sch Biol Sci, Edinburgh EH9 3BF, Midlothian, Scotland.; Oyarzún, DA (corresponding author), Univ Edinburgh, Sch Informat, Edinburgh EH8 9AB, Midlothian, Scotland.; Oyarzún, DA (corresponding author), Univ Edinburgh, SynthSys Ctr Synthet & Syst Biol, Edinburgh EH9 3BF, Midlothian, Scotland. | 1240 | Ceroni, Francesca;Nikolados, Evangelos-Marios;Oyarzun, Diego A;Weiss, Andrea Y | 25 | 6 | 473,115,700,002 | null | UK | ACS SYNTHETIC BIOLOGY | UK | null | null | Univ Edinburgh, Sch Biol Sci, Edinburgh EH9 3BF, Midlothian, Scotland | 2161-5063 | Ceroni, F;Nikolados, E M;Oyarzún, D A;Weiss, A Y | JUN | d.oyarzun@ed.ac.uk | growth Defects;Loss-of-Function;synthetic gene circuits | 4 | J | Biochemistry & Molecular Biology | ALLOCATION;approach;bacterial gene circuits;break down circuit function;cellular burden;cellular capacity;cellular host;circuit output;complex relation;comprehensive framework;critical capacity;design space;DYNAMICS;endogenous processes;equilibrium;ESCHERICHIA-COLI;expense;expression;extensive simulations;extra load;Gene circuits;gene expression;genetic burden;genetic logic gates;growth;growth conditions;growth Defects;growth rate drop;heterologous genes;host;host-circuit interactions;IMPACT;integrated host-circuit models;large regions;leading;limit;Loss-of-Function;mechanistic modeling;MODEL;model-based design;NETWORK;optimization;physiology;point;protein output;reduced biosynthesis;resource allocation;result;ribosomal scarcity;RIBOSOMES;shape;silico;simulations;stronger induction;synthetic gene circuits;transcriptional logic gates;weak induction;wide-ranging implications | Nikolados, E M | ALLOCATION;DYNAMICS;ESCHERICHIA-COLI;EXPRESSION;genetic burden;genetic logic gates;host-circuit interactions;mechanistic modeling;MODEL;model-based design;NETWORK;RIBOSOMES;synthetic gene circuits | 1231 | [Nikolados, Evangelos-Marios; Oyarzun, Diego A.] Univ Edinburgh, Sch Biol Sci, Edinburgh EH9 3BF, Midlothian, Scotland. [Weiss, Andrea Y.] Imperial Coll London, Hammersmith Hosp, Dept Med, London W12 0NN, England. [Ceroni, Francesca] Imperial Coll London, Dept Chem Engn, London SW7 2AZ, England. [Ceroni, Francesca] Imperial Coll London, Imperial Coll Ctr Synthet Biol, London SW7 2AZ, England. [Oyarzun, Diego A.] Univ Edinburgh, Sch Informat, Edinburgh EH8 9AB, Midlothian, Scotland. [Oyarzun, Diego A.] Univ Edinburgh, SynthSys Ctr Synthet & Syst Biol, Edinburgh EH9 3BF, Midlothian, Scotland. | null | approach;bacterial gene circuits;break down circuit function;cellular burden;cellular capacity;cellular host;circuit output;complex relation;comprehensive framework;critical capacity;design space;endogenous processes;equilibrium;expense;extensive simulations;extra load;gene circuits;gene expression;growth;growth conditions;growth defects;growth rate drop;heterologous genes;host;host-circuit interactions;impact;integrated host-circuit models;large regions;leading;limit;optimization;physiology;point;protein output;reduced biosynthesis;resource allocation;result;ribosomal scarcity;shape;silico;simulations;stronger induction;synthetic gene circuits;transcriptional logic gates;weak induction;wide-ranging implications | 10.1002/biot.201200085;10.1006/jmbi.1993.1319;10.1007/s10295-018-2013-9;10.1016/j.bpj.2013.04.049;10.1016/j.bpj.2015.06.034;10.1016/j.bpj.2017.12.010;10.1016/j.cell.2012.05.044;10.1016/j.mib.2016.07.009;10.1021/acssynbio.6b00040;10.1021/acssynbio.6b00361;10.1021/acssynbio.7b00119;10.1021/acssynbio.8b00015;10.1021/sb400055h;10.1038/35002125;10.1038/35002131;10.1038/msb.2011.94;10.1038/msb4100204;10.1038/nbt.4238;10.1038/nchembio.218;10.1038/ncomms1516;10.1038/nmeth.4635;10.1038/s41467-018-02898-6;10.1038/s41467-018-03970-x;10.1038/s41564-017-0022-5;10.1073/pnas.1416533112;10.1073/pnas.1718622115;10.1093/nar/gkv1280;10.1103/PhysRevLett.108.018102;10.1126/science.1192588;10.1128/jb.177.6.1497-1504.1995;10.15252/msb.20167461;[10.1038/NMETH.3339, 10.1038/nmeth.3339] | Univ Edinburgh | Ceroni, F;Nikolados, E M;Oyarzún, D A;Weiss, A Y | Nikolados, E M: Univ Edinburgh, Sch Biol Sci, Edinburgh EH9 3BF, Midlothian, Scotland | Ceroni, Francesca;Oyarzun, Diego A | null | 32 | null | UK | Imperial Coll London;Univ Edinburgh | Nikolados, Evangelos-Marios | Green Submitted, Green Accepted | ALLOCATION;DYNAMICS;ESCHERICHIA-COLI;EXPRESSION;MODEL;NETWORK;RIBOSOMES | Nikolados, Evangelos-Marios; Weiss, Andrea Y.; Ceroni, Francesca; Oyarzun, Diego A.; | null | Imperial Coll London, Dept Chem Engn, London SW7 2AZ, England;Imperial Coll London, Hammersmith Hosp, Dept Med, London W12 0NN, England;Imperial Coll London, Imperial Coll Ctr Synthet Biol, London SW7 2AZ, England;Univ Edinburgh, Sch Biol Sci, Edinburgh EH9 3BF, Midlothian, Scotland;Univ Edinburgh, Sch Informat, Edinburgh EH8 9AB, Midlothian, Scotland;Univ Edinburgh, SynthSys Ctr Synthet & Syst Biol, Edinburgh EH9 3BF, Midlothian, Scotland | Imperial Coll London, Dept Chem Engn, London SW7 2AZ, England;Imperial Coll London, Hammersmith Hosp, Dept Med, London W12 0NN, England;Imperial Coll London, Imperial Coll Ctr Synthet Biol, London SW7 2AZ, England;Univ Edinburgh, Sch Biol Sci, Edinburgh EH9 3BF, Midlothian, Scotland;Univ Edinburgh, Sch Informat, Edinburgh EH8 9AB, Midlothian, Scotland;Univ Edinburgh, SynthSys Ctr Synthet & Syst Biol, Edinburgh EH9 3BF, Midlothian, Scotland | null | host-circuit interactions;genetic burden;genetic logic gate;mechanistic models;model-based design;Synthetic gene circuit | 6 | 1993;1995;2000;2008;2009;2010;2011;2012;2013;2015;2016;2017;2018 | 36 | Univ Edinburgh, Sch Biol Sci, Edinburgh EH9 3BF, Midlothian, Scotland;Univ Edinburgh, Sch Informat, Edinburgh EH8 9AB, Midlothian, Scotland;Univ Edinburgh, SynthSys Ctr Synthet & Syst Biol, Edinburgh EH9 3BF, Midlothian, Scotland | ACS Synth. Biol. | Oyarzun, Diego A | AMER CHEMICAL SOC | ,;a;across;allocation;and;approach;assess;at;bacterial;be;between;beyond;biosynthesis;both;break;built;burden;by;can;capacity;caused;cellular;circuit;circuits;complex;comprehensive;conditions;critical;defects;design;down;drop;endogenous;equilibrium;even;expense;expression;extensive;extent;extra;for;framework;function;gates;gene;genes;growth;here;heterologous;highlights;host;host-circuit;impact;implications;in;increased;induction;integrated;interactions;is;large;leading;limit;load;logic;models;of;offers;on;optimization;our;output;perturb;physiology;point;processes;protein;quantify;rate;reaches;reduced;regions;relation;resource;result;reveal;ribosomal;scarcity;shape;sharply;shifts;silico;simulations;slow;space;stronger;studied;suggest;synthetic;that;the;their;tipping;to;transcriptional;various;we;weak;which;wide-ranging;with;yet | Univ Edinburgh | Synthetic gene circuits perturb the physiology of their cellular host. The extra load on endogenous processes shifts the equilibrium of resource allocation in the host, leading to slow growth and reduced biosynthesis. Here we built integrated host-circuit models to quantify growth defects caused by synthetic gene circuits. Simulations reveal a complex relation between circuit output and cellular capacity for gene expression. For weak induction of heterologous genes, protein output can be increased at the expense of growth defects. Yet for stronger induction, cellular capacity reaches a tipping point, beyond which both gene expression and growth rate drop sharply. Extensive simulations across various growth conditions and large regions of the design space suggest that the critical capacity is a result of ribosomal scarcity. We studied the impact of growth defects on various gene circuits and transcriptional logic gates, which highlights the extent to which cellular burden can limit, shape, and even break down circuit function. Our approach offers a comprehensive framework to assess the impact of host-circuit interactions in silico, with wide-ranging implications for the design and optimization of bacterial gene circuits. | A-7945-2008;J-3835-2014 | ALLOCATION;DYNAMICS;ESCHERICHIA-COLI;EXPRESSION;MODEL;NETWORKS;RIBOSOME | 2 | null | genetic burden;genetic logic gates;host-circuit interactions;mechanistic modeling;model-based design;synthetic gene circuits | 19 | ESCHERICHIA-COLI;ALLOCATION;host-circuit interactions;DYNAMICS;EXPRESSION;genetic burden;genetic logic gates;mechanistic models;MODEL;model-based design;NETWORKS;RIBOSOME;synthetic gene circuits | WOS:000473115700002 | Imperial Coll London, London, England;Univ Edinburgh, Midlothian, Scotland | UK | 2,019 | null | 0000-0001-7237-4982;0000-0003-2303-0889 | null | null | English | null | ACS SYNTH BIOL;BIOPHYS J;BIOTECHNOL J;CELL;CURR OPIN MICROBIOL;J BACTERIOL;J IND MICROBIOL BIOT;J MOL BIOL;MOL SYST BIOL;NAT BIOTECHNOL;NAT CHEM BIOL;NAT COMMUN;NAT METHODS;NAT MICROBIOL;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PHYS REV LETT;SCIENCE | Ceroni, Francesca;Nikolados, Evangelos-Marios;Oyarzun, Diego A;Weiss, Andrea Y | 2024-03-11
ER | Blanchard, A E;Borkowski, O;Cambray, G;Carbonell-Ballestero, M;Cardinale, S;Ceroni, F;Cookson, N A;Darlington, A P S;Del Vecchio, D;Dong, H J;Elowitz, M B;Gardner, T S;Gorochowski, T E;Gyorgy, A;Karr, J R;Liao, C;Liu, D;Mather, W H;Nyström, A;Qian, Y L;Rondelez, Y;Rugbjerg, P;Scott, M;Shopera, T;Sleight, S C;Tan, C;Vind, J;Wang, B J;Weisse, A Y | IF5IY | Midlothian, Scotland;Midlothian, Scotland. | 39 | null | 2 | null | 31,181,895 | Ceroni, Francesca;Nikolados, Evangelos-Marios;Oyarzun, Diego A;Weiss, Andrea Y | ACS SYNTH BIOL | London, England;Midlothian, Scotland |
Holliger, P;Houlihan, G;Taylor, A I | 10.1101/cshperspect.a032490 | a032490 | 1 BUNGTOWN RD, COLD SPRING HARBOR, NY 11724 USA | 5s1k67265x59266r3a4o2z2g2z1j5k115333u5u | Beyond DNA and RNA: The Expanding Toolbox of Synthetic Genetics | MRC | null | Holliger, P (corresponding author), MRC, Lab Mol Biol, Cambridge CB2 0QH, England. | null | Holliger, Philipp;Houlihan, Gillian;Taylor, Alexander I | Cell Biology | MRC [MC_U105178804] Funding Source: UKRI; Medical Research Council [MC_U105178804] Funding Source: Medline | WOS | Holliger, P | MRC, Cambridge, England | 11 | :;and;beyond;DNA;Expanding;Genetics;of;RNA;synthetic;the;Toolbox | 1 | null | COLD SPRING HARBOR LAB PRESS | MRC, Lab Mol Biol, Cambridge CB2 0QH, England | Article | MRC | COLD SPRING HARBOR | null | null | Lab Mol Biol;MRC | Medical Research Council;MRC | Holliger, P (corresponding author), MRC, Lab Mol Biol, Cambridge CB2 0QH, England. | null | Holliger, Philipp;Houlihan, Gillian;Taylor, Alexander I | 42 | 1 | 470,086,600,002 | Medical Research Council [MC_U105178804] Funding Source: Medline;MRC [MC_U105178804] Funding Source: UKRI | UK | COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY | UK | null | null | MRC, Lab Mol Biol, Cambridge CB2 0QH, England | 1943-0264 | Holliger, P;Houlihan, G;Taylor, A I | JUN | ph1@mrc-lmb.cam.ac.uk | DNA;Expanding Toolbox;RNA;Synthetic Genetics | 3 | J | Cell Biology | ability;ALPHABET EXPANSION;application;applications;APTAMERS;biotechnology;catalysts (ribozymes/ DNAzymes);central;development;directed evolution;DNA;DNAZYME;ENZYMATIC-SYNTHESIS;enzymes;evolution;Expanding Toolbox;functional structures;gives rise;INFORMATION;key enabling technology;life's origins;LIGANDS;ligands (aptamers);modern biology;molecular level;molecular medicine;nanostructures;natural nucleic acids;new field;nonnatural alternatives;nucleic acid chemical toolbox;POLYMERASE;PROPAGATION;range;remarkable physicochemical properties;repositories;reverse transcriptase engineering;review;RNA;SELECTION;supporting genetic information storage;synthetic genetics;SYSTEMATIC EVOLUTION;unique;WORLD;xeno nucleic acids (XNAs);XNA polymerase | Taylor, A I | ALPHABET EXPANSION;APTAMERS;directed evolution;DNAZYME;ENZYMATIC-SYNTHESIS;LIGANDS;POLYMERASE;SELECTION;SYSTEMATIC EVOLUTION;WORLD | null | [Taylor, Alexander I.; Houlihan, Gillian; Holliger, Philipp] MRC, Lab Mol Biol, Cambridge CB2 0QH, England. | null | ability;application;applications;aptamers;biotechnology;catalysts (ribozymes/ DNAzymes);central;development;DNA;enzymes;evolution;functional structures;gives rise;information;key enabling technology;life's origins;ligands (aptamers);modern biology;molecular level;molecular medicine;nanostructures;natural nucleic acids;new field;nonnatural alternatives;nucleic acid chemical toolbox;propagation;range;remarkable physicochemical properties;repositories;reverse transcriptase engineering;review;RNA;supporting genetic information storage;synthetic genetics;unique;xeno nucleic acids (XNAs);XNA polymerase | 10.1002/anie.200701369;10.1002/anie.201508678;10.1002/cbdv.200900083;10.1002/cbic.201600136;10.1002/cncr.26730;10.1002/eji.201646450;10.1016/j.addr.2018.04.007;10.1016/j.biomaterials.2014.08.046;10.1016/j.biotechadv.2015.02.008;10.1016/j.cbpa.2004.10.003;10.1016/j.cbpa.2016.08.001;10.1016/j.chembiol.2004.10.017;10.1016/j.chembiol.2012.10.011;10.1016/j.copbio.2017.04.004;10.1016/j.copbio.2017.09.006;10.1016/j.drudis.2014.09.004;10.1016/j.jconrel.2016.10.015;10.1016/j.jmb.2006.06.050;10.1016/j.sbi.2016.01.009;10.1016/j.tibs.2016.04.010;10.1017/S0033583517000038;10.1021/ac400058z;10.1021/acs.accounts.7b00056;10.1021/acs.chemrev.6b00114;10.1021/cb800314v;10.1021/ja100710j;10.1021/ja993688s;10.1021/jacs.5b06696;10.1021/jacs.5b12647;10.1021/jacs.6b10767;10.1021/jacs.6b13132;10.1021/jacs.7b11488;10.1021/nn1024658;10.1038/emm.2016.44;10.1038/natrevmats.2017.68;10.1038/nature01185;10.1038/nature13900;10.1038/nature13982;10.1038/nbt.3765;10.1038/ncomms11235;10.1038/nprot.2015.104;10.1038/nprot.2018.023;10.1038/nrd.2016.199;10.1038/nrg1231;10.1038/nrg3978;10.1038/nrm.2017.77;10.1038/s41467-017-02014-0;10.1038/s41557-018-0008-9;10.1038/s41570017-0076;10.1039/c3sc50574j;10.1039/c7sc03747c;10.1039/c7sc04491g;10.1073/pnas.0408440102;10.1073/pnas.0704211104;10.1073/pnas.1120964109;10.1073/pnas.1610103113;10.1073/pnas.92.25.11509;10.1073/pnas.94.9.4262;10.1080/15476286.2016.1236173;10.1093/nar/gkv1472;10.1093/nar/gkw608;10.1093/nar/gkx368;10.1101/cshperspect.a023770;10.1126/science.1200752;10.1126/science.1217622;10.1126/science.1238149;10.1126/science.271.5257.1854;10.1126/science.284.5423.2118;10.1126/science.aaf5409;10.1146/annurev-cellbio-100616-060758;10.1371/journal.pone.0015004;10.1517/14712598.2015.1025048;10.1557/mrs.2017.276;10.3389/fchem.2016.00018;10.3390/biomedicines5030051;10.3390/cancers10010009;[10.1038/NCHEM.1241, 10.1038/nchem.1241];[10.1038/NCHEM.2493, 10.1038/nchem.2493];[10.1038/NCHEM.2517, 10.1038/nchem.2517];[10.1038/NCHEMBIO.277, 10.1038/nchembio.277];[10.1038/NNANO.2017.99, 10.1038/nnano.2017.99] | MRC | Holliger, P;Houlihan, G;Taylor, A I | Taylor, A I: MRC, Lab Mol Biol, Cambridge CB2 0QH, England | Houlihan, Gillian | MC_U105178804 | 82 | null | UK | MRC | Taylor, Alexander I | Bronze, Green Published | ALPHABET EXPANSION;APTAMERS;DIRECTED EVOLUTION;DNAZYME;ENZYMATIC-SYNTHESIS;LIGANDS;POLYMERASE;SELECTION;SYSTEMATIC EVOLUTION;WORLD | Taylor, Alexander I.; Houlihan, Gillian; Holliger, Philipp; | null | MRC, Lab Mol Biol, Cambridge CB2 0QH, England | MRC, Lab Mol Biol, Cambridge CB2 0QH, England | null | null | 6 | 1995;1996;1997;1999;2000;2002;2003;2004;2005;2006;2007;2009;2010;2011;2012;2013;2014;2015;2016;2017;2018 | 29 | MRC, Lab Mol Biol, Cambridge CB2 0QH, England | Cold Spring Harbor Perspect. Biol. | Holliger, Philipp | COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT | ";(aptamers);(ribozymes/;(XNAs);,;a;ability;acid;acids;also;alternatives;and;application;applications;aptamers;are;as;at;been;believed;biology;biotechnology;both;capable;catalysts;central;chemical;collectively;define;development;DNA;DNAzymes);enabling;engineering;enzymes;evolution;expand;field;for;form;functional;genetic;genetics;gives;have;however;in;information;is;key;level;life's;ligands;medicine;modern;molecular;nanostructures;natural;new;nonnatural;not;nucleic;of;origins;outline;physicochemical;polymerase;propagation;properties;range;remarkable;repositories;reverse;review;rise;RNA;seeks;storage;structures;such;summarize;supporting;synthetic;technology;termed;the;their;this;to;toolbox;transcriptase;unique;we;well;which;widely;xeno;XNA | MRC | The remarkable physicochemical properties of the natural nucleic acids, DNA and RNA, define modern biology at the molecular level and are widely believed to have been central to life's origins. However, their ability to form repositories of information as well as functional structures such as ligands (aptamers) and catalysts (ribozymes/ DNAzymes) is not unique. A range of nonnatural alternatives, collectively termed xeno nucleic acids (XNAs), are also capable of supporting genetic information storage and propagation as well as evolution. This gives rise to a new field of "synthetic genetics," which seeks to expand the nucleic acid chemical toolbox for applications in both biotechnology and molecular medicine. In this review, we outline XNA polymerase and reverse transcriptase engineering as a key enabling technology and summarize the application of "synthetic genetics" to the development of aptamers, enzymes, and nanostructures. | Y-6197-2019 | ALPHABET EXPANSION;APTAMERS;DIRECTED EVOLUTION;DNAZYME;ENZYMATIC-SYNTHESIS;LIGANDS;POLYMERASE;SELECTION;SYSTEMATIC EVOLUTION;WORLD | 4 | null | null | 15 | ALPHABET EXPANSION;aptamer;directed evolution;DNAZYME;ENZYMATIC-SYNTHESIS;LIGANDS;POLYMERASE;SELECTION;SYSTEMATIC EVOLUTION;WORLD | WOS:000470086600002 | MRC, Cambridge, England | UK | 2,019 | null | null | null | null | English | null | ACCOUNTS CHEM RES;ACS CHEM BIOL;ACS NANO;ADV DRUG DELIVER REV;ANAL CHEM;ANGEW CHEM INT EDIT;ANNU REV CELL DEV BI;BIOMATERIALS;BIOMEDICINES;BIOTECHNOL ADV;CANCER-AM CANCER SOC;CANCERS;CHEM BIODIVERS;CHEM BIOL;CHEM REV;CHEM SCI;CHEMBIOCHEM;CSH PERSPECT BIOL;CURR OPIN BIOTECH;CURR OPIN CHEM BIOL;CURR OPIN STRUC BIOL;DRUG DISCOV TODAY;EUR J IMMUNOL;EXP MOL MED;EXPERT OPIN BIOL TH;FRONT CHEM;J AM CHEM SOC;J CONTROL RELEASE;J MOL BIOL;MRS BULL;NAT BIOTECHNOL;NAT CHEM;NAT CHEM BIOL;NAT COMMUN;NAT NANOTECHNOL;NAT PROTOC;NAT REV CHEM;NAT REV DRUG DISCOV;NAT REV GENET;NAT REV MATER;NAT REV MOL CELL BIO;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PLOS ONE;Q REV BIOPHYS;RNA BIOL;SCIENCE;TRENDS BIOCHEM SCI | Holliger, Philipp;Houlihan, Gillian;Taylor, Alexander I | 2024-03-11
ER | Anosova, I;Attwater, J;Benner, S A;Burmeister, P E;Chaput, J C;Chen, T;Chen, T J;Chen, Z;Chim, N;Cozens, C;Darmostuk, M;Dellafiore, M A;Dunn, M R;Ellefson, J W;Eschenmoser, A;Feldman, A W;Fokina, A A;Friedman, A D;Garn, H;Gelinas, A D;Gold, L;Gothelf, K V;Grosjean, H;Herdewijn, P;Hori, S;Horning, D P;Houlihan, G;Howorka, S;Jo, H;Joyce, G F;Kasahara, Y;Khvorova, A;Kim, K R;Koide, S;Larsen, A C;Ledbetter, M P;Lee, K H;Lipi, F;Liu, J;Liu, Z X;Lutz, J F;Matsunaga, K;Mei, H;Meyer, K D;Mi, J;Morrow, P K;Ong, J L;Pan, W H;Pfeiffer, F;Pinheiro, V B;Reader, J S;Röthlisberger, P;Sacerdote, M G;Santoro, S W;Schimmel, P;Schumacher, T N M;Sczepanski, J T;Seeman, N C;Silverman, S K;Szathmáry, E;Tawiah, K D;Taylor, A I;Thirunavukarasu, D;Tsai, C H;Vater, A;Wachowius, F;Wang, Y J;Wang, Z M;Weigele, P;Wittrup, A;Wochner, A;Young, D D;Yu, H Y;Zhou, C;Zhou, J H | IB2GB | Cambridge, England | 30 | null | 1 | null | 31,160,351 | Holliger, Philipp;Houlihan, Gillian;Taylor, Alexander I | CSH PERSPECT BIOL | Cambridge, England |
Boedicker, J;Chavez, M S;Chellamuthu, P;El-Naggar, M Y;Naughton, K;Pirbadian, S;Silva, K P T | 10.3389/fmicb.2019.00938 | 938 | AVENUE DU TRIBUNAL FEDERAL 34, LAUSANNE, CH-1015, SWITZERLAND | 3g3c1n2y4zd1r4l5q64m105r4o3t1u5s703y4r | Biogenic Control of Manganese Doping in Zinc Sulfide Nanomaterial Using <i>Shewanella oneidensis</i> MR-1 | Univ Southern Calif | null | Boedicker, J (corresponding author), Univ Southern Calif, Dept Biol Sci, Los Angeles, CA 90007 USA.;Boedicker, J (corresponding author), Univ Southern Calif, Dept Phys & Astron, Los Angeles, CA 90007 USA. | null | Boedicker, James;Chavez, Marko S;Chellamuthu, Prithiviraj;El-Naggar, Mohamed Y;Naughton, Kyle;Pirbadian, Sahand;Silva, Kalinga Pavan T | Microbiology | Office of Naval Research [N00014-15-1-2573]; Office of Naval Research Multidisciplinary University Research Initiative [N00014-18-1-2632]; Air Force Office of Scientific Research Award [FA9550-14-1-0294] | WOS | Boedicker, J | Univ Southern Calif, Los Angeles, CA USA | 10 | <i>Shewanella;biogenic;control;Doping;in;Manganese;MR-1;Nanomaterial;of;oneidensis</i>;Sulfide;using;Zinc | 1 | Pirbadian, Sahand | FRONTIERS MEDIA SA | Univ Southern Calif, Dept Biol Sci, Los Angeles, CA 90007 USA;Univ Southern Calif, Dept Chem, Los Angeles, CA USA;Univ Southern Calif, Dept Phys & Astron, Los Angeles, CA 90007 USA;Univ Southern Calif, Dept Phys & Astron, Los Angeles, CA 90007 USA.; Boedicker, J (corresponding author), Univ Southern Calif, Dept Biol Sci, Los Angeles, CA 90007 USA | Article | Univ Southern Calif | LAUSANNE | null | null | Univ Southern Calif | Air Force Office of Scientific Research Award;Office of Naval Research;Office of Naval Research Multidisciplinary University Research Initiative | Boedicker, J (corresponding author), Univ Southern Calif, Dept Phys & Astron, Los Angeles, CA 90007 USA.; Boedicker, J (corresponding author), Univ Southern Calif, Dept Biol Sci, Los Angeles, CA 90007 USA. | null | Boedicker, James;Chavez, Marko S;Chellamuthu, Prithiviraj;El-Naggar, Mohamed Y;Naughton, Kyle;Pirbadian, Sahand;Silva, Kalinga Pavan T | 48 | 3 | 467,034,500,001 | Air Force Office of Scientific Research Award [FA9550-14-1-0294];Office of Naval Research [N00014-15-1-2573];Office of Naval Research Multidisciplinary University Research Initiative [N00014-18-1-2632] | USA | FRONTIERS IN MICROBIOLOGY | USA;USA.; | null | null | Univ Southern Calif, Dept Phys & Astron, Los Angeles, CA 90007 USA | 1664-302X | Boedicker, J;Chavez, M S;Chellamuthu, P;El-Naggar, M Y;Naughton, K;Pirbadian, S;Silva, K P T | MAY 7 | boedicke@usc.edu | <i>Shewanella oneidensis</i> MR-1;biogenic Control;Manganese;Zinc Sulfide Nanomaterial | 7 | J | Microbiology | <i>Shewanella oneidensis</i> MR-1;atom-by-atom nanomaterial synthesis;BACTERIA;biogenic;biogenic Control;biogenic quantum dots;biogenically;biological strategies;biological systems;compounds;cytochrome complex MtrCAB;cytochrome expression levels;dopant incorporation;expression;genetic control circuits;genetic engineering;inducer molecule;inducible expression;inorganic materials;interest;Manganese;manganese (KO oxide;manganese doped zinc sulfide nanoparticles (Mn;metals;microbes;MN;NANOCRYSTALS;nanomaterial characteristics;nanomaterials;nanoparticle (NP);NANOPARTICLES;natural synthetic capabilities;optical properties;OPTICAL-PROPERTIES;optoelectronic properties;particles;PHOTOLUMINESCENCE;precise modulation;promise;quantum dot (QD);recent advancements;redox state;reduction;results;semiconductor nanomaterials;shape;Shewanella;Shewanella oneindensis;similar;size;STRAIN;synthetic biology;Synthetic gene circuit;synthetic gene circuits;tunable control;Zinc Sulfide Nanomaterial;ZnS) | Chellamuthu, P | biogenic;EXPRESSION;genetic engineering;METALS;MN;NANOCRYSTALS;nanoparticle (NP);NANOPARTICLES;OPTICAL-PROPERTIES;PHOTOLUMINESCENCE;quantum dot (QD);REDUCTION;Shewanella;Synthetic biology | null | [Chellamuthu, Prithiviraj; Naughton, Kyle; Pirbadian, Sahand; Silva, Kalinga Pavan T.; Chavez, Marko S.; El-Naggar, Mohamed Y.; Boedicker, James] Univ Southern Calif, Dept Phys & Astron, Los Angeles, CA 90007 USA. [Chellamuthu, Prithiviraj; El-Naggar, Mohamed Y.; Boedicker, James] Univ Southern Calif, Dept Biol Sci, Los Angeles, CA 90007 USA. [El-Naggar, Mohamed Y.] Univ Southern Calif, Dept Chem, Los Angeles, CA USA. | This work was supported by Office of Naval Research award number N00014-15-1-2573 and by the Office of Naval Research Multidisciplinary University Research Initiative Grant No. N00014-18-1-2632. SP was supported by Air Force Office of Scientific Research Award No. FA9550-14-1-0294. We thank USC Center for Electron Microscopy and Microanalysis (CEMMA) and California Institute of Technology GPS Division Analytical Facility for their help with sample analysis. | atom-by-atom nanomaterial synthesis;bacteria;biogenic quantum dots;biogenically;biological strategies;biological systems;compounds;cytochrome complex MtrCAB;cytochrome expression levels;dopant incorporation;genetic control circuits;inducer molecule;inducible expression;inorganic materials;interest;manganese (KO oxide;manganese doped zinc sulfide nanoparticles (Mn;microbes;nanomaterial characteristics;nanomaterials;natural synthetic capabilities;optical properties;optoelectronic properties;particles;precise modulation;promise;recent advancements;redox state;reduction;results;semiconductor nanomaterials;shape;Shewanella oneindensis;similar;size;strain;synthetic biology;synthetic gene circuit;synthetic gene circuits;tunable control;ZnS) | 10.1002/adfm.200600163;10.1002/adfm.200600493;10.1002/bio.2801;10.1002/jctb.3934;10.1002/pssb.2221360155;10.1007/BF01569900;10.1007/BF02651190;10.1007/s00203-002-0472-9;10.1007/s00253-016-7756-5;10.1007/s10529-015-2026-7;10.1007/s13204-011-0036-x;10.1016/0022-2313(92)90034-7;10.1016/j.apsusc.2008.04.002;10.1016/j.apt.2012.09.007;10.1016/j.colsurfb.2011.02.030;10.1016/j.jallcom.2009.07.097;10.1016/j.jcis.2015.01.022;10.1016/j.optmat.2005.10.003;10.1016/j.pmatsci.2010.10.001;10.1016/j.spmi.2015.07.043;10.1016/j.stam.2005.03.006;10.1016/j.tim.2010.06.007;10.1016/S0168-6445(03)00044-5;10.1021/acssynbio.6b00349;10.1021/ar9001069;10.1021/ja110996c;10.1021/jz402495h;10.1021/sb4000564;10.1023/A:1020518818647;10.1038/nbt.4111;10.1038/nmat758;10.1038/nrmicro.2015.24;10.1038/nrmicro1947;10.1039/c2cs35331h;10.1063/1.1633347;10.1063/1.2711709;10.1063/1.328642;10.1073/pnas.0832310100;10.1073/pnas.1523633113;10.1080/15533170500471417;10.1103/PhysRevLett.72.416;10.1111/1751-7915.12297;10.1111/j.1365-2958.2010.07266.x;10.1128/AEM.01087-07;10.1128/AEM.50.2.491-497.1985;10.1128/AEM.67.1.260-269.2001;10.1128/AEM.71.8.4935-4937.2005;10.1186/s40643-017-0181-5;10.1371/journal.pone.0106937;10.3389/fmicb.2012.00056;10.3762/bjnano.6.181;10.4236/OJBIPHY.2016.61001, 10.4236/ojbiphy.2016.61001];[10.1007/s11051-006-9183-5, 10.1007/sl1051-006-9183-5];[10.1038/NMAT3912, 10.1038/nmat3912];[10.1039/c6ra13835g, 10.1039/C6RA13835G];[10.1039/c7ee00282c, 10.1039/C7EE00282C] | Univ Southern Calif | Boedicker, J;Chavez, M S;Chellamuthu, P;El-Naggar, M Y;Naughton, K;Pirbadian, S;Silva, K P T | Chellamuthu, P: Univ Southern Calif, Dept Phys & Astron, Los Angeles, CA 90007 USA | null | FA9550-14-1-0294;N00014-15-1-2573;N00014-18-1-2632 | 58 | null | USA | Univ Southern Calif | Chellamuthu, Prithiviraj | gold, Green Published | EXPRESSION;METALS;MN;NANOCRYSTALS;NANOPARTICLES;OPTICAL-PROPERTIES;PHOTOLUMINESCENCE;REDUCTION;SYNTHETIC BIOLOGY | Chellamuthu, Prithiviraj; Naughton, Kyle; Pirbadian, Sahand; Silva, Kalinga Pavan T.; Chavez, Marko S.; El-Naggar, Mohamed Y.; Boedicker, James; | null | Univ Southern Calif, Dept Biol Sci, Los Angeles, CA 90007 USA;Univ Southern Calif, Dept Chem, Los Angeles, CA USA;Univ Southern Calif, Dept Phys & Astron, Los Angeles, CA 90007 USA | Univ Southern Calif, Dept Biol Sci, Los Angeles, CA 90007 USA;Univ Southern Calif, Dept Chem, Los Angeles, CA USA;Univ Southern Calif, Dept Phys & Astron, Los Angeles, CA 90007 USA | null | biogenic;genetic engineering;nanoparticle (NP);quantum dot (QD);Shewanella | null | 1979;1981;1985;1986;1992;1994;1995;2001;2002;2003;2004;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017;2018 | 12 | Univ Southern Calif, Dept Biol Sci, Los Angeles, CA 90007 USA;Univ Southern Calif, Dept Phys & Astron, Los Angeles, CA 90007 USA | Front. Microbiol. | Boedicker, James | FRONTIERS MEDIA SA | (KO;(Mn;,;:;a;advancements;alter;an;and;as;assembled;atom-by-atom;bacteria;biogenic;biogenically;biological;biology;by;capabilities;characteristics;chemically;circuit;circuits;combine;complex;compounds;control;controlled;create;cytochrome;demonstrate;dopant;doped;dots;enabled;engineered;expression;for;gene;genetic;have;here;implementing;in;incorporation;inducer;inducible;inorganic;interest;into;levels;made;manganese;manufacture;many;materials;microbes;modulation;molecule;MtrCAB;nanomaterial;nanomaterials;nanoparticles;natural;naturally;of;oneindensis;optical;optoelectronic;our;oxide;particles;perform;physical;precise;promise;properties;quantum;recent;redox;reduction;regulated;results;semiconductor;shape;Shewanella;similar;size;specify;spurred;state;strain;strategies;such;sulfide;synthesis;synthesized;synthetic;systems;the;thereby;these;to;toward;tunable;using;we;were;which;with;zinc;ZnS) | Univ Southern Calif | Bacteria naturally alter the redox state of many compounds and perform atom-by-atom nanomaterial synthesis to create many inorganic materials. Recent advancements in synthetic biology have spurred interest in using biological systems to manufacture nanomaterials, implementing biological strategies to specify the nanomaterial characteristics such as size, shape, and optical properties. Here, we combine the natural synthetic capabilities of microbes with engineered genetic control circuits toward biogenically synthesized semiconductor nanomaterials. Using an engineered strain of Shewanella oneindensis with inducible expression of the cytochrome complex MtrCAB, we control the reduction of manganese (KO oxide. Cytochrome expression levels were regulated using an inducer molecule, which enabled precise modulation of dopant incorporation into manganese doped zinc sulfide nanoparticles (Mn:ZnS). Thereby, a synthetic gene circuit controlled the optical properties of biogenic quantum dots. These biogenically assembled nanomaterials have similar physical and optoelectronic properties to chemically synthesized particles. Our results demonstrate the promise of implementing synthetic gene circuits for tunable control of nanomaterials made by biological systems. | null | EXPRESSION;METALS;MN;NANOCRYSTALS;NANOPARTICLES;OPTICAL-PROPERTIES;PHOTOLUMINESCENCE;REDUCTION;SYNTHETIC BIOLOGY | 4 | null | biogenic;genetic engineering;nanoparticle (NP);quantum dot (QD);Shewanella | 10 | biogenic;EXPRESSION;genetic engineering;METALS;MN;NANOCRYSTALS;NANOPARTICLES;nanoparticle (NP);OPTICAL-PROPERTIES;PHOTOLUMINESCENCE;quantum dot (QD);REDUCTION;Shewanella;Synthetic biology | WOS:000467034500001 | Univ Southern Calif, Los Angeles, CA USA | USA | 2,019 | null | 0000-0002-4186-3457 | null | null | English | null | ACCOUNTS CHEM RES;ACS SYNTH BIOL;ADV FUNCT MATER;ADV POWDER TECHNOL;ANTON LEEUW INT J G;APPL ENVIRON MICROB;APPL MICROBIOL BIOT;APPL NANOSCI;APPL PHYS LETT;APPL SURF SCI;ARCH MICROBIOL;BEILSTEIN J NANOTECH;BIORESOUR BIOPROCESS;BIOTECHNOL LETT;CHEM SOC REV;COLLOID SURFACE B;ENERG ENVIRON SCI;FEMS MICROBIOL REV;FRONT MICROBIOL;J ALLOY COMPD;J AM CHEM SOC;J APPL PHYS;J CHEM TECHNOL BIOT;J COLLOID INTERF SCI;J ELECTRON MATER;J IND MICROBIOL;J LUMIN;J NANOPART RES;J PHYS CHEM LETT;LUMINESCENCE;METAL CYCLING BACTER;MICROB BIOTECHNOL;MOL MICROBIOL;NAT BIOTECHNOL;NAT MATER;NAT REV MICROBIOL;OPEN J BIOPHYSICS;OPT MATER;P NATL ACAD SCI USA;PHYS REV LETT;PHYS STATUS SOLIDI B;PLOS ONE;PROG MATER SCI;RSC ADV;SCI TECHNOL ADV MAT;SUPERLATTICE MICROST;SYNTH REACT INORG M;THESIS;TRENDS MICROBIOL | Boedicker, James;Chavez, Marko S;Chellamuthu, Prithiviraj;El-Naggar, Mohamed Y;Naughton, Kyle;Pirbadian, Sahand;Silva, Kalinga Pavan T | 2024-03-11
ER | Akid, R;Ali I.M.;Ang, J;Beerman P. A., G;Begum, R;Bhargava, R N;Biswas, S;Bouhenni, R;Bretschger, O;Burdige, D J;Cao, J;Chandrakar, R K;Chen, A Y;Coursolle, D;Da Costa, J P;Deng, Z T;Dunleavy, R;Fang, X S;Francis, C A;Fredrickson, J K;Goede, O;Hazra, C;Hurd, J M;Hussain, I;Jacob, J M;Karar, N;Katiyar, M;Kershaw, S V;Kole, A K;Komada, S;Lloyd, J R;Mao, C B;Marusak, K E;Myers, J M;Naik, R R;Nealson K.;Nealson, K H;Peng, W Q;Rodrigues, L R;Rodríguez-Carmona, E;Sasakura, H;Schuergers, N;Segall-Shapiro, T H;Singh, B N;Singh, B R;Smanski, M J;Smith, A M;Son, D;Spoerke, E D;Stroyuk, A L;Vance, M E;Wakatsuki, T;Wanjari, L;Warad, H C;West, E A;Wu, J W;Xiao, Q | HW9TV | Los Angeles, CA USA;Los Angeles, CA USA. | 15 | null | 1 | null | 31,134,005 | Boedicker, James;Chavez, Marko S;Chellamuthu, Prithiviraj;El-Naggar, Mohamed Y;Naughton, Kyle;Pirbadian, Sahand;Silva, Kalinga Pavan T | FRONT MICROBIOL | Los Angeles, CA USA |
Bhatia, S K;Choi, T R;Gurav, R;Jung, H R;Ko, B J;Lee, J H;Moon, Y M;Park, J Y;Park, Y L;Song, H S;Yang, S Y;Yang, Y H | 10.4014/jmb.1901.01070 | null | KOREA SCI TECHNOL CENTER #402, 635-4 YEOGSAM-DONG, KANGNAM-GU, SEOUL, SOUTH KOREA | 2f4p196e4o3j1a3b2s344r103x5a973596v6v5e | Increased Tolerance to Furfural by Introduction of Polyhydroxybutyrate Synthetic Genes to <i>Escherichia coli</i> | Konkuk Univ | null | Yang, YH (corresponding author), Konkuk Univ, Coll Engn, Dept Biol Engn, Seoul 05029, South Korea.;Yang, YH (corresponding author), Konkuk Univ, Inst Ubiquitous Informat Technol & Applicat CBRU, Seoul 05029, South Korea. | null | Bhatia, Shashi Kant;Choi, Tae-Rim;Gurav, Ranjit;Jung, Hye-Rim;Ko, Byoung Joon;Lee, Ju-Hee;Moon, Yu-Mi;Park, Jun Young;Park, Ye Lim;Song, Hun-Suk;Yang, Soo-Yeon;Yang, Yung-Hun | Biotechnology & Applied Microbiology;Microbiology | Research Program for Solving Social Issues of the National Research Foundation of Korea (NRF) - Ministry of Science and ICT [2017M3A9E4077234]; National Research Foundation of Korea (NRF) [NRF-2015M1A5A1037196, NRF2016R1D1A1B03932301]; Polar Academic Program (PAP) [PE18900] | WOS | Yang, Y H | Konkuk Univ, Seoul, South Korea;Osong Med Innovat Fdn, Cheongju, South Korea | 29 | <i>Escherichia;by;coli</i>;Furfural;genes;increased;Introduction;of;Polyhydroxybutyrate;synthetic;to;Tolerance | 1 | Bhatia, Shashi;Gurav, Ranjit G;Ko, Byoung Joon | KOREAN SOC MICROBIOLOGY & BIOTECHNOLOGY | Konkuk Univ, Coll Engn, Dept Biol Engn, Seoul 05029, South Korea;Konkuk Univ, Coll Engn, Dept Biol Engn, Seoul 05029, South Korea.; Yang, YH (corresponding author), Konkuk Univ, Inst Ubiquitous Informat Technol & Applicat CBRU, Seoul 05029, South Korea;Konkuk Univ, Inst Ubiquitous Informat Technol & Applicat CBRU, Seoul 05029, South Korea;Osong Med Innovat Fdn, New Drug Dev Ctr, Cheongju 28160, South Korea | Article | Konkuk Univ | SEOUL | null | null | Konkuk Univ;Osong Med Innovat Fdn | National Research Foundation of Korea (NRF);Polar Academic Program (PAP);Research Program for Solving Social Issues of the National Research Foundation of Korea (NRF) - Ministry of Science and ICT | Yang, YH (corresponding author), Konkuk Univ, Coll Engn, Dept Biol Engn, Seoul 05029, South Korea.; Yang, YH (corresponding author), Konkuk Univ, Inst Ubiquitous Informat Technol & Applicat CBRU, Seoul 05029, South Korea. | 784 | Bhatia, Shashi Kant;Choi, Tae-Rim;Gurav, Ranjit;Jung, Hye-Rim;Ko, Byoung Joon;Lee, Ju-Hee;Moon, Yu-Mi;Park, Jun Young;Park, Ye Lim;Song, Hun-Suk;Yang, Soo-Yeon;Yang, Yung-Hun | 30 | 3 | 469,201,000,012 | National Research Foundation of Korea (NRF) [NRF-2015M1A5A1037196, NRF2016R1D1A1B03932301];Polar Academic Program (PAP) [PE18900];Research Program for Solving Social Issues of the National Research Foundation of Korea (NRF) - Ministry of Science and ICT [2017M3A9E4077234] | South Korea | JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY | South Korea;South Korea.; | null | null | Konkuk Univ, Coll Engn, Dept Biol Engn, Seoul 05029, South Korea | 1017-7825 | Bhatia, S K;Choi, T R;Gurav, R;Jung, H R;Ko, B J;Lee, J H;Moon, Y M;Park, J Y;Park, Y L;Song, H S;Yang, S Y;Yang, Y H | MAY | seokor@konkuk.ac.kr | <i>Escherichia coli</i>;Furfural;increased Tolerance;Introduction;Polyhydroxybutyrate Synthetic Genes | 12 | J | Biotechnology & Applied Microbiology;Microbiology | 3-HYDROXYVALERATE;4-hydroxybenzaldehyde;<i>Escherichia coli</i>;absence;application;BACTERIA;bio-based;biodegradable polymer;BIOMASS HYDROLYSATE;compound;cost-effective PHB production;E. coli;Escherichia coli;feasibility;FERMENTATION;fermentative production;findings;furfural;glucose;good target product;growth;increased PHB production;increased Tolerance;INHIBITORS;innovative strategy;Introduction;lignocellulose hydrolysate;lignocellulose hydrolysates;mechanisms;non-edible resource;Overexpression;petroleum-based plastics;phaB;phaC;PHB;PHB production;PHB synthetic genes;PHB synthetic genes (bktB;POLY-3-HYDROXYBUTYRATE;POLYHYDROXYALKANOATES;Polyhydroxybutyrate;polyhydroxybutyrate (PHB);Polyhydroxybutyrate Synthetic Genes;potential;pretreatment processes;promising substrate;Ralstonia eutropha H16) improved cell growth;recombinant E. coli;resistance;results;study;sustainable;vanillin;well-known polyhydroxyalkanoate | Jung, H R | 3-HYDROXYVALERATE;BACTERIA;BIOMASS HYDROLYSATE;Escherichia coli;FERMENTATION;furfural;GROWTH;INHIBITORS;lignocellulose hydrolysate;MECHANISMS;Overexpression;POLY-3-HYDROXYBUTYRATE;POLYHYDROXYALKANOATES;Polyhydroxybutyrate;resistance | 776 | [Jung, Hye-Rim; Lee, Ju-Hee; Moon, Yu-Mi; Choi, Tae-Rim; Yang, Soo-Yeon; Song, Hun-Suk; Park, Jun Young; Park, Ye Lim; Bhatia, Shashi Kant; Gurav, Ranjit; Yang, Yung-Hun] Konkuk Univ, Coll Engn, Dept Biol Engn, Seoul 05029, South Korea. [Bhatia, Shashi Kant; Yang, Yung-Hun] Konkuk Univ, Inst Ubiquitous Informat Technol & Applicat CBRU, Seoul 05029, South Korea. [Ko, Byoung Joon] Osong Med Innovat Fdn, New Drug Dev Ctr, Cheongju 28160, South Korea. | This study was supported by the Research Program for Solving Social Issues of the National Research Foundation of Korea (NRF) funded by the Ministry of Science and ICT (2017M3A9E4077234), National Research Foundation of Korea (NRF) (NRF-2015M1A5A1037196, NRF2016R1D1A1B03932301). Consulting service from the Microbial Carbohydrate Resource Bank (MCRB, Seoul, Korea) was kindly appreciated. This work was also supported by the Polar Academic Program (PAP, PE18900). | 4-hydroxybenzaldehyde;absence;application;bio-based;biodegradable polymer;compound;cost-effective PHB production;E. coli;feasibility;fermentative production;findings;furfural;glucose;good target product;increased PHB production;inhibitors;innovative strategy;introduction;lignocellulose hydrolysate;lignocellulose hydrolysates;non-edible resource;petroleum-based plastics;phaB;phaC;PHB;PHB production;PHB synthetic genes;PHB synthetic genes (bktB;polyhydroxybutyrate (PHB);potential;pretreatment processes;promising substrate;Ralstonia eutropha H16) improved cell growth;recombinant E. coli;resistance;results;study;sustainable;vanillin;well-known polyhydroxyalkanoate | 10.1002/(SICI)1097-0290(20000605)68:5<524::AID-BIT6>3.0.CO;2-T;10.1002/yea.3067;10.1007/BF00500854;10.1007/s00253-005-0142-3;10.1007/s00449-017-1743-9;10.1007/s10295-003-0049-x;10.1007/s10295-004-0136-7;10.1007/s10295-015-1718-2;10.1007/s10529-010-0513-4;10.1016/j.biortech.2008.03.071;10.1016/j.biortech.2009.11.046;10.1016/j.biortech.2017.02.061;10.1016/j.biortech.2017.05.197;10.1016/j.biortech.2018.09.122;10.1016/j.jclepro.2017.05.209;10.1016/j.nbt.2013.10.004;10.1016/j.watres.2009.12.031;10.1016/S0079-6700(00)00035-6;10.1016/S0167-7799(98)01194-9;10.1016/S0960-8524(01)00212-7;10.1016/S0960-8524(99)00161-3;10.1016/S1001-0742(09)60295-3;10.1021/acs.biomac.7b01446;10.1021/bm4010244;10.1021/ie801542g;10.1038/nbt0208-169;10.1073/pnas.1217958110;10.1111/1462-2920.12636;10.1111/j.1365-2672.2012.05391.x;10.1126/science.1114736;10.1128/AEM.05008-11;10.1128/JB.183.1.301-308.2001;10.1146/annurev.arplant.043008.092125;10.1186/1475-2859-8-47;10.1186/1754-6834-2-26;10.1186/1756-0500-6-219;10.2174/2212796811206010014;10.2514/6.2013-2933;10.3389/fbioe.2015.00017;10.3389/fmicb.2014.00247;10.3389/fpls.2013.00107;10.4014/jmb.1705.05020;[10.1002/(SICI)1097-0290(1999)66:4<203::AID-BIT1>3.0.CO;2-#, 10.1002/(SICI)1097-0290(1999)66:4<203::AID-BIT1>3.0.CO;2-#] | Konkuk Univ | Bhatia, S K;Choi, T R;Gurav, R;Jung, H R;Ko, B J;Lee, J H;Moon, Y M;Park, J Y;Park, Y L;Song, H S;Yang, S Y;Yang, Y H | Jung, H R: Konkuk Univ, Coll Engn, Dept Biol Engn, Seoul 05029, South Korea | Bhatia, Shashi;Gurav, Ranjit G;Ko, Byoung;Park, Jun;Song, Hun-Suk | 2017M3A9E4077234;NRF-2015M1A5A1037196;NRF2016R1D1A1B03932301;PE18900 | 48 | null | South Korea | Konkuk Univ;Osong Med Innovat Fdn | Jung, Hye-Rim | Bronze | 3-HYDROXYVALERATE;BACTERIA;BIOMASS HYDROLYSATE;FERMENTATION;GROWTH;INHIBITORS;MECHANISMS;OVEREXPRESSION;POLY-3-HYDROXYBUTYRATE;POLYHYDROXYALKANOATES | Jung, Hye-Rim; Lee, Ju-Hee; Moon, Yu-Mi; Choi, Tae-Rim; Yang, Soo-Yeon; Song, Hun-Suk; Park, Jun Young; Park, Ye Lim; Bhatia, Shashi Kant; Gurav, Ranjit; Ko, Byoung Joon; Yang, Yung-Hun; | null | Konkuk Univ, Coll Engn, Dept Biol Engn, Seoul 05029, South Korea;Konkuk Univ, Inst Ubiquitous Informat Technol & Applicat CBRU, Seoul 05029, South Korea;Osong Med Innovat Fdn, New Drug Dev Ctr, Cheongju 28160, South Korea | Konkuk Univ, Coll Engn, Dept Biol Engn, Seoul 05029, South Korea;Konkuk Univ, Inst Ubiquitous Informat Technol & Applicat CBRU, Seoul 05029, South Korea;Osong Med Innovat Fdn, New Drug Dev Ctr, Cheongju 28160, South Korea | 1738-8872 | Escherichia coli;furfural;lignocellulosic hydrolysates;Polyhydroxybutyrate;resistance | 5 | 1978;1997;1998;1999;2000;2001;2002;2003;2004;2006;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017;2018;2019 | 27 | Konkuk Univ, Coll Engn, Dept Biol Engn, Seoul 05029, South Korea;Konkuk Univ, Inst Ubiquitous Informat Technol & Applicat CBRU, Seoul 05029, South Korea | J. Microbiol. Biotechnol. | Yang, Yung-Hun | KOREAN SOC MICROBIOLOGY & BIOTECHNOLOGY | (bktB;(PHB);,;4-hydroxybenzaldehyde;a;absence;addition;an;and;application;as;be;bio-based;biodegradable;by;cell;coli;compound;confer;cost-effective;could;during;E.;especially;eutropha;feasibility;fermentative;findings;for;found;from;furfural;generation;genes;glucose;good;growth;H16);has;however;hydrolysate;hydrolysates;improved;in;increased;indicate;inhibitors;innovative;introduction;investigated;is;its;lignocellulose;limited;most;non-edible;observed;of;opposed;our;petroleum-based;phaB;phaC;PHB;plastics;polyhydroxyalkanoate;polyhydroxybutyrate;polymer;potential;presence;pretreatment;processes;product;production;promising;Ralstonia;recombinant;replace;resistance;resource;results;show;stimulate;strategy;study;substrate;such;suggesting;sustainable;synthetic;target;that;the;these;this;to;used;using;vanillin;was;we;well-known | Konkuk Univ | Polyhydroxybutyrate (PHB), the most well-known polyhydroxyalkanoate, is a bio-based, biodegradable polymer that has the potential to replace petroleum-based plastics. Lignocellulose hydrolysate, a non-edible resource, is a promising substrate for the sustainable, fermentative production of PHB. However, its application is limited by the generation of inhibitors during the pretreatment processes. In this study, we investigated the feasibility of PHB production in E. coli in the presence of inhibitors found in lignocellulose hydrolysates. Our results show that the introduction of PHB synthetic genes (bktB, phaB, and phaC from Ralstonia eutropha H16) improved cell growth in the presence of the inhibitors such as furfural, 4-hydroxybenzaldehyde, and vanillin, suggesting that PHB synthetic genes confer resistance to these inhibitors. In addition, increased PHB production was observed in the presence of furfural as opposed to the absence of furfural, suggesting that this compound could be used to stimulate PHB production. Our findings indicate that PHB production using lignocellulose hydrolysates in recombinant E. coli could be an innovative strategy for cost-effective PHB production, and PHB could be a good target product from lignocellulose hydrolysates, especially glucose. | AAE-9014-2020;ABA-1336-2021;ABG-2763-2020;HPH-3570-2023;N-4550-2018 | 3-HYDROXYVALERATE;BACTERIA;BIOMASS HYDROLYSATE;FERMENTATION;GROWTH;INHIBITOR;MECHANISM;OVEREXPRESSION;POLY(3-HYDROXYBUTYRATE);POLYHYDROXYALKANOATES | 2 | null | Escherichia coli;furfural;lignocellulose hydrolysate;Polyhydroxybutyrate;resistance | 9 | ESCHERICHIA-COLI;3-HYDROXYVALERATE;BACTERIA;BIOMASS HYDROLYSATE;FERMENTATION;furfural;GROWTH;INHIBITOR;LIGNOCELLULOSIC HYDROLYSATE;MECHANISM;Overexpression;Poly(3-hydroxybutyrate);POLYHYDROXYALKANOATES;Polyhydroxybutyrate;resistance | WOS:000469201000012 | Konkuk Univ, Seoul, South Korea;Osong Med Innovat Fdn, Cheongju, South Korea | South Korea | 2,019 | null | 0000-0001-9841-4022;0000-0002-7688-6069;0000-0002-8091-2952 | null | null | English | null | ANNU REV PLANT BIOL;APPL ENVIRON MICROB;APPL MICROBIOL BIOT;BIOMACROMOLECULES;BIOPROC BIOSYST ENG;BIORESOURCE TECHNOL;BIOTECHNOL BIOENG;BIOTECHNOL BIOFUELS;BIOTECHNOL LETT;BMC Res Notes;Br J Hosp Med;CURRENT CHEM BIOL;ENVIRON ENG RES;ENVIRON MICROBIOL;EUR J APPL MICROBIOL;FEBS LETT;FRONT BIOENG BIOTECH;FRONT MICROBIOL;FRONT PLANT SCI;IND ENG CHEM RES;J APPL MICROBIOL;J BACTERIOL;J CLEAN PROD;J ENVIRON SCI;J IND MICROBIOL BIOT;J MICROBIOL BIOTECHN;MICROB CELL FACT;MICROBIOL;NAT BIOTECHNOL;NEW BIOTECHNOL;P NATL ACAD SCI USA;Production of Bio-ethylene;PROG POLYM SCI;SCIENCE;TRENDS BIOTECHNOL;Waste and Biomass Valorization;WATER RES;YEAST | Bhatia, Shashi Kant;Choi, Tae-Rim;Gurav, Ranjit;Jung, Hye-Rim;Ko, Byoung Joon;Lee, Ju-Hee;Moon, Yu-Mi;Park, Jun Young;Park, Ye Lim;Song, Hun-Suk;Yang, Soo-Yeon;Yang, Yung-Hun | 2024-03-11
ER | [Anonymous];Ahn, J;Barciszewski, J;Bhatia, S K;Braunegg, G;Brodin, M;Broeren M.;Carroll, A;Cesário, M T;Dietrich Diane;Dietrich, K;Du C.;Gorsich, S W;Han, M J;Jeon, J M;Johnson, K;Kumar, P;Lynd, L R;Madkour, M H;Mezzina, M P;Mills, T Y;Moon, J;Nieves, L M;Palmqvist, E;Phylactides, M;Ragauskas, A J;Saha, B C;Seo, H M;Sharma H.K.;Silva, L F;Sims, R E H;Song, H S;Steinbüchel, A;Sudesh, K;Sun, Y;Van Der Weijde, T;Wang, Q;Wang, W;Wang, X;Wen, Q X;Yang, Y H;Yu, J;Zaldivar, J | HZ9TT | Seoul, South Korea;Seoul, South Korea. | 28 | null | 2 | null | 31,030,455 | Bhatia, Shashi Kant;Choi, Tae-Rim;Gurav, Ranjit;Jung, Hye-Rim;Ko, Byoung Joon;Lee, Ju-Hee;Moon, Yu-Mi;Park, Jun Young;Park, Ye Lim;Song, Hun-Suk;Yang, Soo-Yeon;Yang, Yung-Hun | J MICROBIOL BIOTECHN | Cheongju, South Korea;Seoul, South Korea |
Bernauer, H S;Hoffmann, M;Pogorevc, D;Popoff, A;Steinmetz, H;Tang, Y;Wenzel, S C;Zipf, G | 10.1021/acssynbio.9b00023 | null | 1155 16TH ST, NW, WASHINGTON, DC 20036 USA | 2453321h6y461hn5p5442l142n5a3s5i3i695q | Biosynthesis and Heterologous Production of Argyrins | Univ Saarland | null | Pogorevc, D (corresponding author), Saarland Univ, Dept Microbial Nat Prod, Helmholtz Inst Pharmaceut Res Saarland HIPS, Helmholtz Ctr Infect Res HZI, D-66123 Saarbrucken, Germany.;Pogorevc, D (corresponding author), Saarland Univ, Dept Pharmaceut Biotechnol, D-66123 Saarbrucken, Germany. | null | Bernauer, Hubert S;Hoffmann, Michael;Pogorevc, Domen;Popoff, Alexander;Steinmetz, Heinrich;Tang, Ying;Wenzel, Silke C;Zipf, Gregor | Biochemical Research Methods | German Federal Ministry of Education and Research [FKZ: 031A155] | WOS | Pogorevc, D | ATG Biosynthet GmbH, Merzhausen, Germany;BASF SE, Ludwigshafen, Germany;Helmholtz Ctr Infect Res HZI, Braunschweig, Germany;Hunan Inst Microbiol, Hunan, Peoples R China;Hunan Normal Univ, Hunan, Peoples R China;Saarland Univ, Saarbrucken, Germany | 8 | and;Argyrins;biosynthesis;Heterologous;of;production | 2 | Popoff, Alexander;Scherzer (Pogorevc), Domen;Tang, Ying | AMER CHEMICAL SOC | ATG Biosynthet GmbH, D-79249 Merzhausen, Germany;BASF SE, D-67056 Ludwigshafen, Germany;Helmholtz Ctr Infect Res HZI, Microbial Strain Collect, D-38124 Braunschweig, Germany;Hunan Inst Microbiol, Changsha 410009, Hunan, Peoples R China;Hunan Normal Univ, Coll Life Sci, State Key Lab Dev Biol Freshwater Fish, Hunan Prov Key Lab Microbial Mol Biol, Changsha 410081, Hunan, Peoples R China;Saarland Univ, Dept Microbial Nat Prod, Helmholtz Inst Pharmaceut Res Saarland HIPS, Helmholtz Ctr Infect Res HZI, D-66123 Saarbrucken, Germany;Saarland Univ, Dept Microbial Nat Prod, Helmholtz Inst Pharmaceut Res Saarland HIPS, Helmholtz Ctr Infect Res HZI, D-66123 Saarbrucken, Germany.; Pogorevc, D (corresponding author), Saarland Univ, Dept Pharmaceut Biotechnol, D-66123 Saarbrucken, Germany;Saarland Univ, Dept Pharmaceut Biotechnol, D-66123 Saarbrucken, Germany | Article | Univ Saarland | WASHINGTON | null | null | ATG Biosynthet GmbH;BASF SE;Helmholtz Ctr Infect Res HZI;Hunan Inst Microbiol;Hunan Normal Univ;Saarland Univ | German Federal Ministry of Education and Research | Pogorevc, D (corresponding author), Saarland Univ, Dept Microbial Nat Prod, Helmholtz Inst Pharmaceut Res Saarland HIPS, Helmholtz Ctr Infect Res HZI, D-66123 Saarbrucken, Germany.; Pogorevc, D (corresponding author), Saarland Univ, Dept Pharmaceut Biotechnol, D-66123 Saarbrucken, Germany. | 1133 | Bernauer, Hubert S;Hoffmann, Michael;Pogorevc, Domen;Popoff, Alexander;Steinmetz, Heinrich;Tang, Ying;Wenzel, Silke C;Zipf, Gregor | 39 | 7 | 468,697,000,022 | German Federal Ministry of Education and Research [FKZ: 031A155] | China;Germany | ACS SYNTHETIC BIOLOGY | Germany | null | null | Saarland Univ, Dept Microbial Nat Prod, Helmholtz Inst Pharmaceut Res Saarland HIPS, Helmholtz Ctr Infect Res HZI, D-66123 Saarbrucken, Germany | 2161-5063 | Bernauer, H S;Hoffmann, M;Pogorevc, D;Popoff, A;Steinmetz, H;Tang, Y;Wenzel, S C;Zipf, G | MAY | domen.pogorevc@helmholtz-hips.de | Argyrins;biosynthesis;Heterologous Production | 8 | J | Biochemistry & Molecular Biology | 160 mg/L;ADENYLATION DOMAIN;antibiotics;antitumorigenic;argyrin;Argyrins;around 20-fold higher yields;BACTERIAL PROTEIN-SYNTHESIS;biosynthesis;chromosomal deletion;COMBINATORIAL BIOSYNTHESIS;cyclic octapeptides;different approaches;F3;FAMILY;future supply;G3;gene synthesis fragments;GENE-CLUSTER;heterologous argyrin production;heterologous expression;heterologous expression system;Heterologous Production;heterologous production platform;host strain Myxococcus xanthus DK1622;IDENTIFICATION;immunosuppressant activities;IMMUNOSUPPRESSIVE CYCLIC-PEPTIDES;J;K;L);led;myxobacteria;myxobacterial producer strain Cystobacter sp;native biosynthetic gene cluster (BGC) sequence;native producer;NATURAL-PRODUCTS;non-ribosomal peptide synthetase pathway;nonribosomal peptide synthetase;novel derivatives;NUCLEOTIDE-SEQUENCE;production system;promising antimicrobial;SBCb004;several novel argyrin derivatives (A2;study;Synthetic gene cluster;template synthetic BGC versions;versatile platform;well-expressed lipopeptide pathway | Pogorevc, D | ADENYLATION DOMAIN;ANTIBIOTICS;argyrin;BACTERIAL PROTEIN-SYNTHESIS;COMBINATORIAL BIOSYNTHESIS;GENE-CLUSTER;heterologous expression;IMMUNOSUPPRESSIVE CYCLIC-PEPTIDES;myxobacteria;NATURAL-PRODUCTS;nonribosomal peptide synthetase;NUCLEOTIDE-SEQUENCE;Synthetic gene cluster | 1121 | [Pogorevc, Domen; Tang, Ying; Hoffmann, Michael; Popoff, Alexander; Wenzel, Silke C.] Saarland Univ, Dept Microbial Nat Prod, Helmholtz Inst Pharmaceut Res Saarland HIPS, Helmholtz Ctr Infect Res HZI, D-66123 Saarbrucken, Germany. [Pogorevc, Domen; Tang, Ying; Hoffmann, Michael; Popoff, Alexander; Wenzel, Silke C.] Saarland Univ, Dept Pharmaceut Biotechnol, D-66123 Saarbrucken, Germany. [Tang, Ying] Hunan Normal Univ, Coll Life Sci, State Key Lab Dev Biol Freshwater Fish, Hunan Prov Key Lab Microbial Mol Biol, Changsha 410081, Hunan, Peoples R China. [Zipf, Gregor; Bernauer, Hubert S.] ATG Biosynthet GmbH, D-79249 Merzhausen, Germany. [Steinmetz, Heinrich] Helmholtz Ctr Infect Res HZI, Microbial Strain Collect, D-38124 Braunschweig, Germany. [Tang, Ying] Hunan Inst Microbiol, Changsha 410009, Hunan, Peoples R China. [Hoffmann, Michael] BASF SE, D-67056 Ludwigshafen, Germany. | We would like to thank Dr. Ronald Garcia for provision and advice on the argyrin producer Cystobacter sp. SBCb004, Irene Kochems and Douglas Gatte Pichi for their efforts in SBCb004 engineering, Sara Andes and Jack Stanley for assistance in arg BGC cloning, Dr. Nestor Zaburannyi for bioinformatics support, and Eva Luxemburger, Daniel Sauer, and Dr. Kirsten Harmrolfs for HPLC MS and NMR measurements. Furthermore, we gratefully acknowledge Prof. Dr. Rolf Muller for constantly supporting and discussing this study. This work was generously funded by a grant from the German Federal Ministry of Education and Research (FKZ: 031A155). | 160 mg/L;antitumorigenic;argyrins;around 20-fold higher yields;chromosomal deletion;cyclic octapeptides;different approaches;F3;family;future supply;G3;gene synthesis fragments;heterologous argyrin production;heterologous expression system;heterologous production platform;host strain Myxococcus xanthus DK1622;identification;immunosuppressant activities;J;K;L);led;myxobacterial producer strain Cystobacter sp;native biosynthetic gene cluster (BGC) sequence;native producer;non-ribosomal peptide synthetase pathway;novel derivatives;production system;promising antimicrobial;SBCb004;several novel argyrin derivatives (A2;study;template synthetic BGC versions;versatile platform;well-expressed lipopeptide pathway | 10.1002/anie.200503737;10.1002/anie.200900406;10.1002/anie.201000140;10.1002/anie.201208344;10.1002/anie.201409964;10.1002/anie.201508277;10.1002/anie.201609079;10.1002/anie.201802479;10.1002/bit.10202;10.1002/bit.25560;10.1002/cbic.201200479;10.1002/cmdc.201000080;10.1007/0-387-30747-8_3;10.1007/BF01030015;10.1007/s00726-014-1846-4;10.1007/s10295-015-1723-5;10.1007/s10529-012-0913-8;10.1007/s12282-016-0717-0;10.1016/0022-2836(69)90288-5;10.1016/0378-1119(82)90023-3;10.1016/j.aca.2008.06.036;10.1016/j.canlet.2017.04.003;10.1016/j.ccr.2008.05.016;10.1016/j.cell.2015.11.031;10.1016/j.chembiol.2005.12.012;10.1016/j.chembiol.2010.01.016;10.1016/j.chembiol.2012.01.007;10.1016/j.chembiol.2015.04.015;10.1016/j.jbiotec.2014.07.447;10.1016/j.ymben.2017.10.004;10.1016/S0022-2836(05)80360-2;10.1016/S0076-6879(09)04803-4;10.1016/S0076-6879(09)04808-3;10.1016/S1074-5521(00)00011-9;10.1016/S1074-5521(00)00118-6;10.1016/S1074-5521(00)80014-9;10.1016/S1074-5521(99)80082-9;10.1016/S1367-5931(00)00235-0;10.1021/acs.jnatprod.5b01055;10.1021/ol017184m;10.1021/sb300080t;10.1038/nature14100;10.1038/nm.3704;10.1039/c001260m;10.1039/c2np20085f;10.1039/c2sc21722h;10.1039/c3sc53163e;10.1039/c4np00007b;10.1039/c4np00011k;10.1039/c4ob02107j;10.1039/c5np00099h;10.1039/c6np00106h;10.1039/c8sc02046a;10.1073/pnas.0608589103;10.1093/nar/16.1.355;10.1093/nar/16.1.356;10.1093/nar/gkn499;10.1093/nar/gkv437;10.1101/PDB.PROT4022;10.1111/j.1365-2958.1995.tb02262.x;10.1126/science.7604280;10.1128/AAC.03326-14;10.1128/AAC.46.9.2772-2778.2002;10.1128/AAC.47.9.2823-2830.2003;10.1128/AEM.01503-06;10.1128/AEM.02841-09;10.1128/JB.181.13.4050-4061.1999;10.1146/annurev.micro.58.030603.123615;10.1186/1471-2148-7-78;10.1186/1471-2180-11-199;10.1371/journal.pone.0042657;10.3109/07853890.2011.579151;10.3390/microorganisms6030084;10.7164/antibiotics.49.145;10.7164/antibiotics.49.150;10.7164/antibiotics.55.543;10.7164/antibiotics.55.715;[10.1038/ja.2012.54, 10.1038/ja.2012.27];[10.1128/AAC.02400-16, 10.1128/aac.02400-16] | Saarland Univ | Bernauer, H S;Hoffmann, M;Pogorevc, D;Popoff, A;Steinmetz, H;Tang, Y;Wenzel, S C;Zipf, G | Pogorevc, D: Saarland Univ, Dept Microbial Nat Prod, Helmholtz Inst Pharmaceut Res Saarland HIPS, Helmholtz Ctr Infect Res HZI, D-66123 Saarbrucken, Germany | null | FKZ: 031A155 | 84 | null | Germany | ATG Biosynthet GmbH;BASF SE;Helmholtz Ctr Infect Res HZI;Hunan Inst Microbiol;Hunan Normal Univ;Saarland Univ | Pogorevc, Domen | null | ADENYLATION DOMAIN;ANTIBIOTICS;BACTERIAL PROTEIN-SYNTHESIS;COMBINATORIAL BIOSYNTHESIS;GENE-CLUSTER;IMMUNOSUPPRESSIVE CYCLIC-PEPTIDES;MYXOBACTERIA;NATURAL-PRODUCTS;NONRIBOSOMAL PEPTIDE SYNTHETASE;NUCLEOTIDE-SEQUENCE | Pogorevc, Domen; Tang, Ying; Hoffmann, Michael; Zipf, Gregor; Bernauer, Hubert S.; Popoff, Alexander; Steinmetz, Heinrich; Wenzel, Silke C.; | null | ATG Biosynthet GmbH, D-79249 Merzhausen, Germany;BASF SE, D-67056 Ludwigshafen, Germany;Helmholtz Ctr Infect Res HZI, Microbial Strain Collect, D-38124 Braunschweig, Germany;Hunan Inst Microbiol, Changsha 410009, Hunan, Peoples R China;Hunan Normal Univ, Coll Life Sci, State Key Lab Dev Biol Freshwater Fish, Hunan Prov Key Lab Microbial Mol Biol, Changsha 410081, Hunan, Peoples R China;Saarland Univ, Dept Microbial Nat Prod, Helmholtz Inst Pharmaceut Res Saarland HIPS, Helmholtz Ctr Infect Res HZI, D-66123 Saarbrucken, Germany;Saarland Univ, Dept Pharmaceut Biotechnol, D-66123 Saarbrucken, Germany | ATG Biosynthet GmbH, D-79249 Merzhausen, Germany;BASF SE, D-67056 Ludwigshafen, Germany;Helmholtz Ctr Infect Res HZI, Microbial Strain Collect, D-38124 Braunschweig, Germany;Hunan Inst Microbiol, Changsha 410009, Hunan, Peoples R China;Hunan Normal Univ, Coll Life Sci, State Key Lab Dev Biol Freshwater Fish, Hunan Prov Key Lab Microbial Mol Biol, Changsha 410081, Hunan, Peoples R China;Saarland Univ, Dept Microbial Nat Prod, Helmholtz Inst Pharmaceut Res Saarland HIPS, Helmholtz Ctr Infect Res HZI, D-66123 Saarbrucken, Germany;Saarland Univ, Dept Pharmaceut Biotechnol, D-66123 Saarbrucken, Germany | null | argyrin;heterologous expression;myxobacteria;nonribosomal peptide synthetase;Synthetic gene cluster | 5 | 1969;1982;1988;1990;1995;1996;1999;2000;2001;2002;2003;2004;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017;2018 | 21 | Saarland Univ, Dept Microbial Nat Prod, Helmholtz Inst Pharmaceut Res Saarland HIPS, Helmholtz Ctr Infect Res HZI, D-66123 Saarbrucken, Germany;Saarland Univ, Dept Pharmaceut Biotechnol, D-66123 Saarbrucken, Germany | ACS Synth. Biol. | Wenzel, Silke C | AMER CHEMICAL SOC | (A2;(BGC);,;160;20-fold;a;activities;after;also;and;antimicrobial;antitumorigenic;applied;approaches;argyrin;argyrins;around;as;assembled;BGC;biosynthetic;characterized;chromosomal;cluster;compared;cyclic;Cystobacter;deletion;derivatives;derive;designed;different;DK1622;engineer;established;exhibiting;expression;F3;family;finally;for;fragments;from;future;G3;gene;heterologous;higher;host;I;identification;identified;immunosuppressant;improve;in;increased;J;K;L);led;lipopeptide;mg/L;myxobacterial;Myxococcus;native;non-ribosomal;novel;octapeptides;of;optimized;pathway;peptide;platform;producer;production;promising;provides;represent;SBCb004;sequence;several;sp;strain;study;supply;synthesis;synthetase;synthetic;system;template;the;thereof;they;this;to;using;versatile;versions;was;well-expressed;were;which;xanthus;yields | Saarland Univ | Argyrins represent a family of cyclic octapeptides exhibiting promising antimicrobial, antitumorigenic and immunosuppressant activities. They derive from a non-ribosomal peptide synthetase pathway, which was identified and characterized in this study from the myxobacterial producer strain Cystobacter sp. SBCb004. Using the native biosynthetic gene cluster (BGC) sequence as template synthetic BGC versions were designed and assembled from gene synthesis fragments. A heterologous expression system was established after chromosomal deletion of a well-expressed lipopeptide pathway from the host strain Myxococcus xanthus DK1622. Different approaches were applied to engineer and improve heterologous argyrin production, which was finally increased to 160 mg/L, around 20-fold higher yields compared to the native producer. Heterologous production platform also led to identification of several novel argyrin derivatives (A2, F3, G3, I, J, K, and L). The optimized production system provides a versatile platform for future supply of argyrins and novel derivatives thereof. | null | ADENYLATION DOMAIN;ANTIBIOTICS;BACTERIAL PROTEIN-SYNTHESIS;COMBINATORIAL BIOSYNTHESIS;GENE-CLUSTER;IMMUNOSUPPRESSIVE CYCLIC-PEPTIDES;MYXOBACTERIA;NATURAL-PRODUCTS;NONRIBOSOMAL PEPTIDE SYNTHETASE;NUCLEOTIDE-SEQUENCE | 3 | null | argyrin;heterologous expression;myxobacteria;nonribosomal peptide synthetase;Synthetic gene cluster | 25 | adenylation domains;ANTIBIOTICS;argyrin;BACTERIAL PROTEIN-SYNTHESIS;COMBINATORIAL BIOSYNTHESIS;GENE-CLUSTER;heterologous expression;IMMUNOSUPPRESSIVE CYCLIC-PEPTIDES;myxobacteria;NATURAL-PRODUCTS;nonribosomal peptide synthetase;NUCLEOTIDE-SEQUENCE;Synthetic gene cluster | WOS:000468697000022 | ATG Biosynthet GmbH, Merzhausen, Germany;BASF SE, Ludwigshafen, Germany;Helmholtz Ctr Infect Res HZI, Braunschweig, Germany;Hunan Inst Microbiol, Hunan, Peoples R China;Hunan Normal Univ, Hunan, Peoples R China;Saarland Univ, Saarbrucken, Germany | China;Germany | 2,019 | null | 0000-0001-5582-059X;0000-0001-8495-1572;0000-0003-0378-9150 | null | null | English | null | 2017 IND BIOTECHNOLO;ACS SYNTH BIOL;AMINO ACIDS;ANAL CHIM ACTA;ANGEW CHEM INT EDIT;ANN MED;ANNU REV MICROBIOL;ANTIMICROB AGENTS CH;APPL ENVIRON MICROB;BIOSYNTHESIS H UNPUB;BIOTECHNOL BIOENG;BIOTECHNOL LETT;BMC EVOL BIOL;BMC MICROBIOL;BREAST CANCER-TOKYO;CANC RES;CANCER CELL;CANCER LETT;CELL;CHEM BIOL;CHEM SCI;CHEMBIOCHEM;CHEMMEDCHEM;CURR OPIN CHEM BIOL;GENE;J ANTIBIOT;J BACTERIOL;J BIOTECHNOL;J IND MICROBIOL BIOT;J MOL BIOL;J NAT PROD;METAB ENG;METHOD ENZYMOL;MICROORGANISMS;MOL CLONING LAB MANU;MOL MICROBIOL;NAT MED;NAT PROD REP;NATURE;NUCLEIC ACIDS RES;ORG BIOMOL CHEM;ORG LETT;P NATL ACAD SCI USA;PLOS ONE;SCIENCE;The Prokaryotes | Bernauer, Hubert S;Hoffmann, Michael;Pogorevc, Domen;Popoff, Alexander;Steinmetz, Heinrich;Tang, Ying;Wenzel, Silke C;Zipf, Gregor | 2024-03-11
ER | [Anonymous];Altschul, S F;Alvarez, R H;Arnison, P G;Bachmann, B O;Baumann, S;Beasley, F C;Beck, E;Berod, L;Bian, X Y;Bielecki, P;Boyer, H W;Bérdy, J;Bülow, L;Chai, Y;Chen, C H;Chen, X;Crüsemann, M;Doekel, S;Du, L C;Ferrari, P;Finking, R;Finn Il D.;Fu, J;Garcia, R O;Gaudelli, N M;Gemperlein, K;Han, J W;Held, J;Herrmann, J;Jones, A K;Julien, B;Kashefi, K;Katz, L;Kries, H;Krug, D;Kudo, F;Lau, J;Ley, S V;Li, J;Magrini, V;Miao, V;Mohr, K I;Newman, D J;Nguyen, K T;Nickeleit, I;Nyfeler, B;Osswald, C;Perlova, O;Rausch, C;Reichenbach;Rose, R E;Sambrook J.;Sasse, F;Schäberle, T F;Selva, E;Shen, B;Shimkets L.J.;Siodlak, D;Stachelhaus, T;Stauch, B;Stevens, D C;Sucipto, H;Süssmuth, R D;Thomas, M G;Tokarski, Z;Ullrich, A;Vollbrecht, L;Von Döhren, H;Walsh, C T;Weber, T;Weissman, K J;Wenzel, S C;Winn, M;Yan, F | HZ2RT | Saarbrucken, Germany;Saarbrucken, Germany. | 26 | null | 6 | null | 30,995,838 | Bernauer, Hubert S;Hoffmann, Michael;Pogorevc, Domen;Popoff, Alexander;Steinmetz, Heinrich;Tang, Ying;Wenzel, Silke C;Zipf, Gregor | ACS SYNTH BIOL | Braunschweig, Germany;Hunan, Peoples R China;Ludwigshafen, Germany;Merzhausen, Germany;Saarbrucken, Germany |
Castro, S;Danino, T;Harimoto, T;Hinchliffe, T E;Mather, W;Singer, Z S;Velazquez, O S;Zhang, J | 10.1073/pnas.1820824116 | null | 2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA | 3x24j85sh1n30573y306l3a366a545g37634m | Rapid screening of engineered microbial therapies in a 3D multicellular model | Columbia Univ | null | Danino, T (corresponding author), Columbia Univ, Data Sci Inst, New York, NY 10027 USA.;Danino, T (corresponding author), Columbia Univ, Dept Biomed Engn, New York, NY 10027 USA.;Danino, T (corresponding author), Columbia Univ, Herbert Irving Comprehens Canc Ctr, New York, NY 10027 USA. | null | Castro, Samuel;Danino, Tal;Harimoto, Tetsuhiro;Hinchliffe, Taylor E;Mather, William;Singer, Zakary S;Velazquez, Oscar S;Zhang, Joanna | Multidisciplinary Sciences | Honjo International Foundation Scholarship; NIH Ruth L. Kirschstein National Research Service Award; NIH [R00CA197649-02]; Department of Defense (DoD) Idea Development Award [LC160314]; DoD Era of Hope Scholar Award [BC160541]; NIH/National Cancer Institute Cancer Center [P30CA013696]; CDMRP [LC160314, 917541] Funding Source: Federal RePORTER | WOS | Danino, T | Columbia Univ, New York, NY USA;Univ Calif San Diego, La Jolla, CA USA | 116 | 3D;a;engineered;in;microbial;model;multicellular;of;rapid;screening;therapies | 1 | Harimoto, Tetsuhiro;Zhang, Joanna | NATL ACAD SCIENCES | Columbia Univ, Data Sci Inst, New York, NY 10027 USA;Columbia Univ, Dept Biomed Engn, New York, NY 10027 USA;Columbia Univ, Dept Biomed Engn, New York, NY 10027 USA.; Danino, T (corresponding author), Columbia Univ, Data Sci Inst, New York, NY 10027 USA.; Danino, T (corresponding author), Columbia Univ, Herbert Irving Comprehens Canc Ctr, New York, NY 10027 USA;Columbia Univ, Herbert Irving Comprehens Canc Ctr, New York, NY 10027 USA;Univ Calif San Diego, BioCircuits Inst, La Jolla, CA 92093 USA | Article | Columbia Univ | WASHINGTON | null | null | Columbia Univ;Univ Calif San Diego | CDMRP;Department of Defense (DoD) Idea Development Award;DoD Era of Hope Scholar Award;Honjo International Foundation Scholarship;NIH;NIH Ruth L. Kirschstein National Research Service Award;NIH/National Cancer Institute Cancer Center | Danino, T (corresponding author), Columbia Univ, Dept Biomed Engn, New York, NY 10027 USA.; Danino, T (corresponding author), Columbia Univ, Data Sci Inst, New York, NY 10027 USA.; Danino, T (corresponding author), Columbia Univ, Herbert Irving Comprehens Canc Ctr, New York, NY 10027 USA. | 9007 | Castro, Samuel;Danino, Tal;Harimoto, Tetsuhiro;Hinchliffe, Taylor E;Mather, William;Singer, Zakary S;Velazquez, Oscar S;Zhang, Joanna | 30 | 4 | 466,446,500,054 | CDMRP [LC160314, 917541] Funding Source: Federal RePORTER;Department of Defense (DoD) Idea Development Award [LC160314];DoD Era of Hope Scholar Award [BC160541];Honjo International Foundation Scholarship;NIH [R00CA197649-02];NIH Ruth L. Kirschstein National Research Service Award;NIH/National Cancer Institute Cancer Center [P30CA013696] | USA | PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA | USA;USA.; | null | null | Columbia Univ, Dept Biomed Engn, New York, NY 10027 USA | 0027-8424 | Castro, S;Danino, T;Harimoto, T;Hinchliffe, T E;Mather, W;Singer, Z S;Velazquez, O S;Zhang, J | APR 30 | td2506@columbia.edu | 3D multicellular model;microbial therapies;rapid screening | 8 | J | Science & Technology - Other Topics | 3D multicellular model;ability;animal-based testing regimes;antitumor therapeutic molecules via several synthetic gene circuits;BACTERIA;bacteria-in-spheroid coculture (BSCC) platform;bacterial dynamics;bacterial therapy;biocontainment;broad applicability;CANCER;cancer therapy;candidates;cells;challenge;clinical applications;clinical translation;critical therapeutic parameters;disease progression;disease sites;diseases;DRUG;efficacies;efficacy;engineer new therapies;engineering living cells;Escherichia coli;high similarity;high-throughput framework;high-throughput screening;host cell types;host-microbe interactions;infections;inflammation;INVASION;library;Listeria monocytogenes;major bottleneck;metabolic disorders;microbes;microbial therapies;multicellular spheroids;outpaces;platform;profile diverse microbial species;Proteus mirabilis;quantitative comparison;rapid screening;Salmonella typhimurium strains;SALMONELLA-TYPHIMURIUM;scalability;sense;serve;significant tumor reduction;syngeneic mouse model;synthetic biology;synthetic gene circuits;tests host species;therapeutic paradigms;therapeutic payloads;throughput;timescale;vitro approaches;weeks | Harimoto, T | BACTERIA;bacterial therapy;CANCER;cancer therapy;CELLS;DRUG;high-throughput screening;INVASION;SALMONELLA-TYPHIMURIUM;Synthetic biology | 9002 | [Harimoto, Tetsuhiro; Singer, Zakary S.; Velazquez, Oscar S.; Zhang, Joanna; Castro, Samuel; Hinchliffe, Taylor E.; Danino, Tal] Columbia Univ, Dept Biomed Engn, New York, NY 10027 USA. [Mather, William] Univ Calif San Diego, BioCircuits Inst, La Jolla, CA 92093 USA. [Danino, Tal] Columbia Univ, Data Sci Inst, New York, NY 10027 USA. [Danino, Tal] Columbia Univ, Herbert Irving Comprehens Canc Ctr, New York, NY 10027 USA. | We thank N. Arpaia, M. Omar Din, and J. Hasty for their helpful comments and suggestions. We thank the Herbert Irving Comprehensive Cancer Center Molecular Pathology Shared Resources Facility for help with histological sample processing. This work was supported in part by the Honjo International Foundation Scholarship (T.H.), NIH Ruth L. Kirschstein National Research Service Award (Z.S.S.), NIH Pathway to Independence Award (R00CA197649-02), Department of Defense (DoD) Idea Development Award LC160314, DoD Era of Hope Scholar Award BC160541, and NIH/National Cancer Institute Cancer Center Support Grant P30CA013696. | ability;animal-based testing regimes;antitumor therapeutic molecules via several synthetic gene circuits;bacteria;bacteria-in-spheroid coculture (BSCC) platform;bacterial dynamics;biocontainment;broad applicability;cancer;candidates;challenge;clinical applications;clinical translation;critical therapeutic parameters;disease progression;disease sites;diseases;efficacies;efficacy;engineer new therapies;engineering living cells;Escherichia coli;high similarity;high-throughput framework;host cell types;host-microbe interactions;infections;inflammation;library;Listeria monocytogenes;major bottleneck;metabolic disorders;microbes;multicellular spheroids;outpaces;platform;profile diverse microbial species;Proteus mirabilis;quantitative comparison;Salmonella typhimurium strains;scalability;sense;serve;significant tumor reduction;syngeneic mouse model;synthetic biology;synthetic gene circuits;tests host species;therapeutic paradigms;therapeutic payloads;throughput;timescale;vitro approaches;weeks | 10.1002/bit.20883;10.1002/bit.25184;10.1016/0264-410X(95)00173-X;10.1016/j.cell.2016.05.082;10.1016/j.cell.2018.05.039;10.1016/j.coisb.2017.05.009;10.1016/j.copbio.2017.06.004;10.1016/j.jamcollsurg.2007.06.283;10.1016/j.jmb.2005.10.076;10.1038/291238a0;10.1038/gt.2008.188;10.1038/nature18930;10.1038/nbt.2284;10.1038/nbt.2989;10.1038/nbt.3805;10.1038/nbt.3879;10.1038/nbt.4222;10.1038/ncomms15028;10.1038/nmicrobiol.2017.83;10.1038/nprot.2008.226;10.1038/nrc2934;10.1038/nrmicro.2017.172;10.1038/s41467-018-03233-9;10.1038/s41589-018-0056-x;10.1038/srep15681;10.1053/j.gastro.2014.09.042;10.1073/pnas.0507681102;10.1073/pnas.1414558112;10.1073/pnas.1522193112;10.1073/pnas.222539699;10.1073/pnas.251543698;10.1098/rsif.2014.0065;10.1126/science.aac7341;10.1126/science.aan4236;10.1126/scitranslmed.aaa3519;10.1126/scitranslmed.aak9537;10.1126/scitranslmed.aao2586;10.1158/0008-5472.CAN-07-2984;10.1177/1087057117696795;10.1186/s12934-015-0383-5;10.1200/JCO.2002.20.1.142;10.12659/MSM.901880;10.1371/journal.pone.0188960;10.15252/msb.20167416;10.1538/expanim.16-0033;10.18632/oncotarget.9935;10.2174/156652310790945539;10.3390/toxins7051702;10.3791/2693 | Columbia Univ | Castro, S;Danino, T;Harimoto, T;Hinchliffe, T E;Mather, W;Singer, Z S;Velazquez, O S;Zhang, J | Harimoto, T: Columbia Univ, Dept Biomed Engn, New York, NY 10027 USA | null | 917541;BC160541;LC160314;P30CA013696;R00CA197649-02 | 50 | null | USA | Columbia Univ;Univ Calif San Diego | Harimoto, Tetsuhiro | Bronze, Green Submitted, Green Published | BACTERIA;CANCER;CELLS;DRUG;INVASION;SALMONELLA-TYPHIMURIUM | Harimoto, Tetsuhiro; Singer, Zakary S.; Velazquez, Oscar S.; Zhang, Joanna; Castro, Samuel; Hinchliffe, Taylor E.; Mather, William; Danino, Tal; | null | Columbia Univ, Data Sci Inst, New York, NY 10027 USA;Columbia Univ, Dept Biomed Engn, New York, NY 10027 USA;Columbia Univ, Herbert Irving Comprehens Canc Ctr, New York, NY 10027 USA;Univ Calif San Diego, BioCircuits Inst, La Jolla, CA 92093 USA | Columbia Univ, Data Sci Inst, New York, NY 10027 USA;Columbia Univ, Dept Biomed Engn, New York, NY 10027 USA;Columbia Univ, Herbert Irving Comprehens Canc Ctr, New York, NY 10027 USA;Univ Calif San Diego, BioCircuits Inst, La Jolla, CA 92093 USA | null | bacterial therapy;cancer therapy;high-throughput screening;Synthetic biology | 18 | 1981;1994;1996;2001;2002;2006;2007;2008;2009;2010;2011;2012;2014;2015;2016;2017;2018 | 22 | Columbia Univ, Data Sci Inst, New York, NY 10027 USA;Columbia Univ, Dept Biomed Engn, New York, NY 10027 USA;Columbia Univ, Herbert Irving Comprehens Canc Ctr, New York, NY 10027 USA | Proc. Natl. Acad. Sci. U. S. A. | Danino, Tal | NATL ACAD SCIENCES | (BSCC);,;a;ability;accelerate;address;and;animal-based;antitumor;applicability;applications;approaches;as;bacteria;bacteria-in-spheroid;bacterial;be;been;biocontainment;biology;bottleneck;broad;by;can;cancer;candidates;cell;cells;challenge;circuits;clinical;coculture;coli;comparison;creating;critical;delivering;demonstrate;disease;diseases;disorders;diverse;dynamically;dynamics;efficacies;efficacy;enables;engineer;engineered;engineering;Escherichia;exhibiting;expanded;expressing;far;for;framework;gene;have;here;high;high-throughput;host;host-microbe;however;identify;in;including;infections;inflammation;intelligently;interactions;is;last;library;limited;Listeria;living;long-term;major;may;metabolic;microbes;microbial;mirabilis;model;molecules;monitoring;monocytogenes;mouse;multicellular;new;of;our;outpaces;over;paradigms;parameters;payloads;platform;present;profile;progression;Proteus;quantitative;rapidly;reduction;regimes;respond;Salmonella;scalability;screen;sense;serve;several;show;significant;similarity;simultaneously;sites;species;specifically;spheroids;strains;such;syngeneic;synthetic;testing;tests;that;the;their;therapeutic;therapies;this;throughput;timescale;to;transforming;translation;tumor;types;typhimurium;understanding;using;various;via;vitro;we;weeks;within | Columbia Univ | Synthetic biology is transforming therapeutic paradigms by engineering living cells and microbes to intelligently sense and respond to diseases including inflammation, infections, metabolic disorders, and cancer. However, the ability to rapidly engineer new therapies far outpaces the throughput of animal-based testing regimes, creating a major bottleneck for clinical translation. In vitro approaches to address this challenge have been limited in scalability and broad applicability. Here, we present a bacteria-in-spheroid coculture (BSCC) platform that simultaneously tests host species, therapeutic payloads, and synthetic gene circuits of engineered bacteria within multicellular spheroids over a timescale of weeks. Long-term monitoring of bacterial dynamics and disease progression enables quantitative comparison of critical therapeutic parameters such as efficacy and biocontainment. Specifically, we screen Salmonella typhimurium strains expressing and delivering a library of antitumor therapeutic molecules via several synthetic gene circuits. We identify candidates exhibiting significant tumor reduction and demonstrate high similarity in their efficacies, using a syngeneic mouse model. Last, we show that our platform can be expanded to dynamically profile diverse microbial species including Listeria monocytogenes, Proteus mirabilis, and Escherichia coli in various host cell types. This high-throughput framework may serve to accelerate synthetic biology for clinical applications and for understanding the host-microbe interactions in disease sites. | null | BACTERIA;CANCER;CELLS;DRUG;INVASION;SALMONELLA-TYPHIMURIUM | 1 | null | bacterial therapy;cancer therapy;high-throughput screening;Synthetic biology | 6 | BACTERIA;bacterial therapy;CANCER;cancer therapy;CELLS;DRUG;high-throughput screening;INVASION;SALMONELLA-TYPHIMURIUM;Synthetic biology | WOS:000466446500054 | Columbia Univ, New York, NY USA;Univ Calif San Diego, La Jolla, CA USA | USA | 2,019 | null | 0000-0001-8859-7494;0009-0009-8032-7487 | null | null | English | null | BIOTECHNOL BIOENG;CANCER RES;CELL;CURR GENE THER;CURR OPIN BIOTECH;Curr Opin Syst Biol;EXP ANIM TOKYO;GASTROENTEROLOGY;GENE THER;J AM COLL SURGEONS;J CLIN ONCOL;J MOL BIOL;J R SOC INTERFACE;JOVE-J VIS EXP;MED SCI MONITOR;METHOD ENZYMOL;MICROB CELL FACT;MOL SYST BIOL;NAT BIOTECHNOL;NAT CHEM BIOL;NAT COMMUN;NAT MICROBIOL;NAT PROTOC;NAT REV CANCER;NAT REV MICROBIOL;NATURE;ONCOTARGET;P NATL ACAD SCI USA;PLOS ONE;SCI REP-UK;SCI TRANSL MED;SCIENCE;SLAS DISCOV;TOXINS;VACCINE | Castro, Samuel;Danino, Tal;Harimoto, Tetsuhiro;Hinchliffe, Taylor E;Mather, William;Singer, Zakary S;Velazquez, Oscar S;Zhang, Joanna | 2024-03-11
ER | Al-Lazikani, B;Anderson, J C;Bartfeld, S;Bhatia, S N;Bhave, M S;Breslin, S;Chien Tiffany;Clevers, H;Daeffler, K N M;Dang, L H;Danino, T;Din, M O;Edwards, A M;Elsinghorst, E A;Fang, Y;Forbes, N S;Friedrich, J;Goers, L;Gopalakrishnan, V;Hohmann, E L;Hoiseth, S K;Hwang, I Y;Isabella, V M;Kasinskas, R W;Khademhosseini, A;Kim, H J;Lee, J W;Li, W Y;Liu, X D;Liu, Y;Mao, N;Nielsen, A A K;Osswald, A;Riglar, D T;Ryan, R M;Scott, S R;Shah, S A;Swofford, C A;Tangney, M;Teixeira, A P;Toso, J F;Verherstraeten, S;Weinberg, B H;Westphal, K;Yamada, T;Zhang, H;Zheng, D W;Zheng, J H | HW1MH | New York, NY USA;New York, NY USA. | 29 | null | 2 | null | 30,996,123 | Castro, Samuel;Danino, Tal;Harimoto, Tetsuhiro;Hinchliffe, Taylor E;Mather, William;Singer, Zakary S;Velazquez, Oscar S;Zhang, Joanna | P NATL ACAD SCI USA | La Jolla, CA USA;New York, NY USA |
Connot, C;Haynes, K A;Livingstone, X;Lopez, B;Mani, A;Smith, C L;Tekel, S J | 10.3389/fbioe.2019.00080 | 80 | AVENUE DU TRIBUNAL FEDERAL 34, LAUSANNE, CH-1015, SWITZERLAND | k26372ne1g1o431k6633313a695i3l5l4c29v | Engineered Orthogonal Quorum Sensing Systems for Synthetic Gene Regulation in <i>Escherichia coil</i> | Arizona State Univ | null | Haynes, KA (corresponding author), Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85281 USA.;Haynes, KA (corresponding author), Emory Univ, WH Coulter Dept Biomed Engn, Atlanta, GA 30322 USA. | null | Connot, Christopher;Haynes, Karmella A;Livingstone, Xylaan;Lopez, Brianna;Mani, Amber;Smith, Christina L;Tekel, Stefan J | Biotechnology & Applied Microbiology;Engineering, Biomedical | Kern Entrepreneurial Engineering Network (KEEN) student research grant (Arizona State University); Fulton Undergraduate Research Initiative (FURI); Western Alliance to Expand Student Opportunities (WAESO, NSF) [HRD 1401190]; School of Biological and Health Systems Engineering (SBHSE) | WOS | Haynes, K A | Arizona State Univ, Tempe, AZ USA;Emory Univ, Atlanta, GA USA | 7 | <i>Escherichia;coil</i>;engineered;for;gene;in;Orthogonal;Quorum;regulation;Sensing;synthetic;systems | 1 | Haynes, Karmella | FRONTIERS MEDIA SA | Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85281 USA;Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85281 USA.; Haynes, KA (corresponding author), Emory Univ, WH Coulter Dept Biomed Engn, Atlanta, GA 30322 USA;Arizona State Univ, Sch Life Sci, Tempe, AZ USA;Emory Univ, WH Coulter Dept Biomed Engn, Atlanta, GA 30322 USA | Article | Arizona State Univ;Emory Univ | LAUSANNE | null | null | Arizona State Univ;Emory Univ | Fulton Undergraduate Research Initiative (FURI);Kern Entrepreneurial Engineering Network (KEEN) student research grant (Arizona State University);School of Biological and Health Systems Engineering (SBHSE);Western Alliance to Expand Student Opportunities (WAESO, NSF) | Haynes, KA (corresponding author), Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85281 USA.; Haynes, KA (corresponding author), Emory Univ, WH Coulter Dept Biomed Engn, Atlanta, GA 30322 USA. | null | Connot, Christopher;Haynes, Karmella A;Livingstone, Xylaan;Lopez, Brianna;Mani, Amber;Smith, Christina L;Tekel, Stefan J | 26 | 3 | 465,358,800,001 | Fulton Undergraduate Research Initiative (FURI);Kern Entrepreneurial Engineering Network (KEEN) student research grant (Arizona State University);School of Biological and Health Systems Engineering (SBHSE);Western Alliance to Expand Student Opportunities (WAESO, NSF) [HRD 1401190] | USA | FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY | USA;USA.; | null | null | Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85281 USA | 2296-4185 | Connot, C;Haynes, K A;Livingstone, X;Lopez, B;Mani, A;Smith, C L;Tekel, S J | APR 17 | kahayne@emory.edu | <i>Escherichia coil</i>;Orthogonal Quorum Sensing Systems;Synthetic Gene Regulation | 7 | J | Biotechnology & Applied Microbiology;Engineering | 10 distinct HSL-synthase enzymes;<i>Escherichia coil</i>;AubR);autoinducer;BACTERIA;Biosensor;BjaR;building synthetic gene;characterized components;CIRCUITS;coordinate behaviors across populations;crosstalk;current study;engineering microbial communities;EsaI/TraR;EsaI/TraR);Escherichia coli BL21;exhibit little;faults;five different regulators (LuxR;gene circuit;gene regulators;homoserine lactone;homoserine lactones (HSLs);identified two sets;investigation;LasI/LasR;LASR;lead;liquid;little;membrane-permeable compounds;microbial quorum signaling pathways;multiple regulators;natural DNA;networks;Orthogonal Quorum Sensing Systems;orthogonal synthase-regulator pairs (BjaI/BjaR;parallel signaling pathways;PATHWAY;popular tools;previous work;protein elements;PSEUDOMONAS-AERUGINOSA;quorum sensing;quorum sensing components;response;responses;results;same set;single HSL;single regulator (LuxR);solid cultures;synthases;Synthetic Gene Regulation;synthetic HSL-signaling systems;synthetic pathways;toolbox;transcription factor;TraR | Tekel, S J | AUTOINDUCER;BACTERIA;Biosensor;CIRCUITS;gene circuit;homoserine lactone;LASR;PATHWAY;PSEUDOMONAS-AERUGINOSA;quorum sensing;transcription factor | null | [Tekel, Stefan J.; Smith, Christina L.; Haynes, Karmella A.] Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85281 USA. [Lopez, Brianna; Mani, Amber; Connot, Christopher; Livingstone, Xylaan] Arizona State Univ, Sch Life Sci, Tempe, AZ USA. [Haynes, Karmella A.] Emory Univ, WH Coulter Dept Biomed Engn, Atlanta, GA 30322 USA. | This project was supported by a Kern Entrepreneurial Engineering Network (KEEN) student research grant (Arizona State University). BL, CS, and AM were supported by the Fulton Undergraduate Research Initiative (FURI). XL was supported by the Western Alliance to Expand Student Opportunities (WAESO, NSF Grant HRD 1401190). ST was supported by the School of Biological and Health Systems Engineering (SBHSE). DNA synthesis and primers were generously provided by Integrated DNA Technologies (IDT) as support for the 2017 International Genetically Engineered Machines (iGEM) competition. | 10 distinct HSL-synthase enzymes;AubR);bacteria;BjaR;building synthetic gene;characterized components;coordinate behaviors across populations;crosstalk;current study;engineering microbial communities;EsaI/TraR;EsaI/TraR);Escherichia coli BL21;exhibit little;faults;five different regulators (LuxR;gene regulators;homoserine lactones (HSLs);identified two sets;investigation;LasI/LasR;LasR;lead;liquid;little;membrane-permeable compounds;microbial quorum signaling pathways;multiple regulators;natural DNA;networks;orthogonal synthase-regulator pairs (BjaI/BjaR;parallel signaling pathways;popular tools;previous work;protein elements;quorum sensing components;response;responses;results;same set;single HSL;single regulator (LuxR);solid cultures;synthases;synthetic HSL-signaling systems;synthetic pathways;toolbox;TraR | 10.1016/j.bios.2012.08.011;10.1016/j.chembiol.2009.09.001;10.1016/j.chembiol.2014.10.008;10.1021/acssynbio.5b00286;10.1021/acssynbio.7b00058;10.1021/acssynbio.8b00271;10.1038/msb.2008.24;10.1038/nature03461;10.1038/nature07088;10.1038/nature09565;10.1038/nbt.3796;10.1038/nbt1413;10.1038/nmicrobiol.2017.83;10.1038/nrm907;10.1073/pnas.1103821108;10.1073/pnas.1114125108;10.1093/nar/gku1388;10.1126/science.1166253;10.1126/science.272.5268.1655;10.1128/AEM.00499-10;10.1128/JB.177.17.5000-5008.1995;10.1128/jb.179.18.5756-5767.1997;10.1128/JB.184.20.5686-5695.2002;10.1128/JB.185.20.5976-5983.2003;10.1128/JB.187.14.5054-5058.2005;10.1186/s12934-015-0379-1;10.1371/journal.pone.0202294;10.1371/journal.ppat.1006504;10.3389/fbioe.2015.00030 | Arizona State Univ | Connot, C;Haynes, K A;Livingstone, X;Lopez, B;Mani, A;Smith, C L;Tekel, S J | Tekel, S J: Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85281 USA | null | HRD 1401190 | 29 | null | USA | Arizona State Univ;Emory Univ | Tekel, Stefan J | Green Submitted, Green Published, gold | AUTOINDUCER;BACTERIA;BIOSENSOR;CIRCUITS;HOMOSERINE LACTONE;LASR;PATHWAY;PSEUDOMONAS-AERUGINOSA | Tekel, Stefan J.; Smith, Christina L.; Lopez, Brianna; Mani, Amber; Connot, Christopher; Livingstone, Xylaan; Haynes, Karmella A.; | null | Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85281 USA;Arizona State Univ, Sch Life Sci, Tempe, AZ USA;Emory Univ, WH Coulter Dept Biomed Engn, Atlanta, GA 30322 USA | Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85281 USA;Arizona State Univ, Sch Life Sci, Tempe, AZ USA;Emory Univ, WH Coulter Dept Biomed Engn, Atlanta, GA 30322 USA | null | Biosensor;Gene circuits;homoserine lactone;quorum sensing;transcription factor | null | 1995;1996;1997;2002;2003;2005;2008;2009;2010;2011;2013;2014;2015;2016;2017;2018 | 15 | Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85281 USA;Emory Univ, WH Coulter Dept Biomed Engn, Atlanta, GA 30322 USA | Front. Bioeng. Biotechnol. | Haynes, Karmella A | FRONTIERS MEDIA SA | (BjaI/BjaR;(HSLs);(LuxR;(LuxR);+;,;10;a;across;activate;an;and;are;AubR);bacteria;become;behaviors;BjaR;BL21;building;by;called;can;characterized;coli;communities;components;composed;compounds;controlled;coordinate;crosstalk;cultures;current;derived;determined;different;distinct;DNA;elements;engineered;engineering;enzymes;EsaI/TraR;EsaI/TraR);Escherichia;exhibit;expand;expressed;faults;five;for;from;gene;have;here;homoserine;HSL;HSL-signaling;HSL-synthase;identified;identify;in;investigation;lactones;LasI/LasR;LasR;lead;liquid;little;membrane-permeable;microbial;multiple;natural;networks;no;of;Orthogonal;our;pairs;parallel;pathways;popular;populations;previous;protein;quorum;regulator;regulators;report;response;responses;results;same;sensing;set;sets;show;signaling;single;solid;study;synthase-regulator;synthases;synthetic;systems;that;the;these;they;to;toolbox;tools;TraR;two;we;when;where;work | Arizona State Univ;Emory Univ | Gene regulators that are controlled by membrane-permeable compounds called homoserine lactones (HSLs) have become popular tools for building synthetic gene networks that coordinate behaviors across populations of engineered bacteria. Synthetic HSL-signaling systems are derived from natural DNA and protein elements from microbial quorum signaling pathways. Crosstalk, where a single HSL can activate multiple regulators, can lead to faults in networks composed of parallel signaling pathways. Here, we report an investigation of quorum sensing components to identify synthetic pathways that exhibit little to no crosstalk in liquid and solid cultures. In previous work, we characterized the response of a single regulator (LuxR) to 10 distinct HSL-synthase enzymes. Our current study determined the responses of five different regulators (LuxR, LasR, TraR, BjaR, and AubR) to the same set of synthases. We identified two sets of orthogonal synthase-regulator pairs (BjaI/BjaR + EsaI/TraR and LasI/LasR + EsaI/TraR) that show little to no crosstalk when they are expressed in Escherichia coli BL21. These results expand the toolbox of characterized components for engineering microbial communities. | null | AUTOINDUCER;BACTERIA;BIOSENSOR;CIRCUITS;HOMOSERINE LACTONE;LASR;PATHWAY;PSEUDOMONAS-AERUGINOSA | 2 | null | Biosensor;gene circuit;homoserine lactone;quorum sensing;transcription factor | 12 | PSEUDOMONAS-AERUGINOSA;AUTOINDUCER;BACTERIA;Biosensor;CIRCUITS;Gene circuits;homoserine lactone;LASR;PATHWAY;quorum sensing;transcription factor | WOS:000465358800001 | Arizona State Univ, Tempe, AZ USA;Emory Univ, Atlanta, GA USA | USA | 2,019 | null | 0000-0002-5975-577X | null | null | English | null | ACS SYNTH BIOL;APPL ENVIRON MICROB;BIOSENS BIOELECTRON;CHEM BIOL;FRONT BIOENG BIOTECH;J BACTERIOL;MICROB CELL FACT;MOL SYST BIOL;NAT BIOTECHNOL;NAT MICROBIOL;NAT REV MOL CELL BIO;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PLOS ONE;PLOS PATHOG;SCIENCE | Connot, Christopher;Haynes, Karmella A;Livingstone, Xylaan;Lopez, Brianna;Mani, Amber;Smith, Christina L;Tekel, Stefan J | 2024-03-11
ER | Ahlgren, N A;Balagadde, F K;Basu, S;Borlee, B R;Canton, B;Daer, R;Davis, R M;Fuqua, C;Gupta, A;Jayaraman, P;Kang, S Y;Kim, S;Lindemann, A;Lindsay, A;Marketon, M M;Medina, G;More, M I;Mukherjee, S;Pearson, J P;Schaefer, A L;Scott, S R;Tamsir, A;Taylor, A F;Vonbodman, S B;Wang, B J;Wu, F Q;Zou, Y Z | HU5ZQ | Atlanta, GA USA;Tempe, AZ USA. | 18 | null | 2 | null | 31,058,147 | Connot, Christopher;Haynes, Karmella A;Livingstone, Xylaan;Lopez, Brianna;Mani, Amber;Smith, Christina L;Tekel, Stefan J | FRONT BIOENG BIOTECH | Atlanta, GA USA;Tempe, AZ USA |
Armstrong, Z;Chen, H M;Hallam, S J;Liu, F;Withers, S G | 10.1021/acscatal.8b05179 | null | 1155 16TH ST, NW, WASHINGTON, DC 20036 USA | 3e4c6p2m1x5j4y1v5y3m5e2m1p6q247291d3y6t | Systematic Screening of Synthetic Gene-Encoded Enzymes for Synthesis of Modified Glycosides | Univ British Columbia | null | Withers, SG (corresponding author), Univ British Columbia, Dept Biochem & Mol Biol, Vancouver, BC V6T 1Z3, Canada.;Withers, SG (corresponding author), Univ British Columbia, Dept Chem, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada.;Withers, SG (corresponding author), Univ British Columbia, Genome Sci & Technol Program, 2329 West Mall, Vancouver, BC V6T 1Z4, Canada.;Withers, SG (corresponding author), Univ British Columbia, Michael Smith Lab, Ctr High Throughput Biol, Vancouver, BC V6T 1Z3, Canada. | null | Armstrong, Zachary;Chen, Hong-Ming;Hallam, Steven J;Liu, Feng;Withers, Stephen G | Chemistry, Physical | Natural Sciences and Engineering Research Council of Canada (NSERC) [DE-AC02-05CH1123] | WOS | Withers, S G | Univ British Columbia, Vancouver BC, Canada | 9 | Enzymes;for;Gene-Encoded;Glycosides;modified;of;screening;synthesis;synthetic;systematic | 1 | Armstrong, Zachary;Withers, Stephen G | AMER CHEMICAL SOC | Univ British Columbia, Dept Biochem & Mol Biol, Vancouver, BC V6T 1Z3, Canada;Univ British Columbia, Dept Chem, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada;Univ British Columbia, Dept Microbiol & Immunol, Vancouver, BC V6T 1Z1, Canada;Univ British Columbia, ECOSCOPE Training Program, Vancouver, BC V6T 1Z3, Canada;Univ British Columbia, Genome Sci & Technol Program, 2329 West Mall, Vancouver, BC V6T 1Z4, Canada;Univ British Columbia, Genome Sci & Technol Program, 2329 West Mall, Vancouver, BC V6T 1Z4, Canada.; Withers, SG (corresponding author), Univ British Columbia, Dept Chem, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada.; Withers, SG (corresponding author), Univ British Columbia, Michael Smith Lab, Ctr High Throughput Biol, Vancouver, BC V6T 1Z3, Canada.; Withers, SG (corresponding author), Univ British Columbia, Dept Biochem & Mol Biol, Vancouver, BC V6T 1Z3, Canada;Univ British Columbia, Grad Program Bioinformat, Vancouver, BC V6T 1Z4, Canada;Univ British Columbia, Michael Smith Lab, Ctr High Throughput Biol, Vancouver, BC V6T 1Z3, Canada | Article | Univ British Columbia | WASHINGTON | null | null | Univ British Columbia | Natural Sciences and Engineering Research Council of Canada (NSERC) | Withers, SG (corresponding author), Univ British Columbia, Genome Sci & Technol Program, 2329 West Mall, Vancouver, BC V6T 1Z4, Canada.; Withers, SG (corresponding author), Univ British Columbia, Dept Chem, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada.; Withers, SG (corresponding author), Univ British Columbia, Michael Smith Lab, Ctr High Throughput Biol, Vancouver, BC V6T 1Z3, Canada.; Withers, SG (corresponding author), Univ British Columbia, Dept Biochem & Mol Biol, Vancouver, BC V6T 1Z3, Canada. | 3227 | Armstrong, Zachary;Chen, Hong-Ming;Hallam, Steven J;Liu, Feng;Withers, Stephen G | 51 | 7 | 464,075,700,049 | Natural Sciences and Engineering Research Council of Canada (NSERC) [DE-AC02-05CH1123] | Canada | ACS CATALYSIS | Canada | null | null | Univ British Columbia, Genome Sci & Technol Program, 2329 West Mall, Vancouver, BC V6T 1Z4, Canada | 2155-5435 | Armstrong, Z;Chen, H M;Hallam, S J;Liu, F;Withers, S G | APR | withers@chem.ubc.ca | Modified Glycosides;synthesis;Synthetic Gene-Encoded Enzymes;systematic Screening | 5 | J | Chemistry | -azido derivatives;1;175 synthetic genes;3-;4-;6-amino;6-positions;active;activity-based probes;alanine;alpha-glucosyl fluoride;amino-;approaches;assembly;azido-glucosides;beta-glucosidase;biocatalysis;carbohydrate-active enzymes;catalysts;catalytic nucleophile glutamate;CAZymes;CHEMOENZYMATIC SYNTHESIS;cloning;creation;detailed kinetic analysis;directed evolution;E. coli clones;eight;enzymes;FAMILY-1;gene products;general framework;glycine;glycolipid analogues;glycosidases;glycoside hydrolase;glycoside hydrolase family GH1;glycosidehydrolase-containing clone libraries;glycosynthase;high-throughput functional screening;hydrolysis;IDENTIFICATION;library;mechanism;Modified Glycosides;modified sugars;mutants;opens;phylogenetically diverse libraries;phylogenomic library;plate-based aglycone specificity screening;rapid evaluation;rare catalytic capabilities;screening;sequence-based family;serine;seven;several useful biocatalysts;subfamilies;subset;substrate specificity;synthesis;synthetic capabilities;Synthetic Gene-Encoded Enzymes;synthetic genes;systematic Screening;taggable disaccharides;three glycosynthase mutants;transfer;trisaccharides;utility | Armstrong, Z | BETA-GLUCOSIDASE;biocatalysis;CAZymes;CHEMOENZYMATIC SYNTHESIS;cloning;directed evolution;FAMILY-1;glycoside hydrolase;glycosynthase;high-throughput functional screening;MECHANISM;phylogenomic library | 3219 | [Armstrong, Zachary; Hallam, Steven J.; Withers, Stephen G.] Univ British Columbia, Genome Sci & Technol Program, 2329 West Mall, Vancouver, BC V6T 1Z4, Canada. [Liu, Feng; Chen, Hong-Ming; Withers, Stephen G.] Univ British Columbia, Dept Chem, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada. [Hallam, Steven J.] Univ British Columbia, Dept Microbiol & Immunol, Vancouver, BC V6T 1Z1, Canada. [Hallam, Steven J.] Univ British Columbia, Grad Program Bioinformat, Vancouver, BC V6T 1Z4, Canada. [Withers, Stephen G.] Univ British Columbia, Michael Smith Lab, Ctr High Throughput Biol, Vancouver, BC V6T 1Z3, Canada. [Withers, Stephen G.] Univ British Columbia, Dept Biochem & Mol Biol, Vancouver, BC V6T 1Z3, Canada. [Hallam, Steven J.] Univ British Columbia, ECOSCOPE Training Program, Vancouver, BC V6T 1Z3, Canada. | We thank the Natural Sciences and Engineering Research Council of Canada (NSERC) for Discovery grants to S.G.W. and S.J.H. We also thank the Joint Genome Institute for provision of the GH1 gene library that was synthesized under Contract No. DE-AC02-05CH1123. | -azido derivatives;1;175 synthetic genes;3-;4-;6-amino;6-positions;active;activity-based probes;alanine;alpha-glucosyl fluoride;amino-;approaches;assembly;azido-glucosides;carbohydrate-active enzymes;catalysts;catalytic nucleophile glutamate;creation;detailed kinetic analysis;E. coli clones;eight;enzymes;gene products;general framework;glycine;glycolipid analogues;glycosidases;glycoside hydrolase family GH1;glycosidehydrolase-containing clone libraries;hydrolysis;identification;library;modified sugars;mutants;opens;phylogenetically diverse libraries;plate-based aglycone specificity screening;rapid evaluation;rare catalytic capabilities;screening;sequence-based family;serine;seven;several useful biocatalysts;subfamilies;subset;substrate specificity;synthetic capabilities;synthetic genes;taggable disaccharides;three glycosynthase mutants;transfer;trisaccharides;utility | 10.1002/1873-3468.12059;10.1002/adsc.201100461;10.1002/anie.201204578;10.1002/anie.201810661;10.1002/bip.22335;10.1002/cbic.201100229;10.1002/ejoc.201402588;10.1007/s00253-006-0526-z;10.1007/s002840010220;10.1016/bs.mie.2017.06.001;10.1016/j.carres.2006.04.049;10.1016/j.carres.2012.02.013;10.1016/j.carres.2018.07.007;10.1016/j.cbpa.2015.06.032;10.1016/j.copbio.2011.02.010;10.1016/j.febslet.2007.03.009;10.1016/j.pep.2005.01.016;10.1016/j.sbi.2009.08.003;10.1016/S1074-5521(01)00038-2;10.1021/acs.chemrev.8b00066;10.1021/acschembio.6b00340;10.1021/bi00049a035;10.1021/bm900215p;10.1021/cb500244v;10.1021/ja00104a060;10.1021/ja00258a047;10.1021/ja980833d;10.1038/nature11117;10.1038/nchembio.203;10.1038/ncomms12482;10.1038/NMETH899;10.1039/c7cc04380e;10.1074/jbc.M116.721597;10.1074/jbc.M406890200;10.1101/gr.108332.110;10.1146/annurev-biochem-062917-012034;10.1371/journal.pone.0132848;10.3389/fmicb.2015.01291;[10.3389/frricb.2015.00275, 10.3389/fmicb.2015.00275] | Univ British Columbia | Armstrong, Z;Chen, H M;Hallam, S J;Liu, F;Withers, S G | Armstrong, Z: Univ British Columbia, Genome Sci & Technol Program, 2329 West Mall, Vancouver, BC V6T 1Z4, Canada | Armstrong, Zachary;Withers, Stephen G | DE-AC02-05CH1123 | 40 | null | Canada | Univ British Columbia | Armstrong, Zachary | null | BETA-GLUCOSIDASE;CHEMOENZYMATIC SYNTHESIS;CLONING;DIRECTED EVOLUTION;FAMILY-1;GLYCOSYNTHASE;MECHANISM | Armstrong, Zachary; Liu, Feng; Chen, Hong-Ming; Hallam, Steven J.; Withers, Stephen G.; | null | Univ British Columbia, Dept Biochem & Mol Biol, Vancouver, BC V6T 1Z3, Canada;Univ British Columbia, Dept Chem, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada;Univ British Columbia, Dept Microbiol & Immunol, Vancouver, BC V6T 1Z1, Canada;Univ British Columbia, ECOSCOPE Training Program, Vancouver, BC V6T 1Z3, Canada;Univ British Columbia, Genome Sci & Technol Program, 2329 West Mall, Vancouver, BC V6T 1Z4, Canada;Univ British Columbia, Grad Program Bioinformat, Vancouver, BC V6T 1Z4, Canada;Univ British Columbia, Michael Smith Lab, Ctr High Throughput Biol, Vancouver, BC V6T 1Z3, Canada | Univ British Columbia, Dept Biochem & Mol Biol, Vancouver, BC V6T 1Z3, Canada;Univ British Columbia, Dept Chem, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada;Univ British Columbia, Dept Microbiol & Immunol, Vancouver, BC V6T 1Z1, Canada;Univ British Columbia, ECOSCOPE Training Program, Vancouver, BC V6T 1Z3, Canada;Univ British Columbia, Genome Sci & Technol Program, 2329 West Mall, Vancouver, BC V6T 1Z4, Canada;Univ British Columbia, Grad Program Bioinformat, Vancouver, BC V6T 1Z4, Canada;Univ British Columbia, Michael Smith Lab, Ctr High Throughput Biol, Vancouver, BC V6T 1Z3, Canada | null | biocatalysis;CAZymes;glycoside hydrolase;glycosynthase;high-throughput functional screening;phylogenomic library | 4 | 1987;1994;1995;1998;2001;2004;2005;2006;2007;2009;2010;2011;2012;2013;2014;2015;2016;2017;2018 | 15 | Univ British Columbia, Dept Biochem & Mol Biol, Vancouver, BC V6T 1Z3, Canada;Univ British Columbia, Dept Chem, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada;Univ British Columbia, Genome Sci & Technol Program, 2329 West Mall, Vancouver, BC V6T 1Z4, Canada;Univ British Columbia, Michael Smith Lab, Ctr High Throughput Biol, Vancouver, BC V6T 1Z3, Canada | ACS Catal. | Withers, Stephen G | AMER CHEMICAL SOC | ,;-azido;1;175;3-;4-;6-amino;6-positions;a;active;activity-based;aglycone;alanine;allows;alpha-glucosyl;also;amino-;analogues;analysis;and;approaches;are;as;assembly;at;azido-glucosides;be;biocatalysts;by;can;capabilities;capable;carbohydrate-active;catalysts;catalytic;catalyzing;characterized;cleave;clone;clones;coli;construction;creation;demonstrated;derivatives;detailed;develop;disaccharides;diverse;does;E.;each;eight;encoded;enzymes;evaluation;exploited;explored;family;fluoride;for;framework;from;further;gene;general;generated;genes;GH1;glutamate;glycine;glycolipid;glycosidases;glycoside;glycosidehydrolase-containing;glycosynthase;harboring;herein;hydrolase;hydrolysis;identification;identify;in;it;kinetic;large;libraries;library;modified;most;mutants;not;nucleophile;of;only;opens;or;other;phylogenetically;plate-based;present;probes;products;provides;rapid;rare;report;represent;screening;search;sequence-based;serine;seven;several;specificity;subfamilies;subset;substituted;substrate;such;sugars;synthetic;taggable;that;the;their;then;these;this;three;through;to;transfer;trisaccharides;up;useful;utility;was;we;were;which;with;within;work | Univ British Columbia | The construction of large, phylogenetically diverse libraries of synthetic genes from a sequence-based family allows rapid evaluation of the substrate specificity encoded within the gene products and identification of rare catalytic capabilities. For carbohydrate-active enzymes such as glycosidases, this opens up approaches to search for enzymes that are capable of catalyzing the hydrolysis and transfer of modified sugars. Herein we report the screening of a library of E. coli clones each harboring 1 of 175 synthetic genes that represent the subfamilies within the glycoside hydrolase family GH1 to identify a subset of enzymes that cleave amino- and azido-glucosides modified at the 3-, 4-, and 6-positions. Eight of the most active such enzymes were further characterized through detailed kinetic analysis and plate-based aglycone specificity screening. Three glycosynthase mutants of each of these enzymes were generated, in which their catalytic nucleophile glutamate was substituted by alanine, glycine, or serine, and their synthetic capabilities were explored with alpha-glucosyl fluoride and 3-, 4-, and 6-amino and -azido derivatives. The utility of seven of the generated mutants was then demonstrated through the assembly of taggable disaccharides, trisaccharides, glycolipid analogues, and activity-based probes. Not only does this work present the creation of several useful biocatalysts, it also provides a general framework that can be exploited to develop catalysts from other glycosidehydrolase-containing clone libraries. | I-7229-2019;U-3635-2019 | BETA-GLUCOSIDASE;CHEMOENZYMATIC SYNTHESIS;CLONING;DIRECTED EVOLUTION;FAMILY-1;GLYCOSYNTHASE;MECHANISM | 1 | null | biocatalysis;CAZymes;glycoside hydrolase;glycosynthase;high-throughput functional screening;phylogenomic library | 17 | BETA-GLUCOSIDASE;biocatalysis;CAZymes;CHEMOENZYMATIC SYNTHESIS;cloning;directed evolution;family 1;glycoside hydrolase;glycosynthase;high-throughput functional screening;MECHANISM;phylogenomic library | WOS:000464075700049 | Univ British Columbia, Vancouver BC, Canada | Canada | 2,019 | null | 0000-0002-4086-2946;0000-0002-6722-5701 | null | null | English | null | ACS CHEM BIOL;ADV SYNTH CATAL;ANGEW CHEM INT EDIT;ANNU REV BIOCHEM;APPL MICROBIOL BIOT;BIOCHEMISTRY-US;BIOMACROMOLECULES;BIOPOLYMERS;CARBOHYD RES;CHEM BIOL;CHEM COMMUN;CHEM REV;CHEMBIOCHEM;CURR MICROBIOL;CURR OPIN BIOTECH;CURR OPIN CHEM BIOL;CURR OPIN STRUC BIOL;EUR J ORG CHEM;EXTREMOPHILES;FEBS LETT;FRONT MICROBIOL;GENOME RES;J AM CHEM SOC;J BIOL CHEM;METHOD ENZYMOL;NAT CHEM BIOL;NAT COMMUN;NAT METHODS;NATURE;PLOS ONE;PROTEIN EXPRES PURIF | Armstrong, Zachary;Chen, Hong-Ming;Hallam, Steven J;Liu, Feng;Withers, Stephen G | 2024-03-11
ER | Aharoni, A;Armstrong, Z;Blanchard, J E;Bornscheuer, U T;Chen, H M;Cobucci-Ponzano, B;Danby, P M;Faijes, M;Giddens, J P;Goddard-Borger, E D;Gullfot, F;Hahm, H S;Heins, R A;Kim, Y W;Kurogochi, M;Kwan, D H;Lauro, B D;Leis, B;Li, K Y;López-López, O;Mackenzie, L F;Namchuk, M N;Naresh, K;Nijikken, Y;Pengthaisong, S;Rich, J R;Spiridonov, N A;Studier, F W;Tasse, L;Taupp, M;Tokuriki, N;Tsukada, T;Turner, N J;Wang, Q P;Wen, L Q;Withers, S G;Zeymer, C;Zhang, J B | HS7UV | Vancouver BC, Canada;Vancouver BC, Canada. | 15 | null | 1 | null | null | Armstrong, Zachary;Chen, Hong-Ming;Hallam, Steven J;Liu, Feng;Withers, Stephen G | ACS CATAL | Vancouver BC, Canada |
Li, W C;Wang, N;Zhang, J M;Zhang, W | 10.1371/journal.pone.0213977 | e0213977 | 1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA | 22584v3ul5w1g2v4z1341q6v5j62582b623q2f | Optimal parameter identification of synthetic gene networks using harmony search algorithm | Zhejiang Univ | null | Zhang, JM (corresponding author), Zhejiang Univ, Dept Control & Engn, Inst Cyber Syst & Control, Hangzhou, Zhejiang, Peoples R China. | null | Li, Wenchao;Wang, Ning;Zhang, Jianming;Zhang, Wei | Multidisciplinary Sciences | National Natural Science Foundation of China (CN) [61573311] | WOS | Zhang, J M | Zhejiang Univ, Zhejiang, Peoples R China | 14 | algorithm;gene;harmony;Identification;networks;of;optimal;parameter;search;synthetic;using | 1 | Li, Wenchao | PUBLIC LIBRARY SCIENCE | Zhejiang Univ, Dept Control & Engn, Inst Cyber Syst & Control, Hangzhou, Zhejiang, Peoples R China | Article | Zhejiang Univ | SAN FRANCISCO | null | null | Zhejiang Univ | National Natural Science Foundation of China (CN) | Zhang, JM (corresponding author), Zhejiang Univ, Dept Control & Engn, Inst Cyber Syst & Control, Hangzhou, Zhejiang, Peoples R China. | null | Li, Wenchao;Wang, Ning;Zhang, Jianming;Zhang, Wei | 10 | 1 | 462,732,300,008 | National Natural Science Foundation of China (CN) [61573311] | China | PLOS ONE | China | null | null | Zhejiang Univ, Dept Control & Engn, Inst Cyber Syst & Control, Hangzhou, Zhejiang, Peoples R China | 1932-6203 | Li, W C;Wang, N;Zhang, J M;Zhang, W | MAR 29 | jmzhang@iipc.zju.edu.cn | harmony search algorithm;optimal parameter identification;synthetic gene networks | 4 | J | Science & Technology - Other Topics | account;analysis;challenged task;CIRCUITS;computational modeling;designed cost function takes two major factors;effectiveness;estimation accuracy;estimation errors;experimental costs;experiments select two types;expression;Gene circuits;Genetic circuits;harmony search algorithm;harmony search(HS)-based OED algorithm;identification outcomes;informative observations;input signals;maximizing Fisher information matrix(FIM)-based optimal criteria;measurement cost;modeling gene networks;MODELS;modified E-optimal criteria;number;optimal experimental design(OED) method;OPTIMAL EXPERIMENTAL-DESIGN;optimal inputs;optimal parameter identification;proposed HS-OED approach;proposed HS-OED method outperforms two candidate OED approaches;proposed optimal identification methodology;reduced computational effort;reliable model parameters;response behaviors;sample size;SELECTION;study focuses;synthetic gene networks;synthetic genetic networks;systems biology;time points;trade-off;two-stage optimization | Zhang, W | CIRCUITS;EXPRESSION;MODELS;OPTIMAL EXPERIMENTAL-DESIGN;SELECTION | null | [Zhang, Wei; Li, Wenchao; Zhang, Jianming; Wang, Ning] Zhejiang Univ, Dept Control & Engn, Inst Cyber Syst & Control, Hangzhou, Zhejiang, Peoples R China. | Author Wei Zhang is partly supported by National Natural Science Foundation of China (CN) 61573311. | account;analysis;challenged task;computational modeling;designed cost function takes two major factors;effectiveness;estimation accuracy;estimation errors;experimental costs;experiments select two types;gene circuits;genetic circuits;harmony search(HS)-based OED algorithm;identification outcomes;informative observations;input signals;maximizing Fisher information matrix(FIM)-based optimal criteria;measurement cost;modeling gene networks;modified E-optimal criteria;number;optimal experimental design(OED) method;optimal inputs;proposed HS-OED approach;proposed HS-OED method outperforms two candidate OED approaches;proposed optimal identification methodology;reduced computational effort;reliable model parameters;response behaviors;sample size;study focuses;synthetic genetic networks;systems biology;time points;trade-off;two-stage optimization | 10.1002/qre.1591;10.1007/s00158-015-1271-7;10.1016/0005-1098(90)90116-Y;10.1016/j.aml.2014.09.013;10.1016/j.bpj.2017.08.057;10.1016/j.cels.2017.01.003;10.1016/j.mbs.2012.01.001;10.1021/sb400139h;10.1038/nbt.3044;10.1038/nbt.4111;10.1038/nrg2102;10.1038/nrg3885;10.1038/s41564-017-0022-5;10.1038/s41580-018-0024-z;10.1042/BSE0450195;10.1093/bioinformatics/btn330;10.1093/bioinformatics/btp358;10.1093/bioinformatics/btt436;10.1093/bioinformatics/btv186;10.1093/bioinformatics/btv672;10.1093/nar/gkv1280;10.1093/synbio/ysx003;10.1109/ACC.2014.6858649;10.1109/TCBB.2014.2377733;10.1109/TMBMC.2016.2633265;10.1126/science.aal2052;10.1128/JB.157.1.283-290.1984;10.1177/003754970107600201;10.1177/0037549703040937;10.1186/1752-0509-1-51;10.1186/1752-0509-4-38;10.1186/1752-0509-8-13;10.1186/1752-0509-8-20;10.1186/1756-0500-5-518;10.1186/s12918-016-0328-6;10.1186/s12918-018-0594-6;10.1371/journal.pcbi.1000558;10.1371/journal.pcbi.1004706;10.1371/journal.pone.0110234;10.1371/journal.pone.0200094 | Zhejiang Univ | Li, W C;Wang, N;Zhang, J M;Zhang, W | Zhang, W: Zhejiang Univ, Dept Control & Engn, Inst Cyber Syst & Control, Hangzhou, Zhejiang, Peoples R China | null | 61573311 | 40 | null | China | Zhejiang Univ | Zhang, Wei | gold, Green Published, Green Submitted | CIRCUITS;EXPRESSION;MODELS;OPTIMAL EXPERIMENTAL-DESIGN;SELECTION | Zhang, Wei; Li, Wenchao; Zhang, Jianming; Wang, Ning; | null | Zhejiang Univ, Dept Control & Engn, Inst Cyber Syst & Control, Hangzhou, Zhejiang, Peoples R China | Zhejiang Univ, Dept Control & Engn, Inst Cyber Syst & Control, Hangzhou, Zhejiang, Peoples R China | null | null | 3 | 1984;1990;2001;2003;2007;2008;2009;2010;2012;2013;2014;2015;2016;2017;2018 | 1 | Zhejiang Univ, Dept Control & Engn, Inst Cyber Syst & Control, Hangzhou, Zhejiang, Peoples R China | PLoS One | Wang, Ning | PUBLIC LIBRARY SCIENCE | ,;a;account;accuracy;algorithm;an;analysis;and;applies;approach;approaches;are;behaviors;between;biology;candidate;challenged;circuits;computational;cost;costs;criteria;describe;design(OED);designed;designs;E-optimal;effectiveness;effort;engineered;errors;estimation;experimental;experiments;factors;Fisher;focuses;function;furthermore;gene;genetic;harmony;HS-OED;identification;important;in;indicate;information;informative;input;inputs;into;involves;is;major;matrix(FIM)-based;maximizing;measurement;method;methodology;minimize;model;modeling;modified;networks;number;observations;obtain;OED;of;on;optimal;optimization;order;outcomes;outperforms;paper;parameters;points;predict;proportional;proposed;provide;pursue;reduced;reliable;response;sample;search(HS)-based;select;signals;size;study;synthetic;systems;takes;task;the;this;time;to;trade-off;two;two-stage;types;using;validate;which;while;with | Zhejiang Univ | Computational modeling of engineered gene circuits is an important while challenged task in systems biology. In order to describe and predict the response behaviors of genetic circuits using reliable model parameters, this paper applies an optimal experimental design(OED) method to obtain input signals. In order to obtain informative observations, this study focuses on maximizing Fisher information matrix(FIM)-based optimal criteria and to provide optimal inputs. Furthermore, this paper designs a two-stage optimization with the modified E-optimal criteria and applies harmony search(HS)-based OED algorithm to minimize estimation errors. The proposed optimal identification methodology involves estimation errors and the sample size to pursue a trade-off between estimation accuracy and measurement cost in modeling gene networks. The designed cost function takes two major factors into account, in which experimental costs are proportional to the number of time points. Experiments select two types of synthetic genetic networks to validate the effectiveness of the proposed HS-OED approach. Identification outcomes and analysis indicate the proposed HS-OED method outperforms two candidate OED approaches, with reduced computational effort. | null | CIRCUITS;EXPRESSION;MODEL;OPTIMAL EXPERIMENTAL-DESIGN;SELECTION | 0 | null | null | 28 | CIRCUITS;EXPRESSION;MODEL;Optimal experimental design;SELECTION | WOS:000462732300008 | Zhejiang Univ, Zhejiang, Peoples R China | China | 2,019 | null | 0000-0002-7956-0742 | null | null | English | null | ACS SYNTH BIOL;APPL MATH LETT;AUTOMATICA;BIOINFORMATICS;BIOPHYS J;BMC Res Notes;BMC SYST BIOL;CELL SYST;ESSAYS BIOCHEM;IEEE ACM T COMPUT BI;IEEE T MOL BIO MULT;J BACTERIOL;MATH BIOSCI;NAT BIOTECHNOL;NAT MICROBIOL;NAT REV GENET;NAT REV MOL CELL BIO;NUCLEIC ACIDS RES;P AMER CONTR CONF;PLOS COMPUT BIOL;PLOS ONE;QUAL RELIAB ENG INT;SCIENCE;SIMUL-T SOC MOD SIM;SIMULATION;STRUCT MULTIDISCIP O;SYN BIOL | Li, Wenchao;Wang, Ning;Zhang, Jianming;Zhang, Wei | 2024-03-11
ER | Adoteye, K;Alon, U;Bandara, S;Banga, J R;Bouffier, A M;Busetto, A G;Carbonell-Ballestero, M;Dehghannasiri, R;Faller, D;Firman, T;Futcher, A B;Geem, Z W;Huang, B;Huynh, L;Le Novère, N;Liao, C;Lin, C D;Liu, Z;Llamosi, A;Mangan Nm.;Marchisio, M A;Meyer, P;Mishra, D;Mohammadi, P;Mélykúti, B;Nimmegeers, P;O'Brien, E L;Pirgazi, J;Raue, A;Segall-Shapiro, T H;Srinivas, N;Steinke, F;Stigter Johannes, D;Ud-Dean, S M M;Vanlier, J;Walter, E;Wilson, A D;Xie, M Q;Yamazaki, K;Zhu, F | HQ9FO | Zhejiang, Peoples R China | 1 | null | 1 | null | 30,925,150 | Li, Wenchao;Wang, Ning;Zhang, Jianming;Zhang, Wei | PLOS ONE | Zhejiang, Peoples R China |
Ayukawa, S;Kiga, D;Moriya, T;Wakao, S;Wakayama, Y;Yamamura, M;Yamaoka, T;Zhang, Z C | 10.3390/life9010030 | 30 | ST ALBAN-ANLAGE 66, CH-4052 BASEL, SWITZERLAND | 215i1i2i2f575r2l1u5y382k6d1j4i354r1i4x6g | Comparison between Effects of Retroactivity and Resource Competition upon Change in Downstream Reporter Genes of Synthetic Genetic Circuits | Tokyo Inst Technol | null | Kiga, D (corresponding author), Tokyo Inst Technol, Dept Computat Intelligence & Syst Sci, Yokohama, Kanagawa 2268503, Japan.;Kiga, D (corresponding author), Waseda Univ, Dept Elect Engn & Biosci, Shinjuku Ku, Tokyo 1698050, Japan. | null | Ayukawa, Shotaro;Kiga, Daisuke;Moriya, Takefumi;Wakao, Shinji;Wakayama, Yuki;Yamamura, Masayuki;Yamaoka, Tomohiro;Zhang, Zicong | Biology;Microbiology | KAKENHI [23119005, 26540152, 15KT0148]; Commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterials from the Ministry of Economy, Trade, and Industry (METI); [12J09398]; Grants-in-Aid for Scientific Research [15KT0148, 26540152] Funding Source: KAKEN | WOS | Kiga, D | Tokyo Inst Technol, Kanagawa, Japan;Waseda Univ, Tokyo, Japan | 9 | and;between;Change;circuits;comparison;competition;Downstream;Effects;genes;genetic;in;of;Reporter;resource;Retroactivity;synthetic;upon | 1 | Kiga, Daisuke;Zhang, Zicong | MDPI | Tokyo Inst Technol, Dept Computat Intelligence & Syst Sci, Yokohama, Kanagawa 2268503, Japan;Tokyo Inst Technol, Dept Computat Intelligence & Syst Sci, Yokohama, Kanagawa 2268503, Japan.; Kiga, D (corresponding author), Waseda Univ, Dept Elect Engn & Biosci, Shinjuku Ku, Tokyo 1698050, Japan;Waseda Univ, Dept Elect Engn & Biosci, Shinjuku Ku, Tokyo 1698050, Japan;Waseda Univ, Waseda Res Inst Sci & Engn, Shinjuku Ku, Tokyo 1698050, Japan | Article | Tokyo Inst Technol;Waseda Univ | BASEL | null | null | Tokyo Inst Technol;Waseda Univ | Commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterials from the Ministry of Economy, Trade, and Industry (METI);Grants-in-Aid for Scientific Research;KAKENHI | Kiga, D (corresponding author), Tokyo Inst Technol, Dept Computat Intelligence & Syst Sci, Yokohama, Kanagawa 2268503, Japan.; Kiga, D (corresponding author), Waseda Univ, Dept Elect Engn & Biosci, Shinjuku Ku, Tokyo 1698050, Japan. | null | Ayukawa, Shotaro;Kiga, Daisuke;Moriya, Takefumi;Wakao, Shinji;Wakayama, Yuki;Yamamura, Masayuki;Yamaoka, Tomohiro;Zhang, Zicong | 3 | 3 | 464,133,600,001 | [12J09398];Commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterials from the Ministry of Economy, Trade, and Industry (METI);Grants-in-Aid for Scientific Research [15KT0148, 26540152] Funding Source: KAKEN;KAKENHI [23119005, 26540152, 15KT0148] | Japan | LIFE-BASEL | Japan | null | null | Tokyo Inst Technol, Dept Computat Intelligence & Syst Sci, Yokohama, Kanagawa 2268503, Japan | null | Ayukawa, S;Kiga, D;Moriya, T;Wakao, S;Wakayama, Y;Yamamura, M;Yamaoka, T;Zhang, Z C | MAR 26 | kiga@waseda.jp;mly-jp.klws@fuji.waseda.jp;my@c.titech.ac.jp;ru10-deka@suou.waseda.jp;shotaroayukawasb@gmail.com;tkfmmry@gmail.com;wakao@waseda.jp;zzhang@ali.c.titech.ac.jp | Change;Downstream Reporter Genes;Effects;Resource Competition;Retroactivity;synthetic genetic circuits | 8 | J | Life Sciences & Biomedicine - Other Topics;Microbiology | activity;advanced design;advancements;altogether;analyses;ARAC;BINDING;cell;Change;circuits' components;combination;competition;component;control;corresponding gene;DEGRADATION;degradation);different copy number;downstream gene;Downstream Reporter Genes;downstream reporter promoter;dual-feedback oscillator;Effects;ESCHERICHIA-COLI;fluorescent protein reporter;Genetic circuits;molecular biology;OSCILLATIONS;phenomenon;protein-binding site;quantification;regulatory protein-binding sites;reporter gene;reporter gene activities;reporter genes;reporter promoters;reporters;resource competition;results;retroactivity;retroactivity (titration;SELECTION;silico;stability;studies;synthetic biology;synthetic genetic circuits;synthetic genetic oscillator;systems biology;two sources;unexpected effects;upstream dynamics;upstream protein;upstream regulatory genes;upstream regulatory protein;vivo experiments;vivo observations | Moriya, T | ARAC;CELL;ESCHERICHIA-COLI;OSCILLATIONS;protein-binding site;reporter gene;resource competition;retroactivity;Synthetic biology;systems biology | null | [Moriya, Takefumi; Zhang, Zicong; Yamamura, Masayuki; Kiga, Daisuke] Tokyo Inst Technol, Dept Computat Intelligence & Syst Sci, Yokohama, Kanagawa 2268503, Japan. [Yamaoka, Tomohiro; Wakayama, Yuki; Wakao, Shinji; Kiga, Daisuke] Waseda Univ, Dept Elect Engn & Biosci, Shinjuku Ku, Tokyo 1698050, Japan. [Ayukawa, Shotaro] Waseda Univ, Waseda Res Inst Sci & Engn, Shinjuku Ku, Tokyo 1698050, Japan. | This work was supported by Grants-in-Aid for Japan Society for the Promotion of Science Fellows (No. 12J09398 to TM) and the KAKENHI programs (23119005 and 26540152 to DK and 15KT0148 to SA) and a grant from the Commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterials from the Ministry of Economy, Trade, and Industry (METI). | activity;advanced design;advancements;altogether;analyses;binding;cell;circuits' components;combination;competition;component;control;corresponding gene;degradation;degradation);different copy number;downstream gene;downstream reporter genes;downstream reporter promoter;dual-feedback oscillator;fluorescent protein reporter;genetic circuits;molecular biology;oscillations;phenomenon;quantification;regulatory protein-binding sites;reporter gene activities;reporter genes;reporter promoters;reporters;results;retroactivity;retroactivity (titration;selection;silico;stability;studies;synthetic biology;synthetic genetic circuits;synthetic genetic oscillator;two sources;unexpected effects;upstream dynamics;upstream protein;upstream regulatory genes;upstream regulatory protein;vivo experiments;vivo observations | 10.1016/0378-1119(80)90100-6;10.1016/B978-0-12-391857-4.00009-4;10.1016/j.bpj.2010.09.057;10.1016/j.bpj.2010.12.3737;10.1016/j.cell.2014.02.022;10.1016/j.compchemeng.2004.08.035;10.1021/j100540a008;10.1021/sb300098w;10.1021/sb400102w;10.1038/35002125;10.1038/35002131;10.1038/msb.2011.94;10.1038/msb.2012.7;10.1038/msb4100204;10.1038/nature07389;10.1038/nature13238;10.1038/nature19841;10.1038/ncomms1687;10.1038/nmeth.2089;10.1073/pnas.1100060108;10.1073/pnas.1105901108;10.1073/pnas.1415685111;10.1073/pnas.83.18.6682;10.1093/nar/25.6.1203;10.1093/nar/8.22.5267;10.1093/nar/gkl393;10.1093/nar/gku735;10.1098/rsif.2018.0157;10.1103/PhysRevE.86.041920;10.1103/PhysRevLett.108.018102;10.1103/PhysRevLett.88.148101;10.1109/ACC.2016.7526834;10.1126/science.1070919;10.1126/science.8303295;10.1128/AEM.00791-07;10.1128/MCB.2.9.1044;10.1128/MCB.6.9.3173;10.1152/ajpcell.1998.274.2.C531;10.1186/1471-2164-11-S4-S16;10.1186/1752-0509-8-S4-S4;10.1186/1754-1611-2-5;10.1186/1754-1611-4-16;10.1371/journal.pbio.0060232;10.1371/journal.pcbi.1003486;10.1371/journal.pone.0041019;10.3389/fbioe.2014.00087 | Tokyo Inst Technol | Ayukawa, S;Kiga, D;Moriya, T;Wakao, S;Wakayama, Y;Yamamura, M;Yamaoka, T;Zhang, Z C | Moriya, T: Tokyo Inst Technol, Dept Computat Intelligence & Syst Sci, Yokohama, Kanagawa 2268503, Japan | ....., ....;Kiga, Daisuke;Wakao, Shinji;Zhang, Zicong | 12J09398;15KT0148;23119005;26540152 | 50 | null | Japan | Tokyo Inst Technol;Waseda Univ | Moriya, Takefumi | gold, Green Submitted, Green Published | ARAC;CELL;ESCHERICHIA-COLI;OSCILLATIONS | Moriya, Takefumi; Yamaoka, Tomohiro; Wakayama, Yuki; Ayukawa, Shotaro; Zhang, Zicong; Yamamura, Masayuki; Wakao, Shinji; Kiga, Daisuke; | null | Tokyo Inst Technol, Dept Computat Intelligence & Syst Sci, Yokohama, Kanagawa 2268503, Japan;Waseda Univ, Dept Elect Engn & Biosci, Shinjuku Ku, Tokyo 1698050, Japan;Waseda Univ, Waseda Res Inst Sci & Engn, Shinjuku Ku, Tokyo 1698050, Japan | Tokyo Inst Technol, Dept Computat Intelligence & Syst Sci, Yokohama, Kanagawa 2268503, Japan;Waseda Univ, Dept Elect Engn & Biosci, Shinjuku Ku, Tokyo 1698050, Japan;Waseda Univ, Waseda Res Inst Sci & Engn, Shinjuku Ku, Tokyo 1698050, Japan | 2075-1729 | protein-binding site;reporter gene;resource competition;retroactivity;Synthetic biology;systems biology | 1 | 1961;1977;1980;1982;1986;1988;1994;1997;1998;2000;2002;2005;2006;2007;2008;2010;2011;2012;2013;2014;2015;2016;2018 | 2 | Tokyo Inst Technol, Dept Computat Intelligence & Syst Sci, Yokohama, Kanagawa 2268503, Japan;Waseda Univ, Dept Elect Engn & Biosci, Shinjuku Ku, Tokyo 1698050, Japan | Life-Basel | Kiga, Daisuke | MDPI | (titration;,;a;achieved;activities;activity;advanced;advancements;allows;altered;altogether;an;analyses;and;as;binding;biology;by;cell;circuits;circuits';combination;competing;competition;component;components;contributed;control;copy;corresponding;degradation;degradation);design;different;downstream;dual-feedback;dynamics;effects;ensure;essential;experiments;fluorescent;for;found;from;furthermore;gene;genes;genetic;have;however;important;in;indicate;interfere;is;level;may;molecular;number;observations;of;on;oscillations;oscillator;our;phenomenon;produced;promoter;promoters;protein;protein-binding;quantification;regulatory;reporter;reporters;results;retroactivity;selection;separating;showed;silico;sites;sources;stability;studies;suggesting;synthetic;termed;that;the;this;to;two;unexpected;upstream;using;vivo;we;with | Tokyo Inst Technol;Waseda Univ | Reporter genes have contributed to advancements in molecular biology. Binding of an upstream regulatory protein to a downstream reporter promoter allows quantification of the activity of the upstream protein produced from the corresponding gene. In studies of synthetic biology, analyses of reporter gene activities ensure control of the cell with synthetic genetic circuits, as achieved using a combination of in silico and in vivo experiments. However, unexpected effects of downstream reporter genes on upstream regulatory genes may interfere with in vivo observations. This phenomenon is termed as retroactivity. Using in silico and in vivo experiments, we found that a different copy number of regulatory protein-binding sites in a downstream gene altered the upstream dynamics, suggesting retroactivity of reporters in this synthetic genetic oscillator. Furthermore, by separating the two sources of retroactivity (titration of the component and competition for degradation), we showed that, in the dual-feedback oscillator, the level of the fluorescent protein reporter competing for degradation with the circuits' components is important for the stability of the oscillations. Altogether, our results indicate that the selection of reporter promoters using a combination of in silico and in vivo experiments is essential for the advanced design of genetic circuits. | HJI-0218-2023;O-1942-2018;T-5361-2018;V-8433-2019 | ARAC;CELLS;ESCHERICHIA-COLI;OSCILLATIONS | 0 | null | protein-binding site;reporter gene;resource competition;retroactivity;Synthetic biology;systems biology | 19 | ESCHERICHIA-COLI;ARAC;CELLS;OSCILLATIONS;protein-binding site;reporter gene;resource competition;retroactivity;Synthetic biology;systems biology | WOS:000464133600001 | Tokyo Inst Technol, Kanagawa, Japan;Waseda Univ, Tokyo, Japan | Japan | 2,019 | null | 0000-0003-1444-5054;0000-0003-3778-5887 | null | null | English | null | ACS SYNTH BIOL;AM J PHYSIOL-CELL PH;ANAL NONLINEAR CONTR;APPL ENVIRON MICROB;BIOPHYS J;BIOTECHNIQUES;BMC GENOMICS;BMC SYST BIOL;CELL;COMPUT CHEM ENG;FRONT BIOENG BIOTECH;GENE;IMAGEJ;J Biol Eng;J PHYS CHEM-US;J R SOC INTERFACE;METHOD ENZYMOL;MOL CELL BIOL;MOL SYST BIOL;NAT COMMUN;NAT METHODS;NATURE;NUCLEIC ACIDS RES;P AMER CONTR CONF;P NATL ACAD SCI USA;PHYS REV E;PHYS REV LETT;PLOS BIOL;PLOS COMPUT BIOL;PLOS ONE;SCIENCE | Ayukawa, Shotaro;Kiga, Daisuke;Moriya, Takefumi;Wakao, Shinji;Wakayama, Yuki;Yamamura, Masayuki;Yamaoka, Tomohiro;Zhang, Zicong | 2024-03-11
ER | Ayukawa, S;Beal, J;Brewster, R C;Burger, A;Chalfie, M;Chen, Y J;Cookson, N A;Del Vecchio, D;Elowitz, M B;Franco, E;Gardner, T S;Gillespie, D T;Gorman, C M;Graham D.;Gyorgy, A;Hasty, J;Hsu, C;Ishimatsu, K;Jayanthi, S;Kim Kyung, H;Kim, K H;Kumar, N S;Le, T T;Lee, S K;Lee, T H;Lutz, R;Mather, W H;Meijering, E;Miyada, C G;Montminy, M R;Moriya, T;Nordeen, S K;Page, K M;Potvin-Trottier, L;Prindle, A;Rasband, W;Rondelez, Y;Saez-Rodriguez, J;Schneider, C A;Sekine, R;Selden, R F;Shetty Reshma, P;Smolen, P;Stricker, J;Tyler J.;Vanzi, F;Wallace, R G;Wong, O K | HS8QG | Kanagawa, Japan.;Tokyo, Japan | 4 | null | 2 | null | 30,917,535 | Ayukawa, Shotaro;Kiga, Daisuke;Moriya, Takefumi;Wakao, Shinji;Wakayama, Yuki;Yamamura, Masayuki;Yamaoka, Tomohiro;Zhang, Zicong | LIFE-BASEL | Kanagawa, Japan;Tokyo, Japan |
Bagh, S;Bonnerjee, D;Mukhopadhyay, S;Sarkar, K;Srivastava, R | 10.1186/s13036-019-0151-x | 20 | CAMPUS, 4 CRINAN ST, LONDON N1 9XW, ENGLAND | 543d674h5q474s611e6v1o4as1p2a3c3a5e15 | A frame-shifted gene, which rescued its function by non-natural start codons and its application in constructing synthetic gene circuits | Saha Inst Nucl Phys | null | Bagh, S (corresponding author), Saha Inst Nucl Phys, Homi Bhabha Natl Inst, Biophys & Struct Genom Div, Block A-F,Sect 1, Kolkata 700064, India. | null | Bagh, Sangram;Bonnerjee, Deepro;Mukhopadhyay, Sayak;Sarkar, Kathakali;Srivastava, Rajkamal | Biochemical Research Methods;Biotechnology & Applied Microbiology | IBOP Project, Department of Atomic Energy, Govt. of India; Ramanujan Fellowship of SB, Department of Science and Technology, Govt. of India | WOS | Bagh, S | Saha Inst Nucl Phys, Kolkata, India | 13 | ,;a;and;application;by;circuits;codons;constructing;frame-shifted;function;gene;in;its;non-natural;rescued;start;synthetic;which | 1 | Bagh, Sangram;Bonnerjee, Deepro;mukhopadhyay, sayak;Sarkar, Kathakali | BMC | Saha Inst Nucl Phys, Homi Bhabha Natl Inst, Biophys & Struct Genom Div, Block A-F,Sect 1, Kolkata 700064, India | Article | Saha Inst Nucl Phys | LONDON | null | null | Saha Inst Nucl Phys | IBOP Project, Department of Atomic Energy, Govt. of India;Ramanujan Fellowship of SB, Department of Science and Technology, Govt. of India | Bagh, S (corresponding author), Saha Inst Nucl Phys, Homi Bhabha Natl Inst, Biophys & Struct Genom Div, Block A-F,Sect 1, Kolkata 700064, India. | null | Bagh, Sangram;Bonnerjee, Deepro;Mukhopadhyay, Sayak;Sarkar, Kathakali;Srivastava, Rajkamal | 9 | 1 | 460,080,300,001 | IBOP Project, Department of Atomic Energy, Govt. of India;Ramanujan Fellowship of SB, Department of Science and Technology, Govt. of India | India | JOURNAL OF BIOLOGICAL ENGINEERING | India | null | null | Saha Inst Nucl Phys, Homi Bhabha Natl Inst, Biophys & Struct Genom Div, Block A-F,Sect 1, Kolkata 700064, India | 1754-1611 | Bagh, S;Bonnerjee, D;Mukhopadhyay, S;Sarkar, K;Srivastava, R | MAR 1 | sangram.bagh@saha.ac.in | application;frame-shifted gene;function;non-natural start codons;synthetic gene circuits | 5 | J | Biochemistry & Molecular Biology;Biotechnology & Applied Microbiology | -repressor cI;3rd codon;application;backgroundFrame-shifted genes resultsin non-functional peptides;BIOLOGY APPLICATIONS;building;building synthetic gene circuits;cI;cI genes;complete loss;demonstrated synthetic genetic NAND;different codon;directed evolution;E coli;effective functionality;Escherichia coli;ESCHERICHIA-COLI;excellent candidate;first report;first several amino acids;frame-shifted cI;Frame-shifted gene;frame-shifted gene.ConclusionsThis study;frame-shifted geneshavenever;function;functional;functions;Gate;gates;Gene circuits;genetic NOT-gates;growth;high regulatory ranges (>300);Hill coefficient (>6.5);large range;library;mutation;new operating mechanism;new view;non-directed evolution;Non-directed evolution of synthetic gene circuit;non-functional synthetic gene circuit;non-natural start codon;Non-natural start codons;NOR logic-gates;novel way;one form;properties;relative copy numbers;Rescued function;serve;SIGNIFICANCE;similar repression behavior;single nucleotide deletion mutation;start codon ACA;starting;starts;synthetic;synthetic gene circuits;synthetic gene circuits.ResultsHere;synthetic genetic circuits;synthetic-gene-circuits;target promoter;translatingfrom;TRANSLATION INITIATION;understanding;whole frame-shifted gene | Sarkar, K | BIOLOGY APPLICATIONS;directed evolution;E coli;ESCHERICHIA-COLI;Frame-shifted gene;Non-directed evolution of synthetic gene circuit;Non-natural start codons;Rescued function;synthetic gene circuits;TRANSLATION INITIATION | null | [Sarkar, Kathakali; Mukhopadhyay, Sayak; Bonnerjee, Deepro; Srivastava, Rajkamal; Bagh, Sangram] Saha Inst Nucl Phys, Homi Bhabha Natl Inst, Biophys & Struct Genom Div, Block A-F,Sect 1, Kolkata 700064, India. | This work was supported by IBOP Project, Department of Atomic Energy, Govt. of India and Ramanujan Fellowship of SB, Department of Science and Technology, Govt. of India. | -repressor cI;3rd codon;backgroundFrame-shifted genes resultsin non-functional peptides;building;building synthetic gene circuits;cI;cI genes;complete loss;demonstrated synthetic genetic NAND;different codon;effective functionality;Escherichia coli;excellent candidate;first report;first several amino acids;frame-shifted cI;frame-shifted gene;frame-shifted gene.ConclusionsThis study;frame-shifted geneshavenever;function;functional;functions;gate;gates;gene circuits;genetic NOT-gates;growth;high regulatory ranges (>300);Hill coefficient (>6.5);large range;library;mutation;new operating mechanism;new view;non-directed evolution;non-functional synthetic gene circuit;non-natural start codon;NOR logic-gates;novel way;one form;properties;relative copy numbers;serve;SIGNIFICANCE;similar repression behavior;single nucleotide deletion mutation;start codon ACA;starting;starts;synthetic;synthetic gene circuits.ResultsHere;synthetic genetic circuits;synthetic-gene-circuits;target promoter;translatingfrom;understanding;whole frame-shifted gene | 10.1002/anie.201708408;10.1002/bit.22969;10.1007/BF00352506;10.1016/j.copbio.2016.03.016;10.1016/j.synbio.2017.09.003;10.1021/sb4000564;10.1038/nbt.1568;10.1038/nbt.2714;10.1038/nchembio.1411;10.1038/nrg2775;10.1038/srep29574;10.1073/pnas.252535999;10.1093/nar/22.23.4953;10.1093/nar/25.6.1203;10.1093/nar/gkt1139;10.1093/nar/gkx070;10.1093/nar/gkx472;10.1099/mic.0.067975-0;10.1103/PhysRevE.77.021919;10.1103/PhysRevE.82.021911;10.1128/AEM.01684-08;10.15252/msb.20145735;10.15252/msb.20167265;[10.1038/NMETH.2926, 10.1038/nmeth.2926] | Saha Inst Nucl Phys | Bagh, S;Bonnerjee, D;Mukhopadhyay, S;Sarkar, K;Srivastava, R | Sarkar, K: Saha Inst Nucl Phys, Homi Bhabha Natl Inst, Biophys & Struct Genom Div, Block A-F,Sect 1, Kolkata 700064, India | mukhopadhyay, sayak | null | 25 | null | India | Saha Inst Nucl Phys | Sarkar, Kathakali | Green Published, gold | BIOLOGY APPLICATIONS;DIRECTED EVOLUTION;ESCHERICHIA-COLI;TRANSLATION INITIATION | Sarkar, Kathakali; Mukhopadhyay, Sayak; Bonnerjee, Deepro; Srivastava, Rajkamal; Bagh, Sangram; | null | Saha Inst Nucl Phys, Homi Bhabha Natl Inst, Biophys & Struct Genom Div, Block A-F,Sect 1, Kolkata 700064, India | Saha Inst Nucl Phys, Homi Bhabha Natl Inst, Biophys & Struct Genom Div, Block A-F,Sect 1, Kolkata 700064, India | null | E. coli;Frame-shifted gene;Non-directed evolution of synthetic gene circuit;Non-natural start codons;Rescued function;Synthetic gene circuit | null | 1981;1994;1997;2002;2004;2008;2009;2010;2011;2013;2014;2016;2017;2018 | 5 | Saha Inst Nucl Phys, Homi Bhabha Natl Inst, Biophys & Struct Genom Div, Block A-F,Sect 1, Kolkata 700064, India | J. Biol. Eng. | Bagh, Sangram | BMC | (>300);(>6.5);,;-repressor;3rd;a;ACA;acids;also;amino;among;an;and;as;backgroundFrame-shifted;became;because;been;behavior;between;building;by;candidate;cI;circuit;circuits;circuits.ResultsHere;codon;coefficient;coli;complete;constructing;copy;deletion;demonstrated;developed;different;during;each;effective;engineered;Escherichia;evidence;evolution;excellent;first;for;form;found;frame-shifted;from;function;functional;functionality;functions;gate;gates;gene;gene.ConclusionsThis;genes;geneshavenever;genetic;growth;had;have;high;Hill;hypothesized;in;inspires;is;it;its;large;library;logic-gates;loss;made;make;may;mechanism;mutation;NAND;new;non-directed;non-functional;non-natural;NOR;not;NOT-gates;novel;nucleotide;numbers;of;on;one;operating;optimizing;over;peptides;promoter;properties;range;ranges;regulatory;relative;report;repression;rescued;resulted;resultsin;series;serve;several;showed;SIGNIFICANCE;similar;single;start;starting;starts;study;synthetic;synthetic-gene-circuits;target;tested;that;the;these;this;through;translated;translatingfrom;understanding;used;view;was;way;we;which;whole;with;within;work;worked | Saha Inst Nucl Phys | BackgroundFrame-shifted genes resultsin non-functional peptides. Because of this complete loss of function, frame-shifted geneshavenever been used in constructing synthetic gene circuits.ResultsHere we report that the function of gene circuits is rescued by a frame-shifted gene, which functions by translatingfrom a non-natural start codon. We report a single nucleotide deletion mutation that developed in the -repressor cI within a synthetic genetic NOT gate in Escherichia coli during growth and through this mutation, a non-functional synthetic gene circuit became functional. This mutation resulted in a frame-shifted cI, which showed effective functionality among genetic NOT-gates in Escherichia coli with high regulatory ranges (>300) and Hill coefficient (>6.5). The cI worked over a large range of relative copy numbers between the frame-shifted gene and its target promoter. These properties make this frame-shifted gene an excellent candidate for building synthetic gene circuits. We hypothesized a new operating mechanism and showed evidence that frame-shifted cI was translated from non-natural start codon. We have engineered and tested a series of NOT gates made from a library of cI genes, each of which starts from a different codon within the first several amino acids of the frame-shifted cI. It is found that one form with start codon ACA, starting from the 3rd codon had similar repression behavior as the whole frame-shifted gene. We demonstrated synthetic genetic NAND and NOR logic-gates with frame-shifted cI. This is the first report of synthetic-gene-circuits made from a frame-shifted gene.ConclusionsThis study inspires a new view on frame-shifted gene and may serve as a novel way of building and optimizing synthetic-gene-circuits. This work may also have significance in the understanding of non-directed evolution of synthetic genetic circuits. | HJI-3440-2023 | BIOLOGY APPLICATIONS;DIRECTED EVOLUTION;ESCHERICHIA-COLI;TRANSLATION INITIATION | 0 | null | E coli;Frame-shifted gene;Non-directed evolution of synthetic gene circuit;Non-natural start codons;Rescued function;synthetic gene circuits | 10 | E. coli;ESCHERICHIA-COLI;BIOLOGY APPLICATIONS;directed evolution;Frame-shifted gene;Non-directed evolution of synthetic gene circuit;Non-natural start codons;Rescued function;synthetic gene circuits;TRANSLATION INITIATION | WOS:000460080300001 | Saha Inst Nucl Phys, Kolkata, India | India | 2,019 | null | 0000-0002-2172-6893;0000-0002-5736-0993;0000-0002-6531-2254;0000-0002-8565-0728 | null | null | English | null | A Genetic Switch;ACS SYNTH BIOL;Angew Chem Int Ed Engl;APPL ENVIRON MICROB;BIOTECHNOL BIOENG;CURR OPIN BIOTECH;MICROBIOL-SGM;MOL GEN GENET;MOL SYST BIOL;NAT BIOTECHNOL;NAT CHEM BIOL;NAT METHODS;NAT REV GENET;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PHYS REV E;SCI REP-UK;SYN SYST BIOTECHNO | Bagh, Sangram;Bonnerjee, Deepro;Mukhopadhyay, Sayak;Sarkar, Kathakali;Srivastava, Rajkamal | 2024-03-11
ER | Ang, J;Arnold Frances, H;Arpino, J A J;Bagh, S;Bassalo, M C;Borujeni, A E;Brophy, J A N;Chen, H Y;Ellefson, J W;Engstrom, M D;He, C G;Hecht, A;Khalil, A S;Lieb, M;Lutz, R;Nielsen, A A;Ptashne M.;Rasmussen, K K;Salis, H M;Sayut, D J;Schreiber, J;Stanton, B C;Yokobayashi, Y | HN3JT | Kolkata, India | 5 | null | 1 | null | 30,867,677 | Bagh, Sangram;Bonnerjee, Deepro;Mukhopadhyay, Sayak;Sarkar, Kathakali;Srivastava, Rajkamal | J BIOL ENG | Kolkata, India |
Cai, Z M;Ding, M T;Fang, L;Gao, Q J;Huang, W R;Liao, X H;Liu, Y C;Liu, Y H;Xie, H B A;Yang, K;Zhan, H J;Zhou, Q | 10.1111/cpr.12552 | e12552 | 111 RIVER ST, HOBOKEN 07030-5774, NJ USA | 555l7256s1341e5r3p35616y4rdk3s6mq57 | A revolutionary tool: CRISPR technology plays an important role in construction of intelligentized gene circuits | Anhui Med Univ | null | Cai, ZM; Huang, WR; Liu, YC (corresponding author), Shenzhen Univ, Affiliated Hosp 1, Dept Urol, Shenzhen, Guangdong, Peoples R China. | null | Cai, Zhiming;Ding, Mengting;Fang, Lan;Gao, Qunjun;Huang, Weiren;Liao, Xinhui;Liu, Yuchen;Liu, Yuhan;Xie, Haibiao;Yang, Kang;Zhan, Hengji;Zhou, Qun | Cell Biology | National Natural Science Foundation of China [81772737]; Guangdong Provincial Department of Science and Technology [2017A020215120]; High Level University's Medical Discipline Construction project [2016031638]; Shenzhen Municipal Government of China [JCYJ20170413161749433, JSGG20160301161836370]; National Key Basic Research Program of China (973 Program) [2014CB745201]; Sanming Project of Shenzhen Health and Family Planning Commission [SZSM201412018, SZSM201512037] | WOS | Cai, Z M;Huang, W R;Liu, Y C | Anhui Med Univ, Shenzhen, Peoples R China;Shenzhen Univ, Guangdong, Peoples R China | 52 | :;a;an;circuits;construction;CRISPR;gene;important;in;intelligentized;of;plays;revolutionary;role;technology;tool | 1 | ding, mengting;Gao, Qunjun;Liu, Haibo;Liu, Yuchen;Liu, Yuhan;Liu, Yujie;Wang, Hao | WILEY | Anhui Med Univ, Dept Urol, Shenzhen Peoples Hosp 2, Clin Med Coll, Shenzhen, Peoples R China;Shenzhen Univ, Affiliated Hosp 1, Dept Urol, Shenzhen, Guangdong, Peoples R China;WR; Liu, YC (corresponding author), Shenzhen Univ, Affiliated Hosp 1, Dept Urol, Shenzhen, Guangdong, Peoples R China | Review | Shenzhen Univ | HOBOKEN | null | null | Anhui Med Univ;Shenzhen Univ | Guangdong Provincial Department of Science and Technology;High Level University's Medical Discipline Construction project;National Key Basic Research Program of China (973 Program);National Natural Science Foundation of China;Sanming Project of Shenzhen Health and Family Planning Commission;Shenzhen Municipal Government of China | Cai, ZM; Huang, WR; Liu, YC (corresponding author), Shenzhen Univ, Affiliated Hosp 1, Dept Urol, Shenzhen, Guangdong, Peoples R China. | null | Cai, Zhiming;Ding, Mengting;Fang, Lan;Gao, Qunjun;Huang, Weiren;Liao, Xinhui;Liu, Yuchen;Liu, Yuhan;Xie, Haibiao;Yang, Kang;Zhan, Hengji;Zhou, Qun | 30 | 2 | 463,046,500,003 | Guangdong Provincial Department of Science and Technology [2017A020215120];High Level University's Medical Discipline Construction project [2016031638];National Key Basic Research Program of China (973 Program) [2014CB745201];National Natural Science Foundation of China [81772737];Sanming Project of Shenzhen Health and Family Planning Commission [SZSM201412018, SZSM201512037];Shenzhen Municipal Government of China [JCYJ20170413161749433, JSGG20160301161836370] | China | CELL PROLIFERATION | China | null | null | Anhui Med Univ, Dept Urol, Shenzhen Peoples Hosp 2, Clin Med Coll, Shenzhen, Peoples R China | 0960-7722 | Cai, Z M;Ding, M T;Fang, L;Gao, Q J;Huang, W R;Liao, X H;Liu, Y C;Liu, Y H;Xie, H B A;Yang, K;Zhan, H J;Zhou, Q | MAR | caizhiming2000@163.com;liuyuchenmdcg@163.com;pony8980@163.com | CRISPR technology;important role;intelligentized gene circuits;revolutionary tool | 12 | J | Cell Biology | activation;application;artificial;artificial switch-inducible Cas9;BIOLOGY;cancer therapy;Cas9;commodity chemicals;complex;CRISPR system;CRISPR technology;CRISPR-associated RNA-guided endonuclease Cas9 (CRISPR-associated protein 9)-targeted genome editing tool;CRISPR-based gene circuit development;CRISPR/Cas systems;CRYSTAL-STRUCTURE;development;efficiency;engineering gene circuits;Gene circuits;gene editing;gene therapy;great applied potential;high efficiency;IDENTIFICATION;important role;integration;intelligentized;intelligentized gene circuits;interspaced short palindromic repeat (CRISPR) system;lack;medicine;networks;new way;normal cells;poor anti-tumour effects;precision cancer therapy;programmability;programmable;prospectives;recent advances;REPRESSION;revolutionary tool;RNA;safety;sequence-specific gene editing tools;single targets;specificity;synthetic biology;synthetic gene circuits;target;traditional single-targeted therapy;TRANSCRIPTIONAL CONTROL;treat tumour cells;tumour cells;tumour-specific targets;ultimate challenge;underlying challenges;unique properties-operability;use | Zhou, Q | ACTIVATION;artificial;CAS9;COMPLEX;CRISPR technology;CRYSTAL-STRUCTURE;Gene circuits;gene editing;IDENTIFICATION;INTEGRATION;intelligentized;NETWORKS;REPRESSION;RNA;TRANSCRIPTIONAL CONTROL | null | [Zhou, Qun; Fang, Lan; Ding, Mengting; Cai, Zhiming; Huang, Weiren] Anhui Med Univ, Dept Urol, Shenzhen Peoples Hosp 2, Clin Med Coll, Shenzhen, Peoples R China. [Zhou, Qun; Zhan, Hengji; Liao, Xinhui; Liu, Yuhan; Xie, Haibiao; Yang, Kang; Gao, Qunjun; Ding, Mengting; Cai, Zhiming; Huang, Weiren; Liu, Yuchen] Shenzhen Univ, Affiliated Hosp 1, Dept Urol, Shenzhen, Guangdong, Peoples R China. | the National Natural Science Foundation of China, Grant/Award Number: 81772737; Guangdong Provincial Department of Science and Technology, Grant/Award Number: 2017A020215120; the High Level University's Medical Discipline Construction project, Grant/Award Number: 2016031638; the Shenzhen Municipal Government of China, Grant/Award Number: JCYJ20170413161749433 and JSGG20160301161836370; the National Key Basic Research Program of China (973 Program), Grant/Award Number: 2014CB745201; the Sanming Project of Shenzhen Health and Family Planning Commission, Grant/Award Number: SZSM201412018 and SZSM201512037 | application;artificial switch-inducible Cas9;biology;cancer therapy;commodity chemicals;CRISPR system;CRISPR technology;CRISPR-associated RNA-guided endonuclease Cas9 (CRISPR-associated protein 9)-targeted genome editing tool;CRISPR-based gene circuit development;CRISPR/Cas systems;development;efficiency;engineering gene circuits;gene circuits;gene therapy;great applied potential;high efficiency;intelligentized gene circuits;interspaced short palindromic repeat (CRISPR) system;lack;medicine;new way;normal cells;poor anti-tumour effects;precision cancer therapy;programmability;programmable;prospectives;recent advances;safety;sequence-specific gene editing tools;single targets;specificity;synthetic biology;synthetic gene circuits;target;traditional single-targeted therapy;treat tumour cells;tumour cells;tumour-specific targets;ultimate challenge;underlying challenges;unique properties-operability;use | 10.1002/hep.30084;10.1016/j.cell.2013.02.022;10.1016/j.cell.2013.06.044;10.1016/j.cell.2014.02.001;10.1016/j.cell.2014.09.029;10.1016/j.cell.2014.11.052;10.1016/j.cell.2015.08.007;10.1016/j.cell.2016.01.012;10.1016/j.cell.2016.02.004;10.1016/j.cell.2017.07.037;10.1016/j.cell.2017.09.049;10.1016/j.chembiol.2014.12.011;10.1016/j.molcel.2014.04.022;10.1016/j.molcel.2015.10.008;10.1016/j.tibtech.2015.12.014;10.1016/j.ymeth.2014.06.014;10.1016/S0092-8674(00)81683-9;10.1016/S1470-2045(09)70240-2;10.1021/acschembio.7b00603;10.1021/acssynbio.7b00425;10.1021/acssynbio.8b00202;10.1021/sb4000417;10.1021/sb4001867;10.1038/cr.2013.122;10.1038/msb.2010.99;10.1038/nature08753;10.1038/nature10886;10.1038/nature11245;10.1038/nature12148;10.1038/nature13011;10.1038/nature14299;10.1038/nature14571;10.1038/nature15544;10.1038/nature16526;10.1038/nature21059;10.1038/nature24268;10.1038/nbt.2808;10.1038/nbt.3199;10.1038/nchembio.1736;10.1038/ncomms13056;10.1038/ncomms3825;10.1038/ncomms4728;10.1038/ncomms5408;10.1038/ncomms6393;10.1038/nprot.2018.007;10.1038/nrmicro3569;10.1038/s41467-017-02075-1;10.1038/s41467-017-02265-x;10.1038/s41467-018-03475-7;10.1073/pnas.1620299114;10.1089/hum.2017.172;10.1105/tpc.15.00852;10.1111/pbi.12981;10.1126/sciadv.1701620;10.1126/science.1172005;10.1126/science.1192128;10.1126/science.1205527;10.1126/science.1207084;10.1126/science.1256272;10.1126/science.aan4672;10.3748/wjg.v22.i3.1179;10.7150/ijbs.16162;10.7554/eLife.31936;[10.1038/nmeth.2184, 10.1038/NMETH.2184];[10.1038/NMETH.2681, 10.1038/nmeth.2681];[10.1038/NMETH.2926, 10.1038/nmeth.2926];[10.1038/NMETH.2969, 10.1038/nmeth.2969];[10.1038/NMETH.3312, 10.1038/nmeth.3312];[10.1038/NMETH.3580, 10.1038/nmeth.3580];[10.1038/NMETH.3994, 10.1038/nmeth.3994] | Anhui Med Univ | Cai, Z M;Ding, M T;Fang, L;Gao, Q J;Huang, W R;Liao, X H;Liu, Y C;Liu, Y H;Xie, H B A;Yang, K;Zhan, H J;Zhou, Q | Zhou, Q: Anhui Med Univ, Dept Urol, Shenzhen Peoples Hosp 2, Clin Med Coll, Shenzhen, Peoples R China | ding, mengting;fang, yu;guo, ppdop;LI, Wenhui;li, xiaofeng;Liu, Haibo;liu, xiao;LIU, YU;liu, yuchen;Liu, Yujie;lu, yang;wang, hang;Wang, Hao;wang, jiajun;Wang, Luyao;wang, xiaoqiang;wang, ya;wang, yi;zhan, xiao;ZHAO, S;zhou, wei;zhou, yang | 2014CB745201;2016031638;2017A020215120;81772737;JCYJ20170413161749433;JSGG20160301161836370;SZSM201412018;SZSM201512037 | 70 | null | China | Anhui Med Univ;Shenzhen Univ | Zhou, Qun | hybrid, Green Published | ACTIVATION;CAS9;COMPLEX;CRYSTAL-STRUCTURE;IDENTIFICATION;INTEGRATION;NETWORKS;REPRESSION;RNA;TRANSCRIPTIONAL CONTROL | Zhou, Qun; Zhan, Hengji; Liao, Xinhui; Fang, Lan; Liu, Yuhan; Xie, Haibiao; Yang, Kang; Gao, Qunjun; Ding, Mengting; Cai, Zhiming; Huang, Weiren; Liu, Yuchen; | null | Anhui Med Univ, Dept Urol, Shenzhen Peoples Hosp 2, Clin Med Coll, Shenzhen, Peoples R China;Shenzhen Univ, Affiliated Hosp 1, Dept Urol, Shenzhen, Guangdong, Peoples R China | Anhui Med Univ, Dept Urol, Shenzhen Peoples Hosp 2, Clin Med Coll, Shenzhen, Peoples R China;Shenzhen Univ, Affiliated Hosp 1, Dept Urol, Shenzhen, Guangdong, Peoples R China | 1365-2184 | artificial;CRISPR technology;Gene circuits;gene editing;intelligentized | 2 | 2000;2009;2010;2011;2012;2013;2014;2015;2016;2017;2018;2019 | 5 | Shenzhen Univ, Affiliated Hosp 1, Dept Urol, Shenzhen, Guangdong, Peoples R China | Cell Prolif. | Liu, Yuchen | WILEY | (CRISPR);(CRISPR-associated;,;9)-targeted;a;advances;also;an;and;anti-tumour;application;applied;artificial;as;assessed;based;be;been;biology;cancer;cannot;Cas9;cells;challenge;challenges;chemicals;circuit;circuits;clustered;commodity;construction;could;CRISPR;CRISPR-associated;CRISPR-based;CRISPR/Cas;currently;design;development;discussed;distinguish;editing;effective;effectively;effects;efficiency;endonuclease;engineering;especially;for;from;gene;genome;great;guarantees;has;have;hence;here;high;if;in;intelligentized;interspaced;is;its;lack;limits;medicine;more;moreover;new;normal;of;on;palindromic;poor;potential;precision;programmability;programmable;properties-operability;prospectives;protein;provides;recent;recently;regularly;repeat;RNA-guided;safety;secure;sequence-specific;severely;short;shown;single;single-targeted;specificity;switch-inducible;synthetic;system;systems;target;targets;technology;the;therapy;to;tool;tools;traditional;treat;tumour;tumour-specific;ultimate;underlying;unique;use;used;using;way;we;which;with | Shenzhen Univ | With the development of synthetic biology, synthetic gene circuits have shown great applied potential in medicine, biology, and as commodity chemicals. An ultimate challenge in the construction of gene circuits is the lack of effective, programmable, secure and sequence-specific gene editing tools. The clustered regularly interspaced short palindromic repeat (CRISPR) system, a CRISPR-associated RNA-guided endonuclease Cas9 (CRISPR-associated protein 9)-targeted genome editing tool, has recently been applied in engineering gene circuits for its unique properties-operability, high efficiency and programmability. The traditional single-targeted therapy cannot effectively distinguish tumour cells from normal cells, and gene therapy for single targets has poor anti-tumour effects, which severely limits the application of gene therapy. Currently, the design of gene circuits using tumour-specific targets based on CRISPR/Cas systems provides a new way for precision cancer therapy. Hence, the application of intelligentized gene circuits based on CRISPR technology effectively guarantees the safety, efficiency and specificity of cancer therapy. Here, we assessed the use of synthetic gene circuits and if the CRISPR system could be used, especially artificial switch-inducible Cas9, to more effectively target and treat tumour cells. Moreover, we also discussed recent advances, prospectives and underlying challenges in CRISPR-based gene circuit development. | ABB-8923-2020;GQI-4698-2022;GXF-9442-2022;GYQ-6286-2022;HMD-7454-2023;HOF-6668-2023;HQZ-7558-2023;HTR-1607-2023;IWE-3635-2023;IWU-6535-2023;IWV-4219-2023;JCD-9947-2023;JED-3951-2023;JEZ-3810-2023;JLL-2001-2023;JMT-2783-2023;JND-8481-2023;JQJ-0490-2023;JRW-6032-2023;JWP-8549-2024;KAL-9865-2024;KCK-2014-2024 | ACTIVATION;CAS9;COMPLEX;TRANSCRIPTION CONTROL;CRYSTAL-STRUCTURE;IDENTIFICATION;INTEGRATION;NETWORKS;REPRESSION;RNA | 2 | null | artificial;CRISPR technology;Gene circuits;gene editing;intelligentized | 8 | ACTIVATION;artificial;CAS9;COMPLEX;TRANSCRIPTION CONTROL;CRISPR technology;CRYSTAL-STRUCTURE;Gene circuits;gene editing;IDENTIFICATION;INTEGRATION;intelligentized;NETWORKS;REPRESSION;RNA | WOS:000463046500003 | Anhui Med Univ, Shenzhen, Peoples R China;Shenzhen Univ, Guangdong, Peoples R China | China | 2,019 | null | 0000-0001-9109-6017;0000-0001-9156-0457;0000-0002-1153-6156;0000-0002-4213-2883;0000-0002-6517-0022;0000-0002-6524-1230;0000-0003-1990-4184 | null | null | English | null | ACS CHEM BIOL;ACS SYNTH BIOL;CELL;CELL RES;CHEM BIOL;ELIFE;HEPATOLOGY;HUM GENE THER;INT J BIOL SCI;LANCET ONCOL;METHODS;MOL CELL;MOL SYST BIOL;NAT BIOTECHNOL;NAT CHEM BIOL;NAT COMMUN;NAT METHODS;NAT PROTOC;NAT REV MICROBIOL;NATURE;P NATL ACAD SCI USA;PLANT BIOTECHNOL J;PLANT CELL;SCI ADV;SCIENCE;TRENDS BIOTECHNOL;WORLD J GASTROENTERO | Cai, Zhiming;Ding, Mengting;Fang, Lan;Gao, Qunjun;Huang, Weiren;Liao, Xinhui;Liu, Yuchen;Liu, Yuhan;Xie, Haibiao;Yang, Kang;Zhan, Hengji;Zhou, Qun | 2024-03-11
ER | Ausländer, D;Biarnes-Carrera, M;Brophy, J A N;Burstein, D;Charpentier, M;Chavez, A;Chen, J S;Cheng, A W;Choi, P S;Culler, S J;Daniel, R;Danino, T;Dunbar, C E;Esvelt, K M;Farzadfard, F;Friedland, A E;Fu, Y F;Gerstein, M B;Gilbert, L A;Grimm, D;Gupta, S;Hanahan, D;Harrington, L B;Hilton, I B;Howden, S E;Jansing, J;Jusiak, B;Kabadi, A M;Kiani, S;Kipniss, N H;Kleinstiver, B P;Lee, S Y;Lenis, T L;Li, Y Q;Lin, F;Liu, C C;Liu, Y C;Ma, D C;Maddalo, D;Makarova, K S;Megraw, M;Morsut, L;Nandagopal, N;Nielsen, J;Nihongaki, Y;Nishimasu, H;Nissim, L;Preziosi, M;Qi, L S;Ran, F A;Rini, B I;Rössger, K;Shin, J;Shmakov, S;Sternberg, S H;Strovas, T J;Wiedenheft, B;Xie, Z;Zalatan, J G;Zhan, H J;Zhou, X X | HR3NW | Guangdong, Peoples R China | 7 | null | 2 | null | 30,520,167 | Cai, Zhiming;Ding, Mengting;Fang, Lan;Gao, Qunjun;Huang, Weiren;Liao, Xinhui;Liu, Yuchen;Liu, Yuhan;Xie, Haibiao;Yang, Kang;Zhan, Hengji;Zhou, Qun | CELL PROLIFERAT | Guangdong, Peoples R China;Shenzhen, Peoples R China |
Gupta, A;Zou, J | 10.1038/s42256-019-0017-4 | null | HEIDELBERGER PLATZ 3, BERLIN, 14197, GERMANY | 37181d4ce3h3yj1260573s6d3w416t583y3m5g | Feedback GAN for DNA optimizes protein functions | Stanford Univ | null | Zou, J (corresponding author), Stanford Univ, Dept Biomed Data Sci, Stanford, CA 94305 USA.;Zou, J (corresponding author), Stanford Univ, Dept Comp Sci, Stanford, CA 94305 USA. | null | Gupta, Anvita;Zou, James | Computer Science, Artificial Intelligence;Computer Science, Interdisciplinary Applications | Chan-Zuckerberg Biohub Investigator grant; National Science Foundation (NSF) grant [CRII 1657155] | WOS | Zou, J | Stanford Univ, Stanford, CA USA | 1 | DNA;feedback;for;functions;GAN;optimizes;protein | 1 | null | NATURE PORTFOLIO | Stanford Univ, Dept Biomed Data Sci, Stanford, CA 94305 USA;Stanford Univ, Dept Comp Sci, Stanford, CA 94305 USA;Stanford Univ, Dept Comp Sci, Stanford, CA 94305 USA.; Zou, J (corresponding author), Stanford Univ, Dept Biomed Data Sci, Stanford, CA 94305 USA | Article | Stanford Univ | BERLIN | null | null | Stanford Univ | Chan-Zuckerberg Biohub Investigator grant;National Science Foundation (NSF) grant | Zou, J (corresponding author), Stanford Univ, Dept Comp Sci, Stanford, CA 94305 USA.; Zou, J (corresponding author), Stanford Univ, Dept Biomed Data Sci, Stanford, CA 94305 USA. | 111 | Gupta, Anvita;Zou, James | 52 | 2 | 567,066,600,008 | Chan-Zuckerberg Biohub Investigator grant;National Science Foundation (NSF) grant [CRII 1657155] | USA | NATURE MACHINE INTELLIGENCE | USA;USA.; | null | null | Stanford Univ, Dept Comp Sci, Stanford, CA 94305 USA | null | Gupta, A;Zou, J | FEB | jamesz@stanford.edu | DNA;feedback GAN;protein functions | 2 | J | Computer Science | advantage;analyser;antimicrobial peptides;applications;coding;DATABASE;desirable biophysical properties;desired properties;differentiable;DNA;DNA sequences;domains;drug discovery;drugs;environmental treatment;external function analyser;FBGAN architecture;feedback GAN;feedback GAN (FBGAN);feedback-loop architecture;feedback-loop mechanism;GAN-generated data points;GAN-generated proteins;GANs;generative adversarial;generative adversarial networks (GANs);generative machine learning models;genes;genomics;gupta;macromolecules;manufacturing;metrics;new structures;novel approach;novel feedback-loop architecture;ones;output;proposed architecture;protein functions;proteins;realistic data;resulting peptides;secondary structure;silico;suite;synthetic biology;synthetic DNA sequences encoding;synthetic gene sequences;synthetic genes;synthetic genes coding;two examples;useful properties;variable length;Zou | Gupta, A | DATABASE | 105 | [Gupta, Anvita; Zou, James] Stanford Univ, Dept Comp Sci, Stanford, CA 94305 USA. [Zou, James] Stanford Univ, Dept Biomed Data Sci, Stanford, CA 94305 USA. | The authors thank A. Kundaje for guidance when initiating the research on GANs and DNA. J.Z. is supported by a Chan-Zuckerberg Biohub Investigator grant and National Science Foundation (NSF) grant CRII 1657155. | advantage;analyser;antimicrobial peptides;applications;coding;desirable biophysical properties;desired properties;differentiable;DNA sequences;domains;drug discovery;drugs;environmental treatment;external function analyser;FBGAN architecture;feedback GAN (FBGAN);feedback-loop architecture;feedback-loop mechanism;GAN-generated data points;GAN-generated proteins;GANs;generative adversarial;generative adversarial networks (GANs);generative machine learning models;genes;genomics;gupta;macromolecules;manufacturing;metrics;new structures;novel approach;novel feedback-loop architecture;ones;output;proposed architecture;proteins;realistic data;resulting peptides;secondary structure;silico;suite;synthetic biology;synthetic DNA sequences encoding;synthetic gene sequences;synthetic genes;synthetic genes coding;two examples;useful properties;variable length;Zou | 10.1002/minf.201700111;10.1002/prot.24065;10.1016/j.jaad.2004.08.026;10.1016/S0734-9750(03)00077-6;10.1021/acs.jcim.7b00414;10.1021/acscentsci.7b00512;10.1038/nrg1637;10.1093/bioinformatics/btx285;10.1093/nar/gkt381;10.1093/nar/gkv1051;10.1093/nar/gkv1278;10.1101/227645V1;10.1101/262501V2];10.1126/science.aan0693;10.1145/3422622;10.1186/s13321-017-0235-x;10.1371/journal.pcbi.1005242;[10.1093/nar/gkh131, 10.1093/nar/gkw1099] | Stanford Univ | Gupta, A;Zou, J | Gupta, A: Stanford Univ, Dept Comp Sci, Stanford, CA 94305 USA | null | CRII 1657155 | 26 | null | USA | Stanford Univ | Gupta, Anvita | null | DATABASE | Gupta, Anvita; Zou, James; | null | Stanford Univ, Dept Biomed Data Sci, Stanford, CA 94305 USA;Stanford Univ, Dept Comp Sci, Stanford, CA 94305 USA | Stanford Univ, Dept Biomed Data Sci, Stanford, CA 94305 USA;Stanford Univ, Dept Comp Sci, Stanford, CA 94305 USA | 2522-5839 | null | 2 | 2003;2004;2005;2012;2013;2016;2017;2018;2020 | 85 | Stanford Univ, Dept Biomed Data Sci, Stanford, CA 94305 USA;Stanford Univ, Dept Comp Sci, Stanford, CA 94305 USA | Nat. Mach. Intell. | Zou, James | NATURE PORTFOLIO | (FBGAN);(GANs);,;:;a;advantage;adversarial;also;an;analyser;and;antimicrobial;applications;apply;approach;architecture;are;as;attractive;be;beyond;biology;biophysical;calculated;can;coding;data;demonstrate;demonstrates;desirable;desired;differentiable;discovery;DNA;does;domains;drug;drugs;encoding;environmental;examples;external;FBGAN;feedback;feedback-loop;find;for;function;GAN;GAN-generated;GANs;gene;generate;generates;generating;generative;genes;genomics;gupta;has;have;here;in;learning;length;machine;macromolecules;manufacturing;mechanism;metrics;models;need;network;networks;new;not;novel;of;ones;optimize;optimizing;or;other;output;peptides;points;produce;properties;propose;proposed;proteins;realistic;represent;resulting;secondary;sequences;silico;specifically;structure;structures;such;suite;synthetic;that;the;their;to;treatment;two;used;useful;using;variable;we;with;Zou | Stanford Univ | Generative adversarial networks (GANs) represent an attractive and novel approach to generate realistic data, such as genes, proteins or drugs, in synthetic biology. Here, we apply GANs to generate synthetic DNA sequences encoding for proteins of variable length. We propose a novel feedback-loop architecture, feedback GAN (FBGAN), to optimize the synthetic gene sequences for desired properties using an external function analyser. The proposed architecture also has the advantage that the analyser does not need to be differentiable. We apply the feedback-loop mechanism to two examples: generating synthetic genes coding for antimicrobial peptides, and optimizing synthetic genes for the secondary structure of their resulting peptides. A suite of metrics, calculated in silico, demonstrates that the GAN-generated proteins have desirable biophysical properties. The FBGAN architecture can also be used to optimize GAN-generated data points for useful properties in domains beyond genomics. Generative machine learning models are used in synthetic biology to find new structures such as DNA sequences, proteins and other macromolecules with applications in drug discovery, environmental treatment and manufacturing. Gupta and Zou propose and demonstrate in silico a feedback-loop architecture to optimize the output of a generative adversarial network that generates synthetic genes to produce ones specifically coding for antimicrobial peptides. | null | DATABASE | 9 | null | null | 7 | DATABASE | WOS:000567066600008 | Stanford Univ, Stanford, CA USA | USA | 2,019 | null | null | null | null | English | null | ABS160603498;ACS CENTRAL SCI;BIOINFORMATICS;BIOTECHNOL ADV;COMMUN ACM;J AM ACAD DERMATOL;J CHEM INF MODEL;J CHEMINFORMATICS;MOL INFORM;NAT REV GENET;NUCLEIC ACIDS RES;PLOS COMPUT BIOL;PR MACH LEARN RES;PREPRINT;PROTEINS;SCIENCE | Gupta, Anvita;Zou, James | 2024-03-11
ER | [Anonymous];Abrusán, G;Apweiler, R;Arjovsky, M;Benner, S A;Buchan, D W A;Esteban C.;Ghahramani A.;Goodfellow, I;Gulrajani, I;Gupta A.;Gupta, A;Izadpanah, A;Killoran N.;Müller, A T;Olivecrona, M;Osokin A.;Papagianni, M;Rocklin, G J;Salimans T.;Segler, M H S;Waghu, F H;Wang, G S;Xu, D;Zhu J. | NK9RV | Stanford, CA USA;Stanford, CA USA. | 104 | null | 1 | null | null | Gupta, Anvita;Zou, James | NAT MACH INTELL | Stanford, CA USA |
Baulcombe, D C;Navarro, F J | 10.1021/acssynbio.8b00393 | null | 1155 16TH ST, NW, WASHINGTON, DC 20036 USA | 23306x204h4jv703o4x4k2f6o1i566zw2t3w4x | miRNA-Mediated Regulation of Synthetic Gene Circuits in the Green Alga <i>Chlamydomonas reinhardtii</i> | Univ Cambridge | null | Baulcombe, DC (corresponding author), Univ Cambridge, Dept Plant Sci, Cambridge CB2 3EA, England. | null | Baulcombe, David C;Navarro, Francisco J | Biochemical Research Methods | OpenPlant from the Biotechnology and Biological Sciences Research Council (BBSRC); Engineering and Physical Sciences Research Council (EPSRC); BBSRC [BB/L014130/1] Funding Source: UKRI | WOS | Baulcombe, D C | Univ Cambridge, Cambridge, England | 8 | <i>Chlamydomonas;Alga;circuits;gene;Green;in;miRNA-Mediated;of;regulation;reinhardtii</i>;synthetic;the | 1 | NAVARRO, FRANCISCO J. | AMER CHEMICAL SOC | Univ Cambridge, Dept Plant Sci, Cambridge CB2 3EA, England | Article | Univ Cambridge | WASHINGTON | null | null | Univ Cambridge | BBSRC;Engineering and Physical Sciences Research Council (EPSRC);OpenPlant from the Biotechnology and Biological Sciences Research Council (BBSRC) | Baulcombe, DC (corresponding author), Univ Cambridge, Dept Plant Sci, Cambridge CB2 3EA, England. | 370 | Baulcombe, David C;Navarro, Francisco J | 26 | 1 | 459,367,000,018 | BBSRC [BB/L014130/1] Funding Source: UKRI;Engineering and Physical Sciences Research Council (EPSRC);OpenPlant from the Biotechnology and Biological Sciences Research Council (BBSRC) | UK | ACS SYNTHETIC BIOLOGY | UK | null | null | Univ Cambridge, Dept Plant Sci, Cambridge CB2 3EA, England | 2161-5063 | Baulcombe, D C;Navarro, F J | FEB | dcb40@cam.ac.uk | Green Alga <i>Chlamydomonas reinhardtii</i>;miRNA-Mediated Regulation;synthetic gene circuits | 2 | J | Biochemistry & Molecular Biology | 20-24 nts;action;alga;ARTIFICIAL MICRORNAS;characterization;Chlamydomonas reinhardtii;CLEAVAGE;COMPLEMENTARITY;engineering;expression;flexible design;gene expression;gene expression pipeline;gene expression regulation small size;Green Alga <i>Chlamydomonas reinhardtii</i>;IDENTIFICATION;improved traits;late stage;mechanism;microRNAs (miRNAs);miRNA;miRNA decoys;miRNA-mediated gene expression regulation;miRNA-Mediated Regulation;miRNA-responsive 3'UTRs;miRNAs;new applications;progress;PROVIDES;RNA;ROBUSTNESS;role;self-regulatory loops;small RNA molecules;synthetic biology approach;Synthetic gene circuit;synthetic gene circuits;synthetic gene networks;synthetic miRNAs;SYSTEM;target predictability;tools;tools will;unicellular green alga Chlamydomonas reinhardtii;useful tools | Navarro, F J | ARTIFICIAL MICRORNAS;Chlamydomonas reinhardtii;CLEAVAGE;COMPLEMENTARITY;EXPRESSION;gene expression;IDENTIFICATION;MECHANISM;miRNA;PROGRESS;PROVIDES;RNA;Synthetic gene circuit;SYSTEM | 358 | [Navarro, Francisco J.; Baulcombe, David C.] Univ Cambridge, Dept Plant Sci, Cambridge CB2 3EA, England. | We would like to thank Ralph Bock (Max Planck Institute for Molecular Plant Physiology, Germany) for the UVM11 strain, Alison Smith and Jim Haseloff (University of Cambridge) for reagents and support, and Adrian Valli and Bruno Martins for critical reading of the manuscript. This work was supported by OpenPlant, which receives its funding from the Biotechnology and Biological Sciences Research Council (BBSRC) and the Engineering and Physical Sciences Research Council (EPSRC). D.C.B. is supported as the Royal Society Edward Penley Abraham Research Professor. | 20-24 nts;action;alga;characterization;engineering;flexible design;gene expression;gene expression pipeline;gene expression regulation small size;improved traits;late stage;microRNAs (miRNAs);miRNA decoys;miRNA-mediated gene expression regulation;miRNA-responsive 3'UTRs;miRNAs;new applications;robustness;role;self-regulatory loops;small RNA molecules;synthetic biology approach;synthetic gene networks;synthetic miRNAs;target predictability;tools;tools will;unicellular green alga Chlamydomonas reinhardtii;useful tools | 10.1002/wdev.223;10.1007/s10529-011-0590-z;10.1007/s11103-015-0425-8;10.1016/B978-0-12-370873-1.00008-3;10.1016/j.bbrc.2003.09.070;10.1016/j.biortech.2014.10.119;10.1016/j.cbpa.2012.05.192;10.1016/j.cell.2009.01.002;10.1016/j.cell.2009.01.035;10.1016/j.cell.2009.01.046;10.1016/j.cell.2017.09.049;10.1016/j.jbiotec.2012.05.010;10.1016/j.molcel.2011.08.023;10.1016/j.omtn.2018.09.009;10.1016/S1097-2765(02)00541-5;10.1021/acssynbio.8b00251;10.1021/sb4001504;10.1038/nature02874;10.1038/nature04785;10.1038/nature05903;10.1038/ncomms3364;10.1038/ng2079;10.1038/nrg1328;10.1038/nrg2504;10.1038/s41477-017-0024-6;10.1038/srep27810;10.1038/srep30620;10.1073/pnas.0506306102;10.1073/pnas.1710597114;10.1073/pnas.2133841100;10.1074/jbc.M111.316729;10.1093/nar/gkq091;10.1093/nar/gkw151;10.1101/gad.1543507;10.1101/gr.199703.115;10.1104/pp.117.2.455;10.1105/tpc.105.039834;10.1105/tpc.111.094144;10.1105/tpc.113.120972;10.1105/tpc.15.00465;10.1105/tpc.9.6.925;10.1111/j.1365-313X.2007.03328.x;10.1111/j.1365-313X.2008.03746.x;10.1111/j.1365-313X.2008.03758.x;10.1111/j.1365-313X.2008.03767.x;10.1111/nph.13532;10.1111/tpj.12354;10.1111/tpj.12606;10.1111/tpj.12781;10.1126/science.1076311;10.1126/science.1143609;10.1126/science.1205527;10.1126/science.aaa1738;10.1146/annurev.arplant.52.1.363;10.1186/1752-0509-6-131;10.1186/gb-2011-12-4-221;10.1261/rna.2414110;10.1261/rna.7135204;10.1371/journal.pone.0003647;10.1371/journal.pone.0016765;10.1371/journal.pone.0021330;[10.1038/NMETH.3100, 10.1038/nmeth.3100] | Univ Cambridge | Baulcombe, D C;Navarro, F J | Navarro, F J: Univ Cambridge, Dept Plant Sci, Cambridge CB2 3EA, England | null | BB/L014130/1 | 66 | null | UK | Univ Cambridge | Navarro, Francisco J | Green Submitted, Green Accepted | ARTIFICIAL MICRORNAS;CLEAVAGE;COMPLEMENTARITY;EXPRESSION;IDENTIFICATION;MECHANISM;PROGRESS;PROVIDES;RNA;SYSTEM | Navarro, Francisco J.; Baulcombe, David C.; | null | Univ Cambridge, Dept Plant Sci, Cambridge CB2 3EA, England | Univ Cambridge, Dept Plant Sci, Cambridge CB2 3EA, England | null | Chlamydomonas reinhardtii;gene expression;miRNA;Synthetic gene circuit | 2 | 1996;1997;1998;2001;2002;2003;2004;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017;2018 | 12 | Univ Cambridge, Dept Plant Sci, Cambridge CB2 3EA, England | ACS Synth. Biol. | Baulcombe, David C | AMER CHEMICAL SOC | (miRNAs);,;20-24;3'UTRs;a;action;addition;alga;and;applications;apply;approach;as;at;based;be;biology;build;can;characterization;characterize;Chlamydomonas;decoys;design;engineering;expression;facilitate;features;fine-tuning;flexible;for;gene;green;harnessed;have;improved;in;increase;is;late;loops;make;many;microRNAs;miRNA;miRNA-mediated;miRNA-responsive;miRNAs;molecules;networks;new;nts;of;on;pipeline;predictability;regulation;reinhardtii;RNA;robustness;role;self-regulatory;size;small;stage;such;synthetic;target;that;the;their;them;then;these;this;to;tools;traits;unicellular;used;useful;we;will;work | Univ Cambridge | MicroRNAs (miRNAs), small RNA molecules of 20-24 nts, have many features that make them useful tools for gene expression regulation small size, flexible design, target predictability, and action at a late stage of the gene expression pipeline. In addition, their role in fine-tuning gene expression can be harnessed to increase robustness of synthetic gene networks. In this work, we apply a synthetic biology approach to characterize miRNA-mediated gene expression regulation in the unicellular green alga Chlamydomonas reinhardtii. This characterization is then used to build tools based on miRNAs, such as synthetic miRNAs, miRNA-responsive 3'UTRs, miRNA decoys, and self-regulatory loops. These tools will facilitate the engineering of gene expression for new applications and improved traits in this alga. | null | ARTIFICIAL MICRORNAS;CLEAVAGE;COMPLEMENTARITY;EXPRESSION;IDENTIFICATION;MECHANISM;PROGRESS;PROVIDES;RNA;SYSTEM | 3 | null | Chlamydomonas reinhardtii;gene expression;miRNA;Synthetic gene circuit | 25 | ARTIFICIAL MICRORNAS;CHLAMYDOMONAS-REINHARDTII;CLEAVAGE;COMPLEMENTARITY;EXPRESSION;GENE-EXPRESSION;IDENTIFICATION;MECHANISM;miRNA;PROGRESS;PROVIDES;RNA;synthetic gene circuits;SYSTEM | WOS:000459367000018 | Univ Cambridge, Cambridge, England | UK | 2,019 | null | 0000-0002-9332-0737 | null | null | English | null | ACS SYNTH BIOL;ANNU REV PLANT PHYS;BIOCHEM BIOPH RES CO;BIORESOURCE TECHNOL;BIOTECHNOL BIOFUELS;BIOTECHNOL LETT;BMC SYST BIOL;CELL;CHLAMYDOMONAS SOURCE;CURR OPIN CHEM BIOL;GENE DEV;GENOME BIOL;GENOME RES;J BIOL CHEM;J BIOTECHNOL;MOL CELL;MOL GEN GENET;MOL THER-NUCL ACIDS;NAT COMMUN;NAT GENET;NAT METHODS;NAT PLANTS;NAT REV GENET;NATURE;NEW PHYTOL;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PLANT CELL;PLANT CELL PHYSL;PLANT J;PLANT MOL BIOL;PLANT PHYSIOL;PLOS ONE;RNA;SCI REP-UK;SCIENCE;SYNTH BIOL SCOP APPL;WIRES DEV BIOL | Baulcombe, David C;Navarro, Francisco J | 2024-03-11
ER | Axtell, M J;Baek, K;Barahimipour, R;Bartel, D P;Baulcombe, D;Benenson, Y;Bloom, R J;Bosia, C;Burgess, S J;Cai, X Z;Carthew, R W;Cerutti, H;Chung, B Y W;Crozet, P;Ebert, M S;Engler, C;Ferenczi, A;Ferrante, P;Franco-Zorrilla, J M;Ghildiyal, M;Harris E.H.;Harris, E H;Hollensen, A K;Hu, J L;Ivashuta, S;Kim, E J;Kitney, R;Li, X B;Liang, J C;Lin, S L;Liu, Q K;Llave, C;Mangan, S;Mckeague, M;Merchant, S S;Molnar, A;Molnár, A;Murphy, K F;Neupert, J;Newman, J R S;Nissim, L;Ossowski, S;Palombella, A L;Patron, N;Reichel, M;Scaife, M A;Schmiedel, J M;Schwab, R;Shin, S E;Siciliano, V;Stegmeier, F;Steinkraus, B R;Stevens, D R;Szczesniak M., W;Valli, A A;Voinnet, O;Wang, C;Weber, E;Xie, Z;Yamasaki, T;Yan, J;Zeng, Y;Zhao, T | HM3IM | Cambridge, England | 12 | null | 1 | null | 30,624,905 | Baulcombe, David C;Navarro, Francisco J | ACS SYNTH BIOL | Cambridge, England |
Fukuda, N;Honda, S | 10.1016/bs.mie.2019.02.036 | null | 525 B STREET, SUITE 1900, SAN DIEGO, CA 92101-4495 USA | 6e6j1m35l3q15443c466r6d1h6i5a2m5ks2l1m | Synthetic gene expression circuits regulating sexual reproduction | Natl Inst Adv Ind Sci & Technol | Methods in Enzymology | Fukuda, N (corresponding author), Natl Inst Adv Ind Sci & Technol, Biomed Res Inst, Tsukuba, Ibaraki, Japan. | null | Fukuda, Nobuo;Honda, Shinya | Biochemical Research Methods;Biochemistry & Molecular Biology;Cell Biology | JSPS KAKENHI [25820406, 16K14497, 18K05424]; Grants-in-Aid for Scientific Research [16K14497, 18K05424, 25820406] Funding Source: KAKEN | WOS | Fukuda, N | Natl Inst Adv Ind Sci & Technol, Ibaraki, Japan | 621 | circuits;expression;gene;regulating;reproduction;sexual;synthetic | 1 | Fukuda, Nobuo;Honda, Shinya | ELSEVIER ACADEMIC PRESS INC | Natl Inst Adv Ind Sci & Technol, Biomed Res Inst, Tsukuba, Ibaraki, Japan | Review; Book Chapter | Natl Inst Adv Ind Sci & Technol | SAN DIEGO | null | null | Natl Inst Adv Ind Sci & Technol | Grants-in-Aid for Scientific Research;JSPS KAKENHI | Fukuda, N (corresponding author), Natl Inst Adv Ind Sci & Technol, Biomed Res Inst, Tsukuba, Ibaraki, Japan. | 30 | Fukuda, Nobuo;Honda, Shinya | 11 | 1 | 500,713,500,003 | Grants-in-Aid for Scientific Research [16K14497, 18K05424, 25820406] Funding Source: KAKEN;JSPS KAKENHI [25820406, 16K14497, 18K05424] | Japan | CHEMICAL AND SYNTHETIC BIOLOGY APPROACHES TO UNDERSTAND CELLULAR FUNCTIONS - PT A | Japan | null | null | Natl Inst Adv Ind Sci & Technol, Biomed Res Inst, Tsukuba, Ibaraki, Japan | 0076-6879 | Fukuda, N;Honda, S | null | nob-fukuda@aist.go.jp | synthetic gene expression circuits regulating sexual reproduction | 2 | S | Biochemistry & Molecular Biology;Cell Biology | alternative methods;ancient times;attractive means;basic guide;budding yeast Saccharomyces cerevisiae;CASSETTES;chapter;combine strain traits;common crossbreeding strategies;crossbreds via mating;crossbreeding;fermentative production;genetic modification;HETEROZYGOSITY;industry exhibit low sporulation rates;isolated yeast strains;isolation;limited crossbreeding efficiency;MAT alpha haploids via sporulation;MAT locus;MATa;MATa/alpha diploids;methods;modification;mutagenesis;numerous technical challenges;parental yeasts;protoplast fusion;purpose;researchers;sequence;several approaches;sexual reproduction;sexual reproduction machinery;sporulation;synthetic gene expression circuits;synthetic gene expression circuits regulating sexual reproduction;TRANSFORMATION;variety;yeast;yeast crossbreeding;yeast resources;yeast strains;yeast traits | Fukuda, N | CASSETTES;HETEROZYGOSITY;TRANSFORMATION | 17 | [Fukuda, Nobuo; Honda, Shinya] Natl Inst Adv Ind Sci & Technol, Biomed Res Inst, Tsukuba, Ibaraki, Japan. | This work was supported by JSPS KAKENHI Grant Number 25820406, 16K14497 and 18K05424. | alternative methods;ancient times;attractive means;basic guide;budding yeast Saccharomyces cerevisiae;chapter;combine strain traits;common crossbreeding strategies;crossbreds via mating;crossbreeding;fermentative production;genetic modification;industry exhibit low sporulation rates;isolated yeast strains;isolation;limited crossbreeding efficiency;MAT alpha haploids via sporulation;MAT locus;MATa;MATa/alpha diploids;methods;modification;mutagenesis;numerous technical challenges;parental yeasts;protoplast fusion;purpose;researchers;sequence;several approaches;sexual reproduction;sexual reproduction machinery;sporulation;synthetic gene expression circuits;variety;yeast;yeast crossbreeding;yeast resources;yeast strains;yeast traits | 10.1016/0027-5107(90)90024-X;10.1016/0092-8674(82)90418-4;10.1021/acssynbio.7b00056;10.1021/acssynbio.8b00020;10.1021/sb400016j;10.1038/s41467-018-05106-7;10.1093/nar/20.6.1425;10.1111/1567-1364.12161;10.1128/MCB.01071-10;10.1128/MCB.11.10.5372;10.1146/annurev.genet.32.1.561;10.1186/1754-1611-7-27;10.1186/s13068-015-0216-0;10.1186/s13568-016-0216-x;10.1371/journal.pone.0068094;10.1534/genetics.108.089250;10.1534/genetics.166.2.653;10.19082/3592;10.2323/jgam.39.285 | Natl Inst Adv Ind Sci & Technol | Fukuda, N;Honda, S | Fukuda, N: Natl Inst Adv Ind Sci & Technol, Biomed Res Inst, Tsukuba, Ibaraki, Japan | Fukuda, Nobuo;Honda, Shinya | 16K14497;18K05424;25820406 | 22 | 978-0-12-818117-1 | Japan | Natl Inst Adv Ind Sci & Technol | Fukuda, Nobuo | null | CASSETTES;HETEROZYGOSITY;TRANSFORMATION | Fukuda, Nobuo; Honda, Shinya; | null | Natl Inst Adv Ind Sci & Technol, Biomed Res Inst, Tsukuba, Ibaraki, Japan | Natl Inst Adv Ind Sci & Technol, Biomed Res Inst, Tsukuba, Ibaraki, Japan | null | null | null | 1982;1983;1990;1991;1992;1993;1998;2000;2004;2008;2011;2013;2014;2015;2016;2017;2018 | 4 | Natl Inst Adv Ind Sci & Technol, Biomed Res Inst, Tsukuba, Ibaraki, Japan | Methods Enzymol. | Honda, Shinya | ELSEVIER ACADEMIC PRESS INC | ,;a;acquire;alpha;alternative;an;ancient;and;approaches;are;as;attempting;attractive;based;basic;been;budding;cerevisiae;challenges;chapter;circuits;combine;common;construction;convert;crossbreds;crossbreeding;developed;diploids;directly;efficiency;enable;exhibit;expand;expression;fermentative;for;fusion;gene;genetic;guide;haploids;has;have;here;improve;in;including;industry;is;isolated;isolation;limited;locus;low;machinery;many;MAT;MATa;MATa/alpha;mate;mating;means;methods;modification;most;mutagenesis;numerous;of;on;parental;production;protoplast;provide;provides;purpose;rates;reproduction;require;researchers;resources;resulting;review;Saccharomyces;sequence;several;sexual;since;sporulation;strain;strains;strategies;subsequently;synthetic;technical;the;these;this;times;to;traits;unable;unfortunately;used;using;utilized;variety;via;we;who;widely;yeast;yeasts | Natl Inst Adv Ind Sci & Technol | The budding yeast Saccharomyces cerevisiae has been widely utilized in fermentative production since ancient times. Several approaches for modification of yeast traits have been developed, including mutagenesis, protoplast fusion, and genetic modification. Crossbreeding provides an attractive means to improve and combine strain traits based on sexual reproduction. Common crossbreeding strategies require the isolation of MATa and MAT alpha haploids via sporulation, as most of parental yeasts are MATa/alpha diploids and unable to mate directly. Unfortunately, many yeast strains used in industry exhibit low sporulation rates resulting in limited crossbreeding efficiency and numerous technical challenges. Here, we review the construction of synthetic gene expression circuits as a means to provide alternative methods for sporulation for yeast crossbreeding. These methods enable researchers to convert the sequence of the MAT locus and subsequently acquire crossbreds via mating of isolated yeast strains. The purpose of this chapter is to provide a basic guide for researchers who are attempting to expand the variety of yeast resources using the sexual reproduction machinery of yeast. | J-1872-2018;K-6894-2016 | CASSETTES;HETEROZYGOSITY;TRANSFORMATION | 4 | null | null | 14 | CASSETTES;HETEROZYGOSITY;TRANSFORMATION | WOS:000500713500003 | Natl Inst Adv Ind Sci & Technol, Ibaraki, Japan | Japan | 2,019 | null | 0000-0001-7053-7194;0000-0002-7878-3944 | null | Shukla, AK | English | null | ACS SYNTH BIOL;AMB EXPRESS;ANNU REV GENET;BIOTECHNOL BIOFUELS;CELL;CURR TOP DEV BIOL;Electron Physician;FEMS YEAST RES;GENETICS;J Biol Eng;J GEN APPL MICROBIOL;MOL CELL BIOL;MUTAT RES;NAT COMMUN;NUCLEIC ACIDS RES;PLOS ONE;YEAST | Fukuda, Nobuo;Honda, Shinya | 2024-03-11
ER | Andersen, M R;Botstein, D;Brachmann, C B;Dashko, S;Duan, S F;Fukuda, N;Gelfand, B;Gietz, D;Haber, J E;Herskowitz, I;Hiraoka, M;Kumaran, R;Mayer, V W;Ogata, T;Ray, B L;Salari Roshanak;Snoek, T;Strathern, J N | BO1KX | Ibaraki, Japan | 4 | null | 1 | null | 31,128,777 | Fukuda, Nobuo;Honda, Shinya | METHOD ENZYMOL | Ibaraki, Japan |
Lu, T K;Purcell, O;Siuti, P;Wang, J | 10.1038/s41467-018-07144-7 | 4942 | HEIDELBERGER PLATZ 3, BERLIN, 14197, GERMANY | 4i45n5t6f6p2d73366746f2yg65205z4w3f59 | Encryption and steganography of synthetic gene circuits | MIT | null | Lu, TK (corresponding author), MIT, Dept Biol Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA.;Lu, TK (corresponding author), MIT, Dept Elect Engn & Comp Sci, Res Lab Elect, 77 Massachusetts Ave, Cambridge, MA 02139 USA.;Lu, TK (corresponding author), MIT, Synthet Biol Ctr, 500 Technol Sq, Cambridge, MA 02139 USA. | null | Lu, Timothy K;Purcell, Oliver;Siuti, Piro;Wang, Jerry | Multidisciplinary Sciences | Defense Advanced Research Projects Agency | WOS | Lu, T K | MIT, Cambridge, MA USA | 9 | and;circuits;encryption;gene;of;steganography;synthetic | 1 | Purcell, Oliver | NATURE PORTFOLIO | MIT, Dept Biol Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA;MIT, Dept Elect Engn & Comp Sci, Res Lab Elect, 77 Massachusetts Ave, Cambridge, MA 02139 USA;MIT, Synthet Biol Ctr, 500 Technol Sq, Cambridge, MA 02139 USA;MIT, Synthet Biol Ctr, 500 Technol Sq, Cambridge, MA 02139 USA.; Lu, TK (corresponding author), MIT, Dept Biol Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA.; Lu, TK (corresponding author), MIT, Dept Elect Engn & Comp Sci, Res Lab Elect, 77 Massachusetts Ave, Cambridge, MA 02139 USA | Article | MIT | BERLIN | null | null | MIT;Synthet Biol Ctr | Defense Advanced Research Projects Agency | Lu, TK (corresponding author), MIT, Synthet Biol Ctr, 500 Technol Sq, Cambridge, MA 02139 USA.; Lu, TK (corresponding author), MIT, Dept Biol Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA.; Lu, TK (corresponding author), MIT, Dept Elect Engn & Comp Sci, Res Lab Elect, 77 Massachusetts Ave, Cambridge, MA 02139 USA. | null | Lu, Timothy K;Purcell, Oliver;Siuti, Piro;Wang, Jerry | 18 | 3 | 450,924,300,004 | Defense Advanced Research Projects Agency | USA | NATURE COMMUNICATIONS | USA;USA.; | null | null | MIT, Synthet Biol Ctr, 500 Technol Sq, Cambridge, MA 02139 USA | null | Lu, T K;Purcell, O;Siuti, P;Wang, J | NOV 22 | timlu@mit.edu | encryption;steganography;synthetic gene circuits | 4 | J | Science & Technology - Other Topics | approach;cells;circuit structure;circuit topology;CIRCUITS;CODE;emerging area;encryption;engineer living cells;first uses encryption;function;genes;goal;integration;intellectual property;interconnections;logic;MEMORY;overlapping uni-directional recombinase sites;PARTS;practicality;present two different approaches;relative strengths;research;second uses steganography;steganography;strategies;synthetic biologists use artificial gene circuits;synthetic circuits;synthetic gene circuits;synthetic genetic codes;third approach;unauthorized third party;weaknesses | Purcell, O | CODE;INTEGRATION;LOGIC;MEMORY;PARTS | null | [Purcell, Oliver; Wang, Jerry; Siuti, Piro; Lu, Timothy K.] MIT, Synthet Biol Ctr, 500 Technol Sq, Cambridge, MA 02139 USA. [Lu, Timothy K.] MIT, Dept Biol Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA. [Lu, Timothy K.] MIT, Dept Elect Engn & Comp Sci, Res Lab Elect, 77 Massachusetts Ave, Cambridge, MA 02139 USA. | This work was supported by the Defense Advanced Research Projects Agency. MK01 and MK02 cells were kind gifts from M. Kogenaru. The bi-stable switch was gift from J. Collins (MIT). We would like to thank J. W. Purcell for help with experimental work, and N. Roquet and F. Farzafard for reading and helping revise the manuscript. | approach;cells;circuit structure;circuit topology;circuits;emerging area;engineer living cells;first uses encryption;function;genes;goal;intellectual property;interconnections;overlapping uni-directional recombinase sites;practicality;present two different approaches;relative strengths;research;second uses steganography;strategies;synthetic biologists use artificial gene circuits;synthetic circuits;synthetic gene circuits;synthetic genetic codes;third approach;unauthorized third party;weaknesses | 10.1002/anie.201105016;10.1007/0-387-25871-X_5;10.1016/j.copbio.2006.09.001;10.1016/j.jmb.2003.09.082;10.1016/S1097-2765(03)00444-1;10.1021/acssynbio.5b00216;10.1021/ja2054034;10.1038/35002131;10.1038/nature08817;10.1038/nature12148;10.1038/nbt.2401;10.1038/nbt.2510;10.1038/nbt1314;10.1038/nchembio.1680;10.1038/nchembio719;10.1038/ncomms7989;10.1038/nrm2005;10.1038/s41565-017-0004-z;10.1073/pnas.0900267106;10.1073/pnas.090527097;10.1073/pnas.1202344109;10.1093/nar/26.2.391;10.1099/mic.0.066308-0;10.1126/science.1205527;10.1126/science.1221761;10.1126/science.1232758;10.1126/science.aad8559;10.1126/science.aaf3639;10.1145/2508859.2516656;10.1186/1754-1611-8-2;[10.1038/NMETH.3147, 10.1038/nmeth.3147] | MIT | Lu, T K;Purcell, O;Siuti, P;Wang, J | Purcell, O: MIT, Synthet Biol Ctr, 500 Technol Sq, Cambridge, MA 02139 USA | Lu, Timothy K | null | 34 | null | USA | MIT | Purcell, Oliver | Green Published, gold | CODE;INTEGRATION;LOGIC;MEMORY;PARTS | Purcell, Oliver; Wang, Jerry; Siuti, Piro; Lu, Timothy K.; | null | MIT, Dept Biol Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA;MIT, Dept Elect Engn & Comp Sci, Res Lab Elect, 77 Massachusetts Ave, Cambridge, MA 02139 USA;MIT, Synthet Biol Ctr, 500 Technol Sq, Cambridge, MA 02139 USA | MIT, Dept Biol Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA;MIT, Dept Elect Engn & Comp Sci, Res Lab Elect, 77 Massachusetts Ave, Cambridge, MA 02139 USA;MIT, Synthet Biol Ctr, 500 Technol Sq, Cambridge, MA 02139 USA | 2041-1723 | null | null | 1998;2000;2002;2003;2004;2005;2006;2007;2009;2010;2011;2012;2013;2014;2015;2016;2018 | 7 | MIT, Dept Biol Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA;MIT, Dept Elect Engn & Comp Sci, Res Lab Elect, 77 Massachusetts Ave, Cambridge, MA 02139 USA;MIT, Synthet Biol Ctr, 500 Technol Sq, Cambridge, MA 02139 USA | Nat. Commun. | Lu, Timothy K | NATURE PORTFOLIO | ,;:;a;adding;also;an;and;approach;approaches;area;artificial;as;be;become;biologists;by;cells;circuit;circuits;codes;commercialized;contained;control;design;desirable;determine;different;difficult;discuss;each;emerging;encryption;engineer;engineered;first;for;function;further;gene;genes;genetic;goal;here;hide;implementation;important;in;increasingly;inspire;intellectual;interconnections;into;introduce;it;living;making;mask;more;obscure;of;overlapping;party;practicality;present;property;protect;recombinase;relative;research;scramble;second;sites;steganography;strategies;strengths;structure;synthetic;the;these;third;this;to;topology;two;unauthorized;uni-directional;use;uses;we;weaknesses;will;with | MIT | Synthetic biologists use artificial gene circuits to control and engineer living cells. As engineered cells become increasingly commercialized, it will be desirable to protect the intellectual property contained in these circuits. Here, we introduce strategies to hide the design of synthetic gene circuits, making it more difficult for an unauthorized third party to determine circuit structure and function. We present two different approaches: the first uses encryption by overlapping uni-directional recombinase sites to scramble circuit topology and the second uses steganography by adding genes and interconnections to obscure circuit topology. We also discuss a third approach: to use synthetic genetic codes to mask the function of synthetic circuits. For each approach, we discuss relative strengths, weaknesses, and practicality of implementation, with the goal to inspire further research into this important and emerging area. | G-4267-2012 | CODE;INTEGRATION;LOGIC;MEMORY;PARTS | 0 | null | null | 10 | CODE;INTEGRATION;LOGIC;MEMORY;PARTS | WOS:000450924300004 | MIT, Cambridge, MA USA | USA | 2,018 | null | 0000-0002-1652-8702 | null | null | English | null | ACS SYNTH BIOL;ANGEW CHEM INT EDIT;CIRC CAM TECHN;COMPLEXITY CHEM BIOL;CURR OPIN BIOTECH;J AM CHEM SOC;J Biol Eng;J MOL BIOL;MICROBIOL-SGM;MOL CELL;NAT BIOTECHNOL;NAT CHEM BIOL;NAT COMMUN;NAT METHODS;NAT NANOTECHNOL;NAT REV MOL CELL BIO;NATURE;NUCLEIC ACIDS RES;P ACM SIGSAC C COMP;P NATL ACAD SCI USA;PERMUTATION MATHWORL;SCIENCE;US patent | Lu, Timothy K;Purcell, Oliver;Siuti, Piro;Wang, Jerry | 2024-03-11
ER | [Anonymous];An, W L;Bonchev, D;Bonnet, J;Caliando, B J;Chin, J W;Clark W.;Cleto, S;Daniel, R;Gardner, T S;Ghosh, P;Greiss, S;Groth, A C;Inside Secure;Kogenaru, M;Lapique, N;Lou, C B;Neumann, H;Nunes-Düby, S E;Ostrov, N;Rackham, O;Roquet, N;Siuti, P;Voigt, C A;Wang, K H;Weisstein E. W.;Wright, O;Xie, J M;Xie, Z;Yang, L | HB3CB | Cambridge, MA USA;Cambridge, MA USA. | 7 | null | 1 | null | 30,467,337 | Lu, Timothy K;Purcell, Oliver;Siuti, Piro;Wang, Jerry | NAT COMMUN | Cambridge, MA USA |
Balázsi, G;Charlebois, D A;Hauser, K;Marshall, S | 10.1073/pnas.1810858115 | null | 2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA | 126x383u173n224y202x6o5n1h3aa3r5r1a42 | Multiscale effects of heating and cooling on genes and gene networks | SUNY Stony Brook | null | Balázsi, G (corresponding author), SUNY Stony Brook, Louis & Beatrice Laufer Ctr Phys & Quantitat Biol, Stony Brook, NY 11794 USA. | null | Balazsi, Gabor;Charlebois, Daniel A;Hauser, Kevin;Marshall, Sylvia | Multidisciplinary Sciences | Natural Sciences and Engineering Research Council of Canada Postdoctoral Fellowship [PDF-453977-2014]; NVIDIA Corporation Titan Xp GPU grant; NIH National Research Service Award Fellowship [F31-GM101946]; National Science Foundation Alliances for Graduate Education; Professoriate-Transformation Fellowship [HRD-1311318]; NIH/National Institute of General Medical Sciences Maximizing Investigators' Research Award [R35GM122561]; Laufer Center for Physical and Quantitative Biology | WOS | Balázsi, G | SUNY Stony Brook, Stony Brook, NY USA | 115 | and;cooling;Effects;gene;genes;heating;multiscale;networks;of;on | 1 | Charlebois, Daniel | NATL ACAD SCIENCES | SUNY Stony Brook, Dept Biochem & Cell Biol, Stony Brook, NY 11794 USA;SUNY Stony Brook, Dept Biomed Engn, Stony Brook, NY 11794 USA;SUNY Stony Brook, Louis & Beatrice Laufer Ctr Phys & Quantitat Biol, Stony Brook, NY 11794 USA | Article | SUNY Stony Brook | WASHINGTON | null | null | SUNY Stony Brook | Laufer Center for Physical and Quantitative Biology;National Science Foundation Alliances for Graduate Education;Natural Sciences and Engineering Research Council of Canada Postdoctoral Fellowship;NIH National Research Service Award Fellowship;NIH/National Institute of General Medical Sciences Maximizing Investigators' Research Award;NVIDIA Corporation Titan Xp GPU grant;Professoriate-Transformation Fellowship | Balázsi, G (corresponding author), SUNY Stony Brook, Louis & Beatrice Laufer Ctr Phys & Quantitat Biol, Stony Brook, NY 11794 USA. | E10806 | Balazsi, Gabor;Charlebois, Daniel A;Hauser, Kevin;Marshall, Sylvia | 19 | 3 | 449,459,000,033 | Laufer Center for Physical and Quantitative Biology;National Science Foundation Alliances for Graduate Education;Natural Sciences and Engineering Research Council of Canada Postdoctoral Fellowship [PDF-453977-2014];NIH National Research Service Award Fellowship [F31-GM101946];NIH/National Institute of General Medical Sciences Maximizing Investigators' Research Award [R35GM122561];NVIDIA Corporation Titan Xp GPU grant;Professoriate-Transformation Fellowship [HRD-1311318] | USA | PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA | USA | null | null | SUNY Stony Brook, Louis & Beatrice Laufer Ctr Phys & Quantitat Biol, Stony Brook, NY 11794 USA | 0027-8424 | Balázsi, G;Charlebois, D A;Hauser, K;Marshall, S | NOV 6 | gabor.balazsi@stonybrook.edu | cooling;gene networks;genes;heating;multiscale effects | 4 | J | Science & Technology - Other Topics | agents;aid future applications;arrest;Arrhenius scaling;cell fate choice;cell fate decision;cellular decision;cellular protection;conformational dynamics;cooling;cooling affect expression;cope;corrupt gene;difficulties;dramatic gene expression bimodality;Effects;experimental observations;expression;FEEDBACK;feedback regulation;GENE;gene expression;gene network function;gene networks;genes;growth arrest;heating;isogenic cell populations;microbes;molecular-dynamics simulations;multiscale effects;multiscale models;noise;nonoptimal temperatures;nonstandard temperatures;ORGANISMS;overall;population dynamics;predictable ways;PROMOTER;reaction rates;regulatory networks;resistant cells;Saccharomyces cerevisiae;SACCHAROMYCES-CEREVISIAE;SHOCK RESPONSE;single genes;stress resistance;Synthetic gene circuit;synthetic gene circuits;temperature;temperature changes;TEMPERATURE COMPENSATION;temperature-dependent growth rates;TetR repressor;toggle switch;TRANSCRIPTION;understanding;yeast | Charlebois, D A | cellular decision;EXPRESSION;FEEDBACK;feedback regulation;NOISE;PROMOTER;REGULATORY NETWORKS;SACCHAROMYCES-CEREVISIAE;SHOCK RESPONSE;Synthetic gene circuit;temperature;TEMPERATURE COMPENSATION;toggle switch;TRANSCRIPTION;YEAST | E10797 | [Charlebois, Daniel A.; Hauser, Kevin; Marshall, Sylvia; Balazsi, Gabor] SUNY Stony Brook, Louis & Beatrice Laufer Ctr Phys & Quantitat Biol, Stony Brook, NY 11794 USA. [Marshall, Sylvia] SUNY Stony Brook, Dept Biochem & Cell Biol, Stony Brook, NY 11794 USA. [Balazsi, Gabor] SUNY Stony Brook, Dept Biomed Engn, Stony Brook, NY 11794 USA. | We thank Todd B. Reynolds for the TBR1 strain, Kevin J. Verstrepen for the KV2695 strain, Sasha F. Levy for the Tsl1-GFP yeast strain, and Lin Chen for inserting the reporter construct into the TBR1 strain. We also thank Kingshuk Ghosh, Andre Ribeiro, Harold Bien, Oleksandra Romanyshyn, Teresa Charlebois, and the Paola Picotti group for helpful discussions; Tamas Szekely, Jr., and Zhihao Cai for acquiring the microfluidics time-lapse images; and the staff at the Flow Cytometry Core Research Facility at the Stony Brook University Hospital for assistance with cell-sorting experiments. This research was supported by a Natural Sciences and Engineering Research Council of Canada Postdoctoral Fellowship (PDF-453977-2014) and NVIDIA Corporation Titan Xp GPU grant (to D.A.C.), NIH National Research Service Award Fellowship (F31-GM101946) and National Science Foundation Alliances for Graduate Education and the Professoriate-Transformation Fellowship (HRD-1311318) (to K.H.), NIH/National Institute of General Medical Sciences Maximizing Investigators' Research Award Grant R35GM122561 (to G.B.), and the Laufer Center for Physical and Quantitative Biology. | agents;aid future applications;arrest;Arrhenius scaling;cell fate choice;cell fate decision;cellular protection;conformational dynamics;cooling;cooling affect expression;cope;corrupt gene;difficulties;dramatic gene expression bimodality;effects;experimental observations;gene;gene expression;gene network function;genes;growth arrest;heating;isogenic cell populations;microbes;molecular-dynamics simulations;multiscale models;nonoptimal temperatures;nonstandard temperatures;organisms;overall;population dynamics;predictable ways;reaction rates;resistant cells;Saccharomyces cerevisiae;single genes;stress resistance;synthetic gene circuits;temperature changes;temperature-dependent growth rates;TetR repressor;understanding | 10.1002/(SICI)1521-1878(199805)20:5<433::AID-BIES10>3.0.CO;2-2;10.1002/biot.201200085;10.1006/jmbi.1994.1468;10.1007/s10867-012-9264-x;10.1016/0378-1119(83)90046-X;10.1016/j.bpj.2011.05.059;10.1016/j.ceb.2013.07.007;10.1016/j.cell.2009.12.001;10.1016/j.cell.2013.02.050;10.1016/j.cell.2014.02.033;10.1016/j.cell.2016.03.006;10.1016/j.celrep.2014.05.018;10.1016/j.molcel.2006.11.003;10.1016/j.molcel.2010.10.006;10.1016/S0022-2836(02)00994-4;10.1016/S0092-8674(03)00346-5;10.1021/acssynbio.5b00154;10.1021/jp0674468;10.1038/346329a0;10.1038/35002125;10.1038/35002131;10.1038/35014651;10.1038/msb.2011.21;10.1038/msb4100173;10.1038/nature01546;10.1038/nature04194;10.1038/nature04640;10.1038/nature04785;10.1038/nature07389;10.1038/nature09937;10.1038/nchembio.1411;10.1038/nchembio.218;10.1038/s41559-016-0016;10.1038/sj/cdd/4400942;10.1042/BJ20060166;10.1046/j.1365-2958.1999.01389.x;10.1073/pnas.0307571101;10.1073/pnas.0408031102;10.1073/pnas.0608451104;10.1073/pnas.0809901106;10.1073/pnas.1114477108;10.1073/pnas.1316298111;10.1073/pnas.1332628100;10.1073/pnas.1508521112;10.1073/pnas.1510328112;10.1073/pnas.1514383113;10.1073/pnas.1517109113;10.1074/jbc.R117.804641;10.1091/mbc.11.12.4241;10.1093/femsle/fnv082;10.1093/nar/25.14.2723;10.1093/nar/gkn545;10.1093/nar/gks583;10.1093/nar/gkv1091;10.1103/PhysRevE.89.052708;10.1109/CDC.2013.6760078;10.1111/j.1365-2958.2012.08192.x;10.1126/science.1154456;10.1126/science.1158684;10.1126/science.1189015;10.1126/science.1192588;10.1126/science.291.5505.878;10.1126/science.aai7825;10.1128/AEM.71.8.4531-4538.2005;10.1128/JB.184.18.5058-5066.2002;10.1128/MCB.13.2.1034;10.1128/MMBR.05018-11;10.1128/MMBR.69.2.326-356.2005;10.1146/annurev.mi.48.100194.002021;10.1186/1472-6750-7-6;10.1186/s12867-015-0048-2;10.1371/journal.pbio.1001325;10.1371/journal.pcbi.1002187;10.1371/journal.pcbi.1002480;10.1371/journal.pcbi.1003979;10.1371/journal.pcbi.1005174;10.1371/journal.pgen.1000673;10.15252/msb.20156185;10.1534/genetics.111.128033;10.1534/genetics.111.130765;10.3109/07420529709001471 | SUNY Stony Brook | Balázsi, G;Charlebois, D A;Hauser, K;Marshall, S | Charlebois, D A: SUNY Stony Brook, Louis & Beatrice Laufer Ctr Phys & Quantitat Biol, Stony Brook, NY 11794 USA | Charlebois, Daniel | F31-GM101946;HRD-1311318;PDF-453977-2014;R35GM122561 | 84 | null | USA | SUNY Stony Brook | Charlebois, Daniel A | hybrid, Green Published, Green Submitted | EXPRESSION;FEEDBACK;PROMOTER;REGULATORY NETWORKS;SACCHAROMYCES-CEREVISIAE;SHOCK RESPONSE;TEMPERATURE COMPENSATION;TOGGLE SWITCH;TRANSCRIPTION;YEAST | Charlebois, Daniel A.; Hauser, Kevin; Marshall, Sylvia; Balazsi, Gabor; | null | SUNY Stony Brook, Dept Biochem & Cell Biol, Stony Brook, NY 11794 USA;SUNY Stony Brook, Dept Biomed Engn, Stony Brook, NY 11794 USA;SUNY Stony Brook, Louis & Beatrice Laufer Ctr Phys & Quantitat Biol, Stony Brook, NY 11794 USA | SUNY Stony Brook, Dept Biochem & Cell Biol, Stony Brook, NY 11794 USA;SUNY Stony Brook, Dept Biomed Engn, Stony Brook, NY 11794 USA;SUNY Stony Brook, Louis & Beatrice Laufer Ctr Phys & Quantitat Biol, Stony Brook, NY 11794 USA | null | cellular decision;feedback regulation;noise;Synthetic gene circuit;temperature | 45 | 1983;1990;1993;1994;1997;1998;1999;2000;2001;2002;2003;2004;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017;2018 | 31 | SUNY Stony Brook, Louis & Beatrice Laufer Ctr Phys & Quantitat Biol, Stony Brook, NY 11794 USA | Proc. Natl. Acad. Sci. U. S. A. | Balazsi, Gabor | NATL ACAD SCIENCES | ,;a;abolishes;affect;agents;aid;alters;and;applications;arrest;Arrhenius;as;between;bimodality;both;but;captured;cell;cells;cellular;cerevisiae;changes;choice;circuits;computationally;conformational;cooling;cope;corrupt;creates;creating;decision;difficulties;discovered;dramatic;dynamics;effects;engineered;experimental;explaining;expression;fate;fully;function;future;gene;genes;growth;heating;here;how;in;incorporating;induce;involves;isogenic;may;microbes;models;molecular-dynamics;most;multiscale;must;network;networks;nonoptimal;nonstandard;not;observations;of;organisms;overall;population;populations;predictable;protection;rates;reaction;repressor;resistance;resistant;revealed;Saccharomyces;scaling;simulations;single;stress;study;subjects;synthetic;temperature;temperature-dependent;temperatures;TetR;that;the;this;those;understanding;ways;we;which;with | SUNY Stony Brook | Most organisms must cope with temperature changes. This involves genes and gene networks both as subjects and agents of cellular protection, creating difficulties in understanding. Here, we study how heating and cooling affect expression of single genes and synthetic gene circuits in Saccharomyces cerevisiae. We discovered that nonoptimal temperatures induce a cell fate choice between stress resistance and growth arrest. This creates dramatic gene expression bimodality in isogenic cell populations, as arrest abolishes gene expression. Multiscale models incorporating population dynamics, temperature-dependent growth rates, and Arrhenius scaling of reaction rates captured the effects of cooling, but not those of heating in resistant cells. Molecular-dynamics simulations revealed how heating alters the conformational dynamics of the TetR repressor, fully explaining the experimental observations. Overall, nonoptimal temperatures induce a cell fate decision and corrupt gene and gene network function in computationally predictable ways, which may aid future applications of engineered microbes in nonstandard temperatures. | R-8264-2016 | EXPRESSION;FEEDBACK;PROMOTER;REGULATORY NETWORKS;SACCHAROMYCES-CEREVISIAE;SHOCK RESPONSE;TEMPERATURE-COMPENSATION;TOGGLE SWITCH;TRANSCRIPTION;YEAST | 4 | null | cellular decision;feedback regulation;noise;Synthetic gene circuit;temperature | 10 | SACCHAROMYCES-CEREVISIAE;YEAST;cellular decision;EXPRESSION;FEEDBACK;FEEDBACK-REGULATION;NOISE;PROMOTER;REGULATORY NETWORKS;SHOCK RESPONSE;synthetic gene circuits;temperature;TEMPERATURE COMPENSATION;toggle switch;TRANSCRIPTION | WOS:000449459000033 | SUNY Stony Brook, Stony Brook, NY USA | USA | 2,018 | null | 0000-0001-7426-1789 | null | null | English | null | ACS SYNTH BIOL;ANNU REV MICROBIOL;APPL ENVIRON MICROB;BIOCHEM J;BIOESSAYS;BIOPHYS J;BIOTECHNOL J;BMC BIOTECHNOL;BMC MOL BIOL;CELL;CELL DEATH DIFFER;CELL REP;CHRONOBIOL INT;CURR OPIN CELL BIOL;FEMS MICROBIOL LETT;GENE;GENETICS;IEEE DECIS CONTR P;J BACTERIOL;J BIOL CHEM;J BIOL PHYS;J MOL BIOL;J PHYS CHEM B;MICROBIOL MOL BIOL R;MOL BIOL CELL;MOL CELL;MOL CELL BIOL;MOL MICROBIOL;MOL SYST BIOL;NAT CHEM BIOL;NAT ECOL EVOL;NAT STRUCT BIOL;NATURE;NEGATIVE FEEDBACK FA;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PHYS REV E;PLOS BIOL;PLOS COMPUT BIOL;PLOS GENET;SCIENCE;WSEAS T BIOL BIOMED | Balazsi, Gabor;Charlebois, Daniel A;Hauser, Kevin;Marshall, Sylvia | 2024-03-11
ER | Abudugupur, A;Al-Fageeh, M B;Anderson, J C;Arnaud, O;Atkinson, M R;Austin, D W;Baron, U;Basu, S;Becskei, A;Bertrand, K P;Blake, W J;Botstein, D;Cao, Y X L;Cardinale, S;Charlebois Da.;Charlebois, D A;Chen, L;Delorme-Axford, E;Diao, J C;Dill, K A;Dowell, R D;Dunlop, M J;Elowitz, M B;Ferrell, J E;Gardner, T S;Gasch, A P;González, C;Hauser, K;Heiland, I;Hillen, W;Hussain, F;Isaacs, F J;Jo, M C;Klumpp, S;Leuenberger, P;Levine, M;Levy, S F;Li, G W;Madrid, C;Marciano, D C;Mensonides, F I C;Mihalik, A;Morano, K A;Murphy, K F;Muthukrishnan, A B;Neupert, J;Nevozhay, D;Newman, J R S;Octavio, L M;Oliveira, S M D;Orth, P;Perezmartin, J;Ptashne, M;Pyatrikas, D V;Raboy, B;Ramos, J L;Reynolds, T B;Richter, K;Ro, D K;Rosenfeld, N;Rowley, A;Ruoff, P;Sawle, L;Saxena, P;Scott, M;Seidel, U;Sen, S;Slomovic, S;Stanton, B C;Stricker, J;Tagkopoulos, I;Tan, C;Thieffry, D;Verghese, J;Voordeckers, K;Watson, E;Windbichler, N;Yaakov, G;Yu, H Y;Zechner, C;Zhou, X | GZ5KM | Stony Brook, NY USA | 34 | null | 1 | null | 30,341,217 | Balazsi, Gabor;Charlebois, Daniel A;Hauser, Kevin;Marshall, Sylvia | P NATL ACAD SCI USA | Stony Brook, NY USA |
Pardee, K | 10.1016/j.bej.2018.07.008 | null | RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS | o411w6m3mx3r401m271440p2m96p5s5r5367 | Perspective: Solidifying the impact of cell-free synthetic biology through lyophilization | Univ Toronto | null | Pardee, K (corresponding author), Univ Toronto, Leslie Dan Fac Pharm, Toronto, ON M5S 3M2, Canada. | null | Pardee, Keith | Biotechnology & Applied Microbiology;Engineering, Chemical | NSERC [RGPIN-2016-06352]; CIHR [201610FDN-375469]; Bill and Melinda Gates Foundation: Grand Challenges Explorations [OPP1160667]; University of Toronto's Connaught Fund; University of Toronto's Medicine by Design initiative; Canada First Research Excellence Fund; Bill and Melinda Gates Foundation [OPP1160667] Funding Source: Bill and Melinda Gates Foundation | WOS | Pardee, K | Univ Toronto, Toronto ON, Canada | 138 | :;biology;Cell-Free;impact;lyophilization;of;perspective;Solidifying;synthetic;the;through | 1 | null | ELSEVIER | Univ Toronto, Leslie Dan Fac Pharm, Toronto, ON M5S 3M2, Canada | Article | Univ Toronto | AMSTERDAM | null | null | Univ Toronto | Bill and Melinda Gates Foundation;Bill and Melinda Gates Foundation: Grand Challenges Explorations;Canada First Research Excellence Fund;CIHR;NSERC;University of Toronto's Connaught Fund;University of Toronto's Medicine by Design initiative | Pardee, K (corresponding author), Univ Toronto, Leslie Dan Fac Pharm, Toronto, ON M5S 3M2, Canada. | 97 | Pardee, Keith | 29 | 1 | 445,980,900,011 | Bill and Melinda Gates Foundation [OPP1160667] Funding Source: Bill and Melinda Gates Foundation;Bill and Melinda Gates Foundation: Grand Challenges Explorations [OPP1160667];Canada First Research Excellence Fund;CIHR [201610FDN-375469];NSERC [RGPIN-2016-06352];University of Toronto's Connaught Fund;University of Toronto's Medicine by Design initiative | Canada | BIOCHEMICAL ENGINEERING JOURNAL | Canada | null | null | Univ Toronto, Leslie Dan Fac Pharm, Toronto, ON M5S 3M2, Canada | 1369-703X | Pardee, K | OCT 15 | keith.pardee@utoronto.ca | cell-free synthetic biology;impact;lyophilization;perspective | 1 | J | Biotechnology & Applied Microbiology;Engineering | ability;abiotic format;advantage;application-focused domain builds;biosafe mode outside;Biosensor;C 2018;cell-free biochemistry;Cell-free synthetic biology;cell-free systems;cellular environments;challenges;chief;community;creative ways;decades;diagnostics;dried pellets;Elsevier B.V;embedded paper-based reactions;EXTRACT PREPARATION;FREE EXPRESSION;FREE PLATFORM;FREE PROTEIN-SYNTHESIS;Freeze-dried cell-free reactions;IMPACT;laboratory;longstanding challenge;lyophilization;MOLECULES;new branch;new efforts;new ideas;newfound venue;opportunities;Paper-based;perspective;poised synthetic gene networks;Portable therapeutic manufacturing;potential;proof-of-concept demonstrations;PROTEIN EXPRESSION;PURIFICATION;recent work;Sensors;significant excitement;synthetic biology;synthetic gene networks outside;taken;thoughts;tools;TRANSCRIPTION-TRANSLATION SYSTEM;translation systems;unexpected advantages;VACCINES;virus;vitro transcription | Pardee, K | Biosensor;Cell-free synthetic biology;Diagnostics;EXTRACT PREPARATION;FREE EXPRESSION;FREE PLATFORM;FREE PROTEIN-SYNTHESIS;Freeze-dried cell-free reactions;MOLECULES;Paper-based;Portable therapeutic manufacturing;PURIFICATION;Sensors;TRANSCRIPTION-TRANSLATION SYSTEM;VACCINES;virus | 91 | [Pardee, Keith] Univ Toronto, Leslie Dan Fac Pharm, Toronto, ON M5S 3M2, Canada. | I would like to thank Hamed Tinafar and Margot Karlikow for their review and helpful comments on the manuscript. Related work in the Pardee lab is support by funding from NSERC (RGPIN-2016-06352), CIHR (201610FDN-375469), Bill and Melinda Gates Foundation: Grand Challenges Explorations (Round 17, OPP1160667), the University of Toronto's Connaught Fund and the University of Toronto's Medicine by Design initiative, which receives funding from the Canada First Research Excellence Fund. | ability;abiotic format;advantage;application-focused domain builds;biosafe mode outside;cell-free biochemistry;cell-free synthetic biology;cell-free systems;cellular environments;challenges;chief;community;creative ways;decades;dried pellets;embedded paper-based reactions;laboratory;longstanding challenge;new branch;new efforts;new ideas;newfound venue;opportunities;poised synthetic gene networks;potential;proof-of-concept demonstrations;protein expression;recent work;significant excitement;synthetic biology;synthetic gene networks outside;taken;thoughts;tools;translation systems;unexpected advantages;vitro transcription | 10.1002/biot.201100155;10.1002/biot.201500214;10.1002/biot.201500237;10.1002/biot.201600678;10.1002/bit.10827;10.1002/bit.10865;10.1002/bit.21567;10.1002/bit.21716;10.1002/bit.24581;10.1002/bit.24947;10.1002/bit.25502;10.1002/bit.26253;10.1002/bit.26439;10.1002/bit.26502;10.1002/btm2.10049;10.1002/btpr.1509;10.1002/btpr.744;10.1002/wnan.1234;10.1006/prep.2001.1400;10.1007/978-1-59745-196-3_15;10.1007/978-1-60327-331-2_12;10.1007/978-1-60327-331-2_2;10.1016/j.bej.2017.11.013;10.1016/j.biochi.2013.11.025;10.1016/j.cell.2014.10.002;10.1016/j.cell.2014.10.004;10.1016/j.cell.2016.04.059;10.1016/j.cell.2016.09.013;10.1016/j.febslet.2014.05.061;10.1016/j.jbiosc.2016.07.015;10.1016/j.jbiotec.2006.05.014;10.1016/j.jbiotec.2011.04.011;10.1016/j.jmb.2011.08.055;10.1016/j.pep.2005.09.021;10.1016/j.pep.2010.01.016;10.1016/j.taap.2018.02.016;10.1016/j.tibtech.2013.09.002;10.1016/j.ymben.2016.09.008;10.1016/S0014-5793(02)02383-9;10.1016/S0956-5663(01)00303-7;10.1021/ac100231a;10.1021/acs.analchem.6b04034;10.1021/acssynbio.5b00296;10.1021/acssynbio.7b00001;10.1021/acssynbio.7b00219;10.1021/acssynbio.7b00253;10.1021/bc100367u;10.1021/bi00905a029;10.1021/bp049789y;10.1021/bp060110v;10.1021/es203511k;10.1021/nl062560n;10.1021/sb200016s;10.1021/sb300049p;10.1021/sb400206c;10.1023/B:JSFG.0000029204.57846.7d;10.1038/90802;10.1038/msb.2008.57;10.1038/msb.2011.55;10.1038/nature24648;10.1038/nchem.2484;10.1038/nrendo.2010.87;10.1038/s41467-018-03469-5;10.1038/s41598-018-27846-8;10.1038/srep08663;10.1038/srep30442;10.1039/c3mb70304e;10.1073/pnas.0905735106;10.1073/pnas.1308701110;10.1073/pnas.1510533112;10.1073/pnas.1715806115;10.1084/jem.186.3.393;10.1093/nar/gkq377;10.1093/synbio/ysy002;10.1093/synbio/ysy003;10.1098/rsif.2016.1039;10.1126/science.290.5499.2148;10.1126/science.aag0804;10.1126/science.aam9321;10.1128/IAI.68.2.986-989.2000;10.1128/JVI.66.11.6527-6532.1992;10.1146/annurev.ge.07.120173.001411;10.1182/blood-2006-07-030593;10.1186/1475-2859-10-56;10.1371/journal.pone.0106232;10.2144/0000113924;10.2144/000114158;10.3389/fmicb.2018.01146;10.3791/50762;10.4161/mabs.4.2.19202;[10.1038/NCHEMBIO.2514, 10.1038/nchembio.2514];[10.1039/c2ra01376b, 10.1039/C2RA01376B] | Univ Toronto | Pardee, K | Pardee, K: Univ Toronto, Leslie Dan Fac Pharm, Toronto, ON M5S 3M2, Canada | null | 201610FDN-375469;OPP1160667;RGPIN-2016-06352 | 93 | null | Canada | Univ Toronto | Pardee, Keith | Green Published, hybrid | BIOSENSOR;EXTRACT PREPARATION;FREE EXPRESSION;FREE PLATFORM;FREE PROTEIN-SYNTHESIS;MOLECULES;PURIFICATION;TRANSCRIPTION-TRANSLATION SYSTEM;VACCINES;VIRUS | Pardee, Keith; | null | Univ Toronto, Leslie Dan Fac Pharm, Toronto, ON M5S 3M2, Canada | Univ Toronto, Leslie Dan Fac Pharm, Toronto, ON M5S 3M2, Canada | 1873-295X | Cell-free synthetic biology;Diagnostics;Freeze-dried cell-free reactions;Paper-based;Portable therapeutic manufacturing;Sensors | null | 1963;1973;1992;1997;2000;2001;2002;2004;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017;2018 | 33 | Univ Toronto, Leslie Dan Fac Pharm, Toronto, ON M5S 3M2, Canada | Biochem. Eng. J. | Pardee, Keith | ELSEVIER | ,;a;ability;abiotic;advantage;advantages;ahead;among;an;and;application-focused;based;begun;biochemistry;biology;biosafe;branch;brought;builds;by;cell-free;cellular;challenge;challenges;chief;community;creative;decades;demonstrations;deploy;domain;dried;efforts;embedded;encoded;environments;even;excitement;exciting;explore;expression;extend;extended;field;for;format;freeze-dried;freeze-drying;gene;genetically;has;have;here;how;I;ideas;important;in;into;is;laboratory;longstanding;mode;my;networks;new;newfound;of;on;operate;opportunities;or;outside;paper-based;pellets;perhaps;poised;potential;proof-of-concept;protein;provide;reactions;recent;significant;solved;sterile;synthetic;systems;taken;the;there;these;this;thoughts;to;together;tools;transcription;translation;unexpected;venue;vitro;ways;work | Univ Toronto | Cell-free synthetic biology is an exciting and new branch in the field of synthetic biology. Based on in vitro transcription and translation systems, this application-focused domain builds on decades of cell-free biochemistry and protein expression to operate synthetic gene networks outside of cellular environments. This has brought new and perhaps even unexpected advantages. Chief among these is the ability to operate genetically encoded tools in a sterile and abiotic format. Recent work has extended this advantage by freeze-drying these cell-free systems into dried pellets or embedded paper-based reactions. Taken together, these new ideas have solved the longstanding challenge of how to deploy poised synthetic gene networks in a biosafe mode outside of the laboratory. There is significant excitement in the potential of this newfound venue and the community has begun to extend proof-of-concept demonstrations in important and creative ways. Here I explore these new efforts and provide my thoughts on the challenges and opportunities ahead for freeze-dried, cell-free synthetic biology. | null | BIOSENSOR;EXTRACT PREPARATION;FREE EXPRESSION;FREE PLATFORM;FREE PROTEIN-SYNTHESIS;MOLECULES;PURIFICATION;TRANSCRIPTION-TRANSLATION SYSTEM;VACCINE;VIRUS | 2 | null | Cell-free synthetic biology;Diagnostics;Freeze-dried cell-free reactions;Paper-based;Portable therapeutic manufacturing;Sensors | 7 | Biosensor;Cell-free synthetic biology;Diagnostics;EXTRACT PREPARATION;FREE EXPRESSION;FREE PLATFORM;FREE PROTEIN-SYNTHESIS;Freeze-dried cell-free reactions;MOLECULES;Paper-based;Portable therapeutic manufacturing;PURIFICATION;SENSOR;TRANSCRIPTION-TRANSLATION SYSTEM;VACCINE;virus | WOS:000445980900011 | Univ Toronto, Toronto ON, Canada | Canada | 2,018 | null | null | null | null | English | null | ACS SYNTH BIOL;ANAL CHEM;ANNU REV GENET;BIOCHEM ENG J;BIOCHEMISTRY-US;BIOCHIMIE;BIOCONJUGATE CHEM;BIOENG TRANSL MED;BIOSENS BIOELECTRON;BIOTECHNIQUES;BIOTECHNOL BIOENG;BIOTECHNOL J;BIOTECHNOL PROGR;BLOOD;CELL;CHANDLER M;ENVIRON SCI TECHNOL;FEBS LETT;FRONT MICROBIOL;INFECT IMMUN;J BIOSCI BIOENG;J BIOTECHNOL;J EXP MED;J MOL BIOL;J R SOC INTERFACE;J VIROL;Journal of Structural and Functional Genomics;JOVE-J VIS EXP;MABS-AUSTIN;METAB ENG;METHODS MOL BIOL;MICROB CELL FACT;MOL BIOSYST;MOL SYST BIOL;NANO LETT;NAT BIOTECHNOL;NAT CHEM;NAT CHEM BIOL;NAT COMMUN;NAT REV ENDOCRINOL;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PLOS ONE;PROTEIN EXPRES PURIF;RSC ADV;SCI REP-UK;SCIENCE;SYN BIOL;TOXICOL APPL PHARM;TRENDS BIOTECHNOL;WIRES NANOMED NANOBI | Pardee, Keith | 2024-03-11
ER | Asahara, H;Bretthauer, R K;Bundy, B C;Buntru, M;Burgenson, D;Caschera, F;Chandler M.;Choi, S H;Clomburg, J M;Daube, S S;Didovyk, A;Duyen, T T M;Ezure, T;Failmezger, J;Garamella, J;Goerke, A R;Gootenberg, J S;Green, A A;Harbers, M;Huppa, J B;Jain, V;Jewett, M C;Jiang, X P;Kanter, G;Karig, D K;Kelwick, R;Kigawa Takanori;Kim, D M;Kim, T W;Kwon, Y C;Lee, K H;Lee, M S;Li, J;Liu, D V;Lu, Y;Makino, S;Martemyanov, K A;Martin, R W;Matthies, D;Mikami, S;Moore, S J;Ong, L L;Pardee, K;Patel, K G;Rohovie, M J;Rustad, M;Saeidi, N;Salehi, A S M;Schoborg, J A;Shimizu, Y;Shin, J;Shinoda, T;Shrestha, P;Siegfried, K;Sitararnan Kalavathy;Smith, M T;Soto, A M;Struss, A;Sullivan, C J;Sun, Z Z;Takahashi, M K;Tanrikulu, I C;Tran, K;Villarreal, F;Wang, H;Welsh, J P;Wen, K Y;Xi, J A;Yan, L;Yang, W C;Yildiz, I;Yin, G;Yonekura, K;Young, C L;Zhao, Q J;Zubay, G | GV3FX | Toronto ON, Canada | 47 | null | 1 | null | 30,740,032 | Pardee, Keith | BIOCHEM ENG J | Toronto ON, Canada |
Du, Y M;Fang, N;Liu, X F;Liu, X M;Liu, Y H;Lu, T G;Sui, J K;Wang, C K;Wang, W J;Yan, N;Zhang, H B;Zhang, Z F | 10.3390/molecules23102511 | 2511 | ST ALBAN-ANLAGE 66, CH-4052 BASEL, SWITZERLAND | d6cfe735q4b3v3504j5i4h4u5v6x5y3o6q4q | Formation of α- and β-Cembratriene-Diols in Tobacco (<i>Nicotiana tabacum</i> L.) Is Regulated by Jasmonate-Signaling Components via Manipulating Multiple Cembranoid Synthetic Genes | Chinese Acad Agr Sci | null | Zhang, HB (corresponding author), Chinese Acad Agr Sci, Tobacco Res Inst, Qingdao 266101, Peoples R China. | null | Du, Yongmei;Fang, Ning;Liu, Xiaofeng;Liu, Xinmin;Liu, Yanhua;Lu, Tiegang;Sui, Jinkai;Wang, Chunkai;Wang, Wenjing;Yan, Ning;Zhang, Hongbo;Zhang, Huai-Bao;Zhang, Zhongfeng | Biochemistry & Molecular Biology;Chemistry, Multidisciplinary | Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences (Elite youth program) [ASTIP-TRIC05]; National Natural Science Foundation of China [31801279]; Fundamental Research Funds for Chinese Academy of Agricultural Sciences [Y2017JC21, 1610232016018, Y2017LM15] | WOS | Zhang, H B | Chinese Acad Agr Sci, Beijing, Peoples R China;Chinese Acad Agr Sci, Qingdao, Peoples R China | 23 | (<i>Nicotiana;and;by;Cembranoid;Components;formation;genes;in;is;Jasmonate-Signaling;L;Manipulating;Multiple;of;Regulated;synthetic;tabacum</i>;Tobacco;via;α-;β-Cembratriene-Diols | 1 | Fang, Ning;Wang, Wenjing | MDPI | Chinese Acad Agr Sci, Biotechnol Res Inst, Beijing 100081, Peoples R China;Chinese Acad Agr Sci, Tobacco Res Inst, Qingdao 266101, Peoples R China | Article | Chinese Acad Agr Sci | BASEL | null | null | Chinese Acad Agr Sci | Fundamental Research Funds for Chinese Academy of Agricultural Sciences;National Natural Science Foundation of China;Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences (Elite youth program) | Zhang, HB (corresponding author), Chinese Acad Agr Sci, Tobacco Res Inst, Qingdao 266101, Peoples R China. | null | Du, Yongmei;Fang, Ning;Liu, Xiaofeng;Liu, Xinmin;Liu, Yanhua;Lu, Tiegang;Sui, Jinkai;Wang, Chunkai;Wang, Wenjing;Yan, Ning;Zhang, Hongbo;Zhang, Huai-Bao;Zhang, Zhongfeng | 26 | 2 | 451,201,400,107 | Fundamental Research Funds for Chinese Academy of Agricultural Sciences [Y2017JC21, 1610232016018, Y2017LM15];National Natural Science Foundation of China [31801279];Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences (Elite youth program) [ASTIP-TRIC05] | China | MOLECULES | China | null | null | Chinese Acad Agr Sci, Tobacco Res Inst, Qingdao 266101, Peoples R China | null | Du, Y M;Fang, N;Liu, X F;Liu, X M;Liu, Y H;Lu, T G;Sui, J K;Wang, C K;Wang, W J;Yan, N;Zhang, H B;Zhang, Z F | OCT | duyongmei@caas.cn;fangning010@163.com;liuxiaofeng626@126.com;liuxinmin@caas.cn;liuyanhua@caas.cn;lutiegang@caas.cn;suijinkai@163.com;wangchunkai1990@outlook.com;wangwenjing@caas.cn;yanning@caas.cn;zhanghongbo@caas.cn;zhanghuaibao@caas.cn;zhangzhongfeng@caas.cn | formation;Jasmonate-Signaling Components via;Multiple Cembranoid Synthetic Genes;Tobacco (<i>Nicotiana tabacum</i> L;α-;β-Cembratriene-Diols | 12 | J | Biochemistry & Molecular Biology;Chemistry | anti-nicotine addiction;ARABIDOPSIS;bioactive derivative;biosynthesis;cembranoid formation;cembranoid production;cembranoid synthetic genes;cembranoid synthetic genes CBTS;cembranoids;cembratriene-diol;cembratriene-diol formation;cembratriene-diol synthetic genes;cembratriene-diols;cembratriene-diols' formation;COI1;critical role;defense responses;display critical roles;DOMAIN PROTEINS INTERACT;downstream regulators MYC2a;dysfunction;encoding MYB transcription factor MYB305;enzymes;expression;findings;formation;gene encoding bHLH transcription factor MYC2a;GLANDULAR TRICHOME;great importance;group;JA;JA (i.e. JA-Ile);JA-signaling components;jasmonate;Jasmonate-Signaling Components via;METABOLISM;molecular regulatory mechanism underlying cembranoid synthesis;Multiple Cembranoid Synthetic Genes;MYB305;MYC2;N. tabacum cv;natural diterpenoid compounds;neuron protection;Nicotiana (tobacco) species display activities;NtLTP1;over-expressing;P450;pharmaceutical potentials;physiological process;phytohormone jasmonic acid (JA);PLANT STRESS-RESPONSE;plants;receptor protein;regulating cembratriene-diol formation;regulating cembratriene-diols' formation;regulatory mechanism;ROLES;secondary metabolism;studies;study;taken;TN90;tobacco;Tobacco (<i>Nicotiana tabacum</i> L;TRANSCRIPTION;TRICHOME INITIATION;trichome secretion;unknown;upregulate;α-;β-Cembratriene-Diols | Sui, J K | ARABIDOPSIS;BIOSYNTHESIS;cembratriene-diol;COI1;DEFENSE RESPONSES;DOMAIN PROTEINS INTERACT;GLANDULAR TRICHOME;jasmonate;METABOLISM;MYC2;PLANT STRESS-RESPONSE;secondary metabolism;tobacco;TRICHOME INITIATION | null | [Sui, Jinkai; Wang, Chunkai; Liu, Xiaofeng; Fang, Ning; Liu, Yanhua; Wang, Wenjing; Yan, Ning; Zhang, Huai-Bao; Du, Yongmei; Liu, Xinmin; Zhang, Zhongfeng; Zhang, Hongbo] Chinese Acad Agr Sci, Tobacco Res Inst, Qingdao 266101, Peoples R China. [Lu, Tiegang] Chinese Acad Agr Sci, Biotechnol Res Inst, Beijing 100081, Peoples R China. | This work was supported by the Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences (Elite youth program to H.Z., ASTIP-TRIC05), the National Natural Science Foundation of China (Grant No. 31801279) and the Fundamental Research Funds for Chinese Academy of Agricultural Sciences (Y2017JC21, 1610232016018, Y2017LM15). | anti-nicotine addiction;bioactive derivative;cembranoid formation;cembranoid production;cembranoid synthetic genes;cembranoid synthetic genes CBTS;cembranoids;cembratriene-diol formation;cembratriene-diol synthetic genes;cembratriene-diols;cembratriene-diols' formation;COI1;critical role;display critical roles;downstream regulators MYC2a;dysfunction;encoding MYB transcription factor MYB305;enzymes;expression;findings;gene encoding bHLH transcription factor MYC2a;great importance;group;JA;JA (i.e. JA-Ile);JA-signaling components;molecular regulatory mechanism underlying cembranoid synthesis;MYB305;N. tabacum cv;natural diterpenoid compounds;neuron protection;Nicotiana (tobacco) species display activities;NtLTP1;over-expressing;P450;pharmaceutical potentials;physiological process;phytohormone jasmonic acid (JA);plants;receptor protein;regulating cembratriene-diol formation;regulating cembratriene-diols' formation;regulatory mechanism;roles;studies;study;taken;TN90;tobacco;transcription;trichome secretion;unknown;upregulate | 10.1007/s00425-002-0904-4;10.1007/s00442-002-0924-6;10.1007/s11103-007-9149-8;10.1016/j.bmc.2017.05.028;10.1016/j.celrep.2017.04.057;10.1016/j.indcrop.2015.12.031;10.1016/j.pbi.2009.07.015;10.1016/j.tplants.2012.03.001;10.1038/86770;10.1038/nature05960;10.1038/nature06006;10.1038/nature09430;10.1038/ncomms13056;10.1038/nprot.2008.73;10.1042/bj0570508;10.1046/j.1365-313X.2002.01432.x;10.1073/pnas.0802332105;10.1080/17429145.2010.544779;10.1093/aob/mcm079;10.1093/aob/mct067;10.1093/jxb/erp270;10.1093/jxb/eru084;10.1093/jxb/erw495;10.1093/jxb/erx068;10.1093/mp/ssr056;10.1093/mp/sss128;10.1093/pcp/pcy004;10.1101/gad.297704;10.1104/pp.103.027086;10.1104/pp.108.125385;10.1104/pp.17.00727;10.1105/tpc.000679;10.1105/tpc.017954;10.1105/tpc.022319;10.1105/tpc.106.048017;10.1105/tpc.108.060079;10.1105/tpc.111.083089;10.1105/tpc.111.083261;10.1105/tpc.112.098749;10.1105/tpc.8.9.1519;10.1111/j.1365-313X.2006.02851.x;10.1111/j.1365-313X.2008.03432.x;10.1111/j.1365-313X.2011.04875.x;10.1111/j.1365-313X.2011.04886.x;10.1111/j.1469-8137.2010.03466.x;10.1111/nph.14205;10.1126/science.1182612;10.1126/science.280.5366.1091;10.1186/1746-4811-9-46;10.1242/dev.016873;10.1242/dev.030585;10.4161/psb.5.2.11214;10.4161/psb.6.12.18120 | Chinese Acad Agr Sci | Du, Y M;Fang, N;Liu, X F;Liu, X M;Liu, Y H;Lu, T G;Sui, J K;Wang, C K;Wang, W J;Yan, N;Zhang, H B;Zhang, Z F | Sui, J K: Chinese Acad Agr Sci, Tobacco Res Inst, Qingdao 266101, Peoples R China | Fang, Ning;liu, yan;Liu, Yiming;Wang, Wenjing;wang, xu | 1610232016018;31801279;ASTIP-TRIC05;Y2017JC21;Y2017LM15 | 54 | null | China | Chinese Acad Agr Sci | Sui, Jinkai | Green Published, Green Submitted, gold | ARABIDOPSIS;BIOSYNTHESIS;COI1;DEFENSE RESPONSES;DOMAIN PROTEINS INTERACT;GLANDULAR TRICHOME;METABOLISM;MYC2;PLANT STRESS-RESPONSE;TRICHOME INITIATION | Sui, Jinkai; Wang, Chunkai; Liu, Xiaofeng; Fang, Ning; Liu, Yanhua; Wang, Wenjing; Yan, Ning; Zhang, Huai-Bao; Du, Yongmei; Liu, Xinmin; Lu, Tiegang; Zhang, Zhongfeng; Zhang, Hongbo; | null | Chinese Acad Agr Sci, Biotechnol Res Inst, Beijing 100081, Peoples R China;Chinese Acad Agr Sci, Tobacco Res Inst, Qingdao 266101, Peoples R China | Chinese Acad Agr Sci, Biotechnol Res Inst, Beijing 100081, Peoples R China;Chinese Acad Agr Sci, Tobacco Res Inst, Qingdao 266101, Peoples R China | 1420-3049 | cembratriene-diol;COI1;jasmonate;secondary metabolism;tobacco | 10 | 1954;1996;1998;2000;2001;2002;2003;2004;2006;2007;2008;2009;2010;2011;2012;2013;2014;2016;2017;2018 | 13 | Chinese Acad Agr Sci, Tobacco Res Inst, Qingdao 266101, Peoples R China | Molecules | Zhang, Hongbo | MDPI | (i.e.;(JA);(tobacco);,;a;acid;activities;addiction;also;although;and;anti-nicotine;are;been;bHLH;bioactive;by;catalyzing;CBTS;cembranoid;cembranoids;cembratriene-diol;cembratriene-diols;cembratriene-diols';COI1;components;compounds;correlated;could;critical;cv;demonstrated;derivative;display;diterpenoid;downstream;dysfunction;either;encoding;enhance;enzymes;expression;factor;findings;formation;found;further;gene;genes;governing;great;group;has;have;importance;in;investigated;is;its;JA;JA-Ile);JA-signaling;jasmonic;mechanism;modulate;molecular;MYB;MYB305;MYC2a;N.;natural;neuron;Nicotiana;NtLTP1;of;or;over-expressing;P450;pharmaceutical;physiological;phytohormone;plants;potentials;process;produced;production;protection;protein;receptor;regulating;regulators;regulatory;remains;reveal;role;roles;secretion;showed;species;studies;study;suggest;synthesis;synthetic;tabacum;taken;that;the;this;TN90;to;tobacco;together;transcription;trichome;underlying;unknown;upregulate;which;with | Chinese Acad Agr Sci | Cembranoids are a group of natural diterpenoid compounds with pharmaceutical potentials, and the cembratriene-diols produced by Nicotiana (tobacco) species display activities in anti-nicotine addiction and neuron protection. Although the enzymes catalyzing cembratriene-diols' formation in tobacco have been investigated, the regulatory mechanism underlying this physiological process remains unknown. This study has investigated the roles of phytohormone jasmonic acid (JA) in regulating cembratriene-diol formation in N. tabacum cv. TN90 and found that JA and COI1, the receptor protein of the bioactive derivative of JA (i.e., JA-Ile), display critical roles in regulating cembratriene-diols' formation and the expression of cembranoid synthetic genes CBTS, P450 and NtLTP1. Further studies showed that over-expressing either the gene encoding bHLH transcription factor MYC2a or that encoding MYB transcription factor MYB305 could upregulate the cembranoid synthetic genes and enhance the cembranoid production in plants with dysfunction of COI1. Further studies suggest that COI1 and its downstream regulators MYC2a and MYB305 also modulate the trichome secretion, which is correlated with cembranoid formation. Taken together, this study has demonstrated a critical role of JA-signaling components in governing the cembratriene-diol formation and the transcription of cembratriene-diol synthetic genes in tobacco. Findings in this study are of great importance to reveal the molecular regulatory mechanism underlying cembranoid synthesis. | AAU-8450-2021;HCI-5542-2022;HGV-1365-2022;IAN-4886-2023;ISU-3780-2023;IXX-1604-2023 | ARABIDOPSIS;BIOSYNTHESIS;COI1;DEFENSE RESPONSES;DOMAIN PROTEINS INTERACT;GLANDULAR TRICHOMES;METABOLISM;MYC2;PLANT STRESS-RESPONSE;TRICHOME INITIATION | 3 | null | cembratriene-diol;COI1;jasmonate;secondary metabolism;tobacco | 14 | ARABIDOPSIS;BIOSYNTHESIS;cembratriene-diol;COI1;DEFENSE RESPONSE;DOMAIN PROTEINS INTERACT;GLANDULAR TRICHOMES;jasmonate;METABOLISM;MYC2;PLANT STRESS-RESPONSE;secondary metabolism;tobacco;TRICHOME INITIATION | WOS:000451201400107 | Chinese Acad Agr Sci, Beijing, Peoples R China;Chinese Acad Agr Sci, Qingdao, Peoples R China | China | 2,018 | null | 0000-0002-4541-5803;0000-0003-4035-8552 | null | null | English | null | ANN BOT-LONDON;BIOCHEM J;BIOORGAN MED CHEM;CELL REP;CURR OPIN PLANT BIOL;DEVELOPMENT;GENE DEV;GENETICS;IND CROP PROD;J EXP BOT;J PLANT INTERACT;MOL PLANT;NAT BIOTECHNOL;NAT COMMUN;NAT PROTOC;NATURE;NEW PHYTOL;OECOLOGIA;P NATL ACAD SCI USA;PLANT CELL;PLANT CELL PHYSIOL;PLANT J;PLANT METHODS;PLANT MOL BIOL;PLANT PHYSIOL;PLANT SIGNAL BEHAV;PLANTA;SCIENCE;TRENDS PLANT SCI | Du, Yongmei;Fang, Ning;Liu, Xiaofeng;Liu, Xinmin;Liu, Yanhua;Lu, Tiegang;Sui, Jinkai;Wang, Chunkai;Wang, Wenjing;Yan, Ning;Zhang, Hongbo;Zhang, Huai-Bao;Zhang, Zhongfeng | 2024-03-11
ER | An, L J;Boter, M;Brückner, K;Campos, M L;Chini, A;Choi, Y E;De Geyter, N;Devoto, A;Dombrecht, B;Graham, I A;Hailat, M M;Hong, G J;Huang, H;Huchelmann, A;Katsir, L;Kazan, K;Li, L;Lian, T F;Liu, G Y;Lorenzo, O;Ma, D C;Maes, L;Moyano, E;Payne, C T;Pesch, M;Qi, T C;Schilmiller, A L;Schmittgen, T D;Sheard, L B;Song, S S;Subramanian, C;Thines, B;Traw, M B;Turner, J G;Van Schie, C C N;Wang, E M;Wang, W J;Wasternack, C;Woldemariam, M G;Xie, D X;Yan, N;Yan, T X;Yemm, E W;Yoshida, Y;Zhang, H B;Zhang, H Y;Zhao, M;Zhu, Z Q | HB6SF | Qingdao, Peoples R China | 15 | null | 1 | null | 30,274,345 | Du, Yongmei;Fang, Ning;Liu, Xiaofeng;Liu, Xinmin;Liu, Yanhua;Lu, Tiegang;Sui, Jinkai;Wang, Chunkai;Wang, Wenjing;Yan, Ning;Zhang, Hongbo;Zhang, Huai-Bao;Zhang, Zhongfeng | MOLECULES | Beijing, Peoples R China;Qingdao, Peoples R China |
Contreras-Llano, L E;Ding, Y F;Mao, M;Morris, E;Tan, C | 10.1021/acsami.8b10029 | null | 1155 16TH ST, NW, WASHINGTON, DC 20036 USA | 6h2w261j21m6f3y6i2s163q612g2j36b4d6f4o | Minimizing Context Dependency of Gene Networks Using Artificial Cells | Univ Calif Davis | null | Tan, C (corresponding author), Univ Calif Davis, Dept Biomed Engn, Davis, CA 95616 USA. | null | Contreras-Llano, Luis E;Ding, Yunfeng;Mao, Michelle;Morris, Eliza;Tan, Cheemeng | Materials Science, Multidisciplinary;Nanoscience & Nanotechnology | Society-in-Science: Branco-Weiss Fellowship; NSF-CHE [1808237-0]; UC MEXUS-CONACYT Doctoral Fellowship; Direct For Mathematical & Physical Scien [1808237] Funding Source: National Science Foundation; Division Of Chemistry [1808237] Funding Source: National Science Foundation | WOS | Tan, C | Univ Calif Davis, Davis, CA USA | 10 | Artificial;Cells;Context;Dependency;gene;minimizing;networks;of;using | 1 | Llano, Luis Eduardo Contreras;Mao, Michelle;Morris, Eliza;Tan, Cheemeng | AMER CHEMICAL SOC | Univ Calif Davis, Dept Biomed Engn, Davis, CA 95616 USA | Article | Univ Calif Davis | WASHINGTON | null | null | Univ Calif Davis | Direct For Mathematical & Physical Scien;Division Of Chemistry;NSF-CHE;Society-in-Science: Branco-Weiss Fellowship;UC MEXUS-CONACYT Doctoral Fellowship | Tan, C (corresponding author), Univ Calif Davis, Dept Biomed Engn, Davis, CA 95616 USA. | 30146 | Contreras-Llano, Luis E;Ding, Yunfeng;Mao, Michelle;Morris, Eliza;Tan, Cheemeng | 46 | 1 | 444,793,000,016 | Direct For Mathematical & Physical Scien [1808237] Funding Source: National Science Foundation;Division Of Chemistry [1808237] Funding Source: National Science Foundation;NSF-CHE [1808237-0];Society-in-Science: Branco-Weiss Fellowship;UC MEXUS-CONACYT Doctoral Fellowship | USA | ACS APPLIED MATERIALS & INTERFACES | USA | null | null | Univ Calif Davis, Dept Biomed Engn, Davis, CA 95616 USA | 1944-8244 | Contreras-Llano, L E;Ding, Y F;Mao, M;Morris, E;Tan, C | SEP 12 | cmtan@ucdavis.edu | Artificial Cells;Context Dependency;gene networks | 5 | J | Materials Science;Science & Technology - Other Topics | antimicrobial;artificial cells;BACTERIA;behavior;bioinspired mechanisms;biomimetics;biomolecules;CHEMICAL COMMUNICATION;chemical-context dependence;circuit;components;concentrations;Context Dependency;controlling robustness;designed functions;different chemical complexity;engineering;expression;extracellular chemical context;extracellular chemical contexts;FEEDBACK;functioning;gene networks;host cells;influences gene transcription;kill bacteria;liposomes;local chemical context;minimal dependency;molecular crowding;new frontier;persistent challenge;PROTOCELL;quorum sensing;ROBUSTNESS;sensitivity;simulated external environments;surrounding milieu;synthetic biological systems;synthetic biology;synthetic biomolecular compartments;synthetic gene circuits;synthetic gene networks;systems;translation;unknown cross talk;VESICLES | Ding, Y F | antimicrobial;artificial cells;BACTERIA;BEHAVIOR;biomimetics;CHEMICAL COMMUNICATION;CIRCUIT;EXPRESSION;FEEDBACK;molecular crowding;PROTOCELL;quorum sensing;ROBUSTNESS;Synthetic biology;synthetic gene circuits;SYSTEMS;VESICLES | 30137 | [Ding, Yunfeng; Contreras-Llano, Luis E.; Morris, Eliza; Mao, Michelle; Tan, Cheemeng] Univ Calif Davis, Dept Biomed Engn, Davis, CA 95616 USA. | We thank Prof. Atul Parikh for sharing organic solvent and functional generator facilities. We appreciate the discussion of the manuscript with Prof. Philip LeDuc, Prof. Atul Parikh, Prof. Robert Smith, and Prof. Erkin Seker. This work is supported by Society-in-Science: Branco-Weiss Fellowship and NSF-CHE 1808237-0 to C.T. L.E.C.-L. is supported through a UC MEXUS-CONACYT Doctoral Fellowship. | artificial cells;bioinspired mechanisms;biomolecules;chemical-context dependence;components;concentrations;controlling robustness;designed functions;different chemical complexity;engineering;extracellular chemical context;extracellular chemical contexts;functioning;gene networks;host cells;influences gene transcription;kill bacteria;liposomes;local chemical context;minimal dependency;new frontier;persistent challenge;sensitivity;simulated external environments;surrounding milieu;synthetic biological systems;synthetic biology;synthetic biomolecular compartments;synthetic gene circuits;synthetic gene networks;translation;unknown cross talk | 10.1002/adhm.201701163;10.1002/anie.201410139;10.1002/biot.201200085;10.1016/0005-2736(85)90521-8;10.1016/j.copbio.2016.02.032;10.1016/j.mattod.2016.02.020;10.1016/S0006-3495(99)77363-7;10.1021/acs.accounts.6b00512;10.1021/acscentsci.6b00330;10.1021/acssynbio.6b00198;10.1021/cb3006402;10.1038/35053176;10.1038/msb4100204;10.1038/nature07018;10.1038/nature09565;10.1038/nbt.2401;10.1038/nbt.3044;10.1038/nbt.4140;10.1038/nchembio.218;10.1038/ncomms5012;10.1038/ncomms6305;10.1038/nnano.2006.180;10.1038/nrd3028;10.1038/nrmicro1838;10.1039/c1cs15211d;10.1039/c3mb70032a;10.1039/c4cc02812k;10.1039/c5cs00361j;10.1039/c5ib00301f;10.1073/pnas.0408236101;10.1073/pnas.1001950107;10.1073/pnas.1300963110;10.1073/pnas.1316298111;10.1074/jbc.M104925200;10.1098/rsfs.2016.0011;10.1126/science.1192588;10.1128/AAC.43.5.1274;10.1146/annurev-biochem-080411-124036;10.1146/annurev.bi.43.070174.001125;[10.1038/NCHEM.1127, 10.1038/nchem.1127];[10.1038/NCHEM.1869, 10.1038/nchem.1869];[10.1038/NCHEM.2617, 10.1038/nchem.2617];[10.1038/NCHEM.2644, 10.1038/nchem.2644];[10.1038/nchem.296, 10.1038/NCHEM.296];[10.1038/NNANO.2013.132, 10.1038/nnano.2013.132];[10.1038/nnano.2013.309, 10.1038/NNANO.2013.309] | Univ Calif Davis | Contreras-Llano, L E;Ding, Y F;Mao, M;Morris, E;Tan, C | Ding, Y F: Univ Calif Davis, Dept Biomed Engn, Davis, CA 95616 USA | Contreras-Llano, Luis Eduardo;ding, yun;Llano, Luis Eduardo Contreras | 1808237;1808237-0 | 46 | null | USA | Univ Calif Davis | Ding, Yunfeng | null | BACTERIA;BEHAVIOR;CHEMICAL COMMUNICATION;CIRCUIT;EXPRESSION;FEEDBACK;PROTOCELL;SYNTHETIC BIOLOGY;SYSTEMS;VESICLES | Ding, Yunfeng; Contreras-Llano, Luis E.; Morris, Eliza; Mao, Michelle; Tan, Cheemeng; | null | Univ Calif Davis, Dept Biomed Engn, Davis, CA 95616 USA | Univ Calif Davis, Dept Biomed Engn, Davis, CA 95616 USA | null | antimicrobial;artificial cell;biomimetics;molecular crowding;quorum sensing;robustness;Synthetic gene circuit | 36 | 1974;1985;1999;2001;2004;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017;2018 | 49 | Univ Calif Davis, Dept Biomed Engn, Davis, CA 95616 USA | ACS Appl. Mater. Interfaces | Tan, Cheemeng | AMER CHEMICAL SOC | ,;a;and;are;arises;artificial;bacteria;be;been;between;bioinspired;biological;biology;biomolecular;biomolecules;bottom-up;by;can;cells;challenge;chemical;chemical-context;circuits;compartments;complexity;components;concentrations;context;contexts;controlling;creates;cross;defined;dependence;dependency;depends;designed;detect;different;enables;encapsulate;engineered;engineering;environmental;environments;external;extracellular;factors;for;from;frontier;functioning;functions;gene;has;here;host;in;influences;interact;kill;liposomes;local;mechanisms;milieu;minimal;minimized;networks;new;of;on;our;persistent;rendered;robust;robustness;sensitivity;show;significant;simulated;surrounding;synthetic;systems;talk;that;the;their;this;to;transcription;translation;types;unknown;using;we;which;with;work;yet | Univ Calif Davis | The functioning of synthetic gene circuits depends on their local chemical context defined by the types and concentrations of biomolecules in the surrounding milieu that influences gene transcription and translation. This chemical-context dependence of synthetic gene circuits arises from significant yet unknown cross talk between engineered components, host cells, and environmental factors and has been a persistent challenge for synthetic biology. Here, we show that the sensitivity of synthetic gene networks to their extracellular chemical contexts can be minimized, and their designed functions rendered robust using artificial cells, which are synthetic biomolecular compartments engineered from the bottom-up using liposomes that encapsulate the gene networks. Our artificial cells detect, interact with, and kill bacteria in simulated external environments with different chemical complexity. Our work enables the engineering of synthetic gene networks with minimal dependency on their extracellular chemical context and creates a new frontier in controlling robustness of synthetic biological systems using bioinspired mechanisms. | HSB-4834-2023;P-6260-2018;P-8005-2019 | BACTERIA;BEHAVIOR;CHEMICAL COMMUNICATION;CIRCUITS;EXPRESSION;FEEDBACK;PROTOCELLS;SYNTHETIC BIOLOGY;SYSTEM;VESICLES | 3 | null | antimicrobial;artificial cells;biomimetics;molecular crowding;quorum sensing;robustness;synthetic gene circuits | 10 | antimicrobial;artificial cell;BACTERIA;BEHAVIOR;biomimetics;CHEMICAL COMMUNICATION;CIRCUITS;EXPRESSION;FEEDBACK;molecular crowding;Protocells;quorum sensing;ROBUST;Synthetic biology;synthetic gene circuits;SYSTEM;VESICLES | WOS:000444793000016 | Univ Calif Davis, Davis, CA USA | USA | 2,018 | null | 0000-0001-9888-2520;0000-0002-4658-502X;0000-0002-9686-7375;0000-0003-1049-1192 | null | null | English | null | ACCOUNTS CHEM RES;ACS CENTRAL SCI;ACS CHEM BIOL;ACS SYNTH BIOL;ADV HEALTHC MATER;ANGEW CHEM INT EDIT;ANNU REV BIOCHEM;ANTIMICROB AGENTS CH;BIOCHIM BIOPHYS ACTA;BIOPHYS J;BIOTECHNOL J;CHEM COMMUN;CHEM SOC REV;CURR OPIN BIOTECH;INTEGR BIOL-UK;INTERFACE FOCUS;J BIOL CHEM;MATER TODAY;MOL BIOSYST;MOL SYST BIOL;NAT BIOTECHNOL;NAT CHEM;NAT CHEM BIOL;NAT COMMUN;NAT NANOTECHNOL;NAT REV DRUG DISCOV;NAT REV MICROBIOL;NATURE;P NATL ACAD SCI USA;SCIENCE | Contreras-Llano, Luis E;Ding, Yunfeng;Mao, Michelle;Morris, Eliza;Tan, Cheemeng | 2024-03-11
ER | Adamala, K P;Black, R A;Blain, J C;Buddingh, B C;Cardinale, S;Chavez, M;Chou, L Y T;Cuatrecasas, P;Del Vecchio, D;Dzieciol, A J;Elani, Y;Gardner, P M;Giacomini, K M;Hope, M J;Hussain, F;Kobori, S;Kolmakov, G V;Krinsky, N;Kurihara, K;Leduc, P R;Lee, K Y;Lentini, R;Lou, C B;Mansy, S S;Martino, C;Mishra, D;Morris, E;Noireaux, V;Qiao, Y;Raffy, S;Schwarz-Schilling, M;Scott, M;Shong, J;Stewart, P S;Studart, A R;Szostak, J W;Tamsir, A;Tan, C;Tan, C M;Van Roekel, H W H;Walde, P;Weitz, M;Wu, M H;Xu, C;Zhang, L J | GT8NA | Davis, CA USA | 52 | null | 1 | null | 30,113,814 | Contreras-Llano, Luis E;Ding, Yunfeng;Mao, Michelle;Morris, Eliza;Tan, Cheemeng | ACS APPL MATER INTER | Davis, CA USA |
Benzinger, D;Khammash, M | 10.1038/s41467-018-05882-2 | 3521 | MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND | 5ia2g2x4t5r3l1s1m5o315h1v232x3s584s3f3x | Pulsatile inputs achieve tunable attenuation of gene expression variability and graded multi-gene regulation | Swiss Fed Inst Technol | null | Khammash, M (corresponding author), Swiss Fed Inst Technol, Dept Biosyst Sci & Engn D BSSE, Mattenstr 26, CH-4058 Basel, Switzerland. | null | Benzinger, Dirk;Khammash, Mustafa | Multidisciplinary Sciences | European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme [743269] | WOS | Khammash, M | Swiss Fed Inst Technol, Basel, Switzerland | 9 | achieve;and;attenuation;expression;gene;graded;inputs;multi-gene;of;pulsatile;regulation;tunable;variability | 1 | null | NATURE PUBLISHING GROUP | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn D BSSE, Mattenstr 26, CH-4058 Basel, Switzerland | Article | Swiss Fed Inst Technol | LONDON | null | null | Swiss Fed Inst Technol | European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme | Khammash, M (corresponding author), Swiss Fed Inst Technol, Dept Biosyst Sci & Engn D BSSE, Mattenstr 26, CH-4058 Basel, Switzerland. | null | Benzinger, Dirk;Khammash, Mustafa | 25 | 1 | 443,154,700,002 | European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme [743269] | Switzerland | NATURE COMMUNICATIONS | Switzerland | null | null | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn D BSSE, Mattenstr 26, CH-4058 Basel, Switzerland | 2041-1723 | Benzinger, D;Khammash, M | AUG 30 | mustafa.khammash@bsse.ethz.ch | gene expression variability;graded multi-gene regulation;pulsatile inputs;tunable attenuation | 2 | J | Science & Technology - Other Topics | activation;beneficial functional behaviors;cell-to-cell variability;dynamic pulsatile signals;dynamic regulation;encoding;expression mean;fast-acting;fixed expression ratios;gene expression;gene expression variability;genetic parts;graded multi-gene regulation;lead;light;light-responsive promoter library;natural transcription factors;noise;optogenetic transcription factor;promoter dose-response characteristics;PROTEIN;pulsatile fashion;pulsatile inputs;pulsatile regulation;pulsatile signaling;REAL-TIME;required laborious optimization;Saccharomyces cerevisiae;SACCHAROMYCES-CEREVISIAE;signals;single input;SINGLE-CELL;synthetic biological systems;synthetic biology;synthetic gene expression systems;synthetic gene networks;SYSTEM;tunable attenuation;tuned;unknown;variability;yeast | Benzinger, D | ACTIVATION;LIGHT;NOISE;PROTEIN;REAL-TIME;SACCHAROMYCES-CEREVISIAE;SINGLE-CELL;Synthetic biology;SYSTEM;YEAST | null | [Benzinger, Dirk; Khammash, Mustafa] Swiss Fed Inst Technol, Dept Biosyst Sci & Engn D BSSE, Mattenstr 26, CH-4058 Basel, Switzerland. | We thank for Peter Buchmann and Marc Rullan for the construction of and help with the LED-setup, Verena Jaggin for assistance with FACS, and Jan Mikelson for providing software for stochastic simulations. We thank members of the Khammash lab, Serge Pelet, and Martin Ackermann for helpful discussion and Stephanie Aoki for critical reading of the manuscript. We would further like to thank Fabian Rudolf (ETH Zurich), Kevin Gardner (City University of New York), Robert H Singer (Albert Einstein College of Medicine), and Daniel Zenklusen (Universite de Montreal) for providing plasmids. D. B. is part of the Life Science Zurich graduate school. This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme grant agreement no. 743269 (CyberGenetics project). | beneficial functional behaviors;cell-to-cell variability;dynamic pulsatile signals;dynamic regulation;encoding;expression mean;fast-acting;fixed expression ratios;gene expression;genetic parts;graded multi-gene regulation;lead;light-responsive promoter library;natural transcription factors;optogenetic transcription factor;promoter dose-response characteristics;pulsatile fashion;pulsatile regulation;pulsatile signaling;required laborious optimization;Saccharomyces cerevisiae;signals;single input;synthetic biological systems;synthetic gene expression systems;synthetic gene networks;tuned;unknown;variability | 10.1002/(SICI)1097-0061(199807)14:10<953::AID-YEA293>3.0.CO;2-U;10.1002/yea.3144;10.1002/yea.3152;10.1016/j.cell.2008.09.050;10.1016/j.celrep.2015.07.035;10.1016/j.jmb.2013.07.036;10.1016/j.mib.2016.07.009;10.1016/j.molcel.2006.11.003;10.1016/j.molcel.2018.04.012;10.1016/j.tibtech.2014.10.002;10.1016/S0031-3203(01)00127-3;10.1021/acssynbio.6b00072;10.1021/acssynbio.6b00251;10.1021/bi200976a;10.1021/j100540a008;10.1021/sb4000564;10.1038/335563a0;10.1038/35014651;10.1038/msb.2013.56;10.1038/nature01546;10.1038/nature04281;10.1038/nature07292;10.1038/nature26141;10.1038/nbt734;10.1038/nchembio.1753;10.1038/NMETH.1253;10.1038/NMETH.1524;10.1038/nmeth.2879;10.1038/nmeth1008;10.1038/s41467-017-01498-0;10.1042/BJ20081949;10.1073/pnas.0504604102;10.1073/pnas.0802601105;10.1073/pnas.0809901106;10.1074/jbc.M102815200;10.1088/0953-8984/23/15/153102;10.1093/nar/gkq091;10.1093/nar/gks1293;10.1093/nar/gks549;10.1093/nar/gku616;10.1103/PhysRevLett.108.108104;10.1126/science.1070919;10.1126/science.1098641;10.1126/science.1109090;10.1126/science.1202142;10.1126/science.1239999;10.1128/MMBR.00025-07;10.1186/1471-2105-10-106;10.3791/50382];10.7554/eLife.06559;[10.1038/nchembio.1337, 10.1038/NCHEMBIO.1337];[10.1038/NCHEMBIO.1430, 10.1038/nchembio.1430];[10.1038/NMETH.2075, 10.1038/nmeth.2075];[10.1038/NMETH.2794, 10.1038/nmeth.2794] | Swiss Fed Inst Technol | Benzinger, D;Khammash, M | Benzinger, D: Swiss Fed Inst Technol, Dept Biosyst Sci & Engn D BSSE, Mattenstr 26, CH-4058 Basel, Switzerland | null | 743269 | 57 | null | Switzerland | Swiss Fed Inst Technol | Benzinger, Dirk | Green Submitted, Green Published, gold | ACTIVATION;LIGHT;NOISE;PROTEIN;REAL-TIME;SACCHAROMYCES-CEREVISIAE;SINGLE-CELL;SYNTHETIC BIOLOGY;SYSTEM;YEAST | Benzinger, Dirk; Khammash, Mustafa; | null | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn D BSSE, Mattenstr 26, CH-4058 Basel, Switzerland | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn D BSSE, Mattenstr 26, CH-4058 Basel, Switzerland | null | null | null | 1977;1988;1989;1998;2000;2001;2002;2003;2004;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017;2018 | 58 | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn D BSSE, Mattenstr 26, CH-4058 Basel, Switzerland | Nat. Commun. | Khammash, Mustafa | NATURE PUBLISHING GROUP | ,;a;also;and;are;at;be;behaviors;beneficial;benefit;biological;but;by;can;cell-to-cell;cerevisiae;characteristics;construct;construction;demonstrate;despite;differences;dose-response;dynamic;enables;encoding;expression;factor;factors;fashion;fast-acting;find;fixed;from;functional;further;gene;genetic;graded;here;how;in;independently;input;into;it;laborious;lead;library;light-responsive;many;mean;multi-gene;natural;networks;of;optimization;optogenetic;or;parts;previously;promoter;pulsatile;ratios;reduce;regulated;regulation;remains;required;Saccharomyces;show;signaling;signals;single;such;synthetic;systems;that;the;then;thus;to;transcription;tuned;unknown;using;variability;we;whether;which | Swiss Fed Inst Technol | Many natural transcription factors are regulated in a pulsatile fashion, but it remains unknown whether synthetic gene expression systems can benefit from such dynamic regulation. Here we find, using a fast-acting, optogenetic transcription factor in Saccharomyces cerevisiae, that dynamic pulsatile signals reduce cell-to-cell variability in gene expression. We then show that by encoding such signals into a single input, expression mean and variability can be independently tuned. Further, we construct a light-responsive promoter library and demonstrate how pulsatile signaling also enables graded multi-gene regulation at fixed expression ratios, despite differences in promoter dose-response characteristics. Pulsatile regulation can thus lead to beneficial functional behaviors in synthetic biological systems, which previously required laborious optimization of genetic parts or the construction of synthetic gene networks. | null | ACTIVATION;LIGHT;NOISE;PROTEIN;REAL-TIME;SACCHAROMYCES-CEREVISIAE;SINGLE-CELL;SYNTHETIC BIOLOGY;SYSTEM;YEAST | 7 | null | null | 10 | SACCHAROMYCES-CEREVISIAE;YEAST;ACTIVATION;LIGHT;NOISE;PROTEIN;REAL-TIME;SINGLE-CELL;Synthetic biology;SYSTEM | WOS:000443154700002 | Swiss Fed Inst Technol, Basel, Switzerland | Switzerland | 2,018 | null | null | null | null | English | null | ACS SYNTH BIOL;BIOCHEM J;BIOCHEMISTRY-US;BMC BIOINFORMATICS;CELL;CELL REP;CURR OPIN MICROBIOL;ELIFE;GENETICS;J BIOL CHEM;J MOL BIOL;J PHYS CHEM-US;J PHYS-CONDENS MAT;JOVE-J VIS EXP;METHOD ENZYMOL;MICROBIOL MOL BIOL R;MOL CELL;MOL SYST BIOL;NAT BIOTECHNOL;NAT CHEM BIOL;NAT COMMUN;NAT METHODS;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PATTERN RECOGN;PHYS REV LETT;SCIENCE;TRENDS BIOTECHNOL;YEAST | Benzinger, Dirk;Khammash, Mustafa | 2024-03-11
ER | Alper, H;Ang, J;Aranda-Díaz, A;Becskei, A;Blake, W J;Boer, V M;Borkowski, O;Brachmann, C B;Cai, L;Davidson, E A;De Chaumont, F;Delvigne, F;Du, J;Elowitz, M B;Fallahi-Sichani, M;Gietz, R D;Gillespie, D T;Gnügge, R;Gordon, A;Griesbeck, O;Hahne, F;Hansen, A S;Hecht, A;Kennedy, M J;Larson, D R;Levine, J H;Liang, J;Liu, J;Longtine, M S;Lugagne, J B;Mcisaac R. S.;Motta-Mena, L B;Murphy, K F;Nevoigt, E;Nevozhay, D;Olivo-Marin, J C;Ottoz, D S M;Pedraza, J M;Polstein, L R;Raj, A;Raser, J M;Rullan, M;Sadowski, I;Shcherbo, D;Shimizu-Sato, S;Sikorski, R S;Tkacik, G;Tostevin, F;Volfson, D;Zechner, C;Zhao, E M;Zoltowski, B D;Zuleta, I A | GS0CZ | Basel, Switzerland | 67 | null | 1 | null | 30,166,548 | Benzinger, Dirk;Khammash, Mustafa | NAT COMMUN | Basel, Switzerland |
Cunha, R C;de Lima, M;Fernandes, M H V;Finger, P F;Fischer, G;Hübner, S O;Vargas, G D | 10.1590/1678-5150-PVB-5343 | null | EMBRAPA-SAUDE ANIMAL, KM47 SEROPEDICA, 23851-970 RIO JANEIRO, BRAZIL | 256i3j673r4w56411r1wg1p4a5j725r3s415s1o | Antigenic and immunogenic properties of the canine distemper virus nucleocapsid protein expressed in <i>Escherichia</i> <i>coli</i> employing codon optimized synthetic gene | Univ Fed Pelotas | null | Hübner, SO (corresponding author), Univ Fed Pelotas UFPel, Dept Vet Prevent, Campus Capao do Leao,Ave Eliseu Maciel S-N, BR-96900010 Capao Do Leao, RS, Brazil. | null | Cunha, Rodrigo C;de Lima, Marcelo;Fernandes, Maureen H, V;Finger, Paula F;Fischer, Geferson;Hubner, Silvia O;Vargas, Gilberto D'Avila | Veterinary Sciences | Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES); Fundacao de Amparo a Pesquisa do Estado do Rio Grande do Sul (FAPERGS); Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq) | WOS | Hübner, S O | Univ Fed Pelotas UFPel, Capao Do Leao RS, Brazil | 38 | <i>coli</i>;<i>Escherichia</i>;and;antigenic;canine;codon;distemper;employing;expressed;gene;immunogenic;in;nucleocapsid;of;optimized;properties;protein;synthetic;the;virus | 1 | Cunha, Rodrigo Casquero | REVISTA PESQUISA VETERINARIA BRASILEIRA | Univ Fed Pelotas UFPel, Ctr Desenvolvimento Tecnol, Biotecnol, Campus Capao do Leao, BR-96900010 Capao Do Leao, RS, Brazil;Univ Fed Pelotas UFPel, Dept Vet Prevent, Campus Capao do Leao,Ave Eliseu Maciel S-N, BR-96900010 Capao Do Leao, RS, Brazil;Univ Fed Pelotas UFPel, Programa Posgrad Med Vet, Fac Vet, Campus Capao do Leao, BR-96900010 Capao Do Leao, RS, Brazil | Article | Univ Fed Pelotas | RIO JANEIRO | null | null | Brazil;Univ Fed Pelotas UFPel | Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq);Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES);Fundacao de Amparo a Pesquisa do Estado do Rio Grande do Sul (FAPERGS) | Hübner, SO (corresponding author), Univ Fed Pelotas UFPel, Dept Vet Prevent, Campus Capao do Leao,Ave Eliseu Maciel S-N, BR-96900010 Capao Do Leao, RS, Brazil. | 1621 | Cunha, Rodrigo C;de Lima, Marcelo;Fernandes, Maureen H, V;Finger, Paula F;Fischer, Geferson;Hubner, Silvia O;Vargas, Gilberto D'Avila | 1 | 3 | 448,939,600,020 | Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq);Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES);Fundacao de Amparo a Pesquisa do Estado do Rio Grande do Sul (FAPERGS) | Brazil | PESQUISA VETERINARIA BRASILEIRA | Brazil | null | null | Univ Fed Pelotas UFPel, Programa Posgrad Med Vet, Fac Vet, Campus Capao do Leao, BR-96900010 Capao Do Leao, RS, Brazil | 0100-736X | Cunha, R C;de Lima, M;Fernandes, M H V;Finger, P F;Fischer, G;Hübner, S O;Vargas, G D | AUG | silviaohubner@yahoo.com.br | <i>Escherichia</i> <i>coli</i>;canine distemper virus nucleocapsid protein;codon;immunogenic properties;synthetic gene | 7 | J | Veterinary Sciences | 28.55mg/mL;<i>Escherichia</i> <i>coli</i>;antigenic;Brazil;canine distemper disease;canine distemper immunodiagnostic assays;canine distemper virus;canine distemper virus (rCDV NP);canine distemper virus nucleocapsid protein;CDV;CDV positive dog sera;CHICKEN IGY;codon;common occurrence;conserved region;development;Diagnosis;Dogs;egg yolk;EGG-YOLK;ELISA;ELISA assays;Escherichia coli;expression;findings;hens;high concentration;His-Tag monoclonal antibodies;IgY;immunogenic;immunogenic characteristics;immunogenic properties;immunoglobulin Y (IgY);importance;infection;LINKED-IMMUNOSORBENT-ASSAY;low sensitivity;majority;mean yield;MONOCLONAL-ANTIBODY;negative control dog sera;NP;nucleocapsid protein;NUCLEOPROTEIN;positive;PROTEIN;purified);rCDVNP;rCDVNP antigenicity;recombinant protein;REGION;results;SDS-PAGE;specific IgY;specific IgY antibodies;specificity;Star strain (mean 300 mu g/mL;study;summary;synthetic gene;taken;useful tools;viroses;vitro;western blot;Western blot analysis | Fernandes, M H V | antigenic;BRAZIL;canine distemper virus;CDV;CHICKEN IGY;codon;Dogs;EGG-YOLK;ELISA;Escherichia coli;EXPRESSION;IgY;immunogenic;INFECTION;LINKED-IMMUNOSORBENT-ASSAY;MONOCLONAL-ANTIBODY;NP;nucleocapsid protein;NUCLEOPROTEIN;REGION;Synthetic gene;viroses | 1615 | [Fernandes, Maureen H., V; Finger, Paula F.] Univ Fed Pelotas UFPel, Programa Posgrad Med Vet, Fac Vet, Campus Capao do Leao, BR-96900010 Capao Do Leao, RS, Brazil. [Cunha, Rodrigo C.] Univ Fed Pelotas UFPel, Ctr Desenvolvimento Tecnol, Biotecnol, Campus Capao do Leao, BR-96900010 Capao Do Leao, RS, Brazil. [Vargas, Gilberto D'Avila; Fischer, Geferson; de Lima, Marcelo; Hubner, Silvia O.] Univ Fed Pelotas UFPel, Dept Vet Prevent, Campus Capao do Leao,Ave Eliseu Maciel S-N, BR-96900010 Capao Do Leao, RS, Brazil. | Financial support was provided by Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES), Fundacao de Amparo a Pesquisa do Estado do Rio Grande do Sul (FAPERGS) and Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq). | 28.55mg/mL;canine distemper disease;canine distemper immunodiagnostic assays;canine distemper virus (rCDV NP);CDV positive dog sera;codon;common occurrence;conserved region;development;diagnosis;egg yolk;ELISA;ELISA assays;Escherichia coli;expression;findings;hens;high concentration;His-Tag monoclonal antibodies;IgY;immunogenic;immunogenic characteristics;immunoglobulin Y (IgY);importance;low sensitivity;majority;mean yield;negative control dog sera;nucleocapsid protein;positive;protein;purified);rCDVNP;rCDVNP antigenicity;recombinant protein;results;SDS-PAGE;specific IgY;specific IgY antibodies;specificity;Star strain (mean 300 mu g/mL;study;summary;synthetic gene;taken;useful tools;vitro;western blot;Western blot analysis | 10.1002/0471140864.ps0501s00;10.1016/0378-1135(95)00014-2;10.1016/j.antiviral.2011.11.005;10.1016/j.cvsm.2008.02.007;10.1016/j.intimp.2014.01.026;10.1016/j.jviromet.2006.05.004;10.1016/j.jviromet.2008.05.023;10.1016/j.jviromet.2008.09.024;10.1016/j.jviromet.2009.07.014;10.1016/j.jviromet.2014.12.004;10.1016/j.pep.2013.10.016;10.1016/j.trstmh.2009.10.005;10.1016/j.vaccine.2007.02.053;10.1016/j.vetimm.2007.06.006;10.1016/j.vetimm.2008.09.023;10.1016/j.vetmic.2006.11.019;10.1016/S0378-1135(97)00194-6;10.1038/emi.2015.26;10.1046/j.1439-0442.1999.00198.x;10.1079/WPS200422;10.1080/09168451.2016.1217144;10.1089/mab.2013.0066;10.1093/bib/5.4.378;10.1093/bioinformatics/bts199;10.1099/0022-1317-78-2-373;10.1101/PDB.PR0T3944;10.1111/j.1365-2621.1992.tb08058.x;10.1111/j.1439-0450.1989.tb00659.x;10.1128/JCM.37.11.3634-3643.1999;10.1128/JCM.37.4.1049-1056.1999;10.1292/jvms.59.51;10.1371/journal.pone.0007002;10.1586/ERM.10.61;10.1590/S0100-736X2008000400005;10.1590/S0100-879X2004000800001;10.1590/S0103-84782007000400016;10.1638/1042-7260(2000)031[0441:CDITCA]2.0.CO;2;10.3109/08820138009066010;10.3791/253;10.4142/jvs.2014.15.4.503;10.4142/jvs.2016.17.3.307 | Univ Fed Pelotas UFPel | Cunha, R C;de Lima, M;Fernandes, M H V;Finger, P F;Fischer, G;Hübner, S O;Vargas, G D | Fernandes, M H V: Univ Fed Pelotas UFPel, Programa Posgrad Med Vet, Fac Vet, Campus Capao do Leao, BR-96900010 Capao Do Leao, RS, Brazil | Cunha, Rodrigo Casquero;Lima, Marcelo | null | 45 | null | Brazil | Univ Fed Pelotas UFPel | Fernandes, Maureen H, V | Green Published, gold | BRAZIL;CHICKEN IGY;DOGS;EGG-YOLK;ELISA;INFECTION;LINKED-IMMUNOSORBENT-ASSAY;MONOCLONAL-ANTIBODY;NUCLEOPROTEIN;REGION | Fernandes, Maureen H., V; Finger, Paula F.; Cunha, Rodrigo C.; Vargas, Gilberto D'Avila; Fischer, Geferson; de Lima, Marcelo; Hubner, Silvia O.; | null | Univ Fed Pelotas UFPel, Ctr Desenvolvimento Tecnol, Biotecnol, Campus Capao do Leao, BR-96900010 Capao Do Leao, RS, Brazil;Univ Fed Pelotas UFPel, Dept Vet Prevent, Campus Capao do Leao,Ave Eliseu Maciel S-N, BR-96900010 Capao Do Leao, RS, Brazil;Univ Fed Pelotas UFPel, Programa Posgrad Med Vet, Fac Vet, Campus Capao do Leao, BR-96900010 Capao Do Leao, RS, Brazil | Univ Fed Pelotas UFPel, Ctr Desenvolvimento Tecnol, Biotecnol, Campus Capao do Leao, BR-96900010 Capao Do Leao, RS, Brazil;Univ Fed Pelotas UFPel, Dept Vet Prevent, Campus Capao do Leao,Ave Eliseu Maciel S-N, BR-96900010 Capao Do Leao, RS, Brazil;Univ Fed Pelotas UFPel, Programa Posgrad Med Vet, Fac Vet, Campus Capao do Leao, BR-96900010 Capao Do Leao, RS, Brazil | 1678-5150 | Escherichia coli;Antigenicity;canine distemper virus;CDV;codon;DOG;expression;IgY;immunogenicity;NP;nucleocapsid protein;Synthetic gene;viroses | 8 | 1980;1989;1992;1995;1997;1998;1999;2000;2001;2004;2006;2007;2008;2009;2010;2012;2014;2015;2016 | 0 | Univ Fed Pelotas UFPel, Dept Vet Prevent, Campus Capao do Leao,Ave Eliseu Maciel S-N, BR-96900010 Capao Do Leao, RS, Brazil | Pesqui. Vet. Bras. | Hubner, Silvia O | REVISTA PESQUISA VETERINARIA BRASILEIRA | (IgY);(mean;(rCDV;,;28.55mg/mL;300;a;additionally;along;analysis;and;antibodies;antigenic;antigenicity;are;as;assays;available;be;being;blot;by;canine;CDV;characteristics;codon;coli;common;concentration;confirmed;conserved;control;could;currently;demonstrated;despite;development;diagnosis;disease;distemper;dog;egg;either;ELISA;employing;Escherichia;evaluated;expressed;expression;findings;for;from;g/mL;gene;hampered;hens;high;His-Tag;IgY;immunodiagnostic;immunogenic;immunoglobulin;importance;in;indicate;inoculated;is;isolate;it;low;majority;mean;monoclonal;mu;negative;NP);nucleocapsid;occurrence;of;optimized;or;our;positive;possible;protein;proved;purified;purified);rCDVNP;reacted;recognized;recombinant;region;results;SDS-PAGE;sensitivity;sera;since;specific;specificity;Star;strain;study;summary;synthetic;taken;tests;that;the;these;this;to;together;tools;useful;using;virus;vitro;was;Western;with;Y;yield;yolk | Univ Fed Pelotas UFPel | Despite common occurrence and importance of canine distemper disease the majority of tests currently available for diagnosis are hampered by either low sensitivity or specificity. In this study it was evaluated antigenic and immunogenic characteristics of a conserved region of nucleocapsid protein of canine distemper virus (rCDV NP) expressed in Escherichia coli employing a codon optimized synthetic gene. The expression of rCDVNP in Star strain (mean 300 mu g/mL, purified) was confirmed by SDS-PAGE and Western blot analysis by using His-Tag monoclonal antibodies. Western blot and ELISA, employing positive and negative control dog sera, demonstrated the rCDVNP antigenicity. The rCDVNP was inoculated in hens and immunoglobulin Y (IgY) was purified from the egg yolk. The mean yield of IgY was 28.55mg/mL. IgY reacted with the recombinant protein as demonstrated by Western blot and ELISA assays. In summary, our findings demonstrated that rCDVNP is antigenic since CDV positive dog sera recognized the protein in vitro. Additionally, the rCDVNP proved to be immunogenic in hens being possible to isolate a high concentration of specific IgY antibodies from the egg yolk. Taken together, these results indicate that the rCDVNP along with the specific IgY could be useful tools for development of the canine distemper immunodiagnostic assays. | AAJ-4965-2021;AFZ-3898-2022 | BRAZIL;CHICKEN IGY;DOGS;EGG-YOLK;ELISA;INFECTION;LINKED-IMMUNOSORBENT-ASSAY;MONOCLONAL-ANTIBODIES;NUCLEOPROTEIN;REGION | 0 | null | antigenic;canine distemper virus;CDV;codon;Dogs;Escherichia coli;expression;IgY;immunogenic;NP;nucleocapsid protein;Synthetic gene;viroses | 7 | ESCHERICHIA-COLI;ANTIGEN;BRAZIL;canine distemper virus;CDV;CHICKEN IGY;codon;Dogs;EGG-YOLK;ELISA;EXPRESSION;IgY;IMMUNOGENICITY;INFECTION;LINKED-IMMUNOSORBENT-ASSAY;MONOCLONAL-ANTIBODIES;NP;nucleocapsid protein;NUCLEOPROTEIN;REGION;Synthetic gene;viroses | WOS:000448939600020 | Univ Fed Pelotas UFPel, Capao Do Leao RS, Brazil | Brazil | 2,018 | null | 0000-0003-0145-0321 | null | null | English | null | ANTIVIR RES;BIOINFORMATICS;BIOSCI BIOTECH BIOCH;BRAZ J MED BIOL RES;BRIEF BIOINFORM;CSH Protoc;Curr Protoc Protein Sci;EMERG MICROBES INFEC;Expert Rev Mol Diagn;Genome Synthesis and Design Futures;IMMUNOL COMMUN;INT COMM TAX VIR;INT IMMUNOPHARMACOL;J CLIN MICROBIOL;J FOOD SCI;J GEN VIROL;J VET MED A;J VET MED B;J VET MED SCI;J VET SCI;J VIROL METHODS;J Vis Exp;J ZOO WILDLIFE MED;Monoclonal Antibodies in Immunodiagnosis and Immunotherapy;NEW MICROBIOL;PESQUI VET BRASIL;PLOS ONE;PROTEIN EXPRES PURIF;REVTA CIENC MED BIOL;T ROY SOC TROP MED H;VACCINE;VET CLIN N AM-SMALL;VET IMMUNOL IMMUNOP;VET MICROBIOL;WORLD POULTRY SCI J | Cunha, Rodrigo C;de Lima, Marcelo;Fernandes, Maureen H, V;Finger, Paula F;Fischer, Geferson;Hubner, Silvia O;Vargas, Gilberto D'Avila | 2024-03-11
ER | Akita, E M;Balamurugan, V;Barben, G;Beineke, A;Bentubo Henri Donnarumma Levy;Chan, K W;Chen, Y;Cho, K H;Deem, S L;Elia, G;Fighera, R A;Frisk, A L;Froger Alexandrine;Guimaraes M. C. C.;Ictv;Iwatsuki, K;Kammila, S;Karlsson, M;Kearse, M;Latha, D;Lavallie E, R;Lee, H;Li, G Q;Martella, V;Newcomb J.;Papaneophytou, C P;Polson, A;Ramos, C R R;Sambrook J.;Schmidt, P;Shin, Y S;Spencer, K A;Stettler, M;Vasconcellos, F A;Veerasami, M;Von Messling, V;Welch, M;Wen, J L;Yadav, V;Yi Li;Yoshida, E;Zhang, R H;Zhang, X Y | GY9DP | Capao Do Leao RS, Brazil | 0 | null | 1 | null | null | Cunha, Rodrigo C;de Lima, Marcelo;Fernandes, Maureen H, V;Finger, Paula F;Fischer, Geferson;Hubner, Silvia O;Vargas, Gilberto D'Avila | PESQUI VET BRASIL | Capao Do Leao RS, Brazil |
Chen, G Y;Chen, Z Y;Jiang, Q T;Li, W;Li, Z;Pu, Z E;Wei, Y M;Zhao, X F;Zheng, Y L | 10.1556/0806.46.2018.09 | null | BUDAFOKI UT 187-189-A-3, H-1117 BUDAPEST, HUNGARY | 5w2l716x654b1r521v2x3i293k126186c5c175z | Characterization of Starch Synthetic Genes and Starch Granule during Seeds Development between Synthetic Hexaploid Wheat and its Parents | Sichuan Agr Univ | null | Zheng, YL (corresponding author), Sichuan Agr Univ, Triticeae Res Inst, Chengdu 611130, Sichuan, Peoples R China. | null | Chen, G Y;Chen, Z Y;Jiang, Q T;Li, W;Li, Z;Pu, Z E;Wei, Y M;Zhao, X F;Zheng, Y L | Agronomy | Key Project of National Natural Science Foundation of China [31230053]; International Science & Technology Cooperation Program of China [2015DFA30600] | WOS | Zheng, Y L | Sichuan Agr Univ, Sichuan, Peoples R China | 46 | and;between;characterization;Development;during;genes;Granule;Hexaploid;its;of;Parents;Seeds;Starch;synthetic;Wheat | 1 | null | AKADEMIAI KIADO ZRT | Sichuan Agr Univ, Coll Agron, Chengdu 611130, Sichuan, Peoples R China;Sichuan Agr Univ, Triticeae Res Inst, Chengdu 611130, Sichuan, Peoples R China | Article | Sichuan Agr Univ | BUDAPEST | null | null | Sichuan Agr Univ | International Science & Technology Cooperation Program of China;Key Project of National Natural Science Foundation of China | Zheng, YL (corresponding author), Sichuan Agr Univ, Triticeae Res Inst, Chengdu 611130, Sichuan, Peoples R China. | 286 | Chen, G Y;Chen, Z Y;Jiang, Q T;Li, W;Li, Z;Pu, Z E;Wei, Y M;Zhao, X F;Zheng, Y L | 24 | 2 | 439,810,300,009 | International Science & Technology Cooperation Program of China [2015DFA30600];Key Project of National Natural Science Foundation of China [31230053] | China | CEREAL RESEARCH COMMUNICATIONS | China | null | null | Sichuan Agr Univ, Triticeae Res Inst, Chengdu 611130, Sichuan, Peoples R China | 0133-3720 | Chen, G Y;Chen, Z Y;Jiang, Q T;Li, W;Li, Z;Pu, Z E;Wei, Y M;Zhao, X F;Zheng, Y L | JUN | ylzheng@sicau.edu.cn | characterization;Parents;Seeds Development;Starch Granule;Starch Synthetic Genes;Synthetic Hexaploid Wheat | 9 | J | Agriculture | AEGILOPS;AGPLSU2;AGPSSU1;AGPSSU2;amount;AS2255;AS60;B-type granule;biosynthesis;characterization;developed starch granules;development;diploid Ae;DURUM;earlier stages;electron microscopy (SEM);ENDOSPERM;expression;expression pattern;GBSSI;genes;grain weight;hexaploid wheat;higher starch content;important role;larger quantity;Parents;parents T. turgidum AS2255;pattern;PHO1;PHO2;plays;polyploid wheats;results;RT-qPCR result;seed;Seeds Development;SHW-L1;SSIII;starch content;starch granule;starch granule development;starch granules;starch quality improvement;starch synthase;starch synthase gene expression;starch synthase genes;Starch Synthetic Genes;starch synthetic genes AGPLSU1;SYNTHASE;synthetic hexaploid wheat;synthetic hexaploid wheat SHW-L1;T-TAUSCHII;tauschii AS60;tetraploid;tetraploid parent;tetraploid wheat;three genotypes;TRITICUM-TURGIDUM;variability;WAXY PROTEINS;wheat grain development | Li, W | AEGILOPS;BIOSYNTHESIS;DURUM;ENDOSPERM;EXPRESSION;seed;starch granule;starch synthase;SYNTHASE;synthetic hexaploid wheat;T-TAUSCHII;tetraploid;TRITICUM-TURGIDUM;VARIABILITY;WAXY PROTEINS | 275 | [Li, W.; Chen, Z. Y.; Li, Z.; Zhao, X. F.; Pu, Z. E.; Chen, G. Y.; Jiang, Q. T.; Wei, Y. M.; Zheng, Y. L.] Sichuan Agr Univ, Triticeae Res Inst, Chengdu 611130, Sichuan, Peoples R China. [Li, W.; Chen, Z. Y.; Li, Z.; Zhao, X. F.; Pu, Z. E.] Sichuan Agr Univ, Coll Agron, Chengdu 611130, Sichuan, Peoples R China. | This work was supported by The Key Project of National Natural Science Foundation of China (No. 31230053) and The International Science & Technology Cooperation Program of China (No. 2015DFA30600). | AGPLSU2;AGPSSU1;AGPSSU2;amount;AS2255;AS60;B-type granule;developed starch granules;development;diploid Ae;earlier stages;electron microscopy (SEM);expression;expression pattern;GBSSI;genes;grain weight;hexaploid wheat;higher starch content;important role;larger quantity;parents;parents T. turgidum AS2255;pattern;PHO1;PHO2;plays;polyploid wheats;results;RT-qPCR result;SHW-L1;SSIII;starch content;starch granule development;starch granules;starch quality improvement;starch synthase gene expression;starch synthase genes;starch synthetic genes;starch synthetic genes AGPLSU1;synthetic hexaploid wheat;synthetic hexaploid wheat SHW-L1;tauschii AS60;tetraploid parent;tetraploid wheat;three genotypes;wheat grain development | 10.1006/anbo.2001.1531;10.1007/BF00027057;10.1007/s10681-008-9864-5;10.1007/s10681-012-0850-6;10.1007/s10722-009-9424-4;10.1007/s10722-011-9787-1;10.1007/s10722-015-0296-5;10.1007/s10725-010-9450-4;10.1007/s11032-009-9314-7;10.1007/s11032-010-9493-2;10.1016/j.jcs.2009.12.002;10.1016/j.jcs.2013.01.001;10.1016/j.jplph.2009.05.004;10.1016/S0065-2296(05)40001-4;10.1016/S0168-9452(03)00076-1;10.1016/S0378-1119(99)00178-X;10.1016/S0733-5210(95)80004-2;10.1016/S1369-5266(03)00042-6;10.1023/A:1018345505142;10.1046/j.1365-313x.2001.01012.x;10.1046/j.1439-0523.2000.00448.x;10.1073/pnas.072223799;10.1093/jxb/erh248;10.1093/jxb/eri065;10.1093/nar/29.9.e45;10.1093/oxfordjournals.aob.a088332;10.1094/CCHEM-85-1-0051;10.1094/CCHEM.2003.80.2.175;10.1104/pp.010363;10.1104/pp.107.3.673;10.1104/pp.120.4.993;10.1105/tpc.10.3.399;10.1105/tpc.107.054007;10.1105/tpc.13.8.1735;10.1105/tpc.7.7.971;10.1111/j.1439-037X.1994.tb00578.x;10.1139/g95-135;10.1139/gen-41-2-272;10.1146/annurev.arplant.54.031902.134927;10.1186/1471-2229-12-147;10.1186/1756-0500-3-140;10.1360/03yc0177 | Sichuan Agr Univ | Chen, G Y;Chen, Z Y;Jiang, Q T;Li, W;Li, Z;Pu, Z E;Wei, Y M;Zhao, X F;Zheng, Y L | Li, W: Sichuan Agr Univ, Triticeae Res Inst, Chengdu 611130, Sichuan, Peoples R China | feng, chen;Jiang, Qiantao;Jiang, Tao;Li, Tao;sheng, chen;SUN, YANLING;Yang, Tian | 2015DFA30600;31230053 | 43 | null | China | Sichuan Agr Univ | Li, W | null | AEGILOPS;BIOSYNTHESIS;DURUM;ENDOSPERM;EXPRESSION;SYNTHASE;T-TAUSCHII;TRITICUM-TURGIDUM;VARIABILITY;WAXY PROTEINS | Li, W.; Chen, Z. Y.; Li, Z.; Zhao, X. F.; Pu, Z. E.; Chen, G. Y.; Jiang, Q. T.; Wei, Y. M.; Zheng, Y. L.; | null | Sichuan Agr Univ, Coll Agron, Chengdu 611130, Sichuan, Peoples R China;Sichuan Agr Univ, Triticeae Res Inst, Chengdu 611130, Sichuan, Peoples R China | Sichuan Agr Univ, Coll Agron, Chengdu 611130, Sichuan, Peoples R China;Sichuan Agr Univ, Triticeae Res Inst, Chengdu 611130, Sichuan, Peoples R China | 1788-9170 | seed;starch granule;starch synthase;synthetic hexaploid wheat;tetraploid | 2 | 1992;1994;1995;1998;1999;2000;2001;2002;2003;2004;2005;2008;2009;2010;2011;2012;2013;2016 | 1 | Sichuan Agr Univ, Triticeae Res Inst, Chengdu 611130, Sichuan, Peoples R China | Cereal Res. Commun. | Zheng, Y L | AKADEMIAI KIADO ZRT | (SEM);,;above;Ae;AGPLSU1;AGPLSU2;AGPSSU1;AGPSSU2;all;also;amount;and;AS2255;AS60;associated;at;B-type;between;content;could;developed;development;diploid;during;earlier;electron;expressed;expression;for;from;GBSSI;gene;genes;genotypes;grain;granule;granules;hexaploid;higher;important;improvement;in;inherited;investigated;its;larger;less;mentioned;microscopy;more;of;parent;parents;pattern;PHO1;PHO2;plays;polyploid;quality;quantity;rapidly;result;results;role;RT-qPCR;scanning;showed;SHW-L1;significantly;slower;SSIII;stages;starch;study;suggest;suggested;synthase;synthetic;T.;tauschii;tetraploid;than;that;the;three;to;turgidum;was;we;weight;wheat;wheats;with | Sichuan Agr Univ | To study the development of starch granules in polyploid wheats, we investigated the expression of starch synthetic genes between the synthetic hexaploid wheat SHW-L1, its parents T. turgidum AS2255 and diploid Ae. tauschii AS60. The synthetic hexaploid wheat SHW-L1 showed significantly higher starch content and grain weight than its parents. Scanning electron microscopy (SEM) showed that SHW-L1 rapidly developed starch granules than AS2255 and AS60. The amount of B-type granule in AS60 was less than that in SHW-L1 and AS2255. RT-qPCR result showed that the starch synthetic genes AGPLSU1, AGPLSU2, AGPSSU1, AGPSSU2, GBSSI, SSIII, PHO1 and PHO2 expressed at earlier stages with larger quantity in SHW-L1 than in its parents during wheat grain development. The expression of the above mentioned genes in AS60 was slower than in SHW-L1 and AS2255. The expression pattern of starch synthase genes was also associated with the grain weight and starch content in all three genotypes. The results suggested that the synthetic hexaploid wheat inherited the pattern of starch granule development and starch synthase gene expression from tetraploid parent. The results suggest that tetraploid wheat could plays more important role for starch quality improvement in hexaploid wheat. | C-6229-2017;IWM-7503-2023;IWU-9607-2023;JEO-8801-2023;JFB-1008-2023;JLM-8296-2023;JTT-9082-2023 | AEGILOPS;BIOSYNTHESIS;DURUM;ENDOSPERM;EXPRESSION;SYNTHASE;T-TAUSCHII;TRITICUM-TURGIDUM;VARIABILITY;WAXY PROTEINS | 4 | null | seed;starch granule;starch synthase;synthetic hexaploid wheat;tetraploid | 12 | AEGILOPS;BIOSYNTHESIS;DURUM;ENDOSPERM;EXPRESSION;SEEDS;starch granule;starch synthase;SYNTHASE;synthetic hexaploid wheat;T-TAUSCHII;tetraploid;TRITICUM-TURGIDUM;VARIABILITY;WAXY PROTEINS | WOS:000439810300009 | Sichuan Agr Univ, Sichuan, Peoples R China | China | 2,018 | null | null | null | null | English | null | ADV BOT RES;ANN BOT-LONDON;ANNU REV PLANT BIOL;BMC PLANT BIOL;BMC Res Notes;CEREAL CHEM;CURR OPIN PLANT BIOL;EUPHYTICA;GENE;GENET RESOUR CROP EV;GENOME;J AGRON CROP SCI;J CEREAL SCI;J EXP BOT;J PLANT PHYSIOL;MOL BREEDING;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PLANT BREEDING;PLANT CELL;PLANT GROWTH REGUL;PLANT J;PLANT PHYSIOL;PLANT SCI;SCI CHINA SER C | Chen, G Y;Chen, Z Y;Jiang, Q T;Li, W;Li, Z;Pu, Z E;Wei, Y M;Zhao, X F;Zheng, Y L | 2024-03-11
ER | Ball, S G;Bechtel, D B;Burton, R A;Colleoni, C;Critchley, J H;Dian, W M;Flood, R G;Gao, M;Gororo, N N;Guo, G F;Guzmán, C;Hogg, A C;Huang Xiu-Qiang;Huang, S;Hurkman, W J;James, M G;Kang, G Z;Konik-Rose, C M;Li Zhongyi;Li, W;Limin, A E;Liu, B;Ma, H;Martin, C;Murai, J;Nieto-Taladriz, M T;Ozkan, H;Pena, R J;Pfaffl, M W;Satoh, H;Sestili, F;Smith, A M;Tetlow, I J;Tickle, P;Tomlinson, K;Villareal, R L;Watanabe, N;Yamamori, M;Zhang, C H;Zhang, L Q;Zhu, T | GO2NI | Sichuan, Peoples R China | 1 | null | 1 | null | null | Chen, G Y;Chen, Z Y;Jiang, Q T;Li, W;Li, Z;Pu, Z E;Wei, Y M;Zhao, X F;Zheng, Y L | CEREAL RES COMMUN | Sichuan, Peoples R China |
Aubel, D;Fussenegger, M;Sedlmayer, F | 10.1038/s41551-018-0215-0 | null | MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND | 6p6w215z3j32n1b5j6p2z155f5l1i4o5m4ua2 | Synthetic gene circuits for the detection, elimination and prevention of disease | Swiss Fed Inst Technol | null | Fussenegger, M (corresponding author), Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland.;Fussenegger, M (corresponding author), Univ Basel, Fac Sci, Basel, Switzerland. | null | Aubel, Dominique;Fussenegger, Martin;Sedlmayer, Ferdinand | Engineering, Biomedical | European Research Council Advanced Grant (ProNet) [321381]; European Research Council (ERC) [321381] Funding Source: European Research Council (ERC) | WOS | Fussenegger, M | Swiss Fed Inst Technol, Basel, Switzerland;Univ Basel, Basel, Switzerland;Univ Claude Bernard Lyon, Lyon, France | 2 | ,;and;circuits;detection;disease;elimination;for;gene;of;prevention;synthetic;the | 2 | Sedlmayer, Ferdinand | NATURE PUBLISHING GROUP | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland;Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland.; Fussenegger, M (corresponding author), Univ Basel, Fac Sci, Basel, Switzerland;Univ Basel, Fac Sci, Basel, Switzerland;Univ Claude Bernard Lyon 1, IUTA Dept Genie Biol, Lyon, France | Review | Swiss Fed Inst Technol;Univ Basel | LONDON | null | null | Swiss Fed Inst Technol;Univ Basel;Univ Claude Bernard Lyon 1 | European Research Council (ERC);European Research Council Advanced Grant (ProNet) | Fussenegger, M (corresponding author), Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland.; Fussenegger, M (corresponding author), Univ Basel, Fac Sci, Basel, Switzerland. | 415 | Aubel, Dominique;Fussenegger, Martin;Sedlmayer, Ferdinand | 146 | 3 | 435,474,500,010 | European Research Council (ERC) [321381] Funding Source: European Research Council (ERC);European Research Council Advanced Grant (ProNet) [321381] | France;Switzerland | NATURE BIOMEDICAL ENGINEERING | Switzerland | null | null | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland | 2157-846X | Aubel, D;Fussenegger, M;Sedlmayer, F | JUN | fussenegger@bsse.ethz.ch | detection;disease;elimination;prevention;synthetic gene circuits | 3 | J | Engineering | applications;autoimmune diseases;AUTOMATED DESIGN;autonomously;basis;BIOLOGY;biomedical applications;cancer remission;changing conditions;clinic;controlled timing;CONTROLLED TRANSGENE EXPRESSION;DELIVERY;DESIGNER CELLS;designing molecular building blocks de novo;detection;devices;diagnostics;disease;disease biomarkers;dosage;elimination;ENGINEERED BACTERIA;experimental animal models;first;human cells;inspired biologists;laboratory;leap;living organisms;major disease areas;MAMMALIAN-CELLS;monitor;natural processes;network's unprecedented specificity;ORGANISMS;pathways;prevention;process environmental cues trigger corrective actions;production;proteins;repurposing;review;RNA;Sensors;synthetic gene circuits;synthetic living sensors;synthetic-biology principles;T-CELLS;tailored genetic networks;therapeutics;TRANSCRIPTIONAL ACTIVATION;unbalanced pathological states;user-defined synthetic gene circuits | Sedlmayer, F | AUTOMATED DESIGN;BIOLOGY;CONTROLLED TRANSGENE EXPRESSION;DELIVERY;DESIGNER CELLS;ENGINEERED BACTERIA;MAMMALIAN-CELLS;RNA;T-CELLS;TRANSCRIPTIONAL ACTIVATION | 399 | [Sedlmayer, Ferdinand; Fussenegger, Martin] Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland. [Aubel, Dominique] Univ Claude Bernard Lyon 1, IUTA Dept Genie Biol, Lyon, France. [Fussenegger, Martin] Univ Basel, Fac Sci, Basel, Switzerland. | We thank D. Fuchs, D. Sequeira, X. Pierrat and S. Auslander for scientific advice. This work was supported by a European Research Council Advanced Grant (ProNet, no. 321381). | applications;autoimmune diseases;autonomously;basis;biomedical applications;cancer remission;changing conditions;clinic;controlled timing;designer cells;designing molecular building blocks de novo;devices;diagnostics;disease biomarkers;dosage;experimental animal models;first;human cells;inspired biologists;laboratory;leap;living organisms;major disease areas;monitor;natural processes;network's unprecedented specificity;organisms;pathways;process environmental cues trigger corrective actions;production;proteins;repurposing;review;sensors;synthetic gene circuits;synthetic living sensors;synthetic-biology principles;tailored genetic networks;therapeutics;unbalanced pathological states;user-defined synthetic gene circuits | 10.1002/anie.201412204;10.1002/anie.201609229;10.1002/bies.201400094;10.1002/bit.26026;10.1002/btpr.2152;10.1002/cncr.28365;10.1002/wsbm.1345;10.1007/978-1-4939-0805-9_11;10.1007/978-1-4939-3271-9_2;10.1007/978-1-61779-412-4_4;10.1016/j.addr.2016.04.032;10.1016/j.addr.2016.05.019;10.1016/j.bios.2015.07.035;10.1016/j.cbpa.2015.05.021;10.1016/j.cell.2016.01.011;10.1016/j.cell.2016.01.012;10.1016/j.cell.2016.04.059;10.1016/j.cell.2016.09.011;10.1016/j.cell.2017.09.049;10.1016/j.celrep.2015.02.049;10.1016/j.celrep.2017.08.044;10.1016/j.cels.2015.06.001;10.1016/j.cels.2015.08.013;10.1016/j.cels.2017.01.003;10.1016/j.chembiol.2017.05.008;10.1016/j.copbio.2015.01.010;10.1016/j.copbio.2015.05.004;10.1016/j.copbio.2015.08.017;10.1016/j.copbio.2016.04.005;10.1016/j.ebiom.2017.05.014;10.1016/j.febslet.2012.02.032;10.1016/j.jbiotec.2009.02.023;10.1016/j.jconrel.2010.11.016;10.1016/j.jhep.2016.03.020;10.1016/j.jmb.2015.08.020;10.1016/j.jmb.2015.10.004;10.1016/j.mib.2017.05.014;10.1016/j.molcel.2014.04.022;10.1016/j.molcel.2014.06.007;10.1016/j.stem.2015.04.005;10.1016/j.tibtech.2012.11.006;10.1016/j.tibtech.2014.10.006;10.1016/j.tig.2016.01.005;10.1016/j.ymben.2011.06.003;10.1016/j.ymben.2013.11.003;10.1016/j.ymben.2015.03.016;10.1016/j.ymthe.2016.10.005;10.1016/j.ymthe.2017.03.012;10.1021/acs.nanolett.5b01943;10.1021/acs.nanolett.7b02270;10.1021/acssynbio.6b00075;10.1021/acssynbio.6b00079;10.1021/acssynbio.6b00296;10.1021/acssynbio.7b00058;10.1021/acssynbio.7b00303;10.1021/ja509263k;10.1021/sb4000417;10.1021/sb400077j;10.1021/sb500090b;10.1021/sb500252a;10.1038/msb.2010.99;10.1038/msb.2012.71;10.1038/mtna.2013.35;10.1038/nature11149;10.1038/nature12148;10.1038/nature13828;10.1038/nature14136;10.1038/nature18930;10.1038/nature20796;10.1038/nature23271;10.1038/nbt.2351;10.1038/nbt.2459;10.1038/nbt.3011;10.1038/nbt.3033;10.1038/nbt.3043;10.1038/nbt.3053;10.1038/nbt.3301;10.1038/nbt.3805;10.1038/nbt.3873;10.1038/nbt.3879;10.1038/nbt840;10.1038/ncomms10243;10.1038/ncomms11247;10.1038/ncomms11658;10.1038/ncomms15028;10.1038/ncomms3825;10.1038/ncomms5408;10.1038/ncomms5729;10.1038/ncomms6392;10.1038/ncomms6393;10.1038/ncomms7989;10.1038/ng.343;10.1038/nm.3471;10.1038/nm0117-5;10.1038/nprot.2014.082;10.1038/nrclinonc.2017.156;10.1038/nrg3094;10.1038/nrmicro3239;10.1038/s41467-017-01211-1;10.1038/s41467-018-04223-7;10.1038/s41551-016-0005;10.1038/s41551-017-0097;10.1039/c5ib00274e;10.1039/c5lc00107b;10.1056/NEJMoa1407222;10.1073/pnas.0704624104;10.1073/pnas.1001294107;10.1073/pnas.1216801110;10.1073/pnas.1217554109;10.1073/pnas.1312414110;10.1073/pnas.1321321111;10.1073/pnas.1402087111;10.1073/pnas.1500107112;10.1073/pnas.1508521112;10.1073/pnas.1514383113;10.1073/pnas.1604391113;10.1073/pnas.89.12.5547;10.1074/jbc.M110.177600;10.1083/jcb.201502074;10.1089/hum.2014.052;10.1093/bioinformatics/btw415;10.1093/nar/gkt002;10.1093/nar/gku1082;10.1093/nar/gkv326;10.1093/nar/gkx298;10.1093/nar/gng069;10.1097/TP.0000000000001016;10.1101/cshperspect.a023895;10.1111/obr.12229;10.1126/science.1205527;10.1126/science.1225829;10.1126/science.aac7341;10.1126/science.aaf4006;10.1126/science.aag0511;10.1126/science.aam9321;10.1126/scitranslmed.3005568;10.1126/scitranslmed.3006368;10.1126/scitranslmed.aaa3519;10.1126/scitranslmed.aaa3601;10.1126/scitranslmed.aac4964;10.1126/scitranslmed.aac5415;10.1126/scitranslmed.aak9537;10.1126/scitranslmed.aal2298;10.1128/JVI.01786-15;10.1172/JCI72517;10.1186/s12866-016-0876-3;10.1186/s12934-015-0288-3;10.1186/s13195-016-0195-9;10.1371/journal.pone.0084081;10.15252/msb.20145508;10.15252/msb.20145735;10.1586/14760584.2015.997714;10.2337/db14-0635;10.3389/fimmu.2016.00091;10.3389/fmicb.2017.01503;[10.1038/nchembio.1979, 10.1038/NCHEMBIO.1979];[10.1038/NCHEMBIO.2253, 10.1038/nchembio.2253];[10.1038/NCHEMBIO.2281, 10.1038/nchembio.2281];[10.1038/nchembio.2498, 10.1038/NCHEMBIO.2498];[10.1038/NMETH.2926, 10.1038/nmeth.2926];[10.1038/nmeth.3136, 10.1038/NMETH.3136];[10.1038/NMETH.3339, 10.1038/nmeth.3339];[10.1038/NMETH.3585, 10.1038/nmeth.3585];[10.1038/NMETH.4505, 10.1038/nmeth.4505];[10.1038/nnano.2014.58, 10.1038/NNANO.2014.58] | Swiss Fed Inst Technol | Aubel, D;Fussenegger, M;Sedlmayer, F | Sedlmayer, F: Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland | null | 321381 | 165 | null | Switzerland | Swiss Fed Inst Technol;Univ Basel;Univ Claude Bernard Lyon 1 | Sedlmayer, Ferdinand | null | AUTOMATED DESIGN;BIOLOGY;CONTROLLED TRANSGENE EXPRESSION;DELIVERY;DESIGNER CELLS;ENGINEERED BACTERIA;MAMMALIAN-CELLS;RNA;T-CELLS;TRANSCRIPTIONAL ACTIVATION | Sedlmayer, Ferdinand; Aubel, Dominique; Fussenegger, Martin; | null | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland;Univ Basel, Fac Sci, Basel, Switzerland;Univ Claude Bernard Lyon 1, IUTA Dept Genie Biol, Lyon, France | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland;Univ Basel, Fac Sci, Basel, Switzerland;Univ Claude Bernard Lyon 1, IUTA Dept Genie Biol, Lyon, France | null | null | 6 | 1992;2003;2007;2009;2010;2011;2012;2013;2014;2015;2016;2017;2018 | 71 | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland;Univ Basel, Fac Sci, Basel, Switzerland | Nat. Biomed. Eng | Fussenegger, Martin | NATURE PUBLISHING GROUP | ,;actions;also;and;animal;applications;are;areas;autoimmune;autonomously;bacterial;basis;being;biologists;biomarkers;biomedical;blocks;building;by;can;cancer;cells;changing;circuits;clinic;conditions;constantly;construct;controlled;coordinate;cope;corrective;cues;customized;de;describe;designer;designing;developed;devices;diagnostics;discuss;disease;diseases;dosage;employ;enable;engineered;environmental;evolved;experimental;explored;first;for;from;furthermore;gene;genetic;genetically;have;how;human;in;infectious;inspired;laboratory;leap;led;living;made;major;metabolic;models;molecular;monitor;natural;naturally;network's;networks;novo;occurring;of;on;operating;or;organisms;other;owing;particular;pathological;pathways;principles;process;processes;production;proteins;re-adjust;remission;repurposing;review;sensors;signalling;specificity;states;such;survey;synthetic;synthetic-biology;tailored;that;the;therapeutics;this;timing;to;trigger;unbalanced;unprecedented;user-defined;we;with | Swiss Fed Inst Technol;Univ Basel | In living organisms, naturally evolved sensors that constantly monitor and process environmental cues trigger corrective actions that enable the organisms to cope with changing conditions. Such natural processes have inspired biologists to construct synthetic living sensors and signalling pathways, by repurposing naturally occurring proteins and by designing molecular building blocks de novo, for customized diagnostics and therapeutics. In particular, designer cells that employ user-defined synthetic gene circuits to survey disease biomarkers and to autonomously re-adjust unbalanced pathological states can coordinate the production of therapeutics, with controlled timing and dosage. Furthermore, tailored genetic networks operating in bacterial or human cells have led to cancer remission in experimental animal models, owing to the network's unprecedented specificity. Other applications of designer cells in infectious, metabolic and autoimmune diseases are also being explored. In this Review, we describe the biomedical applications of synthetic gene circuits in major disease areas, and discuss how the first genetically engineered devices developed on the basis of synthetic-biology principles made the leap from the laboratory to the clinic. | null | AUTOMATED DESIGN;BIOLOGY;CONTROLLING TRANSGENE EXPRESSION;DELIVERY;DESIGNER CELLS;ENGINEERED BACTERIA;MAMMALIAN-CELLS;RNA;T-CELLS;TRANSCRIPTIONAL ACTIVATION | 4 | null | null | 17 | AUTOMATED DESIGN;BIOLOGY;CONTROLLING TRANSGENE EXPRESSION;DELIVERY;DESIGNER CELLS;ENGINEERED BACTERIA;MAMMALIAN-CELLS;RNA;T-CELLS;TRANSCRIPTIONAL ACTIVATION | WOS:000435474500010 | Swiss Fed Inst Technol, Basel, Switzerland;Univ Basel, Basel, Switzerland;Univ Claude Bernard Lyon, Lyon, France | France;Switzerland | 2,018 | null | 0000-0001-9877-5549 | null | null | English | null | ACS SYNTH BIOL;ADV DRUG DELIVER REV;ALZHEIMERS RES THER;ANGEW CHEM INT EDIT;BIOESSAYS;BIOINFORMATICS;BIOSENS BIOELECTRON;BIOTECHNOL BIOENG;BIOTECHNOL PROGR;BMC MICROBIOL;CANCER-AM CANCER SOC;CELL;CELL CHEM BIOL;CELL REP;CELL STEM CELL;CELL SYST;CSH PERSPECT BIOL;CURR OPIN BIOTECH;CURR OPIN CHEM BIOL;CURR OPIN MICROBIOL;DIABETES;EBIOMEDICINE;EXPERT REV VACCINES;FEBS LETT;FRONT IMMUNOL;FRONT MICROBIOL;HUM GENE THER;INTEGR BIOL-UK;J AM CHEM SOC;J BIOL CHEM;J BIOTECHNOL;J CELL BIOL;J CLIN INVEST;J CONTROL RELEASE;J HEPATOL;J MOL BIOL;J VIROL;LAB CHIP;METAB ENG;METHODS MOL BIOL;MICROB CELL FACT;MOL CELL;MOL SYST BIOL;MOL THER;MOL THER-NUCL ACIDS;NANO LETT;NAT BIOMED ENG;NAT BIOTECHNOL;NAT CHEM BIOL;NAT COMMUN;NAT GENET;NAT MED;NAT METHODS;NAT NANOTECHNOL;NAT PROTOC;NAT REV CLIN ONCOL;NAT REV GENET;NAT REV MICROBIOL;NATURE;NEW ENGL J MED;NUCLEIC ACIDS RES;OBES REV;P NATL ACAD SCI USA;PLOS ONE;SCI TRANSL MED;SCIENCE;TRANSPLANTATION;TRENDS BIOTECHNOL;TRENDS GENET;WIRES SYST BIOL MED | Aubel, Dominique;Fussenegger, Martin;Sedlmayer, Ferdinand | 2024-03-11
ER | [Anonymous];Agustín-Pavón, C;Amir, Y;Ando, H;Andries, O;Ausländer, D;Ausländer, S;Bacchus, W;Baeumler, T A;Bai, P;Baig, H;Balazs, A B;Bikard, D;Borrero, J;Bradley, R W;Brazzoli, M;Brophy, J A N;Buffie, C G;Busskamp, V;Caliando, B J;Cameron, D E;Ceroni, F;Chan, C T Y;Chassin, H;Chen, Z Y;Cheng, J K;Citorik, R J;Courbet, A;Daniel, R;Danino, T;Dastor, M;De La Fuente-Nunez, C;Della Peruta, M;Di Bernardo, D;Din, M O;Dormitzer, P R;Duan, F F;Duan, F P;Duportet, X;Ehrhardt, K;Eyjolfsdottir, H;Fischbach, M A;Folcher, M;Gallagher, R R;Geering, B;Gootenberg, J S;Gossen, M;Green, A A;Gröger, A;Gupta, S;Guye, P;Guzmán-Herrador, D L;Haellman, V;Heng, B C;Hirsch, M L;Holowko, M B;Hwang, I Y;Hörner, M;Issa, F;Ittig, S J;Jayaraman, P;Jinek, M;Kawasaki, S;Kemmer, C;Kim, T;Klingemann, H;Kloss, C C;Kojima, R;Konermann, S;Kong, D S;Kong, W;Kotula, J W;Krishnamurthy, M;Krom, R J;Limaye, S A;Liu, Y C;Lu, T K;Luo, X L;Maddalena, A;Manzoni, R;Matsuoka, Y;Maude, S L;Maxmen, A;Miki, K;Mimee, M;Mohammadi, P;Morel, M;Morsut, L;Mátés, L;Müller, K;Müller, M;Nielsen, A A;Nielsen, A A K;Nissim, L;O'Neill, S;Otero-Muras, I;Pardee, K;Park, J S;Perli, S D;Piñero-Lambea, C;Porter, D L;Prasad, V;Prochazka, L;Qudrat, A;Quintero, D;Rajendra, Y;Rezania, A;Riglar, D T;Ronda, C;Roybal, K T;Rubens, J R;Ryu, M H;Rössger, K;Saxena, P;Schukur, L;Schwarz, K A;Sedlmayer, F;Shao, J W;Sheth, R U;Slomovic, S;Smole, A;Steidler, L;Thaiss, C A;Thompson, J A;Wang, H;Weber, W;Weinberg, B H;Wroblewska, L;Wu, H C;Xie, M;Xie, M Q;Xie, Z;Ye, H F;Yin, C R;Yosef, I;You, M X;Zargar, A;Zheng, J H | GJ6DR | Basel, Switzerland;Basel, Switzerland. | 79 | null | 3 | null | 31,011,195 | Aubel, Dominique;Fussenegger, Martin;Sedlmayer, Ferdinand | NAT BIOMED ENG | Basel, Switzerland;Lyon, France |
Kremling, A;Löwe, H;Pflüger-Grau, K;Wagner, S G;Ziegler, M | 10.1371/journal.pone.0197420 | e0197420 | 1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA | 28245l642x631d336c723i4d291c1cg3748649 | pTRA - A reporter system for monitoring the intracellular dynamics of gene expression | Tech Univ Munich | null | Pflüger-Grau, K (corresponding author), Tech Univ Munich, Fac Mech Engn, Syst Biotechnol, Garching, Germany. | null | Kremling, Andreas;Loewe, Hannes;Pflueger-Grau, Katharina;Wagner, Sabine G;Ziegler, Martin | Multidisciplinary Sciences | German Federal Ministry of Education and Research (BMBF) with the Grant SysBioTerp [031A305A] | WOS | Pflüger-Grau, K | Tech Univ Munich, Garching, Germany;Univ Stuttgart, Stuttgart, Germany | 13 | -;a;dynamics;expression;for;gene;intracellular;monitoring;of;pTRA;Reporter;system;the | 1 | Lowe, Hannes;Ziegler, Martin | PUBLIC LIBRARY SCIENCE | Tech Univ Munich, Fac Mech Engn, Syst Biotechnol, Garching, Germany;Univ Stuttgart, Inst Biochem Engn, Stuttgart, Germany | Article | Tech Univ Munich | SAN FRANCISCO | null | null | Tech Univ Munich;Univ Stuttgart | German Federal Ministry of Education and Research (BMBF) with the Grant SysBioTerp | Pflüger-Grau, K (corresponding author), Tech Univ Munich, Fac Mech Engn, Syst Biotechnol, Garching, Germany. | null | Kremling, Andreas;Loewe, Hannes;Pflueger-Grau, Katharina;Wagner, Sabine G;Ziegler, Martin | 5 | 2 | 432,348,900,057 | German Federal Ministry of Education and Research (BMBF) with the Grant SysBioTerp [031A305A] | Germany | PLOS ONE | Germany | null | null | Tech Univ Munich, Fac Mech Engn, Syst Biotechnol, Garching, Germany | 1932-6203 | Kremling, A;Löwe, H;Pflüger-Grau, K;Wagner, S G;Ziegler, M | MAY 17 | k.pflueger-grau@tum.de | gene expression;intracellular dynamics;pTRA;reporter system | 5 | J | Science & Technology - Other Topics | assignment;behaviour;biological parts;BIOLOGY;case study;different genetic setups;end;ESCHERICHIA-COLI;EUROPEAN VECTOR ARCHITECTURE;fluorescent mCherry protein;FLUORESCENT PROTEIN;functions;GENE;gene expression;gene(s);GOI;identified;INFORMATION;interest (GOI);intracellular dynamics;methods;mRNA;optimal combination;plasmid pTRA;potential;prerequisite;protein formation;pTRA;pTRA plasmid;reporter system;SEVA;shortcomings;specific synthetic part;specific transcriptional;standardised tools;successful metabolic engineering;synthetic function;synthetic gene networks;synthetic genetic circuits;toolkit;transcriptional;transcriptional circuits;transcriptional strength;translational activity;translational outputs;understanding;vivo | Wagner, S G | BIOLOGY;ESCHERICHIA-COLI;EUROPEAN VECTOR ARCHITECTURE;FLUORESCENT PROTEIN;SEVA | null | [Wagner, Sabine G.; Ziegler, Martin; Loewe, Hannes; Kremling, Andreas; Pflueger-Grau, Katharina] Tech Univ Munich, Fac Mech Engn, Syst Biotechnol, Garching, Germany. [Ziegler, Martin] Univ Stuttgart, Inst Biochem Engn, Stuttgart, Germany. | This work was supported by the German Federal Ministry of Education and Research (BMBF) with the Grant SysBioTerp (Support Code 031A305A) to AK. | assignment;behaviour;biological parts;case study;different genetic setups;end;fluorescent mCherry protein;functions;gene;gene(s);GOI;identified;information;interest (GOI);intracellular dynamics;methods;mRNA;optimal combination;plasmid pTRA;potential;prerequisite;protein formation;pTRA plasmid;shortcomings;specific synthetic part;specific transcriptional;standardised tools;successful metabolic engineering;synthetic function;synthetic gene networks;synthetic genetic circuits;toolkit;transcriptional;transcriptional circuits;transcriptional strength;translational activity;translational outputs;understanding;vivo | 10.1007/s00253-002-1158-6;10.1007/s10529-007-9384-8;10.1016/0168-1656(91)90032-Q;10.1016/j.chembiol.2015.04.018;10.1016/j.mib.2016.07.009;10.1016/j.nbt.2017.05.001;10.1021/ja508478x;10.1038/227680a0;10.1038/nature04342;10.1038/NMETH1062;10.1093/nar/gks1119;10.1093/nar/gku1114;10.1101/019927];10.1111/1751-7915.12701 | Tech Univ Munich | Kremling, A;Löwe, H;Pflüger-Grau, K;Wagner, S G;Ziegler, M | Wagner, S G: Tech Univ Munich, Fac Mech Engn, Syst Biotechnol, Garching, Germany | null | 031A305A | 15 | null | Germany | Tech Univ Munich;Univ Stuttgart | Wagner, Sabine G | Green Published, gold, Green Submitted | BIOLOGY;ESCHERICHIA-COLI;EUROPEAN VECTOR ARCHITECTURE;FLUORESCENT PROTEIN;SEVA | Wagner, Sabine G.; Ziegler, Martin; Loewe, Hannes; Kremling, Andreas; Pflueger-Grau, Katharina; | null | Tech Univ Munich, Fac Mech Engn, Syst Biotechnol, Garching, Germany;Univ Stuttgart, Inst Biochem Engn, Stuttgart, Germany | Tech Univ Munich, Fac Mech Engn, Syst Biotechnol, Garching, Germany;Univ Stuttgart, Inst Biochem Engn, Stuttgart, Germany | null | null | 5 | 1970;1991;2001;2003;2005;2007;2013;2014;2015;2016;2017;2018 | 2 | Tech Univ Munich, Fac Mech Engn, Syst Biotechnol, Garching, Germany | PLoS One | Pflueger-Grau, Katharina | PUBLIC LIBRARY SCIENCE | (GOI);,;a;accurately;activity;allows;analyse;and;are;as;assignment;based;be;behaviour;biological;by;can;case;circuits;combination;compare;crucial;design;developed;different;discuss;dynamics;encoding;end;engineering;fine-tuning;fluorescent;for;formation;function;functions;gene;gene(s);genetic;GOI;have;identified;important;in;information;interest;intracellular;is;it;many;mCherry;measure;metabolic;methods;mRNA;networks;of;on;optimal;outputs;part;parts;plasmid;potential;predict;prerequisite;presence;protein;pTRA;represent;setups;shortcomings;show;specific;standardised;strength;study;successful;synthetic;systematically;tested;the;this;thus;to;toolkit;tools;transcriptional;translational;understand;understanding;using;vivo;we | Tech Univ Munich | The presence of standardised tools and methods to measure and represent accurately biological parts and functions is a prerequisite for successful metabolic engineering and crucial to understand and predict the behaviour of synthetic genetic circuits. Many synthetic gene networks are based on transcriptional circuits, thus information on transcriptional and translational activity is important for understanding and fine-tuning the synthetic function. To this end, we have developed a toolkit to analyse systematically the transcriptional and translational activity of a specific synthetic part in vivo. It is based on the plasmid pTRA and allows the assignment of specific transcriptional and translational outputs to the gene(s) of interest (GOI) and to compare different genetic setups. By this, the optimal combination of transcriptional strength and translational activity can be identified. The design is tested in a case study using the gene encoding the fluorescent mCherry protein as GOI. We show the intracellular dynamics of mRNA and protein formation and discuss the potential and shortcomings of the pTRA plasmid. | null | BIOLOGY;ESCHERICHIA-COLI;EUROPEAN VECTOR ARCHITECTURE;FLUORESCENT PROTEIN;SEVA | 0 | null | null | 11 | ESCHERICHIA-COLI;BIOLOGY;EUROPEAN VECTOR ARCHITECTURE;FLUORESCENT PROTEIN;SEVA | WOS:000432348900057 | Tech Univ Munich, Garching, Germany;Univ Stuttgart, Stuttgart, Germany | Germany | 2,018 | null | 0000-0003-2137-5234;0000-0003-3867-6391 | null | null | English | null | APPL MICROBIOL BIOT;BioRxiv;BIOTECHNOL LETT;CHEM BIOL;CURR OPIN MICROBIOL;J AM CHEM SOC;J BIOTECHNOL;MICROB BIOTECHNOL;Molecular cloning;NAT METHODS;NATURE;NEW BIOTECHNOL;NUCLEIC ACIDS RES | Kremling, Andreas;Loewe, Hannes;Pflueger-Grau, Katharina;Wagner, Sabine G;Ziegler, Martin | 2024-03-11
ER | Borkowski, O;De Lorenzo, V;Endy, D;Filonov, G S;Gawin, A;Gorii-Moreno, A;Hiller, J;Laemmli, U K;Martínez-García, E;Merzlyak, E M;Riesenberg, D;Sambrook J.;Silva-Rocha, R;Terpe, K | GG0DP | Garching, Germany | 2 | null | 2 | null | 29,772,009 | Kremling, Andreas;Loewe, Hannes;Pflueger-Grau, Katharina;Wagner, Sabine G;Ziegler, Martin | PLOS ONE | Garching, Germany;Stuttgart, Germany |
Dong, K L;Wang, M Y;Wang, Y D;Ye, H F | 10.1002/biot.201700160 | 1700160 | POSTFACH 101161, 69451 WEINHEIM, GERMANY | 3p5t4h2w7121y6u3n3z1x3c3z3t1j3m3r5c2l | Engineering Mammalian Designer Cells for the Treatment of Metabolic Diseases | East China Normal Univ | null | Ye, HF (corresponding author), East China Normal Univ, Inst Biomed Sci, Shanghai Key Lab Regulatory Biol, Dongchuan Rd 500, Shanghai 200241, Peoples R China.;Ye, HF (corresponding author), East China Normal Univ, Sch Life Sci, Dongchuan Rd 500, Shanghai 200241, Peoples R China. | SI | Dong, Kaili;Wang, Meiyan;Wang, Yidan;Ye, Haifeng | Biochemical Research Methods;Biotechnology & Applied Microbiology | National Natural Science Foundation of China (NSFC) [31522017]; National Key Research and Development Program of China, Stem Cell, and Translational Research [2016YFA0100300]; NSFC [31470834, 31670869]; Science and Technology Commission of Shanghai Municipality [15QA1401500, 14JC1401700]; Thousand Youth Talents Plan of China | WOS | Ye, H F | East China Normal Univ, Shanghai, Peoples R China | 13 | Cells;Designer;Diseases;engineering;for;mammalian;Metabolic;of;the;Treatment | 1 | Wang, Meiyan | WILEY-V C H VERLAG GMBH | East China Normal Univ, Inst Biomed Sci, Shanghai Key Lab Regulatory Biol, Dongchuan Rd 500, Shanghai 200241, Peoples R China;East China Normal Univ, Inst Biomed Sci, Shanghai Key Lab Regulatory Biol, Dongchuan Rd 500, Shanghai 200241, Peoples R China.; Ye, HF (corresponding author), East China Normal Univ, Sch Life Sci, Dongchuan Rd 500, Shanghai 200241, Peoples R China;East China Normal Univ, Sch Life Sci, Dongchuan Rd 500, Shanghai 200241, Peoples R China | Review | East China Normal Univ | WEINHEIM | null | null | East China Normal Univ | National Key Research and Development Program of China, Stem Cell, and Translational Research;National Natural Science Foundation of China (NSFC);NSFC;Science and Technology Commission of Shanghai Municipality;Thousand Youth Talents Plan of China | Ye, HF (corresponding author), East China Normal Univ, Inst Biomed Sci, Shanghai Key Lab Regulatory Biol, Dongchuan Rd 500, Shanghai 200241, Peoples R China.; Ye, HF (corresponding author), East China Normal Univ, Sch Life Sci, Dongchuan Rd 500, Shanghai 200241, Peoples R China. | null | Dong, Kaili;Wang, Meiyan;Wang, Yidan;Ye, Haifeng | 35 | 2 | 431,621,000,003 | National Key Research and Development Program of China, Stem Cell, and Translational Research [2016YFA0100300];National Natural Science Foundation of China (NSFC) [31522017];NSFC [31470834, 31670869];Science and Technology Commission of Shanghai Municipality [15QA1401500, 14JC1401700];Thousand Youth Talents Plan of China | China | BIOTECHNOLOGY JOURNAL | China | null | null | East China Normal Univ, Inst Biomed Sci, Shanghai Key Lab Regulatory Biol, Dongchuan Rd 500, Shanghai 200241, Peoples R China | 1860-6768 | Dong, K L;Wang, M Y;Wang, Y D;Ye, H F | MAY | hfye@bio.ecnu.edu.cn | engineering Mammalian Designer Cells;Metabolic Diseases;Treatment | 4 | J | Biochemistry & Molecular Biology;Biotechnology & Applied Microbiology | ability;ACTIVATED RECEPTOR-ALPHA;biological systems;clinical applications;closed-loop gene circuits;COREPRESSOR;current technologies;designed cells;DESIGNER CELLS;development;diabetes;engineering Mammalian Designer Cells;engineering principles;future;future perspectives;GENE-EXPRESSION;GLUCOSE-HOMEOSTASIS;HYPERTENSION;hyperuricemia;intelligent manner;mammalian designer cells;MANAGEMENT;Metabolic Diseases;metabolic disorders;METFORMIN;Mice;new functions;new opportunities;number;obesity;open-;recent advances;reprogram cell activities;review;robust therapeutic behaviors;synthetic biology;synthetic designer cells uploaded;synthetic gene;synthetic gene circuits;TRANSGENE EXPRESSION;treatment;URIC-ACID | Wang, Y D | ACTIVATED RECEPTOR-ALPHA;COREPRESSOR;DESIGNER CELLS;GENE-EXPRESSION;GLUCOSE-HOMEOSTASIS;HYPERTENSION;MANAGEMENT;metabolic disorders;METFORMIN;MICE;synthetic gene circuits;TRANSGENE EXPRESSION;URIC-ACID | null | [Wang, Yidan; Wang, Meiyan; Dong, Kaili; Ye, Haifeng] East China Normal Univ, Inst Biomed Sci, Shanghai Key Lab Regulatory Biol, Dongchuan Rd 500, Shanghai 200241, Peoples R China. [Wang, Yidan; Wang, Meiyan; Dong, Kaili; Ye, Haifeng] East China Normal Univ, Sch Life Sci, Dongchuan Rd 500, Shanghai 200241, Peoples R China. | The authors thank Shuyong Liao for the comments on the manuscript. This work was financially supported by the grants from the National Natural Science Foundation of China (NSFC: No. 31522017) for outstanding young scientists, the National Key Research and Development Program of China, Stem Cell, and Translational Research (No. 2016YFA0100300), the NSFC (No. 31470834, No. 31670869), the Science and Technology Commission of Shanghai Municipality (No. 15QA1401500, No. 14JC1401700), and the Thousand Youth Talents Plan of China to H.Y. | ability;biological systems;clinical applications;closed-loop gene circuits;current technologies;designed cells;designer cells;development;diabetes;engineering principles;future;future perspectives;hypertension;hyperuricemia;intelligent manner;mammalian designer cells;metabolic diseases;metabolic disorders;new functions;new opportunities;number;obesity;open-;recent advances;reprogram cell activities;review;robust therapeutic behaviors;synthetic biology;synthetic designer cells uploaded;synthetic gene;treatment | 10.1002/anie.201609229;10.1002/bit.21235;10.1007/s12272-016-0871-0;10.1016/j.cell.2013.02.022;10.1016/j.cell.2014.07.022;10.1016/j.copbio.2015.01.010;10.1016/j.ejmech.2012.03.055;10.1016/j.jhep.2016.03.020;10.1016/j.jmb.2005.05.027;10.1016/j.molcel.2014.06.007;10.1016/j.ymben.2013.11.003;10.1016/j.ymben.2015.03.016;10.1016/j.ymthe.2016.11.008;10.1016/S0039-128X(99)00014-8;10.1016/S0140-6736(05)67483-1;10.1016/S0140-6736(14)60460-8;10.1021/acssynbio.6b00257;10.1021/bi034472c;10.1021/sb400182x;10.1037/0003-066X.62.3.220;10.1038/27376;10.1038/83348;10.1038/84448;10.1038/nature03461;10.1038/nature03508;10.1038/nature12271;10.1038/nature21070;10.1038/nbt.1617;10.1038/nbt.1775;10.1038/nbt0912-810b;10.1038/ncomms11247;10.1038/ncomms3825;10.1038/ncomms6392;10.1038/nm.3730;10.1038/nm.3782;10.1038/nprot.2014.038;10.1038/nrendo.2010.19;10.1038/nri912;10.1038/nrmicro2073;10.1038/nrrheum.2012.135;10.1038/nsmb.1983;10.1038/s41551-016-0005;10.1042/BJ20090998;10.1056/NEJMc1102475;10.1056/NEJMoa012512;10.1056/NEJMoa072761;10.1056/NEJMra1110560;10.1073/pnas.040552697;10.1073/pnas.0901501106;10.1073/pnas.0908882107;10.1073/pnas.1216801110;10.1073/pnas.1312414110;10.1073/pnas.88.9.3608;10.1074/jbc.274.22.15901;10.1074/jbc.M405586200;10.1074/jbc.M511095200;10.1081/LRST-200029981;10.1089/hum.1998.9.13-1939;10.1093/nar/gkr1251;10.1093/nar/gkt002;10.1093/nar/gku545;10.1093/nar/gkv1343;10.1093/nar/gkv326;10.1097/00004872-200401000-00003;10.1111/j.1399-5448.2007.00224.x;10.1111/j.1467-789X.2011.00981.x;10.1126/sciadv.1601314;10.1126/science.1203535;10.1126/science.1206843;10.1126/science.1216753;10.1126/science.aaf4006;10.1126/scitranslmed.3005568;10.1126/scitranslmed.aal2298;10.1128/MCB.20.5.1868-1876.2000;10.1155/2014/943162;10.13345/j.cjb.160431;10.15252/msb.20156663;10.2169/internalmedicine.48.1817;10.2174/1389200218666170222150555;10.2174/187221412800604644;10.2337/dc08-1171;10.2337/dc12-1707;10.2337/dc14-2898;10.3109/07388551.2015.1084266;[10.1038/NMETH.1892, 10.1038/nmeth.1892];[10.1038/nphoton.2014.166, 10.1038/NPHOTON.2014.166] | East China Normal Univ | Dong, K L;Wang, M Y;Wang, Y D;Ye, H F | Wang, Y D: East China Normal Univ, Inst Biomed Sci, Shanghai Key Lab Regulatory Biol, Dongchuan Rd 500, Shanghai 200241, Peoples R China | null | 14JC1401700;15QA1401500;2016YFA0100300;31470834;31522017;31670869 | 98 | null | China | East China Normal Univ | Wang, Yidan | null | ACTIVATED RECEPTOR-ALPHA;COREPRESSOR;GENE-EXPRESSION;GLUCOSE-HOMEOSTASIS;HYPERTENSION;MANAGEMENT;METFORMIN;MICE;TRANSGENE EXPRESSION;URIC-ACID | Wang, Yidan; Wang, Meiyan; Dong, Kaili; Ye, Haifeng; | null | East China Normal Univ, Inst Biomed Sci, Shanghai Key Lab Regulatory Biol, Dongchuan Rd 500, Shanghai 200241, Peoples R China;East China Normal Univ, Sch Life Sci, Dongchuan Rd 500, Shanghai 200241, Peoples R China | East China Normal Univ, Inst Biomed Sci, Shanghai Key Lab Regulatory Biol, Dongchuan Rd 500, Shanghai 200241, Peoples R China;East China Normal Univ, Sch Life Sci, Dongchuan Rd 500, Shanghai 200241, Peoples R China | 1860-7314 | designer cells;metabolic disorders;Synthetic gene circuit | 5 | 1989;1991;1992;1998;1999;2000;2001;2002;2003;2004;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017 | 7 | East China Normal Univ, Inst Biomed Sci, Shanghai Key Lab Regulatory Biol, Dongchuan Rd 500, Shanghai 200241, Peoples R China;East China Normal Univ, Sch Life Sci, Dongchuan Rd 500, Shanghai 200241, Peoples R China | Biotechnol. J. | Ye, Haifeng | WILEY-V C H VERLAG GMBH | ,;a;ability;activities;advanced;advances;an;and;applications;applies;applying;authors;be;behaviors;biological;biology;brought;can;cell;cells;circuits;clinical;closed-loop;constructed;current;design;designed;designer;development;diabetes;discuss;diseases;disorders;engineer;engineering;for;functions;future;gene;has;highlight;hypertension;hyperuricemia;in;including;intelligent;mammalian;manner;metabolic;more;most;new;number;obesity;of;open-;opportunities;or;perform;perspectives;principles;rationally;recent;reprogram;review;revolutionized;robust;significantly;synthetic;systems;technologies;that;the;therapeutic;these;this;to;treat;treating;treatment;uploaded;will;with | East China Normal Univ | Synthetic biology applies engineering principles to biological systems and has significantly advanced the design of synthetic gene circuits that can reprogram cell activities to perform new functions. The ability to engineer mammalian designer cells with robust therapeutic behaviors has brought new opportunities for treating metabolic diseases. In this review, the authors highlight the most recent advances in the development of synthetic designer cells uploaded with open- or closed-loop gene circuits for the treatment of metabolic disorders including diabetes, hypertension, hyperuricemia, and obesity, and discuss the current technologies and future perspectives in applying these designer cells for clinical applications. In the future, more and more rationally designed cells will be constructed and revolutionized to treat a number of metabolic disorders in an intelligent manner. | null | ACTIVATED RECEPTOR-ALPHA;COREPRESSOR;GENE-EXPRESSION;GLUCOSE-HOMEOSTASIS;HYPERTENSION;MANAGEMENT;METFORMIN;MICE;TRANSGENE EXPRESSION;URIC-ACID | 2 | null | designer cells;metabolic disorders;synthetic gene circuits | 11 | ACTIVATED RECEPTOR-ALPHA;COREPRESSOR;DESIGNER CELLS;GENE-EXPRESSION;GLUCOSE-HOMEOSTASIS;HYPERTENSION;MANAGEMENT;metabolic disorders;METFORMIN;MICE;synthetic gene circuits;TRANSGENE EXPRESSION;URIC-ACID | WOS:000431621000003 | East China Normal Univ, Shanghai, Peoples R China | China | 2,018 | null | 0000-0002-2118-6647 | null | null | English | null | ACS SYNTH BIOL;AM PSYCHOL;ANGEW CHEM INT EDIT;ARCH PHARM RES;BEST PRACT RES CLIN;BIOCHEM J;BIOCHEMISTRY-US;BIOSCI TRENDS;BIOTECHNOL BIOENG;BMJ;CARDIOL RES PRACT;CASE BASED GUIDE CLI;CELL;CRIT REV BIOTECHNOL;CURR DRUG METAB;CURR OPIN BIOTECH;DIABETES CARE;EUR J MED CHEM;GLOB HLTH RISKS MORT;HUM GENE THER;INTERNAL MED;J AM COLL CARDIOL;J BIOL CHEM;J HEPATOL;J HYPERTENS;J MOL BIOL;J RECEPT SIG TRANSD;LANCET;METAB ENG;MOL CELL;MOL CELL BIOL;MOL SYST BIOL;MOL THER;NAT BIOMED ENG;NAT BIOTECHNOL;NAT COMMUN;NAT MED;NAT METHODS;NAT PHOTONICS;NAT PROTOC;NAT REV ENDOCRINOL;NAT REV IMMUNOL;NAT REV MICROBIOL;NAT REV RHEUMATOL;NAT STRUCT MOL BIOL;NATURE;NEW ENGL J MED;NUCLEIC ACIDS RES;OBES REV;P NATL ACAD SCI USA;PEDIATR DIABETES;RECENT PATENTS ENDOC;RES PHARM SCI;REV INVEST CLIN;SCI ADV;SCI TRANSL MED;SCIENCE;Sheng Wu Gong Cheng Xue Bao;STEROIDS | Dong, Kaili;Wang, Meiyan;Wang, Yidan;Ye, Haifeng | 2024-03-11
ER | 2012;[Anonymous];[尹剑丽 Yin Jianli];[邵佳伟 Shao Jiawei];Aguilar, C A;Ausländer, D;Ausländer, S;Bai, P;Basu, S;Beerli, R R;Bellefroid, E J;Bodmer, M;Bothfeld, W;Bouchie, A;Bray G. A.;Chen, X J;Chinetti, G;Daly, M J;Das Kurmi, B;Daynes, R A;Dowell, P;Dumont, J;Fischbach, M A;Folcher, M;Friedman, J M;Fung, E;Gitzinger, M;Gray, L J;Gupta, A;Haas, L;Halford, J C G;Ham, J;Haslam, D W;Heng, B C;Hirsch, I B;Hong, G S;Hsiao, V;Hu, L Y A;Kaur, J;Kearney, P M;Kemmer, C;Khan, A;Kim, T;Knowler, W C;Kumar, R;Lee, H;Legoux, R;Leibiger, I B;Lundberg, C;Mann, T;Messerli, F H;Müller, K;Neve, K A;Ng, M;Nissen, S E;Oberoi, J;Ohno, I;Polonsky, K S;Qi, L S;Roth Ga.;Ruder, W C;Ryu, M H;Rössger, K;Saxena, P;Shao, J W;Singh, M N;Stanley, S A;Stanley, T B;Suh, W;Takebe, T;Terán, W;Therrien, J P;Tschowri, N;Vega, R B;Wang Meiyan;Wang, H;Wang, X;Werner, N S;Wilkinson, S P;Wolfsdorf, J;Xie, M;Xie, M Q;Xue, S;Yamaguchi, T;Yanagisawa R. T.;Yang Linfeng;Yao, F;Ye, H F;Zhang, F;Zhuo, Q | GF0LC | Shanghai, Peoples R China;Shanghai, Peoples R China. | 10 | null | 1 | null | 29,144,600 | Dong, Kaili;Wang, Meiyan;Wang, Yidan;Ye, Haifeng | BIOTECHNOL J | Shanghai, Peoples R China |
Barahona, M;Polizzi, K M;Stan, G B;Tomazou, M | 10.1016/j.cels.2018.03.013 | null | 50 HAMPSHIRE ST, FLOOR 5, CAMBRIDGE, MA 02139 USA | 5v4745123a5hj3n4h1y82d442q6k3m5f2p2e6i | Computational Re-design of Synthetic Genetic Oscillators for Independent Amplitude and Frequency Modulation | Imperial Coll London | null | Stan, GB (corresponding author), Imperial Coll London, Dept Bioengn, London SW7 2AZ, England.;Stan, GB (corresponding author), Imperial Coll London, Imperial Coll Ctr Synthet Biol, London SW7 2AZ, England. | null | Barahona, Mauricio;Polizzi, Karen M;Stan, Guy-Bart;Tomazou, Marios | Biochemistry & Molecular Biology;Cell Biology | EPSRC [EP/N014529/1, EP/P009352/1]; UK EPSRC [EP/M002187/1, EP/I032223/1]; EPSRC [EP/I032223/1, EP/N014529/1, EP/P009352/1, EP/M002187/1] Funding Source: UKRI | WOS | Stan, G B | Imperial Coll London, London, England | 6 | Amplitude;and;computational;for;Frequency;genetic;Independent;modulation;of;Oscillators;Re-design;synthetic | 1 | Barahona, Mauricio;Polizzi, Karen;Stan, Guy-Bart;Tomazou, Marios | CELL PRESS | Imperial Coll London, Dept Bioengn, London SW7 2AZ, England;Imperial Coll London, Dept Bioengn, London SW7 2AZ, England.; Stan, GB (corresponding author), Imperial Coll London, Imperial Coll Ctr Synthet Biol, London SW7 2AZ, England;Imperial Coll London, Dept Life Sci, London SW7 2AZ, England;Imperial Coll London, Dept Math, London SW7 2AZ, England;Imperial Coll London, Imperial Coll Ctr Synthet Biol, London SW7 2AZ, England | Article | Imperial Coll London | CAMBRIDGE | null | null | Imperial Coll London | EPSRC;UK EPSRC | Stan, GB (corresponding author), Imperial Coll London, Dept Bioengn, London SW7 2AZ, England.; Stan, GB (corresponding author), Imperial Coll London, Imperial Coll Ctr Synthet Biol, London SW7 2AZ, England. | + | Barahona, Mauricio;Polizzi, Karen M;Stan, Guy-Bart;Tomazou, Marios | 9 | 4 | 432,192,100,013 | EPSRC [EP/I032223/1, EP/N014529/1, EP/P009352/1, EP/M002187/1] Funding Source: UKRI;EPSRC [EP/N014529/1, EP/P009352/1];UK EPSRC [EP/M002187/1, EP/I032223/1] | UK | CELL SYSTEMS | UK | null | null | Imperial Coll London, Dept Bioengn, London SW7 2AZ, England | 2405-4712 | Barahona, M;Polizzi, K M;Stan, G B;Tomazou, M | APR 25 | g.stan@imperial.ac.uk | computational Re-design;Frequency Modulation;Independent Amplitude;Synthetic Genetic Oscillators | 4 | J | Biochemistry & Molecular Biology;Cell Biology | activation;amplitude;amplitude modulation;amplitudes;approach decouples frequency;behavior;biotechnology applications;broad dynamic range;broad range;broader function;building synthetic genetic oscillators;computational Re-design;control;controllable;DEGRADATION;dials;dual-feedback oscillator;DYNAMICS;enzymatic degradation;ESCHERICHIA-COLI;expression;fast oscillation cycles;Frequency Modulation;general design principles;Independent Amplitude;independent control;independent modulation;input;key molecular species;light;need;oscillator's transcription factors;output;period;periods;physiologically reasonable parameters;re-designed;re-designed oscillators;repressilator;REPRESSOR;ROBUST;sink module;Synthetic Genetic Oscillators;translational coupling;tunability-;two classic genetic oscillators;unmet | Tomazou, M | ACTIVATION;DEGRADATION;DYNAMICS;ESCHERICHIA-COLI;EXPRESSION;LIGHT;REPRESSOR;ROBUST | 508 | [Tomazou, Marios; Stan, Guy-Bart] Imperial Coll London, Dept Bioengn, London SW7 2AZ, England. [Barahona, Mauricio] Imperial Coll London, Dept Math, London SW7 2AZ, England. [Polizzi, Karen M.] Imperial Coll London, Dept Life Sci, London SW7 2AZ, England. [Tomazou, Marios; Barahona, Mauricio; Polizzi, Karen M.; Stan, Guy-Bart] Imperial Coll London, Imperial Coll Ctr Synthet Biol, London SW7 2AZ, England. | M.B. acknowledges funding from EPSRC grant EP/N014529/1 supporting the EPSRC Center for Mathematics of Precision Healthcare. G.B.S. gratefully acknowledges the support of the UK EPSRC through his EPSRC Fellowship for Growth EP/M002187/1, as well as the EPSRC project EP/P009352/1. M.T., M.B., K.P., and G.B.S. gratefully acknowledge the support of the UK EPSRC through project EP/I032223/1. | amplitude;amplitude modulation;amplitudes;approach decouples frequency;behavior;biotechnology applications;broad dynamic range;broad range;broader function;building synthetic genetic oscillators;control;controllable;dials;dual-feedback oscillator;enzymatic degradation;fast oscillation cycles;general design principles;independent control;independent modulation;input;key molecular species;need;oscillator's transcription factors;output;period;periods;physiologically reasonable parameters;re-designed;re-designed oscillators;repressilator;sink module;synthetic genetic oscillators;translational coupling;tunability-;two classic genetic oscillators;unmet | 10.1006/jmbi.1994.1434;10.1006/jmbi.1996.0230;10.1007/s001140050704;10.1016/B978-0-12-417029-2.00005-4;10.1016/j.bbamem.2007.07.015;10.1016/j.jmb.2008.10.081;10.1016/j.jmb.2010.10.038;10.1016/j.jmb.2013.07.036;10.1016/j.mib.2016.07.009;10.1016/j.tibtech.2011.09.001;10.1016/S0092-8674(03)00346-5;10.1016/S0955-0674(03)00017-6;10.1021/acssynbio.5b00147;10.1021/sb300060e;10.1021/sb3000639;10.1021/sb500262f;10.1021/sb500273n;10.1023/A:1020611919599;10.1038/35002125;10.1038/481033a;10.1038/msb.2011.94;10.1038/msb4100204;10.1038/nature03508;10.1038/nature04405;10.1038/nature07389;10.1038/nature07616;10.1038/nature08753;10.1038/nature13238;10.1038/nature19841;10.1038/nbt.1591;10.1038/nbt.3053;10.1038/nmeth.2884;10.1063/1.3574387;10.1063/1.4756221;10.1073/pnas.1005615107;10.1073/pnas.1111221108;10.1093/nar/25.6.1203;10.1093/nar/gkp889;10.1093/nar/gkq121;10.1098/rsif.2009.0487;10.1098/rsif.2010.0183;10.1099/mic.0.067975-0;10.1101/014787];10.1103/PhysRevLett.88.148101;10.1109/CDC.2016.7798359;10.1111/dgd.12262;10.1111/j.1365-2958.2005.04798.x;10.1111/j.1749-6632.1991.tb27261.x;10.1126/science.1156951;10.1126/science.2476847;10.1126/science.aac7341;10.1186/1752-0509-1-57;10.1186/1752-0509-8-63;10.1186/1752-0509-8-S4-S4;10.1371/journal.pcbi.1003658;10.1371/journal.pone.0004882;10.1371/journal.pone.0016140;10.3791/50762;10.7554/eLife.09771;10.7554/eLife.23702;[10.1038/NMETH.3339, 10.1038/nmeth.3339] | Imperial Coll London | Barahona, M;Polizzi, K M;Stan, G B;Tomazou, M | Tomazou, M: Imperial Coll London, Dept Bioengn, London SW7 2AZ, England | Barahona, Mauricio | EP/I032223/1;EP/M002187/1;EP/N014529/1;EP/P009352/1 | 66 | null | UK | Imperial Coll London | Tomazou, Marios | Green Submitted, hybrid, Green Published | ACTIVATION;DEGRADATION;DYNAMICS;ESCHERICHIA-COLI;EXPRESSION;LIGHT;REPRESSOR;ROBUST | Tomazou, Marios; Barahona, Mauricio; Polizzi, Karen M.; Stan, Guy-Bart; | null | Imperial Coll London, Dept Bioengn, London SW7 2AZ, England;Imperial Coll London, Dept Life Sci, London SW7 2AZ, England;Imperial Coll London, Dept Math, London SW7 2AZ, England;Imperial Coll London, Imperial Coll Ctr Synthet Biol, London SW7 2AZ, England | Imperial Coll London, Dept Bioengn, London SW7 2AZ, England;Imperial Coll London, Dept Life Sci, London SW7 2AZ, England;Imperial Coll London, Dept Math, London SW7 2AZ, England;Imperial Coll London, Imperial Coll Ctr Synthet Biol, London SW7 2AZ, England | 2405-4720 | null | 4 | 1963;1989;1991;1994;1996;1997;1999;2000;2002;2003;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017 | 22 | Imperial Coll London, Dept Bioengn, London SW7 2AZ, England;Imperial Coll London, Imperial Coll Ctr Synthet Biol, London SW7 2AZ, England | Cell Syst. | Stan, Guy-Bart | CELL PRESS | ";,;a;accessible;alleviating;allow;amplitude;amplitudes;an;and;applications;approach;are;be;behavior;between;biotechnology;broad;broader;building;by;can;channeled;characterize;classic;computationally;control;controllable;coupling;currently;cycles;decouples;degradation;demonstrate;design;dials;dual-feedback;dynamic;engineered;enzymatic;explain;facilitates;factors;fast;for;frequency;function;general;genetic;here;how;improve;in;incorporating;independent;input;is;key;maintains;modulation;module;molecular;more;must;need;of;Orthogonal;oscillation;oscillator;oscillator's;oscillators;our;output;over;parameters;perform;period;periods;physiologically;precisely;principles;provide;range;re-designed;reasonable;repressilator;sink;species;synthetic;that;the;this;through;to;transcription;translational;tunability-;two;unmet;we;well;where;while;why | Imperial Coll London | To perform well in biotechnology applications, synthetic genetic oscillators must be engineered to allow independent modulation of amplitude and period. This need is currently unmet. Here, we demonstrate computationally how two classic genetic oscillators, the dual-feedback oscillator and the repressilator, can be re-designed to provide independent control of amplitude and period and improve tunability- that is, a broad dynamic range of periods and amplitudes accessible through the input "dials." Our approach decouples frequency and amplitude modulation by incorporating an orthogonal "sink module" where the key molecular species are channeled for enzymatic degradation. This sink module maintains fast oscillation cycles while alleviating the translational coupling between the oscillator's transcription factors and output. We characterize the behavior of our re-designed oscillators over a broad range of physiologically reasonable parameters, explain why this facilitates broader function and control, and provide general design principles for building synthetic genetic oscillators that are more precisely controllable. | C-3638-2008;M-9747-2019 | ACTIVATION;DEGRADATION;DYNAMICS;ESCHERICHIA-COLI;EXPRESSION;LIGHT;REPRESSOR;ROBUST | 0 | null | null | 18 | ESCHERICHIA-COLI;ACTIVATION;DEGRADATION;DYNAMICS;EXPRESSION;LIGHT;REPRESSOR;ROBUST | WOS:000432192100013 | Imperial Coll London, London, England | UK | 2,018 | null | 0000-0001-5435-2667;0000-0002-0836-5579;0000-0002-1089-5675;0000-0002-5560-902X | null | null | English | null | ACS SYNTH BIOL;AIP CONF PROC;ANN NY ACAD SCI;BBA-BIOMEMBRANES;BioRxiv;BMC SYST BIOL;CELL;CHAOS;CURR OPIN CELL BIOL;CURR OPIN MICROBIOL;DEV GROWTH DIFFER;ELIFE;IEEE DECIS CONTR P;Indian Journal of Pharmaceutical Sciences;International Research Journal of Pharmacy;J MOL BIOL;J PROTEIN CHEM;J R SOC INTERFACE;JOVE-J VIS EXP;LIGHT BASED DYNAMIC;METHOD BIOCHEM ANAL;METHOD MICROBIOL;MICROBIOL-SGM;MOL MICROBIOL;MOL SYST BIOL;NAT BIOTECHNOL;NAT METHODS;NATURE;NATURWISSENSCHAFTEN;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PHYS REV LETT;PLOS COMPUT BIOL;PLOS ONE;SCIENCE;TRENDS BIOTECHNOL | Barahona, Mauricio;Polizzi, Karen M;Stan, Guy-Bart;Tomazou, Marios | 2024-03-11
ER | Arora Shweta;Arpino, J A J;Atkinson, M R;Bakken, E E;Borkowski, O;Bozek, K;Cameron, D E;Ceroni, F;Chalfie, M;Chuang, C H;Cookson, N A;Danino, T;Davidson, E A;Del Vecchio, D;Didovyk, A;Elowitz, M B;Farrell, C M;Fung, E;Galkin, V E;Gjuvsland, A B;Goers, L;Goodwin B.;Hasty, J;Hess, B;Kedracka-Krok, S;Levskaya, A;Lewis, D;Lu, T K;Lutz, R;Lux, M W;Milo, R;Moriya, T;Natale, P;Niederholtmeyer, H;Nielsen, A A K;Olson, E J;Potvin-Trottier, L;Prindle, A;Purcell, O;Qian, Y L;Ritika S.;Schmid, S R;Shis, D L;Sowa, S W;Steipe, B;Strelkowa, N;Stricker, J;Sun, Z Z;Tabor, J J;Tigges, M;Toettcher, J E;Tomazou M.;Tsai, T Y C;Tyson, J J;Uriu, K;Utsumi, R;Voigt, C A;Weisse A. Y.;Wu, F Q;Zhang, X | GF8BF | London, England;London, England. | 24 | null | 1 | null | 29,680,377 | Barahona, Mauricio;Polizzi, Karen M;Stan, Guy-Bart;Tomazou, Marios | CELL SYST | London, England |
Song, A G;Zhang, L;Zheng, W B | 10.1063/1.5019297 | 043117 | 1305 WALT WHITMAN RD, STE 300, MELVILLE, NY 11747-4501 USA | 2i2z1l67236zu3w3pm3z4268502g1j4f4i1n51 | Adaptive logical stochastic resonance in time-delayed synthetic genetic networks | Nanjing Normal Univ | null | Zhang, L (corresponding author), Nanjing Normal Univ, Sch Elect & Automat Engn, Nanjing 210046, Jiangsu, Peoples R China. | null | Song, Aiguo;Zhang, Lei;Zheng, Wenbin | Mathematics, Applied;Physics, Mathematical | National Science Foundation of China [61203237]; Industry-Academia Cooperation Innovation Fund Projection of Jiangsu Province [BY2016001-02] | WOS | Zhang, L | Chengdu Univ Informat Technol, Sichuan, Peoples R China;Nanjing Normal Univ, Jiangsu, Peoples R China;Southeast Univ, Jiangsu, Peoples R China | 28 | adaptive;genetic;in;logical;networks;resonance;stochastic;synthetic;time-delayed | 1 | Song, Aiguo;Zhang, Lei | AMER INST PHYSICS | Chengdu Univ Informat Technol, Coll Software Engn, Chengdu 610225, Sichuan, Peoples R China;Nanjing Normal Univ, Sch Elect & Automat Engn, Nanjing 210046, Jiangsu, Peoples R China;Southeast Univ, Sch Instrument Sci & Engn, Sipailou 2, Nanjing 210096, Jiangsu, Peoples R China | Article | Nanjing Normal Univ | MELVILLE | null | null | Chengdu Univ Informat Technol;Nanjing Normal Univ;Southeast Univ | Industry-Academia Cooperation Innovation Fund Projection of Jiangsu Province;National Science Foundation of China | Zhang, L (corresponding author), Nanjing Normal Univ, Sch Elect & Automat Engn, Nanjing 210046, Jiangsu, Peoples R China. | null | Song, Aiguo;Zhang, Lei;Zheng, Wenbin | 42 | 3 | 431,142,000,021 | Industry-Academia Cooperation Innovation Fund Projection of Jiangsu Province [BY2016001-02];National Science Foundation of China [61203237] | China | CHAOS | China | null | null | Nanjing Normal Univ, Sch Elect & Automat Engn, Nanjing 210046, Jiangsu, Peoples R China | 1054-1500 | Song, A G;Zhang, L;Zheng, W B | APR | leizhang@njnu.edu.cn | adaptive logical stochastic resonance;time-delayed synthetic genetic networks | 3 | J | Mathematics;Physics | adaptive logical stochastic resonance;AIP Publishing;background noise;bacteriophage lambda;clear logic operation;concept;contrast;designing new genetic regulatory networks paradigm;desired logic response;hand;larger range;latch operation;length;logic operation;LOGICAL STOCHASTIC RESONANCE;modulated periodic force;NETWORK;noise;one hand;optimal noise plateau;possible help;previous synthetic genetic networks;proposed system;result;stability;SYSTEM;time-delay;time-delayed synthetic genetic networks;tuning time-delay;two advantages;varying noise intensity | Zhang, L | NOISE;STABILITY | null | [Zhang, Lei] Nanjing Normal Univ, Sch Elect & Automat Engn, Nanjing 210046, Jiangsu, Peoples R China. [Zheng, Wenbin] Chengdu Univ Informat Technol, Coll Software Engn, Chengdu 610225, Sichuan, Peoples R China. [Song, Aiguo] Southeast Univ, Sch Instrument Sci & Engn, Sipailou 2, Nanjing 210096, Jiangsu, Peoples R China. | The work was supported by the National Science Foundation of China (No. 61203237) and the Industry-Academia Cooperation Innovation Fund Projection of Jiangsu Province (BY2016001-02). | AIP Publishing;background noise;bacteriophage lambda;clear logic operation;concept;contrast;designing new genetic regulatory networks paradigm;desired logic response;hand;larger range;latch operation;length;logic operation;logical stochastic resonance;modulated periodic force;network;one hand;optimal noise plateau;possible help;previous synthetic genetic networks;proposed system;result;system;time-delay;time-delayed synthetic genetic networks;tuning time-delay;two advantages;varying noise intensity | 10.1007/s11071-013-1136-9;10.1016/j.chemphys.2010.06.015;10.1016/j.cnsns.2013.12.008;10.1016/j.physleta.2012.01.039;10.1021/nl9034175;10.1038/35002125;10.1038/nature01257;10.1038/nature07389;10.1038/nbt1413;10.1063/1.1345702;10.1063/1.3245318;10.1063/1.4984806;10.1103/PhysRevE.71.031106;10.1103/PhysRevE.82.051106;10.1103/PhysRevE.84.055201;10.1103/PhysRevLett.102.104101;10.1103/PhysRevLett.82.2811;10.1103/PhysRevLett.87.250602;10.1103/PhysRevLett.90.020601;10.1109/TCSI.2006.883882;10.1109/TCSII.2007.901631;10.1109/TNNLS.2015.2495155;10.1209/0295-5075/93/18001;10.1371/journal.pone.0076032 | Nanjing Normal Univ | Song, A G;Zhang, L;Zheng, W B | Zhang, L: Nanjing Normal Univ, Sch Elect & Automat Engn, Nanjing 210046, Jiangsu, Peoples R China | Zhang, Lei | 61203237;BY2016001-02 | 25 | null | China | Chengdu Univ Informat Technol;Nanjing Normal Univ;Southeast Univ | Zhang, Lei | null | NOISE;STABILITY | Zhang, Lei; Zheng, Wenbin; Song, Aiguo; | null | Chengdu Univ Informat Technol, Coll Software Engn, Chengdu 610225, Sichuan, Peoples R China;Nanjing Normal Univ, Sch Elect & Automat Engn, Nanjing 210046, Jiangsu, Peoples R China;Southeast Univ, Sch Instrument Sci & Engn, Sipailou 2, Nanjing 210096, Jiangsu, Peoples R China | Chengdu Univ Informat Technol, Coll Software Engn, Chengdu 610225, Sichuan, Peoples R China;Nanjing Normal Univ, Sch Elect & Automat Engn, Nanjing 210046, Jiangsu, Peoples R China;Southeast Univ, Sch Instrument Sci & Engn, Sipailou 2, Nanjing 210096, Jiangsu, Peoples R China | 1089-7682 | null | 4 | 1999;2000;2001;2002;2003;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2016;2017 | 31 | Nanjing Normal Univ, Sch Elect & Automat Engn, Nanjing 210046, Jiangsu, Peoples R China | Chaos | Song, Aiguo | AMER INST PHYSICS | ,;a;adapt;adding;advantages;AIP;and;applied;background;bacteriophage;based;be;by;can;clear;concept;contrast;derived;designing;desired;extend;for;force;from;genetic;hand;has;help;implement;in;increase;intensity;is;lambda;larger;latch;length;logic;logical;make;modulated;network;networks;new;noise;obtained;obtaining;of;on;one;operation;optimal;other;paper;paradigm;periodic;plateau;possible;previous;proposed;provides;published;Publishing;range;regulatory;resonance;response;result;stochastic;synthetic;system;the;time-delay;time-delayed;to;tuned;tuning;two;varying;when;with | Nanjing Normal Univ | In the paper, the concept of logical stochastic resonance is applied to implement logic operation and latch operation in time-delayed synthetic genetic networks derived from a bacteriophage lambda. Clear logic operation and latch operation can be obtained when the network is tuned by modulated periodic force and time-delay. In contrast with the previous synthetic genetic networks based on logical stochastic resonance, the proposed system has two advantages. On one hand, adding modulated periodic force to the background noise can increase the length of the optimal noise plateau of obtaining desired logic response and make the system adapt to varying noise intensity. On the other hand, tuning time-delay can extend the optimal noise plateau to larger range. The result provides possible help for designing new genetic regulatory networks paradigm based on logical stochastic resonance. Published by AIP Publishing. | AGI-2713-2022;C-9699-2009 | NOISE;STABILITY | 2 | null | null | 7 | NOISE;STABILITY | WOS:000431142000021 | Chengdu Univ Informat Technol, Sichuan, Peoples R China;Nanjing Normal Univ, Jiangsu, Peoples R China;Southeast Univ, Jiangsu, Peoples R China | China | 2,018 | null | 0000-0001-8749-7459;0000-0002-1982-6780 | null | null | English | null | APPL PHYS LETT;CHAOS;CHEM PHYS;COMMUN NONLINEAR SCI;EPL-EUROPHYS LETT;IEEE T CIRCUITS-I;IEEE T CIRCUITS-II;IEEE T NEUR NET LEAR;J Biol Eng;NANO LETT;NAT BIOTECHNOL;NATURE;NONLINEAR DYNAM;PHYS LETT A;PHYS REV E;PHYS REV LETT;PLOS ONE | Song, Aiguo;Zhang, Lei;Zheng, Wenbin | 2024-03-11
ER | Bulsara, A R;Canton, B;Dari, A;Elowitz, M B;Frank, T D;Guerra, D N;Gupta, A;Hasty, J;Hellen, E H;Kohar, V;Li, C G;Masoller, C;Murali, K;Nistala G. J.;Ohira, T;Sharma, A;Stricker, J;Tsimring, L S;Wang, N;Wu, J;Zhang, L | GE3VW | Jiangsu, Peoples R China | 36 | null | 3 | null | 31,906,654 | Song, Aiguo;Zhang, Lei;Zheng, Wenbin | CHAOS | Jiangsu, Peoples R China;Sichuan, Peoples R China |
Brandao, R M S D;da Silva, A S;de Andrade, H M;do Monte, S J;Faria, A R;Martins, L M S | 10.2217/fmb-2017-0184 | null | UNITEC HOUSE, 3RD FLOOR, 2 ALBERT PLACE, FINCHLEY CENTRAL, LONDON, N3 1QB, ENGLAND | t4t6i13562w604k166n505v3p4x5z1e6w6y6s12 | Novel recombinant multiepitope proteins for the detection of anti-<i>Cryptococcus </i>antibodies | Univ Fed Piaui | null | Brandao, RMSD (corresponding author), Univ Fed Piaui, Lab Imunogenet & Biol Mol, Campus Ministro Petronio Portella Bloco SG 16, BR-64049550 Teresina, Piaui, Brazil. | null | da Silva, Adalberto Socorro;de Andrade, Helida Monteiro;Faria, Angelica Rosa;Hadad do Monte, Semiramis Jamil;Santos de Serpa Brandao, Rafael Melo;Soares Martins, Liline Maria | Microbiology | Laboratorio de Imunogenetica e Biologia Molecular, Universidade Federal do Piaui, Brazil; Laboratorio de Imunogenetica e Biologia Molecular (LIB/UFPI) | WOS | Brandao, RMSD | Univ Estadual Piaui, Piaui, Brazil;Univ Fed Minas Gerais, Belo Horizonte MG, Brazil;Univ Fed Piaui, Piaui, Brazil | 13 | </i>antibodies;anti-<i>Cryptococcus;detection;for;multiepitope;novel;of;Proteins;recombinant;the | 1 | Brandao, Rafael | FUTURE MEDICINE LTD | Univ Estadual Piaui, Ctr Ciencias Saude, BR-64001280 Teresina, Piaui, Brazil;Univ Fed Minas Gerais, Inst Ciencias Biol, Dept Parasitol, BR-31279910 Belo Horizonte, MG, Brazil;Univ Fed Piaui, Lab Imunogenet & Biol Mol, Campus Ministro Petronio Portella Bloco SG 16, BR-64049550 Teresina, Piaui, Brazil | Article | Univ Fed Piaui | LONDON | null | null | Univ Estadual Piaui;Univ Fed Minas Gerais;Univ Fed Piaui | Laboratorio de Imunogenetica e Biologia Molecular (LIB/UFPI);Laboratorio de Imunogenetica e Biologia Molecular, Universidade Federal do Piaui, Brazil | Brandao, RMSD (corresponding author), Univ Fed Piaui, Lab Imunogenet & Biol Mol, Campus Ministro Petronio Portella Bloco SG 16, BR-64049550 Teresina, Piaui, Brazil. | 436 | da Silva, Adalberto Socorro;de Andrade, Helida Monteiro;Faria, Angelica Rosa;Hadad do Monte, Semiramis Jamil;Santos de Serpa Brandao, Rafael Melo;Soares Martins, Liline Maria | 2 | 3 | 432,198,800,006 | Laboratorio de Imunogenetica e Biologia Molecular (LIB/UFPI);Laboratorio de Imunogenetica e Biologia Molecular, Universidade Federal do Piaui, Brazil | Brazil | FUTURE MICROBIOLOGY | Brazil | null | null | Univ Fed Piaui, Lab Imunogenet & Biol Mol, Campus Ministro Petronio Portella Bloco SG 16, BR-64049550 Teresina, Piaui, Brazil | 1746-0913 | Brandao, R M S D;da Silva, A S;de Andrade, H M;do Monte, S J;Faria, A R;Martins, L M S | MAR | brandaorafael@hotmail.com | anti-<i>Cryptococcus </i>antibodies;detection;novel recombinant multiepitope proteins | 6 | J | Microbiology | 100%;88.57%;aim;alternative assay;anti-<i>Cryptococcus </i>antibodies;anti-Cryptococcus antibodies;antigens;attempt;B;C;coding sequences;conclusion;cryptococcosis;D. Results;detection;Diagnosis;ELISA;Escherichia coil;four genes;GATTII INFECTION;GLOBAL BURDEN;good results;HIV PATIENTS;materials;MENINGITIS;methods;multiepitope protein;multiepitope proteins;novel recombinant multiepitope proteins;peptides;potential antigens;protein D;proteins;PULMONARY CRYPTOCOCCOSIS;recombinant multiepitope proteins;results;sensitivity;SERODIAGNOSIS;serological diagnosis;silico analyses;specificity;synthetic gene;synthetic genes;synthetic peptides;test recombinant multiepitope proteins;union | Brandao, R M S D | antigens;cryptococcosis;DIAGNOSIS;ELISA;GATTII INFECTION;GLOBAL BURDEN;HIV PATIENTS;MENINGITIS;multiepitope protein;PULMONARY CRYPTOCOCCOSIS;SERODIAGNOSIS;serological diagnosis;Synthetic gene | 429 | [Santos de Serpa Brandao, Rafael Melo; Soares Martins, Liline Maria; da Silva, Adalberto Socorro; Hadad do Monte, Semiramis Jamil] Univ Fed Piaui, Lab Imunogenet & Biol Mol, Campus Ministro Petronio Portella Bloco SG 16, BR-64049550 Teresina, Piaui, Brazil. [Faria, Angelica Rosa; de Andrade, Helida Monteiro] Univ Fed Minas Gerais, Inst Ciencias Biol, Dept Parasitol, BR-31279910 Belo Horizonte, MG, Brazil. [Soares Martins, Liline Maria] Univ Estadual Piaui, Ctr Ciencias Saude, BR-64001280 Teresina, Piaui, Brazil. | This work was supported by the Laboratorio de Imunogenetica e Biologia Molecular, Universidade Federal do Piaui, Brazil. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.; The American Journal of Experts conducted the review of the English language of the manuscript, funded by the Laboratorio de Imunogenetica e Biologia Molecular (LIB/UFPI). | 100%;88.57%;aim;alternative assay;anti-Cryptococcus antibodies;attempt;B;C;coding sequences;conclusion;cryptococcosis;D. Results;diagnosis;Escherichia coil;four genes;good results;materials;methods;multiepitope proteins;peptides;potential antigens;protein D;proteins;recombinant multiepitope proteins;results;sensitivity;serological diagnosis;silico analyses;specificity;synthetic genes;synthetic peptides;test recombinant multiepitope proteins;union | 10.1002/jcla.20483;10.1007/s00018-004-4464-6;10.1016/j.bjid.2012.07.004;10.1016/j.bjid.2012.10.020;10.1016/j.fgb.2014.10.003;10.1016/j.idc.2015.10.004;10.1016/S0035-9203(96)90297-7;10.1016/S0167-5877(00)00115-X;10.1038/227680a0;10.1038/nrmicro.2015.6;10.1093/cid/cir379;10.1093/cid/cis529;10.1093/cid/civ041;10.1097/MCP.0b013e32835f1ad1;10.1097/QAD.0b013e328322ffac;10.1111/j.1439-0507.2008.01549.x;10.1128/CDLI.9.4.883-891.2002;10.1128/CVI.00189-08;10.1128/CVI.00383-07;10.1128/CVI.00446-12;10.1128/CVI.05553-11;10.1128/JCM.00751-17;10.1128/microbiolspec.EI10-0016-2016;10.1185/03007995.2012.761134;10.1186/1471-2148-8-19;10.1186/s13071-015-0932-0;10.1371/journal.pntd.0003429;10.1371/journal.pntd.0004885;10.1371/journal.pone.0161100;10.1542/peds.107.5.e66;10.3109/13693786.2011.564216;[10.2217/FMB.13.22, 10.2217/fmb.13.22];[10.2217/fmb.14.49, 10.2217/FMB.14.49] | Univ Fed Piaui | Brandao, R M S D;da Silva, A S;de Andrade, H M;do Monte, S J;Faria, A R;Martins, L M S | Brandao, R M S D: Univ Fed Piaui, Lab Imunogenet & Biol Mol, Campus Ministro Petronio Portella Bloco SG 16, BR-64049550 Teresina, Piaui, Brazil | null | null | 37 | null | Brazil | Univ Estadual Piaui;Univ Fed Minas Gerais;Univ Fed Piaui | Santos de Serpa Brandao, Rafael Melo | null | DIAGNOSIS;GATTII INFECTION;GLOBAL BURDEN;HIV PATIENTS;MENINGITIS;PULMONARY CRYPTOCOCCOSIS;SERODIAGNOSIS | Santos de Serpa Brandao, Rafael Melo; Faria, Angelica Rosa; de Andrade, Helida Monteiro; Soares Martins, Liline Maria; da Silva, Adalberto Socorro; Hadad do Monte, Semiramis Jamil; | null | Univ Estadual Piaui, Ctr Ciencias Saude, BR-64001280 Teresina, Piaui, Brazil;Univ Fed Minas Gerais, Inst Ciencias Biol, Dept Parasitol, BR-31279910 Belo Horizonte, MG, Brazil;Univ Fed Piaui, Lab Imunogenet & Biol Mol, Campus Ministro Petronio Portella Bloco SG 16, BR-64049550 Teresina, Piaui, Brazil | Univ Estadual Piaui, Ctr Ciencias Saude, BR-64001280 Teresina, Piaui, Brazil;Univ Fed Minas Gerais, Inst Ciencias Biol, Dept Parasitol, BR-31279910 Belo Horizonte, MG, Brazil;Univ Fed Piaui, Lab Imunogenet & Biol Mol, Campus Ministro Petronio Portella Bloco SG 16, BR-64049550 Teresina, Piaui, Brazil | 1746-0921 | Antigenicity;cryptococcosis;ELISA;multiepitope protein;serological diagnosis;Synthetic gene | 4 | 1970;1996;2000;2001;2002;2005;2008;2009;2011;2012;2013;2014;2015;2016;2017 | 4 | Univ Fed Piaui, Lab Imunogenet & Biol Mol, Campus Ministro Petronio Portella Bloco SG 16, BR-64049550 Teresina, Piaui, Brazil | Future Microbiol. | Hadad do Monte, Semiramis Jamil | FUTURE MEDICINE LTD | &;,;100%;88.57%;:;;;a;aim;all;alternative;an;analyses;and;anti-Cryptococcus;antibodies;antigens;as;assay;assembled;attempt;B;be;been;best;C;cloned;coding;coil;conclusion;constructs;cryptococcosis;D;D.;detect;diagnosis;Escherichia;expressed;for;four;genes;good;have;here;however;improve;in;into;materials;methods;multiepitope;of;peptides;potential;previously;produce;producing;protein;proteins;recombinant;results;sensitivity;sequences;serological;showed;shown;silico;specificity;synthetic;test;that;the;these;to;union;used;were;with;would;yielded | Univ Fed Piaui | Aim: To produce and test recombinant multiepitope proteins as an alternative assay for the serological diagnosis of cryptococcosis. Materials & methods: Previously, synthetic peptides were used to detect anti-Cryptococcus antibodies, and in silico analyses showed that the union of peptides would improve the results. Here, the coding sequences of these peptides were assembled into synthetic genes. Four genes have been cloned and expressed in Escherichia coil, producing recombinant multiepitope proteins: proteins A, B, C and D. Results: All constructs yielded good results; however, protein D showed the best results, with a sensitivity of 88.57% and specificity of 100%. Conclusion: The multiepitope proteins were shown to be potential antigens for the diagnosis of cryptococcosis in an attempt to detect anti-Cryptococcus antibodies. | null | DIAGNOSIS;GATTII INFECTION;GLOBAL BURDEN;HIV PATIENTS;MENINGITIS;PULMONARY CRYPTOCOCCOSIS;SERODIAGNOSIS | 1 | null | antigens;cryptococcosis;ELISA;multiepitope protein;serological diagnosis;Synthetic gene | 8 | ANTIGEN;cryptococcosis;DIAGNOSIS;ELISA;GATTII INFECTION;GLOBAL BURDEN;HIV PATIENTS;MENINGITIS;multiepitope protein;PULMONARY CRYPTOCOCCOSIS;SERODIAGNOSIS;serological diagnosis;Synthetic gene | WOS:000432198800006 | Univ Estadual Piaui, Piaui, Brazil;Univ Fed Minas Gerais, Belo Horizonte MG, Brazil;Univ Fed Piaui, Piaui, Brazil | Brazil | 2,018 | null | 0000-0002-8718-7140 | null | null | English | null | AIDS;BMC EVOL BIOL;BRAZ J INFECT DIS;CELL MOL LIFE SCI;CLIN DIAGN LAB IMMUN;CLIN INFECT DIS;CLIN VACCINE IMMUNOL;CURR MED RES OPIN;CURR OPIN PULM MED;FUNGAL GENET BIOL;FUTURE MICROBIOL;HEPAT RES TREAT;INDIAN J MED RES;INFECT DIS CLIN N AM;INT J CLIN EXP MED;J CLIN LAB ANAL;J CLIN MICROBIOL;MED MYCOL;MICROBIOL SPECTR;MYCOSES;NAT REV MICROBIOL;NATURE;PARASITE VECTOR;PEDIATRICS;PLOS NEGLECT TROP D;PLOS ONE;PREV VET MED;T ROY SOC TROP MED H;WHO TECH REP SER | da Silva, Adalberto Socorro;de Andrade, Helida Monteiro;Faria, Angelica Rosa;Hadad do Monte, Semiramis Jamil;Santos de Serpa Brandao, Rafael Melo;Soares Martins, Liline Maria | 2024-03-11
ER | Binnicker, M J;Brandao, R M S D;Brocchieri, L;Chai, H C;Chen, S C A;Cheng, Z;Dai, J F;Dubbels, M;Faria, A R;Galdino, A S;Goldman, D L;Greiner, M;Hajissa, K;Hayes, G E;Houghton, R L;Laemmli, U K;Lin, X;Lindsley, M D;Lockhart, S R;Martins, L M S;May, R C;Mayer, M P;Morera, N;Park, B J;Perfect, J R;Phillips, P;Saha, D C;Santos, F L N;Seaton, R A;Souto, A C P;Vallabhaneni, S;Vidal, J E;Who;Xie, X N;Yu, J Q;Zhuang, D | GF8DO | Piaui, Brazil | 4 | null | 3 | null | 29,125,786 | da Silva, Adalberto Socorro;de Andrade, Helida Monteiro;Faria, Angelica Rosa;Hadad do Monte, Semiramis Jamil;Santos de Serpa Brandao, Rafael Melo;Soares Martins, Liline Maria | FUTURE MICROBIOL | Belo Horizonte MG, Brazil;Piaui, Brazil |
Bervoets, I;Charlier, D;De Mey, M;Maertens, J;Van Brempt, M;Van Hove, B;Van Nerom, K | 10.1093/nar/gky010 | null | GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND | 1s3k1bc40s67j4o4v3e632e3c1h2r693y1w5f | A sigma factor toolbox for orthogonal gene expression in <i>Escherichia coli</i> | Vrije Univ Brussel | null | Charlier, D (corresponding author), Vrije Univ Brussel, Dept Bioengn Sci, Res Grp Microbiol, Pl Laan 2, B-1050 Brussels, Belgium. | null | Bervoets, Indra;Charlier, Daniel;De Mey, Marjan;Maertens, Jo;Van Brempt, Maarten;Van Hove, Bob;Van Nerom, Katleen | Biochemistry & Molecular Biology | Fonds voor Wetenschappelijk Onderzoek Vlaanderen [G.0321.13N]; Ghent University Special Research Fund [BOF16/IOP/040]; Fonds voor Wetenschappelijk onderzoek Vlaanderen (FWO-Vlaanderen); Institute for the Promotion of Innovation through Science and Technology in Flanders (IWT-Vlaanderen) | WOS | Charlier, D | Univ Ghent, Ghent, Belgium;Vrije Univ Brussel, Brussels, Belgium | 46 | <i>Escherichia;a;coli</i>;expression;factor;for;gene;in;Orthogonal;sigma;Toolbox | 1 | Bervoets, Indra;Charlier, Daniel;De Mey, Marjan | OXFORD UNIV PRESS | Univ Ghent, Dept Biotechnol, CSB, B-9000 Ghent, Belgium;Vrije Univ Brussel, Dept Bioengn Sci, Res Grp Microbiol, Pl Laan 2, B-1050 Brussels, Belgium | Article | Vrije Univ Brussel | OXFORD | null | null | Univ Ghent;Vrije Univ Brussel | Fonds voor Wetenschappelijk Onderzoek Vlaanderen;Fonds voor Wetenschappelijk onderzoek Vlaanderen (FWO-Vlaanderen);Ghent University Special Research Fund;Institute for the Promotion of Innovation through Science and Technology in Flanders (IWT-Vlaanderen) | Charlier, D (corresponding author), Vrije Univ Brussel, Dept Bioengn Sci, Res Grp Microbiol, Pl Laan 2, B-1050 Brussels, Belgium. | 2144 | Bervoets, Indra;Charlier, Daniel;De Mey, Marjan;Maertens, Jo;Van Brempt, Maarten;Van Hove, Bob;Van Nerom, Katleen | 51 | 2 | 426,293,300,048 | Fonds voor Wetenschappelijk onderzoek Vlaanderen (FWO-Vlaanderen);Fonds voor Wetenschappelijk Onderzoek Vlaanderen [G.0321.13N];Ghent University Special Research Fund [BOF16/IOP/040];Institute for the Promotion of Innovation through Science and Technology in Flanders (IWT-Vlaanderen) | Belgium | NUCLEIC ACIDS RESEARCH | Belgium | null | null | Vrije Univ Brussel, Dept Bioengn Sci, Res Grp Microbiol, Pl Laan 2, B-1050 Brussels, Belgium | 0305-1048 | Bervoets, I;Charlier, D;De Mey, M;Maertens, J;Van Brempt, M;Van Hove, B;Van Nerom, K | FEB 28 | dcharlie@vub.ac.be | <i>Escherichia coli</i>;orthogonal gene expression;sigma factor toolbox | 7 | J | Biochemistry & Molecular Biology | <i>Escherichia coli</i>;analyzed sigma factors;assembly;Bacillus subtilis;BACILLUS-SUBTILIS;CELL-ENVELOPE;circuit;CIRCUITS;complex synthetic genetic systems;conditions;control;DESIGN;different sensory signals;directed evolution;dynamic control;Escherichia coli;EXTRACYTOPLASMIC-FUNCTION SIGMA(X);four;future;gene expression;Genetic circuits;heterologous sigma factors;host;IDENTIFICATION;IN-VIVO;interesting expansion;interference;loss;multigene pathways;multiple outputs;orthogonal expression;orthogonal expression systems;orthogonal gene expression;orthogonal manner;orthogonal nature;orthogonally;PATHWAY;programmable control;promoter libraries;regulation systems;response;result;separate modules;shortage;sigma factor toolbox;size;specific promoter sequences;stay;synthetic biology;synthetic biology toolbox;synthetic genetic sensors;three sigma factors;timing;toolbox;TRANSCRIPTION;transcription initiation frequencies;tuning;undesired crosstalk;use;wide range | Bervoets, I | BACILLUS-SUBTILIS;CELL-ENVELOPE;DESIGN;directed evolution;EXTRACYTOPLASMIC-FUNCTION SIGMA(X);IDENTIFICATION;IN-VIVO;PATHWAY;Synthetic biology;TRANSCRIPTION | 2133 | [Bervoets, Indra; Van Nerom, Katleen; Charlier, Daniel] Vrije Univ Brussel, Dept Bioengn Sci, Res Grp Microbiol, Pl Laan 2, B-1050 Brussels, Belgium. [Van Brempt, Maarten; Van Hove, Bob; Maertens, Jo; De Mey, Marjan] Univ Ghent, Dept Biotechnol, CSB, B-9000 Ghent, Belgium. | Fonds voor Wetenschappelijk Onderzoek Vlaanderen [G.0321.13N to M.D.M., D.C.]; Ghent University Special Research Fund [BOF16/IOP/040 to M.D.M.]; Fonds voor Wetenschappelijk onderzoek Vlaanderen (FWO-Vlaanderen) (to BVH); Institute for the Promotion of Innovation through Science and Technology in Flanders (IWT-Vlaanderen) Ph.D. Grant (to M.V.B.). Funding for open access charge: Fonds Wetenschappelijk Onderzoek [G.0321.13N]. | analyzed sigma factors;assembly;Bacillus subtilis;circuit;circuits;complex synthetic genetic systems;conditions;control;different sensory signals;dynamic control;Escherichia coli;four;future;gene expression;genetic circuits;heterologous sigma factors;host;interesting expansion;interference;loss;multigene pathways;multiple outputs;orthogonal expression;orthogonal expression systems;orthogonal manner;orthogonal nature;orthogonally;programmable control;promoter libraries;regulation systems;response;result;separate modules;shortage;sigma factor toolbox;size;specific promoter sequences;stay;synthetic biology toolbox;synthetic genetic sensors;three sigma factors;timing;toolbox;transcription initiation frequencies;tuning;undesired crosstalk;use;wide range | 10.1006/jmbi.2001.5372;10.1007/s10295-016-1862-3;10.1016/0378-1119(79)90082-9;10.1016/j.biotechadv.2015.02.011;10.1016/j.biotechadv.2016.02.012;10.1016/j.cbpa.2016.08.003;10.1016/j.cell.2013.02.022;10.1016/j.cell.2014.10.002;10.1016/j.copbio.2014.11.013;10.1016/j.enzmictec.2014.10.006;10.1016/j.jbiotec.2013.07.030;10.1016/j.jmb.2006.01.059;10.1016/j.jmb.2015.10.004;10.1016/j.mib.2004.10.001;10.1016/j.mib.2008.10.002;10.1016/j.tibtech.2016.02.010;10.1016/j.ymben.2010.10.006;10.1016/j.ymben.2012.08.007;10.1016/j.ymben.2014.02.012;10.1016/S1369-5274(02)00372-7;10.1021/acssynbio.7b00017;10.1021/ja805203w;10.1021/sb500299c;10.1038/msb.2013.58;10.1038/nature10965;10.1038/nature12051;10.1038/nbt.1555;10.1038/nbt.1568;10.1038/nbt.2461;10.1038/nchembio.1411;10.1038/ncomms2425;10.1038/nrg3227;10.1038/nrmicro3240;10.1038/nrmicro750;10.1038/nrmicro787;10.1073/pnas.0600828103;10.1073/pnas.0900267106;10.1073/pnas.120163297;10.1073/pnas.1220157110;10.1073/pnas.89.11.5123;10.1093/nar/28.18.3497;10.1093/nar/gkg694;10.1093/nar/gkq810;10.1093/nar/gkr1288;10.1093/nar/gks597;10.1093/nar/gkt520;10.1093/nar/gku829;10.1111/j.1365-2958.2007.06090.x;10.1126/science.1191652;10.1126/science.1193990;10.1126/science.1214547;10.1128/jb.173.24.7867-7874.1991;10.1128/jb.174.12.3843-3849.1992;10.1128/JB.180.8.2057-2062.1998;10.1128/JB.181.18.5718-5724.1999;10.1128/JB.183.12.3623-3630.2001;10.1128/JB.183.6.1921-1927.2001;10.1128/JB.184.17.4881-4890.2002;10.1128/JB.186.4.1136-1146.2004;10.1128/MMBR.69.4.527-543.2005;10.1146/annurev-chembioeng-061312-103312;10.1146/annurev.micro.57.030502.090913;10.1186/1472-6750-10-26;10.1186/1472-6750-7-34;10.1186/1475-2859-12-56;10.1371/journal.pcbi.1002811;10.1371/journal.pone.0006441;10.1371/journal.pone.0179181;10.15252/msb.20145299;10.3389/fpls.2015.00007;10.3390/biom5031245;[10.1038/NMETH.2404, 10.1038/nmeth.2404];[10.1371/journal.pone.0016765, 10.4161/bbug.3.1.18223] | Vrije Univ Brussel | Bervoets, I;Charlier, D;De Mey, M;Maertens, J;Van Brempt, M;Van Hove, B;Van Nerom, K | Bervoets, I: Vrije Univ Brussel, Dept Bioengn Sci, Res Grp Microbiol, Pl Laan 2, B-1050 Brussels, Belgium | De Mey, Marjan | BOF16/IOP/040;G.0321.13N | 76 | null | Belgium | Univ Ghent;Vrije Univ Brussel | Bervoets, Indra | Green Published, Green Submitted, gold | BACILLUS-SUBTILIS;CELL-ENVELOPE;DESIGN;DIRECTED EVOLUTION;EXTRACYTOPLASMIC-FUNCTION SIGMA(X);IDENTIFICATION;IN-VIVO;PATHWAY;SYNTHETIC BIOLOGY;TRANSCRIPTION | Bervoets, Indra; Van Brempt, Maarten; Van Nerom, Katleen; Van Hove, Bob; Maertens, Jo; De Mey, Marjan; Charlier, Daniel; | null | Univ Ghent, Dept Biotechnol, CSB, B-9000 Ghent, Belgium;Vrije Univ Brussel, Dept Bioengn Sci, Res Grp Microbiol, Pl Laan 2, B-1050 Brussels, Belgium | Univ Ghent, Dept Biotechnol, CSB, B-9000 Ghent, Belgium;Vrije Univ Brussel, Dept Bioengn Sci, Res Grp Microbiol, Pl Laan 2, B-1050 Brussels, Belgium | 1362-4962 | null | 4 | 1979;1991;1992;1998;1999;2000;2001;2002;2003;2004;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017 | 57 | Vrije Univ Brussel, Dept Bioengn Sci, Res Grp Microbiol, Pl Laan 2, B-1050 Brussels, Belgium | Nucleic Acids Res. | Charlier, Daniel | OXFORD UNIV PRESS | ,;a;additionally;allow;an;analyzed;and;are;as;assembly;Bacillus;based;be;between;biology;but;by;can;circuit;circuits;coli;combined;complex;complexity;conditions;constitutes;contribute;control;covers;creating;crosstalk;different;dynamic;each;enable;enables;Escherichia;expanded;expansion;expression;factor;factors;for;four;frequencies;from;function;future;gene;genetic;growing;heterologous;host;in;incorporated;increasingly;initiation;interesting;interference;into;is;it;libraries;limited;loss;manner;may;minimize;modules;more;multigene;multiple;nature;needed;of;on;Orthogonal;orthogonally;other;outputs;over;parts;pathways;presents;programmable;promoter;range;recognize;regulation;regulatory;response;result;sensors;sensory;separate;sequences;set;shortage;sigma;signals;size;specific;stay;subtilis;synthetic;systems;that;the;their;therefore;this;three;timing;to;toolbox;toward;transcription;tuning;undesired;up;use;used;wide;without;work | Vrije Univ Brussel | Synthetic genetic sensors and circuits enable programmable control over timing and conditions of gene expression and, as a result, are increasingly incorporated into the control of complex and multigene pathways. Size and complexity of genetic circuits are growing, but stay limited by a shortage of regulatory parts that can be used without interference. Therefore, orthogonal expression and regulation systems are needed to minimize undesired crosstalk and allow for dynamic control of separate modules. This work presents a set of orthogonal expression systems for use in Escherichia coli based on heterologous sigma factors from Bacillus subtilis that recognize specific promoter sequences. Up to four of the analyzed sigma factors can be combined to function orthogonally between each other and toward the host. Additionally, the toolbox is expanded by creating promoter libraries for three sigma factors without loss of their orthogonal nature. As this set covers a wide range of transcription initiation frequencies, it enables tuning of multiple outputs of the circuit in response to different sensory signals in an orthogonal manner. This sigma factor toolbox constitutes an interesting expansion of the synthetic biology toolbox and may contribute to the assembly of more complex synthetic genetic systems in the future. | S-8129-2019 | BACILLUS-SUBTILIS;CELL-ENVELOPE;DESIGN;DIRECTED EVOLUTION;EXTRACYTOPLASMIC-FUNCTION SIGMA(X);IDENTIFICATION;IN-VIVO;PATHWAY;SYNTHETIC BIOLOGY;TRANSCRIPTION | 5 | null | null | 12 | BACILLUS-SUBTILIS;cell envelope;DESIGN;directed evolution;EXTRACYTOPLASMIC-FUNCTION SIGMA(X);IDENTIFICATION;IN-VIVO;PATHWAY;Synthetic biology;TRANSCRIPTION | WOS:000426293300048 | Univ Ghent, Ghent, Belgium;Vrije Univ Brussel, Brussels, Belgium | Belgium | 2,018 | null | 0000-0002-1402-7517;0000-0002-6844-376X;0000-0002-8134-9436 | null | null | English | null | ACS SYNTH BIOL;ANNU REV CHEM BIOMOL;ANNU REV MICROBIOL;BIOENGINEERED;BIOMOLECULES;BIOTECHNOL ADV;BMC BIOTECHNOL;CELL;CURR OPIN BIOTECH;CURR OPIN CHEM BIOL;CURR OPIN MICROBIOL;ENZYME MICROB TECH;FRONT PLANT SCI;GENE;J AM CHEM SOC;J BACTERIOL;J BIOTECHNOL;J IND MICROBIOL BIOT;J MOL BIOL;J STAT SOFTW;METAB ENG;MICROB CELL FACT;MICROBIOL MOL BIOL R;MOL MICROBIOL;MOL SYST BIOL;NAT BIOTECHNOL;NAT CHEM BIOL;NAT COMMUN;NAT METHODS;NAT REV GENET;NAT REV MICROBIOL;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PLOS COMPUT BIOL;PLOS ONE;SCI REP UK;SCIENCE;TRENDS BIOTECHNOL | Bervoets, Indra;Charlier, Daniel;De Mey, Marjan;Maertens, Jo;Van Brempt, Maarten;Van Hove, Bob;Van Nerom, Katleen | 2024-03-11
ER | Ajikumar, P K;Amaya, E;An, W L;Arense, P;Bagyan, I;Bikard, D;Bradley, R W;Brewster, R C;Britton, R A;Browning, D F;Cao, M;Chen, Y F;Cheon, S;Coussement, P;Dagert, M;Datsenko, K A;Davis, J H;De Mey, M;De Paepe, B;Eiamphungporn, W;Errington, J;Green, A A;Grigorova, I L;Gruber, T M;Gu, L;Hengge-Aronis, R;Jones, J A;Jullesson, D;Kahm, M;Kazmierczak, M J;Keasling, J D;Li, G W;Lonetto, M;Lucks, J B;Maeda, H;Meyer, A J;Mitchell, J E;Mutalik, V K;Na, D;Paddon, C J;Paget, M S;Pandey, R P;Petersohn, A;Piggot, P J;Qi, L S;Qiu, J;Quan, J Y;Rhodius, V A;Salis, H M;Segall-Shapiro, T H;Sharma, V;Shimada, T;Shis, D L;Singh, A;Slusarczyk, A L;Stanton, B C;Sun, D X;Tai, M;Temme, K;Trantas, E A;Trubitsyna, M;Tyo, K E J;Van Hove, B;Wang, S T;Wargacki, A J;Werner, S;Woolston, B M;Wu, G;Wu, J J;Xu, P;Zhang, Y W;Zou R. | FX7TG | Brussels, Belgium | 66 | null | 2 | null | 29,361,130 | Bervoets, Indra;Charlier, Daniel;De Mey, Marjan;Maertens, Jo;Van Brempt, Maarten;Van Hove, Bob;Van Nerom, Katleen | NUCLEIC ACIDS RES | Brussels, Belgium;Ghent, Belgium |
Wang, X;Wu, F Q;Zhang, Q | 10.1016/j.cels.2018.01.010 | null | 50 HAMPSHIRE ST, FLOOR 5, CAMBRIDGE, MA 02139 USA | 7057195h3de613s6v3q3f1o4q3yq2u5v181e48 | Design of Adjacent Transcriptional Regions to Tune Gene Expression and Facilitate Circuit Construction | Arizona State Univ | null | Wang, X (corresponding author), Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85287 USA. | null | Wang, Xiao;Wu, Fuqing;Zhang, Qi | Biochemistry & Molecular Biology;Cell Biology | American Heart Association [15PRE25710303]; National Science Foundation [DMS-1100309]; NIH [GM106081] | WOS | Wang, X | Arizona State Univ, Tempe, AZ USA | 6 | Adjacent;and;circuit;construction;design;expression;Facilitate;gene;of;Regions;to;Transcriptional;tune | 1 | Wang, Xiao;Wu, Fuqing;Zhang, Qi | CELL PRESS | Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85287 USA | Article | Arizona State Univ | CAMBRIDGE | null | null | Arizona State Univ | American Heart Association;National Science Foundation;NIH | Wang, X (corresponding author), Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85287 USA. | + | Wang, Xiao;Wu, Fuqing;Zhang, Qi | 23 | 1 | 427,421,500,010 | American Heart Association [15PRE25710303];National Science Foundation [DMS-1100309];NIH [GM106081] | USA | CELL SYSTEMS | USA | null | null | Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85287 USA | 2405-4712 | Wang, X;Wu, F Q;Zhang, Q | FEB 28 | xiaowang@asu.edu | Adjacent Transcriptional Regions;Circuit Construction;gene expression | 3 | J | Biochemistry & Molecular Biology;Cell Biology | 300-fold range;account ATRs;Adjacent Transcriptional Regions;adjacent transcriptional regions (ATR);ATRs;BACTERIA;bistability;Circuit Construction;common;complex synthetic gene circuits;comprehensive model;DEGRADATION;degrees;designed synthetic 5'ATRs;different ATRs;different GC content;ESCHERICHIA-COLI;expression;future engineering;gene expression;genes/noncoding regions;high GC content;high gene expression;high sensitivity;INITIATION;logic gates;low basal expression;low folding energy lead;MESSENGER-RNA;networks;nonlinearity;one gene;operon;ORGANIZATION;polycistronic architecture;protein expression levels;reporter gene;results;secondary structure;sizes;small size;synthetic biology;synthetic gene circuits;synthetic operons;synthetic toggle switches;takes;TRANSLATION EFFICIENCY;unknown;varying basal expression | Wu, F Q | BACTERIA;DEGRADATION;ESCHERICHIA-COLI;INITIATION;MESSENGER-RNA;NETWORKS;ORGANIZATION;SECONDARY STRUCTURE;Synthetic biology;TRANSLATION EFFICIENCY | 206 | [Wu, Fuqing; Zhang, Qi; Wang, Xiao] Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85287 USA. | We thank Dr. Alexander Green for helpful suggestions and comments and Josh Cutts, Wei Feng, and Stefan Tekel for technical support for the RT-qPCR experiments. We would also like to thank Dr. John Fricks for inputs on statistical analysis and reasoning. F.W. was supported by an American Heart Association Predoctoral Fellowship (15PRE25710303). This study was financially supported by a National Science Foundation grant (DMS-1100309) and NIH grant (GM106081) (to X.W.). | 300-fold range;account ATRs;adjacent transcriptional regions (ATR);ATRs;bistability;common;complex synthetic gene circuits;comprehensive model;degrees;designed synthetic 5'ATRs;different ATRs;different GC content;expression;future engineering;gene expression;genes/noncoding regions;high GC content;high gene expression;high sensitivity;logic gates;low basal expression;low folding energy lead;nonlinearity;one gene;operon;polycistronic architecture;protein expression levels;reporter gene;results;sizes;small size;synthetic gene circuits;synthetic operons;synthetic toggle switches;takes;unknown;varying basal expression | 10.1002/jcc.21596;10.1016/j.cell.2014.10.004;10.1016/j.cell.2016.03.006;10.1016/j.cell.2016.04.059;10.1016/j.cels.2017.06.001;10.1016/j.chembiol.2014.10.008;10.1016/j.jmb.2016.02.018;10.1016/j.jtbi.2008.02.005;10.1016/j.molcel.2016.06.006;10.1021/bi9809425;10.1021/jacs.6b01453;10.1021/sb4000977;10.1038/35002125;10.1038/35002131;10.1038/509S13a;10.1038/nature13238;10.1038/nature18930;10.1038/nbt.1568;10.1038/nbt.3053;10.1038/nbt0509-450;10.1038/nrmicro.2015.24;10.1038/nrmicro2930;10.1073/pnas.0909910107;10.1073/pnas.1105692108;10.1073/pnas.1205693109;10.1073/pnas.1305590110;10.1073/pnas.87.19.7668;10.1093/femsre/fuv022;10.1093/nar/27.7.1578;10.1093/nar/gku159;10.1101/gad.6.1.135;10.1101/gr.912603;10.1126/science.1170160;10.1126/science.1188308;10.1126/science.1209042;10.1126/science.aaa3794;10.1126/science.aac7341;10.1128/AEM.01055-16;10.1146/annurev.genet.42.110807.091653;10.1186/s13036-017-0068-1;10.1371/journal.pone.0113380;10.1371/journal.pone.0176013;10.15252/msb.20134955;10.15252/msb.20145794;10.15252/msb.20156540;10.3184/003685015X14368807556441;10.3389/fmicb.2014.00451;10.7554/eLife.23702;[10.1038/NMETH.2205, 10.1038/nmeth.2205];[10.1038/NMETH.2404, 10.1038/nmeth.2404];[10.1038/NMETH.2926, 10.1038/nmeth.2926];[10.1038/NMETH.3147, 10.1038/nmeth.3147] | Arizona State Univ | Wang, X;Wu, F Q;Zhang, Q | Wu, F Q: Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85287 USA | Wang, Xiao;Wu, Fuqing | 15PRE25710303;DMS-1100309;GM106081 | 53 | null | USA | Arizona State Univ | Wu, Fuqing | Green Accepted, Bronze | BACTERIA;DEGRADATION;ESCHERICHIA-COLI;INITIATION;MESSENGER-RNA;NETWORKS;ORGANIZATION;SECONDARY STRUCTURE;SYNTHETIC BIOLOGY;TRANSLATION EFFICIENCY | Wu, Fuqing; Zhang, Qi; Wang, Xiao; | null | Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85287 USA | Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85287 USA | 2405-4720 | null | 2 | 1990;1992;1995;1998;1999;2000;2003;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017 | 11 | Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85287 USA | Cell Syst. | Wang, Xiao | CELL PRESS | (ATR);,;300-fold;5'ATRs;a;account;adjacent;affected;and;architecture;ATRs;basal;based;bistability;build;built;by;circuits;common;complex;comprehensive;construct;constructed;content;could;degrees;design;designed;different;energy;engineering;expression;facilitate;flanked;folding;for;found;furthermore;future;gates;GC;gene;generated;genes/noncoding;here;high;how;however;in;into;is;it;lead;levels;logic;low;metric;model;more;nonlinearity;of;on;one;operon;operons;other;our;over;polycistronic;presence;protein;range;rationally;regions;remains;reporter;results;sensitivity;size;sizes;small;switches;synthetic;takes;termed;that;the;these;to;toggle;transcriptional;tune;unknown;used;varying;we;with | Arizona State Univ | Polycistronic architecture is common for synthetic gene circuits, however, it remains unknown how expression of one gene is affected by the presence of other genes/noncoding regions in the operon, termed adjacent transcriptional regions (ATR). Here, we constructed synthetic operons with a reporter gene flanked by different ATRs, and we found that ATRs with high GC content, small size, and low folding energy lead to high gene expression. Based on these results, we built a model of gene expression and generated a metric that takes into account ATRs. We used the metric to design and construct logic gates with low basal expression and high sensitivity and nonlinearity. Furthermore, we rationally designed synthetic 5'ATRs with different GC content and sizes to tune protein expression levels over a 300-fold range and used these to build synthetic toggle switches with varying basal expression and degrees of bistability. Our comprehensive model and gene expression metric could facilitate the future engineering of more complex synthetic gene circuits. | A-8414-2008;AAU-8942-2021;I-9228-2017 | BACTERIA;DEGRADATION;ESCHERICHIA-COLI;INITIATION;MESSENGER-RNA;NETWORKS;ORGANIZATION;SECONDARY STRUCTURE;SYNTHETIC BIOLOGY;TRANSLATION EFFICIENCY | 1 | null | null | 16 | ESCHERICHIA-COLI;BACTERIA;DEGRADATION;INITIATION;MESSENGER-RNA;NETWORKS;ORGANIZATION;SECONDARY STRUCTURE;Synthetic biology;TRANSLATION EFFICIENCY | WOS:000427421500010 | Arizona State Univ, Tempe, AZ USA | USA | 2,018 | null | 0000-0002-2820-3550;0000-0002-4056-0155;0000-0002-8463-1322 | null | null | English | null | ACS SYNTH BIOL;ANNU REV GENET;APPL ENVIRON MICROB;BIOCHEMISTRY-US;CELL;CELL SYST;CHEM BIOL;ELIFE;FEMS MICROBIOL REV;FRONT MICROBIOL;GENE DEV;GENOME RES;J AM CHEM SOC;J Biol Eng;J COMPUT CHEM;J MOL BIOL;J THEOR BIOL;METHOD ENZYMOL;MOL CELL;MOL SYST BIOL;NAT BIOTECHNOL;NAT METHODS;NAT REV MICROBIOL;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PLOS ONE;SCI PROGRESS-UK;SCIENCE | Wang, Xiao;Wu, Fuqing;Zhang, Qi | 2024-03-11
ER | Ahnert, S E;Bennett, M R;Borujeni, A E;Brophy, J A N;Cameron, D E;Cao, Y X L;Carr, S B;Chen, H Y;Chen, Y;Chizzolini, F;Desmit, M H;Din, M O;Egbert, R G;Elowitz, M B;Emory, S A;Farasat, I;Ferreira, J P;Gardner, T S;Kudla, G;Lee, J W;Li, J;Lim, H N;Litcofsky, K D;Liu, C L;Ma, K C;Mackie, G A;Mao, Y H;Mus, F;Mutalik, V K;Nielsen, A A K;Oliva, G;Pardee, K;Prindle, A;Rocha, E P C;Salis, H M;Seffens, W;Selinger, D W;Serra, M J;Smanski, M J;Taniguchi, Y;Trotta, E;Tuller, T;Wright, G;Wu, F Q;Xia, T B;Yang, L;Yeung, E;Zadeh, J N;Zhang, W W | FZ2PG | Tempe, AZ USA | 14 | null | 1 | null | 29,428,414 | Wang, Xiao;Wu, Fuqing;Zhang, Qi | CELL SYST | Tempe, AZ USA |
Boehm, C R;Grant, P K;Haseloff, J | 10.1038/s41467-018-03069-3 | 776 | MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND | 212c6d51374z485r244682q5m701b2f2k1j2o2r | Programmed hierarchical patterning of bacterial populations | Univ Cambridge | null | Haseloff, J (corresponding author), Univ Cambridge, Dept Plant Sci, Downing St, Cambridge CB2 3EA, England. | null | Boehm, Christian R;Grant, Paul K;Haseloff, Jim | Multidisciplinary Sciences | Gates Cambridge Trust; John Templeton Foundation [15619]; Biotechnology and Biological Sciences Research Council; Engineering and Physical Sciences Research Council [BB/L014130/1]; EC [612146]; BBSRC [BB/L014130/1] Funding Source: UKRI | WOS | Haseloff, J | Max Planck Inst Mol Plant Physiol, Potsdam, Germany;Microsoft Res, Cambridge, England;Univ Cambridge, Cambridge, England | 9 | Bacterial;hierarchical;of;patterning;populations;programmed | 2 | Boehm, Christian R.;Grant, Paul;Haseloff, Jim | NATURE PUBLISHING GROUP | Max Planck Inst Mol Plant Physiol, Muhlenberg 1, D-14476 Potsdam, Germany;Microsoft Res, 21 Stn Rd, Cambridge CB1 2FB, England;Univ Cambridge, Dept Plant Sci, Downing St, Cambridge CB2 3EA, England | Article | Univ Cambridge | LONDON | null | null | Max Planck Inst Mol Plant Physiol;Microsoft Res;Univ Cambridge | BBSRC;Biotechnology and Biological Sciences Research Council;EC;Engineering and Physical Sciences Research Council;Gates Cambridge Trust;John Templeton Foundation | Haseloff, J (corresponding author), Univ Cambridge, Dept Plant Sci, Downing St, Cambridge CB2 3EA, England. | null | Boehm, Christian R;Grant, Paul K;Haseloff, Jim | 20 | 3 | 425,787,500,017 | BBSRC [BB/L014130/1] Funding Source: UKRI;Biotechnology and Biological Sciences Research Council;EC [612146];Engineering and Physical Sciences Research Council [BB/L014130/1];Gates Cambridge Trust;John Templeton Foundation [15619] | Germany;UK | NATURE COMMUNICATIONS | UK | null | null | Univ Cambridge, Dept Plant Sci, Downing St, Cambridge CB2 3EA, England | 2041-1723 | Boehm, C R;Grant, P K;Haseloff, J | FEB 22 | jh295@cam.ac.uk | bacterial populations | 3 | J | Science & Technology - Other Topics | autonomous induction;bacterial gene expression domains;bacterial populations;bacteriophage T7 RNA polymerase activity;BACTERIOPHAGE-T7;best-performing variant;biological self-organization;cell suspension;control;date;different;dissection;DNA;emulation;expression;fundamental mechanisms shaping morphogenesis;gate-like behavior;gene expression across bacterial populations;gene expression domains;genes;growth;hierarchical induction;importance;IN-VIVO;little attention;membrane-based spatial assay;modern genetic tools;multicellular;multicellular organisms;population-based AND-logic;POSITIONAL INFORMATION;promoters;ratiometric assay;sequence;several synthetic genetic circuits;split enzyme variants;surface culture;synthetic biologists;synthetic circuit;synthetic genetic system;SYSTEM;T7 RNA-POLYMERASE;three-color;two different homoserine lactones | Boehm, C R | BACTERIOPHAGE-T7;DNA;EXPRESSION;GENES;GROWTH;IN-VIVO;POSITIONAL INFORMATION;PROMOTERS;SEQUENCE;T7 RNA-POLYMERASE | null | [Boehm, Christian R.; Grant, Paul K.; Haseloff, Jim] Univ Cambridge, Dept Plant Sci, Downing St, Cambridge CB2 3EA, England. [Grant, Paul K.] Microsoft Res, 21 Stn Rd, Cambridge CB1 2FB, England. [Boehm, Christian R.] Max Planck Inst Mol Plant Physiol, Muhlenberg 1, D-14476 Potsdam, Germany. | C.R.B. acknowledges support from the Gates Cambridge Trust. P.K.G. acknowledges support from the John Templeton Foundation (Grant No. 15619: "Mind, Mechanism and Mathematics: Turing Centenary Research Project"). J.H. acknowledges support from the Biotechnology and Biological Sciences Research Council and the Engineering and Physical Sciences Research Council (OpenPlant Grant No. BB/L014130/1) and EC FP7 project no. 612146 (PLASWIRES). | autonomous induction;bacterial gene expression domains;bacteriophage T7 RNA polymerase activity;best-performing variant;biological self-organization;cell suspension;control;date;different;dissection;emulation;fundamental mechanisms shaping morphogenesis;gate-like behavior;gene expression across bacterial populations;gene expression domains;hierarchical induction;importance;little attention;membrane-based spatial assay;modern genetic tools;multicellular;multicellular organisms;population-based AND-logic;ratiometric assay;several synthetic genetic circuits;split enzyme variants;surface culture;synthetic biologists;synthetic circuit;synthetic genetic system;system;three-color;two different homoserine lactones | 10.1002/dvg.1020090202;10.1006/jmbi.1996.0399;10.1016/0022-2836(86)90385-2;10.1016/0092-8674(79)90097-7;10.1016/0092-8674(89)90103-7;10.1016/0378-1119(87)90165-X;10.1016/B978-0-12-385120-8.00002-4;10.1016/j.cell.2009.04.048;10.1016/j.cell.2009.12.001;10.1016/j.chembiol.2014.10.008;10.1016/S0022-2836(83)80282-4;10.1016/S0022-5193(69)80016-0;10.1021/acssynbio.5b00116;10.1021/acssynbio.5b00286;10.1021/acssynbio.6b00248;10.1021/bi000365w;10.1021/bi00415a055;10.1021/ja907617a;10.1021/sb200015u;10.1021/sb400152n;10.1038/280035a0;10.1038/353031a0;10.1038/msb.2008.24;10.1038/msb.2013.55;10.1038/nature03461;10.1038/nature11516;10.1038/nbt0102-87;10.1038/ncomms1738;10.1038/ncomms5905;10.1038/nrg1837;10.1038/srep15159;10.1073/pnas.0407229101;10.1073/pnas.0704256104;10.1073/pnas.1220157110;10.1073/pnas.92.26.12250;10.1074/jbc.M311194200;10.1093/nar/gkq671;10.1093/nar/gks597;10.1093/nar/gku884;10.1098/rsif.2014.1041;10.1098/rstb.1952.0012;10.1101/cshperspect.a001990;10.1101/cshperspect.a023929;10.1103/PhysRevLett.94.018103;10.1126/science.aaa3794;10.1128/JB.132.2.734-737.1977;10.1128/jb.174.2.619-622.1992;10.1128/jb.177.6.1497-1504.1995;10.1128/jb.179.2.557-562.1997;10.1146/annurev-genet-102108-134304;10.1186/1754-1611-3-10;10.1242/dev.114991;10.1371/journal.pbio.0030064;10.15252/msb.20145299;10.15252/msb.20156590;10.3389/fbioe.2015.00030;[10.1038/NMETH.1318, 10.1038/nmeth.1318];[10.1038/NMETH.2019, 10.1038/nmeth.2019] | Univ Cambridge | Boehm, C R;Grant, P K;Haseloff, J | Boehm, C R: Univ Cambridge, Dept Plant Sci, Downing St, Cambridge CB2 3EA, England | null | 15619;612146;BB/L014130/1 | 60 | null | UK | Max Planck Inst Mol Plant Physiol;Microsoft Res;Univ Cambridge | Boehm, Christian R | gold, Green Published, Green Submitted | BACTERIOPHAGE-T7;DNA;EXPRESSION;GENES;GROWTH;IN-VIVO;POSITIONAL INFORMATION;PROMOTERS;SEQUENCE;T7 RNA-POLYMERASE | Boehm, Christian R.; Grant, Paul K.; Haseloff, Jim; | null | Max Planck Inst Mol Plant Physiol, Muhlenberg 1, D-14476 Potsdam, Germany;Microsoft Res, 21 Stn Rd, Cambridge CB1 2FB, England;Univ Cambridge, Dept Plant Sci, Downing St, Cambridge CB2 3EA, England | Max Planck Inst Mol Plant Physiol, Muhlenberg 1, D-14476 Potsdam, Germany;Microsoft Res, 21 Stn Rd, Cambridge CB1 2FB, England;Univ Cambridge, Dept Plant Sci, Downing St, Cambridge CB2 3EA, England | null | null | null | 1952;1969;1977;1979;1983;1986;1987;1988;1989;1991;1992;1995;1996;1997;2000;2002;2004;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017 | 25 | Univ Cambridge, Dept Plant Sci, Downing St, Cambridge CB2 3EA, England | Nat. Commun. | Haseloff, Jim | NATURE PUBLISHING GROUP | ,;a;across;activity;allow;and;AND-logic;assay;attention;autonomous;bacterial;bacteriophage;been;behavior;best-performing;biological;biologists;both;build;cell;characterize;circuit;circuits;control;culture;date;demonstrate;despite;develop;different;dissection;domains;emulation;enzyme;expression;finally;for;from;fundamental;gate-like;gene;genetic;has;have;here;hierarchical;homoserine;however;implementing;importance;in;induction;intact;it;its;lactones;little;mechanisms;membrane-based;modern;morphogenesis;multicellular;of;organisms;patterning;polymerase;population-based;populations;programmed;ratiometric;received;report;reported;responsive;RNA;self-organization;several;shaping;spatial;split;surface;suspension;synthetic;system;systematically;T7;the;then;this;three-color;to;tools;two;use;utilize;validate;variant;variants;we | Univ Cambridge | Modern genetic tools allow the dissection and emulation of fundamental mechanisms shaping morphogenesis in multicellular organisms. Several synthetic genetic circuits for control of multicellular patterning have been reported to date. However, hierarchical induction of gene expression domains has received little attention from synthetic biologists, despite its importance in biological self-organization. Here we report a synthetic genetic system implementing population-based AND-logic for programmed autonomous induction of bacterial gene expression domains. We develop a ratiometric assay for bacteriophage T7 RNA polymerase activity and use it to systematically characterize different intact and split enzyme variants. We then utilize the best-performing variant to build a three-color patterning system responsive to two different homoserine lactones. We validate the AND gate-like behavior of this system both in cell suspension and in surface culture. Finally, we use the synthetic circuit in a membrane-based spatial assay to demonstrate programmed hierarchical patterning of gene expression across bacterial populations. | null | BACTERIOPHAGE-T7;DNA;EXPRESSION;GENE;GROWTH;IN-VIVO;POSITIONAL INFORMATION;PROMOTER;SEQUENCE;T7 RNA-POLYMERASE | 0 | null | null | 10 | BACTERIOPHAGE-T7;DNA;EXPRESSION;GENE;GROWTH;IN-VIVO;POSITIONAL INFORMATION;PROMOTER;SEQUENCE;T7 RNA-POLYMERASE | WOS:000425787500017 | Max Planck Inst Mol Plant Physiol, Potsdam, Germany;Microsoft Res, Cambridge, England;Univ Cambridge, Cambridge, England | Germany;UK | 2,018 | null | 0000-0002-1099-0461;0000-0002-6633-7998;0000-0003-4793-8058 | null | null | English | null | ACS SYNTH BIOL;ANNU REV GENET;BIOCHEMISTRY-US;CELL;CHEM BIOL;CSH PERSPECT BIOL;DEV GENET;DEVELOPMENT;FRONT BIOENG BIOTECH;GENE;J AM CHEM SOC;J BACTERIOL;J BIOL CHEM;J Biol Eng;J MOL BIOL;J R SOC INTERFACE;J THEOR BIOL;Mechanisms of Morphogenesis;METHOD ENZYMOL;MOL SYST BIOL;NAT BIOTECHNOL;NAT COMMUN;NAT METHODS;NAT REV GENET;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PHILOS T ROY SOC B;PHYS REV LETT;PLOS BIOL;SCI REP-UK;SCIENCE | Boehm, Christian R;Grant, Paul K;Haseloff, Jim | 2024-03-11
ER | Balagadde, F K;Barkai, N;Basu, S;Bollenbach, T;Brenner, K;Chen, Y;Coen, E S;Cohen, S N;Davies Jamie A.;Davis, R M;Dong, H J;Dunn, J J;Gibson, D G;Goedhart, J;Grant, P K;Greber, D;Green, J B A;Han, T Y;Haughn, G W;Ikeda, R A;Imburgio, D;Iost, I;Isalan, M;Kimelman, D;Klumpp, S;Lo, W C;Makarova, O V;Miroux, B;Moon, T S;Muller, D K;Nagai, T;Ng, W L;Panayotatos, N;Payne, S;Reinke, A W;Rosa, M D;Rosenberg, A H;Rudge, T J;Salis, H M;Schaerli, Y;Schindelin, J;Schuster, M;Scott, S R;Segall-Shapiro, T H;Shis, D L;Sohka Takayuki;Sternberg, P W;Stevens, A M;Studier, F W;Tabor, J J;Teague, B P;Temme, K;Thompson, K E;Turing, A M;Wang, L H;Wang, L Y;Wolpert, L;Wu, F Q;Yordanov, B | FX1DE | Cambridge, England | 27 | null | 3 | null | 29,472,537 | Boehm, Christian R;Grant, Paul K;Haseloff, Jim | NAT COMMUN | Cambridge, England;Potsdam, Germany |
Cole, C M;Devaraj, N K;Joseph, S;Shi, X Y;Wu, T | 10.1038/s41598-018-21739-6 | 3488 | MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND | 1x6x4c55t5l6t6c4ye1q5t3n3s4p6p57554y3q | Optimization of ClpXP activity and protein synthesis in an <i>E-coli</i> extract-based cell-free expression system | Univ Calif San Diego | null | Joseph, S (corresponding author), Univ Calif San Diego, Dept Chem & Biochem, 9500 Gilman Dr, La Jolla, CA 92093 USA. | null | Cole, Christian M;Devaraj, Neal K;Joseph, Simpson;Shi, Xinying;Wu, Ti | Multidisciplinary Sciences | Department of Defense Army Research Office [W911NF-13-1-0383] | WOS | Joseph, S | Univ Calif San Diego, La Jolla, CA USA | 8 | <i>E-coli</i>;activity;an;and;Cell-Free;ClpXP;expression;extract-based;in;of;optimization;protein;synthesis;system | 1 | Wu, Ti | NATURE PUBLISHING GROUP | Univ Calif San Diego, Dept Chem & Biochem, 9500 Gilman Dr, La Jolla, CA 92093 USA | Article | Univ Calif San Diego | LONDON | null | null | Univ Calif San Diego | Department of Defense Army Research Office | Joseph, S (corresponding author), Univ Calif San Diego, Dept Chem & Biochem, 9500 Gilman Dr, La Jolla, CA 92093 USA. | null | Cole, Christian M;Devaraj, Neal K;Joseph, Simpson;Shi, Xinying;Wu, Ti | 17 | 1 | 425,728,600,044 | Department of Defense Army Research Office [W911NF-13-1-0383] | USA | SCIENTIFIC REPORTS | USA | null | null | Univ Calif San Diego, Dept Chem & Biochem, 9500 Gilman Dr, La Jolla, CA 92093 USA | 2045-2322 | Cole, C M;Devaraj, N K;Joseph, S;Shi, X Y;Wu, T | FEB 22 | sjoseph@ucsd.edu | <i>E-coli</i> extract-based cell-free expression system;ClpXP activity;optimization;protein synthesis | 5 | J | Science & Technology - Other Topics | <i>E-coli</i> extract-based cell-free expression system;activity;adenosine triphosphate (ATP);ATP;cell;cell extract;cell-free expression system;cell-free transcription-translation (TX-TL) systems;ClpXP;ClpXP activity;conditions;damaged proteins;DEGRADATION MACHINE;E. coli ClpXP protease;efficient protein expression platform;EMULSION;energy regeneration system;established conditions;exogenous ATP;function;fundamental process;IN-VITRO;intact proteins;living cells;low activity;low proteolytic activity;optimization;POLYPHOSPHATE;protein degradation;protein synthesis;purified ClpXP;rapid consumption;robust protein degradation system;SSPB ADAPTER;studies;synthetic;tunable synthetic genetic circuits;TX-TL system;TX-TL systems;used E. coli S30 cell extract;VESICLES;vitro synthetic biology;will | Shi, X Y | ATP;DEGRADATION MACHINE;EMULSION;IN-VITRO;POLYPHOSPHATE;SSPB ADAPTER;VESICLES | null | [Shi, Xinying; Wu, Ti; Cole, Christian M.; Devaraj, Neal K.; Joseph, Simpson] Univ Calif San Diego, Dept Chem & Biochem, 9500 Gilman Dr, La Jolla, CA 92093 USA. | This work was supported by the Department of Defense Army Research Office contract W911NF-13-1-0383. | activity;adenosine triphosphate (ATP);cell;cell extract;cell-free expression system;cell-free transcription-translation (TX-TL) systems;ClpXP;ClpXP activity;conditions;damaged proteins;E. coli ClpXP protease;efficient protein expression platform;energy regeneration system;established conditions;exogenous ATP;function;fundamental process;intact proteins;living cells;low activity;low proteolytic activity;protein degradation;protein synthesis;purified ClpXP;rapid consumption;robust protein degradation system;studies;synthetic;tunable synthetic genetic circuits;TX-TL system;TX-TL systems;used E. coli S30 cell extract;vitro synthetic biology;will | 10.1002/cbic.201500643;10.1016/0005-2760(74)90091-5;10.1016/B978-0-12-420067-8.00025-8;10.1016/j.bbamcr.2011.06.007;10.1016/j.cell.2009.09.034;10.1016/j.jmb.2015.06.021;10.1016/j.mimet.2005.05.003;10.1016/j.molcel.2004.10.001;10.1016/j.tibs.2016.08.013;10.1016/S0092-8674(00)80431-6;10.1016/S0092-8674(03)00612-3;10.1016/S1097-2765(00)80243-9;10.1016/S1097-2765(03)00060-1;10.1021/acssynbio.5b00296;10.1021/la026100v;10.1038/35002125;10.1038/nature13238;10.1073/pnas.1600098113;10.1073/pnas.1931005100;10.1074/jbc.M109.017624;10.1088/1478-3975/2/3/P01;10.1093/nar/gkh925;10.1101/gad.12.9.1338;10.1101/gad.1240104;10.1126/science.289.5488.2354;10.1128/AEM.66.5.2045-2051.2000;10.1146/annurev-biochem-060408-172623;10.1186/1754-1611-4-8;10.1186/1754-1611-4-9;10.1371/journal.pone.0028707 | Univ Calif San Diego | Cole, C M;Devaraj, N K;Joseph, S;Shi, X Y;Wu, T | Shi, X Y: Univ Calif San Diego, Dept Chem & Biochem, 9500 Gilman Dr, La Jolla, CA 92093 USA | Devaraj, Neal K | W911NF-13-1-0383 | 31 | null | USA | Univ Calif San Diego | Shi, Xinying | gold, Green Published | ATP;DEGRADATION MACHINE;EMULSION;IN-VITRO;POLYPHOSPHATE;SSPB ADAPTER;VESICLES | Shi, Xinying; Wu, Ti; Cole, Christian M.; Devaraj, Neal K.; Joseph, Simpson; | null | Univ Calif San Diego, Dept Chem & Biochem, 9500 Gilman Dr, La Jolla, CA 92093 USA | Univ Calif San Diego, Dept Chem & Biochem, 9500 Gilman Dr, La Jolla, CA 92093 USA | null | null | null | 1974;1997;1998;2000;2003;2004;2005;2006;2009;2010;2011;2012;2013;2014;2015;2016 | 9 | Univ Calif San Diego, Dept Chem & Biochem, 9500 Gilman Dr, La Jolla, CA 92093 USA | Sci Rep | Joseph, Simpson | NATURE PUBLISHING GROUP | (ATP);(TX-TL);,;a;activity;added;adding;adenosine;all;also;an;and;are;ATP;be;biology;both;but;by;cell;cell-free;cells;circuits;ClpXP;coli;conditions;consumption;correlated;creating;damaged;degradation;E.;efficient;energy;essential;established;exogenous;expression;extract;for;function;fundamental;genetic;has;improved;in;intact;interested;is;living;longer;low;needed;no;not;occur;of;only;optimized;our;platform;process;protease;protein;proteins;proteolytic;purified;rapid;regeneration;remove;require;robust;S30;showed;simultaneously;studies;surprisingly;synthesis;synthetic;system;systems;tested;that;the;then;therefore;this;to;transcription-translation;triphosphate;tunable;TX-TL;used;useful;very;vitro;was;we;will;with | Univ Calif San Diego | Protein degradation is a fundamental process in all living cells and is essential to remove both damaged proteins and intact proteins that are no longer needed by the cell. We are interested in creating synthetic genetic circuits that function in a cell-free expression system. This will require not only an efficient protein expression platform but also a robust protein degradation system in cell extract. Therefore, we purified and tested the activity of E. coli ClpXP protease in cell-free transcription-translation (TX-TL) systems that used E. coli S30 cell extract. Surprisingly, our studies showed that purified ClpXP added to the TX-TL system has very low proteolytic activity. The low activity of ClpXP was correlated with the rapid consumption of adenosine triphosphate (ATP) in cell extract. We improved the activity of ClpXP in cell extract by adding exogenous ATP and an energy regeneration system. We then established conditions for both protein synthesis, and protein degradation by ClpXP to occur simultaneously in the TX-TL systems. The optimized conditions for ClpXP activity will be useful for creating tunable synthetic genetic circuits and in vitro synthetic biology. | B-4712-2014 | ATP;DEGRADATION MACHINE;EMULSION;IN-VITRO;POLYPHOSPHATE;SSPB ADAPTER;VESICLES | 1 | null | null | 11 | ATP;DEGRADATION MACHINE;EMULSION;IN-VITRO;POLYPHOSPHATE;SSPB ADAPTER;VESICLES | WOS:000425728600044 | Univ Calif San Diego, La Jolla, CA USA | USA | 2,018 | null | 0000-0001-6427-6418 | null | null | English | null | ACS SYNTH BIOL;ANNU REV BIOCHEM;APPL ENVIRON MICROB;BBA-MOL CELL RES;BIOCHIM BIOPHYS ACTA;BioRxiv;CELL;CHEMBIOCHEM;GENE DEV;J BIOL CHEM;J Biol Eng;J MICROBIOL METH;J MOL BIOL;LANGMUIR;METHOD ENZYMOL;MOL CELL;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PHYS BIOL;PLOS ONE;SCIENCE;TRENDS BIOCHEM SCI | Cole, Christian M;Devaraj, Neal K;Joseph, Simpson;Shi, Xinying;Wu, Ti | 2024-03-11
ER | Baker, T A;Bolon, D N;Chowdhuri, S;Davis, J H;Elowitz, M B;Flynn, J M;Garamella, J;Ge, X M;Glynn, S E;Gottesman, S;Itoh, H;Jendrasi.Gl;Kenniston, J A;Kim, Y I;Levchenko, I;Noireaux, V;Pautot, S;Pontes, M H;Prindle, A;Rajagopal, V;Resnick, S M;Rivas, G;Sauer, R T;Sharp, K A;Shin Jonghyeon;Sun Z.Z.;Thompson, J;Wang, J M | FX0JF | La Jolla, CA USA | 12 | null | 1 | null | 29,472,573 | Cole, Christian M;Devaraj, Neal K;Joseph, Simpson;Shi, Xinying;Wu, Ti | SCI REP-UK | La Jolla, CA USA |
de Lange, O;Klavins, E;Nemhauser, J | 10.1016/j.copbio.2017.07.003 | null | THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND | 30336g6a6wg3f586a47491h1p3g5v6q2r2n4o3c | Synthetic genetic circuits in crop plants | Univ Washington | null | Nemhauser, J (corresponding author), Univ Washington, Dept Biol, Seattle, WA 98195 USA. | null | de Lange, Orlando;Klavins, Eric;Nemhauser, Jennifer | Biochemical Research Methods;Biotechnology & Applied Microbiology | National Science Foundation [MCB-1411949]; National Institutes of Health [R01-GM107084]; Direct For Biological Sciences; Div Of Molecular and Cellular Bioscience [1411949] Funding Source: National Science Foundation; Direct For Computer & Info Scie & Enginr; Division of Computing and Communication Foundations [1317694] Funding Source: National Science Foundation | WOS | Nemhauser, J | Univ Washington, Seattle, WA USA | 49 | circuits;crop;genetic;in;plants;synthetic | 1 | Klavins, Eric | ELSEVIER SCI LTD | Univ Washington, Dept Biol, Seattle, WA 98195 USA;Univ Washington, Dept Elect Engn, Seattle, WA 98195 USA | Review | Univ Washington | OXFORD | null | null | Univ Washington | Direct For Biological Sciences;Direct For Computer & Info Scie & Enginr;Div Of Molecular and Cellular Bioscience;Division of Computing and Communication Foundations;National Institutes of Health;National Science Foundation | Nemhauser, J (corresponding author), Univ Washington, Dept Biol, Seattle, WA 98195 USA. | 22 | de Lange, Orlando;Klavins, Eric;Nemhauser, Jennifer | 35 | 2 | 426,224,300,005 | Direct For Biological Sciences;Direct For Computer & Info Scie & Enginr;Div Of Molecular and Cellular Bioscience [1411949] Funding Source: National Science Foundation;Division of Computing and Communication Foundations [1317694] Funding Source: National Science Foundation;National Institutes of Health [R01-GM107084];National Science Foundation [MCB-1411949] | USA | CURRENT OPINION IN BIOTECHNOLOGY | USA | null | null | Univ Washington, Dept Elect Engn, Seattle, WA 98195 USA | 0958-1669 | de Lange, O;Klavins, E;Nemhauser, J | FEB | jn7@uw.edu | crop plants;synthetic genetic circuits | 3 | J | Biochemistry & Molecular Biology;Biotechnology & Applied Microbiology | AGROBACTERIUM-MEDIATED TRANSFORMATION;ARABIDOPSIS;century;coding DNA;combinations;complex traits;considerable barrier;CONSTRUCTION;continued;crop breeding;crop improvement;crop plant;crop plants;desired function;ENRICHMENT;exploratory laboratory testing;future developments necessary;Genetic circuits;genetics;genome;genome modifications;interest;love affair;mass selection programs;mutagenesis;promoters;recent development;requisite DNA parts;RICE;STACKING;standardized pipeline;successes;synthetic genetic circuits;technologies;TRANSGENE EXPRESSION;transgenic products;trials;viable crop improvement technology | de Lange, O | AGROBACTERIUM-MEDIATED TRANSFORMATION;ARABIDOPSIS;CONSTRUCTION;ENRICHMENT;mutagenesis;PROMOTERS;RICE;STACKING;TECHNOLOGIES;TRANSGENE EXPRESSION | 16 | [de Lange, Orlando; Klavins, Eric] Univ Washington, Dept Elect Engn, Seattle, WA 98195 USA. [Nemhauser, Jennifer] Univ Washington, Dept Biol, Seattle, WA 98195 USA. | Funding for plant synthetic biology in the Klavins and Nemhauser groups is provided by collaborative grants from the National Science Foundation (MCB-1411949) and the National Institutes of Health (R01-GM107084). JLN is also supported in this work as an HHMI faculty scholar. The authors would like to thank A Lanctot, C Wright and L Adam for critical reading of the manuscript. | century;coding DNA;combinations;complex traits;considerable barrier;continued;crop breeding;crop improvement;crop plant;desired function;exploratory laboratory testing;future developments necessary;genetic circuits;genetics;genome;genome modifications;interest;love affair;mass selection programs;recent development;requisite DNA parts;standardized pipeline;successes;synthetic genetic circuits;transgenic products;trials;viable crop improvement technology | 10.1002/biot.201100487;10.1007/s00412-013-0403-3;10.1007/s11032-005-4929-9;10.1007/s11103-011-9767-z;10.1007/s11105-008-0044-5;10.1007/s11627-012-9459-7;10.1016/j.cell.2016.01.011;10.1016/j.copbio.2015.10.001;10.1016/j.copbio.2015.11.007;10.1016/j.pbi.2014.02.004;10.1016/j.tibtech.2011.02.003;10.1016/j.tibtech.2014.12.010;10.1016/j.tplants.2008.09.004;10.1017/S1742170515000198;10.1038/35002125;10.1038/35002131;10.1038/514S55a;10.1038/nature13776;10.1038/nbt.1506;10.1038/nbt.2467;10.1038/nbt1082;10.1038/nprot.2007.241;10.1073/pnas.0809737105;10.1093/jxb/eru138;10.1093/mp/ssu107;10.1093/pcp/pcw201;10.1098/rstb.2007.2170;10.1101/gr.145557.112;10.1104/pp.119.1.133;10.1104/pp.123.3.895;10.1104/pp.15.01542;10.1104/pp.15.01663;10.1105/tpc.010412;10.1111/j.1365-313X.2012.04916.x;10.1111/j.1467-7652.2003.00061.x;10.1111/j.1467-7652.2010.00577.x;10.1111/pbi.12107;10.1111/pbi.12176;10.1111/pbi.12242;10.1111/tpj.12356;10.1126/science.aac7341;10.1186/1754-6834-5-84;10.1186/s40064-015-1369-9;10.1371/journal.pgen.0030179;10.1371/journal.pone.0000350;10.3389/fpls.2014.00169;10.3389/fpls.2016.01949;10.3390/v7082819;10.3791/52189;10.7554/eLife.13664;[10.1038/NMETH.2918, 10.1038/nmeth.2918];[10.1038/NMETH.3659, 10.1038/nmeth.3659] | Univ Washington | de Lange, O;Klavins, E;Nemhauser, J | de Lange, O: Univ Washington, Dept Elect Engn, Seattle, WA 98195 USA | null | 1317694;1411949;MCB-1411949;R01-GM107084 | 55 | null | USA | Univ Washington | de Lange, Orlando | hybrid, Green Accepted | AGROBACTERIUM-MEDIATED TRANSFORMATION;ARABIDOPSIS;CONSTRUCTION;ENRICHMENT;MUTAGENESIS;PROMOTERS;RICE;STACKING;TECHNOLOGIES;TRANSGENE EXPRESSION | de Lange, Orlando; Klavins, Eric; Nemhauser, Jennifer; | null | Univ Washington, Dept Biol, Seattle, WA 98195 USA;Univ Washington, Dept Elect Engn, Seattle, WA 98195 USA | Univ Washington, Dept Biol, Seattle, WA 98195 USA;Univ Washington, Dept Elect Engn, Seattle, WA 98195 USA | 1879-0429 | null | null | 1999;2000;2002;2004;2005;2007;2008;2009;2011;2012;2013;2014;2015;2016;2017 | 29 | Univ Washington, Dept Biol, Seattle, WA 98195 USA | Curr. Opin. Biotechnol. | Nemhauser, Jennifer | ELSEVIER SCI LTD | ,;a;accelerate;achieve;affair;ago;allowing;and;are;barrier;be;began;between;breeding;bringing;century;circuits;coding;combinations;complex;considerable;continued;could;crop;delivered;designed;desired;development;developments;directly;DNA;exploratory;far;from;function;future;genetic;genetics;genome;has;highlight;however;improvement;interest;into;introduced;is;laboratory;love;make;market;mass;modifications;necessary;not;of;over;parts;pipeline;plant;products;programs;rationally;recent;regulatory;remains;requisite;selection;so;standardized;successes;synthetic;targeted;technology;testing;the;there;this;to;traits;transgenic;trials;unabated;viable;we;yet | Univ Washington | The love affair between crop breeding and genetics began over a century ago and has continued unabated, from mass selection programs to targeted genome modifications. Synthetic genetic circuits, a recent development, are combinations of regulatory and coding DNA introduced into a crop plant to achieve a desired function. Genetic circuits could accelerate crop improvement, allowing complex traits to be rationally designed and requisite DNA parts delivered directly into a genome of interest. However, there is not yet a standardized pipeline from exploratory laboratory testing to crop trials, and bringing transgenic products to market remains a considerable barrier. We highlight successes so far and future developments necessary to make genetic circuits a viable crop improvement technology over this century. | null | AGROBACTERIUM-MEDIATED TRANSFORMATION;ARABIDOPSIS;CONSTRUCTION;ENRICHMENT;MUTAGENESIS;PROMOTER;RICE;STACKING;TECHNOLOGIES;TRANSGENE EXPRESSION | 1 | null | null | 7 | AGROBACTERIUM-MEDIATED TRANSFORMATION;ARABIDOPSIS;CONSTRUCTION;ENRICHMENT;mutagenesis;PROMOTER;RICE;STACKING;TECHNOLOGIES;TRANSGENE EXPRESSION | WOS:000426224300005 | Univ Washington, Seattle, WA USA | USA | 2,018 | null | 0000-0002-3805-5117 | null | null | English | null | BIOTECHNOL BIOFUELS;BIOTECHNOL J;CELL;CHROMOSOMA;CURR OPIN BIOTECH;CURR OPIN PLANT BIOL;ELIFE;FRONT PLANT SCI;GENOME RES;IN VITRO CELL DEV-PL;J EXP BOT;JOVE-J VIS EXP;MOL BREEDING;MOL PLANT;NAT;NAT BIOTECHNOL;NAT METHODS;NAT PROTOC;NATURE;P NATL ACAD SCI USA;PHILOS T R SOC B;PLANT BIOTECHNOL J;PLANT CELL;PLANT CELL PHYSIOL;PLANT J;PLANT MOL BIOL;PLANT MOL BIOL REP;PLANT PHYSIOL;PLOS GENET;PLOS ONE;RENEW AGR FOOD SYST;REVOLUTION FARM TRAN;SCIENCE;SPRINGERPLUS;TRENDS BIOTECHNOL;TRENDS PLANT SCI;VIRUSES-BASEL | de Lange, Orlando;Klavins, Eric;Nemhauser, Jennifer | 2024-03-11
ER | Ainley, W M;Bastaki, N K;Birchler, J A;Brouwer, B O;Butaye, K M J;Butelli, E;Carlson, S R;Cermak T.;Clarke, J L;Collard, B C Y;Conkin Paul K.;Delmans, M;Desfeux, C;Diretto, G;Eisenstein, M;Elowitz, M B;Endo, M;Fossati, E;Fuentes, P;Gaeta, R T;Gardner, T S;Hou, L L;Ishida, Y;Kanevski, I;Kosuri, S;Kwit, C;Lin, M T;Liu, W S;Liu, X J;Llorca, C M;Lombardo, L;Lucht, J M;Morey, K J;Nandy, S;Nelissen, H;Nielsen, A A K;Nishizawa-Yokoi, A;Paine, J A;Pardey, P;Patron, N J;Petersen, P D;Qi, Y P;Roybal, K T;Rushton, P J;Scharff, L B;Schaumberg, K A;Srivastava, V;Wang, C;Wijnker, E;Xu, C H;Yadava, P;Yasmeen, A;Zhu, C F;Zuniga-Soto, E | FX6VB | Seattle, WA USA | 31 | null | 1 | null | 28,772,191 | de Lange, Orlando;Klavins, Eric;Nemhauser, Jennifer | CURR OPIN BIOTECH | Seattle, WA USA |
Chang, C C;Chen, B S;Liao, W X;Lin, L J;Ling, C;Liu, B;Xie, Z | 10.1021/acssynbio.7b00134 | null | 1155 16TH ST, NW, WASHINGTON, DC 20036 USA | 343m5k6u4n3e5z5y111314hqs3w6r5t2x5v4j | Functional Characterization of Insulation Effect for Synthetic Gene Circuits in Mammalian Cells | Tsinghua Univ | null | Xie, Z (corresponding author), Tsinghua Univ, Tsinghua Natl Lab Informat Sci & Technol, Ctr Synthet & Syst Biol, Dept Automat,MOE Key Lab Bioinformat & Bioinforma, Beijing 100084, Peoples R China. | null | Chang, Chih-Chun;Chen, Bor-Sen;Liao, Weixi;Lin, Ling-Jun;Ling, Che;Liu, Bing;Xie, Zhen | Biochemical Research Methods | Cross-strait Tsinghua Foundation; National Key Basic Research Program of China [2014CB745200]; Basic Research Program of Tsinghua National Lab for Information Science and Technology; National Science Council [NSC 98-221-E-007-113-MY3] | WOS | Xie, Z | Natl Tsing Hua Univ, Hsinchu, Taiwan;Syngentech Inc, Beijing, Peoples R China;Tsinghua Univ, Beijing, Peoples R China | 7 | Cells;characterization;circuits;effect;for;functional;gene;in;Insulation;mammalian;of;synthetic | 2 | null | AMER CHEMICAL SOC | Natl Tsing Hua Univ, Dept Elect Engn, Hsinchu 30013, Taiwan;Syngentech Inc, Zhongguancun Life Sci Pk, Beijing 102206, Peoples R China;Tsinghua Univ, Tsinghua Natl Lab Informat Sci & Technol, Ctr Synthet & Syst Biol, Dept Automat,MOE Key Lab Bioinformat & Bioinforma, Beijing 100084, Peoples R China | Article | Tsinghua Univ | WASHINGTON | null | null | Natl Tsing Hua Univ;Syngentech Inc;Tsinghua Univ | Basic Research Program of Tsinghua National Lab for Information Science and Technology;Cross-strait Tsinghua Foundation;National Key Basic Research Program of China;National Science Council | Xie, Z (corresponding author), Tsinghua Univ, Tsinghua Natl Lab Informat Sci & Technol, Ctr Synthet & Syst Biol, Dept Automat,MOE Key Lab Bioinformat & Bioinforma, Beijing 100084, Peoples R China. | 418 | Chang, Chih-Chun;Chen, Bor-Sen;Liao, Weixi;Lin, Ling-Jun;Ling, Che;Liu, Bing;Xie, Zhen | 16 | 3 | 426,012,600,014 | Basic Research Program of Tsinghua National Lab for Information Science and Technology;Cross-strait Tsinghua Foundation;National Key Basic Research Program of China [2014CB745200];National Science Council [NSC 98-221-E-007-113-MY3] | China;Taiwan | ACS SYNTHETIC BIOLOGY | China | null | null | Tsinghua Univ, Tsinghua Natl Lab Informat Sci & Technol, Ctr Synthet & Syst Biol, Dept Automat,MOE Key Lab Bioinformat & Bioinforma, Beijing 100084, Peoples R China | 2161-5063 | Chang, C C;Chen, B S;Liao, W X;Lin, L J;Ling, C;Liu, B;Xie, Z | FEB | zhenxie@tsinghua.edu.cn | functional Characterization;Insulation Effect;mammalian cells;synthetic gene circuits | 7 | J | Biochemistry & Molecular Biology | affected;BETA-GLOBIN INSULATOR;BIOLOGY;block interference across different chromatin domains;cascade;cascade circuit;chromatin partitioning boundaries;cross-regulations;CTCF;deviation;different cassettes;effect;ENHANCER-BLOCKING ACTIVITY;episomal plasmid vectors;episomal synthetic gene circuits;eukaryotic genome;expression;first regulatory;function;functional Characterization;functional effect;general guide;Insulation Effect;insulators;mammalian cells;modular construction;multiple transcription cassettes;noncoding gene regulatory elements;promoters;quantitative method;response curve;response intensity;results;SELECTION;sensory switch circuit;sensory switch circuits;six promoters;synthetic gene;synthetic gene circuits;three insulators;threshold position;threshold-like effect;unwanted cross-regulations;varying promoters | Liao, W X | BETA-GLOBIN INSULATOR;BIOLOGY;CTCF;ENHANCER-BLOCKING ACTIVITY;EXPRESSION | 412 | [Liao, Weixi; Xie, Zhen] Tsinghua Univ, Tsinghua Natl Lab Informat Sci & Technol, Ctr Synthet & Syst Biol, Dept Automat,MOE Key Lab Bioinformat & Bioinforma, Beijing 100084, Peoples R China. [Liu, Bing] Syngentech Inc, Zhongguancun Life Sci Pk, Beijing 102206, Peoples R China. [Chang, Chih-Chun; Lin, Ling-Jun; Ling, Che; Chen, Bor-Sen] Natl Tsing Hua Univ, Dept Elect Engn, Hsinchu 30013, Taiwan. | We thank members of Xie lab for helpful discussions. We thank Yun Jiang and Huiya Huang for technical support. We thank Xiaowo Wang for insightful discussions. The research was supported by the Cross-strait Tsinghua Foundation (Z.X.), the National Key Basic Research Program of China (2014CB745200), the Basic Research Program of Tsinghua National Lab for Information Science and Technology, and the National Science Council (B.C., NSC 98-221-E-007-113-MY3). | affected;block interference across different chromatin domains;cascade;cascade circuit;chromatin partitioning boundaries;cross-regulations;deviation;different cassettes;effect;episomal plasmid vectors;episomal synthetic gene circuits;eukaryotic genome;first regulatory;function;functional effect;general guide;insulation effect;insulators;mammalian cells;modular construction;multiple transcription cassettes;noncoding gene regulatory elements;promoters;quantitative method;response curve;response intensity;results;selection;sensory switch circuit;sensory switch circuits;six promoters;synthetic gene;three insulators;threshold position;threshold-like effect;unwanted cross-regulations;varying promoters | 10.1016/j.gde.2011.12.007;10.1016/S0092-8674(00)81967-4;10.1021/sb500263b;10.1038/emboj.2011.406;10.1038/msb.2011.49;10.1038/nbt.2355;10.1038/nbt.2401;10.1038/nbt957;10.1038/nrm3738;10.1038/nrmicro3140;10.1038/sj.mt.6300399;10.1073/pnas.0402938101;10.1073/pnas.1413896112;10.1073/pnas.94.2.575;10.1073/pnas.96.25.14354;10.1089/hgtb.2012.152;10.1093/nar/gkt605;10.1126/science.1140871;10.1126/science.1205527;10.1139/O10-111;10.1146/annurev-chembioeng-061010-114145 | Tsinghua Univ | Chang, C C;Chen, B S;Liao, W X;Lin, L J;Ling, C;Liu, B;Xie, Z | Liao, W X: Tsinghua Univ, Tsinghua Natl Lab Informat Sci & Technol, Ctr Synthet & Syst Biol, Dept Automat,MOE Key Lab Bioinformat & Bioinforma, Beijing 100084, Peoples R China | Chen, Bor-Sen;Xie, Zhen | 2014CB745200;NSC 98-221-E-007-113-MY3 | 23 | null | China | Natl Tsing Hua Univ;Syngentech Inc;Tsinghua Univ | Liao, Weixi | null | BETA-GLOBIN INSULATOR;BIOLOGY;CTCF;ENHANCER-BLOCKING ACTIVITY;EXPRESSION | Liao, Weixi; Liu, Bing; Chang, Chih-Chun; Lin, Ling-Jun; Ling, Che; Chen, Bor-Sen; Xie, Zhen; | null | Natl Tsing Hua Univ, Dept Elect Engn, Hsinchu 30013, Taiwan;Syngentech Inc, Zhongguancun Life Sci Pk, Beijing 102206, Peoples R China;Tsinghua Univ, Tsinghua Natl Lab Informat Sci & Technol, Ctr Synthet & Syst Biol, Dept Automat,MOE Key Lab Bioinformat & Bioinforma, Beijing 100084, Peoples R China | Natl Tsing Hua Univ, Dept Elect Engn, Hsinchu 30013, Taiwan;Syngentech Inc, Zhongguancun Life Sci Pk, Beijing 102206, Peoples R China;Tsinghua Univ, Tsinghua Natl Lab Informat Sci & Technol, Ctr Synthet & Syst Biol, Dept Automat,MOE Key Lab Bioinformat & Bioinforma, Beijing 100084, Peoples R China | null | null | 2 | 1997;1999;2004;2007;2008;2010;2011;2012;2013;2014;2015 | 3 | Tsinghua Univ, Tsinghua Natl Lab Informat Sci & Technol, Ctr Synthet & Syst Biol, Dept Automat,MOE Key Lab Bioinformat & Bioinforma, Beijing 100084, Peoples R China | ACS Synth. Biol. | Xie, Zhen | AMER CHEMICAL SOC | ,;a;across;affected;along;and;are;as;assembled;avoided;be;between;block;both;boundaries;but;cascade;cassettes;cells;characterize;chromatin;circuit;circuits;composed;construction;context;cross-regulations;curve;developed;deviation;different;displayed;domains;effect;elements;episomal;eukaryotic;facilitate;first;function;functional;gene;general;genome;guide;here;in;insulation;insulators;intensity;interference;is;layer;mainly;mammalian;may;method;modular;multiple;noncoding;not;observed;of;on;or;our;partitioning;plasmid;position;promoters;provided;quantitative;reduce;regulatory;response;results;revealed;selection;sensory;should;showed;six;some;switch;synthetic;tested;that;the;therefore;three;threshold;threshold-like;to;transcription;unwanted;useful;usually;varied;varying;vectors;was;we;were;which;with;without | Tsinghua Univ | Insulators are noncoding gene regulatory elements in eukaryotic genome, which function as chromatin partitioning boundaries, and block interference across different chromatin domains. To facilitate modular construction of synthetic gene circuit that is usually composed of multiple transcription cassettes, unwanted cross-regulations between different cassettes should be avoided. Here, we developed a quantitative method to characterize the functional effect of three insulators on the cross-regulations of six promoters in mammalian cells. We showed that the unwanted cross-regulations displayed a threshold-like effect, and the threshold position varied along with the context of promoters and insulators. We tested the function of insulators in both cascade and sensory switch circuits assembled in episomal plasmid vectors, and showed that the insulation effect was mainly revealed on the first regulatory layer of the cascade circuit. A deviation on the response curve of the sensory switch circuit with or without insulators was observed, but response intensity of some sensory switch circuits were not affected. Therefore, our results provided a general guide on the selection of insulators with varying promoters in episomal synthetic gene circuits in mammalian cells, which may be useful to reduce the effect of the unwanted cross-regulations. | D-9114-2017;GPW-5925-2022 | BETA-GLOBIN INSULATOR;BIOLOGY;CTCF;ENHANCER-BLOCKING ACTIVITY;EXPRESSION | 1 | null | null | 13 | BETA-GLOBIN INSULATOR;BIOLOGY;CTCF;ENHANCER-BLOCKING ACTIVITY;EXPRESSION | WOS:000426012600014 | Natl Tsing Hua Univ, Hsinchu, Taiwan;Syngentech Inc, Beijing, Peoples R China;Tsinghua Univ, Beijing, Peoples R China | China;Taiwan | 2,018 | null | null | null | null | English | null | ACS SYNTH BIOL;ANNU REV CHEM BIOMOL;BIOCHEM CELL BIOL;CELL;CURR OPIN GENET DEV;EMBO J;HUM GENE THER METHOD;MOL SYST BIOL;MOL THER;NAT BIOTECHNOL;NAT CHEM BIOL;NAT REV MICROBIOL;NAT REV MOL CELL BIO;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;REV CELL BIOL MOL ME;SCIENCE | Chang, Chih-Chun;Chen, Bor-Sen;Liao, Weixi;Lin, Ling-Jun;Ling, Che;Liu, Bing;Xie, Zhen | 2024-03-11
ER | [Anonymous];Amouyal, M;Bell, A C;Bleris, L;Chen, Z Y;Chung, J H;Davidsohn, N;Guye, P;Lienert, F;Lou, C B;Lunyak, V V;Miest, T S;Qi, L;Raab, J R;Recillas-Targa, F;Szymczak, A L;Uchida, N;Wieland, M;Xie Z.;Xie, Z;Yang, J P;Yuan, Y;Yusufzai, T M | FX3ZX | Beijing, Peoples R China | 5 | null | 3 | null | 29,193,957 | Chang, Chih-Chun;Chen, Bor-Sen;Liao, Weixi;Lin, Ling-Jun;Ling, Che;Liu, Bing;Xie, Zhen | ACS SYNTH BIOL | Beijing, Peoples R China;Hsinchu, Taiwan |
Del Vecchio, D;Qian, Y L | 10.1098/rsif.2017.0902 | 20170902 | 6-9 CARLTON HOUSE TERRACE, LONDON SW1Y 5AG, ENGLAND | 5u5z5p4k1n2a3vh3w6g3w4y5c1p5n2v2m5rt55 | Realizing 'integral control' in living cells: how to overcome leaky integration due to dilution? | MIT | null | Del Vecchio, D (corresponding author), MIT, Dept Mech Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA. | null | Del Vecchio, Domitilla;Qian, Yili | Multidisciplinary Sciences | AFOSR [FA9550-140-1-0060] | WOS | Del Vecchio, D | MIT, Cambridge, MA USA | 15 | 'integral;:;?;Cells;control';dilution;due;how;in;integration;leaky;living;overcome;realizing;to | 1 | /0000-0002-1097-0401;Del Vecchio, Domitilla | ROYAL SOC | MIT, Dept Mech Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA;MIT, Synthet Biol Ctr, 500 Technol Sq, Cambridge, MA 02139 USA | Article | MIT | LONDON | null | null | Dept Mech Engn;MIT | AFOSR | Del Vecchio, D (corresponding author), MIT, Dept Mech Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA. | null | Del Vecchio, Domitilla;Qian, Yili | 4 | 2 | 426,464,000,013 | AFOSR [FA9550-140-1-0060] | USA | JOURNAL OF THE ROYAL SOCIETY INTERFACE | USA | null | null | MIT, Dept Mech Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA | 1742-5689 | Del Vecchio, D;Qian, Y L | FEB | ddv@mit.edu | 'integral control';dilution;leaky integration;living cells | 2 | J | Science & Technology - Other Topics | 'integral control';'leaky' memory;'memory' element;ability;accumulation (integral);adaptation;adaptation error;adaptation property;biomolecular;biomolecules;cells;cellular resources;concrete guidance;consequence;CONSTRAINTS;CONTEXT;DESIGN;design principle;designing integral controllers;desired set-point;dilution;disturbances;error;fades;finding approaches;fluctuations;gene expression;GENE-EXPRESSION;general principle;Genetic circuits;growth;homeostasis;integral control;integral controller;integral controllers;integration leakiness;key aspect;leaky integration;living cells;lost;major problem;memory element;negligible;output;perturbations;process;reaching adaptation;reactions;recent years;results;RNA;ROBUST PERFECT ADAPTATION;ROBUSTNESS;significant efforts;synthetic biology;synthetic genetic circuits;time-scale separation;two synthetic genetic circuits;uncertainty;unique ability | Qian, Y L | adaptation;CONSTRAINTS;CONTEXT;DESIGN;GENE-EXPRESSION;GROWTH;HOMEOSTASIS;integral control;RNA;ROBUST PERFECT ADAPTATION;ROBUSTNESS;Synthetic biology;time-scale separation | null | [Qian, Yili; Del Vecchio, Domitilla] MIT, Dept Mech Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA. [Del Vecchio, Domitilla] MIT, Synthet Biol Ctr, 500 Technol Sq, Cambridge, MA 02139 USA. | This work is supported by AFOSR grant no. FA9550-140-1-0060. | 'leaky' memory;'memory' element;ability;accumulation (integral);adaptation error;adaptation property;biomolecular;biomolecules;cells;cellular resources;concrete guidance;consequence;design principle;designing integral controllers;desired set-point;dilution;disturbances;error;fades;finding approaches;fluctuations;gene expression;general principle;genetic circuits;integral control;integral controller;integral controllers;integration leakiness;key aspect;living cells;lost;major problem;memory element;negligible;output;perturbations;process;reaching adaptation;reactions;recent years;results;robustness;significant efforts;synthetic genetic circuits;two synthetic genetic circuits;uncertainty;unique ability | 10.1002/biot.201200085;10.1016/0005-1098(76)90006-6;10.1016/0006-3002(52)90227-8;10.1016/j.bpj.2012.12.015;10.1016/j.bpj.2015.06.034;10.1016/j.cell.2009.04.047;10.1016/j.cell.2009.12.001;10.1016/j.cels.2017.06.001;10.1016/j.ifacol.2017.08.2466;10.1016/j.jtbi.2010.07.034;10.1016/j.jtbi.2016.06.036;10.1016/S0022-2836(02)00994-4;10.1016/S0167-6911(03)00136-1;10.1021/acssynbio.6b00014;10.1021/acssynbio.6b00361;10.1021/acssynbio.7b00119;10.1021/jp3004568;10.1038/msb.2008.58;10.1038/msb4100181;10.1038/nature11478;10.1038/nbt.2461;10.1038/nprot.2013.105;10.1038/nrm2698;10.1038/nrmicro2930;10.1049/sb:20045016;10.1073/pnas.97.9.4649;10.1093/nar/gks439;10.1098/rsif.2015.1062;10.1098/rsif.2016.0380;10.1101/222042;10.1101/gad.1127103;10.1109/CDC.2010.5717525;10.1109/CDC.2014.7039358;10.1371/journal.pbio.0050229;10.23943/PRINCETON/9780691161532.001.0001;[10.1016/j.cels.2016.01.004, 10.1016/j.cels.2016.02.010] | MIT | Del Vecchio, D;Qian, Y L | Qian, Y L: MIT, Dept Mech Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA | Qian, Yili | FA9550-140-1-0060 | 41 | null | USA | MIT | Qian, Yili | Green Submitted, Bronze, Green Published | CONSTRAINTS;CONTEXT;DESIGN;GENE-EXPRESSION;GROWTH;HOMEOSTASIS;RNA;ROBUST PERFECT ADAPTATION;SYNTHETIC BIOLOGY | Qian, Yili; Del Vecchio, Domitilla; | null | MIT, Dept Mech Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA;MIT, Synthet Biol Ctr, 500 Technol Sq, Cambridge, MA 02139 USA | MIT, Dept Mech Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA;MIT, Synthet Biol Ctr, 500 Technol Sq, Cambridge, MA 02139 USA | 1742-5662 | adaptation;integral control;robustness;Synthetic biology;time-scale separation | 139 | 1952;1976;1995;2000;2002;2003;2004;2006;2007;2008;2009;2010;2012;2013;2014;2015;2016;2017 | 65 | MIT, Dept Mech Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA | J. R. Soc. Interface | Del Vecchio, Domitilla | ROYAL SOC | 'leaky';'memory';(integral);,;a;ability;accumulation;adapt;adaptation;aimed;all;an;and;any;approaches;appropriate;are;as;aspect;at;away;because;becomes;been;between;biomolecular;biomolecules;by;cells;cellular;challenged;challenging;circuits;concrete;consequence;control;controller;controllers;design;designing;desired;dilute;dilution;disturbances;due;efforts;element;error;exemplify;expression;fact;fades;faster;finding;fluctuations;for;fundamentally;gene;general;genetic;gradually;grow;guidance;have;here;however;if;implement;implementing;in;integral;integration;is;its;key;leakiness;living;lost;major;make;mathematically;memory;most;much;negligible;of;on;our;output;particular;perfectly;performance;perturbations;practically;principle;problem;process;processes;property;propose;prove;provide;reaching;reactions;realize;recent;resources;resulting;results;robustness;set-point;significant;stores;such;synthetic;than;that;the;then;there;this;to;two;unaffected;uncertainty;unique;we;with;years | MIT | A major problem in the design of synthetic genetic circuits is robustness to perturbations and uncertainty. Because of this, there have been significant efforts in recent years in finding approaches to implement integral control in genetic circuits. Integral controllers have the unique ability to make the output of a process adapt perfectly to disturbances. However, implementing an integral controller is challenging in living cells. This is because a key aspect of any integral controller is a 'memory' element that stores the accumulation (integral) of the error between the output and its desired set-point. The ability to realize such a memory element in living cells is fundamentally challenged by the fact that all biomolecules dilute as cells grow, resulting in a 'leaky' memory that gradually fades away. As a consequence, the adaptation property is lost. Here, we propose a general principle for designing integral controllers such that the performance is practically unaffected by dilution. In particular, we mathematically prove that if the reactions implementing the integral controller are all much faster than dilution, then the adaptation error due to integration leakiness becomes negligible. We exemplify this design principle with two synthetic genetic circuits aimed at reaching adaptation of gene expression to fluctuations in cellular resources. Our results provide concrete guidance on the biomolecular processes that are most appropriate for implementing integral controllers in living cells. | L-5558-2019 | CONSTRAINTS;CONTEXT;DESIGN;GENE-EXPRESSION;GROWTH;HOMEOSTASIS;RNA;ROBUST PERFECT ADAPTATION;SYNTHETIC BIOLOGY | 0 | null | adaptation;integral control;robustness;Synthetic biology;time-scale separation | 8 | adaptation;CONSTRAINTS;CONTEXT;DESIGN;GENE-EXPRESSION;GROWTH;HOMEOSTASIS;integral control;RNA;ROBUST;ROBUST PERFECT ADAPTATION;Synthetic biology;time-scale separation | WOS:000426464000013 | MIT, Cambridge, MA USA | USA | 2,018 | null | 0000-0001-6472-8576;0000-0002-1097-0401 | null | null | English | null | ACS SYNTH BIOL;AUTOMATICA;BIOCHIM BIOPHYS ACTA;BIOPHYS J;BioRxiv;BIOTECHNOL J;CELL;CELL SYST;FEMS MICROBIOL REV;GENE DEV;IEEE DECIS CONTR P;IFAC PAPERSONLINE;INTRO SYSTEMS BIOL D;J MOL BIOL;J PHYS CHEM B;J R SOC INTERFACE;J THEOR BIOL;MOL SYST BIOL;NAT BIOTECHNOL;NAT PROTOC;NAT REV MICROBIOL;NAT REV MOL CELL BIO;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PLOS BIOL;SINGULAR PERTURBATIO;SYST CONTROL LETT;SYSTEMS BIOL | Del Vecchio, Domitilla;Qian, Yili | 2024-03-11
ER | Alon U.;Ang, J;Astrom K. J.;Briat, C;Cardinale, S;Del Vecchio D.;Del Vecchio, D;Drengstig, T;Francis, B A;Giladi, H;Gyorgy, A;Hussein, R;Klavins, E;Klumpp, S;Kokotovic P. K.;Levine, E;Lu, T;Mackie, G A;Massé, E;Mehta, P;Monod, J;Muzzey, D;Na, D;Olsman Noah.;Peralta-Yahya, P P;Purnick, P E M;Qian, Y L;Raveh, A;Ren, X;Rivera-Ortiz, P;Rosenfeld, N;Samaniego, C C;Shimoni, Y;Shopera, T;Sontag, E D;Tang, Z F;Yeung, E;Yi, T M;Yoo, S M | FX9XJ | Cambridge, MA USA | 71 | null | 1 | null | 29,436,515 | Del Vecchio, Domitilla;Qian, Yili | J R SOC INTERFACE | Cambridge, MA USA |
Bleris, L;Ehrhardt, K;Kannan, S;Lee, J;Li, Y;Ma, L;Quarton, T | 10.1038/s41540-017-0043-y | 6 | MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND | 526f342t1li3t423h1v5x5v2d22331p2jwg6s | Mapping the operational landscape of microRNAs in synthetic gene circuits | Univ Texas Dallas | null | Bleris, L (corresponding author), Univ Texas Dallas, Bioengn Dept, Richardson, TX 75083 USA.;Bleris, L (corresponding author), Univ Texas Dallas, Ctr Syst Biol, Richardson, TX 75083 USA.;Bleris, L (corresponding author), Univ Texas Dallas, Dept Biol Sci, Richardson, TX 75083 USA. | null | Bleris, Leonidas;Ehrhardt, Kristina;Kannan, Srijaa;Lee, James;Li, Yi;Ma, Lan;Quarton, Tyler | Mathematical & Computational Biology | US National Science Foundation (NSF) CAREER grant [1351354]; NSF [1361355]; University of Texas at Dallas; Direct For Mathematical & Physical Scien; Division Of Mathematical Sciences [1361355] Funding Source: National Science Foundation; Div Of Chem, Bioeng, Env, & Transp Sys; Directorate For Engineering [1351354] Funding Source: National Science Foundation | WOS | Bleris, L | Univ Texas Dallas, Richardson, TX USA | 4 | circuits;gene;in;landscape;Mapping;microRNAs;of;operational;synthetic;the | 1 | Li, Yi;Quarton, Tyler | NATURE PUBLISHING GROUP | Univ Texas Dallas, Bioengn Dept, Richardson, TX 75083 USA;Univ Texas Dallas, Bioengn Dept, Richardson, TX 75083 USA.; Bleris, L (corresponding author), Univ Texas Dallas, Ctr Syst Biol, Richardson, TX 75083 USA.; Bleris, L (corresponding author), Univ Texas Dallas, Dept Biol Sci, Richardson, TX 75083 USA;Univ Texas Dallas, Ctr Syst Biol, Richardson, TX 75083 USA;Univ Texas Dallas, Dept Biol Sci, Richardson, TX 75083 USA;Univ Texas Dallas, Sch Behav & Brain Sci, Richardson, TX 75083 USA | Article | Univ Texas Dallas | LONDON | null | null | Univ Texas Dallas | Direct For Mathematical & Physical Scien;Directorate For Engineering;Div Of Chem, Bioeng, Env, & Transp Sys;Division Of Mathematical Sciences;NSF;University of Texas at Dallas;US National Science Foundation (NSF) CAREER grant | Bleris, L (corresponding author), Univ Texas Dallas, Bioengn Dept, Richardson, TX 75083 USA.; Bleris, L (corresponding author), Univ Texas Dallas, Ctr Syst Biol, Richardson, TX 75083 USA.; Bleris, L (corresponding author), Univ Texas Dallas, Dept Biol Sci, Richardson, TX 75083 USA. | null | Bleris, Leonidas;Ehrhardt, Kristina;Kannan, Srijaa;Lee, James;Li, Yi;Ma, Lan;Quarton, Tyler | 8 | 4 | 459,652,500,002 | Direct For Mathematical & Physical Scien;Directorate For Engineering [1351354] Funding Source: National Science Foundation;Div Of Chem, Bioeng, Env, & Transp Sys;Division Of Mathematical Sciences [1361355] Funding Source: National Science Foundation;NSF [1361355];University of Texas at Dallas;US National Science Foundation (NSF) CAREER grant [1351354] | USA | NPJ SYSTEMS BIOLOGY AND APPLICATIONS | USA;USA.; | null | null | Univ Texas Dallas, Bioengn Dept, Richardson, TX 75083 USA | null | Bleris, L;Ehrhardt, K;Kannan, S;Lee, J;Li, Y;Ma, L;Quarton, T | JAN 11 | bleris@utdallas.edu | microRNAs;operational landscape;synthetic gene circuits | 7 | J | Mathematical & Computational Biology | abundances;BIOLOGY;characterization;class;combination;complete operational landscape;development;disease;endogenous information;endogenous microRNAs;endogenous milieu;engineering;expression;extensive trial-and-error;function;gene expression;homeostasis;human embryonic kidney cells;input genetic template abundance;insight;interface;mathematical models;mediators;microRNA concentration;microRNA control;microRNA function;microRNA targets;MICRORNAS;miRNAs;multi-component genetic circuits;NETWORK;new insights;noncoding RNAs;observed nonlinearities;OPERATION;operational landscape;output;perfect complementarity;phenomenological;points;PROTEIN-SYNTHESIS;quantitative analysis;regulators;regulatory modules;relationship;RNA;ROBUSTNESS;ROLES;sensor systems;sequence;short;single-cell level;stepwise development;synthetic biology;synthetic biology experimentation;Synthetic gene circuit;synthetic gene circuits;ubiquitous modulators | Quarton, T | BIOLOGY;EXPRESSION;MIRNAS;NETWORK;PROTEIN-SYNTHESIS;RNA;ROBUSTNESS;SEQUENCE | null | [Quarton, Tyler; Ehrhardt, Kristina; Li, Yi; Ma, Lan; Bleris, Leonidas] Univ Texas Dallas, Bioengn Dept, Richardson, TX 75083 USA. [Quarton, Tyler; Ehrhardt, Kristina; Li, Yi; Bleris, Leonidas] Univ Texas Dallas, Ctr Syst Biol, Richardson, TX 75083 USA. [Lee, James; Bleris, Leonidas] Univ Texas Dallas, Dept Biol Sci, Richardson, TX 75083 USA. [Kannan, Srijaa] Univ Texas Dallas, Sch Behav & Brain Sci, Richardson, TX 75083 USA. | This work was funded by the US National Science Foundation (NSF) CAREER grant 1351354, NSF 1361355, and the University of Texas at Dallas. | abundances;characterization;class;combination;complete operational landscape;development;disease;endogenous information;endogenous microRNAs;endogenous milieu;engineering;extensive trial-and-error;function;gene expression;homeostasis;human embryonic kidney cells;input genetic template abundance;insight;interface;mathematical models;mediators;microRNA concentration;microRNA control;microRNA function;microRNA targets;microRNAs;multi-component genetic circuits;new insights;noncoding RNAs;observed nonlinearities;operation;output;perfect complementarity;phenomenological;points;quantitative analysis;regulators;regulatory modules;relationship;roles;sensor systems;short;single-cell level;stepwise development;synthetic biology;synthetic biology experimentation;synthetic gene circuit;synthetic gene circuits;ubiquitous modulators | 10.1007/978-1-61779-412-4_10;10.1016/j.bios.2015.07.035;10.1016/j.cbpa.2012.05.192;10.1016/j.cell.2007.05.045;10.1016/j.cell.2009.01.002;10.1016/j.cell.2009.01.035;10.1016/j.cell.2009.01.058;10.1016/j.cell.2011.01.030;10.1016/j.cell.2012.04.005;10.1016/j.cels.2017.01.003;10.1016/j.molcel.2007.05.018;10.1016/j.tcb.2006.12.007;10.1021/sb4001596;10.1021/sb4001867;10.1038/35888;10.1038/msb.2008.62;10.1038/msb.2011.49;10.1038/nature02872;10.1038/nature07242;10.1038/nature09267;10.1038/nbt1307;10.1038/ncb0309-228;10.1038/ncomms2471;10.1038/ng.905;10.1038/nrg1328;10.1038/nrg3094;10.1038/nrm3611;10.1038/srep32823;10.1039/c3mb70043g;10.1073/pnas.1205693109;10.1073/pnas.1304840111;10.1073/pnas.1413896112;10.1126/science.1190544;10.1126/science.1205527;10.1126/science.1206843;10.1126/science.aaa1738;10.1371/journal.pcbi.1001101;10.1371/journal.pcbi.1004653;10.15252/msb.20167265;10.2307/2965437;[10.1038/nnano.2010.135, 10.1038/NNANO.2010.135] | Univ Texas Dallas | Bleris, L;Ehrhardt, K;Kannan, S;Lee, J;Li, Y;Ma, L;Quarton, T | Quarton, T: Univ Texas Dallas, Bioengn Dept, Richardson, TX 75083 USA | Bleris, Leonidas | 1351354;1361355 | 42 | null | USA | Univ Texas Dallas | Quarton, Tyler | gold, Green Published | BIOLOGY;EXPRESSION;MIRNAS;NETWORK;PROTEIN-SYNTHESIS;RNA;ROBUSTNESS;SEQUENCE | Quarton, Tyler; Ehrhardt, Kristina; Lee, James; Kannan, Srijaa; Li, Yi; Ma, Lan; Bleris, Leonidas; | null | Univ Texas Dallas, Bioengn Dept, Richardson, TX 75083 USA;Univ Texas Dallas, Ctr Syst Biol, Richardson, TX 75083 USA;Univ Texas Dallas, Dept Biol Sci, Richardson, TX 75083 USA;Univ Texas Dallas, Sch Behav & Brain Sci, Richardson, TX 75083 USA | Univ Texas Dallas, Bioengn Dept, Richardson, TX 75083 USA;Univ Texas Dallas, Ctr Syst Biol, Richardson, TX 75083 USA;Univ Texas Dallas, Dept Biol Sci, Richardson, TX 75083 USA;Univ Texas Dallas, Sch Behav & Brain Sci, Richardson, TX 75083 USA | 2056-7189 | null | null | 1995;1998;2004;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017 | 12 | Univ Texas Dallas, Bioengn Dept, Richardson, TX 75083 USA;Univ Texas Dallas, Ctr Syst Biol, Richardson, TX 75083 USA;Univ Texas Dallas, Dept Biol Sci, Richardson, TX 75083 USA | npj Syst. Biol. Appl. | Bleris, Leonidas | NATURE PUBLISHING GROUP | ,;a;abundance;abundances;an;analysis;and;are;as;at;between;biology;cells;characterization;circuit;circuits;class;combination;complementarity;complete;concentration;contains;control;derive;development;disease;embryonic;employs;enables;endogenous;engineered;engineering;equipped;establish;experimentally;experimentation;expression;extensive;facilitates;features;framework;frequently;function;gene;genetic;here;homeostasis;human;in;information;input;insight;insights;interface;into;investigate;is;kidney;landscape;level;mathematical;mediators;microRNA;microRNAs;milieu;model;models;modulators;modules;moreover;multi-component;new;noncoding;nonlinearities;now;observed;of;on;operation;operational;optimized;our;output;perfect;phenomenological;points;provide;quantitative;recapitulates;regulators;regulatory;relationship;RNAs;roles;sensor;short;single-cell;specifically;stepwise;synthetic;systems;targets;template;that;the;through;to;trial-and-error;typically;ubiquitous;under;used;using;various;we;with;work | Univ Texas Dallas | MicroRNAs are a class of short, noncoding RNAs that are ubiquitous modulators of gene expression, with roles in development, homeostasis, and disease. Engineered microRNAs are now frequently used as regulatory modules in synthetic biology. Moreover, synthetic gene circuits equipped with engineered microRNA targets with perfect complementarity to endogenous microRNAs establish an interface with the endogenous milieu at the single-cell level. The function of engineered microRNAs and sensor systems is typically optimized through extensive trial-and-error. Here, using a combination of synthetic biology experimentation in human embryonic kidney cells and quantitative analysis, we investigate the relationship between input genetic template abundance, microRNA concentration, and output under microRNA control. We provide a framework that employs the complete operational landscape of a synthetic gene circuit and enables the stepwise development of mathematical models. We derive a phenomenological model that recapitulates experimentally observed nonlinearities and contains features that provide insight into the microRNA function at various abundances. Our work facilitates the characterization and engineering of multi-component genetic circuits and specifically points to new insights on the operation of microRNAs as mediators of endogenous information and regulators of gene expression in synthetic biology. | A-6761-2009 | BIOLOGY;EXPRESSION;MIRNA;NETWORKS;PROTEIN-SYNTHESIS;RNA;ROBUST;SEQUENCE | 0 | null | null | 7 | BIOLOGY;EXPRESSION;miRNA;NETWORKS;PROTEIN-SYNTHESIS;RNA;ROBUST;SEQUENCE | WOS:000459652500002 | Univ Texas Dallas, Richardson, TX USA | USA | 2,018 | null | 0000-0001-6389-7888;0000-0003-2086-3519 | null | null | English | null | ACS SYNTH BIOL;BIOSENS BIOELECTRON;CELL;CELL SYST;CURR OPIN CHEM BIOL;J Biol Eng;METHODS MOL BIOL;MOL BIOSYST;MOL CELL;MOL SYST BIOL;NAT BIOTECHNOL;NAT CELL BIOL;NAT COMMUN;NAT GENET;NAT NANOTECHNOL;NAT REV GENET;NAT REV MOL CELL BIO;NATURE;P NATL ACAD SCI USA;PLOS COMPUT BIOL;SCI REP-UK;SCIENCE;TRENDS CELL BIOL | Bleris, Leonidas;Ehrhardt, Kristina;Kannan, Srijaa;Lee, James;Li, Yi;Ma, Lan;Quarton, Tyler | 2024-03-11
ER | Acar, M;Ameres, S L;Baek, D;Balázsi, G;Bartel, D P;Beisel, C L;Benenson, Y;Bishop C.M.;Bleris, L;Bloom R., J;Carthew, R W;Deans, T L;Del Rosario, R C H;Ebert, M S;Egbert, R G;Ehrhardt, K;Fire, A;Guinn, M;Guo, H L;Kashyap, N;Lee, J;Leisner, M;Li, X;Mello, C C;Mohammadi, P;Moore, R;Mukherji, S;Nevozhay, D;Osella, M;Pillai, R S;Rinaudo, K;Ruder, W C;Schmiedel, J M;Schreiber, J;Strovas, T J;Tsang, J;Weber, W;Winter, J;Xie, Z;Yuan, Y | HM7IT | Richardson, TX USA;Richardson, TX USA. | 14 | null | 1 | null | 29,354,284 | Bleris, Leonidas;Ehrhardt, Kristina;Kannan, Srijaa;Lee, James;Li, Yi;Ma, Lan;Quarton, Tyler | NPJ SYST BIOL APPL | Richardson, TX USA |
Bashor, C J;Collins, J J | 10.1146/annurev-biophys-070816-033903 | null | 4139 EL CAMINO WAY, PO BOX 10139, PALO ALTO, CA 94303-0897 USA | 1a271g2p3k256v392c5d6t1l4oy1d1k314f3p13 | Understanding Biological Regulation Through Synthetic Biology | MIT | Annual Review of Biophysics | Bashor, CJ (corresponding author), MIT, Inst Med Engn & Sci, Dept Biol Engn, Cambridge, MA 02139 USA.;Bashor, CJ (corresponding author), MIT, Synthet Biol Ctr, Cambridge, MA 02139 USA. | null | Bashor, Caleb J;Collins, James J | Biophysics | null | WOS | Bashor, C J | Broad Inst MIT & Harvard, Cambridge, MA USA;Harvard MIT Program Hlth Sci & Technol, Cambridge, MA USA;Harvard Univ, Boston, MA USA;MIT, Cambridge, MA USA | 47 | biological;biology;regulation;synthetic;through;understanding | 1 | null | ANNUAL REVIEWS | Broad Inst MIT & Harvard, Cambridge, MA 02142 USA;Harvard MIT Program Hlth Sci & Technol, Cambridge, MA 02139 USA;Harvard Univ, Wyss Inst Biologically Inspired Engn, Boston, MA 02115 USA;MIT, Inst Med Engn & Sci, Dept Biol Engn, Cambridge, MA 02139 USA;MIT, Inst Med Engn & Sci, Dept Biol Engn, Cambridge, MA 02139 USA.; Bashor, CJ (corresponding author), MIT, Synthet Biol Ctr, Cambridge, MA 02139 USA;MIT, Synthet Biol Ctr, Cambridge, MA 02139 USA | Review; Book Chapter | MIT | PALO ALTO | null | null | Broad Inst MIT & Harvard;Harvard MIT Program Hlth Sci & Technol;Harvard Univ;Inst Med Engn & Sci;MIT | null | Bashor, CJ (corresponding author), MIT, Inst Med Engn & Sci, Dept Biol Engn, Cambridge, MA 02139 USA.; Bashor, CJ (corresponding author), MIT, Synthet Biol Ctr, Cambridge, MA 02139 USA. | 423 | Bashor, Caleb J;Collins, James J | 63 | 5 | 433,056,800,019 | null | USA | ANNUAL REVIEW OF BIOPHYSICS, VOL 47 | USA;USA.; | null | null | MIT, Inst Med Engn & Sci, Dept Biol Engn, Cambridge, MA 02139 USA | 1936-122X | Bashor, C J;Collins, J J | null | cbashor@mit.edu;jimjc@mit.edu | synthetic biology;understanding Biological Regulation | 2 | S | Biophysics | biological discovery;building;cellular phenotype;cellular regulation;cellular regulation serves;circuit engineering;CIRCUITS;engineering cycle;engineering synthetic gene regulatory circuits;ESCHERICHIA-COLI;furnished biologists;gene circuit engineering;initial circuit designs;iterative cycles;living cells;logic gates;MAMMALIAN-CELLS;motif;natural network function;natural systems;network structure;networks;observed circuit behavior;often-incomplete models;POSITIVE-FEEDBACK;precision manipulation;predictively;process;PROTEIN MODULES;reductive inquiry-biochemistry;refactoring;regulation;REGULATORY NETWORK;rely;resynthesis;single-cell level;STOCHASTIC GENE-EXPRESSION;synthetic biology;Synthetic gene circuit;synthetic gene circuit engineering research;systems biology;systems-level network function;testing;toolkit;turn;ultimate means;understanding;understanding Biological Regulation | Bashor, C J | CIRCUITS;engineering cycle;ESCHERICHIA-COLI;LIVING CELLS;logic gates;MAMMALIAN-CELLS;motif;NETWORKS;POSITIVE-FEEDBACK;PROTEIN MODULES;refactoring;REGULATORY NETWORK;SINGLE-CELL LEVEL;STOCHASTIC GENE-EXPRESSION;Synthetic biology;Synthetic gene circuit | 399 | [Bashor, Caleb J.; Collins, James J.] MIT, Inst Med Engn & Sci, Dept Biol Engn, Cambridge, MA 02139 USA. [Bashor, Caleb J.; Collins, James J.] MIT, Synthet Biol Ctr, Cambridge, MA 02139 USA. [Collins, James J.] Harvard MIT Program Hlth Sci & Technol, Cambridge, MA 02139 USA. [Collins, James J.] Broad Inst MIT & Harvard, Cambridge, MA 02142 USA. [Collins, James J.] Harvard Univ, Wyss Inst Biologically Inspired Engn, Boston, MA 02115 USA. | null | biological discovery;building;cellular phenotype;cellular regulation;cellular regulation serves;circuit engineering;engineering cycle;engineering synthetic gene regulatory circuits;furnished biologists;gene circuit engineering;initial circuit designs;iterative cycles;natural network function;natural systems;network structure;observed circuit behavior;often-incomplete models;precision manipulation;predictively;process;reductive inquiry-biochemistry;regulation;rely;resynthesis;synthetic gene circuit engineering research;systems biology;systems-level network function;testing;toolkit;turn;ultimate means;understanding | 10.1002/biot.201000181;10.1016/j.cell.2005.06.006;10.1016/j.cell.2008.06.030;10.1016/j.cell.2009.07.046;10.1016/j.cell.2010.12.014;10.1016/j.cell.2011.01.032;10.1016/j.cell.2012.05.045;10.1016/j.cell.2012.08.040;10.1016/j.cell.2013.02.022;10.1016/j.cell.2014.04.047;10.1016/j.cell.2014.10.002;10.1016/j.cell.2014.10.004;10.1016/j.cell.2015.02.009;10.1016/j.cell.2016.02.004;10.1016/j.cell.2016.04.059;10.1016/j.cell.2016.09.013;10.1016/j.cels.2017.06.001;10.1016/j.copbio.2006.08.001;10.1016/j.copbio.2009.07.009;10.1016/j.molcel.2016.06.006;10.1016/j.sbi.2007.12.002;10.1016/j.sbi.2016.06.012;10.1016/j.tibtech.2015.12.014;10.1016/S0006-3495(00)76519-2;10.1016/S0022-2836(61)80072-7;10.1016/S0092-8674(00)80566-8;10.1038/35002125;10.1038/35002131;10.1038/35011540;10.1038/35014651;10.1038/373573a0;10.1038/468889a;10.1038/nature01546;10.1038/nature02870;10.1038/nature04342;10.1038/nature04473;10.1038/nature04588;10.1038/nature05851;10.1038/nature06847;10.1038/nature07389;10.1038/nature08753;10.1038/nature09906;10.1038/nature13238;10.1038/nature19841;10.1038/nature20777;10.1038/nbt.2510;10.1038/nbt.3053;10.1038/nbt.3063;10.1038/nbt.3199;10.1038/nbt.3805;10.1038/nbt986;10.1038/nchembio.1411;10.1038/ng869;10.1038/nrg2499;10.1038/nrg2775;10.1038/nrm2203;10.1038/nrm2698;10.1038/nrm2746;10.1038/nrmicro3239;10.1038/scientificamerican1182-128;10.1039/c0ib00070a;10.1073/pnas.1009747107;10.1073/pnas.1202344109;10.1073/pnas.1332628100;10.1073/pnas.1508521112;10.1073/pnas.1610973113;10.1073/pnas.1934711100;10.1073/pnas.94.3.814;10.1073/pnas.95.15.8420;10.1088/1468-6996/15/1/014401;10.1093/emboj/20.10.2528;10.1093/nar/25.6.1203;10.1098/rsif.2016.0380;10.1101/cshperspect.a023978;10.1101/sqb.2015.80.027557;10.1103/PhysRevLett.88.148101;10.1113/jphysiol.1952.sp004764;10.1126/science.1063127;10.1126/science.1070919;10.1126/science.1076979;10.1126/science.1085945;10.1126/science.1089072;10.1126/science.1106914;10.1126/science.1109090;10.1126/science.1137455;10.1126/science.1151153;10.1126/science.1172005;10.1126/science.1205527;10.1126/science.1206843;10.1126/science.1232758;10.1126/science.1255301;10.1126/science.1256272;10.1126/science.131.3412.1503;10.1126/science.298.5594.824;10.1126/science.aaa3794;10.1126/science.aab2956;10.1126/science.aac7341;10.1126/science.aad8559;10.1126/scitranslmed.3005568;10.1146/annurev.bioeng.5.040202.121553;10.1146/annurev.biophys.050708.133652;10.1529/biophysj.107.118687;[10.1038/NMETH.2969, 10.1038/nmeth.2969];[10.1038/NMETH.3312, 10.1038/nmeth.3312];[10.1038/NMETH.3339, 10.1038/nmeth.3339];[10.1038/NMETH.3585, 10.1038/nmeth.3585];[10.1038/nprot.2013.021, 10.1038/nprot.nprot.2013.021] | MIT | Bashor, C J;Collins, J J | Bashor, C J: MIT, Inst Med Engn & Sci, Dept Biol Engn, Cambridge, MA 02139 USA | null | null | 108 | 978-0-8243-1847-5 | USA | Broad Inst MIT & Harvard;Harvard MIT Program Hlth Sci & Technol;Harvard Univ;MIT | Bashor, Caleb J | Bronze, Green Published | CIRCUITS;ESCHERICHIA-COLI;LIVING CELLS;LOGIC GATES;MAMMALIAN-CELLS;NETWORKS;POSITIVE-FEEDBACK;PROTEIN MODULES;SINGLE-CELL LEVEL;STOCHASTIC GENE-EXPRESSION | Bashor, Caleb J.; Collins, James J.; | null | Broad Inst MIT & Harvard, Cambridge, MA 02142 USA;Harvard MIT Program Hlth Sci & Technol, Cambridge, MA 02139 USA;Harvard Univ, Wyss Inst Biologically Inspired Engn, Boston, MA 02115 USA;MIT, Inst Med Engn & Sci, Dept Biol Engn, Cambridge, MA 02139 USA;MIT, Synthet Biol Ctr, Cambridge, MA 02139 USA | Broad Inst MIT & Harvard, Cambridge, MA 02142 USA;Harvard MIT Program Hlth Sci & Technol, Cambridge, MA 02139 USA;Harvard Univ, Wyss Inst Biologically Inspired Engn, Boston, MA 02115 USA;MIT, Inst Med Engn & Sci, Dept Biol Engn, Cambridge, MA 02139 USA;MIT, Synthet Biol Ctr, Cambridge, MA 02139 USA | null | engineering cycle;motif;refactoring;regulatory network;Synthetic biology;Synthetic gene circuit | null | 1952;1960;1961;1982;1995;1997;1998;1999;2000;2001;2002;2003;2004;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017 | 65 | MIT, Inst Med Engn & Sci, Dept Biol Engn, Cambridge, MA 02139 USA;MIT, Synthet Biol Ctr, Cambridge, MA 02139 USA | Annu. Rev. Biophys. | Collins, James J | ANNUAL REVIEWS | ,;a;advance;and;are;as;at;be;behavior;biological;biologists;biology;building;but;by;can;cellular;circuit;circuits;cycle;cycles;design;designed;designs;differences;directed;discovery;discuss;each;emerges;encountered;engineering;established;exact;experimentally;fields;force;from;function;furnished;gene;has;here;how;in;inevitably;initial;inquiry-biochemistry;investigated;iterative;manipulation;means;models;molecular;must;natural;network;not;observed;of;often-incomplete;on;only;our;outline;phenotype;precision;predictively;proceeds;process;reconstruct;reductive;refined;regulation;regulatory;rely;reorganize;research;resolved;resynthesis;rewire;serves;structure;synthetic;systems;systems-level;testing;that;the;through;to;toolkit;turn;ultimate;understanding;uses;using;we;with | MIT | Engineering synthetic gene regulatory circuits proceeds through iterative cycles of design, building, and testing. Initial circuit designs must rely on often-incomplete models of regulation established by fields of reductive inquiry-biochemistry and molecular and systems biology. As differences in designed and experimentally observed circuit behavior are inevitably encountered, investigated, and resolved, each turn of the engineering cycle can force a resynthesis in understanding of natural network function. Here, we outline research that uses the process of gene circuit engineering to advance biological discovery. Synthetic gene circuit engineering research has not only refined our understanding of cellular regulation but furnished biologists with a toolkit that can be directed at natural systems to exact precision manipulation of network structure. As we discuss, using circuit engineering to predictively reorganize, rewire, and reconstruct cellular regulation serves as the ultimate means of testing and understanding how cellular phenotype emerges from systems-level network function. | null | CIRCUITS;ESCHERICHIA-COLI;LIVING CELLS;LOGIC GATES;MAMMALIAN-CELLS;NETWORKS;POSITIVE FEEDBACK;PROTEIN MODULES;SINGLE-CELL LEVEL;STOCHASTIC GENE-EXPRESSION | 2 | null | engineering cycle;motif;refactoring;regulatory network;Synthetic biology;Synthetic gene circuit | 25 | ESCHERICHIA-COLI;CIRCUITS;engineering cycle;LIVING CELLS;logic gates;MAMMALIAN-CELLS;MOTIFS;NETWORKS;Positive feedback;PROTEIN MODULES;refactoring;REGULATORY NETWORKS;SINGLE-CELL LEVEL;STOCHASTIC GENE-EXPRESSION;Synthetic biology;synthetic gene circuits | WOS:000433056800019 | Broad Inst MIT & Harvard, Cambridge, MA USA;Harvard MIT Program Hlth Sci & Technol, Cambridge, MA USA;Harvard Univ, Boston, MA USA;MIT, Cambridge, MA USA | USA | 2,018 | null | null | null | Dill, KA | English | null | ANNU REV BIOMED ENG;ANNU REV BIOPHYS;BIOPHYS J;BIOTECHNOL J;CELL;CELL SYST;COLD SH Q B;CSH PERSPECT BIOL;CURR OPIN BIOTECH;CURR OPIN STRUC BIOL;EMBO J;INTEGR BIOL-UK;J MOL BIOL;J PHYSIOL-LONDON;J R SOC INTERFACE;MOL CELL;NAT BIOTECHNOL;NAT CHEM BIOL;NAT GENET;NAT METHODS;NAT PROTOC;NAT REV GENET;NAT REV MICROBIOL;NAT REV MOL CELL BIO;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PHYS REV LETT;SCI AM;SCI TECHNOL ADV MAT;SCI TRANSL MED;SCIENCE;TRENDS BIOTECHNOL | Bashor, Caleb J;Collins, James J | 2024-03-11
ER | Alon, U;Appleton, E;Barrett, C L;Bashor, C J;Becskei, A;Bintu, L;Blake, W J;Bonnet, J;Brophy, J A N;Callura, J M;Cameron, D E;Carroll, S B;Ceroni, F;Chau, A H;Chavez, A;Chen, Y;Danino, T;Del Vecchio, D;Detwiler, P B;Dueber, J E;Dunlap, J C;Ellis, T;Elowitz, M;Elowitz, M B;Endy, D;Ernst, J;Erwin, D H;Farzadfard, F;Fischbach, M;Fischbach, M A;Frieda, K L;Friedland, A E;Gardner, T S;Gordley, R M;Green, A A;Guido, N J;Hannon, G J;Hartwell, L H;Hasty, J;Hilton, I B;Hodgkin, A L;Howard, P L;Isaacs, F J;Isalan, M;Jacob, F;Jenuwein, T;Jones, D L;Jusiak, B;Keung, A J;Khalil, A S;Kiani, S;Kirschner, M;Kornberg, A;Kærn, M;Lee, J W;Liu, A P;Lutz, R;Mcadams, H H;Milo, R;Nielsen, A A K;Nielsen, J;Nocedal, I;O'Shaughnessy, E C;Ozbudak, E M;Panne, D;Pardee, K;Park, S H;Pawson, T;Pedraza, J M;Potvin-Trottier, L;Prindle, A;Ptashne, M;Purnick, P E M;Qi, L S;Razooky, B S;Rice, M K;Roquet, N;Rosenfeld, N;Ruder, W C;Siuti, P;Slomovic, S;Smanski, M J;Stanton, B C;Stricker, J;Süel, G M;Tigges, M;Toprak, E;Ubersax, J A;Weinberg, B H;Weinberger, L S;Xie, Z;Yeh, B J;Yeung, E;Young, R A | BK2KQ | Cambridge, MA USA;Cambridge, MA USA. | 78 | null | 4 | null | 29,547,341 | Bashor, Caleb J;Collins, James J | ANNU REV BIOPHYS | Boston, MA USA;Cambridge, MA USA |
Ellis, T;Pothoulakis, G | 10.1038/s42003-017-0008-0 | 7 | 75 VARICK ST, 9TH FLR, NEW YORK, NY 10013-1917 USA | m6n5s2e2o4x6x4i414o136c7133712v2t6o6k3z | Synthetic gene regulation for independent external induction of the <i>Saccharomyces cerevisiae</i> pseudohyphal growth phenotype | Imperial Coll London | null | Ellis, T (corresponding author), Imperial Coll London, Ctr Synthet Biol & Innovat, South Kensington Campus,Exhibit Rd, London SW7 2AZ, England.;Ellis, T (corresponding author), Imperial Coll London, Dept Bioengn, South Kensington Campus,Exhibit Rd, London SW7 2AZ, England. | null | Ellis, Tom;Pothoulakis, Georgios | Biology;Multidisciplinary Sciences | Leverhulme Trust [RPG-2012-562]; BBSRC [BB/K006290/1]; BBSRC [BB/K006290/1] Funding Source: UKRI; Biotechnology and Biological Sciences Research Council [BB/K006290/1] Funding Source: researchfish | WOS | Ellis, T | Imperial Coll London, London, England | 1 | <i>Saccharomyces;cerevisiae</i>;external;for;gene;growth;Independent;induction;of;phenotype;pseudohyphal;regulation;synthetic;the | 1 | Pothoulakis, Georgios | NATURE PUBLISHING GROUP | Imperial Coll London, Ctr Synthet Biol & Innovat, South Kensington Campus,Exhibit Rd, London SW7 2AZ, England;Imperial Coll London, Ctr Synthet Biol & Innovat, South Kensington Campus,Exhibit Rd, London SW7 2AZ, England.; Ellis, T (corresponding author), Imperial Coll London, Dept Bioengn, South Kensington Campus,Exhibit Rd, London SW7 2AZ, England;Imperial Coll London, Dept Bioengn, South Kensington Campus,Exhibit Rd, London SW7 2AZ, England | Article | Imperial Coll London | NEW YORK | null | null | Imperial Coll London | BBSRC;Biotechnology and Biological Sciences Research Council;Leverhulme Trust | Ellis, T (corresponding author), Imperial Coll London, Ctr Synthet Biol & Innovat, South Kensington Campus,Exhibit Rd, London SW7 2AZ, England.; Ellis, T (corresponding author), Imperial Coll London, Dept Bioengn, South Kensington Campus,Exhibit Rd, London SW7 2AZ, England. | null | Ellis, Tom;Pothoulakis, Georgios | 4 | 2 | 461,126,500,007 | BBSRC [BB/K006290/1];BBSRC [BB/K006290/1] Funding Source: UKRI;Biotechnology and Biological Sciences Research Council [BB/K006290/1] Funding Source: researchfish;Leverhulme Trust [RPG-2012-562] | UK | COMMUNICATIONS BIOLOGY | UK | null | null | Imperial Coll London, Ctr Synthet Biol & Innovat, South Kensington Campus,Exhibit Rd, London SW7 2AZ, England | null | Ellis, T;Pothoulakis, G | null | t.ellis@imperial.ac.uk | <i>Saccharomyces cerevisiae</i> pseudohyphal growth phenotype;independent external induction;Synthetic Gene Regulation | 2 | J | Life Sciences & Biomedicine - Other Topics;Science & Technology - Other Topics | <i>Saccharomyces cerevisiae</i> pseudohyphal growth phenotype;branched filament structures;BUD gene family control filamentation;BUD-SITE-SELECTION;complex multigene phenotype;connected cells;CONSTRUCTION;control;different types;differentiation;diploid;expression;external induction;FILAMENTOUS GROWTH;FLO8 genes;gene regulation;gross changes;haploid cells;HAPLOID INVASIVE GROWTH;haploid yeast;independent external induction;members;multicellular phenotype;natural PHD1;networks;offers opportunities;pattern;PROTEIN;pseudohyphal growth;response;resulting multicellular structure;reversibility;rich media;Saccharomyces cerevisiae;Stress;Synthetic Gene Regulation;synthetic gene regulation systems;synthetic genetic timer network;synthetic regulation;SYSTEM;TRANSCRIPTION;unicellular yeast cells;wild budding yeast cells;yeast | Pothoulakis, G | BUD-SITE-SELECTION;CONSTRUCTION;EXPRESSION;FILAMENTOUS GROWTH;HAPLOID INVASIVE GROWTH;NETWORKS;PATTERN;PROTEIN;TRANSCRIPTION;YEAST | null | [Pothoulakis, Georgios; Ellis, Tom] Imperial Coll London, Ctr Synthet Biol & Innovat, South Kensington Campus,Exhibit Rd, London SW7 2AZ, England. [Pothoulakis, Georgios; Ellis, Tom] Imperial Coll London, Dept Bioengn, South Kensington Campus,Exhibit Rd, London SW7 2AZ, England. | The authors wish to thank William Shaw (Imperial College London) for his assistance on the implementation of the Yeast ToolKit and providing certain YTK part plasmids. We also thank Marios Tomazou, Felix Jonas and all other helpful members of CSynBI at Imperial College London. This work was funded by The Leverhulme Trust under project grant RPG-2012-562 and by the BBSRC via grant BB/K006290/1. | branched filament structures;BUD gene family control filamentation;complex multigene phenotype;connected cells;control;different types;differentiation;diploid;expression;external induction;FLO8 genes;gene regulation;gross changes;haploid cells;haploid yeast;members;multicellular phenotype;natural PHD1;offers opportunities;pseudohyphal growth;response;resulting multicellular structure;reversibility;rich media;Saccharomyces cerevisiae;stress;synthetic gene regulation systems;synthetic genetic timer network;synthetic regulation;system;unicellular yeast cells;wild budding yeast cells | 10.1002/j.1460-2075.1991.tb04901.x;10.1007/s004380050220;10.1016/j.febslet.2012.01.053;10.1016/j.ymeth.2012.08.004;10.1016/S0168-6445(00)00056-5;10.1016/S1369-5274(02)00300-4;10.1021/sb500366v;10.1038/274765a0;10.1038/nbt.1536;10.1038/nbt1162;10.1038/nrmicro1578;10.1046/j.1365-2958.2003.03478.x;10.1073/pnas.0407097102;10.1073/pnas.0608451104;10.1073/pnas.1305423110;10.1073/pnas.1522679113;10.1073/pnas.240345197;10.1083/jcb.134.2.413;10.1091/mbc.11.3.833;10.1091/mbc.12.7.2147;10.1091/mbc.12.8.2497;10.1091/mbc.5.9.1003;10.1091/mbc.E02-03-0151;10.1093/nar/gks1313;10.1093/nar/gkt1402;10.1101/PDB.T0P065482;10.1111/j.1574-6976.2011.00275.x;10.1111/jam.13078;10.1126/science.1224339;10.1128/AEM.00425-07;10.1128/EC.00284-06;10.1128/EC.4.6.1018-1028.2005;10.1128/EC.4.8.1328-1342.2005;10.1128/MCB.05420-11;10.1128/MCB.10.9.4757;10.1128/MCB.14.3.2100;10.1128/MCB.8.10.4048;10.1128/MMBR.00037-06;10.1128/MMBR.69.2.326-356.2005;10.1242/dev.00425;10.1371/journal.pgen.1005684;10.1534/genetics.111.127456 | Imperial Coll London | Ellis, T;Pothoulakis, G | Pothoulakis, G: Imperial Coll London, Ctr Synthet Biol & Innovat, South Kensington Campus,Exhibit Rd, London SW7 2AZ, England | Pothoulakis, Georgios | BB/K006290/1;RPG-2012-562 | 45 | null | UK | Imperial Coll London | Pothoulakis, Georgios | Green Published, gold | BUD-SITE-SELECTION;CONSTRUCTION;EXPRESSION;FILAMENTOUS GROWTH;HAPLOID INVASIVE GROWTH;NETWORKS;PATTERN;PROTEIN;TRANSCRIPTION;YEAST | Pothoulakis, Georgios; Ellis, Tom; | null | Imperial Coll London, Ctr Synthet Biol & Innovat, South Kensington Campus,Exhibit Rd, London SW7 2AZ, England;Imperial Coll London, Dept Bioengn, South Kensington Campus,Exhibit Rd, London SW7 2AZ, England | Imperial Coll London, Ctr Synthet Biol & Innovat, South Kensington Campus,Exhibit Rd, London SW7 2AZ, England;Imperial Coll London, Dept Bioengn, South Kensington Campus,Exhibit Rd, London SW7 2AZ, England | 2399-3642 | null | null | 1978;1988;1990;1991;1994;1996;1997;2000;2001;2002;2003;2005;2007;2009;2011;2012;2013;2014;2015;2016 | 14 | Imperial Coll London, Ctr Synthet Biol & Innovat, South Kensington Campus,Exhibit Rd, London SW7 2AZ, England;Imperial Coll London, Dept Bioengn, South Kensington Campus,Exhibit Rd, London SW7 2AZ, England | Commun. Biol. | Ellis, Tom | NATURE PUBLISHING GROUP | ,;a;able;also;and;are;both;branched;BUD;budding;by;can;cells;cerevisiae;changes;complex;connected;consisting;construct;control;controlling;demonstrates;different;differentiation;diploid;elongate;employ;enable;even;exert;explore;expression;external;family;filament;filamentation;finally;FLO8;for;form;further;gene;genes;genetic;gross;growth;haploid;here;how;in;induction;investigate;is;media;members;modifying;multicellular;multigene;natural;naturally;network;of;offers;opportunities;our;over;performed;PHD1;phenotype;pseudohyphal;rationally;regulation;response;resulting;reversibility;rich;Saccharomyces;stress;structure;structures;synthetic;system;systems;that;the;their;this;timer;to;trigger;types;undergo;unicellular;using;we;wild;work;yeast | Imperial Coll London | Pseudohyphal growth is a multicellular phenotype naturally performed by wild budding yeast cells in response to stress. Unicellular yeast cells undergo gross changes in their gene regulation and elongate to form branched filament structures consisting of connected cells. Here, we construct synthetic gene regulation systems to enable external induction of pseudohyphal growth in Saccharomyces cerevisiae. By controlling the expression of the natural PHD1 and FLO8 genes we are able to trigger pseudohyphal growth in both diploid and haploid yeast, even in different types of rich media. Using this system, we also investigate how members of the BUD gene family control filamentation in haploid cells. Finally, we employ a synthetic genetic timer network to control pseudohyphal growth and further explore the reversibility of differentiation. Our work demonstrates that synthetic regulation can exert control over a complex multigene phenotype and offers opportunities for rationally modifying the resulting multicellular structure. | HLQ-6280-2023 | BUD-SITE-SELECTION;CONSTRUCTION;EXPRESSION;FILAMENTOUS GROWTH;HAPLOID INVASIVE GROWTH;NETWORKS;PATTERNS;PROTEIN;TRANSCRIPTION;YEAST | 0 | null | null | 11 | YEAST;BUD-SITE-SELECTION;CONSTRUCTION;EXPRESSION;FILAMENTOUS GROWTH;HAPLOID INVASIVE GROWTH;NETWORKS;PATTERNS;PROTEIN;TRANSCRIPTION | WOS:000461126500007 | Imperial Coll London, London, England | UK | 2,018 | null | 0000-0003-2950-3990 | null | null | English | null | ACS SYNTH BIOL;APPL ENVIRON MICROB;Cold Spring Harb Protoc;CURR OPIN MICROBIOL;DEVELOPMENT;EMBO J;EUKARYOT CELL;FEBS LETT;FEMS MICROBIOL REV;GENETICS;J APPL MICROBIOL;J CELL BIOL;METHODS;MICROBIOL MOL BIOL R;MOL BIOL CELL;MOL CELL BIOL;MOL GEN GENET;MOL MICROBIOL;NAT BIOTECHNOL;NAT REV MICROBIOL;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PLOS GENET;SCIENCE | Ellis, Tom;Pothoulakis, Georgios | 2024-03-11
ER | Albers, E;Ashe, M P;Bahn, Y S;Basu, S;Blount, B A;Brückner, S;Casamayor, A;Chen, M T;Cullen, P J;Dang, C V;Douglas, L M;Dranginis, A M;Ellis, T;Farabaugh, P J;Flick, J S;Gancedo, J M;Gimeno, C J;Harkins, H A;Hughes, R M;Kim, J;Kobayashi, O;Kron, S J;Kumamoto, C A;Lee, M E;Liu, H P;Mcisaac, R S;Mosch, H U;Murphy, K F;Nehlin, J O;Ni, L;Park, Y N;Raithatha, S;Ramos, J L;Rines Danielr.;Ryan, O;Salazar-Ciudad, I;Sanders, S L;Sharma, G;Voth, W P;Wu, M;Yin, Z K;Zahner, J E | HO7LC | London, England;London, England. | 15 | null | 1 | null | 30,271,894 | Ellis, Tom;Pothoulakis, Georgios | COMMUN BIOL | London, England |
Arangundy-Franklin, S;Holliger, P;Houlihan, G | 10.1016/j.copbio.2017.04.004 | null | THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND | 6v366y246u4b5p1c2dp51u2034o1t143u5s23 | Engineering and application of polymerases for synthetic genetics | MRC Lab Mol Biol | null | Holliger, P (corresponding author), MRC Lab Mol Biol, Francis Crick Ave,Cambridge Biomed Campus, Cambridge CB2 0QH, England. | null | Arangundy-Franklin, Sebastian;Holliger, Philipp;Houlihan, Gillian | Biochemical Research Methods;Biotechnology & Applied Microbiology | Medical Research Council [MC_U105178804]; MRC-AstraZeneca/MedImmune Blue Sky Grant; Medical Research Council [MC_U105178804] Funding Source: researchfish; MRC [MC_U105178804] Funding Source: UKRI | WOS | Holliger, P | MRC Lab Mol Biol, Cambridge, England | 48 | and;application;engineering;for;Genetics;of;polymerases;synthetic | 1 | null | ELSEVIER SCI LTD | MRC Lab Mol Biol, Francis Crick Ave,Cambridge Biomed Campus, Cambridge CB2 0QH, England | Review | MRC Lab Mol Biol | OXFORD | null | null | MRC Lab Mol Biol | Medical Research Council;MRC;MRC-AstraZeneca/MedImmune Blue Sky Grant | Holliger, P (corresponding author), MRC Lab Mol Biol, Francis Crick Ave,Cambridge Biomed Campus, Cambridge CB2 0QH, England. | 179 | Arangundy-Franklin, Sebastian;Holliger, Philipp;Houlihan, Gillian | 55 | 1 | 418,313,200,023 | Medical Research Council [MC_U105178804];Medical Research Council [MC_U105178804] Funding Source: researchfish;MRC [MC_U105178804] Funding Source: UKRI;MRC-AstraZeneca/MedImmune Blue Sky Grant | UK | CURRENT OPINION IN BIOTECHNOLOGY | UK | null | null | MRC Lab Mol Biol, Francis Crick Ave,Cambridge Biomed Campus, Cambridge CB2 0QH, England | 0958-1669 | Arangundy-Franklin, S;Holliger, P;Houlihan, G | DEC | ph1@mrc-lmb.cam.ac.uk | application;engineering;polymerases;Synthetic Genetics | 3 | J | Biochemistry & Molecular Biology;Biotechnology & Applied Microbiology | application;backbone moieties;chemical determinants;COMBINATORIAL SELECTION;concomitantly;conjunction;crosstalk;CRYSTAL-STRUCTURE;directed evolution;discovery;DNA-POLYMERASE;engineering;engineering polymerases;ENZYMATIC-SYNTHESIS;evolution;exploration;function;genetic alphabet;genetic information;given rise;IN-VITRO SELECTION;information exchange;investigation;modified nucleotide analogs;molecular biology;natural genetic system;new field;novel;novel unnatural basepairs;nucleic acids;NUCLEIC-ACIDS;nucleobase;nucleotide chemistry;organic chemistry;polymerases;progress;PROPAGATION;protein engineering;recent progress;reverse transcription;REVERSE-TRANSCRIPTASE;SEMISYNTHETIC ORGANISM;STORAGE;sugar ring;synthetic genetic polymers;synthetic genetics;synthetic nucleic acids;T7 RNA-POLYMERASE;templated synthesis;two lines;variation | Houlihan, G | COMBINATORIAL SELECTION;CRYSTAL-STRUCTURE;directed evolution;DNA-POLYMERASE;ENZYMATIC-SYNTHESIS;IN-VITRO SELECTION;NUCLEIC-ACIDS;REVERSE-TRANSCRIPTASE;SEMISYNTHETIC ORGANISM;T7 RNA-POLYMERASE | 168 | [Houlihan, Gillian; Arangundy-Franklin, Sebastian; Holliger, Philipp] MRC Lab Mol Biol, Francis Crick Ave,Cambridge Biomed Campus, Cambridge CB2 0QH, England. | The authors acknowledge support by the Medical Research Council (G.H., P.H., program no. MC_U105178804) and an MRC-AstraZeneca/MedImmune Blue Sky Grant supporting the salary of S.A-F. | backbone moieties;chemical determinants;concomitantly;conjunction;crosstalk;discovery;engineering polymerases;evolution;exploration;function;genetic alphabet;genetic information;given rise;information exchange;investigation;modified nucleotide analogs;molecular biology;natural genetic system;new field;novel;novel unnatural basepairs;nucleic acids;nucleobase;nucleotide chemistry;organic chemistry;polymerases;progress;propagation;protein engineering;recent progress;reverse transcription;storage;sugar ring;synthetic genetic polymers;synthetic genetics;synthetic nucleic acids;templated synthesis;two lines;variation | 10.1002/1439-7633(20010302)2:3<212::AID-CBIC212>3.0.CO;2-R;10.1002/anie.201503652;10.1002/anie.201508678;10.1002/anie.201606242;10.1002/cbdv.200900185;10.1002/cbic.201000384;10.1002/cbic.201600136;10.1002/j.1460-2075.1995.tb00140.x;10.1007/s00216-013-7350-y;10.1007/s00253-015-6781-0;10.1016/j.bbrc.2014.09.053;10.1016/j.bbrc.2015.03.019;10.1016/j.biomaterials.2014.08.046;10.1016/j.cbpa.2008.06.028;10.1016/j.cbpa.2016.08.001;10.1016/j.cell.2013.04.046;10.1016/j.chembiol.2004.10.017;10.1016/j.jbiotec.2013.07.005;10.1016/j.jmb.2006.06.050;10.1016/S0040-4020(98)00094-5;10.1021/acs.biochem.5b00689;10.1021/acschembio.5b00949;10.1021/acssynbio.6b00228;10.1021/ar040004z;10.1021/bi0507074;10.1021/bi1009503;10.1021/bi101915z;10.1021/bi400558c;10.1021/ja038525p;10.1021/ja0428255;10.1021/ja045364w;10.1021/ja412079b;10.1021/ja508015a;10.1021/ja9039696;10.1021/ja906186f;10.1021/jacs.5b02251;10.1021/jacs.5b03482;10.1021/jacs.6b10767;10.1038/nature12306;10.1038/nature13314;10.1038/nature13982;10.1038/nature21022;10.1038/nbt.2556;10.1038/nbt1001;10.1038/nbt974;10.1038/ncomms11235;10.1038/ncomms7923;10.1038/nrd.2016.199;10.1038/nrd1955;10.1039/c4mb00436a;10.1039/c5mb00045a;10.1042/EBC20160013;10.1073/pnas.071052198;10.1073/pnas.102577799;10.1073/pnas.1120964109;10.1073/pnas.1311778111;10.1073/pnas.132067399;10.1073/pnas.1616443114;10.1074/jbc.M112.442350;10.1074/jbc.M113.532697;10.1074/jbc.R400006200;10.1093/molbev/msu271;10.1093/nar/gkn1070;10.1093/nar/gkn956;10.1093/nar/gkv1057;10.1093/nar/gkv1472;10.1093/nar/gkv367;10.1093/nar/gkv719;10.1093/nar/gkv734;10.1093/nar/gkv798;10.1093/nar/gkx079;10.1093/nar/gnf138;10.1126/science.1217622;10.1126/science.290.5495.1347;10.1126/science.aad9633;10.1126/science.aaf5409;10.1146/annurev.biochem.66.1.337;10.1371/journal.pone.0015004;10.3389/fmicb.2014.00305;10.4161/rna.27447;[10.1038/NCHEM.1241, 10.1038/nchem.1241];[10.1038/NCHEM.2493, 10.1038/nchem.2493];[10.1038/NCHEM.2517, 10.1038/nchem.2517];[10.1038/NCHEMBIO.277, 10.1038/nchembio.277] | MRC Lab Mol Biol | Arangundy-Franklin, S;Holliger, P;Houlihan, G | Houlihan, G: MRC Lab Mol Biol, Francis Crick Ave,Cambridge Biomed Campus, Cambridge CB2 0QH, England | Houlihan, Gillian | MC_U105178804 | 89 | null | UK | MRC Lab Mol Biol | Houlihan, Gillian | null | COMBINATORIAL SELECTION;CRYSTAL-STRUCTURE;DIRECTED EVOLUTION;DNA-POLYMERASE;ENZYMATIC-SYNTHESIS;IN-VITRO SELECTION;NUCLEIC-ACIDS;REVERSE-TRANSCRIPTASE;SEMISYNTHETIC ORGANISM;T7 RNA-POLYMERASE | Houlihan, Gillian; Arangundy-Franklin, Sebastian; Holliger, Philipp; | null | MRC Lab Mol Biol, Francis Crick Ave,Cambridge Biomed Campus, Cambridge CB2 0QH, England | MRC Lab Mol Biol, Francis Crick Ave,Cambridge Biomed Campus, Cambridge CB2 0QH, England | 1879-0429 | null | null | 1995;1997;1998;2000;2001;2002;2004;2005;2006;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017 | 34 | MRC Lab Mol Biol, Francis Crick Ave,Cambridge Biomed Campus, Cambridge CB2 0QH, England | Curr. Opin. Biotechnol. | Holliger, Philipp | ELSEVIER SCI LTD | ,;a;acids;advanced;allow;alphabet;analogs;and;as;backbone;basepairs;biology;build;by;capable;capacity;chemical;chemistry;concomitantly;conjunction;crosstalk;dedicated;design;determinants;discovery;engineering;evolution;exchange;expand;exploration;field;for;function;genetic;genetics;given;has;here;in;information;investigation;is;lines;modified;moieties;molecular;natural;new;novel;nucleic;nucleobase;nucleotide;of;organic;polymerases;polymers;probed;progress;propagation;protein;recent;reverse;ring;rise;specifically;storage;sugar;summarize;synthesis;synthetic;system;systematically;templated;that;the;these;to;transcription;two;unnatural;utilizing;variation;we;well;with | MRC Lab Mol Biol | Organic chemistry has systematically probed the chemical determinants of function in nucleic acids by variation to the nucleobase, sugar ring and backbone moieties to build synthetic genetic polymers. Concomitantly, protein engineering has advanced to allow the discovery of polymerases capable of utilizing modified nucleotide analogs. A conjunction of these two lines of investigation in nucleotide chemistry and molecular biology has given rise to a new field of synthetic genetics dedicated to the exploration of the capacity of these novel, synthetic nucleic acids for the storage and propagation of genetic information, for evolution and for crosstalk, that is, information exchange with the natural genetic system. Here we summarize recent progress in synthetic genetics, specifically in the design of novel unnatural basepairs to expand the genetic alphabet as well as progress in engineering polymerases capable of templated synthesis, reverse transcription and evolution of synthetic genetic polymers. | Y-6197-2019 | COMBINATORIAL SELECTION;CRYSTAL-STRUCTURE;DIRECTED EVOLUTION;DNA-POLYMERASE;ENZYMATIC-SYNTHESIS;IN-VITRO SELECTION;NUCLEIC-ACIDS;REVERSE-TRANSCRIPTASE;SEMISYNTHETIC ORGANISM;T7 RNA-POLYMERASE | 3 | null | null | 12 | COMBINATORIAL SELECTION;CRYSTAL-STRUCTURE;directed evolution;DNA-POLYMERASE;ENZYMATIC-SYNTHESIS;IN-VITRO SELECTION;NUCLEIC-ACIDS;REVERSE-TRANSCRIPTASE;SEMISYNTHETIC ORGANISM;T7 RNA-POLYMERASE | WOS:000418313200023 | MRC Lab Mol Biol, Cambridge, England | UK | 2,017 | null | null | null | null | English | null | ACCOUNTS CHEM RES;ACS CHEM BIOL;ACS SYNTH BIOL;ANAL BIOANAL CHEM;ANGEW CHEM INT EDIT;ANNU REV BIOCHEM;APPL MICROBIOL BIOT;BIOCHEM BIOPH RES CO;BIOCHEMISTRY-US;BIOMATERIALS;CELL;CHEM BIODIVERS;CHEM BIOL;CHEMBIOCHEM;COLD SPRING HARBOR P;COLD SPRING HERB PER;CURR OPIN CHEM BIOL;CURR PROTOC NUCL ACI;EMBO J;ESSAYS BIOCHEM;FRONT MICROBIOL;J AM CHEM SOC;J BIOL CHEM;J BIOTECHNOL;J MOL BIOL;J SYST CHEM;MOL BIOL EVOL;MOL BIOSYST;NAT BIOTECHNOL;NAT CHEM;NAT CHEM BIOL;NAT COMMUN;NAT REV DRUG DISCOV;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PLOS ONE;POLYM ENG PCR SEQUEN;RNA BIOL;SCIENCE;TETRAHEDRON | Arangundy-Franklin, Sebastian;Holliger, Philipp;Houlihan, Gillian | 2024-03-11
ER | Ablasser, A;Anosova, I;Benner, S A;Brakmann, S;Brown, J A;Burmeister, P E;Chelliserrykattil, J;Chen, C Y;Chen, T;Chen, T J;Cozens, C;Delespaul, W;Dunn, M R;Elle, I C;Ellefson, J W;Fa, M;Ferreira-Bravo, I A;Friedman, A D;Gandham, S H A;Gao, P;Gao, Y;Gelinas, A D;Georgiadis, M M;Ghadessy, F J;Gold, L;Hagiwara, K;Herdewijn, P;Hollenstein, M;Horhota, A;Ibach, J;Ichida, J K;Keefe, A D;Khanal, A;Kimoto, M;Koshkin, A A;Kreil, G;Kunkel, T A;Laos, R;Larsen, A C;Li, L;Loakes, D;Maiti, M;Malyshev, D A;Matsunaga, K;Matsuura, M F;Mauer, J;Meyer, A J;Meyer, C;Mi, J;Millar, D;Murciano-Calles, J;Ng, E W M;Oberthür, D;Ong, J L;Padilla, R;Pech, A;Pinheiro, V B;Schultz, H J;Schöning, K U;Sefah, K;Sheng, J;Somasunderam, A;Sousa, R;Staiger, N;Svobodova, M;Szostak, J W;Taylor, A I;Tolle, F;Torres, L;Wang, Z M;Wlotzka, B;Xia, G;Yu, H Y;Zhang, L K;Zhang, L Q;Zhang, Y K;Zhou, J H;Zhu, B | FQ4FN | Cambridge, England | 36 | null | 1 | null | 28,601,700 | Arangundy-Franklin, Sebastian;Holliger, Philipp;Houlihan, Gillian | CURR OPIN BIOTECH | Cambridge, England |
Blanchard, A E;Liao, C;Lu, T | 10.1038/s41564-017-0022-5 | null | MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND | 3i566u6e446r691961l674t5m5gh1d384t2i24 | An integrative circuit-host modelling framework for predicting synthetic gene network behaviours | Univ Illinois | null | Lu, T (corresponding author), Univ Illinois, Carl R Woese Inst Genom Biol, Urbana, IL 61801 USA.;Lu, T (corresponding author), Univ Illinois, Ctr Biophys & Quantitat Biol, Urbana, IL 61801 USA.;Lu, T (corresponding author), Univ Illinois, Dept Bioengn, Urbana, IL 61801 USA.;Lu, T (corresponding author), Univ Illinois, Dept Phys, Urbana, IL 61801 USA. | null | Blanchard, Andrew E;Liao, Chen;Lu, Ting | Microbiology | National Science Foundation [1553649, 1227034]; Office of Naval Research [N000141612525]; American Heart Association [12SDG12090025]; Brain and Behavior Research Foundation (NARSAD Young Investigator Award); National Center for Supercomputing Applications (Faculty Fellowship); Direct For Biological Sciences; Div Of Molecular and Cellular Bioscience [1553649] Funding Source: National Science Foundation; Div Of Engineering Education and Centers; Directorate For Engineering [1227034] Funding Source: National Science Foundation; U.S. Department of Defense (DOD) [N000141612525] Funding Source: U.S. Department of Defense (DOD) | WOS | Lu, T | Univ Illinois, Urbana, IL USA | 2 | an;behaviours;circuit-host;for;Framework;gene;integrative;modelling;network;predicting;synthetic | 1 | Liao, Chen | NATURE PUBLISHING GROUP | Univ Illinois, Carl R Woese Inst Genom Biol, Urbana, IL 61801 USA;Univ Illinois, Ctr Biophys & Quantitat Biol, Urbana, IL 61801 USA;Univ Illinois, Dept Bioengn, Urbana, IL 61801 USA;Univ Illinois, Dept Bioengn, Urbana, IL 61801 USA.; Lu, T (corresponding author), Univ Illinois, Carl R Woese Inst Genom Biol, Urbana, IL 61801 USA.; Lu, T (corresponding author), Univ Illinois, Dept Phys, Urbana, IL 61801 USA.; Lu, T (corresponding author), Univ Illinois, Ctr Biophys & Quantitat Biol, Urbana, IL 61801 USA;Univ Illinois, Dept Phys, Urbana, IL 61801 USA | Article | Univ Illinois | LONDON | null | null | Univ Illinois | American Heart Association;Brain and Behavior Research Foundation (NARSAD Young Investigator Award);Direct For Biological Sciences;Directorate For Engineering;Div Of Engineering Education and Centers;Div Of Molecular and Cellular Bioscience;National Center for Supercomputing Applications (Faculty Fellowship);National Science Foundation;Office of Naval Research;U.S. Department of Defense (DOD) | Lu, T (corresponding author), Univ Illinois, Dept Bioengn, Urbana, IL 61801 USA.; Lu, T (corresponding author), Univ Illinois, Carl R Woese Inst Genom Biol, Urbana, IL 61801 USA.; Lu, T (corresponding author), Univ Illinois, Dept Phys, Urbana, IL 61801 USA.; Lu, T (corresponding author), Univ Illinois, Ctr Biophys & Quantitat Biol, Urbana, IL 61801 USA. | 1666 | Blanchard, Andrew E;Liao, Chen;Lu, Ting | 27 | 4 | 417,976,600,017 | American Heart Association [12SDG12090025];Brain and Behavior Research Foundation (NARSAD Young Investigator Award);Direct For Biological Sciences;Directorate For Engineering [1227034] Funding Source: National Science Foundation;Div Of Engineering Education and Centers;Div Of Molecular and Cellular Bioscience [1553649] Funding Source: National Science Foundation;National Center for Supercomputing Applications (Faculty Fellowship);National Science Foundation [1553649, 1227034];Office of Naval Research [N000141612525];U.S. Department of Defense (DOD) [N000141612525] Funding Source: U.S. Department of Defense (DOD) | USA | NATURE MICROBIOLOGY | USA;USA.; | null | null | Univ Illinois, Dept Bioengn, Urbana, IL 61801 USA | 2058-5276 | Blanchard, A E;Liao, C;Lu, T | DEC | luting@illinois.edu | integrative circuit-host modelling framework;synthetic gene network behaviours | 3 | J | Microbiology | behaviours;bidirectional circuit-host coupling;BIOLOGY;challenge;circuit behaviours;circuit-host interactions;CIRCUITS;complex interdependence;detailed kinetic module;dynamic resource partitioning;DYNAMICS;ESCHERICHIA-COLI;exogenous circuits;experimental data;expression;extended version;foreign gene overexpression;gene circuit behaviours;gene circuit modelling framework;Gene circuits;growth-modulating feedback;GROWTH-RATE;host;host physiology;IN-VIVO;integrative circuit-host modelling framework;lack;large set;leading cause;mechanistic description;multilayered circuit-host coupling;multiple factors;one fundamental challenge;population structure;PPGPP;PROTEIN-SYNTHESIS;quantitative understanding;rational design;single-cell dynamics;SOURCE SHIFT-DOWN;spatial ecology;synthetic biology;synthetic gene network behaviours;synthetic gene networks;system-specific interactions;toggle switch;toggle switch across scales;training;TRANSCRIPTION INITIATION;utility | Liao, C | BIOLOGY;ESCHERICHIA-COLI;EXPRESSION;GROWTH-RATE;IN-VIVO;PPGPP;PROTEIN-SYNTHESIS;SOURCE SHIFT-DOWN;toggle switch;TRANSCRIPTION INITIATION | 1658 | [Liao, Chen; Lu, Ting] Univ Illinois, Dept Bioengn, Urbana, IL 61801 USA. [Liao, Chen; Blanchard, Andrew E.; Lu, Ting] Univ Illinois, Carl R Woese Inst Genom Biol, Urbana, IL 61801 USA. [Blanchard, Andrew E.; Lu, Ting] Univ Illinois, Dept Phys, Urbana, IL 61801 USA. [Lu, Ting] Univ Illinois, Ctr Biophys & Quantitat Biol, Urbana, IL 61801 USA. | This work was supported by the National Science Foundation (No. 1553649 and 1227034), the Office of Naval Research (No. N000141612525), the American Heart Association (No. 12SDG12090025), the Brain and Behavior Research Foundation (NARSAD Young Investigator Award), and the National Center for Supercomputing Applications (Faculty Fellowship). | behaviours;bidirectional circuit-host coupling;challenge;circuit behaviours;circuit-host interactions;circuits;complex interdependence;detailed kinetic module;dynamic resource partitioning;dynamics;exogenous circuits;experimental data;extended version;foreign gene overexpression;gene circuit behaviours;gene circuit modelling framework;gene circuits;growth-modulating feedback;host;host physiology;lack;large set;leading cause;mechanistic description;multilayered circuit-host coupling;multiple factors;one fundamental challenge;population structure;quantitative understanding;rational design;single-cell dynamics;spatial ecology;synthetic biology;synthetic gene networks;system-specific interactions;toggle switch across scales;training;utility | 10.1002/biot.201200085;10.1006/jmbi.2000.4327;10.1016/0022-2836(71)90336-6;10.1016/0734-9750(95)00004-A;10.1016/j.cbpa.2013.09.012;10.1016/j.cell.2004.07.009;10.1016/j.cell.2009.04.048;10.1016/j.cell.2009.10.025;10.1016/j.cell.2009.12.001;10.1016/j.cell.2012.05.044;10.1016/j.cell.2014.02.033;10.1016/j.febslet.2008.02.057;10.1016/S1097-2765(03)00266-1;10.1021/j100540a008;10.1038/35002125;10.1038/35002131;10.1038/463288a;10.1038/468889a;10.1038/msb.2013.14;10.1038/msb4100173;10.1038/nature03461;10.1038/nature10317;10.1038/nature11478;10.1038/nbt.1591;10.1038/nchembio.218;10.1038/ncomms15128;10.1038/nrg2775;10.1039/c5ib00275c;10.1073/pnas.0706115104;10.1073/pnas.0804953105;10.1073/pnas.1416533112;10.1073/pnas.1421138111;10.1099/00221287-19-3-592;10.1099/mic.0.26560-0;10.1111/j.1365-2958.2008.06229.x;10.1111/j.1462-2920.2010.02357.x;10.1126/science.1192588;10.1126/science.1206843;10.1126/science.1237435;10.1128/AAC.34.1.111;10.1128/JB.131.1.18-29.1977;10.1128/JB.131.1.7-17.1977;10.1128/jb.177.6.1497-1504.1995;10.1128/MMBR.55.2.316-333.1991;10.1146/annurev.micro.62.081307.162903;10.1186/1741-7007-4-30;10.1186/s12918-015-0188-5;[10.1038/NMETH.2926, 10.1038/nmeth.2926] | Univ Illinois | Blanchard, A E;Liao, C;Lu, T | Liao, C: Univ Illinois, Dept Bioengn, Urbana, IL 61801 USA | null | 1227034;12SDG12090025;1553649;N000141612525 | 50 | null | USA | Univ Illinois | Liao, Chen | null | BIOLOGY;ESCHERICHIA-COLI;EXPRESSION;GROWTH-RATE;IN-VIVO;PPGPP;PROTEIN-SYNTHESIS;SOURCE SHIFT-DOWN;TOGGLE SWITCH;TRANSCRIPTION INITIATION | Liao, Chen; Blanchard, Andrew E.; Lu, Ting; | null | Univ Illinois, Carl R Woese Inst Genom Biol, Urbana, IL 61801 USA;Univ Illinois, Ctr Biophys & Quantitat Biol, Urbana, IL 61801 USA;Univ Illinois, Dept Bioengn, Urbana, IL 61801 USA;Univ Illinois, Dept Phys, Urbana, IL 61801 USA | Univ Illinois, Carl R Woese Inst Genom Biol, Urbana, IL 61801 USA;Univ Illinois, Ctr Biophys & Quantitat Biol, Urbana, IL 61801 USA;Univ Illinois, Dept Bioengn, Urbana, IL 61801 USA;Univ Illinois, Dept Phys, Urbana, IL 61801 USA | null | null | 12 | 1958;1971;1975;1977;1990;1991;1995;2000;2001;2003;2004;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017 | 54 | Univ Illinois, Carl R Woese Inst Genom Biol, Urbana, IL 61801 USA;Univ Illinois, Ctr Biophys & Quantitat Biol, Urbana, IL 61801 USA;Univ Illinois, Dept Bioengn, Urbana, IL 61801 USA;Univ Illinois, Dept Phys, Urbana, IL 61801 USA | NAT. MICROBIOL | Lu, Ting | NATURE PUBLISHING GROUP | ,;a;able;accurately;across;advances;also;altered;among;an;and;applied;arises;behaviours;benefits;bidirectional;biology;both;but;by;capture;cause;challenge;circuit;circuit-host;circuits;coarse-grained;complex;concerning;consists;coupling;data;demonstrate;describe;description;design;detailed;dynamic;dynamics;ecology;engineered;examine;exogenous;experimental;explicitly;extended;factors;feedback;following;foreign;framework;from;fundamental;further;gene;generic;growth-modulating;here;host;in;including;integrates;interactions;interdependence;involves;is;its;kinetic;lack;large;leading;mechanistic;modelling;module;multilayered;multiple;networks;of;one;our;overexpression;partitioning;physiology;population;predict;present;qualitatively;quantitative;rational;resource;revealed;scales;set;showed;single-cell;spatial;structure;switch;synthetic;system-specific;systematically;that;the;their;this;through;to;toggle;tools;training;understanding;using;utility;version;was;we;which;whose;with;work | Univ Illinois | One fundamental challenge in synthetic biology is the lack of quantitative tools that accurately describe and predict the behaviours of engineered gene circuits. This challenge arises from multiple factors, among which the complex interdependence of circuits and their host is a leading cause. Here we present a gene circuit modelling framework that explicitly integrates circuit behaviours with host physiology through bidirectional circuit-host coupling. The framework consists of a coarse-grained but mechanistic description of host physiology that involves dynamic resource partitioning, multilayered circuit-host coupling including both generic and system-specific interactions, and a detailed kinetic module of exogenous circuits. We showed that, following training, the framework was able to capture and predict a large set of experimental data concerning the host and its foreign gene overexpression. To demonstrate its utility, we applied the framework to examine a growth-modulating feedback circuit whose dynamics is qualitatively altered by circuit-host interactions. Using an extended version of the framework, we further systematically revealed the behaviours of a toggle switch across scales from single-cell dynamics to population structure and to spatial ecology. This work advances our quantitative understanding of gene circuit behaviours and also benefits the rational design of synthetic gene networks. | null | BIOLOGY;ESCHERICHIA-COLI;EXPRESSION;GROWTH-RATE;IN-VIVO;PPGPP;PROTEIN-SYNTHESIS;SOURCE SHIFT-DOWN;TOGGLE SWITCH;TRANSCRIPTION INITIATION | 1 | null | null | 9 | ESCHERICHIA-COLI;BIOLOGY;EXPRESSION;GROWTH-RATE;IN-VIVO;PPGPP;PROTEIN-SYNTHESIS;SOURCE SHIFT-DOWN;toggle switch;TRANSCRIPTION INITIATION | WOS:000417976600017 | Univ Illinois, Urbana, IL USA | USA | 2,017 | null | 0000-0001-8474-1196 | null | null | English | null | ANNU REV MICROBIOL;ANTIMICROB AGENTS CH;BIOTECHNOL ADV;BIOTECHNOL J;BMC BIOL;BMC SYST BIOL;CELL;CURR OPIN CHEM BIOL;ECOSAL PLUS;ENVIRON MICROBIOL;FEBS LETT;INTEGR BIOL-UK;J BACTERIOL;J BIOL CHEM;J GEN MICROBIOL;J MOL BIOL;J PHYS CHEM-US;MICROBIOL REV;MICROBIOL-SGM;MOL CELL;MOL MICROBIOL;MOL SYST BIOL;NAT BIOTECHNOL;NAT CHEM BIOL;NAT COMMUN;NAT METHODS;NAT REV GENET;NATURE;P NATL ACAD SCI USA;SCIENCE | Blanchard, Andrew E;Liao, Chen;Lu, Ting | 2024-03-11
ER | Anderson, J C;Arkin, A P;Barker, M M;Basu, S;Blanchard, A E;Bollenbach, T;Bremer H.;Brophy, J A N;Cardinale, S;Chopra, I;Cox, R A;Deris, J B;Dong, H J;Elowitz, M;Elowitz, M B;Friesen, J D;Gardner, T S;Gerosa, L;Gillespie, D T;Glick, B R;Hartl, F U;Johnsen, K;Karpinets, T V;Karr, J R;Khalil, A S;Klumpp, S;Koch, A L;Kwok, R;Li, G W;Lu, T;Lu, T K;Maitra, A;Marr, A G;Molin, S;Murray, H D;Paul, B J;Peralta-Yahya, P P;Potrykus, K;Ruder, W C;Schaechter, M;Scott, M;Tabor, J J;Tan, C;Tozaki, H;Traxler, M F;Venturelli, O S;Weisse, A Y;Zhang, C | FP9NU | Urbana, IL USA;Urbana, IL USA. | 61 | null | 1 | null | 28,947,816 | Blanchard, Andrew E;Liao, Chen;Lu, Ting | NAT MICROBIOL | Urbana, IL USA |
Cambray, G;Cardinale, S | 10.1186/s12918-017-0494-1 | 112 | CAMPUS, 4 CRINAN ST, LONDON N1 9XW, ENGLAND | 35gq3k23o63156o5v1kx1k06f1e422m4i4s | Genome-wide analysis of <i>E</i>. <i>coli</i> cell-gene interactions | Univ Calif Berkeley | null | Cardinale, S (corresponding author), Tech Univ Denmark, Novo Nordisk Fdn, Ctr Biosustainabil, Bldg 220, DK-2800 Lyngby, Denmark.;Cardinale, S (corresponding author), Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA. | null | Cambray, G;Cardinale, S | Mathematical & Computational Biology | National Science Foundation as part of the Synthetic Biology Engineering Research Center [04570/0540879]; Novo Nordisk Foundation (NNF) [11355-444]; Human Frontier Science Program [LT000873/2011-L] | WOS | Cardinale, S | Tech Univ Denmark, Lyngby, Denmark;Univ Calif Berkeley, Berkeley, CA USA;Univ Montpellier, Montpellier, France | 11 | <i>E</i>;Analysis;cell-gene;genome-wide;i>coli</i>;interactions;of | 3 | Cambray, Guillaume;Cardinale, Stefano | BMC | Tech Univ Denmark, Novo Nordisk Fdn, Ctr Biosustainabil, Bldg 220, DK-2800 Lyngby, Denmark;Univ Calif Berkeley, Calif Inst Quantitat Biosci, Berkeley, CA 94720 USA;Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA;Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA.; Cardinale, S (corresponding author), Tech Univ Denmark, Novo Nordisk Fdn, Ctr Biosustainabil, Bldg 220, DK-2800 Lyngby, Denmark;Univ Montpellier, INRA, DGIMI, Montpellier, France | Article | Tech Univ Denmark;Univ Calif Berkeley | LONDON | null | null | Tech Univ Denmark;Univ Calif Berkeley;Univ Montpellier | Human Frontier Science Program;National Science Foundation as part of the Synthetic Biology Engineering Research Center;Novo Nordisk Foundation (NNF) | Cardinale, S (corresponding author), Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA.; Cardinale, S (corresponding author), Tech Univ Denmark, Novo Nordisk Fdn, Ctr Biosustainabil, Bldg 220, DK-2800 Lyngby, Denmark. | null | Cambray, G;Cardinale, S | 8 | 4 | 416,045,700,001 | Human Frontier Science Program [LT000873/2011-L];National Science Foundation as part of the Synthetic Biology Engineering Research Center [04570/0540879];Novo Nordisk Foundation (NNF) [11355-444] | Denmark;France;USA | BMC SYSTEMS BIOLOGY | Denmark;USA.; | null | null | Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA | null | Cambray, G;Cardinale, S | NOV 23 | cardinale.stefano@gmail.com | <i>E</i>;genome-wide analysis;i>coli</i> cell-gene interactions | 2 | J | Mathematical & Computational Biology | 3822 single-gene deletion strains;<i>E</i>;background;biological circuits;BIOLOGY;Biosynthesis (DB) system led;cell division;Cell growth;cell size;cellular endogenous systems;cellular functions;cellular size;Cellular systems;conclusions;contrast;development;disruptions;distinct primary influence;division;dual fluorescent reporter gene;dual impact;effect;Energy;ESCHERICHIA-COLI;existence;expression;expression-specific;FEEDBACK;feedbacks;foundations;functions;gene disruptions proximally affect one component;gene expression;gene-specific effects;generic Size-Expression interaction;genes;genome-wide analysis;growth;high-expression phenotype;high-throughput screening methods;i>coli</i> cell-gene interactions;KEIO collection;KEIO gene knockouts;large-cell;low-expression phenotypes;Membrane;model prokaryote Escherichia coli;Motility (MM) system;number;perturbations;physiological systems;Positive feedback;predictable genetic parts;protein synthesis;pursuit;putting;recent years;regression analyses;reliability;results;ribosomal content;Ribosome (EPR) system;ribosome function;single cells via flow cytometry;Size-Expression interaction;Size-Expression map;small-cell;smaller cells;standardization;study;synthetic;synthetic biology;Synthetic gene expression;synthetic genes;systematic perturbations;systematic understanding;three systems;tight control;TRANSCRIPTION;whole-cell models;widespread across cell systems | Cardinale, S | BIOLOGY;Cell growth;Cellular systems;ESCHERICHIA-COLI;EXPRESSION;KEIO gene knockouts;Positive feedback;Synthetic gene expression;TRANSCRIPTION | null | [Cardinale, S.] Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA. [Cardinale, S.] Tech Univ Denmark, Novo Nordisk Fdn, Ctr Biosustainabil, Bldg 220, DK-2800 Lyngby, Denmark. [Cambray, G.] Univ Calif Berkeley, Calif Inst Quantitat Biosci, Berkeley, CA 94720 USA. [Cambray, G.] Univ Montpellier, INRA, DGIMI, Montpellier, France. | This work was funded by the National Science Foundation as part of the Synthetic Biology Engineering Research Center grant number 04570/0540879. SC also acknowledges funding from the Novo Nordisk Foundation (NNF) grant no. 11355-444 "Biobase". GC acknowledges funding by the Human Frontier Science Program (LT000873/2011-L). | 3822 single-gene deletion strains;background;biological circuits;Biosynthesis (DB) system led;cell division;cell growth;cell size;cellular endogenous systems;cellular functions;cellular size;conclusions;contrast;development;disruptions;distinct primary influence;division;dual fluorescent reporter gene;dual impact;effect;Energy;existence;expression;expression-specific;Feedback;feedbacks;foundations;functions;gene disruptions proximally affect one component;gene expression;gene-specific effects;generic Size-Expression interaction;genes;genome-wide analysis;growth;high-expression phenotype;high-throughput screening methods;KEIO collection;large-cell;low-expression phenotypes;Membrane;model prokaryote Escherichia coli;Motility (MM) system;number;perturbations;physiological systems;positive feedback;predictable genetic parts;protein synthesis;pursuit;putting;recent years;regression analyses;reliability;results;ribosomal content;Ribosome (EPR) system;ribosome function;single cells via flow cytometry;Size-Expression interaction;Size-Expression map;small-cell;smaller cells;standardization;study;synthetic;synthetic biology;synthetic genes;systematic perturbations;systematic understanding;three systems;tight control;whole-cell models;widespread across cell systems | 10.1002/biot.201200085;10.1016/j.cbpa.2013.09.012;10.1016/j.cell.2009.12.001;10.1016/j.celrep.2013.06.023;10.1016/j.celrep.2017.07.015;10.1016/j.cels.2016.04.004;10.1016/j.copbio.2014.01.001;10.1016/j.molcel.2016.11.007;10.1016/j.ymben.2013.01.006;10.1038/msb4100050;10.1038/nbt.3177;10.1038/nprot.2008.211;10.1093/bioinformatics/btr465;10.1128/JB.00259-17;10.1128/JB.130.1.212-222.1977;10.1128/jb.177.16.4696-4702.1995;10.1146/annurev.genet.38.072902.091347;10.1186/1754-1611-4-12;10.1186/1754-1611-7-22;10.15252/msb.20145379;[10.1038/NMETH.2404, 10.1038/nmeth.2404] | Univ Calif Berkeley | Cambray, G;Cardinale, S | Cardinale, S: Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA | Cambray, Guillaume;Cardinale, Stefano | 04570/0540879;11355-444;LT000873/2011-L | 28 | null | USA | Tech Univ Denmark;Univ Calif Berkeley;Univ Montpellier | Cardinale, S | Green Published, gold, Green Submitted | BIOLOGY;ESCHERICHIA-COLI;EXPRESSION;TRANSCRIPTION | Cardinale, S.; Cambray, G.; | null | Tech Univ Denmark, Novo Nordisk Fdn, Ctr Biosustainabil, Bldg 220, DK-2800 Lyngby, Denmark;Univ Calif Berkeley, Calif Inst Quantitat Biosci, Berkeley, CA 94720 USA;Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA;Univ Montpellier, INRA, DGIMI, Montpellier, France | Tech Univ Denmark, Novo Nordisk Fdn, Ctr Biosustainabil, Bldg 220, DK-2800 Lyngby, Denmark;Univ Calif Berkeley, Calif Inst Quantitat Biosci, Berkeley, CA 94720 USA;Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA;Univ Montpellier, INRA, DGIMI, Montpellier, France | 1752-0509 | Cell growth;Cellular systems;KEIO gene knockouts;Positive feedback;Synthetic gene expression | null | 1977;1995;1996;1998;2000;2003;2004;2006;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017 | 2 | Tech Univ Denmark, Novo Nordisk Fdn, Ctr Biosustainabil, Bldg 220, DK-2800 Lyngby, Denmark;Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA | BMC Syst. Biol. | Cambray, G | BMC | (DB);(EPR);(MM);,;3822;:;a;achieved;across;advances;affect;affected;all;an;analyses;analysis;and;aspects;associated;background;between;biological;biology;biosynthesis;both;broadly;by;caused;cell;cells;cellular;circuits;coli;collection;component;comprised;conclusions;construct;content;contrast;control;cytometry;deleted;deletion;describe;design;development;discriminate;disruptions;distinct;division;dual;each;effect;effects;elucidate;endogenous;energy;Escherichia;even;existence;expression;expression-specific;feedback;feedbacks;finally;flow;fluorescent;for;forward;found;foundations;function;functions;gene;gene-specific;generic;genes;genetic;genome-wide;growth;has;high-expression;high-throughput;how;however;impact;in;indirectly;influence;inserting;interaction;interacts;into;is;it;KEIO;large-cell;led;low-expression;map;mapped;measured;Membrane;methods;model;models;modulate;more;most;motility;not;number;of;on;one;onto;parts;perturbations;phenotype;phenotypes;physiological;positive;possible;predict;predictable;predominantly;presents;primary;prokaryote;propagates;protein;provides;proximally;pursuit;putting;quantified;recent;regression;reliability;reliably;reporter;results;ribosomal;Ribosome;screening;single;single-gene;size;Size-Expression;small-cell;smaller;specifically;standardization;still;strains;study;swarming;synthesis;synthetic;system;systematic;systems;that;the;therefore;this;though;three;through;tight;to;ultimately;understanding;used;via;was;we;were;whole-cell;widespread;with;work;years | Tech Univ Denmark;Univ Calif Berkeley | Background: The pursuit of standardization and reliability in synthetic biology has achieved, in recent years, a number of advances in the design of more predictable genetic parts for biological circuits. However, even with the development of high-throughput screening methods and whole-cell models, it is still not possible to predict reliably how a synthetic genetic construct interacts with all cellular endogenous systems. This study presents a genome-wide analysis of how the expression of synthetic genes is affected by systematic perturbations of cellular functions. We found that most perturbations modulate expression indirectly through an effect on cell size, putting forward the existence of a generic Size-Expression interaction in the model prokaryote Escherichia coli. Results: The Size-Expression interaction was quantified by inserting a dual fluorescent reporter gene construct into each of the 3822 single-gene deletion strains comprised in the KEIO collection. Cellular size was measured for single cells via flow cytometry. Regression analyses were used to discriminate between expression-specific and gene-specific effects. Functions of the deleted genes broadly mapped onto three systems with distinct primary influence on the Size-Expression map. Perturbations in the Division and Biosynthesis (DB) system led to a large-cell and high-expression phenotype. In contrast, disruptions of the Membrane and Motility (MM) system caused small-cell and low-expression phenotypes. The Energy, Protein synthesis and Ribosome (EPR) system was predominantly associated with smaller cells and positive feedback on ribosome function. Conclusions: Feedback between cell growth and gene expression is widespread across cell systems. Even though most gene disruptions proximally affect one component of the Size-Expression interaction, the effect therefore ultimately propagates to both. More specifically, we describe the dual impact of growth on cell size and gene expression through cell division and ribosomal content. Finally, we elucidate aspects of the tight control between swarming, gene expression and cell growth. This work provides foundations for a systematic understanding of feedbacks between genetic and physiological systems. | A-9476-2015;F-4024-2014 | BIOLOGY;ESCHERICHIA-COLI;EXPRESSION;TRANSCRIPTION | 1 | null | Cell growth;Cellular systems;KEIO gene knockouts;Positive feedback;Synthetic gene expression | 8 | ESCHERICHIA-COLI;BIOLOGY;CELL-GROWTH;Cellular systems;EXPRESSION;KEIO gene knockouts;Positive feedback;Synthetic gene expression;TRANSCRIPTION | WOS:000416045700001 | Tech Univ Denmark, Lyngby, Denmark;Univ Calif Berkeley, Berkeley, CA USA;Univ Montpellier, Montpellier, France | Denmark;France;USA | 2,017 | null | 0000-0003-0087-2469;0000-0003-4357-9246 | null | null | English | null | ANNU REV GENET;APPL ENVIRON MICROB;BIOINFORMATICS;BioRxiv;BIOTECHNOL J;CELL;CELL REP;CELL SYST;CURR OPIN BIOTECH;CURR OPIN CHEM BIOL;ECOSAL PLUS;J BACTERIOL;J Biol Eng;METAB ENG;MOL CELL;MOL SYST BIOL;NAT BIOTECHNOL;NAT METHODS;NAT PROTOC;PRACTICAL APPROACH F;PRACTICAL SH CYTOMET | Cambray, G;Cardinale, S | 2024-03-11
ER | [Anonymous];Arkin A. P.;Arkin, A P;Baba, T;Brunk, E;Cardinale, S;Castle S.;Dennis, P P;Frumkin, I;Hintsche, M;Huang, D W;Klumpp, S;Mutalik, V K;Ormerod M.;Paul, B J;Pruss, B M;Prüss, B M;Robertson, B R;Scott, M;Shin, S;Sleight Sean, C;Wanner, B L;Woodruff, L B A;Wu, C H;Zeitoun, R I | FN5KG | Berkeley, CA USA.;Lyngby, Denmark | 3 | null | 3 | null | 29,169,395 | Cambray, G;Cardinale, S | BMC SYST BIOL | Berkeley, CA USA;Lyngby, Denmark;Montpellier, France |
Gemperlein, K;Hoffmann, M;Huo, L J;Müller, R;Petzke, L;Pilak, P;Wenzel, S C | 10.1016/j.ymben.2017.09.009 | null | 525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA | 2bj6l4j3l595p29201d332w6240t14256kr3z | Synthetic biology approaches to establish a heterologous production system for coronatines | Univ Saarland | null | Wenzel, SC (corresponding author), Saarland Univ, Dept Pharmaceut Biotechnol, D-66123 Saarbrucken, Germany.;Wenzel, SC (corresponding author), Saarland Univ, Helmholtz Ctr Infect Res, Helmholtz Inst Pharmaceut Res Saarland, Dept Microbial Nat Prod, D-66123 Saarbrucken, Germany. | null | Gemperlein, Katja;Hoffmann, Michael;Huo, Liujie;Mueller, Rolf;Petzke, Lutz;Pilak, Patrick;Wenzel, Silke C | Biotechnology & Applied Microbiology | BASF SE | WOS | Wenzel, S C | BASF SE, Ludwigshafen, Germany;Saarland Univ, Saarbrucken, Germany;Shandong Univ Helmholtz Joint Inst Biotechnol, Qingdao, Peoples R China;Tech Univ Munich, Weihenstephan, Germany | 44 | a;approaches;biology;coronatines;Establish;for;Heterologous;production;synthetic;system;to | 2 | Huo, Liujie;Muller, Rolf | ACADEMIC PRESS INC ELSEVIER SCIENCE | BASF SE, D-67056 Ludwigshafen, Germany;Saarland Univ, Dept Pharmaceut Biotechnol, D-66123 Saarbrucken, Germany;Saarland Univ, Helmholtz Ctr Infect Res, Helmholtz Inst Pharmaceut Res Saarland, Dept Microbial Nat Prod, D-66123 Saarbrucken, Germany;Saarland Univ, Helmholtz Ctr Infect Res, Helmholtz Inst Pharmaceut Res Saarland, Dept Microbial Nat Prod, D-66123 Saarbrucken, Germany.; Wenzel, SC (corresponding author), Saarland Univ, Dept Pharmaceut Biotechnol, D-66123 Saarbrucken, Germany;Shandong Univ Helmholtz Joint Inst Biotechnol, Qingdao, Peoples R China;Tech Univ Munich, Chair Biol Chem, D-85354 Freising Weihenstephan, Weihenstephan, Germany;Tech Univ Munich, Munich Ctr Integrated Prot Sci CiPSM, D-85354 Freising Weihenstephan, Weihenstephan, Germany | Article | Univ Saarland | SAN DIEGO | null | null | BASF SE;Saarland Univ;Shandong Univ Helmholtz Joint Inst Biotechnol;Tech Univ Munich | BASF SE | Wenzel, SC (corresponding author), Saarland Univ, Helmholtz Ctr Infect Res, Helmholtz Inst Pharmaceut Res Saarland, Dept Microbial Nat Prod, D-66123 Saarbrucken, Germany.; Wenzel, SC (corresponding author), Saarland Univ, Dept Pharmaceut Biotechnol, D-66123 Saarbrucken, Germany. | 222 | Gemperlein, Katja;Hoffmann, Michael;Huo, Liujie;Mueller, Rolf;Petzke, Lutz;Pilak, Patrick;Wenzel, Silke C | 20 | 6 | 416,513,600,023 | BASF SE | China;Germany | METABOLIC ENGINEERING | Germany | null | null | Saarland Univ, Helmholtz Ctr Infect Res, Helmholtz Inst Pharmaceut Res Saarland, Dept Microbial Nat Prod, D-66123 Saarbrucken, Germany | 1096-7176 | Gemperlein, K;Hoffmann, M;Huo, L J;Müller, R;Petzke, L;Pilak, P;Wenzel, S C | NOV | silke.wenzel@helmholtz-hzi.de | coronatines;heterologous production system;synthetic biology approaches | 7 | J | Biotechnology & Applied Microbiology | >90 mg/l;additional engineering;amide bond;applied constructional design facilitated versatile pathway modifications;ARABIDOPSIS-THALIANA;ASSEMBLY-LINE;bicyclic polyketide moiety;BIOSYNTHETIC GENE-CLUSTER;CARRIER PROTEIN DOMAINS;CFA;CFA production platforms;COMPLETE GENOME SEQUENCE;constitutive PrpsH promoter;COR;COR biosynthesis;COR biosynthetic gene cluster;Coronafacic acid;coronafacic acid (CFA);coronamic acid (CMA);Coronatine;coronatine (COR);coronatines;derivatives;development;engineering;expression;expression strain;expression vector features;function;gene cluster composition production profiles;genetic information;heterologous COR;heterologous expression;heterologous production system;host;IMPACT;led;modifications;multiple virulence activities;native producer P. syringae pv;P. putida KT2440;p15Aori-based transposon backbone;phytotoxin;PHYTOTOXIN CORONATINE;plant stress hormone jasmonoyl-L-isoleucine;Polyketide synthase;production;promising CFA production yields;Pseudomonads;Pseudomonas syringae;PSEUDOMONAS-PUTIDA KT2440;PV. TOMATO DC3000;reconstituted;selected pathway proteins;several pathovars;studies;synthetic biology approaches;synthetic DNA fragments;Synthetic gene cluster;target compounds;tomato DC3000;unusual ethylcyclopropyl amino acid moiety;use;valuable information;via | Gemperlein, K | ARABIDOPSIS-THALIANA;ASSEMBLY-LINE;BIOSYNTHETIC GENE-CLUSTER;CARRIER PROTEIN DOMAINS;COMPLETE GENOME SEQUENCE;Coronafacic acid;Coronatine;heterologous expression;PHYTOTOXIN CORONATINE;Polyketide synthase;Pseudomonads;PSEUDOMONAS-PUTIDA KT2440;PV. TOMATO DC3000;Synthetic gene cluster | 213 | [Gemperlein, Katja; Hoffmann, Michael; Mueller, Rolf; Wenzel, Silke C.] Saarland Univ, Helmholtz Ctr Infect Res, Helmholtz Inst Pharmaceut Res Saarland, Dept Microbial Nat Prod, D-66123 Saarbrucken, Germany. [Gemperlein, Katja; Hoffmann, Michael; Mueller, Rolf; Wenzel, Silke C.] Saarland Univ, Dept Pharmaceut Biotechnol, D-66123 Saarbrucken, Germany. [Huo, Liujie] Shandong Univ Helmholtz Joint Inst Biotechnol, Qingdao, Peoples R China. [Pilak, Patrick] Tech Univ Munich, Munich Ctr Integrated Prot Sci CiPSM, D-85354 Freising Weihenstephan, Weihenstephan, Germany. [Pilak, Patrick] Tech Univ Munich, Chair Biol Chem, D-85354 Freising Weihenstephan, Weihenstephan, Germany. [Petzke, Lutz] BASF SE, D-67056 Ludwigshafen, Germany. | We thank Nestor Zaburannyi for analysis of Illumina sequence data. We also thank Hubert S. Bernauer and Gregor Zipf from ATG:biosynthetics GmbH for the competent service regarding COR gene cluster design and DNA synthesis. This work was generously funded by BASF SE, we gratefully acknowledge all members of the project consortium for constant support of this study. | >90 mg/l;additional engineering;amide bond;applied constructional design facilitated versatile pathway modifications;bicyclic polyketide moiety;CFA;CFA production platforms;constitutive PrpsH promoter;COR;COR biosynthesis;COR biosynthetic gene cluster;coronafacic acid (CFA);coronamic acid (CMA);coronatine (COR);derivatives;development;engineering;expression;expression strain;expression vector features;function;gene cluster composition production profiles;genetic information;heterologous COR;host;impact;led;modifications;multiple virulence activities;native producer P. syringae pv;P. putida KT2440;p15Aori-based transposon backbone;phytotoxin;plant stress hormone jasmonoyl-L-isoleucine;production;promising CFA production yields;Pseudomonas syringae;reconstituted;selected pathway proteins;several pathovars;studies;synthetic DNA fragments;target compounds;tomato DC3000;unusual ethylcyclopropyl amino acid moiety;use;valuable information;via | 10.1006/plas.1997.1294;10.1007/s00203-005-0059-3;10.1007/s00253-004-1836-7;10.1007/s00253-014-5952-8;10.1016/0048-4059(82)90026-1;10.1016/0378-1119(94)00661-B;10.1016/j.cell.2006.06.054;10.1016/j.chembiol.2004.12.012;10.1016/j.chembiol.2006.09.014;10.1016/j.chembiol.2012.01.007;10.1016/j.micres.2012.09.006;10.1016/j.pbi.2008.05.004;10.1016/j.ymben.2015.11.001;10.1016/S0031-9422(00)80702-5;10.1016/S0031-9422(00)81049-3;10.1016/S0031-9422(00)85028-1;10.1016/S0040-4020(98)01002-3;10.1016/S0378-1119(01)00476-0;10.1021/bi061930j;10.1021/bi700243h;10.1021/cr0503097;10.1021/ja00444a067;10.1021/ja8077945;10.1021/ja9536330;10.1021/sb3000657;10.1038/nature03797;10.1038/nchembio.161;10.1038/nchembio.734;10.1046/j.1365-2958.1999.01249.x;10.1046/j.1462-2920.2002.00366.x;10.1071/BI9700585;10.1073/pnas.0409450102;10.1073/pnas.1731982100;10.1073/pnas.95.26.15469;10.1073/pnas.96.4.1645;10.1093/nar/gkn499;10.1094/MPMI-8-0165;10.1094/MPMI.2004.17.2.162;10.1099/00221287-146-10-2447;10.1099/mic.0.2008/018820-0;10.1101/PDB.PROT4022;10.1104/pp.114.239061;10.1111/J.1364-3703.2005.00311.X;10.1111/j.1462-2920.2011.02430.x;10.1111/j.1574-6968.1997.tb12625.x;10.1111/j.1751-7915.2009.00107.x;10.1128/AEM.01503-06;10.1128/AEM.02315-08;10.1128/JB.01352-12;10.1128/JB.134.3.1141-1156.1978;10.1128/jb.172.7.3859-3867.1990;10.1128/JB.186.1.35-42.2004;10.1128/MMBR.63.2.266-292.1999;10.1186/1471-2091-10-26 | Saarland Univ | Gemperlein, K;Hoffmann, M;Huo, L J;Müller, R;Petzke, L;Pilak, P;Wenzel, S C | Gemperlein, K: Saarland Univ, Helmholtz Ctr Infect Res, Helmholtz Inst Pharmaceut Res Saarland, Dept Microbial Nat Prod, D-66123 Saarbrucken, Germany | Huo, Liujie;Muller, Rolf | null | 56 | null | Germany | BASF SE;Saarland Univ;Shandong Univ Helmholtz Joint Inst Biotechnol;Tech Univ Munich | Gemperlein, Katja | null | ARABIDOPSIS-THALIANA;ASSEMBLY-LINE;BIOSYNTHETIC GENE-CLUSTER;CARRIER PROTEIN DOMAINS;COMPLETE GENOME SEQUENCE;CORONAFACIC ACID;PHYTOTOXIN CORONATINE;POLYKETIDE SYNTHASE;PSEUDOMONAS-PUTIDA KT2440;PV. TOMATO DC3000 | Gemperlein, Katja; Hoffmann, Michael; Huo, Liujie; Pilak, Patrick; Petzke, Lutz; Mueller, Rolf; Wenzel, Silke C.; | null | BASF SE, D-67056 Ludwigshafen, Germany;Saarland Univ, Dept Pharmaceut Biotechnol, D-66123 Saarbrucken, Germany;Saarland Univ, Helmholtz Ctr Infect Res, Helmholtz Inst Pharmaceut Res Saarland, Dept Microbial Nat Prod, D-66123 Saarbrucken, Germany;Shandong Univ Helmholtz Joint Inst Biotechnol, Qingdao, Peoples R China;Tech Univ Munich, Chair Biol Chem, D-85354 Freising Weihenstephan, Weihenstephan, Germany;Tech Univ Munich, Munich Ctr Integrated Prot Sci CiPSM, D-85354 Freising Weihenstephan, Weihenstephan, Germany | BASF SE, D-67056 Ludwigshafen, Germany;Saarland Univ, Dept Pharmaceut Biotechnol, D-66123 Saarbrucken, Germany;Saarland Univ, Helmholtz Ctr Infect Res, Helmholtz Inst Pharmaceut Res Saarland, Dept Microbial Nat Prod, D-66123 Saarbrucken, Germany;Shandong Univ Helmholtz Joint Inst Biotechnol, Qingdao, Peoples R China;Tech Univ Munich, Chair Biol Chem, D-85354 Freising Weihenstephan, Weihenstephan, Germany;Tech Univ Munich, Munich Ctr Integrated Prot Sci CiPSM, D-85354 Freising Weihenstephan, Weihenstephan, Germany | 1096-7184 | Coronafacic acid;Coronatine;heterologous expression;Polyketide synthase;Pseudomonads;Synthetic gene cluster | null | 1970;1977;1978;1982;1984;1985;1986;1990;1995;1996;1997;1998;1999;2000;2001;2002;2003;2004;2005;2006;2007;2008;2009;2011;2012;2013;2014;2016 | 13 | Saarland Univ, Dept Pharmaceut Biotechnol, D-66123 Saarbrucken, Germany;Saarland Univ, Helmholtz Ctr Infect Res, Helmholtz Inst Pharmaceut Res Saarland, Dept Microbial Nat Prod, D-66123 Saarbrucken, Germany | Metab. Eng. | Wenzel, Silke C | ACADEMIC PRESS INC ELSEVIER SCIENCE | (CFA);(CMA);(COR);,;>90;a;about;acid;activities;additional;aimed;amide;amino;an;and;applied;as;at;backbone;based;bicyclic;biosynthesis;biosynthetic;bond;by;CFA;cluster;composition;compounds;consists;constitutive;constructional;constructs;COR;coronafacic;coronamic;coronatine;DC3000;derivatives;design;designed;development;directed;DNA;engineering;establishing;ethylcyclopropyl;evaluated;expression;facilitated;features;for;fragments;from;function;gene;generation;genetic;heterologous;hormone;host;impact;in;including;information;is;it;its;jasmonoyl-L-isoleucine;KT2440;led;linked;mediates;mg/L;mimicking;modifications;moiety;multiple;native;obtained;of;on;our;P.;p15Aori-based;pathovars;pathway;phytotoxin;plant;platforms;polyketide;produced;producer;production;profiles;promising;promoter;proteins;PrpsH;Pseudomonas;putida;pv;reconstituted;represents;selected;several;strain;stress;structurally;studies;synthetic;syringae;target;the;to;tomato;towards;transposon;unusual;use;using;valuable;various;vector;versatile;via;virulence;was;we;were;which;with;yields | Saarland Univ | Coronatine (COR) represents a phytotoxin produced by several pathovars of Pseudomonas syringae. It mediates multiple virulence activities by mimicking the plant stress hormone jasmonoyl-L-isoleucine. Structurally, COR consists of a bicyclic polyketide moiety, coronafacic acid (CFA), which is linked via an amide bond to an unusual ethylcyclopropyl amino acid moiety, coronamic acid (CMA). In our studies, we aimed at establishing and engineering of heterologous COR and CFA production platforms using P. putida KT2440 as host. Based on genetic information of the native producer P. syringae pv. tomato DC3000 a COR biosynthetic gene cluster was designed and reconstituted from synthetic DNA fragments. The applied constructional design facilitated versatile pathway modifications and the generation of various expression constructs, which were evaluated for the production of CFA, COR and its derivatives. By modifications of the gene cluster composition production profiles were directed towards target compounds and valuable information about the function and impact of selected pathway proteins on COR biosynthesis were obtained. Additional engineering of expression vector features, including the use of the constitutive PrpsH promoter and a p15Aori-based transposon backbone, led to the development of an expression strain with promising CFA production yields of >90 mg/l. | B-1559-2008;GSN-6252-2022;L-6090-2019 | ARABIDOPSIS-THALIANA;ASSEMBLY-LINE;BIOSYNTHETIC GENE-CLUSTER;CARRIER PROTEIN DOMAINS;COMPLETE GENOME SEQUENCE;CORONAFACIC ACID;PHYTOTOXIN CORONATINE;POLYKETIDE SYNTHASE;PSEUDOMONAS-PUTIDA KT2440;PV. TOMATO DC3000 | 1 | null | Coronafacic acid;Coronatine;heterologous expression;Polyketide synthase;Pseudomonads;Synthetic gene cluster | 10 | ARABIDOPSIS-THALIANA;ASSEMBLY-LINE;BIOSYNTHETIC GENE-CLUSTER;CARRIER PROTEIN DOMAINS;COMPLETE GENOME SEQUENCE;Coronafacic acid;Coronatine;heterologous expression;PHYTOTOXIN CORONATINE;Polyketide synthase;Pseudomonads;PSEUDOMONAS-PUTIDA KT2440;PV. TOMATO DC3000;Synthetic gene cluster | WOS:000416513600023 | BASF SE, Ludwigshafen, Germany;Saarland Univ, Saarbrucken, Germany;Shandong Univ Helmholtz Joint Inst Biotechnol, Qingdao, Peoples R China;Tech Univ Munich, Weihenstephan, Germany | China;Germany | 2,017 | null | 0000-0002-1042-5665;0000-0002-1406-8466 | null | null | English | null | ACS SYNTH BIOL;APPL ENVIRON MICROB;APPL MICROBIOL BIOT;ARCH MICROBIOL;AUST J BIOL SCI;BIOCHEMISTRY-US;BMC BIOCHEM;CELL;CHEM BIOL;CHEM REV;CURR OPIN PLANT BIOL;ENVIRON MICROBIOL;FEMS MICROBIOL LETT;GENE;J AM CHEM SOC;J BACTERIOL;J GEN MICROBIOL;J MOL MICROB BIOTECH;METAB ENG;MICROB BIOTECHNOL;MICROBIOL MOL BIOL R;MICROBIOL RES;MICROBIOL-SGM;MOL CLONING LAB MANU;MOL MICROBIOL;MOL PLANT MICROBE IN;MOL PLANT PATHOL;NAT CHEM BIOL;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PHYSIOL PLANT PATHOL;PHYTOCHEMISTRY;PLANT PHYSIOL;PLASMID;TETRAHEDRON | Gemperlein, Katja;Hoffmann, Michael;Huo, Liujie;Mueller, Rolf;Petzke, Lutz;Pilak, Patrick;Wenzel, Silke C | 2024-03-11
ER | Bakke, I;Bender, C L;Berg, L;Blatny, J M;Braun, Y;Brooks, D M;Buell, C R;Chai, Y;Chang, A C Y;Couch, R;Cui, J;Dayan, F E;Dudnik, A;Durland, R H;Fischbach, M A;Fonseca, S;Frank, S;Fu, J;Gemperlein, K;Gross, F;Ichihara, A;Jiralerspong, S;Katsir, L;Keane, P J;Kelly, W L;Kotowska, M;Liyanage, H;Loeschcke, A;Marqués, S;Melotto, M;Mitchell, R E;Mittal, S;Nelson, K E;Parry, R J;Patel, J;Perlova, O;Peñaloza-Vázquez, A;Quade, N;Ramel, C;Rangaswamy, V;Rubin, E J;Sambrook J.;Smirnova, A V;Strieter, E R;Vaillancourt, F H;Wenzel, S C;Worley, J N | FO1IX | Saarbrucken, Germany;Saarbrucken, Germany. | 16 | null | 4 | null | 28,951,265 | Gemperlein, Katja;Hoffmann, Michael;Huo, Liujie;Mueller, Rolf;Petzke, Lutz;Pilak, Patrick;Wenzel, Silke C | METAB ENG | Ludwigshafen, Germany;Qingdao, Peoples R China;Saarbrucken, Germany;Weihenstephan, Germany |
Chen, W C W;Higashikuni, Y;Lu, T K | 10.1016/j.copbio.2017.06.011 | null | THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND | 1j1f5h4t3c572kd6c5j4f5c246j5v28vp6j71 | Advancing therapeutic applications of synthetic gene circuits | MIT | null | Lu, TK (corresponding author), MIT, Dept Biol Engn, Cambridge, MA 02139 USA.;Lu, TK (corresponding author), MIT, Elect Res Lab, Cambridge, MA 02139 USA. | null | Chen, William C W;Higashikuni, Yasutomi;Lu, Timothy K | Biochemical Research Methods;Biotechnology & Applied Microbiology | Japan Heart Foundation; Uehara Memorial Foundation; NIH Ruth L Kirschstein NRSA postdoctoral fellowship [5T32HL007208]; American Heart Association Collaborative Sciences Award [14CSA20500002] | WOS | Lu, T K | Massachusetts Gen Hosp, Boston, MA USA;MIT, Cambridge, MA USA | 47 | advancing;applications;circuits;gene;of;synthetic;therapeutic | 1 | HIGASHIKUNI, YASUTOMI | ELSEVIER SCI LTD | Massachusetts Gen Hosp, Cardiovasc Res Ctr, Boston, MA 02114 USA;MIT, Dept Biol Engn, Cambridge, MA 02139 USA;MIT, Elect Res Lab, Cambridge, MA 02139 USA;MIT, Elect Res Lab, Cambridge, MA 02139 USA.; Lu, TK (corresponding author), MIT, Dept Biol Engn, Cambridge, MA 02139 USA | Review | MIT | OXFORD | null | null | Elect Res Lab;Massachusetts Gen Hosp;MIT | American Heart Association Collaborative Sciences Award;Japan Heart Foundation;NIH Ruth L Kirschstein NRSA postdoctoral fellowship;Uehara Memorial Foundation | Lu, TK (corresponding author), MIT, Elect Res Lab, Cambridge, MA 02139 USA.; Lu, TK (corresponding author), MIT, Dept Biol Engn, Cambridge, MA 02139 USA. | 141 | Chen, William C W;Higashikuni, Yasutomi;Lu, Timothy K | 59 | 3 | 413,381,100,017 | American Heart Association Collaborative Sciences Award [14CSA20500002];Japan Heart Foundation;NIH Ruth L Kirschstein NRSA postdoctoral fellowship [5T32HL007208];Uehara Memorial Foundation | USA | CURRENT OPINION IN BIOTECHNOLOGY | USA;USA.; | null | null | MIT, Elect Res Lab, Cambridge, MA 02139 USA | 0958-1669 | Chen, W C W;Higashikuni, Y;Lu, T K | OCT | timlu@mit.edu | advancing therapeutic applications;synthetic gene circuits | 3 | J | Biochemistry & Molecular Biology;Biotechnology & Applied Microbiology | acid;advancing therapeutic applications;BACTERIA;biomedicine;Boolean logic gate circuits;cells;challenges;closed loop circuits;DESIGN;development;devices;disease;effector screening technologies;expression;extracellular environment;future opportunities;gene networks;homeostasis;inflammation;intracellular signaling;living cells;local delivery;mammalian cells;MICROBIOME;modified microbes;new sense-and-respond capabilities;novel therapeutic strategies;ORGANISMS;recent advances;regulatory elements;researchers;response;restoration;review;spatiotemporal control;specific functions;synthetic biology aims;synthetic gene circuits;T-CELLS;therapeutic applications;therapeutic molecules;tools | Higashikuni, Y | ACID;BACTERIA;DESIGN;DISEASE;EXPRESSION;HOMEOSTASIS;INFLAMMATION;MICROBIOME;T-CELLS;TOOLS | 133 | [Higashikuni, Yasutomi; Chen, William C. W.; Lu, Timothy K.] MIT, Elect Res Lab, Cambridge, MA 02139 USA. [Higashikuni, Yasutomi; Chen, William C. W.; Lu, Timothy K.] MIT, Dept Biol Engn, Cambridge, MA 02139 USA. [Chen, William C. W.] Massachusetts Gen Hosp, Cardiovasc Res Ctr, Boston, MA 02114 USA. | YH was supported in part by the research fellowships from the Japan Heart Foundation and the Uehara Memorial Foundation. WC was supported by the NIH Ruth L Kirschstein NRSA postdoctoral fellowship (5T32HL007208). This work was supported by the American Heart Association Collaborative Sciences Award (14CSA20500002). | biomedicine;Boolean logic gate circuits;cells;challenges;closed loop circuits;development;devices;effector screening technologies;extracellular environment;future opportunities;gene networks;homeostasis;intracellular signaling;living cells;local delivery;mammalian cells;modified microbes;new sense-and-respond capabilities;novel therapeutic strategies;organisms;recent advances;regulatory elements;researchers;response;restoration;review;spatiotemporal control;specific functions;synthetic biology aims;synthetic gene circuits;therapeutic applications;therapeutic molecules | 10.1002/anie.201507634;10.1002/anie.201507978;10.1002/biot.201400642;10.1002/biot.201600099;10.1016/j.addr.2016.04.006;10.1016/j.cell.2015.02.010;10.1016/j.cell.2016.01.011;10.1016/j.cell.2016.01.012;10.1016/j.cell.2016.09.011;10.1016/j.cell.2016.09.013;10.1016/j.cell.2017.03.041;10.1016/j.cell.2017.03.045;10.1016/j.cels.2015.06.001;10.1016/j.ejphar.2017.04.021;10.1016/j.it.2015.06.004;10.1016/j.jhep.2016.03.020;10.1016/j.jmb.2015.10.004;10.1016/j.molcel.2014.03.030;10.1016/j.neuron.2015.03.065;10.1016/j.pharmthera.2013.12.014;10.1016/j.tig.2014.09.004;10.1016/j.ymthe.2016.10.005;10.1016/S0140-6736(07)61128-3;10.1021/acschembio.6b00234;10.1021/sb400077j;10.1021/sb400128g;10.1021/sb500090b;10.1021/sb500173f;10.1038/boneres.2016.9;10.1038/mi.2013.73;10.1038/nature18930;10.1038/nbt.3301;10.1038/nbt.3326;10.1038/ncomms10624;10.1038/ncomms15028;10.1038/npp.2015.293;10.1038/nrd.2016.245;10.1038/nrendo.2013.193;10.1038/nrendo.2015.227;10.1038/srep18950;10.1039/c5mb00763a;10.1056/NEJMra1110560;10.1056/NEJMra1600266;10.1073/pnas.1508521112;10.1073/pnas.1514383113;10.1073/pnas.1517883113;10.1093/nar/gkw117;10.1097/MOG.0000000000000139;10.1098/rsif.2014.1000;10.1101/gad.284828.116;10.1111/j.1440-1746.2010.06549.x;10.1126/science.aab4077;10.1126/science.aac7341;10.1126/science.aaf4006;10.1126/scisignal.aaf7593;10.1126/scitranslmed.3005975;10.1126/scitranslmed.aac4964;10.1146/annurev-pharmtox-010814-124803;10.1152/physrev.00030.2013;10.1155/2015/375187;10.1172/JCI72517;10.1586/14760584.2015.997714;10.2337/db13-1236;10.2337/db14-0635;10.3748/wjg.v19.i25.3931;10.4161/hv.28549;[10.1038/NMETH.3585, 10.1038/nmeth.3585] | MIT | Chen, W C W;Higashikuni, Y;Lu, T K | Higashikuni, Y: MIT, Elect Res Lab, Cambridge, MA 02139 USA | Lu, Timothy K | 14CSA20500002;5T32HL007208 | 69 | null | USA | Massachusetts Gen Hosp;MIT | Higashikuni, Yasutomi | null | ACID;BACTERIA;DESIGN;DISEASE;EXPRESSION;HOMEOSTASIS;INFLAMMATION;MICROBIOME;T-CELLS;TOOLS | Higashikuni, Yasutomi; Chen, William C. W.; Lu, Timothy K.; | null | Massachusetts Gen Hosp, Cardiovasc Res Ctr, Boston, MA 02114 USA;MIT, Dept Biol Engn, Cambridge, MA 02139 USA;MIT, Elect Res Lab, Cambridge, MA 02139 USA | Massachusetts Gen Hosp, Cardiovasc Res Ctr, Boston, MA 02114 USA;MIT, Dept Biol Engn, Cambridge, MA 02139 USA;MIT, Elect Res Lab, Cambridge, MA 02139 USA | 1879-0429 | null | null | 2007;2010;2011;2012;2013;2014;2015;2016;2017 | 19 | MIT, Dept Biol Engn, Cambridge, MA 02139 USA;MIT, Elect Res Lab, Cambridge, MA 02139 USA | Curr. Opin. Biotechnol. | Lu, Timothy K | ELSEVIER SCI LTD | ,;addition;advances;aims;and;applications;as;be;biology;biomedicine;Boolean;can;capabilities;cells;challenges;circuits;closed;computing;control;delivery;design;designed;development;devices;discuss;effector;elements;enable;enabled;engineered;environment;extracellular;for;functions;future;gate;gene;genetically;has;homeostasis;in;including;into;intracellular;introduce;living;local;logic;loop;mammalian;many;microbes;modified;molecular;molecules;networks;new;novel;of;opportunities;or;organisms;perform;program;recent;regulatory;researchers;response;restoration;review;screening;sense-and-respond;signaling;spatiotemporal;specific;strategies;such;synthetic;technologies;the;therapeutic;this;to;used;we;well;which;will;with;would | MIT | Synthetic biology aims to introduce new sense-and-respond capabilities into living cells, which would enable novel therapeutic strategies. The development of regulatory elements, molecular computing devices, and effector screening technologies has enabled researchers to design synthetic gene circuits in many organisms, including mammalian cells. Engineered gene networks, such as closed loop circuits or Boolean logic gate circuits, can be used to program cells to perform specific functions with spatiotemporal control and restoration of homeostasis in response to the extracellular environment and intracellular signaling. In addition, genetically modified microbes can be designed as local delivery of therapeutic molecules. In this review, we will discuss recent advances in therapeutic applications of synthetic gene circuits, as well as challenges and future opportunities for biomedicine. | G-4267-2012 | ACID;BACTERIA;DESIGN;DISEASE;EXPRESSION;HOMEOSTASIS;INFLAMMATION;MICROBIOME;T-CELLS;TOOL | 3 | null | null | 9 | ACID;BACTERIA;DESIGN;DISEASE;EXPRESSION;HOMEOSTASIS;INFLAMMATION;MICROBIOME;T-CELLS;TOOL | WOS:000413381100017 | Massachusetts Gen Hosp, Boston, MA USA;MIT, Cambridge, MA USA | USA | 2,017 | null | 0000-0002-2232-567X | null | null | English | null | ACS CHEM BIOL;ACS SYNTH BIOL;ADV DRUG DELIVER REV;ANGEW CHEM INT EDIT;ANNU REV PHARMACOL;BIOTECHNOL J;BONE RES;CELL;CELL SYST;COLD SPRING HARB PER;CURR OPIN GASTROEN;DIABETES;EUR J PHARMACOL;EXPERT REV VACCINES;GENE DEV;HUM VACC IMMUNOTHER;J CLIN INVEST;J GASTROEN HEPATOL;J HEPATOL;J MOL BIOL;J R SOC INTERFACE;LANCET;MOL BIOSYST;MOL CELL;MOL THER;MUCOSAL IMMUNOL;NAT BIOTECHNOL;NAT COMMUN;NAT METHODS;NAT REV DRUG DISCOV;NAT REV ENDOCRINOL;NATURE;NEURON;NEUROPSYCHOPHARMACOL;NEW ENGL J MED;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PHARMACOL THERAPEUT;PHYSIOL REV;ROBBINS COTRAN PATHO;SCI REP-UK;SCI SIGNAL;SCI TRANSL MED;SCIENCE;STEM CELLS INT;TRENDS GENET;TRENDS IMMUNOL;WORLD J GASTROENTERO | Chen, William C W;Higashikuni, Yasutomi;Lu, Timothy K | 2024-03-11
ER | Andries, O;Auslander S.;Ausländer, S;Bai, P;Bartalena, L;Beal, J;Bhatia, S N;Borrero, J;Bradley, R W;Braff, D;Chen, W C W;Chen, Z Y;Chovatiya, R;Daringer, N M;Din, M O;Duan, F F;Foo, J L;Gosselin, P;Griffiths, C E M;Hwang, I Y;Juillerat, A;Juillot, S;Kis, Z;Kotas, M E;Kumar, V;Lai, A C;Lim, B;Liu, K W;Lynch, S V;Marlow, G J;Maroun, C R;Martín, R;Mimee, M;Morsut, L;Mullur, R;Nakamura, T;Navarro, R;Neurath, M F;Nielsen, A A K;Niopek, D;Pardee, K;Polonsky, K S;Raman, S;Robert, S;Roybal, K T;Saxena, P;Schukur, L;Shi, Y;Shreiner, A B;Slomovic, S;Smole, A;Srivastava, S;Sun, X;Toure, M;Tuomilehto, J;Urban, D J;Vardy, E;Whitaker, W R;Wong, A S L;Wroblewska, L;Wu, C Y;Wu, M R;Xie, M;Xie, M Q | FK3JJ | Cambridge, MA USA;Cambridge, MA USA. | 21 | null | 2 | null | 28,750,201 | Chen, William C W;Higashikuni, Yasutomi;Lu, Timothy K | CURR OPIN BIOTECH | Boston, MA USA;Cambridge, MA USA |
Boucher, N;Derbyshire, K M;Gray, T A;Judd, J;Van Roey, E | 10.1128/JB.00410-17 | e00410 | 1752 N ST NW, WASHINGTON, DC 20036-2904 USA | gz4ak561p9485w5i70d572k2v304d39576r | Application of Distributive Conjugal DNA Transfer in <i>Mycobacterium smegmatis</i> To Establish a Genome-Wide Synthetic Genetic Array | New York State Dept Hlth | null | Derbyshire, KM (corresponding author), New York State Dept Hlth, Wadsworth Ctr, Div Genet, Albany, NY 12201 USA.;Derbyshire, KM (corresponding author), SUNY Albany, Dept Biomed Sci, Albany, NY 12222 USA. | null | Boucher, Nathalie;Derbyshire, Keith M;Gray, Todd A;Judd, Julius;Van Roey, Erik | Microbiology | NIAID [R21AI07258, R01AI097191] | WOS | Derbyshire, K M | New York State Dept Hlth, Albany, NY USA;SUNY Albany, Albany, NY USA | 199 | <i>Mycobacterium;a;application;Array;Conjugal;Distributive;DNA;Establish;genetic;genome-wide;in;of;smegmatis</i>;synthetic;to;Transfer | 1 | Judd, Julius | AMER SOC MICROBIOLOGY | New York State Dept Hlth, Wadsworth Ctr, Div Genet, Albany, NY 12201 USA;New York State Dept Hlth, Wadsworth Ctr, Div Genet, Albany, NY 12201 USA.; Derbyshire, KM (corresponding author), SUNY Albany, Dept Biomed Sci, Albany, NY 12222 USA;SUNY Albany, Dept Biomed Sci, Albany, NY 12222 USA | Article | New York State Dept Hlth;SUNY Albany | WASHINGTON | null | null | New York State Dept Hlth;SUNY Albany | NIAID | Derbyshire, KM (corresponding author), New York State Dept Hlth, Wadsworth Ctr, Div Genet, Albany, NY 12201 USA.; Derbyshire, KM (corresponding author), SUNY Albany, Dept Biomed Sci, Albany, NY 12222 USA. | null | Boucher, Nathalie;Derbyshire, Keith M;Gray, Todd A;Judd, Julius;Van Roey, Erik | 8 | 2 | 411,075,700,009 | NIAID [R21AI07258, R01AI097191] | USA | JOURNAL OF BACTERIOLOGY | USA;USA.; | null | null | New York State Dept Hlth, Wadsworth Ctr, Div Genet, Albany, NY 12201 USA | 0021-9193 | Boucher, N;Derbyshire, K M;Gray, T A;Judd, J;Van Roey, E | OCT | keith.derbyshire@health.ny.gov | <i>Mycobacterium smegmatis</i>;application;Distributive Conjugal DNA Transfer;Genome-Wide Synthetic Genetic Array | 5 | J | Microbiology | <i>Mycobacterium smegmatis</i>;advantage;analysis;application;arrayed library;chromosomal conjugation system;CHROMOSOMAL DNA;combination;combines mutations;conjugation;conserved hypothetical genes;conserved hypothetical protein annotations;defined mutations;Distributive Conjugal DNA Transfer;double mutant strains;essential process;esx3;fast-growing nonpathogenic species;feasibility;function;functions;fxbA;gene interactions;genes;genesencoding;genetic redundancy;genome-scale SGA;genome-wide scale;Genome-Wide Synthetic Genetic Array;great potential;high efficiency;high number;high-throughput mycobacterial SGA (mSGA) screen;hypothetical genes;IDENTIFICATION;identified novel;IMPORTANCE Mycobacterium smegmatis;individual donor;initial assignment;IRON;iron utilization pathways;known genes;M. smegmatis;model organism;molecular genetic approaches;mSGA;mutants;Mycobacteria;mycobacterial genomes;mycobacterial pathogens;mycobacterial pathways;mycobacterial species;Mycobacterium smegmatis;noncoding RNA (ncRNA);novel genetic interactions;obscure phenotypic effects;pathways;powerful approach;powerful genetic tool;proteins;query genes;RecA;recipient mutations;redundant biological pathways;redundant pathways;single-gene mutations;study;SURVIVAL;synthetic genetic array;synthetic genetic array (mSGA) approach;synthetic genetic arrays (SGAs);transposon mutants;TUBERCULOSIS;two gene products;two individual mutations;uncovering interactions | Judd, J | CHROMOSOMAL DNA;conjugation;IDENTIFICATION;IRON;iron utilization pathways;Mycobacteria;RecA;SURVIVAL;synthetic genetic array;TUBERCULOSIS | null | [Judd, Julius; Boucher, Nathalie; Van Roey, Erik; Gray, Todd A.; Derbyshire, Keith M.] New York State Dept Hlth, Wadsworth Ctr, Div Genet, Albany, NY 12201 USA. [Gray, Todd A.; Derbyshire, Keith M.] SUNY Albany, Dept Biomed Sci, Albany, NY 12222 USA. | This work was supported by funding from NIAID R21AI07258 and R01AI097191. The Wadsworth Center Core Facilities performed the sequencing and bioinformatics and provided media. | advantage;analysis;arrayed library;chromosomal conjugation system;combination;combines mutations;conjugation;conserved hypothetical genes;conserved hypothetical protein annotations;defined mutations;double mutant strains;essential process;esx3;fast-growing nonpathogenic species;feasibility;function;functions;fxbA;gene interactions;genes;genesencoding;genetic redundancy;genome-scale SGA;genome-wide scale;great potential;high efficiency;high number;high-throughput mycobacterial SGA (mSGA) screen;hypothetical genes;identification;identified novel;IMPORTANCE Mycobacterium smegmatis;individual donor;initial assignment;known genes;M. smegmatis;model organism;molecular genetic approaches;mSGA;mutants;mycobacteria;mycobacterial genomes;mycobacterial pathogens;mycobacterial pathways;mycobacterial species;Mycobacterium smegmatis;noncoding RNA (ncRNA);novel genetic interactions;obscure phenotypic effects;pathways;powerful approach;powerful genetic tool;proteins;query genes;recA;recipient mutations;redundant biological pathways;redundant pathways;single-gene mutations;study;synthetic genetic array (mSGA) approach;synthetic genetic arrays (SGAs);transposon mutants;two gene products;two individual mutations;uncovering interactions | 10.1016/j.cell.2005.08.031;10.1016/j.cell.2010.11.052;10.1016/j.mib.2009.11.006;10.1016/j.tube.2015.01.004;10.1038/nchembio.340;10.1038/ng1844;10.1038/NMETH.1240;10.1038/nmeth0908-759;10.1038/nmeth996;10.1046/j.1365-2958.1998.00818.x;10.1073/pnas.0404892101;10.1073/pnas.0503272102;10.1073/pnas.0603179103;10.1073/pnas.0900589106;10.1073/pnas.1514135112;10.1073/pnas.231275498;10.1093/nar/gkg595;10.1111/j.1365-2958.2005.04824.x;10.1111/j.1365-2958.2007.05935.x;10.1111/j.1365-2958.2008.06299.x;10.1126/science.1065810;10.1126/science.1106753;10.1126/science.1162609;10.1128/genomeA.00148-13;10.1128/JB.00024-09;10.1128/JB.00216-07;10.1128/JB.01222-07;10.1128/JB.181.11.3402-3408.1999;10.1128/JB.181.14.4266-4274.1999;10.1261/rna.034116.112;10.1371/journal.pbio.1001602;10.1371/journal.pgen.1002377;10.1371/journal.pgen.1004120;10.1371/journal.pgen.1005641;10.1371/journal.ppat.1002251;10.1371/journal.ppat.1003120;10.2144/000112601;[10.1038/nmeth.1239, 10.1038/NMETH.1239];[10.1039/B907407d, 10.1039/b907407d] | New York State Dept Hlth | Boucher, N;Derbyshire, K M;Gray, T A;Judd, J;Van Roey, E | Judd, J: New York State Dept Hlth, Wadsworth Ctr, Div Genet, Albany, NY 12201 USA | null | R01AI097191;R21AI07258 | 40 | null | USA | New York State Dept Hlth;SUNY Albany | Judd, Julius | Bronze, Green Published | CHROMOSOMAL DNA;IDENTIFICATION;IRON;SURVIVAL;TUBERCULOSIS | Judd, Julius; Boucher, Nathalie; Van Roey, Erik; Gray, Todd A.; Derbyshire, Keith M.; | null | New York State Dept Hlth, Wadsworth Ctr, Div Genet, Albany, NY 12201 USA;SUNY Albany, Dept Biomed Sci, Albany, NY 12222 USA | New York State Dept Hlth, Wadsworth Ctr, Div Genet, Albany, NY 12201 USA;SUNY Albany, Dept Biomed Sci, Albany, NY 12222 USA | 1098-5530 | conjugation;iron utilization pathways;Mycobacteria;RecA;synthetic genetic array | 20 | 1991;1998;1999;2001;2003;2004;2005;2006;2007;2008;2009;2010;2011;2013;2014;2015 | 3 | New York State Dept Hlth, Wadsworth Ctr, Div Genet, Albany, NY 12201 USA;SUNY Albany, Dept Biomed Sci, Albany, NY 12222 USA | J. Bacteriol. | Derbyshire, Keith M | AMER SOC MICROBIOLOGY | (mSGA);(ncRNA);(SGAs);,;a;advantage;all;an;analysis;and;annotations;approach;approaches;are;array;arrayed;arrays;as;assigned;assignment;be;because;biological;both;but;by;can;choice;chromosomal;combination;combine;combined;combines;conjugation;conserved;define;defined;demonstrated;describe;donor;double;effects;efficiency;enables;essential;esx3;fast-growing;feasibility;for;found;function;functions;further;fxbA;gene;genes;genesencoding;genetic;genome-scale;genome-wide;genomes;great;had;harboring;has;here;hidden;high;high-throughput;hypothetical;identification;identified;identify;importance;importantly;in;individual;initial;interacting;interactions;is;it;known;lethal;library;linking;M.;many;may;model;molecular;most;mSGA;mutant;mutants;mutations;mycobacteria;mycobacterial;Mycobacterium;noncoding;nonpathogenic;normally;novel;number;obscure;of;offer;on;or;organism;other;pathogens;pathways;phenotypic;potential;powerful;predicted;process;products;protein;proteins;provide;query;recA;recipient;reduce;redundancy;redundant;RNA;scale;screen;separately;SGA;single-gene;smegmatis;species;strains;study;synthetic;synthetically;system;take;that;the;this;throughout;thus;to;tool;transposon;two;uncovering;using;viable;we;were;when;which;with;work | New York State Dept Hlth;SUNY Albany | Genetic redundancy can obscure phenotypic effects of single-gene mutations. Two individual mutations may be viable separately but are lethal when combined, thus synthetically linking the two gene products in an essential process. Synthetic genetic arrays (SGAs), in which defined mutations are combined, provide a powerful approach to identify novel genetic interactions and redundant pathways. A genome-scale SGA can offer an initial assignment of function to hypothetical genes by uncovering interactions with known genes or pathways. Here, we take advantage of the chromosomal conjugation system of Mycobacterium smegmatis to combine individual donor and recipient mutations on a genome-wide scale. We demonstrated the feasibility of a high-throughput mycobacterial SGA (mSGA) screen by using mutants of esx3, fxbA, and recA as query genes, which were combined with an arrayed library of transposon mutants by conjugation. The mSGA identified interacting genes that we had predicted and, most importantly, identified novel interacting genesencoding both proteins and a noncoding RNA (ncRNA). In combination with other molecular genetic approaches, the mSGA has great potential to both reduce the high number of conserved hypothetical protein annotations in mycobacterial genomes and further define mycobacterial pathways and gene interactions. IMPORTANCE Mycobacterium smegmatis is the model organism of choice for the study of mycobacterial pathogens, because it is a fast-growing nonpathogenic species harboring many genes that are conserved throughout mycobacteria. In this work, we describe a synthetic genetic array (mSGA) approach for M. smegmatis, which combines mutations on a genome-wide scale with high efficiency. Analysis of the double mutant strains enables the identification of interacting genes and pathways that are normally hidden by redundant biological pathways. The mSGA is a powerful genetic tool that enables functions to be assigned to the many conserved hypothetical genes found in all mycobacterial species. | null | CHROMOSOMAL DNA;IDENTIFICATION;IRON;SURVIVAL;TUBERCULOSIS | 0 | null | conjugation;iron utilization pathways;Mycobacteria;RecA;synthetic genetic array | 15 | CHROMOSOMAL DNA;conjugation;IDENTIFICATION;IRON;iron utilization pathways;Mycobacteria;RecA;SURVIVAL;synthetic genetic array;TUBERCULOSIS | WOS:000411075700009 | New York State Dept Hlth, Albany, NY USA;SUNY Albany, Albany, NY USA | USA | 2,017 | null | 0000-0002-4602-0205 | null | null | English | null | BIOTECHNIQUES;CELL;CURR OPIN MICROBIOL;GENOME ANNOUNCEMENTS;J BACTERIOL;METHOD ENZYMOL;MOL BIOSYST;MOL MICROBIOL;NAT CHEM BIOL;NAT GENET;NAT METHODS;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PLOS BIOL;PLOS GENET;PLOS PATHOG;RNA;SCIENCE;TUBERCULOSIS | Boucher, Nathalie;Derbyshire, Keith M;Gray, Todd A;Judd, Julius;Van Roey, Erik | 2024-03-11
ER | Andries, K;Babu, M;Butland, G;Chowdhury, R P;Coros, A;Dussurget, O;Fang, Z;Fernandes, N D;Flint, J L;Gray, T A;Griffin, J E;Guo, X V;Jacobs, W R;Joshi, S M;Kalscheuer, R;Kieser, K J;Lehner, B;Li, S K;Liu, Y G;Nguyen, K T;Nichols, R J;Ojha, A;Parsons, L M;Rengarajan, J;Roguev, A;Sassetti, C M;Schuldiner, M;Shell, S S;Shiloh, M U;Siegrist, M S;Silhavy, T J;Tong, A H Y;Typas, A;Van Kessel, J C;Wang, J;Wells, R M;Zuker, M | FH3UO | Albany, NY USA;Albany, NY USA. | 4 | null | 2 | null | 28,784,812 | Boucher, Nathalie;Derbyshire, Keith M;Gray, Todd A;Judd, Julius;Van Roey, Erik | J BACTERIOL | Albany, NY USA |
Tei, H;Uriu, K | 10.1016/j.jtbi.2017.06.005 | null | 24-28 OVAL RD, LONDON NW1 7DX, ENGLAND | 1u2vs3458u1c2272m6e4s1y172p5l581f2n2f | Feedback loops interlocked at competitive binding sites amplify and facilitate genetic oscillations | Kanazawa Univ | null | Uriu, K (corresponding author), Kanazawa Univ, Grad Sch Nat Sci & Technol, Kakuma Machi, Kanazawa, Ishikawa 9201192, Japan. | null | Tei, Hajime;Uriu, Koichiro | Biology;Mathematical & Computational Biology | JSPS KAKENHI [26840085]; Grants-in-Aid for Scientific Research [26840085, 17H05762] Funding Source: KAKEN | WOS | Uriu, K | Kanazawa Univ, Ishikawa, Japan | 428 | amplify;and;at;binding;competitive;Facilitate;feedback;genetic;interlocked;loops;oscillations;sites | 1 | Uriu, Koichiro | ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD | Kanazawa Univ, Grad Sch Nat Sci & Technol, Kakuma Machi, Kanazawa, Ishikawa 9201192, Japan | Article | Kanazawa Univ | LONDON | null | null | Kanazawa Univ | Grants-in-Aid for Scientific Research;JSPS KAKENHI | Uriu, K (corresponding author), Kanazawa Univ, Grad Sch Nat Sci & Technol, Kakuma Machi, Kanazawa, Ishikawa 9201192, Japan. | 64 | Tei, Hajime;Uriu, Koichiro | 10 | 1 | 406,079,800,007 | Grants-in-Aid for Scientific Research [26840085, 17H05762] Funding Source: KAKEN;JSPS KAKENHI [26840085] | Japan | JOURNAL OF THEORETICAL BIOLOGY | Japan | null | null | Kanazawa Univ, Grad Sch Nat Sci & Technol, Kakuma Machi, Kanazawa, Ishikawa 9201192, Japan | 0022-5193 | Tei, H;Uriu, K | SEP 7 | tei@staff.kanazawa-u.ac.jp;uriu@staff.kanazawa-u.ac.jp | competitive binding sites;feedback loops;genetic oscillations | 2 | J | Life Sciences & Biomedicine - Other Topics;Mathematical & Computational Biology | activator;activator ROR;additional mechanisms;amplification;amplitude;binding sites;Bmal1;Bmal1 oscillations;Bmal1 promoter;Bmal1 regulation;C 2017 Elsevier Ltd;Circadian clock;competitive binding sites;contrast;dissociation constants;expression levels;fast activator;fast repressor;feedback loops;genetic oscillations;integration;key;key clock gene Bmal1;large time scale separation;MAMMALIAN CIRCADIAN CLOCK;mechanism;METABOLISM;MODEL;necessary;negative feedback loops;noncompetitive binding sites;noncompetitive sites;optimal ratio;oscillation;OSCILLATIONS;peak phase difference;Phase difference;positive;preference;present;previous experiments;previous study;principles;regulation;regulatory networks;relative time;relative time scales;REPRESSOR;repressor REV-ERB;results;REV-ERB;REV-ERB-ALPHA;rights reserved;ROBUST;robust oscillations;ROR;ROR peaks;same binding sites;slow activator;slow repressor;small;small phase difference;SYNCHRONIZATION;Synthetic Genetic Oscillators;time scales;TRANSCRIPTION;transcription patterns | Uriu, K | AMPLITUDE;Bmal1;Circadian clock;MAMMALIAN CIRCADIAN CLOCK;MECHANISM;METABOLISM;MODEL;Phase difference;PRINCIPLES;REV-ERB-ALPHA;ROBUST;SYNCHRONIZATION;Synthetic genetic oscillators;TRANSCRIPTION | 56 | [Uriu, Koichiro; Tei, Hajime] Kanazawa Univ, Grad Sch Nat Sci & Technol, Kakuma Machi, Kanazawa, Ishikawa 9201192, Japan. | We thank Gen Kurosawa and Andrew Oates for their helpful comments on the manuscript. This work was supported by JSPS KAKENHI [26840085] to K.U. | activator;activator ROR;additional mechanisms;amplification;amplitude;binding sites;Bmal1;Bmal1 oscillations;Bmal1 promoter;Bmal1 regulation;circadian clock;competitive binding sites;contrast;dissociation constants;expression levels;fast activator;fast repressor;feedback loops;genetic oscillations;integration;key;key clock gene Bmal1;large time scale separation;mammalian circadian clock;necessary;negative feedback loops;noncompetitive binding sites;noncompetitive sites;optimal ratio;oscillation;oscillations;peak phase difference;positive;preference;present;previous experiments;previous study;regulation;regulatory networks;relative time;relative time scales;repressor;repressor REV-ERB;results;REV-ERB;robust oscillations;ROR;ROR peaks;same binding sites;slow activator;slow repressor;small;small phase difference;synthetic genetic oscillators;time scales;transcription patterns | 10.1016/j.bpj.2014.07.022;10.1016/j.bpj.2015.09.024;10.1016/j.cell.2010.12.019;10.1016/j.cell.2016.05.012;10.1016/j.celrep.2013.03.013;10.1016/j.cmet.2016.10.003;10.1016/j.jtbi.2008.04.011;10.1016/j.molcel.2015.10.024;10.1016/j.neuron.2004.07.018;10.1016/j.physa.2015.02.091;10.1016/S0092-8674(02)00825-5;10.1016/S0092-8674(03)00074-6;10.1016/S0092-8674(03)00346-5;10.1038/msb.2012.62;10.1038/nature07389;10.1038/nature07616;10.1038/nature11048;10.1038/ng1504;10.1038/nrm2530;10.1038/nrm2995;10.1038/nsmb.3324;10.1038/srep05782;10.1073/pnas.0904837106;10.1073/pnas.1132112100;10.1073/pnas.1603799113;10.1073/pnas.2036281100;10.1088/1478-3975/13/3/035005;10.1103/PhysRevE.80.011926;10.1103/PhysRevE.94.052413;10.1103/PhysRevLett.102.068105;10.1126/science.1156951;10.1126/science.1226339;10.1126/science.aab3021;10.1186/1471-2199-5-18;10.1186/1752-0509-4-66;10.1371/journal.pbio.1000595;10.1371/journal.pcbi.0020030;10.1371/journal.pcbi.0030068;10.1371/journal.pcbi.1002309;10.1371/journal.pcbi.1002787;10.1371/journal.pcbi.1005266;10.1371/journal.pone.0018663;10.1371/journal.pone.0046835;10.1371/journal.pone.0104761;10.1529/biophysj.104.058388;10.1529/biophysj.106.094086 | Kanazawa Univ | Tei, H;Uriu, K | Uriu, K: Kanazawa Univ, Grad Sch Nat Sci & Technol, Kakuma Machi, Kanazawa, Ishikawa 9201192, Japan | Uriu, Koichiro | 17H05762;26840085 | 48 | null | Japan | Kanazawa Univ | Uriu, Koichiro | null | AMPLITUDE;MAMMALIAN CIRCADIAN CLOCK;MECHANISM;METABOLISM;MODEL;PRINCIPLES;REV-ERB-ALPHA;ROBUST;SYNCHRONIZATION;TRANSCRIPTION | Uriu, Koichiro; Tei, Hajime; | null | Kanazawa Univ, Grad Sch Nat Sci & Technol, Kakuma Machi, Kanazawa, Ishikawa 9201192, Japan | Kanazawa Univ, Grad Sch Nat Sci & Technol, Kakuma Machi, Kanazawa, Ishikawa 9201192, Japan | 1095-8541 | Bmal1;Circadian clock;Phase difference;synthetic genetic oscillator | null | 1982;2002;2003;2004;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017 | 5 | Kanazawa Univ, Grad Sch Nat Sci & Technol, Kakuma Machi, Kanazawa, Ishikawa 9201192, Japan | J. Theor. Biol. | Tei, Hajime | ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD | ,;a;activates;activator;additional;advantageous;amplification;amplifying;amplitude;an;and;are;arises;as;at;between;binding;Bmal1;both;by;circadian;clock;compensate;compete;competitive;comprise;constants;contrast;conversely;demonstrated;depends;difference;disadvantage;dissociation;enhance;examples;experiments;expression;facilitate;fast;feedback;for;forming;from;further;gene;generate;genetic;here;in;indicate;integration;interlocked;is;key;large;larger;later;levels;likely;loops;mammalian;mathematical;mechanisms;modeling;more;moreover;necessary;negative;networks;noncompetitive;of;often;on;only;optimal;oscillation;oscillations;oscillators;our;patterns;peak;peaks;phase;positive;predict;preferable;preference;present;previous;promoter;ratio;regulated;regulation;regulatory;relative;repressor;results;REV-ERB;reveal;robust;ROR;same;scale;scales;secondly;separation;show;similar;sites;slow;small;study;synthetic;than;that;the;their;them;therefore;these;this;time;to;transcription;under;using;we;when;with | Kanazawa Univ | Positive and negative feedback loops are often present in regulatory networks for genetic oscillations. Relative time scales and integration of these feedback loops are key to robust oscillations in expression levels. Using examples from the circadian clock and synthetic genetic oscillators, we study positive and negative feedback loops interlocked at competitive binding sites. In the mammalian circadian clock, a key clock gene Bmal1 is regulated by the activator ROR and the repressor REV-ERB. Conversely, Bmal1 activates both of them, forming interlocked feedback loops. Previous experiments indicate that the activator and repressor compete for the same binding sites in the Bmal1 promoter. Transcription patterns predict that ROR peaks later than REV-ERB and, moreover, the peak phase difference between them is small. Using mathematical modeling we reveal an optimal ratio of dissociation constants of an activator and a repressor for the competitive binding sites to enhance the amplitude of Bmal1 oscillations. This optimal ratio arises only when the amplitude of the repressor is larger than that of the activator. Secondly, we reveal that the preference of binding sites for an activator and a repressor depends on their relative time scales. A previous study demonstrated that noncompetitive binding sites are preferable for synthetic genetic oscillators that comprise a fast activator and a slow repressor with a large time scale separation. Here we show that when their time scales are similar, competitive binding sites are more likely to generate oscillation than noncompetitive sites. In contrast, for a slow activator and a fast repressor with a small phase difference as in Bmal1 regulation, noncompetitive binding sites are advantageous for amplifying oscillations. Our results, therefore, predict that additional mechanisms are necessary to compensate the disadvantage of the Bmal1 promoter and further facilitate amplification under the regulation by ROR and REV-ERB. | L-3596-2015 | AMPLITUDE;MAMMALIAN CIRCADIAN CLOCK;MECHANISM;METABOLISM;MODEL;PRINCIPLES;REV-ERB-ALPHA;ROBUST;SYNCHRONIZATION;TRANSCRIPTION | 0 | null | Bmal1;Circadian clock;Phase difference;Synthetic genetic oscillators | 9 | AMPLITUDE;Bmal1;Circadian clock;MAMMALIAN CIRCADIAN CLOCK;MECHANISM;METABOLISM;MODEL;Phase difference;PRINCIPLES;REV-ERB-ALPHA;ROBUST;SYNCHRONIZATION;synthetic genetic oscillator;TRANSCRIPTION | WOS:000406079800007 | Kanazawa Univ, Ishikawa, Japan | Japan | 2,017 | null | 0000-0003-1802-2470 | null | null | English | null | BIOPHYS J;BMC MOL BIOL;BMC SYST BIOL;CELL;CELL METAB;CELL REP;J THEOR BIOL;Models of biological pattern formation;MOL CELL;MOL SYST BIOL;NAT GENET;NAT REV MOL CELL BIO;NAT STRUCT MOL BIOL;NATURE;NEURON;P NATL ACAD SCI USA;PAP PHYS;PHYS BIOL;PHYS REV E;PHYS REV LETT;PHYSICA A;PLOS BIOL;PLOS COMPUT BIOL;PLOS ONE;SCI REP-UK;SCIENCE | Tei, Hajime;Uriu, Koichiro | 2024-03-11
ER | Ananthasubramaniam, B;Atkinson, M R;Bernard, S;Cho, H;Cyran, S A;Forger, D B;Gonze, D;Guantes, R;Huang, B;Jolley, C C;Kim, J K;Koike, N;Korencic, A;Leloup, J C;Lengyel I. M.;Li, Y;Marino, S;Mather, W;Meinhardt H.;Mirsky, H P;Monti, M;Munteanu, A;Narumi, R;Novák, B;Ogawa, Y;Papazyan, R;Pett, J P;Preitner, N;Relógio, A;Rey, G;Sato, T K;Stricker, J;Tian, X J;Tigges, M;To, T L;Tokuda, I T;Tsai, T Y C;Ueda, H R;Ukai-Tadenuma, M;Wang, J K;Webb, A B;Westermark, P O;Yamamoto, T;Zhang, E E;Zhang, Y X;Zhao, X;Zhu, B K | FB3YX | Ishikawa, Japan | 6 | null | 1 | null | 28,625,476 | Tei, Hajime;Uriu, Koichiro | J THEOR BIOL | Ishikawa, Japan |
Aisyah;Alisjahbana, B;Damayanti, R R R;Handali, S;Ihsanawati;Natalia, D;Puspasari, F;Putri, R D;Yuwita, A | 10.1016/j.apjtb.2017.07.017 | null | WOLTERS KLUWER INDIA PVT LTD , A-202, 2ND FLR, QUBE, C T S NO 1498A-2 VILLAGE MAROL, ANDHERI EAST, MUMBAI, 400059, INDIA | 2h5d2yk125e58394e254j1ie5t5h3a19xa6q | Construction and expression of a synthetic gene encoding nonstructural glycoprotein NS1 of dengue 2 virus in <i>Pichia</i> <i>pastoris</i> | Inst Technol Bandung | null | Natalia, D (corresponding author), Inst Technol Bandung, Fac Math & Nat Sci, Biochem Res Div, Jl Ganesha 10, Bandung 40132, Indonesia. | null | Aisyah;Alisjahbana, Bachti;Damayanti, Raden Roro Rika;Handali, Sukwan;Ihsanawati;Natalia, Dessy;Puspasari, Fernita;Putri, Riski Dwimalida;Yuwita, Anita | Tropical Medicine | Ministry of Research, Technology, and Higher Education of Indonesia [0400/I1/B04/SPK-WRRI/VI/2014] | WOS | Natalia, D | Inst Technol Bandung, Bandung, Indonesia;Padjadjaran State Univ, Jatinangor, Indonesia;Pakar Biomed Indonesia, Bandung, Indonesia | 7 | 2;<i>pastoris</i>;<i>Pichia</i>;a;and;construction;dengue;encoding;expression;gene;glycoprotein;in;nonstructural;NS1;of;synthetic;virus | 1 | Puspasari, Fernita | WOLTERS KLUWER MEDKNOW PUBLICATIONS | Inst Technol Bandung, Fac Math & Nat Sci, Biochem Res Div, Jl Ganesha 10, Bandung 40132, Indonesia;Padjadjaran State Univ, Fac Med, Jl Raya Bandung Sumedang KM21, Jatinangor, Indonesia;Pakar Biomed Indonesia, Jl Rancabentang 12B, Bandung 40142, Indonesia | Article | Inst Technol Bandung | MUMBAI | null | null | Inst Technol Bandung;Padjadjaran State Univ;Pakar Biomed Indonesia | Ministry of Research, Technology, and Higher Education of Indonesia | Natalia, D (corresponding author), Inst Technol Bandung, Fac Math & Nat Sci, Biochem Res Div, Jl Ganesha 10, Bandung 40132, Indonesia. | 693 | Aisyah;Alisjahbana, Bachti;Damayanti, Raden Roro Rika;Handali, Sukwan;Ihsanawati;Natalia, Dessy;Puspasari, Fernita;Putri, Riski Dwimalida;Yuwita, Anita | 3 | 3 | 408,640,800,004 | Ministry of Research, Technology, and Higher Education of Indonesia [0400/I1/B04/SPK-WRRI/VI/2014] | Indonesia | ASIAN PACIFIC JOURNAL OF TROPICAL BIOMEDICINE | Indonesia | null | null | Inst Technol Bandung, Fac Math & Nat Sci, Biochem Res Div, Jl Ganesha 10, Bandung 40132, Indonesia | 2221-1691 | Aisyah;Alisjahbana, B;Damayanti, R R R;Handali, S;Ihsanawati;Natalia, D;Puspasari, F;Putri, R D;Yuwita, A | AUG | dessy@chem.itb.ac.id | <i>Pichia</i> <i>pastoris</i>;dengue 2 virus;expression;synthetic gene encoding nonstructural glycoprotein NS1 | 9 | J | Tropical Medicine | 2% (v/v) methanol;45 kDa;72 h;<i>Pichia</i> <i>pastoris</i>;antigenicity;codon;commercial rapid test;conclusions;dengue 2 virus;dengue diagnostic kit;DENV-2 NS1 amino acid sequences;development;expression;expression vector;Indonesian-specific DENV2 virus;induction;methods;molecular weight;monoclonal antibody;Ni-NTA affinity chromatography;NS1;optimal expression condition;P. pastoris KM71;P. pastoris pPICZ alpha;pastoris);Pichia pastoris (P;potential candidate;PROTEIN;purified recombinant DENV-2 NS1 protein;recombinant DENV-2 NS1 protein;resulting recombinant DENV-2 NS1 protein;results;synthetic gene;synthetic gene encoding nonstructural glycoprotein NS1;tested;use;vaccine | Puspasari, F | null | 689 | [Puspasari, Fernita; Putri, Riski Dwimalida; Aisyah; Damayanti, Raden Roro Rika; Ihsanawati; Natalia, Dessy] Inst Technol Bandung, Fac Math & Nat Sci, Biochem Res Div, Jl Ganesha 10, Bandung 40132, Indonesia. [Yuwita, Anita; Handali, Sukwan] Pakar Biomed Indonesia, Jl Rancabentang 12B, Bandung 40142, Indonesia. [Alisjahbana, Bachti] Padjadjaran State Univ, Fac Med, Jl Raya Bandung Sumedang KM21, Jatinangor, Indonesia. | We thank "Penelitian Unggulan Strategis Nasional 2013" under the contract number of 0400/I1/B04/SPK-WRRI/VI/2014, Ministry of Research, Technology, and Higher Education of Indonesia, for funding this work. | 2% (v/v) methanol;45 kDa;72 h;antigenicity;codon;commercial rapid test;conclusions;dengue diagnostic kit;DENV-2 NS1 amino acid sequences;development;expression vector;Indonesian-specific DENV2 virus;induction;methods;molecular weight;monoclonal antibody;Ni-NTA affinity chromatography;NS1;optimal expression condition;P. pastoris KM71;P. pastoris pPICZ alpha;pastoris);Pichia pastoris (P;potential candidate;protein;purified recombinant DENV-2 NS1 protein;recombinant DENV-2 NS1 protein;resulting recombinant DENV-2 NS1 protein;results;synthetic gene;tested;use;vaccine | 10.1007/s00253-014-5963-5;10.1007/s11262-005-0036-6;10.1007/s11262-012-0851-5;10.1016/j.antiviral.2009.11.009;10.1016/j.antiviral.2013.03.008;10.1016/j.antiviral.2013.09.013;10.1016/j.jviromet.2010.04.003;10.1016/j.pep.2009.02.003;10.1093/nar/15.3.1281;10.1155/2013/343195;10.1371/journal.pone.0080891;10.1385/MB:16:1:23;10.2144/04361DD02 | Inst Technol Bandung | Aisyah;Alisjahbana, B;Damayanti, R R R;Handali, S;Ihsanawati;Natalia, D;Puspasari, F;Putri, R D;Yuwita, A | Puspasari, F: Inst Technol Bandung, Fac Math & Nat Sci, Biochem Res Div, Jl Ganesha 10, Bandung 40132, Indonesia | null | 0400/I1/B04/SPK-WRRI/VI/2014 | 13 | null | Indonesia | Inst Technol Bandung;Padjadjaran State Univ;Pakar Biomed Indonesia | Puspasari, Fernita | gold | null | Puspasari, Fernita; Putri, Riski Dwimalida; Aisyah; Damayanti, Raden Roro Rika; Yuwita, Anita; Alisjahbana, Bachti; Handali, Sukwan; Ihsanawati; Natalia, Dessy; | null | Inst Technol Bandung, Fac Math & Nat Sci, Biochem Res Div, Jl Ganesha 10, Bandung 40132, Indonesia;Padjadjaran State Univ, Fac Med, Jl Raya Bandung Sumedang KM21, Jatinangor, Indonesia;Pakar Biomed Indonesia, Jl Rancabentang 12B, Bandung 40142, Indonesia | Inst Technol Bandung, Fac Math & Nat Sci, Biochem Res Div, Jl Ganesha 10, Bandung 40132, Indonesia;Padjadjaran State Univ, Fac Med, Jl Raya Bandung Sumedang KM21, Jatinangor, Indonesia;Pakar Biomed Indonesia, Jl Rancabentang 12B, Bandung 40142, Indonesia | 2588-9222 | null | 8 | 1987;2000;2004;2006;2009;2010;2013;2015 | 2 | Inst Technol Bandung, Fac Math & Nat Sci, Biochem Res Div, Jl Ganesha 10, Bandung 40132, Indonesia | Asian Pac. Trop. Biomed. | Natalia, Dessy | WOLTERS KLUWER MEDKNOW PUBLICATIONS | (p;(v/v);,;2%;45;72;:;a;able;achieved;acid;affinity;alpha;amino;and;antibody;antigenicity;as;by;candidate;characterize;chromatography;codon;commercial;commercially;conclusions;condition;dengue;DENV-2;DENV2;derived;development;diagnostic;express;expression;for;from;gene;h;in;Indonesian-specific;induction;inserted;interact;into;is;its;kDa;kit;KM71;methanol;methods;molecular;monoclonal;Ni-NTA;NS1;objectives;of;optimal;optimized;P.;pastoris;pastoris);Pichia;potential;pPICZ;produced;protein;purified;rapid;recombinant;resulting;results;secreted;sequences;similar;synthesized;synthetic;test;tested;the;to;use;vaccine;vector;virus;was;weight;with | Inst Technol Bandung | Objectives: To express and characterize NS1 of Indonesian-specific DENV2 virus in Pichia pastoris (P. pastoris). Methods: A codon optimized synthetic gene derived from the DENV-2 NS1 amino acid sequences was synthesized commercially and inserted into the P. pastoris pPICZ alpha A expression vector. The recombinant DENV-2 NS1 protein was purified by Ni-NTA affinity chromatography, and its antigenicity was tested. Results: The recombinant DENV-2 NS1 protein was secreted as a protein with a molecular weight of similar to 45 kDa, and the optimal expression condition was achieved by induction with 2% (v/v) methanol for 72 h. The purified recombinant DENV-2 NS1 protein was able to interact with a monoclonal antibody of NS1 in a commercial rapid test. Conclusions: The resulting recombinant DENV-2 NS1 protein produced in P. pastoris KM71 is a potential candidate for use in the development of a dengue diagnostic kit and vaccine. | null | null | 0 | null | null | 5 | null | WOS:000408640800004 | Inst Technol Bandung, Bandung, Indonesia;Padjadjaran State Univ, Jatinangor, Indonesia;Pakar Biomed Indonesia, Bandung, Indonesia | Indonesia | 2,017 | null | 0000-0002-8953-8805 | null | null | English | null | ANTIVIR RES;APPL MICROBIOL BIOT;BIOMED RES INT;BIOTECHNIQUES;J VIROL METHODS;MOL BIOTECHNOL;NUCLEIC ACIDS RES;PLOS ONE;PROTEIN EXPRES PURIF;VIRUS GENES | Aisyah;Alisjahbana, Bachti;Damayanti, Raden Roro Rika;Handali, Sukwan;Ihsanawati;Natalia, Dessy;Puspasari, Fernita;Putri, Riski Dwimalida;Yuwita, Anita | 2024-03-11
ER | Amorim, J H;Athmaram, T N;Bollati, M;Bragança, C R S;Cregg, J M;Das, D;Kosasih, H;Lim, S P;Muller, D A;Sankar, S G;Sharp, P M;Wu, S X;Zhou, J M | FF1DU | Bandung, Indonesia | 2 | null | 3 | null | null | Aisyah;Alisjahbana, Bachti;Damayanti, Raden Roro Rika;Handali, Sukwan;Ihsanawati;Natalia, Dessy;Puspasari, Fernita;Putri, Riski Dwimalida;Yuwita, Anita | ASIAN PAC J TROP BIO | Bandung, Indonesia;Jatinangor, Indonesia |
Beck, J L;Collins, J J;Del Vecchio, D;Dy, A J;Martin, K B;Murray, R M;Ng, A H;Yeung, E | 10.1016/j.cels.2017.06.001 | null | 50 HAMPSHIRE ST, FLOOR 5, CAMBRIDGE, MA 02139 USA | 3z81y1j3b2k2w684r4j2r2z6k1nl5u6nz5q31 | Biophysical Constraints Arising from Compositional Context in Synthetic Gene Networks | Pacific Northwest Natl Lab | null | Yeung, E (corresponding author), Pacific Northwest Natl Lab, Computat & Stat Analyt Div, Data Sci & Analyt Grp, Richland, WA 99352 USA. | null | Beck, James L;Collins, James J;Del Vecchio, Domitilla;Dy, Aaron J;Martin, Kyle B;Murray, Richard M;Ng, Andrew H;Yeung, Enoch | Biochemistry & Molecular Biology;Cell Biology | Charles Lee Powell Foundation Fellowship; Kanel Foundation Fellowship; National Science Foundation Graduate Fellowship; National Defense Science and Engineering Graduate Fellowship; Air Force Office of Scientific Research grant (AFOSR) [FA9550-14-1-0060]; Defense Threat Reduction Agency [HDTRA1-14-1-0006]; Defense Advanced Research Projects Agency [HR0011-12-C-0065]; Direct For Computer & Info Scie & Enginr; Division of Computing and Communication Foundations [1317694] Funding Source: National Science Foundation | WOS | Yeung, E | Broad Inst MIT & Harvard, Cambridge, MA USA;CALTECH, Pasadena, CA USA;Harvard MIT Program Hlth Sci & Technol, Cambridge, MA USA;Harvard Univ, Cambridge, MA USA;MIT, Cambridge, MA USA;Pacific Northwest Natl Lab, Richland, WA USA;Univ Calif Berkeley, Berkeley, CA USA | 5 | Arising;biophysical;Compositional;Constraints;Context;From;gene;in;networks;synthetic | 1 | null | CELL PRESS | Broad Inst MIT & Harvard, Cambridge, MA USA;CALTECH, Dept Civil & Mech Engn, Pasadena, CA 91125 USA;CALTECH, Dept Comp & Math Sci, Control & Dynam Syst, Pasadena, CA 91125 USA;CALTECH, Div Biol & Biol Engn, Pasadena, CA 91125 USA;Harvard MIT Program Hlth Sci & Technol, Cambridge, MA USA;Harvard Univ, Wyss Inst Biol Inspired Engn, Cambridge, MA 02138 USA;MIT, Inst Med Engn & Sci, Synthet Biol Ctr, Dept Biol Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA;MIT, Synthet Biol Ctr, Dept Mech Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA;Pacific Northwest Natl Lab, Computat & Stat Analyt Div, Data Sci & Analyt Grp, Richland, WA 99352 USA;Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA | Article | Pacific Northwest Natl Lab | CAMBRIDGE | null | null | Broad Inst MIT & Harvard;CALTECH;Harvard MIT Program Hlth Sci & Technol;Harvard Univ;MIT;Pacific Northwest Natl Lab;Univ Calif Berkeley | Air Force Office of Scientific Research grant (AFOSR);Charles Lee Powell Foundation Fellowship;Defense Advanced Research Projects Agency;Defense Threat Reduction Agency;Direct For Computer & Info Scie & Enginr;Division of Computing and Communication Foundations;Kanel Foundation Fellowship;National Defense Science and Engineering Graduate Fellowship;National Science Foundation Graduate Fellowship | Yeung, E (corresponding author), Pacific Northwest Natl Lab, Computat & Stat Analyt Div, Data Sci & Analyt Grp, Richland, WA 99352 USA. | + | Beck, James L;Collins, James J;Del Vecchio, Domitilla;Dy, Aaron J;Martin, Kyle B;Murray, Richard M;Ng, Andrew H;Yeung, Enoch | 12 | 10 | 406,295,900,003 | Air Force Office of Scientific Research grant (AFOSR) [FA9550-14-1-0060];Charles Lee Powell Foundation Fellowship;Defense Advanced Research Projects Agency [HR0011-12-C-0065];Defense Threat Reduction Agency [HDTRA1-14-1-0006];Direct For Computer & Info Scie & Enginr;Division of Computing and Communication Foundations [1317694] Funding Source: National Science Foundation;Kanel Foundation Fellowship;National Defense Science and Engineering Graduate Fellowship;National Science Foundation Graduate Fellowship | USA | CELL SYSTEMS | USA | null | null | Pacific Northwest Natl Lab, Computat & Stat Analyt Div, Data Sci & Analyt Grp, Richland, WA 99352 USA | 2405-4712 | Beck, J L;Collins, J J;Del Vecchio, D;Dy, A J;Martin, K B;Murray, R M;Ng, A H;Yeung, E | JUL 26 | enoch.yeung@pnnl.gov | biophysical Constraints;Compositional Context;synthetic gene networks | 8 | J | Biochemistry & Molecular Biology;Cell Biology | 30%;400% higher expression;biophysical Constraints;cells;coding sequences;Compositional Context;convergent genes;divergent-;DNA TOPOLOGY;DNA);dynamic range;Effects;ELEMENTS;entire genes;ESCHERICHIA-COLI;expression;expression levels;FLUORESCENT PROTEIN;gene expression;genes;greater ultrasensitivity;gyrase;hypothesis;ILVYC OPERON;induced;induced genes;induction;intergenic compositional context (spatial arrangement;intergenic context effects;intragenic compositional context (promoter structure;modeling;one;orientation;PROMOTER;promoters;ribosome binding sites);RNA;spacing regions;supercoiling;supercoiling effects;switch stability;Synthetic gene expression;synthetic gene networks;taking advantage;tandem genes;tandem orientations;tandem- oriented genes;threshold detection;toggle switch;TRANSCRIPTION;transcriptional interference;treatment;vitro supercoiling relaxation experiments | Yeung, E | CELLS;DNA TOPOLOGY;ELEMENTS;ESCHERICHIA-COLI;EXPRESSION;FLUORESCENT PROTEIN;ILVYC OPERON;PROMOTERS;RNA;TRANSCRIPTION | 11 | [Yeung, Enoch] Pacific Northwest Natl Lab, Computat & Stat Analyt Div, Data Sci & Analyt Grp, Richland, WA 99352 USA. [Murray, Richard M.] CALTECH, Dept Comp & Math Sci, Control & Dynam Syst, Pasadena, CA 91125 USA. [Dy, Aaron J.; Collins, James J.] MIT, Inst Med Engn & Sci, Synthet Biol Ctr, Dept Biol Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA. [Martin, Kyle B.; Murray, Richard M.] CALTECH, Div Biol & Biol Engn, Pasadena, CA 91125 USA. [Ng, Andrew H.] Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA. [Del Vecchio, Domitilla] MIT, Synthet Biol Ctr, Dept Mech Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA. [Beck, James L.] CALTECH, Dept Civil & Mech Engn, Pasadena, CA 91125 USA. [Collins, James J.] Harvard MIT Program Hlth Sci & Technol, Cambridge, MA USA. [Collins, James J.] Harvard Univ, Wyss Inst Biol Inspired Engn, Cambridge, MA 02138 USA. [Dy, Aaron J.; Collins, James J.] Broad Inst MIT & Harvard, Cambridge, MA USA. | We thank Ophelia Venturelli for her invaluable inspiration and guidance in this project; Victoria Hsiao, Jin Park, Anu Thubagere, and Adam Rosenthal for great advice on imaging; David Younger, Ania Baetica, Vincent Noireaux, Clarmyra Hayes, and Zachary Z. Sun for guidance and assistance with TX-TL experiments; and Lea Goentoro, Johann Pauls-son, Long Cai, Jennifer Brophy, John Doyle, Eric Klavins, and Julius Lucks for insightful conversations. This work was supported in part by a Charles Lee Powell Foundation Fellowship, a Kanel Foundation Fellowship, a National Science Foundation Graduate Fellowship, a National Defense Science and Engineering Graduate Fellowship, Air Force Office of Scientific Research grant (AFOSR) FA9550-14-1-0060, Defense Threat Reduction Agency grant HDTRA1-14-1-0006, and Defense Advanced Research Projects Agency grant HR0011-12-C-0065. | 30%;400% higher expression;coding sequences;convergent genes;divergent-;DNA);dynamic range;effects;entire genes;expression;expression levels;gene expression;genes;greater ultrasensitivity;gyrase;hypothesis;induced;induced genes;induction;intergenic compositional context (spatial arrangement;intergenic context effects;intragenic compositional context (promoter structure;modeling;one;orientation;promoter;ribosome binding sites);spacing regions;supercoiling;supercoiling effects;switch stability;synthetic gene expression;synthetic gene networks;taking advantage;tandem genes;tandem orientations;tandem- oriented genes;threshold detection;toggle switch;transcriptional interference;treatment;vitro supercoiling relaxation experiments | 10.1002/biot.201200085;10.1016/0022-2836(92)90721-U;10.1016/0092-8674(85)90112-6;10.1016/j.bpj.2015.06.034;10.1016/j.cell.2008.01.027;10.1016/j.cell.2014.05.038;10.1016/j.chembiol.2015.04.018;10.1016/j.gde.2005.02.007;10.1016/j.tig.2005.04.009;10.1021/bi00332a018;10.1021/ja037994o;10.1021/ja411060p;10.1021/sb200016s;10.1021/sb400203p;10.1038/35002131;10.1038/msb.2011.38;10.1038/nature11516;10.1038/nbt988;10.1038/nprot.2011.432;10.1038/nrm976;10.1046/j.1365-2958.2001.02249.x;10.1073/pnas.0402940101;10.1073/pnas.1301301110;10.1073/pnas.2135496100;10.1073/pnas.84.20.7024;10.1073/pnas.96.25.14294;10.1088/1478-3975/4/4/001;10.1093/nar/25.6.1203;10.1093/nar/gkq810;10.1093/nar/gks014;10.1109/CDC.2013.6760079;10.1111/j.1365-2958.2005.05006.x;10.1126/science.1207339;10.1128/AEM.70.11.6809-6815.2004;10.1128/jb.169.10.4499-4506.1987;10.1146/annurev.genet.36.032902.111815;10.1186/1754-1611-5-12;10.1371/journal.pcbi.1003785;10.1371/journal.pone.0003647;10.15252/msb.20156540;[10.1038/NMETH.1318, 10.1038/nmeth.1318];[10.1038/nmeth.2403, 10.1038/NMETH.2403];[10.1038/NMETH.2404, 10.1038/nmeth.2404];[10.1038/NMETH.3339, 10.1038/nmeth.3339] | Pacific Northwest Natl Lab | Beck, J L;Collins, J J;Del Vecchio, D;Dy, A J;Martin, K B;Murray, R M;Ng, A H;Yeung, E | Yeung, E: Pacific Northwest Natl Lab, Computat & Stat Analyt Div, Data Sci & Analyt Grp, Richland, WA 99352 USA | Dy, Aaron J | 1317694;FA9550-14-1-0060;HDTRA1-14-1-0006;HR0011-12-C-0065 | 47 | null | USA | Broad Inst MIT & Harvard;CALTECH;Harvard MIT Program Hlth Sci & Technol;Harvard Univ;MIT;Pacific Northwest Natl Lab;Univ Calif Berkeley | Yeung, Enoch | Green Submitted, Bronze | CELLS;DNA TOPOLOGY;ELEMENTS;ESCHERICHIA-COLI;EXPRESSION;FLUORESCENT PROTEIN;ILVYC OPERON;PROMOTERS;RNA;TRANSCRIPTION | Yeung, Enoch; Dy, Aaron J.; Martin, Kyle B.; Ng, Andrew H.; Del Vecchio, Domitilla; Beck, James L.; Collins, James J.; Murray, Richard M.; | null | Broad Inst MIT & Harvard, Cambridge, MA USA;CALTECH, Dept Civil & Mech Engn, Pasadena, CA 91125 USA;CALTECH, Dept Comp & Math Sci, Control & Dynam Syst, Pasadena, CA 91125 USA;CALTECH, Div Biol & Biol Engn, Pasadena, CA 91125 USA;Harvard MIT Program Hlth Sci & Technol, Cambridge, MA USA;Harvard Univ, Wyss Inst Biol Inspired Engn, Cambridge, MA 02138 USA;MIT, Inst Med Engn & Sci, Synthet Biol Ctr, Dept Biol Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA;MIT, Synthet Biol Ctr, Dept Mech Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA;Pacific Northwest Natl Lab, Computat & Stat Analyt Div, Data Sci & Analyt Grp, Richland, WA 99352 USA;Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA | Broad Inst MIT & Harvard, Cambridge, MA USA;CALTECH, Dept Civil & Mech Engn, Pasadena, CA 91125 USA;CALTECH, Dept Comp & Math Sci, Control & Dynam Syst, Pasadena, CA 91125 USA;CALTECH, Div Biol & Biol Engn, Pasadena, CA 91125 USA;Harvard MIT Program Hlth Sci & Technol, Cambridge, MA USA;Harvard Univ, Wyss Inst Biol Inspired Engn, Cambridge, MA 02138 USA;MIT, Inst Med Engn & Sci, Synthet Biol Ctr, Dept Biol Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA;MIT, Synthet Biol Ctr, Dept Mech Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA;Pacific Northwest Natl Lab, Computat & Stat Analyt Div, Data Sci & Analyt Grp, Richland, WA 99352 USA;Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA | 2405-4720 | null | 1 | 1985;1987;1992;1997;1999;2000;2001;2002;2003;2004;2005;2006;2007;2008;2009;2011;2012;2013;2014;2015;2016 | 68 | Pacific Northwest Natl Lab, Computat & Stat Analyt Div, Data Sci & Analyt Grp, Richland, WA 99352 USA | Cell Syst. | Murray, Richard M | CELL PRESS | (promoter;(spatial;,;30%;400%;about;abrogated;advantage;affects;and;are;arranged;arrangement;between;binding;both;bringing;by;can;coding;compare;compositional;context;convergent;detection;differences;divergent;divergent-;DNA);dynamic;each;effects;entire;experiments;explain;expression;gene;genes;greater;gyrase;higher;highly;however;hypothesis;improve;in;induced;induction;interference;intergenic;intragenic;is;known;less;levels;mediated;modeling;much;networks;of;on;one;or;orientation;orientations;oriented;other;postulate;promoter;range;rebuilt;regions;relaxation;Ribosome;sensitive;sequences;sites);spacing;stability;structure;supercoiling;switch;synthetic;taking;tandem;tandem-;than;that;the;this;threshold;through;to;toggle;transcriptional;treatment;ultrasensitivity;up;validate;vitro;we;whether;with;within;yielded | Pacific Northwest Natl Lab | Synthetic gene expression is highly sensitive to intragenic compositional context (promoter structure, spacing regions between promoter and coding sequences, and ribosome binding sites). However, much less is known about the effects of intergenic compositional context (spatial arrangement and orientation of entire genes on DNA) on expression levels in synthetic gene networks. We compare expression of induced genes arranged in convergent, divergent, or tandem orientations. Induction of convergent genes yielded up to 400% higher expression, greater ultrasensitivity, and dynamic range than divergent- or tandem- oriented genes. Orientation affects gene expression whether one or both genes are induced. We postulate that transcriptional interference in divergent and tandem genes, mediated by supercoiling, can explain differences in expression and validate this hypothesis through modeling and in vitro supercoiling relaxation experiments. Treatment with gyrase abrogated intergenic context effects, bringing expression levels within 30% of each other. We rebuilt the toggle switch with convergent genes, taking advantage of supercoiling effects to improve threshold detection and switch stability. | H-7052-2016 | CELLS;DNA TOPOLOGY;ELEMENTS;ESCHERICHIA-COLI;EXPRESSION;FLUORESCENT PROTEIN;ILVYC OPERON;PROMOTER;RNA;TRANSCRIPTION | 0 | null | null | 26 | ESCHERICHIA-COLI;CELLS;DNA TOPOLOGY;ELEMENTS;EXPRESSION;FLUORESCENT PROTEIN;ILVYC OPERON;PROMOTER;RNA;TRANSCRIPTION | WOS:000406295900003 | Broad Inst MIT & Harvard, Cambridge, MA USA;CALTECH, Pasadena, CA USA;Harvard MIT Program Hlth Sci & Technol, Cambridge, MA USA;Harvard Univ, Cambridge, MA USA;MIT, Cambridge, MA USA;Pacific Northwest Natl Lab, Richland, WA USA;Univ Calif Berkeley, Berkeley, CA USA | USA | 2,017 | null | null | null | null | English | null | ACS SYNTH BIOL;ANNU REV GENET;APPL ENVIRON MICROB;BIOCHEMISTRY-US;BIOPHYS J;BIOTECHNOL J;CELL;CHEM BIOL;CURR OPIN GENET DEV;ECOSAL PLUS;IEEE DECIS CONTR P;J AM CHEM SOC;J BACTERIOL;J Biol Eng;J BIOL METHODS;J MOL BIOL;MOL MICROBIOL;MOL SYST BIOL;NAT BIOTECHNOL;NAT METHODS;NAT PROTOC;NAT REV MOL CELL BIO;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PHYS BIOL;PLOS COMPUT BIOL;PLOS ONE;SCIENCE;TRENDS GENET | Beck, James L;Collins, James J;Del Vecchio, Domitilla;Dy, Aaron J;Martin, Kyle B;Murray, Richard M;Ng, Andrew H;Yeung, Enoch | 2024-03-11
ER | [Anonymous];Babendure, J R;Balke, V L;Berg J.M.;Bintu, L;Brophy, J A N;Buc, H;Cardinale, S;Ceroni, F;Chong, S S;Davis, J H;Drolet, M;Edelstein A. D.;Engler, C;Filonov, G S;Gardner, T S;Gibson, D G;Gyorgy, A;Han, K Y;Hatfield, G W;Kalisky, T;Kobayashi, H;Korbel, J O;Kosuri, S;Larson, M H;Lee, T S;Liu, L F;Lutz, R;Maier, T;Meyer, S;Moon, T S;Mutalik, V K;Nelson, H C M;Noireaux, V;Opel, M L;Ouafa, Z A;Paige, J S;Rahmouni, A R;Rhee, K Y;Shearwin, K E;Shin, J;Siegal-Gaskins, D;Tuza, Z A;Veening, J W;Young, J W;Zhang, J | FB7BK | Richland, WA USA | 81 | null | 7 | null | 28,734,826 | Beck, James L;Collins, James J;Del Vecchio, Domitilla;Dy, Aaron J;Martin, Kyle B;Murray, Richard M;Ng, Andrew H;Yeung, Enoch | CELL SYST | Berkeley, CA USA;Cambridge, MA USA;Pasadena, CA USA;Richland, WA USA |
Ding, Y F;Fan, J Z;Li, B Q;Li, J N;Pan, T R;Tan, C M;Tseng, K H;Villarreal, F;Weyers, B | 10.1039/c7lc00382j | null | THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND | 253k4d2f5l2k4q1r3w6x5743v39212f2p125x1u | Multi-dimensional studies of synthetic genetic promoters enabled by microfluidic impact printing | Univ Calif Davis | null | Li, BQ (corresponding author), Univ Sci & Technol China, Dept Precis Machinery Precis Instrumentat, Hefei 230027, Anhui, Peoples R China.;Li, BQ; Tan, CM; Pan, TR (corresponding author), Univ Calif Davis, Dept Biomech Engn, Davis, CA 95616 USA. | null | Ding, Yunfeng;Fan, Jinzhen;Li, Baoqing;Li, Jiannan;Pan, Tingrui;Tan, Cheemeng;Tseng, Kuo Hao;Villarreal, Fernando;Weyers, Brent | Biochemical Research Methods;Chemistry, Analytical;Chemistry, Multidisciplinary;Instruments & Instrumentation;Nanoscience & Nanotechnology | National Science Foundation [ECCS-0846502, DBI-1256193]; National Institute of Environmental Health Sciences of the NIH Superfund Research Program [P42ES004699]; National Natural Science Foundation of China [51675505]; Branco Weiss Fellowship | WOS | Li, B Q;Pan, T R;Tan, C M | Univ Calif Davis, Davis, CA USA;Univ Sci & Technol China, Anhui, Peoples R China | 17 | by;enabled;genetic;impact;Microfluidic;multi-dimensional;of;printing;promoters;studies;synthetic | 2 | Fan, Jinzhen;Li, Jiannan;Tan, Cheemeng;Villarreal, Fernando;Weyers, Brent William | ROYAL SOC CHEMISTRY | CM; Pan, TR (corresponding author), Univ Calif Davis, Dept Biomech Engn, Davis, CA 95616 USA.; Li, BQ (corresponding author), Univ Sci & Technol China, Dept Precis Machinery Precis Instrumentat, Hefei 230027, Anhui, Peoples R China;Univ Calif Davis, Dept Biomech Engn, Davis, CA 95616 USA;Univ Sci & Technol China, Dept Precis Machinery Precis Instrumentat, Hefei 230027, Anhui, Peoples R China | Article | Univ Calif Davis;Univ Sci & Technol China | CAMBRIDGE | null | null | Univ Calif Davis;Univ Sci & Technol China | Branco Weiss Fellowship;National Institute of Environmental Health Sciences of the NIH Superfund Research Program;National Natural Science Foundation of China;National Science Foundation | Li, BQ; Tan, CM; Pan, TR (corresponding author), Univ Calif Davis, Dept Biomech Engn, Davis, CA 95616 USA.; Li, BQ (corresponding author), Univ Sci & Technol China, Dept Precis Machinery Precis Instrumentat, Hefei 230027, Anhui, Peoples R China. | 2207 | Ding, Yunfeng;Fan, Jinzhen;Li, Baoqing;Li, Jiannan;Pan, Tingrui;Tan, Cheemeng;Tseng, Kuo Hao;Villarreal, Fernando;Weyers, Brent | 41 | 2 | 404,469,800,005 | Branco Weiss Fellowship;National Institute of Environmental Health Sciences of the NIH Superfund Research Program [P42ES004699];National Natural Science Foundation of China [51675505];National Science Foundation [ECCS-0846502, DBI-1256193] | China;USA | LAB ON A CHIP | China;USA.; | null | null | Univ Calif Davis, Dept Biomech Engn, Davis, CA 95616 USA | 1473-0197 | Ding, Y F;Fan, J Z;Li, B Q;Li, J N;Pan, T R;Tan, C M;Tseng, K H;Villarreal, F;Weyers, B | JUL 7 | bqli@ustc.edu.cn;cmtan@ucdavis.edu;tingrui@ucdavis.edu | microfluidic impact printing;multi-dimensional studies;synthetic genetic promoters | 9 | J | Biochemistry & Molecular Biology;Chemistry;Instruments & Instrumentation;Science & Technology - Other Topics | 1 mu L drop;1-10000-fold;100 pL-10 nL;ability;accurate direct dilutions;BIOLOGY;cell;cell-free systems;CHIP;combinatorial interactions;concentration;dilution;dose response;droplet printing;droplets;drug discovery;experimental combinations;experiments;factor;FREE PROTEIN EXPRESSION;gene regulatory modules;GENERATION;genetic promoters;GRADIENT;gradient printing system;impact printing;interactions;intractable number;limitation;major limitation;mathematical model;microfluidic impact printing;multi-dimensional data;multi-dimensional studies;multi-parametric;multifactorial design;multiple cis;multiple regulatory factors;natural genetic promoters;new frontier;parallel piezoelectric cantilever beams;platform;promoters;quantitative studies;range;scalable actuator array;SERIAL;single factor;synthetic;synthetic genetic promoter;synthetic genetic promoters;three regulatory factors;trans regulatory factors;transfer function;tunable volumes;use | Fan, J Z | BIOLOGY;CELL;CHIP;DILUTION;DRUG DISCOVERY;FREE PROTEIN EXPRESSION;GENERATION;GRADIENT;PLATFORM;SERIAL | 2198 | [Fan, Jinzhen; Villarreal, Fernando; Weyers, Brent; Ding, Yunfeng; Tseng, Kuo Hao; Li, Jiannan; Li, Baoqing; Tan, Cheemeng; Pan, Tingrui] Univ Calif Davis, Dept Biomech Engn, Davis, CA 95616 USA. [Li, Baoqing] Univ Sci & Technol China, Dept Precis Machinery Precis Instrumentat, Hefei 230027, Anhui, Peoples R China. | This research work has been supported in part by the National Science Foundation Awards ECCS-0846502 and DBI-1256193 to TP. JF acknowledges traineeship support from the National Institute of Environmental Health Sciences of the NIH Superfund Research Program (No. P42ES004699). BL acknowledges grant support from the National Natural Science Foundation of China (No. 51675505). CT acknowledges grant support from the Branco Weiss Fellowship. The authors would like to acknowledge Ray Lin for his assistance in software programming and circuit board design and Samantha Kennedy for her assistance in mechanical printer-head designs. | 1 mu L drop;1-10000-fold;100 pL-10 nL;ability;accurate direct dilutions;cell-free systems;combinatorial interactions;concentration;dose response;droplet printing;droplets;experimental combinations;experiments;factor;gene regulatory modules;genetic promoters;gradient printing system;impact printing;interactions;intractable number;limitation;major limitation;mathematical model;multi-dimensional data;multi-dimensional studies;multi-parametric;multifactorial design;multiple cis;multiple regulatory factors;natural genetic promoters;new frontier;parallel piezoelectric cantilever beams;promoters;quantitative studies;range;scalable actuator array;single factor;synthetic;synthetic genetic promoter;three regulatory factors;trans regulatory factors;transfer function;tunable volumes;use | 10.1002/cbic.200400321;10.1007/s10544-009-9385-6;10.1007/s11705-017-1610-x;10.1016/j.cell.2009.02.007;10.1016/j.copbio.2012.02.002;10.1016/j.ymben.2011.09.002;10.1016/S0006-3495(97)78307-3;10.1016/S0168-1605(02)00022-3;10.1016/S1359-6446(99)01388-4;10.1021/ac035114i;10.1021/ac2029198;10.1021/acssynbio.5b00296;10.1021/bp070133p;10.1021/ja037166v;10.1021/la000600b;10.1038/nature10315;10.1038/nchembio.218;10.1038/nrd1985;10.1039/b715524g;10.1039/b806140h;10.1039/b813582g;10.1039/c2ib00102k;10.1039/c5lc00432b;10.1039/c6lc00265j;10.1039/c6lc00636a;10.1039/c6ra08472a;10.1063/1.3580756;10.1063/1.4847815;10.1063/1.4928298;10.1073/pnas.0306752101;10.1073/pnas.1106752109;10.1088/1478-3975/2/3/P01;10.1093/nar/gkt052;10.1098/rsif.2009.0083.focus;10.1109/TCAD.2012.2202396;10.1109/TCAD.2013.2263035;10.1111/j.1556-4029.2010.01460.x;10.1128/JB.00994-09;10.1128/JCM.00932-16;10.1177/2211068211435302;10.2116/analsci.10.881 | Univ Calif Davis | Ding, Y F;Fan, J Z;Li, B Q;Li, J N;Pan, T R;Tan, C M;Tseng, K H;Villarreal, F;Weyers, B | Fan, J Z: Univ Calif Davis, Dept Biomech Engn, Davis, CA 95616 USA | ding, yun;Li, baoqing;Weyers, Brent William | 51675505;DBI-1256193;ECCS-0846502;P42ES004699 | 43 | null | USA | Univ Calif Davis;Univ Sci & Technol China | Fan, Jinzhen | Green Accepted | BIOLOGY;CELL;CHIP;DILUTION;DRUG DISCOVERY;FREE PROTEIN EXPRESSION;GENERATION;GRADIENT;PLATFORM;SERIAL | Fan, Jinzhen; Villarreal, Fernando; Weyers, Brent; Ding, Yunfeng; Tseng, Kuo Hao; Li, Jiannan; Li, Baoqing; Tan, Cheemeng; Pan, Tingrui; | null | Univ Calif Davis, Dept Biomech Engn, Davis, CA 95616 USA;Univ Sci & Technol China, Dept Precis Machinery Precis Instrumentat, Hefei 230027, Anhui, Peoples R China | Univ Calif Davis, Dept Biomech Engn, Davis, CA 95616 USA;Univ Sci & Technol China, Dept Precis Machinery Precis Instrumentat, Hefei 230027, Anhui, Peoples R China | 1473-0189 | null | 13 | 1994;1997;1999;2000;2002;2003;2004;2005;2006;2007;2008;2009;2010;2011;2012;2013;2015;2016;2017 | 17 | Univ Calif Davis, Dept Biomech Engn, Davis, CA 95616 USA;Univ Sci & Technol China, Dept Precis Machinery Precis Instrumentat, Hefei 230027, Anhui, Peoples R China | Lab Chip | Pan, Tingrui | ROYAL SOC CHEMISTRY | ,;1;1-10000-fold;100;a;ability;accurate;actuator;and;apply;are;arise;array;as;at;beams;between;by;cantilever;cell-free;cis;combinations;combinatorial;comprises;concentration;constructs;creates;data;design;dilutions;direct;dose;drop;droplet;droplets;due;enable;established;experimental;experiments;facilitates;factor;factors;finally;first;for;from;frontier;function;gene;generate;genetic;gradient;has;highly;impact;in;integrate;interactions;intractable;is;L;limitation;limited;major;mathematical;model;modules;mu;multi-dimensional;multi-parametric;multifactorial;multiple;natural;new;next;nL;number;obtain;of;only;or;our;overcome;parallel;piezoelectric;pL-10;present;primarily;printing;promoter;promoters;quantitative;range;regulated;regulatory;respect;response;scalable;single;studies;study;such;synthetic;system;systems;technology;that;the;these;this;three;to;trans;transfer;tunable;typically;understand;use;using;varied;volumes;we;which;with;work | Univ Calif Davis;Univ Sci & Technol China | Natural genetic promoters are regulated by multiple cis and trans regulatory factors. For quantitative studies of these promoters, the concentration of only a single factor is typically varied to obtain the dose response or transfer function of the promoters with respect to the factor. Such design of experiments has limited our ability to understand quantitative, combinatorial interactions between multiple regulatory factors at promoters. This limitation is primarily due to the intractable number of experimental combinations that arise from multifactorial design of experiments. To overcome this major limitation, we integrate impact printing and cell-free systems to enable multi-dimensional studies of genetic promoters. We first present a gradient printing system which comprises parallel piezoelectric cantilever beams as a scalable actuator array to generate droplets with tunable volumes in the range of 100 pL-10 nL, which facilitates highly accurate direct dilutions in the range of 1-10000-fold in a 1 mu L drop. Next, we apply this technology to study interactions between three regulatory factors at a synthetic genetic promoter. Finally, a mathematical model of gene regulatory modules is established using the multi-parametric and multi-dimensional data. Our work creates a new frontier in the use of cell-free systems and droplet printing for multi-dimensional studies of synthetic genetic constructs. | ABE-8742-2021;GVR-9616-2022;HSB-4834-2023 | BIOLOGY;CELLS;CHIP;DILUTION;DRUG DISCOVERY;FREE PROTEIN EXPRESSION;GENERATION;GRADIENTS;PLATFORM;SERIAL | 0 | null | null | 10 | BIOLOGY;CELLS;CHIP;DILUTION;DRUG DISCOVERY;FREE PROTEIN EXPRESSION;GENERATION;GRADIENTS;PLATFORM;SERIAL | WOS:000404469800005 | Univ Calif Davis, Davis, CA USA;Univ Sci & Technol China, Anhui, Peoples R China | China;USA | 2,017 | null | 0000-0002-1939-3401;0000-0002-4034-1243;0000-0002-6089-4785;0000-0002-7280-533X;0000-0003-1049-1192 | null | null | English | null | ACS SYNTH BIOL;ANAL CHEM;ANAL SCI;BIOMED MICRODEVICES;BIOMICROFLUIDICS;BIOPHYS J;BIOTECHNOL PROGR;CELL;CHEMBIOCHEM;CURR OPIN BIOTECH;DRUG DISCOV TODAY;FRONT CHEM SCI ENG;IEEE T COMPUT AID D;INT J FOOD MICROBIOL;INTEGR BIOL-UK;J AM CHEM SOC;J BACTERIOL;J CLIN MICROBIOL;J FORENSIC SCI;J R SOC INTERFACE;JALA-J LAB AUTOM;LAB CHIP;LAB CHIP MINIATURIZE;LANGMUIR;METAB ENG;NAT CHEM BIOL;NAT REV DRUG DISCOV;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PHYS BIOL;RSC ADV;US Pat | Ding, Yunfeng;Fan, Jinzhen;Li, Baoqing;Li, Jiannan;Pan, Tingrui;Tan, Cheemeng;Tseng, Kuo Hao;Villarreal, Fernando;Weyers, Brent | 2024-03-11
ER | Angenendt, P;Bsoul, A;Cai, L F;Chappell, J;Dittrich, P S;Dutka, F;Fan, J Z;Garamella, J;Grgicak, C M;Gulati, S;Harris, D C;Hayashi, Y;Hedges, A J;Hodgman, C E;Hsieh, Y L;Hu, S W;Huang, J D;Jeon, N L;Kong, F W;La D.;Lee, K;Leung, K;Li, B Q;Li, G W;Mei, Q;Noireaux, V;Oosterbroek E.;Patterson, G H;Rose, D;Schu, D J;Seidi, A;Sharp, P A;Smith, K P;Stögbauer, T;Sun, K;Tan, C;Teh, S Y;Vaughn, B S;Villarreal, F;Yeger-Lotem, E;Zheng, B | EZ1KL | Anhui, Peoples R China;Davis, CA USA. | 22 | null | 2 | null | 28,613,297 | Ding, Yunfeng;Fan, Jinzhen;Li, Baoqing;Li, Jiannan;Pan, Tingrui;Tan, Cheemeng;Tseng, Kuo Hao;Villarreal, Fernando;Weyers, Brent | LAB CHIP | Anhui, Peoples R China;Davis, CA USA |
Baym, M;Bronson, R T;Gerber, G K;Giessen, T W;Kerns, S J;Kotula, J W;Niederhuber, M J;Riglar, D T;Silver, P A;Way, J C | 10.1038/nbt.3879 | null | 75 VARICK ST, 9TH FLR, NEW YORK, NY 10013-1917 USA | 3zi1h133p6k6d6k53g13n6zw4t3p4u3e6d34 | Engineered bacteria can function in the mammalian gut long-term as live diagnostics of inflammation | Harvard Med Sch | null | Silver, PA (corresponding author), Harvard Med Sch, Dept Syst Biol, Boston, MA 02115 USA.;Silver, PA (corresponding author), Harvard Univ, Wyss Inst Biol Inspired Engn, Boston, MA 02115 USA. | null | Baym, Michael;Bronson, Roderick T;Gerber, Georg K;Giessen, Tobias W;Kerns, S Jordan;Kotula, Jonathan W;Niederhuber, Matthew J;Riglar, David T;Silver, Pamela A;Way, Jeffrey C | Biotechnology & Applied Microbiology | NCI Cancer Center Support Grant [NIH 5 P30 CA06516]; Human Frontier Science Program Long-Term Fellowship; NHMRC/RG Menzies Early Career Fellowship from Menzies Foundation through Australian National Health and Medical Research Council; Leopoldina Research Fellowship from German National Academy of Sciences Leopoldina [LPDS 2014-05]; Defense Advanced Research Projects Agency [HR0011-15-C-0094]; Wyss Institute for Biologically Inspired Engineering | WOS | Silver, P A | Emulate Inc, Boston, MA USA;Harvard Med Sch, Boston, MA USA;Harvard Univ, Boston, MA USA;SynLogic, Cambridge, MA USA | 35 | as;bacteria;can;diagnostics;engineered;function;gut;in;inflammation;live;long-term;mammalian;of;the | 1 | Baym, Michael;Giessen, Tobias;Riglar, David | NATURE PUBLISHING GROUP | Emulate Inc, Boston, MA USA;Harvard Med Sch, Brigham & Womens Hosp, Dept Pathol, Massachusetts Host Microbiome Ctr, Boston, MA USA;Harvard Med Sch, Dept Biomed Informat, Boston, MA USA;Harvard Med Sch, Dept Microbiol & Immunol, Boston, MA USA;Harvard Med Sch, Dept Syst Biol, Boston, MA 02115 USA;Harvard Med Sch, Dept Syst Biol, Boston, MA 02115 USA.; Silver, PA (corresponding author), Harvard Univ, Wyss Inst Biol Inspired Engn, Boston, MA 02115 USA;Harvard Univ, Wyss Inst Biol Inspired Engn, Boston, MA 02115 USA;SynLogic, Cambridge, MA USA | Article | Harvard Med Sch;Harvard Univ | NEW YORK | null | null | Emulate Inc;Harvard Med Sch;Harvard Univ;SynLogic | Defense Advanced Research Projects Agency;Human Frontier Science Program Long-Term Fellowship;Leopoldina Research Fellowship from German National Academy of Sciences Leopoldina;NCI Cancer Center Support Grant;NHMRC/RG Menzies Early Career Fellowship from Menzies Foundation through Australian National Health and Medical Research Council;Wyss Institute for Biologically Inspired Engineering | Silver, PA (corresponding author), Harvard Med Sch, Dept Syst Biol, Boston, MA 02115 USA.; Silver, PA (corresponding author), Harvard Univ, Wyss Inst Biol Inspired Engn, Boston, MA 02115 USA. | + | Baym, Michael;Bronson, Roderick T;Gerber, Georg K;Giessen, Tobias W;Kerns, S Jordan;Kotula, Jonathan W;Niederhuber, Matthew J;Riglar, David T;Silver, Pamela A;Way, Jeffrey C | 186 | 7 | 405,310,300,017 | Defense Advanced Research Projects Agency [HR0011-15-C-0094];Human Frontier Science Program Long-Term Fellowship;Leopoldina Research Fellowship from German National Academy of Sciences Leopoldina [LPDS 2014-05];NCI Cancer Center Support Grant [NIH 5 P30 CA06516];NHMRC/RG Menzies Early Career Fellowship from Menzies Foundation through Australian National Health and Medical Research Council;Wyss Institute for Biologically Inspired Engineering | USA | NATURE BIOTECHNOLOGY | USA;USA.; | null | null | Harvard Med Sch, Dept Syst Biol, Boston, MA 02115 USA | 1087-0156 | Baym, M;Bronson, R T;Gerber, G K;Giessen, T W;Kerns, S J;Kotula, J W;Niederhuber, M J;Riglar, D T;Silver, P A;Way, J C | JUL | pamela_silver@hms.harvard.edu | bacteria;function;inflammation;live diagnostics;mammalian gut | 10 | J | Biotechnology & Applied Microbiology | 6 months;analysis;BACTERIA;CELL RECRUITMENT;commensal murine Escherichia coli strain;commercial translation;detected tetrathionate;diagnostic strain;diagnostics;disease;durable performance;DYNAMICS;ELECTRON-ACCEPTOR;ENTERICA SEROVAR TYPHIMURIUM;ESCHERICHIA-COLI;exposure;extended gut colonization;fecal testing;function;genetic mouse models;growth;gut;infection-induced;inflammation;live diagnostics;living diagnostics;mammalian gut;MEMORY;MICROBIOTA;mouse gut;mutation;potential;SALMONELLA-TYPHIMURIUM;stable;STRAIN;STRAINS;susceptibility;synthetic genetic circuits;technologies;tetrathionate;therapeutics;time;unpredictable function | Riglar, D T | CELL RECRUITMENT;DISEASE;DYNAMICS;ELECTRON-ACCEPTOR;ENTERICA SEROVAR TYPHIMURIUM;ESCHERICHIA-COLI;GROWTH;MICROBIOTA;SALMONELLA-TYPHIMURIUM;STRAIN | 653 | [Riglar, David T.; Giessen, Tobias W.; Baym, Michael; Kerns, S. Jordan; Niederhuber, Matthew J.; Kotula, Jonathan W.; Silver, Pamela A.] Harvard Med Sch, Dept Syst Biol, Boston, MA 02115 USA. [Riglar, David T.; Giessen, Tobias W.; Kerns, S. Jordan; Niederhuber, Matthew J.; Kotula, Jonathan W.; Way, Jeffrey C.; Silver, Pamela A.] Harvard Univ, Wyss Inst Biol Inspired Engn, Boston, MA 02115 USA. [Baym, Michael] Harvard Med Sch, Dept Biomed Informat, Boston, MA USA. [Bronson, Roderick T.] Harvard Med Sch, Dept Microbiol & Immunol, Boston, MA USA. [Gerber, Georg K.] Harvard Med Sch, Brigham & Womens Hosp, Dept Pathol, Massachusetts Host Microbiome Ctr, Boston, MA USA. [Kerns, S. Jordan] Emulate Inc, Boston, MA USA. [Kotula, Jonathan W.] SynLogic, Cambridge, MA USA. | We thank A. Graveline and L. Bry for discussions and assistance with mouse experiments and A. Verdegaal for experimental assistance. S. typhimurium TT22470 was a gift from J. Roth. We thank Dana-Farber/Harvard Cancer Center in Boston for the use of the Rodent Histopathology Core, which provided histology preparation service. Dana-Farber/Harvard Cancer Center is supported in part by a NCI Cancer Center Support Grant # NIH 5 P30 CA06516. D.T.R. was supported by a Human Frontier Science Program Long-Term Fellowship and an NHMRC/RG Menzies Early Career Fellowship from the Menzies Foundation through the Australian National Health and Medical Research Council. T.W.G. was supported by a Leopoldina Research Fellowship (LPDS 2014-05) from the German National Academy of Sciences Leopoldina. The research was funded by Defense Advanced Research Projects Agency Grant HR0011-15-C-0094 (P.A.S.) and the Wyss Institute for Biologically Inspired Engineering. | 6 months;analysis;bacteria;commensal murine Escherichia coli strain;commercial translation;detected tetrathionate;diagnostic strain;diagnostics;durable performance;exposure;extended gut colonization;fecal testing;function;genetic mouse models;gut;infection-induced;inflammation;living diagnostics;mammalian gut;memory;mouse gut;mutation;potential;stable;strain;strains;susceptibility;synthetic genetic circuits;technologies;tetrathionate;therapeutics;time;unpredictable function | 10.1007/978-1-4939-0554-6_12;10.1007/s00011-008-7062-5;10.1016/j.addr.2016.04.032;10.1016/j.cels.2015.06.001;10.1016/j.chom.2015.12.006;10.1016/S0008-6215(00)90109-5;10.1021/sb3000595;10.1021/sb3000832;10.1021/sb400055h;10.1021/sb4001245;10.1038/35002131;10.1038/embor.2013.27;10.1038/ismej.2014.3;10.1038/nature09415;10.1038/nature11225;10.1038/ncomms10039;10.1046/j.1365-2958.1999.01345.x;10.1073/pnas.120163297;10.1073/pnas.1210309109;10.1073/pnas.1321321111;10.1086/315497;10.1097/MIB.0000000000000468;10.1111/mmi.12176;10.1126/science.1256272;10.1128/IAI.71.5.2839-2858.2003;10.1128/JB.183.8.2463-2475.2001;10.1136/gut.34.7.865;10.1186/1754-1611-4-12;10.1186/s13059-016-0980-6;10.1371/journal.pone.0044328;10.1371/journal.pone.0128036;10.4049/jimmunol.168.2.869;[10.1038/NMETH.3147, 10.1038/nmeth.3147];[10.1038/NMETH.3339, 10.1038/nmeth.3339] | Harvard Med Sch | Baym, M;Bronson, R T;Gerber, G K;Giessen, T W;Kerns, S J;Kotula, J W;Niederhuber, M J;Riglar, D T;Silver, P A;Way, J C | Riglar, D T: Harvard Med Sch, Dept Syst Biol, Boston, MA 02115 USA | Young, Richard A | HR0011-15-C-0094;LPDS 2014-05;NIH 5 P30 CA06516 | 36 | null | USA | Emulate Inc;Harvard Med Sch;Harvard Univ;SynLogic | Riglar, David T | Green Accepted | CELL RECRUITMENT;DISEASE;DYNAMICS;ELECTRON-ACCEPTOR;ENTERICA SEROVAR TYPHIMURIUM;ESCHERICHIA-COLI;GROWTH;MICROBIOTA;SALMONELLA-TYPHIMURIUM;STRAIN | Riglar, David T.; Giessen, Tobias W.; Baym, Michael; Kerns, S. Jordan; Niederhuber, Matthew J.; Bronson, Roderick T.; Kotula, Jonathan W.; Gerber, Georg K.; Way, Jeffrey C.; Silver, Pamela A.; | null | Emulate Inc, Boston, MA USA;Harvard Med Sch, Brigham & Womens Hosp, Dept Pathol, Massachusetts Host Microbiome Ctr, Boston, MA USA;Harvard Med Sch, Dept Biomed Informat, Boston, MA USA;Harvard Med Sch, Dept Microbiol & Immunol, Boston, MA USA;Harvard Med Sch, Dept Syst Biol, Boston, MA 02115 USA;Harvard Univ, Wyss Inst Biol Inspired Engn, Boston, MA 02115 USA;SynLogic, Cambridge, MA USA | Emulate Inc, Boston, MA USA;Harvard Med Sch, Brigham & Womens Hosp, Dept Pathol, Massachusetts Host Microbiome Ctr, Boston, MA USA;Harvard Med Sch, Dept Biomed Informat, Boston, MA USA;Harvard Med Sch, Dept Microbiol & Immunol, Boston, MA USA;Harvard Med Sch, Dept Syst Biol, Boston, MA 02115 USA;Harvard Univ, Wyss Inst Biol Inspired Engn, Boston, MA 02115 USA;SynLogic, Cambridge, MA USA | 1546-1696 | null | 7 | 1980;1986;1993;1998;1999;2000;2001;2002;2003;2008;2010;2012;2013;2014;2015;2016 | 202 | Harvard Med Sch, Dept Syst Biol, Boston, MA 02115 USA;Harvard Univ, Wyss Inst Biol Inspired Engn, Boston, MA 02115 USA | Nat. Biotechnol. | Silver, Pamela A | NATURE PUBLISHING GROUP | ,;6;a;accomplish;analysis;and;as;bacteria;bacterial;be;been;both;but;by;can;circuits;coli;colonization;commensal;commercial;confirms;detect;detected;diagnostic;diagnostics;durable;during;engineered;Escherichia;exposure;extended;fecal;for;function;functioned;genetic;genetically;gut;has;here;hindered;in;infection-induced;inflammation;intended;is;living;maintain;mammalian;memory;models;months;mouse;murine;mutation;of;or;our;over;performance;potential;produced;report;retains;stable;strain;strains;susceptibility;synthetic;technologies;testing;tetrathionate;that;the;their;therapeutics;these;this;time;to;translation;unpredictable;using;we;were;which | Harvard Med Sch;Harvard Univ | Bacteria can be engineered to function as diagnostics or therapeutics in the mammalian gut but commercial translation of technologies to accomplish this has been hindered by the susceptibility of synthetic genetic circuits to mutation and unpredictable function during extended gut colonization. Here, we report stable, engineered bacterial strains that maintain their function for 6 months in the mouse gut. We engineered a commensal murine Escherichia coli strain to detect tetrathionate, which is produced during inflammation. Using our engineered diagnostic strain, which retains memory of exposure in the gut for analysis by fecal testing, we detected tetrathionate in both infection-induced and genetic mouse models of inflammation over 6 months. The synthetic genetic circuits in the engineered strain were genetically stable and functioned as intended over time. The durable performance of these strains confirms the potential of engineered bacteria as living diagnostics. | F-6495-2012 | CELL RECRUITMENT;DISEASE;DYNAMICS;ELECTRON-ACCEPTOR;ENTERICA SEROVAR TYPHIMURIUM;ESCHERICHIA-COLI;GROWTH;MICROBIOTA;SALMONELLA-TYPHIMURIUM;STRAINS | 17 | null | null | 8 | ESCHERICHIA-COLI;CELL RECRUITMENT;DISEASE;DYNAMICS;ELECTRON-ACCEPTOR;ENTERICA SEROVAR TYPHIMURIUM;GROWTH;MICROBIOTA;SALMONELLA-TYPHIMURIUM;STRAINS | WOS:000405310300017 | Emulate Inc, Boston, MA USA;Harvard Med Sch, Boston, MA USA;Harvard Univ, Boston, MA USA;SynLogic, Cambridge, MA USA | USA | 2,017 | null | 0000-0001-6328-2031;0000-0002-5004-4373;0000-0003-1303-5598 | null | null | English | null | ACS SYNTH BIOL;ADV BACTERIAL GENET;ADV DRUG DELIVER REV;CARBOHYD RES;CELL HOST MICROBE;CELL SYST;EMBO REP;GENETICS;GENOME BIOL;GUT;INFECT IMMUN;INFLAMM BOWEL DIS;INFLAMM RES;ISME J;J BACTERIOL;J Biol Eng;J IMMUNOL;J INFECT DIS;METHODS MOL BIOL;MOL MICROBIOL;NAT COMMUN;NAT METHODS;NATURE;P NATL ACAD SCI USA;PLOS ONE;SCIENCE | Baym, Michael;Bronson, Roderick T;Gerber, Georg K;Giessen, Tobias W;Kerns, S Jordan;Kotula, Jonathan W;Niederhuber, Matthew J;Riglar, David T;Silver, Pamela A;Way, Jeffrey C | 2024-03-11
ER | Archer, E J;Barthel, M;Baym, M;Bucci, V;Ceroni, F;Chassaing, B;Clairmont, C;Datsenko, K A;Davis R.W.;Deatherage, D E;Devkota, S;Drake, J W;Farzadfard, F;Gardner, T S;Gorochowski, T E;Hensel, M;Hoover-Plow, J L;Kamdar, K;Keubler, L M;Kotula, J W;Kuo, M S;Lee, H;Liu, Y W;Mimee, M;Moser, F;Myhrvold, C;Price-Carter, M;Rooks, M G;Simmonds, N J;Sleight Sean, C;Sleight, S C;White, P;Winter, S E;Yang, L | FA2ZJ | Boston, MA USA;Boston, MA USA. | 264 | null | 4 | null | 28,553,941 | Baym, Michael;Bronson, Roderick T;Gerber, Georg K;Giessen, Tobias W;Kerns, S Jordan;Kotula, Jonathan W;Niederhuber, Matthew J;Riglar, David T;Silver, Pamela A;Way, Jeffrey C | NAT BIOTECHNOL | Boston, MA USA;Cambridge, MA USA |
Dana, S K;Hellen, E H;Kurths, J | 10.1140/epjst/e2016-60396-5 | null | TIERGARTENSTRASSE 17, D-69121 HEIDELBERG, GERMANY | 3h3d734633m6n4gh6b56u663414r16k61s | Electronic circuit analog of synthetic genetic networks: Revisited | Univ North Carolina Greensboro | null | Hellen, EH (corresponding author), Univ North Carolina Greensboro, Dept Phys & Astron, Greensboro, NC 27402 USA. | null | Dana, Syamal K;Hellen, Edward H;Kurths, Jurgen | Physics, Multidisciplinary | University Grants Commission (India) Emeritus Fellowship | WOS | Hellen, E H | Jadavpur Univ, Kolkata, India;Potsdam Inst Climate Impact Res, Potsdam, Germany;Univ North Carolina Greensboro, Greensboro, NC USA | 226 | :;analog;circuit;electronic;genetic;networks;of;Revisited;synthetic | 3 | Hellen, Edward | SPRINGER HEIDELBERG | Jadavpur Univ, Dept Math, Kolkata 700032, India;Potsdam Inst Climate Impact Res, Potsdam, Germany;Univ North Carolina Greensboro, Dept Phys & Astron, Greensboro, NC 27402 USA | Article | Univ North Carolina Greensboro | HEIDELBERG | null | null | Jadavpur Univ;Potsdam Inst Climate Impact Res;Univ North Carolina Greensboro | University Grants Commission (India) Emeritus Fellowship | Hellen, EH (corresponding author), Univ North Carolina Greensboro, Dept Phys & Astron, Greensboro, NC 27402 USA. | 1828 | Dana, Syamal K;Hellen, Edward H;Kurths, Jurgen | 4 | 3 | 403,684,400,010 | University Grants Commission (India) Emeritus Fellowship | Germany;India;USA | EUROPEAN PHYSICAL JOURNAL-SPECIAL TOPICS | USA | null | null | Univ North Carolina Greensboro, Dept Phys & Astron, Greensboro, NC 27402 USA | 1951-6355 | Dana, S K;Hellen, E H;Kurths, J | JUN | ehhellen@uncg.edu | electronic circuit analog;synthetic genetic networks | 3 | J | Physics | 3-gene Repressilator;additive noise;chemical kinetics;circuit design;circuit models;conversions;coupled Repressilators;dynamical behavior's complexity;DYNAMICAL BEHAVIORS;dynamical systems' behavior;electrical systems;electronic analog;electronic circuit analog;electronic circuits;experiment;experiments;extrinsic noise;Hill function inhibition;important features;improved electronic analog;improved version;incorporation;initial conditions;investigations;isolated Repressilator;model parameters;multistability;networks;numerical results;numerical simulations;previous design;quorum sensing coupling;real circuit component values;REPRESSILATORS;studies;studying potential dynamical behaviors;SYNCHRONIZATION;synthetic genetic network;synthetic genetic networks;systematic change;useful tools;verification | Hellen, E H | REPRESSILATORS;SYNCHRONIZATION | 1811 | [Hellen, Edward H.] Univ North Carolina Greensboro, Dept Phys & Astron, Greensboro, NC 27402 USA. [Kurths, Jurgen] Potsdam Inst Climate Impact Res, Potsdam, Germany. [Dana, Syamal K.] Jadavpur Univ, Dept Math, Kolkata 700032, India. | S.K.D. acknowledges support by the University Grants Commission (India) Emeritus Fellowship. The authors thank Evgeny Volkov for valuable contributions. | 3-gene Repressilator;additive noise;chemical kinetics;circuit design;circuit models;conversions;coupled Repressilators;dynamical behavior's complexity;dynamical behaviors;dynamical systems' behavior;electrical systems;electronic analog;electronic circuits;experiment;experiments;extrinsic noise;Hill function inhibition;important features;improved electronic analog;improved version;incorporation;initial conditions;investigations;isolated Repressilator;model parameters;multistability;networks;numerical results;numerical simulations;previous design;quorum sensing coupling;real circuit component values;studies;studying potential dynamical behaviors;synthetic genetic network;synthetic genetic networks;systematic change;useful tools;verification | 10.1038/35002125;10.1038/35002131;10.1038/468889a;10.1038/nrg3197;10.1038/scientificamerican1293-102;10.1063/1.1345702;10.1063/1.1786683;10.1063/1.2173048;10.1063/1.4705085;10.1073/pnas.0307095101;10.1103/PhysRevE.78.031904;10.1103/PhysRevE.83.031901;10.1103/PhysRevE.95.022408;10.1103/PhysRevLett.99.148103;10.1142/S0218127407019275;10.1142/S0218127410026800;10.1146/annurev.cellbio.21.012704.131001;10.1371/journal.pone.0023286;10.1371/journal.pone.0062997;10.1371/journal.pone.0076032 | Univ North Carolina Greensboro | Dana, S K;Hellen, E H;Kurths, J | Hellen, E H: Univ North Carolina Greensboro, Dept Phys & Astron, Greensboro, NC 27402 USA | Hellen, Edward | null | 21 | null | USA | Jadavpur Univ;Potsdam Inst Climate Impact Res;Univ North Carolina Greensboro | Hellen, Edward H | Green Submitted | REPRESSILATORS;SYNCHRONIZATION | Hellen, Edward H.; Kurths, Jurgen; Dana, Syamal K.; | null | Jadavpur Univ, Dept Math, Kolkata 700032, India;Potsdam Inst Climate Impact Res, Potsdam, Germany;Univ North Carolina Greensboro, Dept Phys & Astron, Greensboro, NC 27402 USA | Jadavpur Univ, Dept Math, Kolkata 700032, India;Potsdam Inst Climate Impact Res, Potsdam, Germany;Univ North Carolina Greensboro, Dept Phys & Astron, Greensboro, NC 27402 USA | 1951-6401 | null | 9 | 1993;2000;2001;2002;2004;2005;2006;2007;2008;2010;2011;2012;2013;2017 | 4 | Univ North Carolina Greensboro, Dept Phys & Astron, Greensboro, NC 27402 USA | Eur. Phys. J.-Spec. Top. | Dana, Syamal K | SPRINGER HEIDELBERG | ,;3-gene;a;additive;allows;an;analog;and;are;behavior;behavior's;behaviors;between;change;chemical;circuit;circuits;complementary;complexity;component;conditions;conversions;coupled;coupling;critically;design;dynamical;electrical;electronic;especially;experiment;experiments;extend;extrinsic;features;for;framework;from;function;genetic;here;Hill;important;improved;in;include;includes;incorporation;inhibition;initial;intrinsic;investigations;is;isolated;it;kinetics;make;mimic;model;models;multistability;network;networks;noise;numerical;of;our;parameters;particularly;potential;presence;present;previous;providing;quorum;real;representing;repressilator;Repressilators;results;reveal;sensing;show;shows;simulations;studies;studying;synthetic;systematic;systems;systems';that;the;this;to;tools;us;useful;values;verification;version;we;when;which | Univ North Carolina Greensboro | Electronic circuits are useful tools for studying potential dynamical behaviors of synthetic genetic networks. The circuit models are complementary to numerical simulations of the networks, especially providing a framework for verification of dynamical behaviors in the presence of intrinsic and extrinsic noise of the electrical systems. Here we present an improved version of our previous design of an electronic analog of genetic networks that includes the 3-gene Repressilator and we show conversions between model parameters and real circuit component values to mimic the numerical results in experiments. Important features of the circuit design include the incorporation of chemical kinetics representing Hill function inhibition, quorum sensing coupling, and additive noise. Especially, we make a circuit design for a systematic change of initial conditions in experiment, which is critically important for studies of dynamical systems' behavior, particularly, when it shows multistability. This improved electronic analog of the synthetic genetic network allows us to extend our investigations from an isolated Repressilator to coupled Repressilators and to reveal the dynamical behavior's complexity. | AAN-7714-2021 | REPRESSILATORS;SYNCHRONIZATION | 0 | null | null | 18 | repressilator;SYNCHRONIZATION | WOS:000403684400010 | Jadavpur Univ, Kolkata, India;Potsdam Inst Climate Impact Res, Potsdam, Germany;Univ North Carolina Greensboro, Greensboro, NC USA | Germany;India;USA | 2,017 | null | 0000-0001-5060-7220 | null | null | English | null | ANNU REV CELL DEV BI;CHAOS;INT J BIFURCAT CHAOS;NAT REV GENET;NATURE;P NATL ACAD SCI USA;PHYS REV E;PHYS REV LETT;PLOS ONE;SCI AM;SIMULATING ANAL ANIM | Dana, Syamal K;Hellen, Edward H;Kurths, Jurgen | 2024-03-11
ER | Benenson, Y;Buldu, J M;Elowitz, M;Elowitz, M B;Ermentrout G. B.;Garcia-Ojalvo, J;Gardner, T S;Hasty, J;Hellen, E H;Mason, J;Potapov, I;Strogatz, S H;Tokuda, I T;Ullner, E;Wagemakers, A;Waters, C M | EY0XO | Greensboro, NC USA | 4 | null | 3 | null | null | Dana, Syamal K;Hellen, Edward H;Kurths, Jurgen | EUR PHYS J-SPEC TOP | Greensboro, NC USA;Kolkata, India;Potsdam, Germany |
Kurths, J;Wang, H Y;Wu, J;Xu, Y | 10.1063/1.4984806 | 063105 | 1305 WALT WHITMAN RD, STE 300, MELVILLE, NY 11747-4501 USA | 5w3f4a16h34176x3p1d3x2n1h20g03g343566 | Information-based measures for logical stochastic resonance in a synthetic gene network under Levy flight superdiffusion | Northwestern Polytech Univ | null | Xu, Y (corresponding author), Beifang Univ Nationalities, Sch Math & Informat Sci, Yinchuan 750021, Peoples R China.;Xu, Y (corresponding author), Humboldt Univ, Dept Phys, D-12489 Berlin, Germany.;Xu, Y (corresponding author), Northwestern Polytech Univ, Dept Appl Math, Xian 710072, Peoples R China.;Xu, Y (corresponding author), Potsdam Inst Climate Impact Res, D-14412 Potsdam, Germany. | null | Kurths, Juergen;Wang, Haiyan;Wu, Juan;Xu, Yong | Mathematics, Applied;Physics, Mathematical | National Natural Science Foundation of China [11602003, 11372247] | WOS | Xu, Y | Beifang Univ Nationalities, Yinchuan, Peoples R China;Humboldt Univ, Berlin, Germany;Northwestern Polytech Univ, Xian, Peoples R China;Potsdam Inst Climate Impact Res, Potsdam, Germany | 27 | a;flight;for;gene;in;information-based;Levy;logical;measures;network;resonance;stochastic;superdiffusion;synthetic;under | 2 | Kurths, Juergen;Xu, Yong | AMER INST PHYSICS | Beifang Univ Nationalities, Sch Math & Informat Sci, Yinchuan 750021, Peoples R China;Humboldt Univ, Dept Phys, D-12489 Berlin, Germany;Northwestern Polytech Univ, Dept Appl Math, Xian 710072, Peoples R China;Northwestern Polytech Univ, Dept Appl Math, Xian 710072, Peoples R China.; Xu, Y (corresponding author), Beifang Univ Nationalities, Sch Math & Informat Sci, Yinchuan 750021, Peoples R China.; Xu, Y (corresponding author), Potsdam Inst Climate Impact Res, D-14412 Potsdam, Germany.; Xu, Y (corresponding author), Humboldt Univ, Dept Phys, D-12489 Berlin, Germany;Northwestern Polytech Univ, Sch Marine Sci & Technol, Xian 710072, Peoples R China;Potsdam Inst Climate Impact Res, D-14412 Potsdam, Germany | Article | Beifang Univ Nationalities;Humboldt Univ;Northwestern Polytech Univ;Potsdam Inst Climate Impact Res | MELVILLE | null | null | Beifang Univ Nationalities;Humboldt Univ;Northwestern Polytech Univ;Potsdam Inst Climate Impact Res | National Natural Science Foundation of China | Xu, Y (corresponding author), Northwestern Polytech Univ, Dept Appl Math, Xian 710072, Peoples R China.; Xu, Y (corresponding author), Beifang Univ Nationalities, Sch Math & Informat Sci, Yinchuan 750021, Peoples R China.; Xu, Y (corresponding author), Potsdam Inst Climate Impact Res, D-14412 Potsdam, Germany.; Xu, Y (corresponding author), Humboldt Univ, Dept Phys, D-12489 Berlin, Germany. | null | Kurths, Juergen;Wang, Haiyan;Wu, Juan;Xu, Yong | 38 | 5 | 404,630,200,007 | National Natural Science Foundation of China [11602003, 11372247] | China;Germany | CHAOS | China;Germany | null | null | Northwestern Polytech Univ, Dept Appl Math, Xian 710072, Peoples R China | 1054-1500 | Kurths, J;Wang, H Y;Wu, J;Xu, Y | JUN | hsux3@nwpu.edu.cn | information-based measures;Levy flight superdiffusion;logical stochastic resonance;synthetic gene network | 4 | J | Mathematics;Physics | accomplished logical stochastic resonance;AIP Publishing;DYNAMICS;information-based measures;information-based methodology;Levy flight superdiffusion;Levy noise;logic gates;logical information transmission;LOGICAL STOCHASTIC RESONANCE;MODEL;mutual information;mutual information changes;noise;noise entropy;potential;repressive proteins;square wave signal;stochastic synthetic gene network model;symbol error rate;synchronization degree;synchronization variances;synthetic gene network;SYSTEM;toggle switch;two repressive proteins | Wu, J | DYNAMICS;MODEL;NOISE;SYSTEM;toggle switch | null | [Wu, Juan; Xu, Yong] Northwestern Polytech Univ, Dept Appl Math, Xian 710072, Peoples R China. [Wu, Juan; Xu, Yong] Beifang Univ Nationalities, Sch Math & Informat Sci, Yinchuan 750021, Peoples R China. [Wu, Juan; Xu, Yong; Kurths, Juergen] Potsdam Inst Climate Impact Res, D-14412 Potsdam, Germany. [Xu, Yong; Kurths, Juergen] Humboldt Univ, Dept Phys, D-12489 Berlin, Germany. [Wang, Haiyan] Northwestern Polytech Univ, Sch Marine Sci & Technol, Xian 710072, Peoples R China. | This work was supported by the National Natural Science Foundation of China under Grant Nos. 11602003 and 11372247. Y. Xu acknowledges the Alexander von Humboldt Foundation and the Fundamental Research Funds for the Central Universities. | accomplished logical stochastic resonance;AIP Publishing;information-based methodology;Levy flight superdiffusion;Levy noise;logic gates;logical information transmission;logical stochastic resonance;mutual information;mutual information changes;noise entropy;potential;repressive proteins;square wave signal;stochastic synthetic gene network model;symbol error rate;synchronization degree;synchronization variances;synthetic gene network;two repressive proteins | 10.1007/s10955-013-0782-0;10.1007/s11071-012-0473-4;10.1007/s11071-013-1136-9;10.1007/s11431-015-6001-2;10.1016/j.bpj.2011.11.4000;10.1016/j.chaos.2016.09.015;10.1016/j.cnsns.2012.07.010;10.1016/j.physa.2014.08.042;10.1016/j.physrep.2006.12.004;10.1038/35002131;10.1038/srep31505;10.1063/1.3660159;10.1063/1.4775758;10.1063/1.4945420;10.1063/1.4948461;10.1073/pnas.0402940101;10.1073/pnas.040411297;10.1088/1751-8113/40/26/005;10.1103/PhysRevE.83.041909;10.1103/PhysRevE.88.052721;10.1103/PhysRevE.94.042222;10.1103/PhysRevLett.102.104101;10.1142/S021797920603576X;10.1142/S0217979214502233;10.1142/S0218127408021877;10.1186/1752-0509-1-50;10.1209/0295-5075/113/30009;10.1209/0295-5075/93/50001;10.1371/journal.pone.0016168;10.1371/journal.pone.0076032 | Northwestern Polytech Univ | Kurths, J;Wang, H Y;Wu, J;Xu, Y | Wu, J: Northwestern Polytech Univ, Dept Appl Math, Xian 710072, Peoples R China | Xu, Yong | 11372247;11602003 | 33 | null | China | Beifang Univ Nationalities;Humboldt Univ;Northwestern Polytech Univ;Potsdam Inst Climate Impact Res | Wu, Juan | null | DYNAMICS;MODEL;NOISE;SYSTEM;TOGGLE SWITCH | Wu, Juan; Xu, Yong; Wang, Haiyan; Kurths, Juergen; | null | Beifang Univ Nationalities, Sch Math & Informat Sci, Yinchuan 750021, Peoples R China;Humboldt Univ, Dept Phys, D-12489 Berlin, Germany;Northwestern Polytech Univ, Dept Appl Math, Xian 710072, Peoples R China;Northwestern Polytech Univ, Sch Marine Sci & Technol, Xian 710072, Peoples R China;Potsdam Inst Climate Impact Res, D-14412 Potsdam, Germany | Beifang Univ Nationalities, Sch Math & Informat Sci, Yinchuan 750021, Peoples R China;Humboldt Univ, Dept Phys, D-12489 Berlin, Germany;Northwestern Polytech Univ, Dept Appl Math, Xian 710072, Peoples R China;Northwestern Polytech Univ, Sch Marine Sci & Technol, Xian 710072, Peoples R China;Potsdam Inst Climate Impact Res, D-14412 Potsdam, Germany | 1089-7682 | null | 6 | 1982;1986;1994;2000;2004;2006;2007;2008;2009;2011;2012;2013;2014;2016 | 36 | Beifang Univ Nationalities, Sch Math & Informat Sci, Yinchuan 750021, Peoples R China;Humboldt Univ, Dept Phys, D-12489 Berlin, Germany;Northwestern Polytech Univ, Dept Appl Math, Xian 710072, Peoples R China;Potsdam Inst Climate Impact Res, D-14412 Potsdam, Germany | Chaos | Kurths, Juergen | AMER INST PHYSICS | ";,;a;accomplished;achieve;addition;AIP;almost;an;analyze;and;as;based;between;by;calculate;can;caused;changes;complementary;consequently;degree;demonstrate;driven;entropy;error;first;flight;for;furthermore;gates;gene;in;information;information-based;investigate;Levy;logic;logical;methodology;model;mutual;network;noise;numerically;obtain;of;off;on;potential;present;proteins;published;Publishing;quantify;rate;repressive;resonance;reveal;shown;shows;signal;some;square;states;stochastic;superdiffusion;symbol;synchronization;synchronously;synthetic;that;the;then;theoretically;those;to;transmission;two;under;variances;wave;we;well;which | Beifang Univ Nationalities;Humboldt Univ;Northwestern Polytech Univ;Potsdam Inst Climate Impact Res | We investigate the logical information transmission of a synthetic gene network under Levy flight superdiffusion by an information-based methodology. We first present the stochastic synthetic gene network model driven by a square wave signal under Levy noise caused by Levy flight superdiffusion. Then, to quantify the potential of logical information transmission and logical stochastic resonance, we theoretically obtain an information-based methodology of the symbol error rate, the noise entropy, and the mutual information of the logical information transmission. Consequently, based on the complementary "on" and "off" states shown in the logical information transmission for the repressive proteins, we numerically calculate the symbol error rate for logic gates, which demonstrate that the synthetic gene network under Levy noise can achieve some logic gates as well as logical stochastic resonance. Furthermore, we calculate the noise entropy and the mutual information between the square wave signal and the logical information transmission, which reveal and quantify the potential of logical information transmission and logical stochastic resonance. In addition, we analyze the synchronization degree of the mutual information for the accomplished logical stochastic resonance of two repressive proteins of the synthetic gene network by synchronization variances, which shows that those mutual information changes almost synchronously. Published by AIP Publishing. | D-7348-2017 | DYNAMICS;MODEL;NOISE;SYSTEM;TOGGLE SWITCH | 1 | null | null | 9 | DYNAMICS;MODEL;NOISE;SYSTEM;toggle switch | WOS:000404630200007 | Beifang Univ Nationalities, Yinchuan, Peoples R China;Humboldt Univ, Berlin, Germany;Northwestern Polytech Univ, Xian, Peoples R China;Potsdam Inst Climate Impact Res, Potsdam, Germany | China;Germany | 2,017 | null | 0000-0002-5926-4276;0000-0002-8407-4650 | null | null | English | null | BIOPHYS J;BMC SYST BIOL;CHAOS;CHAOS SOLITON FRACT;COMMUN NONLINEAR SCI;EPL-EUROPHYS LETT;INT J BIFURCAT CHAOS;INT J MOD PHYS B;J CHEM PHYS;J PHYS A-MATH THEOR;J STAT PHYS;LEVY WALKS VERSUS LE;NATURE;NONLINEAR DYNAM;P NATL ACAD SCI USA;PHYS REP;PHYS REV E;PHYS REV LETT;PHYSICA A;PLOS ONE;SCI CHINA TECHNOL SC;SCI REP-UK;SIMULATION CHAOTIC B;The fractal geometry of nature | Kurths, Juergen;Wang, Haiyan;Wu, Juan;Xu, Yong | 2024-03-11
ER | Ando, H;Andrecut, M;Bianco-Martinez, E;Chen, H;Dari, A;Daza, A;Dubkov, A A;Gardner, T S;Hasty, J;Hellen, E H;Hlavácková-Schindler, K;Janicki, A;Klafter, J;Kobayashi, H;Li, Y G;Mandelbrot B. B.;Murali, K;Nurzaman, S G;Sharma, A;Strasser, M;Wang, J W;Wang, Z Q;Xu, Y;Zeng, C H;Zeng, L Z | EZ3SH | Berlin, Germany;Potsdam, Germany.;Xian, Peoples R China.;Yinchuan, Peoples R China. | 39 | null | 4 | null | 28,679,222 | Kurths, Juergen;Wang, Haiyan;Wu, Juan;Xu, Yong | CHAOS | Berlin, Germany;Potsdam, Germany;Xian, Peoples R China;Yinchuan, Peoples R China |
Allgöwer, F;Halter, W;Montenbruck, J M;Tuza, Z A | 10.1016/j.jtbi.2017.03.004 | null | 24-28 OVAL RD, LONDON NW1 7DX, ENGLAND | a4e3a4d2g2s4g364214184t2962c2x6y6s4434 | A resource dependent protein synthesis model for evaluating synthetic circuits | Univ Stuttgart | null | Halter, W (corresponding author), Univ Stuttgart, Inst Syst Theory & Automat Control, Pfaffenwaldring 9, Stuttgart, Germany. | null | Allgoewer, Frank;Halter, Wolfgang;Montenbruck, Jan Maximilian;Tuza, Zoltan A | Biology;Mathematical & Computational Biology | Ministry for Science, Research and Art Baden-Wurttemberg | WOS | Halter, W | Univ Stuttgart, Stuttgart, Germany | 420 | a;circuits;dependent;evaluating;for;model;protein;resource;synthesis;synthetic | 1 | Allgöwer, Frank;Halter, Wolfgang | ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD | Univ Stuttgart, Inst Syst Theory & Automat Control, Pfaffenwaldring 9, Stuttgart, Germany | Article | Univ Stuttgart | LONDON | null | null | Univ Stuttgart | Ministry for Science, Research and Art Baden-Wurttemberg | Halter, W (corresponding author), Univ Stuttgart, Inst Syst Theory & Automat Control, Pfaffenwaldring 9, Stuttgart, Germany. | 278 | Allgoewer, Frank;Halter, Wolfgang;Montenbruck, Jan Maximilian;Tuza, Zoltan A | 4 | 1 | 400,952,700,027 | Ministry for Science, Research and Art Baden-Wurttemberg | Germany | JOURNAL OF THEORETICAL BIOLOGY | Germany | null | null | Univ Stuttgart, Inst Syst Theory & Automat Control, Pfaffenwaldring 9, Stuttgart, Germany | 0022-5193 | Allgöwer, F;Halter, W;Montenbruck, J M;Tuza, Z A | MAY 7 | wolfgang.halter@ist.uni-stuttgart.de | resource dependent protein synthesis model;synthetic circuits | 4 | J | Life Sciences & Biomedicine - Other Topics;Mathematical & Computational Biology | convergence properties;different loading scenarios;DNA templates;dynamic mechanisms;DYNAMICS;expression;Genetic regulatory networks;geometric considerations;host-circuit interactions;influence;limited resources;LIVE ESCHERICHIA-COLI;movement;mRNA;Normally hyperbolic manifolds;novel approaches;novel protein synthesis;present additional insights;process;protein synthesis;Resource dependence;resource dependent protein synthesis model;Ribosome Flow Model;RIBOSOMES;RNA-POLYMERASE;silico design;synthetic biology;synthetic circuits;synthetic gene circuits;synthetic gene networks | Halter, W | DYNAMICS;EXPRESSION;Genetic regulatory networks;host-circuit interactions;LIVE ESCHERICHIA-COLI;Normally hyperbolic manifolds;Resource dependence;RNA-POLYMERASE;Synthetic biology | 267 | [Halter, Wolfgang; Montenbruck, Jan Maximilian; Tuza, Zoltan A.; Allgoewer, Frank] Univ Stuttgart, Inst Syst Theory & Automat Control, Pfaffenwaldring 9, Stuttgart, Germany. | This work was supported by the research cluster BW<SUP>2</SUP> (www.bwbiosyn.de) of the Ministry for Science, Research and Art Baden-Wurttemberg. | convergence properties;different loading scenarios;DNA templates;dynamic mechanisms;geometric considerations;influence;limited resources;movement;mRNA;novel approaches;novel protein synthesis;present additional insights;process;protein synthesis;Ribosome Flow Model;ribosomes;RNA-polymerase;silico design;synthetic gene circuits;synthetic gene networks | 10.1006/jsbi.1997.3845;10.1007/BF01403247;10.1016/0022-2836(77)90279-0;10.1016/j.bpj.2013.10.024;10.1016/j.bpj.2015.06.034;10.1016/j.ydbio.2008.10.043;10.1021/acssynbio.6b00040;10.1038/35002125;10.1038/ismej.2012.94;10.1073/pnas.1416533112;10.1073/pnas.94.3.814;10.1090/S0002-9939-1960-0121542-7;10.1093/nar/25.4.787;10.1093/nar/gkf549;10.1093/nar/gkp889;10.1098/rsif.2014.0713;10.1098/rsif.2015.1062;10.1103/PhysRevE.68.021910;10.1109/TBCAS.2013.2290063;10.1109/TCBB.2012.88;10.1111/j.1365-2958.2012.08081.x;10.1126/science.282.5390.902;10.1128/ecosal.5.2.3;10.1128/JB.181.20.6425-6440.1999;10.1137/0513013;10.1371/journal.pcbi.1002127;10.1371/journal.pone.0096039 | Univ Stuttgart | Allgöwer, F;Halter, W;Montenbruck, J M;Tuza, Z A | Halter, W: Univ Stuttgart, Inst Syst Theory & Automat Control, Pfaffenwaldring 9, Stuttgart, Germany | Allgöwer, Frank;Tuza, Zoltan Andras | null | 31 | null | Germany | Univ Stuttgart | Halter, Wolfgang | Green Submitted | DYNAMICS;EXPRESSION;LIVE ESCHERICHIA-COLI;RNA-POLYMERASE | Halter, Wolfgang; Montenbruck, Jan Maximilian; Tuza, Zoltan A.; Allgoewer, Frank; | null | Univ Stuttgart, Inst Syst Theory & Automat Control, Pfaffenwaldring 9, Stuttgart, Germany | Univ Stuttgart, Inst Syst Theory & Automat Control, Pfaffenwaldring 9, Stuttgart, Germany | 1095-8541 | host-circuit interactions;Genetic regulatory networks;Normally hyperbolic manifolds;Resource dependence;Synthetic biology | null | 1960;1967;1970;1977;1982;1997;1998;1999;2000;2002;2003;2008;2009;2010;2011;2012;2013;2014;2015;2016 | 4 | Univ Stuttgart, Inst Syst Theory & Automat Control, Pfaffenwaldring 9, Stuttgart, Germany | J. Theor. Biol. | Allgoewer, Frank | ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD | ,;a;additional;among;analyzing;and;approaches;based;be;by;can;circuits;considerations;convergence;demonstrate;describes;design;different;DNA;dynamic;evaluate;flow;from;further;gene;geometric;how;in;influence;insights;into;limited;loading;mechanisms;model;movement;mRNA;necessitates;networks;novel;of;on;originates;other;performance;present;process;properties;protein;reliable;resources;respectively;Ribosome;ribosomes;RNA-polymerase;scenarios;silico;such;synthesis;synthetic;templates;the;things;this;to;under;upon;used;we;which | Univ Stuttgart | Reliable in silico design of synthetic gene networks necessitates novel approaches to model the process of protein synthesis under the influence of limited resources. We present such a novel protein synthesis model which originates from the Ribosome Flow Model and among other things describes the movement of RNA-polymerase and ribosomes on mRNA and DNA templates, respectively. By analyzing the convergence properties of this model based upon geometric considerations, we present additional insights into the dynamic mechanisms of the process of protein synthesis. Further, we demonstrate how this model can be used to evaluate the performance of synthetic gene circuits under different loading scenarios. | F-3909-2011;G-2627-2014 | DYNAMICS;EXPRESSION;LIVE ESCHERICHIA-COLI;RNA-POLYMERASE | 0 | null | Genetic regulatory networks;host-circuit interactions;Normally hyperbolic manifolds;Resource dependence;Synthetic biology | 12 | host-circuit interactions;DYNAMICS;EXPRESSION;Genetic regulatory networks;LIVE ESCHERICHIA-COLI;Normally hyperbolic manifolds;Resource dependence;RNA-POLYMERASE;Synthetic biology | WOS:000400952700027 | Univ Stuttgart, Stuttgart, Germany | Germany | 2,017 | null | 0000-0001-9902-5782;0000-0002-3702-3658 | null | null | English | null | ACS SYNTH BIOL;BIOPHYS J;DEV BIOL;Die Grundlehren der mathematischen Wissenschaften;ECOSAL PLUS;IEEE ACM T COMPUT BI;IEEE T BIOMED CIRC S;INVENT MATH;ISME J;J BACTERIOL;J MOL BIOL;J R SOC INTERFACE;J STRUCT BIOL;MOL MICROBIOL;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PHYS REV E;PLOS COMPUT BIOL;PLOS ONE;Proc Amer Math Soc;SCIENCE;SIAM J MATH ANAL;The theory of matrices | Allgoewer, Frank;Halter, Wolfgang;Montenbruck, Jan Maximilian;Tuza, Zoltan A | 2024-03-11
ER | [Anonymous];Bakshi, S;Bremer Hans;De-Leon, S B T;Edri, S;Elowitz, M B;Gantmacher F.R.;Gorochowski, T E;Gyorgy, A;Hahn W.;Hartman, P;Hirsch, M W;Kennell, D;Margaliot, M;Mcadams, H H;Milo, R;Moran, M A;Poker, G;Pugh, C;Raveh, A;Reuveni, S;Rogozin, I B;Selby, C P;Shaw, L B;Tao, H;Wang, M D;Weisse, A Y;Zhu, J | EU3TA | Stuttgart, Germany | 4 | null | 1 | null | 28,286,216 | Allgoewer, Frank;Halter, Wolfgang;Montenbruck, Jan Maximilian;Tuza, Zoltan A | J THEOR BIOL | Stuttgart, Germany |
Dapper, A L;Drury, D W;Siniard, D J;Wade, M J;Zentner, G E | 10.1126/sciadv.1601910 | e1601910 | 1200 NEW YORK AVE, NW, WASHINGTON, DC 20005 USA | e3p4k3g38582468324z5d6j1l4u3iw4135f1f | CRISPR/Cas9 gene drives in genetically variable and nonrandomly mating wild populations | Indiana Univ | null | Wade, MJ (corresponding author), Indiana Univ, Dept Biol, Bloomington, IN 47405 USA. | null | Dapper, Amy L;Drury, Douglas W;Siniard, Dylan J;Wade, Michael J;Zentner, Gabriel E | Multidisciplinary Sciences | Indiana University startup funds [NIH R01 GM084238]; NSF Doctora lDissertation Improvement Grant [1311167]; Division Of Environmental Biology; Direct For Biological Sciences [1311167] Funding Source: National Science Foundation | WOS | Wade, M J | Indiana Univ, Bloomington, IN USA;Univ Wisconsin, Madison, WI USA | 3 | and;CRISPR/Cas9;Drives;gene;genetically;in;mating;nonrandomly;populations;variable;wild | 1 | Zentner, Gabriel | AMER ASSOC ADVANCEMENT SCIENCE | Indiana Univ, Dept Biol, Bloomington, IN 47405 USA;Univ Wisconsin, Genet Lab, Madison, WI 53706 USA | Article | Indiana Univ | WASHINGTON | null | null | Indiana Univ;Univ Wisconsin | Direct For Biological Sciences;Division Of Environmental Biology;Indiana University startup funds;NSF Doctora lDissertation Improvement Grant | Wade, MJ (corresponding author), Indiana Univ, Dept Biol, Bloomington, IN 47405 USA. | null | Dapper, Amy L;Drury, Douglas W;Siniard, Dylan J;Wade, Michael J;Zentner, Gabriel E | 23 | 2 | 401,955,300,006 | Direct For Biological Sciences [1311167] Funding Source: National Science Foundation;Division Of Environmental Biology;Indiana University startup funds [NIH R01 GM084238];NSF Doctora lDissertation Improvement Grant [1311167] | USA | SCIENCE ADVANCES | USA | null | null | Indiana Univ, Dept Biol, Bloomington, IN 47405 USA | 2375-2548 | Dapper, A L;Drury, D W;Siniard, D J;Wade, M J;Zentner, G E | MAY | mjwade@indiana.edu | CRISPR/Cas9 gene drives;nonrandomly mating wild populations;variable | 5 | J | Science & Technology - Other Topics | (ITD);BINDING;Cas9;Cas9 target sites;characteristic;characterization;CRISPR/Cas9;CRISPR/Cas9 gene drives;CRISPR/Cas9-based synthetic gene drive;crop pests;designing;disease vectors;disease-vectoring arthropods;drives will;effect;efficacy;equivalent;flour beetle Tribolium castaneum;four populations;function;genetic data;genetic variability;genome-wide analysis;immune;mating system;mild inbreeding;MUTAGENIC CHAIN-REACTION;MUTATIONS;nonrandomly mating wild populations;OFF-TARGET SITES;POPULATIONS;populations harbor genetic variants;potential;rare ITD allele;RNA-GUIDED ENDONUCLEASE;synthetic gene drives;SYSTEM;TRIBOLIUM-CASTANEUM;variable;vector;wild populations | Drury, D W | BINDING;CAS9;GENOME-WIDE ANALYSIS;MUTAGENIC CHAIN-REACTION;MUTATIONS;OFF-TARGET SITES;RNA-GUIDED ENDONUCLEASE;SYSTEM;TRIBOLIUM-CASTANEUM;VECTOR | null | [Drury, Douglas W.; Dapper, Amy L.; Siniard, Dylan J.; Zentner, Gabriel E.; Wade, Michael J.] Indiana Univ, Dept Biol, Bloomington, IN 47405 USA. [Dapper, Amy L.] Univ Wisconsin, Genet Lab, Madison, WI 53706 USA. | This work was supported by Indiana University startup funds (G.E.Z.) and NIH R01 GM084238 (M.J.W.). The sequencing was supported by an NSF Doctora lDissertation Improvement Grant (1311167 to M.J.W and A.L.D). | (ITD);Cas9 target sites;characteristic;characterization;CRISPR/Cas9;CRISPR/Cas9-based synthetic gene drive;crop pests;designing;disease vectors;disease-vectoring arthropods;drives will;effect;efficacy;equivalent;flour beetle Tribolium castaneum;four populations;function;genetic data;genetic variability;immune;mating system;mild inbreeding;populations;populations harbor genetic variants;potential;rare ITD allele;synthetic gene drives;wild populations | 10.1016/j.cell.2015.09.038;10.1016/j.cell.2016.10.044;10.1016/j.gene.2005.04.025;10.1016/S0005-2736(99)00064-4;10.1038/154607a0;10.1038/nature13011;10.1038/nature14299;10.1038/nature14592;10.1038/nbt.2889;10.1038/nbt.2916;10.1038/nbt.3439;10.1038/sj.hdy.6885930;10.1038/srep00288;10.1038/srep05405;10.1046/j.1365-2540.2000.00676.x;10.1073/pnas.1521077112;10.1093/bioinformatics/btp324;10.1093/bioinformatics/btr589;10.1093/bioinformatics/btu743;10.1093/emph/eow030;10.1093/nar/gkp807;10.1093/nar/gkv137;10.1111/eva.12219;10.1111/j.1420-9101.2011.02394.x;10.1126/science.122.3163.287;10.1126/science.130.3380.902;10.1126/science.aaa5945;10.1146/annurev.ge.01.120167.000345;10.1371/journal.pone.0077904;10.1371/journal.pone.0128036;10.1534/genetics.115.177592;10.4269/ajtmh.2001.65.491;10.7554/eLife.03401 | Indiana Univ | Dapper, A L;Drury, D W;Siniard, D J;Wade, M J;Zentner, G E | Drury, D W: Indiana Univ, Dept Biol, Bloomington, IN 47405 USA | null | 1311167;NIH R01 GM084238 | 40 | null | USA | Indiana Univ;Univ Wisconsin | Drury, Douglas W | Green Published, gold, Green Submitted | BINDING;CAS9;GENOME-WIDE ANALYSIS;MUTAGENIC CHAIN-REACTION;MUTATIONS;OFF-TARGET SITES;RNA-GUIDED ENDONUCLEASE;SYSTEM;TRIBOLIUM-CASTANEUM;VECTOR | Drury, Douglas W.; Dapper, Amy L.; Siniard, Dylan J.; Zentner, Gabriel E.; Wade, Michael J.; | null | Indiana Univ, Dept Biol, Bloomington, IN 47405 USA;Univ Wisconsin, Genet Lab, Madison, WI 53706 USA | Indiana Univ, Dept Biol, Bloomington, IN 47405 USA;Univ Wisconsin, Genet Lab, Madison, WI 53706 USA | null | null | 5 | 1927;1944;1955;1959;1960;1967;1979;1987;1994;1999;2000;2001;2005;2009;2010;2011;2012;2013;2014;2015;2016;2017 | 78 | Indiana Univ, Dept Biol, Bloomington, IN 47405 USA | Sci. Adv. | Wade, Michael J | AMER ASSOC ADVANCEMENT SCIENCE | (ITD);,;a;accentuated;allele;alter;among;and;arthropods;based;beetle;but;by;can;Cas9;castaneum;characteristic;characterization;conclude;control;CRISPR/Cas9;CRISPR/Cas9-based;crop;data;designing;disease;disease-vectoring;drive;drives;effect;efficacy;eliminate;equivalent;even;flour;four;from;function;gene;genetic;harbor;have;how;immune;in;inbreeding;is;it;ITD;many;mating;mild;most;of;on;or;pests;populations;potential;rare;reduce;render;require;show;sites;some;such;suppress;synthetic;system;target;targeted;that;the;them;they;this;to;Tribolium;unclear;using;variability;variants;vectors;we;which;wild;will;within;would | Indiana Univ | Synthetic gene drives based on CRISPR/Cas9 have the potential to control, alter, or suppress populations of crop pests and disease vectors, but it is unclear how they will function in wild populations. Using genetic data from four populations of the flour beetle Tribolium castaneum, we show that most populations harbor genetic variants in Cas9 target sites, some of which would render them immune to drive (ITD). We show that even a rare ITD allele can reduce or eliminate the efficacy of a CRISPR/Cas9-based synthetic gene drive. This effect is equivalent to and accentuated by mild inbreeding, which is a characteristic of many disease-vectoring arthropods. We conclude that designing such drives will require characterization of genetic variability and the mating system within and among targeted populations. | null | BINDING;CAS9;GENOME-WIDE ANALYSIS;MUTAGENIC CHAIN-REACTION;MUTATIONS;OFF-TARGET SITES;RNA-GUIDED ENDONUCLEASE;SYSTEM;TRIBOLIUM-CASTANEUM;VECTORS | 3 | null | null | 7 | BINDING;CAS9;GENOME-WIDE ANALYSIS;MUTAGENIC CHAIN-REACTION;MUTATIONS;OFF-TARGET SITES;RNA-GUIDED ENDONUCLEASE;SYSTEM;Tribolium castaneum;VECTORS | WOS:000401955300006 | Indiana Univ, Bloomington, IN USA;Univ Wisconsin, Madison, WI USA | USA | 2,017 | null | 0000-0002-0801-7646 | null | null | English | null | AM J TROP MED HYG;ANNU REV GENET;BBA-BIOMEMBRANES;BIOINFORMATICS;CELL;CR SOC BIOL;ELEMENTS EVOLUTIONAR;ELIFE;EVOL APPL;EVOL MED PUBLIC HLTH;GENE;GENETICS;HEREDITY;J EVOLUTION BIOL;NAT BIOTECHNOL;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;Phytochemical Bulletin;PLOS ONE;QUANT BIOL;SCI REP-UK;SCIENCE | Dapper, Amy L;Drury, Douglas W;Siniard, Dylan J;Wade, Michael J;Zentner, Gabriel E | 2024-03-11
ER | Baym, M;Bull, J J;Bushland, R C;Chan, S W;Charlesworth B.;Dobrovolskaïa-Zavadskaïa, N;Donnelly, M J;Doyle J.J.;Drury, D W;Esvelt, K M;Gantz, V M;Hammond, A;Hiraizumi, Y;Kim, H S;Kleinstiver, B P;Knipling, E F;Kofler, R;Komor, A C;Krstic, D;Kuscu, C;Lewontin R. C.;Li, H;Lu, Y H;Mackenzie, S M;Naito, Y;O'Geen, H;Ran, F A;Robert, M A;Sternberg, S H;Turner, B C;Unckless, R L;Urbanelli, S;Vanderplank, F L;Vazeille, M;Wade, M J;Wu Xuebing;Wu, X B;Zetsche, B;Zhang, Y L | EV7KW | Bloomington, IN USA | 84 | null | 2 | null | 28,560,324 | Dapper, Amy L;Drury, Douglas W;Siniard, Dylan J;Wade, Michael J;Zentner, Gabriel E | SCI ADV | Bloomington, IN USA;Madison, WI USA |
Andrews, B;Boone, C;Costanzo, M;Myers, C L;Tan, Y Z;Usaj, M;VanderSluis, B;Wang, W;Zou, A | 10.1534/g3.117.040220 | null | 9650 ROCKVILLE AVE, BETHESDA, MD 20814 USA | 5bl63371g2rl5v5p1e5p15f37g3j58q4o2 | TheCellMap. org: A Web-Accessible Database for Visualizing and Mining the Global Yeast Genetic Interaction Network | Univ Toronto | null | Costanzo, M; Andrews, B; Boone, C (corresponding author), Univ Toronto, Donnelly Ctr, 160 Coll St,Room 13212, Toronto, ON M5S 3E1, Canada.;Myers, CL (corresponding author), Univ Minnesota Twin Cities, Dept Comp Sci & Engn, 200 Union St, Minneapolis, MN 55455 USA. | null | Andrews, Brenda;Boone, Charles;Costanzo, Michael;Myers, Chad L;Tan, Yizhao;Usaj, Matej;VanderSluis, Benjamin;Wang, Wen;Zou, Albert | Genetics & Heredity | National Institutes of Health [R01HG005853, R01HG005084]; Canadian Institutes of Health Research [FDN-143264, FDN-143265]; National Science Foundation [DBI\0953881]; Direct For Biological Sciences; Div Of Biological Infrastructure [0953881] Funding Source: National Science Foundation | WOS | Andrews, B;Boone, C;Costanzo, M;Myers, C L | Princeton Univ, Princeton, NJ USA;Simons Fdn, New York, NY USA;Univ Minnesota Twin Cities, Minneapolis, MN USA;Univ Toronto, Toronto ON, Canada | 7 | :;a;and;Database;for;genetic;Global;Interaction;Mining;network;org;the;theCellMap;Visualizing;Web-Accessible;yeast | 2 | Usaj, Matej;Wang, Wen | GENETICS SOCIETY AMERICA | B; Boone, C (corresponding author), Univ Toronto, Donnelly Ctr, 160 Coll St,Room 13212, Toronto, ON M5S 3E1, Canada.; Myers, CL (corresponding author), Univ Minnesota Twin Cities, Dept Comp Sci & Engn, 200 Union St, Minneapolis, MN 55455 USA;Princeton Univ, Lewis Sigler Inst Integrat Genom, Princeton, NJ 08544 USA;Simons Fdn, Simons Ctr Data Anal, New York, NY 10010 USA;Univ Minnesota Twin Cities, Dept Comp Sci & Engn, 200 Union St, Minneapolis, MN 55455 USA;Univ Toronto, Dept Mol Genet, Toronto, ON M5S 3E1, Canada;Univ Toronto, Donnelly Ctr, 160 Coll St,Room 13212, Toronto, ON M5S 3E1, Canada | Article | Univ Minnesota Twin Cities;Univ Toronto | BETHESDA | null | null | Princeton Univ;Simons Fdn;Univ Minnesota Twin Cities;Univ Toronto | Canadian Institutes of Health Research;Direct For Biological Sciences;Div Of Biological Infrastructure;National Institutes of Health;National Science Foundation | Costanzo, M; Andrews, B; Boone, C (corresponding author), Univ Toronto, Donnelly Ctr, 160 Coll St,Room 13212, Toronto, ON M5S 3E1, Canada.; Myers, CL (corresponding author), Univ Minnesota Twin Cities, Dept Comp Sci & Engn, 200 Union St, Minneapolis, MN 55455 USA. | 1549 | Andrews, Brenda;Boone, Charles;Costanzo, Michael;Myers, Chad L;Tan, Yizhao;Usaj, Matej;VanderSluis, Benjamin;Wang, Wen;Zou, Albert | 6 | 5 | 400,822,200,014 | Canadian Institutes of Health Research [FDN-143264, FDN-143265];Direct For Biological Sciences;Div Of Biological Infrastructure [0953881] Funding Source: National Science Foundation;National Institutes of Health [R01HG005853, R01HG005084];National Science Foundation [DBI\0953881] | Canada;USA | G3-GENES GENOMES GENETICS | Canada;USA | null | null | Univ Toronto, Donnelly Ctr, 160 Coll St,Room 13212, Toronto, ON M5S 3E1, Canada | 2160-1836 | Andrews, B;Boone, C;Costanzo, M;Myers, C L;Tan, Y Z;Usaj, M;VanderSluis, B;Wang, W;Zou, A | MAY | brenda.andrews@utoronto.ca;charlie.boone@utoronto.ca;cmyers@cs.umn.edu;michael.costanzo@utoronto.ca | Global Yeast Genetic Interaction Network;org;theCellMap;Web-Accessible Database | 9 | J | Genetics & Heredity | access;ANNOTATION ERRORS;budding yeast Saccharomyces cerevisiae;cell;central repository;data-driven network layouts;deletion;genetic interactions;genetic network;genome-scale Synthetic Genetic Array (SGA) experiments;Global Yeast Genetic Interaction Network;INTERACTION MAP;interactive manner;key;large-scale data validation;localization;MISSING HERITABILITY;mutants;new discoveries;ONTOLOGY;org;org serves;providing access;quantitative genetic interaction data;quantitative genomic data;SACCHAROMYCES-CEREVISIAE GENOME;storing;subnetworks;synthetic genetic array SGA;systematic Identification;theCellMap;users;Web-Accessible Database;yeast genetics | Usaj, M | ANNOTATION ERRORS;CELL;DELETION;genetic interactions;genetic network;INTERACTION MAP;LOCALIZATION;MISSING HERITABILITY;MUTANTS;ONTOLOGY;SACCHAROMYCES-CEREVISIAE GENOME;synthetic genetic array SGA;SYSTEMATIC IDENTIFICATION;yeast genetics | 1539 | [Usaj, Matej; Tan, Yizhao; Zou, Albert; Costanzo, Michael; Andrews, Brenda; Boone, Charles] Univ Toronto, Donnelly Ctr, 160 Coll St,Room 13212, Toronto, ON M5S 3E1, Canada. [Andrews, Brenda; Boone, Charles] Univ Toronto, Dept Mol Genet, Toronto, ON M5S 3E1, Canada. [Wang, Wen; VanderSluis, Benjamin; Myers, Chad L.] Univ Minnesota Twin Cities, Dept Comp Sci & Engn, 200 Union St, Minneapolis, MN 55455 USA. [VanderSluis, Benjamin] Simons Fdn, Simons Ctr Data Anal, New York, NY 10010 USA. [VanderSluis, Benjamin] Princeton Univ, Lewis Sigler Inst Integrat Genom, Princeton, NJ 08544 USA. | We thank A. Baryshnikova, D. Botstein, and members of the Andrews, Boone, and Myers labs for helpful discussions and critical comments. This work was supported by the National Institutes of Health (R01HG005853 to C.B., B.A., and C.L.M., and R01HG005084 to C.L.M.), the Canadian Institutes of Health Research (FDN-143264 and FDN-143265 to C.B. and B.A.), and the National Science Foundation (DBI\0953881 to C.L.M.). B.A., C.B., and C.L.M. are Senior Fellows in the Genetic Networks program of the Canadian Institute for Advanced Research, and C.B. is co-Director of the Program. | access;budding yeast Saccharomyces cerevisiae;central repository;data-driven network layouts;genetic interactions;genome-scale Synthetic Genetic Array (SGA) experiments;interactive manner;key;large-scale data validation;new discoveries;org;org serves;providing access;quantitative genetic interaction data;quantitative genomic data;storing;subnetworks;theCellMap;users | 10.1007/978-1-4939-1363-3_10;10.1016/0092-8674(85)90154-0;10.1016/j.cels.2016.04.014;10.1016/j.copbio.2010.11.001;10.1038/75556;10.1038/msb.2013.54;10.1038/nature00935;10.1038/nature02026;10.1038/nature11867;10.1038/ncomms9712;10.1038/NMETH.1534;10.1073/pnas.0712255105;10.1073/pnas.1119675109;10.1093/nar/gkh036;10.1093/nar/gkv1284;10.1126/science.1065810;10.1126/science.1180823;10.1126/science.285.5429.901;10.1126/science.291.5506.1001;10.1126/science.aaf1420;10.1242/jcs.00611;10.1534/g3.115.017830;[10.1038/nmeth.1890, 10.1038/NMETH.1890] | Univ Toronto | Andrews, B;Boone, C;Costanzo, M;Myers, C L;Tan, Y Z;Usaj, M;VanderSluis, B;Wang, W;Zou, A | Usaj, M: Univ Toronto, Donnelly Ctr, 160 Coll St,Room 13212, Toronto, ON M5S 3E1, Canada | Usaj, Matej;Wang, Wen;Ｂｏｏｎｅ, Ｃｈａｒｌｅｓ | 0953881;DBI\0953881;FDN-143264;FDN-143265;R01HG005084;R01HG005853 | 25 | null | Canada | Princeton Univ;Simons Fdn;Univ Minnesota Twin Cities;Univ Toronto | Usaj, Matej | Green Published, gold | ANNOTATION ERRORS;CELL;DELETION;INTERACTION MAP;LOCALIZATION;MISSING HERITABILITY;MUTANTS;ONTOLOGY;SACCHAROMYCES-CEREVISIAE GENOME;SYSTEMATIC IDENTIFICATION | Usaj, Matej; Tan, Yizhao; Wang, Wen; VanderSluis, Benjamin; Zou, Albert; Myers, Chad L.; Costanzo, Michael; Andrews, Brenda; Boone, Charles; | null | Princeton Univ, Lewis Sigler Inst Integrat Genom, Princeton, NJ 08544 USA;Simons Fdn, Simons Ctr Data Anal, New York, NY 10010 USA;Univ Minnesota Twin Cities, Dept Comp Sci & Engn, 200 Union St, Minneapolis, MN 55455 USA;Univ Toronto, Dept Mol Genet, Toronto, ON M5S 3E1, Canada;Univ Toronto, Donnelly Ctr, 160 Coll St,Room 13212, Toronto, ON M5S 3E1, Canada | Princeton Univ, Lewis Sigler Inst Integrat Genom, Princeton, NJ 08544 USA;Simons Fdn, Simons Ctr Data Anal, New York, NY 10010 USA;Univ Minnesota Twin Cities, Dept Comp Sci & Engn, 200 Union St, Minneapolis, MN 55455 USA;Univ Toronto, Dept Mol Genet, Toronto, ON M5S 3E1, Canada;Univ Toronto, Donnelly Ctr, 160 Coll St,Room 13212, Toronto, ON M5S 3E1, Canada | null | genetic interaction;Genetic networks;Synthetic genetic array (SGA);yeast genetics | 5 | 1985;1999;2000;2001;2002;2003;2004;2008;2010;2011;2012;2013;2014;2015;2016 | 78 | Univ Minnesota Twin Cities, Dept Comp Sci & Engn, 200 Union St, Minneapolis, MN 55455 USA;Univ Toronto, Donnelly Ctr, 160 Coll St,Room 13212, Toronto, ON M5S 3E1, Canada | G3-Genes Genomes Genet. | Boone, Charles | GENETICS SOCIETY AMERICA | (SGA);,;a;access;allows;an;analyzing;and;annotate;array;as;budding;by;central;cerevisiae;data;data-driven;discoveries;easily;ensure;experiments;explore;extract;for;functionally;genetic;genome-scale;genomic;in;interaction;interactions;interactive;intuitive;is;key;large-scale;layouts;manner;network;new;or;org;particular;produced;promote;providing;quantitative;reorganize;repository;Saccharomyces;serves;storing;subnetworks;synthetic;the;theCellMap;to;users;using;validation;visualize;with;yeast | Univ Minnesota Twin Cities;Univ Toronto | Providing access to quantitative genomic data is key to ensure large-scale data validation and promote new discoveries. TheCellMap. org serves as a central repository for storing and analyzing quantitative genetic interaction data produced by genome-scale Synthetic Genetic Array (SGA) experiments with the budding yeast Saccharomyces cerevisiae. In particular, TheCellMap. org allows users to easily access, visualize, explore, and functionally annotate genetic interactions, or to extract and reorganize subnetworks, using data-driven network layouts in an intuitive and interactive manner. | E-6320-2012;IQX-0075-2023;J-5454-2015 | ANNOTATION ERRORS;CELLS;DELETION;INTERACTION MAP;LOCALIZATION;MISSING HERITABILITY;MUTANTS;ONTOLOGY;SACCHAROMYCES-CEREVISIAE GENOME;SYSTEMATIC IDENTIFICATION | 0 | null | genetic interactions;genetic network;synthetic genetic array SGA;yeast genetics | 11 | ANNOTATION ERRORS;CELLS;DELETION;genetic interactions;Genetic networks;INTERACTION MAP;LOCALIZATION;MISSING HERITABILITY;MUTANTS;ONTOLOGY;SACCHAROMYCES-CEREVISIAE GENOME;Synthetic genetic array (SGA);SYSTEMATIC IDENTIFICATION;yeast genetics | WOS:000400822200014 | Princeton Univ, Princeton, NJ USA;Simons Fdn, New York, NY USA;Univ Minnesota Twin Cities, Minneapolis, MN USA;Univ Toronto, Toronto ON, Canada | Canada;USA | 2,017 | null | 0000-0002-5812-6744;0000-0003-0675-2847 | null | null | English | null | CELL;CELL SYST;CURR OPIN BIOTECH;Epistasis and the Evolutionary Process;J CELL SCI;METHODS MOL BIOL;MOL SYST BIOL;NAT COMMUN;NAT GENET;NAT METHODS;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;SCIENCE;SPRING EMBEDDERS FOR | Andrews, Brenda;Boone, Charles;Costanzo, Michael;Myers, Chad L;Tan, Yizhao;Usaj, Matej;VanderSluis, Benjamin;Wang, Wen;Zou, Albert | 2024-03-11
ER | Ashburner, M;Atias, N;Baryshnikova, A;Ben-Shitrit, T;Bloom, J S;Costanzo, M;Evangelista, M;Giaever, G;Harris, M A;Hartman, J L;Huh, W K;Kobourov S. G.;Koh, J L Y;Kuzmin, E;Mani, R;Novick, P;Phillips Pc.;Tong, A H Y;Vizeacoumar, F J;Winzeler, E A;Zuk, O | EU1YN | Minneapolis, MN USA;Toronto ON, Canada. | 95 | null | 4 | null | 28,325,812 | Andrews, Brenda;Boone, Charles;Costanzo, Michael;Myers, Chad L;Tan, Yizhao;Usaj, Matej;VanderSluis, Benjamin;Wang, Wen;Zou, Albert | G3-GENES GENOM GENET | Minneapolis, MN USA;New York, NY USA;Princeton, NJ USA;Toronto ON, Canada |
Arangundy-Franklin, S;Holliger, P;Houlihan, G | 10.1021/acs.accounts.7b00056 | null | 1155 16TH ST, NW, WASHINGTON, DC 20036 USA | 31s4m1a10681um4i3a3q2m1q2l70121f3t6j4z | Exploring the Chemistry of Genetic Information Storage and Propagation through Polymerase Engineering | MRC | null | Holliger, P (corresponding author), MRC, Lab Mol Biol, Francis Crick Ave,Cambridge Biomed Campus, Cambridge CB2 0QH, England. | null | Arangundy-Franklin, Sebastian;Holliger, Philipp;Houlihan, Gillian | Chemistry, Multidisciplinary | Medical Research Council [MC_U105178804]; MRC-AstraZeneca/MedImmune Blue Sky Grant; MRC [MC_U105178804] Funding Source: UKRI; Medical Research Council [MC_U105178804] Funding Source: researchfish | WOS | Holliger, P | MRC, Cambridge, England | 50 | and;chemistry;engineering;exploring;genetic;Information;of;polymerase;Propagation;Storage;the;through | 1 | Holliger, Philipp | AMER CHEMICAL SOC | MRC, Lab Mol Biol, Francis Crick Ave,Cambridge Biomed Campus, Cambridge CB2 0QH, England | Review | MRC | WASHINGTON | null | null | Lab Mol Biol;MRC | Medical Research Council;MRC;MRC-AstraZeneca/MedImmune Blue Sky Grant | Holliger, P (corresponding author), MRC, Lab Mol Biol, Francis Crick Ave,Cambridge Biomed Campus, Cambridge CB2 0QH, England. | 1087 | Arangundy-Franklin, Sebastian;Holliger, Philipp;Houlihan, Gillian | 46 | 1 | 399,859,800,045 | Medical Research Council [MC_U105178804];Medical Research Council [MC_U105178804] Funding Source: researchfish;MRC [MC_U105178804] Funding Source: UKRI;MRC-AstraZeneca/MedImmune Blue Sky Grant | UK | ACCOUNTS OF CHEMICAL RESEARCH | UK | null | null | MRC, Lab Mol Biol, Francis Crick Ave,Cambridge Biomed Campus, Cambridge CB2 0QH, England | 0001-4842 | Arangundy-Franklin, S;Holliger, P;Houlihan, G | APR | phl@mrc-lmb.cam.ac.uk | Chemistry;Genetic Information Storage;Polymerase Engineering;Propagation | 3 | J | Chemistry | 3D folding;ability;analysis;applications;area will;backbone linkages;basic level;biological information;biopolymers;biotechnology;carriers;catalysis;catalysts;CHEMICAL ETIOLOGY;chemical parameter range;CHEMISTRY;chemists;CONSPECTUS;decoding information;degree;described;determination;devices;different chemistries;directed evolution;distinct form;DNA;DNA-POLYMERASE;en-;encoding genetic information;engineering;enzymatic synthesis;ENZYMATIC-SYNTHESIS;established DNA designs;evolution;exploration;fidelity;first tentative forays;function;fundamental property;genetic information;genetic information (molecular heredity);Genetic Information Storage;Goldilocks;good efficiency;high throughput plate-based screens;ideal;inception;information transfer;investigation;large (if finite) number;lead;leads;least;life;ligands (aptamers);medicine;molecular embodiment;molecular heredity;molecular parameters;nanostructures;natural nucleic acids DNA;natural polymerases;nature;non-cognate nucleotide substrates;non-enzymatic synthesis;novel sequence spaces;novel strategies;nucleic acids;NUCLEIC-ACIDS;nucleobases;number;origin;panoply;phage display;phenotypic space;Polymerase Engineering;polymerase enzymes;polymerase function;polymerases;polymers;polypeptides;polysaccharides;potential;powerful method;progress;PROPAGATION;providing access;question;questions;range;realized;related nucleic acids;replication;repositories;reverse;REVERSE-TRANSCRIPTASE ACTIVITY;rich sequence;RNA;RNA-POLYMERASE;screening;SELECTION;sequence-defined biopolymer;several catalysts;simple polyhedron nanostructures;spaces;store;structure;synthetic genetic polymers;synthetic genetics;synthetic nucleic acids comprising unnatural sugar ring congeners;SYSTEM;TARGETS;TNA;two;unique capacity;variation;water-in-oil emulsion technology based methods;will;yield novel ligands | Houlihan, G | CHEMICAL ETIOLOGY;directed evolution;DNA-POLYMERASE;ENZYMATIC-SYNTHESIS;NUCLEIC-ACIDS;REVERSE-TRANSCRIPTASE ACTIVITY;RNA-POLYMERASE;SELECTION;SYSTEM;TNA | 1079 | [Houlihan, Gillian; Arangundy-Franklin, Sebastian; Holliger, Philipp] MRC, Lab Mol Biol, Francis Crick Ave,Cambridge Biomed Campus, Cambridge CB2 0QH, England. | The authors acknowledge support by the Medical Research Council (G.H. and P.H., program no. MC_U105178804) and an MRC-AstraZeneca/MedImmune Blue Sky Grant supporting the salary of S.A.-F. | 3D folding;ability;analysis;applications;area will;backbone linkages;basic level;biological information;biopolymers;biotechnology;carriers;catalysis;catalysts;chemical parameter range;chemistry;chemists;CONSPECTUS;decoding information;degree;described;determination;devices;different chemistries;distinct form;DNA;en-;encoding genetic information;engineering;enzymatic synthesis;established DNA designs;evolution;exploration;fidelity;first tentative forays;function;fundamental property;genetic information;genetic information (molecular heredity);Goldilocks;good efficiency;high throughput plate-based screens;ideal;inception;information transfer;investigation;large (if finite) number;lead;leads;least;life;ligands (aptamers);medicine;molecular embodiment;molecular heredity;molecular parameters;nanostructures;natural nucleic acids DNA;natural polymerases;nature;non-cognate nucleotide substrates;non-enzymatic synthesis;novel sequence spaces;novel strategies;nucleic acids;nucleobases;number;origin;panoply;phage display;phenotypic space;polymerase enzymes;polymerase function;polymerases;polymers;polypeptides;polysaccharides;potential;powerful method;progress;providing access;question;questions;range;realized;related nucleic acids;replication;repositories;reverse;rich sequence;RNA;screening;sequence-defined biopolymer;several catalysts;simple polyhedron nanostructures;spaces;store;structure;synthetic genetic polymers;synthetic genetics;synthetic nucleic acids comprising unnatural sugar ring congeners;targets;two;unique capacity;variation;water-in-oil emulsion technology based methods;will;yield novel ligands | 10.1002/(SICI)1521-3773(19990419)38:8<1124::AID-ANIE1124>3.0.CO;2-W;10.1002/1521-3773(20021004)41:19<3620::AID-ANIE3620>3.0.CO;2-C;10.1002/anie.200500047;10.1002/anie.200601217;10.1002/anie.200602772;10.1002/anie.200900953;10.1002/anie.201503652;10.1002/anie.201508678;10.1002/anie.201604641;10.1002/cbic.201000384;10.1002/cbic.201600136;10.1007/978-1-4939-3197-2_4;10.1016/0022-2836(84)90425-X;10.1016/0968-0004(89)90130-8;10.1016/j.jbiotec.2013.07.005;10.1016/j.jmb.2006.06.050;10.1021/ar040004z;10.1021/bi400558c;10.1021/ja035917n;10.1021/ja038525p;10.1021/ja0428255;10.1021/ja045364w;10.1021/ja053322h;10.1021/ja3017889;10.1021/ja9039696;10.1021/ja909180c;10.1021/jp3056834;10.1038/nature12306;10.1038/nature13314;10.1038/nature13982;10.1038/nature21022;10.1038/nbt.2556;10.1038/nbt1321;10.1038/nbt974;10.1038/ncomms11235;10.1039/c2cc35028a;10.1039/c5ob01540e;10.1073/pnas.071052198;10.1073/pnas.1013804107;10.1073/pnas.1120964109;10.1073/pnas.1133470100;10.1073/pnas.1213933109;10.1073/pnas.1319590110;10.1073/pnas.93.18.9670;10.1073/pnas.95.7.3402;10.1073/pnas.96.17.9491;10.1073/pnas.97.10.5095;10.1073/pnas.97.8.3868;10.1074/jbc.M005757200;10.1074/jbc.M113.532697;10.1093/nar/30.2.605;10.1093/nar/gki840;10.1093/nar/gkq1053;10.1093/nar/gkq1360;10.1093/nar/gkr1068;10.1093/nar/gkv1057;10.1093/nar/gkv1472;10.1093/nar/gkv798;10.1093/nar/gkw812;10.1093/protein/gzw052;10.1101/cshperspect.a023770;10.1126/science.1200752;10.1126/science.1217622;10.1126/science.1241888;10.1126/science.2434996;10.1126/science.284.5423.2118;10.1126/science.286.5438.295;10.1126/science.290.5495.1347;10.1126/science.aaf5409;10.1186/1759-2208-3-2];[10.1038/NCHEM.1241, 10.1038/nchem.1241];[10.1038/NCHEM.2493, 10.1038/nchem.2493];[10.1038/NCHEMBIO.280, 10.1038/nchembio.280];[10.1038/NCHEMBIO.966, 10.1038/nchembio.966] | MRC | Arangundy-Franklin, S;Holliger, P;Houlihan, G | Houlihan, G: MRC, Lab Mol Biol, Francis Crick Ave,Cambridge Biomed Campus, Cambridge CB2 0QH, England | Houlihan, Gillian | MC_U105178804 | 77 | null | UK | MRC | Houlihan, Gillian | Green Published, hybrid | CHEMICAL ETIOLOGY;DIRECTED EVOLUTION;DNA-POLYMERASE;ENZYMATIC-SYNTHESIS;NUCLEIC-ACIDS;REVERSE-TRANSCRIPTASE ACTIVITY;RNA-POLYMERASE;SELECTION;SYSTEM;TNA | Houlihan, Gillian; Arangundy-Franklin, Sebastian; Holliger, Philipp; | null | MRC, Lab Mol Biol, Francis Crick Ave,Cambridge Biomed Campus, Cambridge CB2 0QH, England | MRC, Lab Mol Biol, Francis Crick Ave,Cambridge Biomed Campus, Cambridge CB2 0QH, England | 1520-4898 | null | 4 | 1984;1987;1989;1996;1998;1999;2000;2001;2002;2003;2004;2005;2006;2007;2009;2010;2011;2012;2013;2014;2015;2016;2017 | 53 | MRC, Lab Mol Biol, Francis Crick Ave,Cambridge Biomed Campus, Cambridge CB2 0QH, England | Accounts Chem. Res. | Holliger, Philipp | AMER CHEMICAL SOC | ";(aptamers);(if;(molecular;,;3D;:;a;ability;access;acids;address;against;although;an;analysis;and;anticipate;apart;applications;are;area;as;at;backbone;based;basic;be;been;biological;biopolymer;biopolymers;biotechnology;but;can;capacity;carriers;catalysis;catalysts;chemical;chemistries;chemistry;chemists;closely;compatible;comprising;congeners;CONSPECTUS;created;currently;decoding;deeper;degree;demonstrates;described;designs;determination;devices;different;directed;discuss;display;distinct;DNA;efficiency;efficiently;efforts;elaborated;embodiment;emergence;emulsion;en-;encode;encoding;endow;engineered;engineering;enzymatic;enzymes;establish;established;establishing;evolution;evolved;expand;exploration;fidelity;finally;finite);first;folding;for;forays;form;found;from;function;fundamental;further;genetic;genetics;Goldilocks;good;has;have;here;heredity;heredity);high;ideal;illuminate;in;inception;increasingly;information;investigation;is;it;its;just;large;largely;lead;leads;least;level;life;ligands;linkages;may;means;medicine;method;methods;molecular;nanostructures;natural;naturally;nature;non-cognate;non-enzymatic;not;novel;nucleic;nucleobases;nucleotide;number;of;opened;or;order;origin;other;panoply;parameter;parameters;phage;phenotypic;plate-based;polyhedron;polymerase;polymerases;polymers;polypeptides;polysaccharides;potential;powerful;progress;propagate;property;providing;question;questions;range;realized;regarding;related;remains;replicated;replication;repositories;requires;restricted;reverse;rich;ring;RNA;screening;screens;seemingly;sequence;sequence-defined;sets;several;short;simple;some;space;spaces;still;store;strategies;structure;substrates;such;sugar;synthesis;synthesize;synthesized;synthetic;taking;targets;technology;tentative;that;the;their;them;therefore;these;they;this;through;throughput;to;toward;transcribe;transfer;two;unexplored;unique;unnatural;up;utilize;variation;water-in-oil;we;what;which;while;will;with;would;yield;yielded | MRC | CONSPECTUS: Nucleic acids are a distinct form of sequence-defined biopolymer. What sets them apart from other biopolymers such as polypeptides or polysaccharides is their unique capacity to encode, store, and propagate genetic information (molecular heredity). In nature, just two closely related nucleic acids, DNA and RNA, function as repositories and carriers of genetic information. They therefore are the molecular embodiment of biological information. This naturally leads to questions regarding the degree of variation from this seemingly ideal "Goldilocks" chemistry that would still be compatible with the fundamental property of molecular heredity. To address this question, chemists have created a panoply of synthetic nucleic acids comprising unnatural sugar ring congeners, backbone linkages, and nucleobases in order to establish the molecular parameters for encoding genetic information and its emergence at the origin of life. A deeper analysis of the potential of these synthetic genetic polymers for molecular heredity requires a means of replication and a determination of the fidelity of information transfer. While non-enzymatic synthesis is an increasingly powerful method, it currently remains restricted to short polymers. Here we discuss efforts toward establishing enzymatic synthesis, replication, and evolution of synthetic genetic polymers through the engineering of polymerase enzymes found in nature. To endow natural polymerases with the ability to efficiently utilize non-cognate nucleotide substrates, novel strategies for the screening and directed evolution of polymerase function have been realized. High throughput plate-based screens, phage display, and water-in-oil emulsion technology based methods have yielded a number of engineered polymerases, some of which can synthesize and reverse transcribe synthetic genetic polymers with good efficiency and fidelity. The inception of such polymerases demonstrates that, at a basic level at least, molecular heredity is not restricted to the natural nucleic acids DNA and RNA, but may be found in a large (if finite) number of synthetic genetic polymers. And it has opened up these novel sequence spaces for investigation. Although largely unexplored, first tentative forays have yielded ligands (aptamers) against a range of targets and several catalysts elaborated in a range of different chemistries. Finally, taking the lead from established DNA designs, simple polyhedron nanostructures have been described. We anticipate that further progress in this area will expand the range of synthetic genetic polymers that can be synthesized, replicated, and evolved providing access to a rich sequence, structure, and phenotypic space. "Synthetic genetics", that is, the exploration of these spaces, will illuminate the chemical parameter range for en- and decoding information, 3D folding, and catalysis and yield novel ligands, catalysts, and nanostructures and devices for applications in biotechnology and medicine. | Y-6197-2019 | CHEMICAL ETIOLOGY;DIRECTED EVOLUTION;DNA-POLYMERASE;ENZYMATIC-SYNTHESIS;NUCLEIC-ACIDS;REVERSE-TRANSCRIPTASE ACTIVITY;RNA-POLYMERASE;SELECTION;SYSTEM;TNA | 1 | null | null | 9 | CHEMICAL ETIOLOGY;directed evolution;DNA-POLYMERASE;ENZYMATIC-SYNTHESIS;NUCLEIC-ACIDS;REVERSE-TRANSCRIPTASE ACTIVITY;RNA-POLYMERASE;SELECTION;SYSTEM;TNA | WOS:000399859800045 | MRC, Cambridge, England | UK | 2,017 | null | 0000-0002-3440-9854 | null | null | English | null | ACCOUNTS CHEM RES;ANGEW CHEM INT EDIT;BIOCHEMISTRY-US;CHEM COMMUN;CHEMBIOCHEM;CSH PERSPECT BIOL;CURR PROTOC NUCL ACI;J AM CHEM SOC;J BIOL CHEM;J BIOTECHNOL;J MOL BIOL;J PHYS CHEM B;J SYST CHEM;METHODS MOL BIOL;NAT BIOTECHNOL;NAT CHEM;NAT CHEM BIOL;NAT COMMUN;NATURE;NUCLEIC ACIDS RES;ORG BIOMOL CHEM;P NATL ACAD SCI USA;POLYM ENG PCR SEQUEN;PROTEIN ENG DES SEL;SCIENCE;TRENDS BIOCHEM SCI | Arangundy-Franklin, Sebastian;Holliger, Philipp;Houlihan, Gillian | 2024-03-11
ER | Ablasser, A;Adamala, K;Anosova, I;Arezi B.;Astatke, M;Baar, C;Benner, S A;Bergen, K;Betz, K;Brudno, Y;Chaput, J C;Chen, T J;Cozens, C;D'Abbadie, M;Davies, D R;Dressman, D;Eckstein, F;Ellefson, J W;Eschenmoser, A;Fa, M;Ferreira-Bravo, I A;Gardner, A F;Gelinas, A D;Ghadessy, F J;Hansen, C J;Hollenstein, M;Horhota, A;Huber, C;Ibach, J;Ichida, J K;Jestin, J L;Joyce, G F;Kimoto, M;Kranaster, R;Laos, R;Larsen, A C;Leconte, A M;Li, Y;Loakes, D;Lockless, S W;Lou, D I;Malyshev, D A;Mauer, J;Millar, D;Nelson, K E;Obeid, S;Ong, J L;Patel, P H;Pinheiro V. B.;Pinheiro, V B;Povilaitis, T;Ramsay, N;Sauter, K B M;Schöning, K U;Siegmund, V;Smith, D A;Staiger, N;Summerer, D;Suzuki, M;Szostak J. W.;Taylor, A I;Tolle, F;Vichier-Guerre, S;Welter, M;Westheimer, F H;Wochner, A;Yamashige, R;Yu, H Y | ES9EV | Cambridge, England | 60 | null | 1 | null | 28,383,245 | Arangundy-Franklin, Sebastian;Holliger, Philipp;Houlihan, Gillian | ACCOUNTS CHEM RES | Cambridge, England |
Izuhara-Kihara, H;Matoba, Y;Noda, M;Sugiyama, M;Yoshida, T | 10.1002/pro.3123 | null | 111 RIVER ST, HOBOKEN 07030-5774, NJ USA | 294h623m4o1w6ro292b3hg113u615m2w2c6u | Crystallographic and mutational analyses of cystathionine β-synthase in the H<sub>2</sub>S-synthetic gene cluster in <i>Lactobacillus plantarum</i> | Hiroshima Univ | null | Matoba, Y (corresponding author), Hiroshima Univ, Grad Sch Biomed & Hlth Sci, Dept Microbiol, Minami Ku, Kasumi 1-2-3, Hiroshima 7348551, Japan.;Sugiyama, M (corresponding author), Hiroshima Univ, Grad Sch Biomed & Hlth Sci, Dept Probiot Sci Prevent Med, Minami Ku, Kasumi 1-2-3, Hiroshima 7348551, Japan. | null | Izuhara-Kihara, Hisae;Matoba, Yasuyuki;Noda, Masafumi;Sugiyama, Masanori;Yoshida, Tomoki | Biochemistry & Molecular Biology | Japan Society for the Promotion of Science [15K07997]; Grants-in-Aid for Scientific Research [15K07997, 15H00947] Funding Source: KAKEN | WOS | Matoba, Y;Sugiyama, M | Hiroshima Univ, Hiroshima, Japan | 26 | <i>Lactobacillus;analyses;and;Cluster;crystallographic;cystathionine;gene;H<sub>2</sub>S-synthetic;in;mutational;of;plantarum</i>;the;β-synthase | 1 | null | WILEY | Hiroshima Univ, Grad Sch Biomed & Hlth Sci, Dept Microbiol, Minami Ku, Kasumi 1-2-3, Hiroshima 7348551, Japan.; Sugiyama, M (corresponding author), Hiroshima Univ, Grad Sch Biomed & Hlth Sci, Dept Probiot Sci Prevent Med, Minami Ku, Kasumi 1-2-3, Hiroshima 7348551, Japan;Hiroshima Univ, Grad Sch Biomed & Hlth Sci, Minami Ku, Kasumi 1-2-3, Hiroshima 7348551, Japan | Article | Hiroshima Univ | HOBOKEN | null | null | Hiroshima Univ | Grants-in-Aid for Scientific Research;Japan Society for the Promotion of Science | Matoba, Y (corresponding author), Hiroshima Univ, Grad Sch Biomed & Hlth Sci, Dept Microbiol, Minami Ku, Kasumi 1-2-3, Hiroshima 7348551, Japan.; Sugiyama, M (corresponding author), Hiroshima Univ, Grad Sch Biomed & Hlth Sci, Dept Probiot Sci Prevent Med, Minami Ku, Kasumi 1-2-3, Hiroshima 7348551, Japan. | 783 | Izuhara-Kihara, Hisae;Matoba, Yasuyuki;Noda, Masafumi;Sugiyama, Masanori;Yoshida, Tomoki | 10 | 1 | 398,183,800,011 | Grants-in-Aid for Scientific Research [15K07997, 15H00947] Funding Source: KAKEN;Japan Society for the Promotion of Science [15K07997] | Japan | PROTEIN SCIENCE | Japan | null | null | Hiroshima Univ, Grad Sch Biomed & Hlth Sci, Minami Ku, Kasumi 1-2-3, Hiroshima 7348551, Japan | 0961-8368 | Izuhara-Kihara, H;Matoba, Y;Noda, M;Sugiyama, M;Yoshida, T | APR | sugi@hiroshima-u.ac.jp;ymatoba@hiroshima-u.ac.jp | <i>Lactobacillus plantarum</i>;crystallographic;cystathionine β-synthase;H<sub>2</sub>S-synthetic gene cluster;mutational analyses | 5 | J | Biochemistry & Molecular Biology | -ketobutylic acid;<i>Lactobacillus plantarum</i>;ACTIVE-SITE;Ala70;ALPHA-AMINOACRYLATE INTERMEDIATE;amino acid;amino acid sequence;AMINO-ACIDS;ammonia;antibiotics;BACTERIA;CBS;CBS-;CGL;CGL-encoding genes;CLUSTER;crystal structure;CRYSTAL-STRUCTURES;crystallographic;cystathionine -lyase (CGL);cystathionine beta-synthase;cystathionine beta-synthase (CBS);cystathionine β-synthase;enzymatic ability;enzymatic properties;enzymes;ESCHERICHIA-COLI;eukaryotic CBS;eukaryotic cells;first substrate;formation;genomes;Glu223 residues;H2S;H2S production;H2S suppression;H2S-generating activity;H<sub>2</sub>S-synthetic gene cluster;high affinity;hydrogen sulfide;hydrogen sulfide (H2S);inactivation;l-cystathionine;l-cysteine;l-cysteine-dependent CBS activities;l-homocysteine;l-OAS-;l-serine;L. plantarum CBS;LACTIC-ACID BACTERIA;Lactobacillus plantarum;major physiological enzymes;mutational analyses;O-acetyl-l-serine (l-OAS);O-acetyl-l-serine sulfhydrylase (OASS);O-ACETYLSERINE SULFHYDRYLASE;OASS activity;plant-derived lactic acid bacterium Lactobacillus plantarum;present study;REACTION SPECIFICITY;resulting l-cystathionine;reverse transsulfuration pathway;SALMONELLA-TYPHIMURIUM LT-2;second substrate;similarity;STRUCTURAL-BASIS;substrate binding pocket;susceptibility;tendency | Matoba, Y | ACTIVE-SITE;ALPHA-AMINOACRYLATE INTERMEDIATE;amino acid;AMINO-ACIDS;crystal structure;CRYSTAL-STRUCTURES;cystathionine beta-synthase;ESCHERICHIA-COLI;hydrogen sulfide;LACTIC-ACID BACTERIA;Lactobacillus plantarum;O-ACETYLSERINE SULFHYDRYLASE;REACTION SPECIFICITY;SALMONELLA-TYPHIMURIUM LT-2;STRUCTURAL-BASIS | 763 | [Matoba, Yasuyuki; Yoshida, Tomoki; Izuhara-Kihara, Hisae; Noda, Masafumi; Sugiyama, Masanori] Hiroshima Univ, Grad Sch Biomed & Hlth Sci, Minami Ku, Kasumi 1-2-3, Hiroshima 7348551, Japan. | Grant sponsor: Grant-in-Aid for Scientific Research from the Japan Society for the Promotion of Science; Grant number: 15K07997. | -ketobutylic acid;Ala70;amino acid sequence;ammonia;antibiotics;bacteria;CBS;CBS-;CGL;CGL-encoding genes;cluster;crystallographic;cystathionine -lyase (CGL);cystathionine beta-synthase (CBS);enzymatic ability;enzymatic properties;enzymes;eukaryotic CBS;eukaryotic cells;first substrate;formation;genomes;Glu223 residues;H2S;H2S production;H2S suppression;H2S-generating activity;high affinity;hydrogen sulfide (H2S);inactivation;l-cystathionine;l-cysteine;l-cysteine-dependent CBS activities;l-homocysteine;l-OAS-;l-serine;L. plantarum CBS;major physiological enzymes;mutational analyses;O-acetyl-l-serine (l-OAS);O-acetyl-l-serine sulfhydrylase (OASS);OASS activity;plant-derived lactic acid bacterium Lactobacillus plantarum;present study;resulting l-cystathionine;reverse transsulfuration pathway;second substrate;similarity;substrate binding pocket;susceptibility;tendency | 10.1002/yea.320100306;10.1006/jmbi.1993.1489;10.1006/jmbi.1999.3002;10.1007/s10545-006-0106-5;10.1016/0003-2697(75)90213-4;10.1016/0003-2697(92)90590-4;10.1016/0005-2744(70)90255-X;10.1016/j.abb.2004.08.024;10.1016/j.abb.2004.09.037;10.1016/j.bbapap.2011.03.006;10.1016/j.bbapap.2011.04.011;10.1016/j.febslet.2008.12.019;10.1016/S0076-6879(97)76066-X;10.1016/S0969-2126(00)00085-X;10.1021/bi00038a008;10.1021/bi00076a017;10.1021/bi00123a013;10.1021/bi035496m;10.1021/bi050485+;10.1021/bi100473v;10.1021/bi1010893;10.1021/bi952938o;10.1038/355472a0;10.1038/nrd2425;10.1073/pnas.1011448107;10.1073/pnas.1313683110;10.1073/pnas.1414545111;10.1073/pnas.85.8.2444;10.1074/jbc.C000056200;10.1074/jbc.M109.010868;10.1074/jbc.M112.414722;10.1074/jbc.M114.610782;10.1074/jbc.M505313200;10.1074/jbc.M703518200;10.1074/jbc.M805459200;10.1074/jbc.R400001200;10.1074/jbc.R400005200;10.1093/nar/25.24.4876;10.1107/s0907444994003112;10.1107/s0907444998003254;10.1126/science.1209855;10.1128/AEM.00150-08;10.1128/JB.01273-06;10.1128/JB.01372-09;10.1248/bpb.33.289;10.1271/bbb.64.1628;10.1371/journal.pone.0030696;10.1515/BC.2003.043;[10.1139/O09-003, 10.1139/o09-003] | Hiroshima Univ | Izuhara-Kihara, H;Matoba, Y;Noda, M;Sugiyama, M;Yoshida, T | Matoba, Y: Hiroshima Univ, Grad Sch Biomed & Hlth Sci, Minami Ku, Kasumi 1-2-3, Hiroshima 7348551, Japan | null | 15H00947;15K07997 | 52 | null | Japan | Hiroshima Univ | Matoba, Yasuyuki | Bronze, Green Published | ACTIVE-SITE;ALPHA-AMINOACRYLATE INTERMEDIATE;AMINO-ACIDS;CRYSTAL-STRUCTURES;ESCHERICHIA-COLI;LACTIC-ACID BACTERIA;O-ACETYLSERINE SULFHYDRYLASE;REACTION SPECIFICITY;SALMONELLA-TYPHIMURIUM LT-2;STRUCTURAL-BASIS | Matoba, Yasuyuki; Yoshida, Tomoki; Izuhara-Kihara, Hisae; Noda, Masafumi; Sugiyama, Masanori; | null | Hiroshima Univ, Grad Sch Biomed & Hlth Sci, Minami Ku, Kasumi 1-2-3, Hiroshima 7348551, Japan | Hiroshima Univ, Grad Sch Biomed & Hlth Sci, Minami Ku, Kasumi 1-2-3, Hiroshima 7348551, Japan | 1469-896X | Amino acids;crystal structure;cystathionine beta-synthase;hydrogen sulfide;Lactobacillus plantarum | 4 | 1966;1970;1975;1976;1988;1992;1993;1994;1995;1996;1997;1998;1999;2000;2003;2004;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014 | 17 | Hiroshima Univ, Grad Sch Biomed & Hlth Sci, Dept Microbiol, Minami Ku, Kasumi 1-2-3, Hiroshima 7348551, Japan;Hiroshima Univ, Grad Sch Biomed & Hlth Sci, Dept Probiot Sci Prevent Med, Minami Ku, Kasumi 1-2-3, Hiroshima 7348551, Japan | Protein Sci. | Sugiyama, Masanori | WILEY | (CBS);(CGL);(H2S);(l-OAS);(OASS);,;-ketobutylic;-lyase;;;a;ability;acid;activities;activity;affinity;Ala70;amino;ammonia;analyses;and;antibiotics;are;as;associated;at;bacteria;bacterium;be;been;beta-synthase;binding;both;by;catalyzed;catalyzes;CBS;CBS-;cells;CGL;CGL-encoding;characterized;cluster;crystallographic;cystathionine;decomposed;displays;enzymatic;enzymes;especially;eukaryotic;first;for;form;formation;from;generate;generation;genes;genomes;Glu223;H2S;H2S-generating;has;have;high;hydrogen;important;in;inactivation;including;increases;indicate;interestingly;into;is;it;its;l-cystathionine;l-cysteine;l-cysteine-dependent;l-homocysteine;l-OAS-;l-serine;L.;lactic;Lactobacillus;mainly;major;might;mutational;O-acetyl-l-serine;OASS;occurs;of;pathway;physiological;plant-derived;plantarum;pocket;presence;present;production;properties;recently;recognized;reported;residues;resulting;reverse;second;sequence;shown;shows;similarity;some;study;substrate;sulfhydrylase;sulfide;suppress;suppression;susceptibility;tendency;that;the;their;these;this;those;to;together;toward;transsulfuration;use;various;we;which;whose;with | Hiroshima Univ | Cystathionine beta-synthase (CBS) catalyzes the formation of l-cystathionine from l-serine and l-homocysteine. The resulting l-cystathionine is decomposed into l-cysteine, ammonia, and -ketobutylic acid by cystathionine -lyase (CGL). This reverse transsulfuration pathway, which is catalyzed by both enzymes, mainly occurs in eukaryotic cells. The eukaryotic CBS and CGL have recently been recognized as major physiological enzymes for the generation of hydrogen sulfide (H2S). In some bacteria, including the plant-derived lactic acid bacterium Lactobacillus plantarum, the CBS- and CGL-encoding genes form a cluster in their genomes. Inactivation of these enzymes has been reported to suppress H2S production in bacteria; interestingly, it has been shown that H2S suppression increases their susceptibility to various antibiotics. In the present study, we characterized the enzymatic properties of the L. plantarum CBS, whose amino acid sequence displays a similarity with those of O-acetyl-l-serine sulfhydrylase (OASS) that catalyzes the generation of l-cysteine from O-acetyl-l-serine (l-OAS) and H2S. The L. plantarum CBS shows l-OAS- and l-cysteine-dependent CBS activities together with OASS activity. Especially, it catalyzes the formation of H2S in the presence of l-cysteine and l-homocysteine, together with the formation of l-cystathionine. The high affinity toward l-cysteine as a first substrate and tendency to use l-homocysteine as a second substrate might be associated with its enzymatic ability to generate H2S. Crystallographic and mutational analyses of CBS indicate that the Ala70 and Glu223 residues at the substrate binding pocket are important for the H2S-generating activity. | null | ACTIVE-SITE;ALPHA-AMINOACRYLATE INTERMEDIATE;AMINO-ACIDS;CRYSTAL-STRUCTURE;ESCHERICHIA-COLI;LACTIC-ACID BACTERIA;O-ACETYLSERINE SULFHYDRYLASE;REACTION SPECIFICITY;SALMONELLA-TYPHIMURIUM LT-2;STRUCTURAL BASIS | 1 | null | amino acid;crystal structure;cystathionine beta-synthase;hydrogen sulfide;Lactobacillus plantarum | 21 | ESCHERICHIA-COLI;ACTIVE-SITE;ALPHA-AMINOACRYLATE INTERMEDIATE;AMINO-ACIDS;CRYSTAL-STRUCTURE;cystathionine beta-synthase;hydrogen sulfide;LACTIC-ACID BACTERIA;LACTOBACILLUS-PLANTARUM;O-ACETYLSERINE SULFHYDRYLASE;REACTION SPECIFICITY;SALMONELLA-TYPHIMURIUM LT-2;STRUCTURAL BASIS | WOS:000398183800011 | Hiroshima Univ, Hiroshima, Japan | Japan | 2,017 | null | null | null | null | English | null | ACTA CRYSTALLOGR D;ANAL BIOCHEM;APPL ENVIRON MICROB;ARCH BIOCHEM BIOPHYS;BBA-PROTEINS PROTEOM;BIOCHEM CELL BIOL;BIOCHEMISTRY-US;BIOCHIM BIOPHYS ACTA;BIOL CHEM;BIOL PHARM BULL;BIOSCI BIOTECH BIOCH;FEBS LETT;J BACTERIOL;J BIOL CHEM;J INHERIT METAB DIS;J MOL BIOL;METHOD ENZYMOL;NAT REV DRUG DISCOV;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PLOS ONE;SCIENCE;STRUCT FOLD DES;YEAST | Izuhara-Kihara, Hisae;Matoba, Yasuyuki;Noda, Masafumi;Sugiyama, Masanori;Yoshida, Tomoki | 2024-03-11
ER | Aitken, S M;Bailey, S;Bonner, E R;Brunger, A T;Burkhard, P;Canevari, L;Castro, R;Claus, M T;Cook, P F;Doherty, N C;Ereño-Orbea, J;Holm, L;Hui, T A;Hullo, M F;Jhee, K H;Jin, H K;Kashiwamata, S;Koutmos, M;Kredich, N M;Liu, M;Lodha, P H;Mccorvie, T J;Mcree D.E.;Messerschmidt, A;Miles, E W;Mino, K;Mozzarelli, A;Ono, B I;Otwinowski, Z;Pearson, W R;Rabeh, W M;Schnackerz, K D;Schneider, G;Schnell, R;Shatalin, K;Singh, S;Sun, Q X;Szabó, C;Tai, C H;Thompson, J D;Toney, M D;Willhardt, I;Woehl, E U;Yadav, P K;Zhao, X R;Ågren, D | EQ6IA | Hiroshima, Japan;Hiroshima, Japan. | 17 | null | 1 | null | 28,127,810 | Izuhara-Kihara, Hisae;Matoba, Yasuyuki;Noda, Masafumi;Sugiyama, Masanori;Yoshida, Tomoki | PROTEIN SCI | Hiroshima, Japan |
Tan, C M;Villarreal, F | 10.1007/s11705-017-1610-x | null | ONE NEW YORK PLAZA, SUITE 4600, NEW YORK, NY, UNITED STATES | 3h361l1643w533y5d394l4n5d5n650k201i3f | Cell-free systems in the new age of synthetic biology | Univ Calif Davis | null | Tan, CM (corresponding author), Univ Calif Davis, Dept Biomed Engn, One Shields Ave, Davis, CA 95616 USA. | null | Tan, Cheemeng;Villarreal, Fernando | Engineering, Chemical | Branco-Weiss Fellowship; Human Frontier Science Program | WOS | Tan, C M | Univ Calif Davis, Davis, CA USA | 11 | age;biology;Cell-Free;in;new;of;synthetic;systems;the | 1 | Tan, Cheemeng;Villarreal, Fernando | SPRINGER | Univ Calif Davis, Dept Biomed Engn, One Shields Ave, Davis, CA 95616 USA | Review | Univ Calif Davis | NEW YORK | null | null | Univ Calif Davis | Branco-Weiss Fellowship;Human Frontier Science Program | Tan, CM (corresponding author), Univ Calif Davis, Dept Biomed Engn, One Shields Ave, Davis, CA 95616 USA. | 65 | Tan, Cheemeng;Villarreal, Fernando | 119 | 1 | 398,723,700,007 | Branco-Weiss Fellowship;Human Frontier Science Program | USA | FRONTIERS OF CHEMICAL SCIENCE AND ENGINEERING | USA | null | null | Univ Calif Davis, Dept Biomed Engn, One Shields Ave, Davis, CA 95616 USA | 2095-0179 | Tan, C M;Villarreal, F | MAR | cmtan@ucdavis.edu | cell-free systems;new age;synthetic biology | 2 | J | Engineering | advent;application;biomolecules;Cell-free synthetic biology;cell-free system;cell-free systems;cell-free transcription-translation systems;cellular proteins;COMPARTMENTALIZATION;components;composition;COUPLED TRANSCRIPTION;Diagnosis;directed evolution;DIRECTED PEPTIDE-SYNTHESIS;evolution;FREE EXPRESSION SYSTEM;FREE PROTEIN-SYNTHESIS;future direction;GENE-EXPRESSION;historical advancement;IN-VITRO SELECTION;infectious diseases;MESSENGER-RNA;modular control;new age;new applications;rapid design;reconstituted;synthesis;synthetic biology;synthetic genetic circuits;TRANSCRIPTION-TRANSLATION SYSTEM;VACCINES;vision | Villarreal, F | application;cell-free system;COMPARTMENTALIZATION;COUPLED TRANSCRIPTION;DIRECTED PEPTIDE-SYNTHESIS;EVOLUTION;FREE EXPRESSION SYSTEM;FREE PROTEIN-SYNTHESIS;GENE-EXPRESSION;IN-VITRO SELECTION;MESSENGER-RNA;TRANSCRIPTION-TRANSLATION SYSTEM | 58 | [Villarreal, Fernando; Tan, Cheemeng] Univ Calif Davis, Dept Biomed Engn, One Shields Ave, Davis, CA 95616 USA. | This work is supported by the Branco-Weiss Fellowship (CT) and the Human Frontier Science Program (CT). | advent;biomolecules;cell-free synthetic biology;cell-free systems;cell-free transcription-translation systems;cellular proteins;components;composition;diagnosis;directed evolution;future direction;historical advancement;infectious diseases;modular control;new applications;rapid design;reconstituted;synthesis;synthetic biology;synthetic genetic circuits;vaccines;vision | 10.1002/anie.200701369;10.1002/biot.201400330;10.1002/bit.22385;10.1002/bit.23103;10.1002/bit.24903;10.1002/bit.25587;10.1002/bit.25814;10.1007/978-3-319-27216-0_10;10.1007/S00253-011-3863-5;10.1016/0005-2787(67)90706-X;10.1016/0014-5793(91)81297-L;10.1016/0092-8674(86)90271-0;10.1016/j.bbrc.2012.12.107;10.1016/j.bbrc.2012.12.108;10.1016/j.biotechadv.2014.10.009;10.1016/j.cell.2007.05.045;10.1016/j.cell.2014.10.004;10.1016/j.cell.2016.04.059;10.1016/j.copbio.2010.05.005;10.1016/j.febslet.2014.06.007;10.1016/j.jbiosc.2014.04.019;10.1016/j.jbiotec.2014.02.009;10.1016/j.pep.2005.01.013;10.1016/j.sbi.2015.04.008;10.1016/j.tibtech.2006.06.009;10.1016/j.ymben.2016.03.002;10.1016/j.ymeth.2015.05.020;10.1016/S0378-1119(99)00508-9;10.1021/acssynbio.5b00051;10.1021/acssynbio.5b00296;10.1021/ja301017y;10.1021/jz3019379;10.1021/sb200003v;10.1021/sb200016s;10.1021/sb400131a;10.1038/269532a0;10.1038/35002125;10.1038/90802;10.1038/nbt.1536;10.1038/nbt0798-652;10.1038/ncomms9168;10.1038/NMETH897;10.1038/srep08663;10.1038/srep26257;10.1039/c5lc00700c;10.1073/pnas.0408782102;10.1073/pnas.1201380109;10.1073/pnas.1314585110;10.1073/pnas.57.4.1010;10.1073/pnas.58.4.1669;10.1073/pnas.70.9.2678;10.1073/pnas.71.4.1219;10.1073/pnas.72.5.1922;10.1073/pnas.77.12.7029;10.1073/pnas.94.10.4937;10.1073/pnas.94.23.12297;10.1093/nar/15.8.3257;10.1093/nar/gkt052;10.1093/protein/gzu002;10.1107/S1744309111032143;10.1111/j.1432-1033.1979.tb12791.x;10.1126/science.1255550;10.1126/science.2649980;10.1128/JVI.62.8.2636-2643.1988;10.1128/MCB.9.11.5073;10.1155/2012/371379;10.1162/ARTL_a_00198;10.1182/blood-2006-07-030593;10.1186/1472-6750-8-58;10.1186/1752-0509-6-134;10.1263/jbb.106.8;10.1371/journal.pone.0014388;10.1371/journal.pone.0096635;10.1371/journal.pone.0154614;10.3389/fbioe.2014.00066;10.3389/fchem.2014.00034;10.7554/eLife.09771;[10.1038/NCHEM.1869, 10.1038/nchem.1869];[10.1038/NMETH.1318, 10.1038/nmeth.1318];[10.1038/NNANO.2013.132, 10.1038/nnano.2013.132];[10.1371/journal.pone.0096185, 10.1371/journal.pone.0090225] | Univ Calif Davis | Tan, C M;Villarreal, F | Villarreal, F: Univ Calif Davis, Dept Biomed Engn, One Shields Ave, Davis, CA 95616 USA | null | null | 86 | null | USA | Univ Calif Davis | Villarreal, Fernando | null | COMPARTMENTALIZATION;COUPLED TRANSCRIPTION;DIRECTED PEPTIDE-SYNTHESIS;EVOLUTION;FREE EXPRESSION SYSTEM;FREE PROTEIN-SYNTHESIS;GENE-EXPRESSION;IN-VITRO SELECTION;MESSENGER-RNA;TRANSCRIPTION-TRANSLATION SYSTEM | Villarreal, Fernando; Tan, Cheemeng; | null | Univ Calif Davis, Dept Biomed Engn, One Shields Ave, Davis, CA 95616 USA | Univ Calif Davis, Dept Biomed Engn, One Shields Ave, Davis, CA 95616 USA | 2095-0187 | Applications;cell-free systems | 1 | 1967;1973;1974;1975;1977;1979;1980;1983;1986;1987;1988;1989;1991;1997;1998;2000;2001;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016 | 18 | Univ Calif Davis, Dept Biomed Engn, One Shields Ave, Davis, CA 95616 USA | Front. Chem. Sci. Eng. | Tan, Cheemeng | SPRINGER | ,;advancement;advent;amenable;and;applications;are;as;biology;biomolecules;cell-free;cellular;circuits;components;composition;control;design;diagnosis;directed;direction;discuss;diseases;evolution;finally;future;genetic;has;here;historical;in;infectious;modular;new;of;on;our;present;proteins;rapid;reconstituted;synthesis;synthetic;systems;the;their;these;to;transcription-translation;ushered;using;vaccines;vision;we;well | Univ Calif Davis | The advent of synthetic biology has ushered in new applications of cell-free transcription-translation systems. These cell-free systems are reconstituted using cellular proteins, and are amenable to modular control of their composition. Here, we discuss the historical advancement of cell-free systems, as well as their new applications in the rapid design of synthetic genetic circuits and components, directed evolution of biomolecules, diagnosis of infectious diseases, and synthesis of vaccines. Finally, we present our vision on the future direction of cell-free synthetic biology. | null | COMPARTMENTALIZATION;COUPLED TRANSCRIPTION;DIRECTED PEPTIDE-SYNTHESIS;EVOLUTION;FREE EXPRESSION SYSTEM;FREE PROTEIN-SYNTHESIS;GENE-EXPRESSION;IN-VITRO SELECTION;MESSENGER-RNA;TRANSCRIPTION-TRANSLATION SYSTEM | 5 | null | application;cell-free system | 8 | Applications;cell-free systems;COMPARTMENTALIZATION;COUPLED TRANSCRIPTION;DIRECTED PEPTIDE-SYNTHESIS;EVOLUTION;FREE EXPRESSION SYSTEM;FREE PROTEIN-SYNTHESIS;GENE-EXPRESSION;IN-VITRO SELECTION;MESSENGER-RNA;TRANSCRIPTION-TRANSLATION SYSTEM | WOS:000398723700007 | Univ Calif Davis, Davis, CA USA | USA | 2,017 | null | 0000-0002-4034-1243;0000-0003-1049-1192 | null | null | English | null | ACS SYNTH BIOL;ACSYNTHETIC BIOL;ACTA CRYSTALLOGR F;ADV EXP MED BIOL;ANGEW CHEM INT EDIT;ARTIF LIFE;BIOCHEM BIOPH RES CO;BIOCHIM BIOPHYS ACTA;BIOTECHNOL ADV;BIOTECHNOL BIOENG;BIOTECHNOL J;BLOOD;BMC BIOTECHNOL;BMC SYST BIOL;CELL;CURR OPIN BIOTECH;CURR OPIN STRUC BIOL;Current Protocols in Molecular Biology;ELIFE;EUR J BIOCHEM;FEBS LETT;Front Bioeng Biotechnol;FRONT CHEM;GENE;J AGRON;J AM CHEM SOC;J BIOSCI BIOENG;J BIOTECHNOL;J NUCLEIC ACIDS;J PHYS CHEM LETT;J SCI FOOD AGR;J VIROL;JOVE-J VIS EXP;LAB CHIP;METAB ENG;METHODS;MOL CELL BIOL;NAT BIOTECHNOL;NAT CHEM;NAT COMMUN;NAT METHODS;NAT NANOTECHNOL;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;P NATL ACAD SCI-BIOL;PLOS ONE;PROTEIN ENG DES SEL;PROTEIN EXPRES PURIF;SCI REP-UK;SCIENCE;TRENDS BIOTECHNOL | Tan, Cheemeng;Villarreal, Fernando | 2024-03-11
ER | Albayrak, C;Bottomley, W;Caschera, F;Chappell, J;Chemla, Y;Chung, B K S;Davies, D H;Deans, T L;Devries, J K;Dodevski, I;Dudley Q, M;Dudley, Q M;Ellis, T;Elowitz, M B;Fujii, S;Fujiwara, K;Gagoski, D;Gallie, D R;Garamella, J;Georgi, V;Gibson, D G;Griffiths, A D;Guild, K;Hanes, J;Hillebrecht, J R;Hong, S H;Hovijitra, N T;Ishihara, G;Jang, S K;Joyce, G F;Kanter, G;Kapsner, K;Karim, A S;Karzbrun, E;Kazuta, Y;Kovtun, O;Kozak, M;Kwon, Y C;Lederman, M;Lewis Daniel, D;Li, J;Lu, Y;Maeda, Y T;Matsuda, T;Miller, O J;Nevin, D E;Niederholtmeyer, H;Niimi, T;Niwa, T;Noren, C J;Oza, J P;Pachuk, C J;Pardee, K;Pelham, H R B;Reichman, M;Roberts, B E;Roberts, R W;Rothblatt, J A;Sachse, R;Schlippe, Y V G;Sharma, B;Shimizu, Y;Shin, J;Singh-Blom, A;Soh, S;Stafford, R L;Stech, M;Steggles, A W;Sumida, T;Sun, Z Z;Tabor S.;Takahashi, M K;Tan, C M;Tawfik, D S;Wang H.;Wang, X;Weitz, M;Yadavalli, R;Yang, H L;Yost, C S;Zawada, J F;Zhang, Y H P;Zhou, H;Zubay, G | ER3UD | Davis, CA USA | 23 | null | 1 | null | null | Tan, Cheemeng;Villarreal, Fernando | FRONT CHEM SCI ENG | Davis, CA USA |
Bandiera, L;Bevilacqua, A;Cortesi, M;Furini, S;Gherardi, A;Giordano, E;Pasini, A | 10.1186/s13036-017-0050-y | 8 | 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND | x204vw1j5g35355w2h493e613q644q6c2k1063 | Reliable measurement of <i>E-coli</i> single cell fluorescence distribution using a standard microscope set-up | Univ Bologna | null | Cortesi, M (corresponding author), Univ Bologna, Dept Elect, Lab Cellular & Mol Engn S Cavalcanti Elect & Info, Cesena, Italy. | null | Bandiera, Lucia;Bevilacqua, Alessandro;Cortesi, Marilisa;Furini, Simone;Gherardi, Alessandro;Giordano, Emanuele;Pasini, Alice | Biochemical Research Methods;Biotechnology & Applied Microbiology | University of Bologna [RFO 2015] | WOS | Cortesi, M | Univ Bologna, Bologna, Italy;Univ Bologna, Cesena, Italy;Univ Bologna, Ozzano Dell Emilia, Italy;Univ Edinburgh, Midlothian, Scotland;Univ Nottingham, Nottingham, England;Univ Siena, Siena, Italy | 11 | <i>E-coli</i>;a;cell;distribution;fluorescence;measurement;microscope;of;reliable;set-up;Single;standard;using | 2 | Bandiera, Lucia;Bevilacqua, Alessandro;Cortesi, Marilisa;Furini, Simone;Gherardi, Alessandro;Giordano, Emanuele;Pasini, Alice | BIOMED CENTRAL LTD | Univ Bologna, Adv Res Ctr Elect Syst Informat & Commun Technol, Bologna, Italy;Univ Bologna, Dept Comp Sci & Engn DISI, Bologna, Italy;Univ Bologna, Dept Elect, Lab Cellular & Mol Engn S Cavalcanti Elect & Info, Cesena, Italy;Univ Bologna, Hlth Sci & Technol Interdept Ctr Ind Res HST CIRI, BioEngLab, Ozzano Dell Emilia, Italy;Univ Edinburgh, Sch Biol Sci, Edinburgh, Midlothian, Scotland;Univ Edinburgh, SynthSys Ctr Synthet & Syst Biol, Edinburgh, Midlothian, Scotland;Univ Nottingham, Sch Med, Div Resp Med, Nottingham, England;Univ Siena, Dept Med Biotechnol, Siena, Italy | Article | Univ Bologna | LONDON | null | null | Univ Bologna;Univ Edinburgh;Univ Nottingham;Univ Siena | University of Bologna | Cortesi, M (corresponding author), Univ Bologna, Dept Elect, Lab Cellular & Mol Engn S Cavalcanti Elect & Info, Cesena, Italy. | null | Bandiera, Lucia;Bevilacqua, Alessandro;Cortesi, Marilisa;Furini, Simone;Gherardi, Alessandro;Giordano, Emanuele;Pasini, Alice | 11 | 8 | 395,925,900,001 | University of Bologna [RFO 2015] | Italy;UK | JOURNAL OF BIOLOGICAL ENGINEERING | Italy | null | null | Univ Bologna, Dept Elect, Lab Cellular & Mol Engn S Cavalcanti Elect & Info, Cesena, Italy | 1754-1611 | Bandiera, L;Bevilacqua, A;Cortesi, M;Furini, S;Gherardi, A;Giordano, E;Pasini, A | FEB 20 | marilisa.cortesi2@unibo.it | <i>E-coli</i> single cell fluorescence distribution;reliable measurement;standard microscope set-up | 7 | J | Biochemistry & Molecular Biology;Biotechnology & Applied Microbiology | 0.99;<i>E-coli</i> single cell fluorescence distribution;acquisition;affordable;affordable measurement/quantification;appropriate software;background;bacterial population;calibration;cellular behaviors;commercial set-ups;complete characterization;comprehension;conclusions;correlation coefficient;custom-made software;data;described;expensive apparatuses;experimental protocol;flow cytometer;Fluorescence microscopy;fluorescent data;fluorescent signal;fundamental;Gene circuits;gene expression;high correlation;image processing-;inter-cellular variability;intercellular variability;laboratories;method;methods;microscope set-up;noise;paper makes quantitative measurement;phenomenon will;Phenotypic noise;presented;protocol;quantitative microscopes);quantitative single-cell fluorescence measurements;reliable measurement;required software;results;same gene circuitry;set-up;significant impact;single cell;single cell fluorescence;single cell fluorescence values;single cell level;single cell level (flow cytometers;Single-cell fluorescence;small laboratories;standard microscope set-up;standard optical microscope;standard optical microscope set-ups;standard optical microscope-;synthetic biology;synthetic biology community (MUSIQ Microscope flUorescence SIngle cell Quantification);synthetic gene circuitry;synthetic gene circuits;system's functionality;tested dynamic range;two experimental set-ups;understanding;validation | Cortesi, M | Fluorescence microscopy;Gene circuits;Phenotypic noise;Single-cell fluorescence;Synthetic biology | null | [Cortesi, Marilisa] Univ Bologna, Dept Elect, Lab Cellular & Mol Engn S Cavalcanti Elect & Info, Cesena, Italy. [Bevilacqua, Alessandro; Gherardi, Alessandro; Giordano, Emanuele] Univ Bologna, Adv Res Ctr Elect Syst Informat & Commun Technol, Bologna, Italy. [Bevilacqua, Alessandro] Univ Bologna, Dept Comp Sci & Engn DISI, Bologna, Italy. [Furini, Simone] Univ Siena, Dept Med Biotechnol, Siena, Italy. [Giordano, Emanuele] Univ Bologna, Hlth Sci & Technol Interdept Ctr Ind Res HST CIRI, BioEngLab, Ozzano Dell Emilia, Italy. [Bandiera, Lucia] Univ Edinburgh, SynthSys Ctr Synthet & Syst Biol, Edinburgh, Midlothian, Scotland. [Bandiera, Lucia] Univ Edinburgh, Sch Biol Sci, Edinburgh, Midlothian, Scotland. [Pasini, Alice] Univ Nottingham, Sch Med, Div Resp Med, Nottingham, England. | University of Bologna RFO 2015 to EG. | 0.99;acquisition;affordable;affordable measurement/quantification;appropriate software;background;bacterial population;calibration;cellular behaviors;commercial set-ups;complete characterization;comprehension;conclusions;correlation coefficient;custom-made software;data;described;expensive apparatuses;experimental protocol;flow cytometer;fluorescent data;fluorescent signal;fundamental;gene expression;high correlation;image processing-;inter-cellular variability;intercellular variability;laboratories;method;methods;microscope set-up;noise;paper makes quantitative measurement;phenomenon will;presented;protocol;quantitative microscopes);quantitative single-cell fluorescence measurements;required software;results;same gene circuitry;set-up;significant impact;single cell;single cell fluorescence;single cell fluorescence values;single cell level;single cell level (flow cytometers;small laboratories;standard optical microscope;standard optical microscope set-ups;standard optical microscope-;synthetic biology community (MUSIQ Microscope flUorescence SIngle cell Quantification);synthetic gene circuitry;synthetic gene circuits;system's functionality;tested dynamic range;two experimental set-ups;understanding;validation | 10.1007/10_2007_073;10.1007/978-1-61779-567-1_2;10.1016/0378-1119(95)00685-0;10.1016/j.cub.2014.07.036;10.1016/j.jtbi.2016.02.004;10.1021/ac5030232;10.1021/sb200021s;10.1021/sb400089c;10.1038/nprot.2011.432;10.1038/nrmicro2056;10.1088/1742-6596/90/1/012068;10.1098/rspb.1980.0020;10.1172/JCI115251;10.1186/1754-1611-4-14;10.3389/fmicb.2016.00479 | Univ Bologna | Bandiera, L;Bevilacqua, A;Cortesi, M;Furini, S;Gherardi, A;Giordano, E;Pasini, A | Cortesi, M: Univ Bologna, Dept Elect, Lab Cellular & Mol Engn S Cavalcanti Elect & Info, Cesena, Italy | Bandiera, Lucia;Bevilacqua, Alessandro;Cortesi, Marilisa;Furini, Simone;Gherardi, Alessandro;Giordano, Emanuele | RFO 2015 | 20 | null | Italy | Univ Bologna;Univ Edinburgh;Univ Nottingham;Univ Siena | Cortesi, Marilisa | Green Published, gold | GENE CIRCUITS | Cortesi, Marilisa; Bandiera, Lucia; Pasini, Alice; Bevilacqua, Alessandro; Gherardi, Alessandro; Furini, Simone; Giordano, Emanuele; | null | Univ Bologna, Adv Res Ctr Elect Syst Informat & Commun Technol, Bologna, Italy;Univ Bologna, Dept Comp Sci & Engn DISI, Bologna, Italy;Univ Bologna, Dept Elect, Lab Cellular & Mol Engn S Cavalcanti Elect & Info, Cesena, Italy;Univ Bologna, Hlth Sci & Technol Interdept Ctr Ind Res HST CIRI, BioEngLab, Ozzano Dell Emilia, Italy;Univ Edinburgh, Sch Biol Sci, Edinburgh, Midlothian, Scotland;Univ Edinburgh, SynthSys Ctr Synthet & Syst Biol, Edinburgh, Midlothian, Scotland;Univ Nottingham, Sch Med, Div Resp Med, Nottingham, England;Univ Siena, Dept Med Biotechnol, Siena, Italy | Univ Bologna, Adv Res Ctr Elect Syst Informat & Commun Technol, Bologna, Italy;Univ Bologna, Dept Comp Sci & Engn DISI, Bologna, Italy;Univ Bologna, Dept Elect, Lab Cellular & Mol Engn S Cavalcanti Elect & Info, Cesena, Italy;Univ Bologna, Hlth Sci & Technol Interdept Ctr Ind Res HST CIRI, BioEngLab, Ozzano Dell Emilia, Italy;Univ Edinburgh, Sch Biol Sci, Edinburgh, Midlothian, Scotland;Univ Edinburgh, SynthSys Ctr Synthet & Syst Biol, Edinburgh, Midlothian, Scotland;Univ Nottingham, Sch Med, Div Resp Med, Nottingham, England;Univ Siena, Dept Med Biotechnol, Siena, Italy | null | Fluorescence microscopy;Phenotypic noise;Single-cell fluorescence;Synthetic biology | null | 1980;1991;1996;1998;1999;2007;2008;2009;2010;2011;2012;2013;2014;2016 | 7 | Univ Bologna, Dept Elect, Lab Cellular & Mol Engn S Cavalcanti Elect & Info, Cesena, Italy | J. Biol. Eng. | Giordano, Emanuele | BIOMED CENTRAL LTD | (flow;(MUSIQ;,;0.99;:;>;a;able;accessible;acquire;acquired;acquisition;affordable;all;allow;allows;an;and;apparatuses;appropriate;are;at;available;background;bacterial;be;behaviors;better;between;biology;by;calibration;cell;cellular;characterization;circuitry;circuits;coefficient;commercial;community;compared;complete;comprehension;computed;conclusions;correlation;coupled;custom-made;cytometer;cytometers;data;described;design;due;dynamic;equipped;expensive;experimental;expression;flow;fluorescence;fluorescent;for;freely;from;functionality;fundamental;gene;hardly;high;image;impact;improve;in;inter-cellular;intercellular;is;its;laboratories;level;makes;measurement;measurement/quantification;measurements;method;methods;microscope;microscope-;microscopes);might;noise;obtained;of;on;optical;or;our;over;paper;phenomenon;population;presented;processed;processing-;protocol;proves;Quantification);Quantifying;quantitative;range;required;results;same;set-up;set-ups;signal;significant;single;single-cell;small;software;standard;synthetic;system's;tested;that;the;this;to;together;transformed;two;understanding;used;validation;values;variability;were;when;whose;will;with | Univ Bologna | Background: Quantifying gene expression at single cell level is fundamental for the complete characterization of synthetic gene circuits, due to the significant impact of noise and inter-cellular variability on the system's functionality. Commercial set-ups that allow the acquisition of fluorescent signal at single cell level (flow cytometers or quantitative microscopes) are expensive apparatuses that are hardly affordable by small laboratories. Methods: A protocol that makes a standard optical microscope able to acquire quantitative, single cell, fluorescent data from a bacterial population transformed with synthetic gene circuitry is presented. Single cell fluorescence values, acquired with a microscope set-up and processed with custom-made software, are compared with results that were obtained with a flow cytometer in a bacterial population transformed with the same gene circuitry. Results: The high correlation between data from the two experimental set-ups, with a correlation coefficient computed over the tested dynamic range > 0.99, proves that a standard optical microscope- when coupled with appropriate software for image processing- might be used for quantitative single-cell fluorescence measurements. The calibration of the set-up, together with its validation, is described. Conclusions: The experimental protocol described in this paper makes quantitative measurement of single cell fluorescence accessible to laboratories equipped with standard optical microscope set-ups. Our method allows for an affordable measurement/quantification of intercellular variability, whose better understanding of this phenomenon will improve our comprehension of cellular behaviors and the design of synthetic gene circuits. All the required software is freely available to the synthetic biology community (MUSIQ Microscope flUorescence SIngle cell Quantification). | A-3021-2012;AAE-3932-2021;AAH-6448-2021;AAU-6456-2020;ABE-3400-2021;B-7851-2013 | GENE CIRCUITS | 0 | null | Fluorescence microscopy;Phenotypic noise;Single-cell fluorescence;Synthetic biology | 9 | Fluorescence microscopy;Gene circuits;Phenotypic noise;Single-cell fluorescence;Synthetic biology | WOS:000395925900001 | Univ Bologna, Bologna, Italy;Univ Bologna, Cesena, Italy;Univ Bologna, Ozzano Dell Emilia, Italy;Univ Edinburgh, Midlothian, Scotland;Univ Nottingham, Nottingham, England;Univ Siena, Siena, Italy | Italy;UK | 2,017 | null | 0000-0002-1099-8279;0000-0002-3731-7760;0000-0002-5347-3851;0000-0002-8054-2875;0000-0002-8811-4816;0000-0003-2567-2981;0000-0003-2938-5058 | null | null | English | null | ACS SYNTH BIOL;ADV BIOCHEM ENG BIOT;ANAL CHEM;CURR BIOL;FRONT MICROBIOL;GENE;IEEE COMP SOC C;IFMBE PROC;IM PROC THEOR TOOLS;INT J COMPUT CORP RE;J Biol Eng;J CLIN INVEST;J THEOR BIOL;MATLAB TOOLBOX ANAL;METHODS MOL BIOL;NAT PROTOC;NAT REV MICROBIOL;PROC R SOC SER B-BIO | Bandiera, Lucia;Bevilacqua, Alessandro;Cortesi, Marilisa;Furini, Simone;Gherardi, Alessandro;Giordano, Emanuele;Pasini, Alice | 2024-03-11
ER | Bandiera, L;Bevilacqua, A;Ceroni Francesca;Ceroni, F;Cohen, S E;Cormack, B P;Giordano, E;Hansen, P C;Ibrahim, S F;Lindstrom Sara;Locke, J C W;Marr, D;Mitsunaga T.;Pothoulakis, G;Selvaggio, G;Singh, P;Vadez, T A;Vicente Nathalie B.;Young Jonathan, W | EN3RP | Cesena, Italy | 8 | null | 4 | null | 28,239,411 | Bandiera, Lucia;Bevilacqua, Alessandro;Cortesi, Marilisa;Furini, Simone;Gherardi, Alessandro;Giordano, Emanuele;Pasini, Alice | J BIOL ENG | Bologna, Italy;Cesena, Italy;Midlothian, Scotland;Nottingham, England;Ozzano Dell Emilia, Italy;Siena, Italy |
Chaplain, M A J;Macnamara, C K | 10.3934/mbe.2017016 | null | PO BOX 2604, SPRINGFIELD, MO 65801-2604 USA | 63561k2s5s471sx192534y5v4hs5h363g1t61 | SPATIO-TEMPORAL MODELS OF SYNTHETIC GENETIC OSCILLATORS | Univ St Andrews | null | Chaplain, MAJ (corresponding author), Univ St Andrews, Sch Math & Stat, Math Inst, St Andrews KY16 9SS, Fife, Scotland. | null | Chaplain, Mark A J;Macnamara, Cicely K | Mathematical & Computational Biology | null | WOS | Chaplain, M A J | Univ St Andrews, Fife, Scotland | 14 | genetic;MODELS;of;Oscillators;SPATIO-TEMPORAL;synthetic | 1 | Chaplain, Mark;Macnamara, Cicely Krystyna | AMER INST MATHEMATICAL SCIENCES-AIMS | Univ St Andrews, Sch Math & Stat, Math Inst, St Andrews KY16 9SS, Fife, Scotland | Article; Proceedings Paper | Univ St Andrews | SPRINGFIELD | null | International Conference on Micro and Macro Systems in Life Sciences | Univ St Andrews | null | Chaplain, MAJ (corresponding author), Univ St Andrews, Sch Math & Stat, Math Inst, St Andrews KY16 9SS, Fife, Scotland. | 262 | Chaplain, Mark A J;Macnamara, Cicely K | 19 | 1 | 387,005,500,017 | null | UK | MATHEMATICAL BIOSCIENCES AND ENGINEERING | UK | Bedlewo, POLAND | null | Univ St Andrews, Sch Math & Stat, Math Inst, St Andrews KY16 9SS, Fife, Scotland | 1547-1063 | Chaplain, M A J;Macnamara, C K | FEB | ckm@st-andrews.ac.uk;majc@st-andrews.ac.uk | SPATIO-TEMPORAL MODELS;Synthetic Genetic Oscillators | 2 | J | Mathematical & Computational Biology | (e.g;activator-repressor systems;ACTIVE-TRANSPORT;apoptosis;approach;bifurcation parameter;BINDING;canonical GRN (the Hesl protein);cell division;cellular function;DIFFERENTIATION RESPONSES;DIFFUSION;diffusion coefficient;diffusion-driven oscillations;DYNAMICS;effect;expression;GENE;gene regulatory networks;gene regulatory networks (GRNs);gene sites;gives rise;GRNs;HES1;Hopf bifurcation;i.e;important aspects;major role;MOLECULES;mRNA;n-gene repressilators;NEGATIVE FEEDBACK;negative feedback leading;NETWORK;nucleus;numerical findings;observing fluo-rescently labelled molecules;observing protein/mRNA levels;one important class;OSCILLATIONS;oscillatory behaviour;P53;positive-negative feedback;protein levels;protein production sites;protein/mRNA acts;proteins;proteins bind;recent computational modelling;REPRESSILATORS;signal transduction pathways;single cells);spatial location;spatial movement;SPATIO-TEMPORAL MODELS;synthetic gene networks;synthetic gene regulatory networks;Synthetic Genetic Oscillators;TIME DELAYS;time);transcription factors;transcription rate;vital component | Macnamara, C K | ACTIVE-TRANSPORT;DIFFERENTIATION RESPONSES;DIFFUSION;diffusion-driven oscillations;DYNAMICS;EXPRESSION;gene regulatory networks;HES1;NEGATIVE FEEDBACK;NETWORK;P53;positive-negative feedback;REPRESSILATORS;synthetic gene networks;TIME DELAYS | 249 | [Macnamara, Cicely K.; Chaplain, Mark A. J.] Univ St Andrews, Sch Math & Stat, Math Inst, St Andrews KY16 9SS, Fife, Scotland. | null | (e.g;activator-repressor systems;apoptosis;approach;bifurcation parameter;binding;canonical GRN (the Hesl protein);cell division;cellular function;diffusion coefficient;effect;gene;gene regulatory networks (GRNs);gene sites;gives rise;GRNs;Hopf bifurcation;i.e;important aspects;major role;molecules;mRNA;n-gene repressilators;negative feedback leading;nucleus;numerical findings;observing fluo-rescently labelled molecules;observing protein/mRNA levels;one important class;oscillations;oscillatory behaviour;protein levels;protein production sites;protein/mRNA acts;proteins;proteins bind;recent computational modelling;signal transduction pathways;single cells);spatial location;spatial movement;spatio-temporal models;synthetic gene regulatory networks;time);transcription factors;transcription rate;vital component | 10.1007/BF00275860;10.1007/BF00276489;10.1007/s11538-012-9725-1;10.1016/0022-5193(68)90189-6;10.1016/0022-5193(72)90157-9;10.1016/0025-5564(88)90081-8;10.1016/0065-2571(65)90067-1;10.1016/j.bbapap.2013.09.019;10.1016/j.csbj.2014.05.007;10.1016/j.jtbi.2008.07.013;10.1016/j.jtbi.2010.08.017;10.1016/j.jtbi.2010.12.016;10.1016/j.jtbi.2012.08.035;10.1016/j.jtbi.2014.07.022;10.1016/j.mbs.2012.01.001;10.1016/S0014-5793(03)00279-5;10.1016/S0960-9822(03)00494-9;10.1021/sb400152n;10.1038/35002125;10.1038/ncomms5905;10.1038/ng1293;10.1051/mmnp/20094304;10.1063/1.1681157;10.1088/1478-3975/11/4/045001;10.1098/rsif.2010.0183;10.1098/rsif.2012.0988;10.1101/gad.1823109;10.1103/PhysRevE.85.046210;10.1111/j.1365-2443.2010.01413.x;10.1126/science.1074560;10.1126/science.1155998;10.1126/science.1181369;10.1126/science.298.5594.824;10.1137/0911001;10.1140/epjb/e2002-00271-1;10.1142/S021820251550030X;10.1186/gb-2012-13-2-240;10.1242/dev.000786;10.3390/genes2010219;10.3938/jkps.50.234 | Univ St Andrews | Chaplain, M A J;Macnamara, C K | Macnamara, C K: Univ St Andrews, Sch Math & Stat, Math Inst, St Andrews KY16 9SS, Fife, Scotland | Chaplain, Mark | null | 40 | null | UK | Univ St Andrews | Macnamara, Cicely K | Green Accepted, gold, Green Submitted | ACTIVE-TRANSPORT;DIFFERENTIATION RESPONSES;DIFFUSION;DYNAMICS;EXPRESSION;HES1;NEGATIVE FEEDBACK;NETWORK;P53;TIME DELAYS | Macnamara, Cicely K.; Chaplain, Mark A. J.; | null | Univ St Andrews, Sch Math & Stat, Math Inst, St Andrews KY16 9SS, Fife, Scotland | Univ St Andrews, Sch Math & Stat, Math Inst, St Andrews KY16 9SS, Fife, Scotland | 1551-0018 | diffusion-driven oscillations;gene regulatory networks;positive-negative feedback;repressilator;Synthetic gene network | 1 | 1965;1968;1972;1974;1984;1985;1988;1990;2000;2002;2003;2004;2007;2008;2009;2010;2011;2012;2013;2014;2015 | 5 | Univ St Andrews, Sch Math & Stat, Math Inst, St Andrews KY16 9SS, Fife, Scotland | Math. Biosci. Eng. | Chaplain, Mark A J | AMER INST MATHEMATICAL SCIENCES-AIMS | (e.g;(GRNs);(the;,;a;activator-repressor;acts;altering;and;apoptosis;approach;are;as;aspects;been;behaviour;bifurcation;bind;binding;both;by;canonical;cause;cell;cells);cellular;class;coefficient;component;computational;demonstrated;diffusion;division;e.g.;effect;examine;extend;factors;feedback;findings;first;fluo-rescently;function;gene;gives;GRN;GRNs;has;have;Hesl;Hopf;i.e;if;important;in;is;known;labelled;leading;levels;location;major;many;may;model;modelling;models;molecules;movement;mRNA;n-gene;negative;networks;nucleus;numerical;observing;of;on;one;oscillations;oscillatory;over;paper;parameter;pathways;play;present;production;protein;protein);protein/mRNA;proteins;proved;rate;recent;reduces;regulatory;Repressilators;rigorously;rise;role;show;signal;single;sites;spatial;spatially;spatio-temporal;subsequently;such;synthetic;systems;temporally;that;the;then;there;thereby;these;this;time);to;transcription;transduction;varying;vital;we | Univ St Andrews | Signal transduction pathways play a major role in many important aspects of cellular function e.g. cell division, apoptosis. One important class of signal transduction pathways is gene regulatory networks (GRNs). In many GRNs, proteins bind to gene sites in the nucleus thereby altering the transcription rate. Such proteins are known as transcription factors. If the binding reduces the transcription rate there is a negative feedback leading to oscillatory behaviour in mRNA and protein levels, both spatially (e.g. by observing fluo-rescently labelled molecules in single cells) and temporally (e.g. by observing protein/mRNA levels over time). Recent computational modelling has demonstrated that spatial movement of the molecules is a vital component of GRNs and may cause the oscillations. These numerical findings have subsequently been proved rigorously i.e. the diffusion coefficient of the protein/mRNA acts as a bifurcation parameter and gives rise to a Hopf bifurcation. In this paper we first present a model of the canonical GRN (the Hesl protein) and show the effect of varying the spatial location of gene and protein production sites on the oscillations. We then extend the approach to examine spatio-temporal models of synthetic gene regulatory networks e.g. n-gene repressilators and activator-repressor systems. | A-5355-2010 | ACTIVE-TRANSPORT;DIFFERENTIATION RESPONSES;DIFFUSION;DYNAMICS;EXPRESSION;HES1;NEGATIVE FEEDBACK;NETWORKS;P53;TIME DELAYS | 0 | JUN 08-12, 2015 | diffusion-driven oscillations;gene regulatory networks;positive-negative feedback;repressilators;synthetic gene networks | 14 | ACTIVE-TRANSPORT;DIFFERENTIATION RESPONSES;DIFFUSION;diffusion-driven oscillations;DYNAMICS;EXPRESSION;gene regulatory networks;HES1;NEGATIVE FEEDBACK;NETWORKS;P53;positive-negative feedback;repressilator;synthetic gene networks;TIME DELAYS | WOS:000387005500017 | Univ St Andrews, Fife, Scotland | UK | 2,017 | null | 0000-0001-5727-2160;0000-0003-4961-6052 | null | null | English | null | ACS SYNTH BIOL;ADVANCE ENZYME REGULAT;B MATH BIOL;BBA-PROTEINS PROTEOM;COMPUT STRUCT BIOTEC;CURR BIOL;DEVELOPMENT;EUR PHYS J B;FEBS LETT;GENE DEV;GENES CELLS;GENES-BASEL;GENOME BIOL;J CHEM PHYS;J KOREAN PHYS SOC;J MATH BIOL;J R SOC INTERFACE;J THEOR BIOL;MATH BIOSCI;MATH MOD METH APPL S;MATH MODEL NAT PHENO;NAT COMMUN;NAT GENET;NATURE;PHYS BIOL;PHYS REV E;SCIENCE;SIAM J SCI STAT COMP | Chaplain, Mark A J;Macnamara, Cicely K | 2024-03-11
ER | Busenberg, S;Cangiani, A;Chaplain, M;Chen, Y Y;Dimitrio, L;Elias, J;Elowitz, M B;Glass, L;Goodwin Brian C.;Gordon, K E;Griffith, J S;Hirata, H;Jensen, M H;Kageyama, R;Kobayashi, T;Lahav, G;Lieberman-Aiden, E;Liu, R T;Mahaffy, J M;Milo, R;Momiji, H;Monk, N A M;Naqib, F;O'Brien, E L;Purcell, O;Sang, L Y;Schaerli, Y;Shymko, R M;Skeel, R D;Sturrock, M;Szymanska, Z;Tiana, G;Yordanov, B | EB0AJ | Fife, Scotland | 5 | null | 1 | null | 27,879,131 | Chaplain, Mark A J;Macnamara, Cicely K | MATH BIOSCI ENG | Fife, Scotland |
Abdallah, H;Collins, J J;Del Vecchio, D;Qian, Y L | 10.1016/j.cels.2016.12.001 | null | 600 TECHNOLOGY SQUARE, 5TH FLOOR, CAMBRIDGE, MA 02139 USA | 3i4v5w6a6x5k602i5x5u3p566t2f6x6m2k3l166n | A Blueprint for a Synthetic Genetic Feedback Controller to Reprogram Cell Fate | MIT | null | Del Vecchio, D (corresponding author), MIT, Dept Mech Engn, Cambridge, MA 02139 USA.;Del Vecchio, D (corresponding author), MIT, Synthet Biol Ctr, Cambridge, MA 02139 USA. | null | Abdallah, Hussein;Collins, James J;Del Vecchio, Domitilla;Qian, Yili | Biochemistry & Molecular Biology;Cell Biology | NIGMS [P50 GMO98792] | WOS | Del Vecchio, D | Broad Inst MIT & Harvard, Cambridge, MA USA;Harvard MIT Program Hlth Sci & Technol, Cambridge, MA USA;Harvard Univ, Boston, MA USA;MIT, Cambridge, MA USA | 4 | a;Blueprint;cell;controller;fate;feedback;for;genetic;Reprogram;synthetic;to | 1 | /0000-0002-1097-0401;Abdallah, Hussein | CELL PRESS | Broad Inst MIT & Harvard, 415 Main St, Cambridge, MA 02142 USA;Harvard MIT Program Hlth Sci & Technol, Cambridge, MA 02139 USA;Harvard Univ, Wyss Inst Biol Inspired Engn, 3 Blackfan Circle, Boston, MA 02115 USA;MIT, Dept Biol Engn, Cambridge, MA 02139 USA;MIT, Dept Elect Engn & Comp Sci, Cambridge, MA 02139 USA;MIT, Dept Mech Engn, Cambridge, MA 02139 USA;MIT, Dept Mech Engn, Cambridge, MA 02139 USA.; Del Vecchio, D (corresponding author), MIT, Synthet Biol Ctr, Cambridge, MA 02139 USA;MIT, Inst Med Engn & Sci, Cambridge, MA 02139 USA;MIT, Synthet Biol Ctr, Cambridge, MA 02139 USA | Article | MIT | CAMBRIDGE | null | null | Broad Inst MIT & Harvard;Dept Mech Engn;Harvard MIT Program Hlth Sci & Technol;Harvard Univ;MIT | NIGMS | Del Vecchio, D (corresponding author), MIT, Dept Mech Engn, Cambridge, MA 02139 USA.; Del Vecchio, D (corresponding author), MIT, Synthet Biol Ctr, Cambridge, MA 02139 USA. | + | Abdallah, Hussein;Collins, James J;Del Vecchio, Domitilla;Qian, Yili | 9 | 8 | 395,783,200,013 | NIGMS [P50 GMO98792] | USA | CELL SYSTEMS | USA;USA.; | null | null | MIT, Dept Mech Engn, Cambridge, MA 02139 USA | 2405-4712 | Abdallah, H;Collins, J J;Del Vecchio, D;Qian, Y L | JAN 25 | ddv@mit.edu | Blueprint;Reprogram Cell Fate;Synthetic Genetic Feedback Controller | 4 | J | Biochemistry & Molecular Biology;Cell Biology | actual TF concentrations;alternative reprogramming strategy;Blueprint;case study;cell's phenotype;concentration;constant overexpression;controller;controller works;desired value;differentiation;discrepancy;EMBRYONIC STEM-CELLS;experimentalists;expression;feedback gain;gene regulatory networks (GRNs);general;GRN's key TFs;GRN's structure;high;independent;induced pluripotency;inefficient;LINEAGES;MAMMALIAN-CELLS;mathematical analysis;NANOG;new approach;parameters;PLURIPOTENCY;practice;problemby;process;Reprogram Cell Fate;reprogramming;reprogramming GRNs;reprogramming strategy;SELF-RENEWAL;specific transcription factors (TFs);stem cells;Synthetic Genetic Feedback Controller;TF expression;theory;transcription factor;TROPHECTODERM | Del Vecchio, D | DIFFERENTIATION;EMBRYONIC STEM-CELLS;EXPRESSION;LINEAGES;MAMMALIAN-CELLS;NANOG;PLURIPOTENCY;SELF-RENEWAL;transcription factor;TROPHECTODERM | 109 | [Del Vecchio, Domitilla; Qian, Yili] MIT, Dept Mech Engn, Cambridge, MA 02139 USA. [Del Vecchio, Domitilla; Collins, James J.] MIT, Synthet Biol Ctr, Cambridge, MA 02139 USA. [Abdallah, Hussein] MIT, Dept Elect Engn & Comp Sci, Cambridge, MA 02139 USA. [Collins, James J.] MIT, Inst Med Engn & Sci, Cambridge, MA 02139 USA. [Collins, James J.] MIT, Dept Biol Engn, Cambridge, MA 02139 USA. [Collins, James J.] Harvard MIT Program Hlth Sci & Technol, Cambridge, MA 02139 USA. [Collins, James J.] Broad Inst MIT & Harvard, 415 Main St, Cambridge, MA 02142 USA. [Collins, James J.] Harvard Univ, Wyss Inst Biol Inspired Engn, 3 Blackfan Circle, Boston, MA 02115 USA. | The authors would like to thank Prof. Eduardo Sontag and Prof. Ron Weiss for discussions on the monotone cooperative nature of the pluripotency network and on the siRNA technology for the implementation of the feedback controller, respectively. The authors would also like to thank Prof. George Daley for a number of useful discussions both on the reprogrammability property of the pluripotency network and on the feedback controller concept. Finally, the authors would like to thank Ms. Narmada Herath for technical support with the stochastic analysis. This work was supported in part by NIGMS grant P50 GMO98792. | actual TF concentrations;alternative reprogramming strategy;case study;cell's phenotype;concentration;constant overexpression;controller;controller works;desired value;discrepancy;experimentalists;feedback gain;gene regulatory networks (GRNs);general;GRN's key TFs;GRN's structure;high;independent;induced pluripotency;inefficient;mathematical analysis;new approach;parameters;practice;problemby;process;reprogram cell fate;reprogramming;reprogramming GRNs;reprogramming strategy;specific transcription factors (TFs);stem cells;synthetic genetic feedback controller;TF expression;theory | 10.1002/bies.200800189;10.1006/dbio.1994.1312;10.1016/j.cell.2005.08.020;10.1016/j.cell.2005.08.040;10.1016/j.cell.2006.07.024;10.1016/j.cell.2008.01.015;10.1016/j.cell.2008.02.039;10.1016/j.cell.2009.01.035;10.1016/j.cell.2009.12.029;10.1016/j.cell.2010.10.008;10.1016/j.cell.2011.05.017;10.1016/j.cell.2012.09.045;10.1016/j.cell.2013.05.001;10.1016/j.stem.2011.11.003;10.1016/j.stem.2014.05.002;10.1016/j.stem.2015.01.013;10.1016/S0092-8674(03)00392-1;10.1017/CBO9780511809088;10.1021/acssynbio.6b00014;10.1038/74199;10.1038/cr.2013.1;10.1038/msb.2013.49;10.1038/mt.2010.314;10.1038/nature08533;10.1038/nature08592;10.1038/nature10098;10.1038/nbt.2018;10.1038/nbt.3070;10.1038/ncb2742;10.1038/NMETH1079;10.1038/nrg3853;10.1038/nrm.2016.8;10.1038/nrm3584;10.1038/nsmb1280;10.1038/nsmb780;10.1038/srep00550;10.1038/srep13533;10.1042/BJ20080134;10.1063/1.481811;10.1073/pnas.0802288105;10.1073/pnas.1017017108;10.1093/dnares/dsn030;10.1093/nar/gkp889;10.1101/gad.1833510;10.1109/TAC.2003.817920;10.1109/TAC.2012.2211444;10.1128/JVI.65.1.483-488.1991;10.1186/1752-0509-5-19;10.1371/journal.pbio.1000149;10.1371/journal.pcbi.0020123;10.1371/journal.pcbi.1003165;10.1371/journal.pcbi.1003625;10.1371/journal.pcbi.1004881;10.1371/journal.pone.0003478;10.1371/journal.pone.0081622;10.1371/journal.pone.0092496;10.1371/journal.pone.0102873;10.23943/PRINCETON/9780691161532.001.0001;[10.1016/j.cels.2016.01.004, 10.1016/j.cels.2016.02.010] | MIT | Abdallah, H;Collins, J J;Del Vecchio, D;Qian, Y L | Del Vecchio, D: MIT, Dept Mech Engn, Cambridge, MA 02139 USA | Qian, Yili | P50 GMO98792 | 69 | null | USA | Broad Inst MIT & Harvard;Harvard MIT Program Hlth Sci & Technol;Harvard Univ;MIT | Del Vecchio, Domitilla | Green Accepted, hybrid | DIFFERENTIATION;EMBRYONIC STEM-CELLS;EXPRESSION;LINEAGES;MAMMALIAN-CELLS;NANOG;PLURIPOTENCY;SELF-RENEWAL;TRANSCRIPTION FACTOR;TROPHECTODERM | Del Vecchio, Domitilla; Abdallah, Hussein; Qian, Yili; Collins, James J.; | null | Broad Inst MIT & Harvard, 415 Main St, Cambridge, MA 02142 USA;Harvard MIT Program Hlth Sci & Technol, Cambridge, MA 02139 USA;Harvard Univ, Wyss Inst Biol Inspired Engn, 3 Blackfan Circle, Boston, MA 02115 USA;MIT, Dept Biol Engn, Cambridge, MA 02139 USA;MIT, Dept Elect Engn & Comp Sci, Cambridge, MA 02139 USA;MIT, Dept Mech Engn, Cambridge, MA 02139 USA;MIT, Inst Med Engn & Sci, Cambridge, MA 02139 USA;MIT, Synthet Biol Ctr, Cambridge, MA 02139 USA | Broad Inst MIT & Harvard, 415 Main St, Cambridge, MA 02142 USA;Harvard MIT Program Hlth Sci & Technol, Cambridge, MA 02139 USA;Harvard Univ, Wyss Inst Biol Inspired Engn, 3 Blackfan Circle, Boston, MA 02115 USA;MIT, Dept Biol Engn, Cambridge, MA 02139 USA;MIT, Dept Elect Engn & Comp Sci, Cambridge, MA 02139 USA;MIT, Dept Mech Engn, Cambridge, MA 02139 USA;MIT, Inst Med Engn & Sci, Cambridge, MA 02139 USA;MIT, Synthet Biol Ctr, Cambridge, MA 02139 USA | 2405-4720 | null | 1 | 1964;1991;1994;1995;2000;2002;2003;2004;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016 | 51 | MIT, Dept Mech Engn, Cambridge, MA 02139 USA;MIT, Synthet Biol Ctr, Cambridge, MA 02139 USA | Cell Syst. | Collins, James J | CELL PRESS | (GRNs);(TFs);,;:;a;actual;address;adjusting;alternative;an;analysis;and;any;apply;approach;artificially;as;based;be;between;by;can;case;cell;cell's;cells;concentration;concentrations;constant;controller;demonstrate;desired;discrepancy;dynamically;experimentalists;expression;factors;fate;feedback;gain;gene;general;genetic;GRN's;GRNs;guaranteed;here;high;in;independent;induced;inefficient;instead;introducing;is;its;key;maintain;manipulate;mathematical;may;model;networks;new;not;of;often;on;overexpression;parameters;performance;performed;phenotype;pluripotency;practice;predicts;problemby;process;propose;provided;regulatory;reprogram;reprogramming;specific;steers;stem;strategy;structure;study;succeed;sufficiently;synthetic;TF;TFs;that;the;theory;this;to;transcription;unreliable;using;value;we;works | MIT | To artificially reprogram cell fate, experimentalists manipulate the gene regulatory networks (GRNs) that maintain a cell's phenotype. In practice, reprogramming is often performed by constant overexpression of specific transcription factors (TFs). This process can be unreliable and inefficient. Here, we address this problemby introducing a new approach to reprogramming based on mathematical analysis. We demonstrate that reprogramming GRNs using constant overexpression may not succeed in general. Instead, we propose an alternative reprogramming strategy: a synthetic genetic feedback controller that dynamically steers the concentration of a GRN's key TFs to any desired value. The controller works by adjusting TF expression based on the discrepancy between desired and actual TF concentrations. Theory predicts that this reprogramming strategy is guaranteed to succeed, and its performance is independent of the GRN's structure and parameters, provided that feedback gain is sufficiently high. As a case study, we apply the controller to a model of induced pluripotency in stem cells. | L-5558-2019 | DIFFERENTIATION;EMBRYONIC STEM-CELLS;EXPRESSION;LINEAGE;MAMMALIAN-CELLS;NANOG;PLURIPOTENCY;SELF-RENEWAL;TRANSCRIPTION FACTORS;TROPHECTODERM | 1 | null | null | 23 | DIFFERENTIATION;EMBRYONIC STEM-CELLS;EXPRESSION;LINEAGE;MAMMALIAN-CELLS;NANOG;PLURIPOTENCY;SELF-RENEWAL;transcription factor;TROPHECTODERM | WOS:000395783200013 | Broad Inst MIT & Harvard, Cambridge, MA USA;Harvard MIT Program Hlth Sci & Technol, Cambridge, MA USA;Harvard Univ, Boston, MA USA;MIT, Cambridge, MA USA | USA | 2,017 | null | 0000-0002-1097-0401;0000-0003-3860-3598 | null | null | English | null | ACS SYNTH BIOL;AM MATH SOC MATH SUR;BIOCHEM J;BIOESSAYS;BMC SYST BIOL;CELL;CELL RES;CELL STEM CELL;CELL SYST;DEV BIOL;DIFFERENTIAL INTEGRA;DNA RES;GENE DEV;IEEE T AUTOMAT CONTR;INTRO SYSTEMS BIOL D;Introduction to Lattices and Order;J CHEM PHYS;J VIROL;MOL SYST BIOL;MOL THER;NAT BIOTECHNOL;NAT CELL BIOL;NAT GENET;NAT METHODS;NAT REV GENET;NAT REV MOL CELL BIO;NAT STRUCT MOL BIOL;NATURE;Nonlinear Systems;NUCLEIC ACIDS RES;NUMERICAL OPTIMIZATI;Numerical Solution of Stochastic Differential Equations;P NATL ACAD SCI USA;PLOS BIOL;PLOS COMPUT BIOL;PLOS ONE;Real-time optimization by extremum-seeking control;SCI REP-UK;The Strategy of the Genes | Abdallah, Hussein;Collins, James J;Del Vecchio, Domitilla;Qian, Yili | 2024-03-11
ER | Alon, U;Angeli, D;Ariyur Kb.;Boyer, L A;Briat, C;Cahan, P;Carey, B W;Carthew, R W;Chambers, I;Chickarmane, V;Cuccato, G;Darzacq, X;Davey B.A.;Del Vecchio D.;Del Vecchio, D;Descalzo, S M;Ebert, M S;Faucon, P C;Feng, H D;Gillespie, D T;Goh, P A;Graf, T;Haley, B;Hanna, J;Hanna, J H;Herberg, M;Holtz, W J;Huang, S;Jaenisch, R;Jens, M;Kalmar, T;Khalil H. K.;Kim, J W;Kloeden P.;Li, C H;Menolascina, F;Milias-Argeitis, A;Milo, R;Morris, S A;Mullin, N P;Murray Richardm.;Niakan, K K;Nikolaev, E V;Niwa, H;Nocedal J.;Palmieri, S L;Radzisheuskaya, A;Schlaeger, T M;Schwanhäusser, B;Sharova, L V;Shu, J;Siwiak M.;Smith H.L.;Soufi, A;Takahashi, K;Tapia, N;Theunissen, T W;Thomson, M;Waddington C.;Walter, W;Wang, J;Warlich, E;Xu, J;Yates, J L | EN1PV | Cambridge, MA USA;Cambridge, MA USA. | 62 | null | 4 | null | 28,065,574 | Abdallah, Hussein;Collins, James J;Del Vecchio, Domitilla;Qian, Yili | CELL SYST | Boston, MA USA;Cambridge, MA USA |
Blanchard, A E;Kong, W T;Liao, C;Lu, T | 10.1093/nar/gkw1045 | null | GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND | 6kmz6v4i2z6b626de5a5u401g3q176y32y26 | Engineering robust and tunable spatial structures with synthetic gene circuits | Univ Illinois | null | Lu, T (corresponding author), Univ Illinois, Carl R Woese Inst Genom Biol, Urbana, IL 61801 USA.;Lu, T (corresponding author), Univ Illinois, Dept Bioengn, Urbana, IL 61801 USA.;Lu, T (corresponding author), Univ Illinois, Dept Phys, Urbana, IL 61801 USA. | null | Blanchard, Andrew E;Kong, Wentao;Liao, Chen;Lu, Ting | Biochemistry & Molecular Biology | National Science Foundation [1227034, 1553649]; Office of Naval Research [N000141612525]; American Heart Association [12SDG12090025]; Brain and Behavior Research Foundation (NARSAD Young Investigator Award); U.S. Department of Defense (DOD) [N000141612525] Funding Source: U.S. Department of Defense (DOD); Direct For Biological Sciences; Div Of Molecular and Cellular Bioscience [1553649] Funding Source: National Science Foundation; Directorate For Engineering; Div Of Engineering Education and Centers [1227034] Funding Source: National Science Foundation | WOS | Lu, T | Univ Illinois, Urbana, IL USA | 45 | and;circuits;engineering;gene;robust;spatial;structures;synthetic;tunable;with | 1 | Liao, Chen | OXFORD UNIV PRESS | Univ Illinois, Carl R Woese Inst Genom Biol, Urbana, IL 61801 USA;Univ Illinois, Dept Bioengn, Urbana, IL 61801 USA;Univ Illinois, Dept Bioengn, Urbana, IL 61801 USA.; Lu, T (corresponding author), Univ Illinois, Carl R Woese Inst Genom Biol, Urbana, IL 61801 USA.; Lu, T (corresponding author), Univ Illinois, Dept Phys, Urbana, IL 61801 USA;Univ Illinois, Dept Phys, Urbana, IL 61801 USA | Article | Univ Illinois | OXFORD | null | null | Univ Illinois | American Heart Association;Brain and Behavior Research Foundation (NARSAD Young Investigator Award);Direct For Biological Sciences;Directorate For Engineering;Div Of Engineering Education and Centers;Div Of Molecular and Cellular Bioscience;National Science Foundation;Office of Naval Research;U.S. Department of Defense (DOD) | Lu, T (corresponding author), Univ Illinois, Dept Bioengn, Urbana, IL 61801 USA.; Lu, T (corresponding author), Univ Illinois, Carl R Woese Inst Genom Biol, Urbana, IL 61801 USA.; Lu, T (corresponding author), Univ Illinois, Dept Phys, Urbana, IL 61801 USA. | 1014 | Blanchard, Andrew E;Kong, Wentao;Liao, Chen;Lu, Ting | 23 | 3 | 396,576,300,045 | American Heart Association [12SDG12090025];Brain and Behavior Research Foundation (NARSAD Young Investigator Award);Direct For Biological Sciences;Directorate For Engineering;Div Of Engineering Education and Centers [1227034] Funding Source: National Science Foundation;Div Of Molecular and Cellular Bioscience [1553649] Funding Source: National Science Foundation;National Science Foundation [1227034, 1553649];Office of Naval Research [N000141612525];U.S. Department of Defense (DOD) [N000141612525] Funding Source: U.S. Department of Defense (DOD) | USA | NUCLEIC ACIDS RESEARCH | USA;USA.; | null | null | Univ Illinois, Dept Bioengn, Urbana, IL 61801 USA | 0305-1048 | Blanchard, A E;Kong, W T;Liao, C;Lu, T | JAN | luting@illinois.edu | engineering;synthetic gene circuits;tunable spatial structures | 4 | J | Biochemistry & Molecular Biology | antibiotic features;band widths;biological systems;BIOLOGY;biosynthesis;cells;cellular context perturbations;cellular nisin immunity;cellular stripes;circuit robustness;CIRCUITS;controllable;controllable arrays;deep mining;DESIGN;designed patterns;direct cells;direct Lactococcus lactis populations;dual signaling;engineering;external nisin gradient;foundations;functional robustness;future applications;goal;GRADIENT;living systems;major goal;mathematical model;multiple species;natural functionalities;nisin;observed patterns;patterns;predictable structures;promising tools;simple synthetic circuits;SPACE;spatial band-pass;spatial structures;spots;structured nisin-producing bacteria;study offers new synthetic biology tools;synthetic communities;synthetic gene circuits;tunability;tunable;tunable spatial structures;valuable route | Kong, W T | BIOLOGY;BIOSYNTHESIS;DESIGN;FOUNDATIONS;SPACE | 1005 | [Kong, Wentao; Liao, Chen; Lu, Ting] Univ Illinois, Dept Bioengn, Urbana, IL 61801 USA. [Kong, Wentao; Blanchard, Andrew E.; Liao, Chen; Lu, Ting] Univ Illinois, Carl R Woese Inst Genom Biol, Urbana, IL 61801 USA. [Blanchard, Andrew E.; Lu, Ting] Univ Illinois, Dept Phys, Urbana, IL 61801 USA. | National Science Foundation [1227034, 1553649]; Office of Naval Research [N000141612525]; American Heart Association [12SDG12090025]; Brain and Behavior Research Foundation (NARSAD Young Investigator Award). Funding for open access charge: National Science Foundation. | antibiotic features;band widths;biological systems;cells;cellular context perturbations;cellular nisin immunity;cellular stripes;circuit robustness;circuits;controllable;controllable arrays;deep mining;designed patterns;direct cells;direct Lactococcus lactis populations;dual signaling;engineering;external nisin gradient;functional robustness;future applications;goal;gradient;living systems;major goal;mathematical model;multiple species;natural functionalities;nisin;observed patterns;patterns;predictable structures;promising tools;simple synthetic circuits;space;spatial band-pass;spatial structures;spots;structured nisin-producing bacteria;study offers new synthetic biology tools;synthetic communities;synthetic gene circuits;tunability;tunable;valuable route | 10.1007/s00018-007-7171-2;10.1016/j.cell.2009.04.048;10.1016/j.cell.2016.03.006;10.1016/j.tibtech.2008.05.004;10.1021/sb300044r;10.1021/sb500225r;10.1038/463288a;10.1038/msb.2008.24;10.1038/msb4100202;10.1038/nature03461;10.1038/nature04342;10.1038/nature08753;10.1038/nbt.1591;10.1038/nbt0708-771;10.1038/ncomms5905;10.1038/nrg1471;10.1038/nrg3227;10.1073/pnas.0901246106;10.1093/nar/gkq671;10.1093/nar/gkv1093;10.1103/RevModPhys.66.1481;10.1126/science.1206843;10.1126/science.1209042;10.1126/science.8493529;10.1126/science.aaa3794;10.1128/AEM.55.1.224-228.1989;10.1128/AEM.58.6.1952-1961.1992;10.1128/JB.180.7.1895-1903.1998;10.1146/annurev.micro.52.1.779;[10.1038/NMETH.2926, 10.1038/nmeth.2926] | Univ Illinois | Blanchard, A E;Kong, W T;Liao, C;Lu, T | Kong, W T: Univ Illinois, Dept Bioengn, Urbana, IL 61801 USA | null | 1227034;12SDG12090025;1553649;N000141612525 | 34 | null | USA | Univ Illinois | Kong, Wentao | Green Published, gold, Green Submitted | BIOLOGY;BIOSYNTHESIS;DESIGN;FOUNDATIONS;SPACE | Kong, Wentao; Blanchard, Andrew E.; Liao, Chen; Lu, Ting; | null | Univ Illinois, Carl R Woese Inst Genom Biol, Urbana, IL 61801 USA;Univ Illinois, Dept Bioengn, Urbana, IL 61801 USA;Univ Illinois, Dept Phys, Urbana, IL 61801 USA | Univ Illinois, Carl R Woese Inst Genom Biol, Urbana, IL 61801 USA;Univ Illinois, Dept Bioengn, Urbana, IL 61801 USA;Univ Illinois, Dept Phys, Urbana, IL 61801 USA | 1362-4962 | null | 2 | 1989;1992;1993;1994;1998;2001;2004;2005;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016 | 35 | Univ Illinois, Carl R Woese Inst Genom Biol, Urbana, IL 61801 USA;Univ Illinois, Dept Bioengn, Urbana, IL 61801 USA;Univ Illinois, Dept Phys, Urbana, IL 61801 USA | Nucleic Acids Res. | Lu, Ting | OXFORD UNIV PRESS | ,;;;a;achieve;additionally;against;all;allow;also;although;and;antibiotic;applications;are;arrays;bacteria;band;band-pass;become;biological;biology;both;build;by;can;cells;cellular;circuit;circuits;communities;composed;consistently;context;controllable;deep;demonstrates;designed;direct;do;driven;dual;engineering;environmental;establish;even;external;facilitate;features;fine-tuning;for;form;functional;functionalities;furthermore;future;gene;generate;goal;gradient;harnessing;have;here;highly;however;immunity;in;is;it;lactis;Lactococcus;living;major;mathematical;mining;model;multiple;natural;need;new;nisin;nisin-producing;not;observed;of;offers;order;patterning;patterns;perturbations;populations;possess;predictable;program;programmed;promising;recently;reproduces;require;robust;robustness;route;show;signaling;simple;space;spatial;species;specified;spots;stripes;structured;structures;study;successfully;synthetic;systems;that;the;their;they;this;to;tools;tunability;tunable;us;valuable;we;when;widths;with | Univ Illinois | Controllable spatial patterning is a major goal for the engineering of biological systems. Recently, synthetic gene circuits have become promising tools to achieve the goal; however, they need to possess both functional robustness and tunability in order to facilitate future applications. Here we show that, by harnessing the dual signaling and antibiotic features of nisin, simple synthetic circuits can direct Lactococcus lactis populations to form programmed spatial band-pass structures that do not require fine-tuning and are robust against environmental and cellular context perturbations. Although robust, the patterns are highly tunable, with their band widths specified by the external nisin gradient and cellular nisin immunity. Additionally, the circuits can direct cells to consistently generate designed patterns, even when the gradient is driven by structured nisin-producing bacteria and the patterning cells are composed of multiple species. A mathematical model successfully reproduces all of the observed patterns. Furthermore, the circuits allow us to establish predictable structures of synthetic communities and controllable arrays of cellular stripes and spots in space. This study offers new synthetic biology tools to program spatial structures. It also demonstrates that a deep mining of natural functionalities of living systems is a valuable route to build circuit robustness and tunability. | null | BIOLOGY;BIOSYNTHESIS;DESIGN;FOUNDATIONS;SPACE | 2 | null | null | 10 | BIOLOGY;BIOSYNTHESIS;DESIGN;FOUNDATIONS;SPACE | WOS:000396576300045 | Univ Illinois, Urbana, IL USA | USA | 2,017 | null | 0000-0001-8474-1196 | null | null | English | null | ABSTR APPL AN;ACS SYNTH BIOL;ANNU REV MICROBIOL;APPL ENVIRON MICROB;BIORESOUR BIOPROCESS;CELL;CELL MOL LIFE SCI;EMBRYONIC DEV DROSOP;J BACTERIOL;MATH BIOL;MOL SYST BIOL;NAT BIOTECHNOL;NAT COMMUN;NAT METHODS;NAT REV GENET;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;REV MOD PHYS;SCIENCE;TRENDS BIOTECHNOL | Blanchard, Andrew E;Kong, Wentao;Liao, Chen;Lu, Ting | 2024-03-11
ER | [Anonymous];Arkin, A;Balagadde, F K;Basu, S;Ben-Jacob, E;Brenner, K;Brophy, J A N;Campos-Ortega J. A.;Cao, Y X L;Chen, Y;Danino, T;Endy, D;Greber, D;Kitano, H;Koch, A J;Kong, W;Kong, W T;Kwok, R;Langer, R;Le Loir, Y;Liu, C L;Lu, T K;Lubelski, J;Murray J.D;Riccione, K A;Ruder, W C;Schaerli, Y;Serrano, L;Slusarczyk, A L;Sohka, T;Stoddard, G W;Tabor, J J;Vandeguchte, M | EO3DY | Urbana, IL USA;Urbana, IL USA. | 44 | null | 1 | null | 27,899,571 | Blanchard, Andrew E;Kong, Wentao;Liao, Chen;Lu, Ting | NUCLEIC ACIDS RES | Urbana, IL USA |
MacPherson, M;Saka, Y | 10.1021/acssynbio.6b00165 | null | 1155 16TH ST, NW, WASHINGTON, DC 20036 USA | 74b5q696i316h54f1s1h4l3o3d6np71285c | Short Synthetic Terminators for Assembly of Transcription Units <i>in Vitro</i> and Stable Chromosomal Integration in Yeast <i>S</i>. <i>cerevisiae</i> | Univ Aberdeen | null | Saka, Y (corresponding author), Univ Aberdeen, Sch Med Med Sci & Nutr, Inst Med Sci, Aberdeen AB25 2ZD, Scotland. | null | MacPherson, Murray;Saka, Yasushi | Biochemical Research Methods | Scottish Universities Life Sciences Alliance (SULSA) | WOS | Saka, Y | Univ Aberdeen, Aberdeen AB25 2ZD, Scotland | 6 | <i>in;<i>S</i>;and;Assembly;Chromosomal;for;i>cerevisiae</i>;in;integration;of;short;Stable;synthetic;Terminators;transcription;Units;Vitro</i>;yeast | 1 | null | AMER CHEMICAL SOC | Univ Aberdeen, Sch Med Med Sci & Nutr, Inst Med Sci, Aberdeen AB25 2ZD, Scotland | Article | Univ Aberdeen | WASHINGTON | null | null | Univ Aberdeen | Scottish Universities Life Sciences Alliance (SULSA) | Saka, Y (corresponding author), Univ Aberdeen, Sch Med Med Sci & Nutr, Inst Med Sci, Aberdeen AB25 2ZD, Scotland. | 138 | MacPherson, Murray;Saka, Yasushi | 36 | 1 | 392,575,700,015 | Scottish Universities Life Sciences Alliance (SULSA) | UK | ACS SYNTHETIC BIOLOGY | UK | null | null | Univ Aberdeen, Sch Med Med Sci & Nutr, Inst Med Sci, Aberdeen AB25 2ZD, Scotland | 2161-5063 | MacPherson, M;Saka, Y | JAN | y.saka@abdn.ac.uk | Assembly;i>cerevisiae</i>;short Synthetic Terminators;Stable Chromosomal Integration;Transcription Units <i>in Vitro</i>;Yeast <i>S</i> | 2 | J | Biochemistry & Molecular Biology | assembled DNA;assembling multiple transcription units;assembly;bacterial artificial chromosome;BINDING PROTEINS NRD1;central;common consensus;consensus sequence;CONSTRUCTION;CRYPTIC UNSTABLE TRANSCRIPTS;DESIGN;different activities;DNA;efficient assembly;efficient homologous recombination;expression vectors;few homologous segments;Gateway recombination reactions;gene assembly;GENE-EXPRESSION;genome;genomic integration;i>cerevisiae</i>;ideal chassis;identical length;impacts;influence;integration;issue;lead;library;method;multigene assemblies;neighboring transcription units;orthogonal genetic components;PATHWAY;problem;property;proximal transcription units;random linkers;rearrangements;RECOMBINATION;repeated usage;repeats;repetitive sequences;Saccharomyces cerevisiae;SACCHAROMYCES-CEREVISIAE;short Synthetic Terminators;stable;Stable Chromosomal Integration;standard parts;synthetic;synthetic biology;synthetic genes;synthetic genetic circuits;synthetic genome assemblies;synthetic terminators;SYSTEM;tandem array;transcription units;Transcription Units <i>in Vitro</i>;transcriptional terminator;transcriptional terminators;two BAC (bacterial artificial chromosome) vectors;vitro;vivo;yeast;Yeast <i>S</i>;yeast genome;yeast S. cerevisiae | MacPherson, M | bacterial artificial chromosome;BINDING PROTEINS NRD1;CONSTRUCTION;CRYPTIC UNSTABLE TRANSCRIPTS;DESIGN;DNA;gene assembly;GENE-EXPRESSION;PATHWAY;RECOMBINATION;Saccharomyces cerevisiae;SACCHAROMYCES-CEREVISIAE;SYSTEM;transcriptional terminator;YEAST | 130 | [MacPherson, Murray; Saka, Yasushi] Univ Aberdeen, Sch Med Med Sci & Nutr, Inst Med Sci, Aberdeen AB25 2ZD, Scotland. | The authors acknowledge the assistance of the lain Fraser Cytometry Centre at the University of Aberdeen. We also thank Claire MacGregor, Diane Massie, and Yvonne Turnbull for technical assistance, Alexander Lorenz and Ryohei Sekido for critical reading of the manuscript, and Richard Newton for preliminary results. This work was supported by the Scottish Universities Life Sciences Alliance (SULSA). | assembled DNA;assembling multiple transcription units;assembly;central;common consensus;consensus sequence;different activities;efficient assembly;efficient homologous recombination;expression vectors;few homologous segments;Gateway recombination reactions;genome;genomic integration;ideal chassis;identical length;impacts;influence;integration;issue;lead;library;method;multigene assemblies;neighboring transcription units;orthogonal genetic components;problem;property;proximal transcription units;random linkers;rearrangements;repeated usage;repeats;repetitive sequences;short synthetic terminators;stable;standard parts;synthetic;synthetic biology;synthetic genes;synthetic genetic circuits;synthetic genome assemblies;synthetic terminators;system;tandem array;transcription units;transcriptional terminators;two BAC (bacterial artificial chromosome) vectors;vitro;vivo;yeast;yeast genome;yeast S. cerevisiae | 10.1002/1097-0061(200010)16:14<1313::AID-YEA626>3.0.CO;2-O;10.1002/yea.1469;10.1016/0378-1119(87)90376-3;10.1016/j.cell.2005.04.030;10.1016/j.cell.2013.10.024;10.1016/j.molcel.2006.07.024;10.1016/j.molcel.2006.07.029;10.1016/j.ymben.2013.07.001;10.1016/S0968-0004(96)10057-8;10.1021/acssynbio.5b00007;10.1021/acssynbio.5b00174;10.1021/sb300116y;10.1021/sb4001323;10.1021/sb500255k;10.1021/sb5003357;10.1021/sb500356d;10.1021/sb500366v;10.1021/sb500372z;10.1038/nature09652;10.1038/ncomms5002;10.1038/nprot.2014.145;10.1073/pnas.0507783103;10.1073/pnas.1100507108;10.1073/pnas.76.10.4951;10.1074/jbc.M109.007948;10.1093/nar/23.15.3079;10.1093/nar/gkt1101;10.1093/nar/gkt135;10.1093/nar/gkt605;10.1093/nar/gkt860;10.1093/nar/gkt915;10.1093/nar/gku1082;10.1093/nar/gku829;10.1093/nar/gkv466;10.1101/gr.182477.114;10.1111/1567-1364.12188;10.1126/science.1151721;10.1126/science.1224350;10.1126/science.1249252;10.1186/1471-2105-11-346;10.1261/rna.338407;10.1371/journal.pone.0016765;10.1371/journal.pone.0021622;10.1371/journal.pone.0064419;10.7554/eLife.03703;[10.1038/NMETH.1318, 10.1038/nmeth.1318];[10.1038/NMETH.3339, 10.1038/nmeth.3339] | Univ Aberdeen | MacPherson, M;Saka, Y | MacPherson, M: Univ Aberdeen, Sch Med Med Sci & Nutr, Inst Med Sci, Aberdeen AB25 2ZD, Scotland | null | null | 51 | null | UK | Univ Aberdeen | MacPherson, Murray | Green Accepted | BINDING PROTEINS NRD1;CONSTRUCTION;CRYPTIC UNSTABLE TRANSCRIPTS;DESIGN;DNA;GENE-EXPRESSION;PATHWAY;RECOMBINATION;SACCHAROMYCES-CEREVISIAE;SYSTEM | MacPherson, Murray; Saka, Yasushi; | null | Univ Aberdeen, Sch Med Med Sci & Nutr, Inst Med Sci, Aberdeen AB25 2ZD, Scotland | Univ Aberdeen, Sch Med Med Sci & Nutr, Inst Med Sci, Aberdeen AB25 2ZD, Scotland | null | Saccharomyces cerevisiae;yeast;bacterial artificial chromosome;gene assembly;transcription termination | 1 | 1979;1987;1989;1995;1996;2000;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016 | 17 | Univ Aberdeen, Sch Med Med Sci & Nutr, Inst Med Sci, Aberdeen AB25 2ZD, Scotland | ACS Synth. Biol. | Saka, Yasushi | AMER CHEMICAL SOC | (bacterial;,;a;activities;address;all;also;although;an;and;are;array;artificial;as;assembled;assemblies;assembling;assembly;avoid;BAC;based;be;because;biology;by;can;central;cerevisiae;chassis;chromosome);circuits;common;components;consensus;constructed;constructs;designed;developing;different;DNA;efficient;exploiting;expression;few;for;Gateway;genes;genetic;genome;genomic;has;have;highly;homologous;however;ideal;identical;impacts;in;influence;integrated;integration;is;issue;its;lead;length;library;linkers;method;multigene;multiple;neighboring;of;on;Orthogonal;particular;parts;poses;problem;property;proven;proximal;random;reactions;rearrangements;recombination;repeated;repeats;repetitive;S.;segments;sequence;sequences;series;set;short;showed;since;stable;standard;such;synthetic;system;tandem;terminators;tested;the;their;there;these;they;this;to;transcription;transcriptional;two;units;usage;using;vectors;vitro;vivo;we;with;yeast | Univ Aberdeen | Assembly of synthetic genetic circuits is central to synthetic biology. Yeast S. cerevisiae, in particular, has proven to be an ideal chassis for synthetic genome assemblies by exploiting its efficient homologous recombination. However, this property of efficient homologous recombination poses a problem for multigene assemblies in yeast, since repeated usage of standard parts, such as transcriptional terminators, can lead to rearrangements of the repeats in assembled DNA constructs in vivo. To address this issue in developing a library of orthogonal genetic components for yeast, we designed a set of short synthetic terminators based on a consensus sequence with random linkers to avoid repetitive sequences. We constructed a series of expression vectors with these synthetic terminators for efficient assembly of synthetic genes using Gateway recombination reactions. We also constructed two BAC (bacterial artificial chromosome) vectors for assembling multiple transcription units with the synthetic terminators in vitro and their integration in the yeast genome. The tandem array of synthetic genes integrated in the genome by this method is highly stable because there are few homologous segments in the synthetic constructs. Using this system of assembly and genomic integration of transcription units, we tested the synthetic terminators and their influence on the proximal transcription units. Although all the synthetic terminators have the common consensus with the identical length, they showed different activities and impacts on the neighboring transcription units. | null | BINDING PROTEINS NRD1;CONSTRUCTION;CRYPTIC UNSTABLE TRANSCRIPTS;DESIGN;DNA;GENE-EXPRESSION;PATHWAY;RECOMBINATION;SACCHAROMYCES-CEREVISIAE;SYSTEM | 2 | null | bacterial artificial chromosome;gene assembly;Saccharomyces cerevisiae;transcriptional terminator;yeast | 9 | SACCHAROMYCES-CEREVISIAE;YEAST;bacterial artificial chromosome;BINDING PROTEINS NRD1;CONSTRUCTION;CRYPTIC UNSTABLE TRANSCRIPTS;DESIGN;DNA;gene assembly;GENE-EXPRESSION;PATHWAY;RECOMBINATION;SYSTEM;transcription termination | WOS:000392575700015 | Univ Aberdeen, Aberdeen AB25 2ZD, Scotland | UK | 2,017 | null | null | null | null | English | null | ACS SYNTH BIOL;BMC BIOINFORMATICS;CELL;ELIFE;FEMS YEAST RES;GENE;GENETICS;GENOME RES;J BIOL CHEM;METAB ENG;MOL CELL;MOL CELL BIOL;NAT COMMUN;NAT METHODS;NAT PROTOC;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PLOS ONE;RNA;SCIENCE;TRENDS BIOCHEM SCI;YEAST | MacPherson, Murray;Saka, Yasushi | 2024-03-11
ER | Agmon, N;Amberg Dc.;Annaluru, N;Arigo, J T;Bao, Z H;Carroll, K L;Casini, A;Ceroni, F;Churchman, L S;Colloms, S D;Curran, K A;Davis, C A;Dicarlo, J E;Duportet, X;El Kaderi, B;Gibson, D G;Giuraniuc, C V;Guo, Z J;Guye, P;Jakociunas, T;Langlerouault, F;Lee, M E;Li, M;Lin, M T;Ma, H;Mateus, C;Mitchell, L A;Redden, H;Ryan, O W;Sadowski, I;Sarrion-Perdigones, A;Scherer, S;Schulz, D;Sikorski, R S;Storch, M;Suzuki, Y;Tan-Wong, S M;Thiebaut, M;Torella, J P;Trubitsyna, M;Weber, E;Wingler, L M;Wyers, F;Xi, L Q;Yamanishi, M | EI5ZV | Aberdeen AB25 2ZD, Scotland | 23 | null | 1 | null | 27,529,501 | MacPherson, Murray;Saka, Yasushi | ACS SYNTH BIOL | Aberdeen AB25 2ZD, Scotland |
Re, A | 10.3389/fcell.2017.00077 | 77 | AVENUE DU TRIBUNAL FEDERAL 34, LAUSANNE, CH-1015, SWITZERLAND | 5t2l23661j64182g53305gf624d6d261u6r6673 | nSynthetic Gene Expression Circuits for Designing Precision Tools in Oncology | Ist Italiano Tecnol | null | Re, A (corresponding author), Ist Italiano Tecnol, Ctr Sustainable Future Technol, Turin, Italy. | null | Re, Angela | Cell Biology;Developmental Biology | Istituto Italiano di Tecnologia | WOS | Re, A | Ist Italiano Tecnol, Turin, Italy | 5 | circuits;Designing;expression;for;gene;in;nSynthetic;Oncology;Precision;Tools | 1 | RE, ANGELA | FRONTIERS MEDIA SA | Ist Italiano Tecnol, Ctr Sustainable Future Technol, Turin, Italy | Review | Ist Italiano Tecnol | LAUSANNE | null | null | Ist Italiano Tecnol | Istituto Italiano di Tecnologia | Re, A (corresponding author), Ist Italiano Tecnol, Ctr Sustainable Future Technol, Turin, Italy. | null | Re, Angela | 9 | 1 | 455,238,900,077 | Istituto Italiano di Tecnologia | Italy | FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY | Italy | null | null | Ist Italiano Tecnol, Ctr Sustainable Future Technol, Turin, Italy | 2296-634X | Re, A | null | angela.re@iit.it | Designing Precision Tools;nSynthetic Gene Expression Circuits;Oncology | 1 | J | Cell Biology;Developmental Biology | ANTICANCER DRUGS;ANTITUMOR EFFICACY;AUTOMATED DESIGN;basic biological elements decoupled;biological engineering;brief overview;capabilities;control;DELIVERY;Designing Precision Tools;drug delivery;drug discovery;enabling methodology;engineering;engineering synthetic circuits;enhanced mechanism clarity;functionalized devices;gene expression;gene-based therapy;individual patients;logic;major advances;MAMMALIAN-CELLS;MESSENGER-RNA;natural context;new capabilities;nSynthetic Gene Expression Circuits;Oncology;oncology needs;portability;post-transcriptional/translational;post-translational levels;precision cancer medicine implementations;precision medicine;precision technologies;prospects;rational engineering;remarkable improvements;review;ROBUSTNESS;scalability;sensitivity;significant advancements;specific applications;standardization;successful establishment;synthetic biology;synthetic circuit;synthetic devices;synthetic genetic circuits;T-CELLS;therapeutic technologies;transcriptional;TRANSCRIPTIONAL REGULATORS;tumor cell-;tumor diagnosis;tumor therapy | Re, A | ANTICANCER DRUGS;ANTITUMOR EFFICACY;AUTOMATED DESIGN;biological engineering;DELIVERY;drug delivery;DRUG DISCOVERY;LOGIC;MAMMALIAN-CELLS;MESSENGER-RNA;precision medicine;Synthetic biology;synthetic circuit;T-CELLS;TRANSCRIPTIONAL REGULATORS;tumor diagnosis;tumor therapy | null | [Re, Angela] Ist Italiano Tecnol, Ctr Sustainable Future Technol, Turin, Italy. | This manuscript has been funded by the Istituto Italiano di Tecnologia. | basic biological elements decoupled;brief overview;capabilities;control;drug delivery;enabling methodology;engineering;engineering synthetic circuits;enhanced mechanism clarity;functionalized devices;gene expression;gene-based therapy;individual patients;major advances;natural context;new capabilities;oncology;oncology needs;portability;post-transcriptional/translational;post-translational levels;precision cancer medicine implementations;precision medicine;precision technologies;prospects;rational engineering;remarkable improvements;review;robustness;scalability;sensitivity;significant advancements;specific applications;standardization;successful establishment;synthetic biology;synthetic devices;synthetic genetic circuits;therapeutic technologies;transcriptional;tumor cell-;tumor diagnosis | 10.1002/adfm.201100731;10.1002/anie.200704121;10.1002/cbic.200700478;10.1007/s10875-012-9689-9;10.1016/j.addr.2016.05.004;10.1016/j.addr.2016.08.004;10.1016/j.bioeng.2007.06.001;10.1016/j.biomaterials.2013.11.083;10.1016/j.cbpa.2012.05.179;10.1016/j.cell.2012.05.045;10.1016/j.cell.2013.02.022;10.1016/j.cell.2014.02.022;10.1016/j.cell.2016.01.011;10.1016/j.cell.2017.01.016;10.1016/j.celrep.2013.06.023;10.1016/j.cels.2017.01.003;10.1016/j.chembiol.2009.02.011;10.1016/j.copbio.2015.02.004;10.1016/j.febslet.2012.01.057;10.1016/j.molimm.2014.12.009;10.1016/j.tcb.2012.07.002;10.1016/j.tibtech.2012.11.006;10.1016/j.ymthe.2017.06.014;10.1017/S1355838299990246;10.1021/acs.accounts.6b00386;10.1021/acscentsci.7b00009;10.1021/acssynbio.5b00259;10.1021/acssynbio.7b00105;10.1021/cb800025k;10.1021/co100069t;10.1021/jacs.6b11273;10.1021/sb300107h;10.1021/sb4001273;10.1021/sb500263b;10.1023/B:DRUG.0000026251.00854.77;10.1038/35002131;10.1038/468889a;10.1038/msb.2010.99;10.1038/msb4100168;10.1038/nature04342;10.1038/nature07521;10.1038/nature11149;10.1038/nature11259;10.1038/nature23271;10.1038/nbt.1568;10.1038/nbt.2459;10.1038/nbt.2510;10.1038/nbt.2891;10.1038/nbt.3301;10.1038/nbt.3805;10.1038/nbt1307;10.1038/nbt986;10.1038/nchembio.1551;10.1038/nchembio.1736;10.1038/nchembio719;10.1038/ncomms1157;10.1038/ncomms11658;10.1038/ncomms14633;10.1038/ncomms3393;10.1038/nprot.2011.431;10.1038/nrd3499;10.1038/nrg2697;10.1038/nrm3738;10.1038/nrmicro3239;10.1038/sj.cgt.7700735;10.1039/b706973a;10.1039/c5mb00127g;10.1042/BCJ20160762;10.1046/j.1365-2958.2003.03656.x;10.1056/NEJMoa1106152;10.1073/pnas.0601755103;10.1073/pnas.0703961104;10.1073/pnas.0900267106;10.1073/pnas.1001721107;10.1073/pnas.1015741108;10.1073/pnas.1301301110;10.1073/pnas.1305590110;10.1073/pnas.1311166110;10.1073/pnas.1604391113;10.1080/15476286.2015.1060395;10.1088/1478-3975/aa6f21;10.1093/nar/gkq954;10.1093/nar/gks734;10.1093/nar/gkt520;10.1093/nar/gku1082;10.1093/nar/gku884;10.1093/nar/gkv125;10.1093/nar/gkv287;10.1093/nar/gkv601;10.1093/nar/gkw507;10.1093/nar/gkx008;10.1098/rsif.2014.1000;10.1126/science.1151153;10.1126/science.1172005;10.1126/science.1192128;10.1126/science.1205527;10.1126/science.1214081;10.1126/science.1232758;10.1126/science.282.5387.296;10.1126/science.aac7341;10.1126/scisignal.aab3397;10.1126/scitranslmed.3005568;10.1126/scitranslmed.aaa3519;10.1126/scitranslmed.aaa3601;10.1146/annurev-chembioeng-061312-103351;10.1158/0008-5472.CAN-06-2526;10.1158/0008-5472.CAN-07-5723;10.1158/0008-5472.CAN-13-1365;10.1158/1078-0432.CCR-05-1757;10.1158/1535-7163.MCT-09-0214;10.1159/000341794;10.1371/journal.pcbi.1005198;10.1371/journal.pone.0030940;10.1371/journal.pone.0082742;10.15252/msb.20145299;10.15252/msb.20156777;10.15252/msb.20167265;10.2147/DDDT.S58049;10.3389/fphar.2016.00533;10.4161/rna.27102;[10.1038/NCHEM.2420, 10.1038/nchem.2420];[10.1038/NCHEMBIO.273, 10.1038/nchembio.273];[10.1038/NCHEMBIO.919, 10.1038/nchembio.919];[10.1038/NMAT2614, 10.1038/nmat2614];[10.1038/nnano.2013.44, 10.1038/NNANO.2013.44] | Ist Italiano Tecnol | Re, A | Re, A: Ist Italiano Tecnol, Ctr Sustainable Future Technol, Turin, Italy | RE, ANGELA | null | 126 | null | Italy | Ist Italiano Tecnol | Re, Angela | gold, Green Published | ANTICANCER DRUGS;ANTITUMOR EFFICACY;AUTOMATED DESIGN;DELIVERY;LOGIC;MAMMALIAN-CELLS;MESSENGER-RNA;SYNTHETIC BIOLOGY;T-CELLS;TRANSCRIPTIONAL REGULATORS | Re, Angela; | null | Ist Italiano Tecnol, Ctr Sustainable Future Technol, Turin, Italy | Ist Italiano Tecnol, Ctr Sustainable Future Technol, Turin, Italy | null | biological engineering;drug delivery;drug discovery;precision medicine;Synthetic biology;synthetic circuits;tumor diagnosis;tumor therapy | null | 1998;1999;2000;2003;2004;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017 | 8 | Ist Italiano Tecnol, Ctr Sustainable Future Technol, Turin, Italy | Front. Cell. Dev. Biol. | Re, Angela | FRONTIERS MEDIA SA | ,;a;advancements;advances;aimed;an;and;applications;as;at;availability;basic;begin;biological;biology;brief;bring;by;cancer;capabilities;cell-;circuits;clarity;construction;context;control;decoupled;delivery;describe;design;devices;diagnosis;diagnostic;drug;elements;enabling;engineering;enhance;enhanced;establishment;expression;focus;for;from;functionalized;gene;gene-based;genetic;have;implementations;improvements;in;individual;its;levels;major;match;mechanism;medicine;methodology;might;natural;needs;new;of;on;oncology;opened;operating;our;overview;patients;portability;post-transcriptional/translational;post-translational;precision;presenting;prospects;rational;remarkable;review;robustness;scalability;sensitivity;significant;some;specific;standardization;streamlines;successful;synthetic;tailor;technologies;the;their;then;therapeutic;therapy;this;through;to;transcriptional;tumor;we;well;which | Ist Italiano Tecnol | Precision medicine in oncology needs to enhance its capabilities to match diagnostic and therapeutic technologies to individual patients. Synthetic biology streamlines the design and construction of functionalized devices through standardization and rational engineering of basic biological elements decoupled from their natural context. Remarkable improvements have opened the prospects for the availability of synthetic devices of enhanced mechanism clarity, robustness, sensitivity, as well as scalability and portability, which might bring new capabilities in precision cancer medicine implementations. In this review, we begin by presenting a brief overview of some of the major advances in the engineering of synthetic genetic circuits aimed to the control of gene expression and operating at the transcriptional, post-transcriptional/translational, and post-translational levels. We then focus on engineering synthetic circuits as an enabling methodology for the successful establishment of precision technologies in oncology. We describe significant advancements in our capabilities to tailor synthetic genetic circuits to specific applications in tumor diagnosis, tumor cell- and gene-based therapy, and drug delivery. | A-4767-2018 | ANTICANCER DRUG;ANTITUMOR EFFICACY;AUTOMATED DESIGN;DELIVERY;LOGIC;MAMMALIAN-CELLS;MESSENGER-RNA;TRANSCRIPTIONAL REGULATION;SYNTHETIC BIOLOGY;T-CELLS | 1 | null | biological engineering;drug delivery;drug discovery;precision medicine;Synthetic biology;synthetic circuit;tumor diagnosis;tumor therapy | 9 | anticancer drug;ANTITUMOR EFFICACY;AUTOMATED DESIGN;biological engineering;DELIVERY;DRUG-DELIVERY;DRUG DISCOVERY;LOGIC;MAMMALIAN-CELLS;MESSENGER-RNA;precision medicine;Transcriptional regulation;Synthetic biology;SYNTHETIC CIRCUITS;T-CELLS;tumor diagnosis;tumor therapy | WOS:000455238900077 | Ist Italiano Tecnol, Turin, Italy | Italy | 2,017 | null | 0000-0002-3179-6967 | null | null | English | null | ACCOUNTS CHEM RES;ACS CENTRAL SCI;ACS CHEM BIOL;ACS COMB SCI;ACS SYNTH BIOL;ADV DRUG DELIVER REV;ADV FUNCT MATER;ANGEW CHEM INT EDIT;ANNU REV CHEM BIOMOL;BIOCHEM J;BIOMATERIALS;BIOMOL ENG;CANCER GENE THER;CANCER RES;CELL;CELL REP;CELL SYST;CHEM BIOL;CHEMBIOCHEM;CLIN CANCER RES;CURR OPIN BIOTECH;CURR OPIN CHEM BIOL;DRUG DES DEV THER;FEBS LETT;Front Bioeng Biotechnol;FRONT PHARMACOL;INVEST NEW DRUG;J AM CHEM SOC;J CLIN IMMUNOL;J MATER CHEM;J R SOC INTERFACE;MED PRIN PRACT;MOL BIOSYST;MOL CANCER THER;MOL IMMUNOL;MOL MICROBIOL;MOL SYST BIOL;MOL THER;NAT BIOTECHNOL;NAT CHEM;NAT CHEM BIOL;NAT COMMUN;NAT MATER;NAT NANOTECHNOL;NAT PROTOC;NAT REV DRUG DISCOV;NAT REV GENET;NAT REV MICROBIOL;NAT REV MOL CELL BIO;NATURE;NEW ENGL J MED;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PHYS BIOL;PLOS COMPUT BIOL;PLOS ONE;RNA;RNA BIOL;SCI SIGNAL;SCI TRANSL MED;SCIENCE;TRENDS BIOTECHNOL;TRENDS CELL BIOL | Re, Angela | 2024-03-11
ER | Afonin, K A;An, W L;Ausländer, S;Bashor, C J;Beisel, C L;Bikard, D;Bonnet, J;Breitling, R;Brewster, R C;Budde, L E;Cameron, D E;Carbonell, P;Cardinale, S;Chandrasekaran, S;Chen, A H;Chen, Y Y;Christen, E H;Collins, I;Comeau, M A;Cora, D;Costales, M G;Courbet, A;Cronin, M;Culler, S J;Danino, T;Davidsohn, N;Di Stasi, A;Douglas, S M;Duong, C P M;Duportet, X;Edwardson, T G W;Elowitz, M;Endo, K;Endy, D;Farokhzad, O C;Fern, J;Ferreira, J P;Ferry, Q R V;Firman, K;Fischbach, M A;Foster, A E;Friedland, A E;Fu, X;Galdzicki, M;Gardner, T S;Gertz, J;Gonzalez-Nicolini, V;Green, A A;Grilly, C;Halman, J R;Hanson, S;Hockenberry, A J;Huh, J H;Isaacs, F J;Jain, K K;Kasap, C;Katuri, J;Ketzer, P;Khalil, A S;Kis, Z;Kloss, C C;Kosuri, S;Kudo, K;Kumaresan, P R;Kwak, H;Lebar, T;Lee, E S;Lee, H K;Lee, N S;Li, Y H;Li, Y Q;Lienert, F;Lim, W A;Los, G V;Lucks, J B;Mohammadi, P;Morel, M;Mukherji, S;Mutalik, V K;Niederholtmeyer, H;Nielsen, A A K;Nissim, L;Ogawa, A;Oishi, M;Qi, L S;Rackham, O;Re, A;Rinaudo, K;Roybal, K T;Rubens, J R;Ryan, P C;Ryu, J;Saito, H;Salis, H M;Sanjana, N E;Schaerli, Y;Schreiber, J;Segall-Shapiro, T H;Shen, S S;Siuti, P;Soundararajan, S;Stoltenburg, R;Stuart, M A C;Tai, W Y;Tian, Y H;Trosset Jean-Yves;Trosset, J Y;Truong, D J J;Vazquez-Anderson, J;Velagapudi, S P;Wagner, H J;Wang, J H;Wang, Y H;Wei, P;Weinberg, B H;Werstuck, G;Wilkie, S;Win, M N;Wroblewska, L;Xie, Z;Yao, Y;Yoo, J W;Zucchelli, S | VH8AQ | Turin, Italy | 9 | null | 1 | null | 28,894,736 | Re, Angela | FRONT CELL DEV BIOL | Turin, Italy |
Charpin-El Hamri, G;Fussenegger, M;Xie, M Q;Xue, S;Ye, H F;Yin, J L;Zulewski, H | 10.1038/s41551-016-0005 | 0005 | HEIDELBERGER PLATZ 3, BERLIN, 14197, GERMANY | w4z4o2o4d6p5t1n6b4j52484p471f1y2p1x2g43 | Self-adjusting synthetic gene circuit for correcting insulin resistance | Swiss Fed Inst Technol | null | Ye, HF (corresponding author), Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland. | null | Charpin-El Hamri, Ghislaine;Fussenegger, Martin;Xie, Mingqi;Xue, Shuai;Ye, Haifeng;Yin, Jianli;Zulewski, Henryk | Engineering, Biomedical | European Research Council (ERC) advanced grant [321381]; Cantons of Basel; Cantons of Swiss Confederation within the INTERREG IV A.20 tri-national research program; National Key Research and Development Program of China, Stem Cell and Translational Research [2016YFA0100300]; National Natural Science Foundation of China (NSFC) [31470834, 31522017, 31670869]; Science and Technology Commission of Shanghai Municipality [15QA1401500, 14JC1401700]; Thousand Youth Talents Plan | WOS | Ye, H F | East China Normal Univ, Shanghai, Peoples R China;IUT, Villeurbanne, France;Stadtspital Triemli, Zurich, Switzerland;Swiss Fed Inst Technol, Basel, Switzerland;Univ Basel Hosp, Basel, Switzerland;Univ Basel, Basel, Switzerland | 1 | circuit;correcting;for;gene;insulin;resistance;self-adjusting;synthetic | 3 | Ye, Haifeng | NATURE PORTFOLIO | East China Normal Univ, Inst Biomed Sci, Shanghai Key Lab Regulatory Biol, Dongchuan Rd 500, Shanghai 200241, Peoples R China;East China Normal Univ, Sch Life Sci, Dongchuan Rd 500, Shanghai 200241, Peoples R China;IUT, Dept Genie Biol, F-69622 Villeurbanne, France;Stadtspital Triemli, Div Endocrinol & Diabet, Birmensdorferstr 497, CH-8063 Zurich, Switzerland;Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland;Univ Basel Hosp, Div Endocrinol Diabet & Metab, Petersgraben 4, CH-4031 Basel, Switzerland;Univ Basel, Fac Sci, Mattenstr 26, CH-4058 Basel, Switzerland | Article | Swiss Fed Inst Technol | BERLIN | null | null | East China Normal Univ;IUT;Stadtspital Triemli;Swiss Fed Inst Technol;Univ Basel;Univ Basel Hosp | Cantons of Basel;Cantons of Swiss Confederation within the INTERREG IV A.20 tri-national research program;European Research Council (ERC) advanced grant;National Key Research and Development Program of China, Stem Cell and Translational Research;National Natural Science Foundation of China (NSFC);Science and Technology Commission of Shanghai Municipality;Thousand Youth Talents Plan | Ye, HF (corresponding author), Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland. | null | Charpin-El Hamri, Ghislaine;Fussenegger, Martin;Xie, Mingqi;Xue, Shuai;Ye, Haifeng;Yin, Jianli;Zulewski, Henryk | 76 | 7 | 418,850,600,005 | Cantons of Basel;Cantons of Swiss Confederation within the INTERREG IV A.20 tri-national research program;European Research Council (ERC) advanced grant [321381];National Key Research and Development Program of China, Stem Cell and Translational Research [2016YFA0100300];National Natural Science Foundation of China (NSFC) [31470834, 31522017, 31670869];Science and Technology Commission of Shanghai Municipality [15QA1401500, 14JC1401700];Thousand Youth Talents Plan | China;France;Switzerland | NATURE BIOMEDICAL ENGINEERING | Switzerland | null | null | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland | 2157-846X | Charpin-El Hamri, G;Fussenegger, M;Xie, M Q;Xue, S;Ye, H F;Yin, J L;Zulewski, H | JAN | fussenegger@bsse.ethz.ch;hfye@bio.ecnu.edu.cn | correcting insulin resistance;self-adjusting synthetic gene circuit | 7 | J | Engineering | acute experimental hyperinsulinaemia;ADIPONECTIN LEVELS;cells;coordinating expression;correcting insulin resistance;different mouse models;engineering synthetic gene circuits;expression;future gene-and cell-based treatments;human ELK1-derived transactivation domain (TetR-Elk1);Hybrid transcription factor;increased blood insulin levels;insulin-resistance syndrome;insulin-sensitizing compound adiponectin;life;MAPK-mediated activation;mitogen-activated protein kinase (MAPK);multifactorial metabolic disorders;opportunities;pathologic markers;PATHWAY;reprogram mammalian cell activities;reversible expression;self-adjusting synthetic gene circuit;self-sufficiently;sophisticated genetic devices;synthetic biology;synthetic insulin-sensing designer circuit;synthetic insulin-sensitive transcriptioncontrol device;synthetic TetR-ELK1-specific promoters;TetR;tetracycline repressor;therapeutic transgenes;tools | Ye, H F | ADIPONECTIN LEVELS;CELLS;EXPRESSION;LIFE | null | [Ye, Haifeng; Xie, Mingqi; Zulewski, Henryk; Fussenegger, Martin] Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland. [Ye, Haifeng; Xue, Shuai; Yin, Jianli] East China Normal Univ, Inst Biomed Sci, Shanghai Key Lab Regulatory Biol, Dongchuan Rd 500, Shanghai 200241, Peoples R China. [Ye, Haifeng; Xue, Shuai; Yin, Jianli] East China Normal Univ, Sch Life Sci, Dongchuan Rd 500, Shanghai 200241, Peoples R China. [Charpin-El Hamri, Ghislaine] IUT, Dept Genie Biol, F-69622 Villeurbanne, France. [Zulewski, Henryk] Univ Basel Hosp, Div Endocrinol Diabet & Metab, Petersgraben 4, CH-4031 Basel, Switzerland. [Zulewski, Henryk] Stadtspital Triemli, Div Endocrinol & Diabet, Birmensdorferstr 497, CH-8063 Zurich, Switzerland. [Fussenegger, Martin] Univ Basel, Fac Sci, Mattenstr 26, CH-4058 Basel, Switzerland. | We thank T. Abel for providing the pTetR-ELK1 (MKp37) plasmid, B. Geering for providing human serum from healthy individuals, Y. Lai for providing the DyLight 800-labelled goat anti-mouse IgG, B.M. Lang and L. Scheller for assistance with the statistical analyses and M. Daoud-El Baba for skilful assistance with the animal study. This work was supported by a European Research Council (ERC) advanced grant (no. 321381), the Cantons of Basel and the Swiss Confederation within the INTERREG IV A.20 tri-national research program and the Gutenberg Chair (awarded to M.F.). This work was also supported by the National Key Research and Development Program of China, Stem Cell and Translational Research (no. 2016YFA0100300), the National Natural Science Foundation of China (NSFC; nos 31470834, 31522017 and 31670869), the Science and Technology Commission of Shanghai Municipality (nos 15QA1401500 and 14JC1401700) and Thousand Youth Talents Plan (awarded to H.Y.). | acute experimental hyperinsulinaemia;coordinating expression;different mouse models;engineering synthetic gene circuits;expression;future gene-and cell-based treatments;human ELK1-derived transactivation domain (TetR-Elk1);hybrid transcription factor;increased blood insulin levels;insulin-resistance syndrome;insulin-sensitizing compound adiponectin;MAPK-mediated activation;mitogen-activated protein kinase (MAPK);multifactorial metabolic disorders;opportunities;pathologic markers;pathway;reprogram mammalian cell activities;reversible expression;self-adjusting synthetic gene circuit;self-sufficiently;sophisticated genetic devices;synthetic biology;synthetic insulin-sensing designer circuit;synthetic insulin-sensitive transcriptioncontrol device;synthetic TetR-ELK1-specific promoters;TetR;tetracycline repressor;therapeutic transgenes;tools | 10.1001/jama.2009.976;10.1002/(SICI)1096-9136(199807)15:7<539::AID-DIA668>3.0.CO;2-S;10.1002/anie.201412204;10.1007/BF00280883;10.1016/j.biomaterials.2013.09.071;10.1016/j.cbpa.2013.10.006;10.1016/j.cbpa.2015.05.021;10.1016/j.cell.2012.02.017;10.1016/j.cell.2013.01.041;10.1016/j.cmet.2011.07.015;10.1016/j.coi.2015.06.015;10.1016/j.copbio.2015.01.010;10.1016/j.jconrel.2010.11.016;10.1016/j.jhep.2016.03.020;10.1016/j.jmb.2010.03.062;10.1016/j.molcel.2014.06.007;10.1016/j.ymeth.2012.01.005;10.1016/S0140-6736(07)61721-8;10.1016/S0140-6736(16)00618-8;10.1016/S0303-7207(01)00674-8;10.1016/S0378-1119(01)00824-1;10.1038/81208;10.1038/msb.2013.48;10.1038/nature12656;10.1038/nbt0602-592;10.1038/nbt1021;10.1038/ng.343;10.1038/nrg3094;10.1038/nrm.2016.10;10.1038/nrm3072;10.1073/pnas.1216801110;10.1073/pnas.1508521112;10.1093/nar/gkt405;10.1126/science.1206843;10.1136/bmj.d1309;10.1136/bmj.f5934;10.1172/JCI29103;10.1210/jc.86.5.1930;10.1530/JME-11-0022;10.2144/000112002;10.2337/db12-0935;10.3945/ajcn.2009.28449C | Swiss Fed Inst Technol | Charpin-El Hamri, G;Fussenegger, M;Xie, M Q;Xue, S;Ye, H F;Yin, J L;Zulewski, H | Ye, H F: Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland | null | 14JC1401700;15QA1401500;2016YFA0100300;31470834;31522017;31670869;321381 | 42 | null | Switzerland | East China Normal Univ;IUT;Stadtspital Triemli;Swiss Fed Inst Technol;Univ Basel;Univ Basel Hosp | Ye, Haifeng | Green Accepted | ADIPONECTIN LEVELS;CELLS;EXPRESSION;LIFE | Ye, Haifeng; Xie, Mingqi; Xue, Shuai; Charpin-El Hamri, Ghislaine; Yin, Jianli; Zulewski, Henryk; Fussenegger, Martin; | null | East China Normal Univ, Inst Biomed Sci, Shanghai Key Lab Regulatory Biol, Dongchuan Rd 500, Shanghai 200241, Peoples R China;East China Normal Univ, Sch Life Sci, Dongchuan Rd 500, Shanghai 200241, Peoples R China;IUT, Dept Genie Biol, F-69622 Villeurbanne, France;Stadtspital Triemli, Div Endocrinol & Diabet, Birmensdorferstr 497, CH-8063 Zurich, Switzerland;Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland;Univ Basel Hosp, Div Endocrinol Diabet & Metab, Petersgraben 4, CH-4031 Basel, Switzerland;Univ Basel, Fac Sci, Mattenstr 26, CH-4058 Basel, Switzerland | East China Normal Univ, Inst Biomed Sci, Shanghai Key Lab Regulatory Biol, Dongchuan Rd 500, Shanghai 200241, Peoples R China;East China Normal Univ, Sch Life Sci, Dongchuan Rd 500, Shanghai 200241, Peoples R China;IUT, Dept Genie Biol, F-69622 Villeurbanne, France;Stadtspital Triemli, Div Endocrinol & Diabet, Birmensdorferstr 497, CH-8063 Zurich, Switzerland;Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland;Univ Basel Hosp, Div Endocrinol Diabet & Metab, Petersgraben 4, CH-4031 Basel, Switzerland;Univ Basel, Fac Sci, Mattenstr 26, CH-4058 Basel, Switzerland | null | null | 1 | 1985;1998;2000;2001;2002;2004;2005;2006;2007;2009;2010;2011;2012;2013;2014;2015;2016 | 72 | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland | Nat. Biomed. Eng | Fussenegger, Martin | NATURE PORTFOLIO | (MAPK);(TetR-Elk1);,;a;activation;activities;acute;adiponectin;and;assembled;be;between;biology;blood;by;can;cell;cell-based;circuit;circuits;compound;consisting;coordinate;coordinating;Correspondingly;demonstrate;designed;designer;device;devices;different;disorders;distinguished;domain;ELK1-derived;engineering;experimental;expression;factor;fine-tuned;for;from;functionally;fused;future;gene;gene-and;genetic;here;human;hybrid;hyperinsulinaemia;in;increased;insulin;insulin-resistance;insulin-sensing;insulin-sensitive;insulin-sensitizing;kinase;levels;mammalian;MAPK-mediated;Markers;may;metabolic;mitogen-activated;models;mouse;multifactorial;of;opportunities;pathologic;pathway;physiological;produce;promoters;protein;provide;repressor;reprogram;reverse;reversed;reversible;rewiring;self-adjusting;self-sufficiently;sense;signalling;sophisticated;syndrome;synthetic;TetR;TetR-ELK1-specific;tetracycline;that;the;therapeutic;to;tools;transactivation;transcription;transcriptioncontrol;transgenes;treatments;using;we | Swiss Fed Inst Technol | Sophisticated genetic devices can be assembled to reprogram mammalian cell activities using tools from synthetic biology. Here, we demonstrate that a self-adjusting synthetic gene circuit can be designed to sense and reverse the insulin-resistance syndrome in different mouse models. By functionally rewiring the mitogen-activated protein kinase (MAPK) signalling pathway to produce MAPK-mediated activation of a hybrid transcription factor consisting of the tetracycline repressor, TetR, fused to the human ELK1-derived transactivation domain (TetR-Elk1), we assembled a synthetic insulin-sensitive transcriptioncontrol device that self-sufficiently distinguished between physiological and increased blood insulin levels and correspondingly fine-tuned the reversible expression of therapeutic transgenes from synthetic TetR-ELK1-specific promoters. In acute experimental hyperinsulinaemia, the synthetic insulin-sensing designer circuit reversed the insulin-resistance syndrome by coordinating expression of the insulin-sensitizing compound adiponectin. Engineering synthetic gene circuits to sense pathologic markers and coordinate the expression of therapeutic transgenes may provide opportunities for future gene-and cell-based treatments of multifactorial metabolic disorders. | null | ADIPONECTIN LEVELS;CELLS;EXPRESSION;LIFE | 7 | null | null | 9 | ADIPONECTIN LEVELS;CELLS;EXPRESSION;LIFE | WOS:000418850600005 | East China Normal Univ, Shanghai, Peoples R China;IUT, Villeurbanne, France;Stadtspital Triemli, Zurich, Switzerland;Swiss Fed Inst Technol, Basel, Switzerland;Univ Basel Hosp, Basel, Switzerland;Univ Basel, Basel, Switzerland | China;France;Switzerland | 2,017 | null | 0000-0002-5482-8116 | null | null | English | null | AM J CLIN NUTR;ANGEW CHEM INT EDIT;BIOMATERIALS;BIOTECHNIQUES;BMJ;BMJ-BRIT MED J;CELL;CELL METAB;CURR OPIN BIOTECH;CURR OPIN CHEM BIOL;CURR OPIN IMMUNOL;DIABETES;DIABETIC MED;DIABETOLOGIA;GENE;J CLIN ENDOCR METAB;J CLIN INVEST;J CONTROL RELEASE;J HEPATOL;J MOL BIOL;J MOL ENDOCRINOL;JAMA-J AM MED ASSOC;LANCET;METHODS;MOL CELL;MOL CELL ENDOCRINOL;MOL SYST BIOL;NAT BIOTECHNOL;NAT GENET;NAT REV GENET;NAT REV MOL CELL BIO;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;SCIENCE | Charpin-El Hamri, Ghislaine;Fussenegger, Martin;Xie, Mingqi;Xue, Shuai;Ye, Haifeng;Yin, Jianli;Zulewski, Henryk | 2024-03-11
ER | Alberti, K G M M;Altarejos, J Y;Ausländer, D;Bacchus, W;Bai, P;Bornfeldt, K E;Christensen, R;Folcher, M;Fussenegger, M;Gao, H;Ge, H F;Gloy, V L;Heng, B C;Jacob, K K;Johnson, A M F;Keeley, M B;Kemmer, C;Kim, T;Kojima, R;Lathuilière, A;Li, S S;Loke Yoon Kong;Matthews, D R;Mátés, L;Okada-Iwabu, M;Prentki, M;Ruder, W C;Samuel, V T;Schlatter, S;Siddle, K;Simonsen, J L;Slomovic, S;Trounson, A;Weber, W;Weyer, C;Wieland, M;Wu, C Y;Ye, H F;Zhou, B;Ziemke, F | FR1TQ | Basel, Switzerland | 85 | null | 6 | null | 28,480,128 | Charpin-El Hamri, Ghislaine;Fussenegger, Martin;Xie, Mingqi;Xue, Shuai;Ye, Haifeng;Yin, Jianli;Zulewski, Henryk | NAT BIOMED ENG | Basel, Switzerland;Shanghai, Peoples R China;Villeurbanne, France;Zurich, Switzerland |
Agnew, C;Brady, R L;Burley, G A;Burton, N;de Ornellas, S;Eperon, I C;Eperon, L P;Reichenbach, L F;Sobri, A A;Zaccai, N R | 10.1016/j.chempr.2016.11.009 | null | 50 HAMPSHIRE ST, FLOOR 5, CAMBRIDGE, MA 02139 USA | 2s2z14p113x2y5j7041574q4z5v4t3m4d705l1z | Structural Basis of the Mispairing of an Artificially Expanded Genetic Information System | Univ Strathclyde | null | Brady, RL (corresponding author), Univ Bristol, Sch Biochem, Bristol BS8 1TD, Avon, England.;Burley, GA (corresponding author), Univ Strathclyde, Dept Pure & Appl Chem, Thomas Graham Bldg,295 Cathedral St, Glasgow G1 1XL, Lanark, Scotland.;Eperon, IC (corresponding author), Univ Leicester, Dept Mol & Cellular Biol, Leicester Inst Struct & Chem Biol, Henry Wellcome Bldg,Lancaster Rd, Leicester LE1 7RH, Leics, England. | null | Agnew, Christopher;Brady, R Leo;Burley, Glenn A;Burton, Nicholas;de Ornellas, Sara;Eperon, Ian C;Eperon, Lucy P;Reichenbach, Linus F;Sobri, Ahmad Ahmad;Zaccai, Nathan R | Chemistry, Multidisciplinary | Biotechnology and Biological Sciences Research Council [BB/J020087/1, BB/J02080X/1]; Leverhulme Trust [RPG-2014-001]; Biotechnology and Biological Sciences Research Council [BB/J020087/1, BB/J02080X/1] Funding Source: researchfish; BBSRC [BB/J020087/1, BB/J02080X/1] Funding Source: UKRI | WOS | Brady, R L;Burley, G A;Eperon, I C | Univ Bristol, Avon, England;Univ Leicester, Leics, England;Univ Strathclyde, Lanark, Scotland | 1 | an;Artificially;Basis;Expanded;genetic;Information;Mispairing;of;structural;system;the | 1 | Burley, Glenn;De Ornellas, Sara;Zaccai, Nathan | CELL PRESS | Univ Bristol, Sch Biochem, Bristol BS8 1TD, Avon, England;Univ Leicester, Dept Mol & Cellular Biol, Leicester Inst Struct & Chem Biol, Henry Wellcome Bldg,Lancaster Rd, Leicester LE1 7RH, Leics, England;Univ Strathclyde, Dept Pure & Appl Chem, Thomas Graham Bldg,295 Cathedral St, Glasgow G1 1XL, Lanark, Scotland;Univ Strathclyde, Dept Pure & Appl Chem, Thomas Graham Bldg,295 Cathedral St, Glasgow G1 1XL, Lanark, Scotland.; Brady, RL (corresponding author), Univ Bristol, Sch Biochem, Bristol BS8 1TD, Avon, England.; Eperon, IC (corresponding author), Univ Leicester, Dept Mol & Cellular Biol, Leicester Inst Struct & Chem Biol, Henry Wellcome Bldg,Lancaster Rd, Leicester LE1 7RH, Leics, England | Article | Univ Bristol;Univ Leicester;Univ Strathclyde | CAMBRIDGE | null | null | Univ Bristol;Univ Leicester;Univ Strathclyde | BBSRC;Biotechnology and Biological Sciences Research Council;Leverhulme Trust | Burley, GA (corresponding author), Univ Strathclyde, Dept Pure & Appl Chem, Thomas Graham Bldg,295 Cathedral St, Glasgow G1 1XL, Lanark, Scotland.; Brady, RL (corresponding author), Univ Bristol, Sch Biochem, Bristol BS8 1TD, Avon, England.; Eperon, IC (corresponding author), Univ Leicester, Dept Mol & Cellular Biol, Leicester Inst Struct & Chem Biol, Henry Wellcome Bldg,Lancaster Rd, Leicester LE1 7RH, Leics, England. | 958 | Agnew, Christopher;Brady, R Leo;Burley, Glenn A;Burton, Nicholas;de Ornellas, Sara;Eperon, Ian C;Eperon, Lucy P;Reichenbach, Linus F;Sobri, Ahmad Ahmad;Zaccai, Nathan R | 18 | 3 | 389,801,600,014 | BBSRC [BB/J020087/1, BB/J02080X/1] Funding Source: UKRI;Biotechnology and Biological Sciences Research Council [BB/J020087/1, BB/J02080X/1];Biotechnology and Biological Sciences Research Council [BB/J020087/1, BB/J02080X/1] Funding Source: researchfish;Leverhulme Trust [RPG-2014-001] | UK | CHEM | UK | null | null | Univ Strathclyde, Dept Pure & Appl Chem, Thomas Graham Bldg,295 Cathedral St, Glasgow G1 1XL, Lanark, Scotland | 2451-9294 | Agnew, C;Brady, R L;Burley, G A;Burton, N;de Ornellas, S;Eperon, I C;Eperon, L P;Reichenbach, L F;Sobri, A A;Zaccai, N R | DEC 8 | eci@le.ac.uk;glenn.burley@strath.ac.uk;l.brady@bristol.ac.uk | Expanded Genetic Information System;Mispairing;structural Basis | 10 | J | Chemistry | 7.8;ALPHABET;B-DNA DODECAMER;CLICK CHEMISTRY;conversion;development;DNA duplexes;double-hydrogen-bonded;Expanded Genetic Information System;EXPANSION;functional methods;G-C base pair;G-Z mispair;HYDROGEN-BONDING PATTERN;loss;mechanisms;Mispairing;mutation;need;next-generation synthetic genetic base pairs;NUCLEIC-ACID;P-Z;PAIR SYSTEMS;PCR AMPLIFICATION;PCR results;pH;pH 7.8;pH dependent;plastic;relative;replication;RNA;ROBUST;slipped'' pair;STRUCTURAL BASIS;study;synthetic genetic information;synthetic nucleotide P pairs;triple-hydrogen-bonded Z-G pair;unique hydrogen-bond arrangement;viaG-Z mispairing;Watson-Crick base pairs;Z | Reichenbach, L F | ALPHABET;B-DNA DODECAMER;CLICK CHEMISTRY;EXPANSION;HYDROGEN-BONDING PATTERN;NUCLEIC-ACID;PAIR SYSTEMS;PCR AMPLIFICATION;REPLICATION;RNA | 946 | [Reichenbach, Linus F.; de Ornellas, Sara; Burley, Glenn A.] Univ Strathclyde, Dept Pure & Appl Chem, Thomas Graham Bldg,295 Cathedral St, Glasgow G1 1XL, Lanark, Scotland. [Sobri, Ahmad Ahmad; Zaccai, Nathan R.; Agnew, Christopher; Burton, Nicholas; Brady, R. Leo] Univ Bristol, Sch Biochem, Bristol BS8 1TD, Avon, England. [Eperon, Lucy P.; Eperon, Ian C.] Univ Leicester, Dept Mol & Cellular Biol, Leicester Inst Struct & Chem Biol, Henry Wellcome Bldg,Lancaster Rd, Leicester LE1 7RH, Leics, England. | This work was supported by the Biotechnology and Biological Sciences Research Council (BB/J020087/1 to R.L.B. and G.A.B.; BB/J02080X/1 to G.A.B. and E.C.I.) and the Leverhulme Trust (RPG-2014-001 to E.C.I. and G.A.B.). We thank Dr. Sharon Kelly (University of Glasgow) for measurement of the CD spectra. We also thank Diamond Light Source for beamtime (proposals mx8922 and mx12342) and the staff of beamlines I02, I03, and I04-1 for assistance with crystal testing and data collection. | 7.8;conversion;development;DNA duplexes;double-hydrogen-bonded;functional methods;G-C base pair;G-Z mispair;loss;mechanisms;mutation;need;next-generation synthetic genetic base pairs;P-Z;PCR results;pH;pH 7.8;pH dependent;plastic;relative;robust;slipped'' pair;study;synthetic genetic information;synthetic nucleotide P pairs;triple-hydrogen-bonded Z-G pair;unique hydrogen-bond arrangement;viaG-Z mispairing;Watson-Crick base pairs;Z | 10.1002/anie.200905173;10.1002/anie.201502890;10.1007/978-1-4020-6316-9_4;10.1016/j.str.2003.11.008;10.1021/ar200257x;10.1021/ar200262x;10.1021/bi00532a002;10.1021/bi201710q;10.1021/bi501534x;10.1021/ja073830m;10.1021/ja204910n;10.1021/ja207907d;10.1021/ja3125299;10.1021/ja408814g;10.1021/jacs.5b02251;10.1021/jacs.5b03482;10.1021/jo300230z;10.1021/sb500268n;10.1038/171737a0;10.1038/171964b0;10.1038/287755a0;10.1038/2930;10.1038/nature13314;10.1038/nbt.2556;10.1038/nprot.2008.104;10.1038/nrg1637;10.1039/b605414e;10.1039/b811159f;10.1039/c2cc36293g;10.1073/pnas.1205176109;10.1073/pnas.1311778111;10.1073/pnas.78.4.2179;10.1073/pnas.94.20.10506;10.1074/jbc.274.35.24749;10.1093/nar/gkl633;10.1093/nar/gkm395;10.1093/nar/gkn956;10.1093/nar/gkp026;10.1093/nar/gkr1068;10.1093/nar/gks322;10.1093/nar/gkt738;10.1093/nar/gku715;10.1093/nar/gkv638;10.1107/S0021889807021206;10.1107/S0907444910045749;10.1146/annurev.biochem.69.1.497;10.2183/pjab.88.345;[10.1038/NCHEM.1117, 10.1038/nchem.1117] | Univ Strathclyde | Agnew, C;Brady, R L;Burley, G A;Burton, N;de Ornellas, S;Eperon, I C;Eperon, L P;Reichenbach, L F;Sobri, A A;Zaccai, N R | Reichenbach, L F: Univ Strathclyde, Dept Pure & Appl Chem, Thomas Graham Bldg,295 Cathedral St, Glasgow G1 1XL, Lanark, Scotland | Burley, Glenn;Burton, Nick;De Ornellas, Sara;Eperon, Ian C. | BB/J020087/1;BB/J02080X/1;RPG-2014-001 | 51 | null | UK | Univ Bristol;Univ Leicester;Univ Strathclyde | Reichenbach, Linus F | Green Submitted, hybrid, Green Accepted | ALPHABET;B-DNA DODECAMER;CLICK CHEMISTRY;EXPANSION;HYDROGEN-BONDING PATTERN;NUCLEIC-ACID;PAIR SYSTEMS;PCR AMPLIFICATION;REPLICATION;RNA | Reichenbach, Linus F.; Sobri, Ahmad Ahmad; Zaccai, Nathan R.; Agnew, Christopher; Burton, Nicholas; Eperon, Lucy P.; de Ornellas, Sara; Eperon, Ian C.; Brady, R. Leo; Burley, Glenn A.; | null | Univ Bristol, Sch Biochem, Bristol BS8 1TD, Avon, England;Univ Leicester, Dept Mol & Cellular Biol, Leicester Inst Struct & Chem Biol, Henry Wellcome Bldg,Lancaster Rd, Leicester LE1 7RH, Leics, England;Univ Strathclyde, Dept Pure & Appl Chem, Thomas Graham Bldg,295 Cathedral St, Glasgow G1 1XL, Lanark, Scotland | Univ Bristol, Sch Biochem, Bristol BS8 1TD, Avon, England;Univ Leicester, Dept Mol & Cellular Biol, Leicester Inst Struct & Chem Biol, Henry Wellcome Bldg,Lancaster Rd, Leicester LE1 7RH, Leics, England;Univ Strathclyde, Dept Pure & Appl Chem, Thomas Graham Bldg,295 Cathedral St, Glasgow G1 1XL, Lanark, Scotland | null | null | 6 | 1953;1980;1981;1982;1987;1997;1998;1999;2000;2003;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015 | 16 | Univ Bristol, Sch Biochem, Bristol BS8 1TD, Avon, England;Univ Leicester, Dept Mol & Cellular Biol, Leicester Inst Struct & Chem Biol, Henry Wellcome Bldg,Lancaster Rd, Leicester LE1 7RH, Leics, England;Univ Strathclyde, Dept Pure & Appl Chem, Thomas Graham Bldg,295 Cathedral St, Glasgow G1 1XL, Lanark, Scotland | Chem | Burley, Glenn A | CELL PRESS | ";,;7.8;;;a;above;and;arrangement;at;base;both;by;conversion;dependent;development;DNA;double-hydrogen-bonded;duplexes;elucidate;evidence;for;forms;functional;G-C;G-Z;genetic;here;highlights;hydrogen-bond;in;information;into;is;it;loss;mechanisms;methods;mispair;mispairing;mutation;naturally;need;next-generation;nucleotide;occurring;occurs;of;P;P-Z;pair;pairs;PCR;pH;plastic;relative;remarkably;results;robust;show;slipped'';spectroscopic;structural;study;synthetic;that;the;this;through;to;triple-hydrogen-bonded;unique;viaG-Z;Watson-Crick;we;when;with;within;Z;Z-G | Univ Bristol;Univ Leicester;Univ Strathclyde | Relative to naturally occurring Watson-Crick base pairs, the synthetic nucleotide P pairs with Z within DNA duplexes through a unique hydrogen-bond arrangement. The loss of this synthetic genetic information by PCR results in the conversion of P-Z into a G-C base pair. Here, we show structural and spectroscopic evidence that the loss of this synthetic genetic information occurs viaG-Z mispairing. Remarkably, the G-Z mispair is both plastic and pH dependent; it forms a double-hydrogen-bonded "slipped'' pair at pH 7.8 and a triple-hydrogen-bonded Z-G pair when the pH is above 7.8. This study highlights the need for robust structural and functional methods to elucidate the mechanisms of mutation in the development of next-generation synthetic genetic base pairs. | AAV-8541-2021;C-7064-2013;E-8799-2011;M-2412-2014 | ALPHABET;B-DNA DODECAMER;CLICK CHEMISTRY;EXPANSION;HYDROGEN-BONDING PATTERN;NUCLEIC-ACIDS;PAIR SYSTEMS;PCR AMPLIFICATION;REPLICATION;RNA | 0 | null | null | 13 | ALPHABET;B-DNA DODECAMER;CLICK CHEMISTRY;EXPANSION;HYDROGEN-BONDING PATTERN;NUCLEIC-ACIDS;PAIR SYSTEMS;PCR AMPLIFICATION;REPLICATION;RNA | WOS:000389801600014 | Univ Bristol, Avon, England;Univ Leicester, Leics, England;Univ Strathclyde, Lanark, Scotland | UK | 2,016 | null | 0000-0002-1476-2044;0000-0002-4896-113X;0000-0002-7333-5456 | null | null | English | null | ACCOUNTS CHEM RES;ACS SYNTH BIOL;ACTA CRYSTALLOGR D;ANGEW CHEM INT EDIT;ANNU REV BIOCHEM;BIOCHEMISTRY-US;CHEM COMMUN;J AM CHEM SOC;J APPL CRYSTALLOGR;J BIOL CHEM;J ORG CHEM;NAT BIOTECHNOL;NAT CHEM;NAT PROTOC;NAT REV GENET;NAT STRUCT BIOL;NATO SCI SER II-MATH;NATURE;NUCLEIC ACIDS RES;P JPN ACAD B-PHYS;P NATL ACAD SCI USA;P NATL ACAD SCI-BIOL;PYMOL MOL GRAPH SYST;STRUCTURE | Agnew, Christopher;Brady, R Leo;Burley, Glenn A;Burton, Nicholas;de Ornellas, Sara;Eperon, Ian C;Eperon, Lucy P;Reichenbach, Linus F;Sobri, Ahmad Ahmad;Zaccai, Nathan R | 2024-03-11
ER | [Anonymous];Benner, S A;Derose, E F;Dhami, K;Drew, H R;Emsley P.;Georgiadis, M M;Geyer, C R;Guckian, K M;Hirao, I;Hodson, M J;Hunter W. N.;Ishizuka, T;Kaul, C;Kim, H J;Kimoto, M;Kool, E T;Krishnamurthy, R;Kunkel, T A;Kypr, J;Leal, N A;Leslie, A G W;Li, L J;Liu, J;Lu, X J;Malyshev, D A;Mccoy, A J;Moran, S;Patel, D J;Renciuk, D;Sefah, K;Seo, Y J;Sheng, P P;Someya, T;Szulik, M W;Watson, J D;Wilcox, J L;Wing, R;Winn, M D;Yamashige, R;Yang, Z Y;Zhang, L Q | EE7MH | Avon, England.;Lanark, Scotland.;Leics, England | 16 | null | 3 | null | null | Agnew, Christopher;Brady, R Leo;Burley, Glenn A;Burton, Nicholas;de Ornellas, Sara;Eperon, Ian C;Eperon, Lucy P;Reichenbach, Linus F;Sobri, Ahmad Ahmad;Zaccai, Nathan R | CHEM-US | Avon, England;Lanark, Scotland;Leics, England |
Inouye, S;Suzuki, T | 10.1016/j.pep.2016.08.006 | null | 525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA | 6e185r3v1l2d1k1s4035e2f6r3v2g5u3x6r3bz | Protein expression of preferred human codon-optimized <i>Gaussia</i> luciferase genes with an artificial open-reading frame in mammalian and bacterial cells | JNC Co | null | Inouye, S (corresponding author), JNC Co, Yokohama Res Ctr, Kanazawa Ku, 5-1 Okawa, Yokohama, Kanagawa 2368605, Japan. | null | Inouye, Satoshi;Suzuki, Takahiro | Biochemical Research Methods;Biochemistry & Molecular Biology;Biotechnology & Applied Microbiology | JSPS KAKENHI Grant [26462828]; Research Foundation for Aichi-Gakuin University; Grants-in-Aid for Scientific Research [26462828] Funding Source: KAKEN | WOS | Inouye, S | Aichi Gakuin Univ, Aichi, Japan;JNC Co, Kanagawa, Japan | 128 | <i>Gaussia</i>;an;and;Artificial;Bacterial;Cells;codon-optimized;expression;frame;genes;human;in;luciferase;mammalian;of;open-reading;preferred;protein;with | 1 | Inouye, Satoshi | ACADEMIC PRESS INC ELSEVIER SCIENCE | Aichi Gakuin Univ, Sch Dent, Dept Biochem, Chikusa Ku, 1-100 Kusumoto Cho, Nagoya, Aichi 4648650, Japan;JNC Co, Yokohama Res Ctr, Kanazawa Ku, 5-1 Okawa, Yokohama, Kanagawa 2368605, Japan | Article | JNC Co | SAN DIEGO | null | null | Aichi Gakuin Univ;JNC Co | Grants-in-Aid for Scientific Research;JSPS KAKENHI Grant;Research Foundation for Aichi-Gakuin University | Inouye, S (corresponding author), JNC Co, Yokohama Res Ctr, Kanazawa Ku, 5-1 Okawa, Yokohama, Kanagawa 2368605, Japan. | 100 | Inouye, Satoshi;Suzuki, Takahiro | 21 | 2 | 384,629,700,014 | Grants-in-Aid for Scientific Research [26462828] Funding Source: KAKEN;JSPS KAKENHI Grant [26462828];Research Foundation for Aichi-Gakuin University | Japan | PROTEIN EXPRESSION AND PURIFICATION | Japan | null | null | JNC Co, Yokohama Res Ctr, Kanazawa Ku, 5-1 Okawa, Yokohama, Kanagawa 2368605, Japan | 1046-5928 | Inouye, S;Suzuki, T | DEC | sinouye@jnc-corp.co.jp | artificial open-reading frame;bacterial cells;preferred human codon-optimized <i>Gaussia</i> luciferase genes;protein expression | 2 | J | Biochemistry & Molecular Biology;Biotechnology & Applied Microbiology | 60% activities;65% GC content;ALGA CHLAMYDOMONAS-REINHARDTII;artificial open-reading frame;bacterial cells;C 2016 Elsevier Inc;Codon optimization;complete preferred human codons;EpGLuc;ESCHERICHIA-COLI;hGLuc;human codon-optimized Gaussia luciferase gene (hGLuc);IN-VIVO;KpGLuc;KpGLuc);Luciferase;mammalian cells;NANOKAZ;OPLOPHORUS LUCIFERASE;pGLuc;Photoprotein;preferred human codon-optimized <i>Gaussia</i> luciferase genes;PRINCEPS;PROTEIN EXPRESSION;protein expressions;reporter gene;rights reserved;secretion;similar protein expression levels;SUBSTRATE;synthetic gene;three preferred human codon-optimized Gaussia luciferase genes (pGLuc;two synthetic genes;wGLuc;wild-type Gaussia luciferase gene (wGLuc) | Inouye, S | ALGA CHLAMYDOMONAS-REINHARDTII;Codon optimization;ESCHERICHIA-COLI;IN-VIVO;Luciferase;NANOKAZ;OPLOPHORUS LUCIFERASE;Photoprotein;PRINCEPS;reporter gene;SECRETION;SUBSTRATE;Synthetic gene | 93 | [Inouye, Satoshi] JNC Co, Yokohama Res Ctr, Kanazawa Ku, 5-1 Okawa, Yokohama, Kanagawa 2368605, Japan. [Suzuki, Takahiro] Aichi Gakuin Univ, Sch Dent, Dept Biochem, Chikusa Ku, 1-100 Kusumoto Cho, Nagoya, Aichi 4648650, Japan. | This work was supported in part by grants from JSPS KAKENHI Grant Number 26462828 (T.S.), and Research Foundation for Aichi-Gakuin University (T.S.). | 60% activities;65% GC content;artificial open-reading frame;bacterial cells;complete preferred human codons;EpGLuc;hGLuc;human codon-optimized Gaussia luciferase gene (hGLuc);KpGLuc;KpGLuc);mammalian cells;pGLuc;protein expression;protein expressions;similar protein expression levels;three preferred human codon-optimized Gaussia luciferase genes (pGLuc;two synthetic genes;wGLuc;wild-type Gaussia luciferase gene (wGLuc) | 10.1007/978-1-62703-718-1_6;10.1007/s00294-008-0189-7;10.1007/s00438-008-0352-3;10.1016/j.ab.2011.03.039;10.1016/j.bbrc.2007.10.152;10.1016/j.bbrc.2008.08.149;10.1016/j.bbrc.2013.06.026;10.1016/j.bbrc.2014.06.140;10.1016/j.febslet.2007.08.036;10.1016/j.jbiosc.2014.08.006;10.1016/j.pep.2009.01.010;10.1016/j.pep.2012.12.006;10.1016/j.pep.2015.02.002;10.1016/j.ymthe.2004.10.016;10.1038/nbt984;10.1093/bioinformatics/btu192;10.1093/nar/gkm219;10.1128/AEM.06670-11;10.1128/IAI.00223-09;10.1371/journal.pone.0017596;10.1371/journal.pone.0025243;10.4161/viru.3.1.18799 | JNC Co | Inouye, S;Suzuki, T | Inouye, S: JNC Co, Yokohama Res Ctr, Kanazawa Ku, 5-1 Okawa, Yokohama, Kanagawa 2368605, Japan | null | 26462828 | 23 | null | Japan | Aichi Gakuin Univ;JNC Co | Inouye, Satoshi | null | ALGA CHLAMYDOMONAS-REINHARDTII;ESCHERICHIA-COLI;IN-VIVO;NANOKAZ;OPLOPHORUS LUCIFERASE;PRINCEPS;SECRETION;SUBSTRATE | Inouye, Satoshi; Suzuki, Takahiro; | null | Aichi Gakuin Univ, Sch Dent, Dept Biochem, Chikusa Ku, 1-100 Kusumoto Cho, Nagoya, Aichi 4648650, Japan;JNC Co, Yokohama Res Ctr, Kanazawa Ku, 5-1 Okawa, Yokohama, Kanagawa 2368605, Japan | Aichi Gakuin Univ, Sch Dent, Dept Biochem, Chikusa Ku, 1-100 Kusumoto Cho, Nagoya, Aichi 4648650, Japan;JNC Co, Yokohama Res Ctr, Kanazawa Ku, 5-1 Okawa, Yokohama, Kanagawa 2368605, Japan | 1096-0279 | Codon optimization;Luciferase;Photoprotein;reporter gene;Synthetic gene | null | 1999;2004;2005;2007;2008;2009;2011;2012;2013;2014;2015 | 6 | JNC Co, Yokohama Res Ctr, Kanazawa Ku, 5-1 Okawa, Yokohama, Kanagawa 2368605, Japan | Protein Expr. Purif. | Suzuki, Takahiro | ACADEMIC PRESS INC ELSEVIER SCIENCE | (hGLuc);(pGLuc;(wGLuc);,;60%;65%;;;activities;affect;an;and;approximately;artificial;bacterial;by;cells;characterized;codon-optimized;codons;comparing;complete;containing;content;did;EpGLuc;expression;expressions;frame;Gaussia;GC;gene;genes;had;have;hGLuc;however;human;in;KpGLuc;KpGLuc);levels;luciferase;mammalian;not;of;open-reading;pGLuc;preferred;protein;same;showed;similar;synthetic;the;them;they;those;three;to;two;were;wGLuc;wild-type;with | JNC Co | The protein expressions of three preferred human codon-optimized Gaussia luciferase genes (pGLuc, EpGLuc, and KpGLuc) were characterized in mammalian and bacterial cells by comparing them with those of wild-type Gaussia luciferase gene (wGLuc) and human codon-optimized Gaussia luciferase gene (hGLuc). Two synthetic genes of EpGLuc and KpGLuc containing the complete preferred human codons have an artificial open-reading frame; however, they had the similar protein expression levels to those of pGLuc and hGLuc in mammalian cells. In bacterial cells, the protein expressions of pGLuc, EpGLuc, and KpGLuc with approximately 65% GC content were the same and showed approximately 60% activities of wGLuc and hGLuc. The artificial open-reading frame in EpGLuc and KpGLuc did not affect the protein expression in mammalian and bacterial cells. | null | ALGA CHLAMYDOMONAS-REINHARDTII;ESCHERICHIA-COLI;IN-VIVO;NANOKAZ;OPLOPHORUS LUCIFERASE;PRINCEPS;SECRETION;SUBSTRATE | 1 | null | Codon optimization;Luciferase;Photoprotein;reporter gene;Synthetic gene | 8 | ESCHERICHIA-COLI;ALGA CHLAMYDOMONAS-REINHARDTII;Codon optimization;IN-VIVO;Luciferase;NANOKAZ;OPLOPHORUS LUCIFERASE;Photoprotein;PRINCEPS;reporter gene;SECRETION;SUBSTRATE;Synthetic gene | WOS:000384629700014 | Aichi Gakuin Univ, Aichi, Japan;JNC Co, Kanagawa, Japan | Japan | 2,016 | null | 0000-0001-8732-7839 | null | null | English | null | ANAL BIOCHEM;APPL ENVIRON MICROB;BIOCHEM BIOPH RES CO;BIOINFORMATICS;CURR GENET;FEBS LETT;INFECT IMMUN;J BIOSCI BIOENG;METHODS MOL BIOL;MOL GENET GENOMICS;MOL THER;NAT BIOTECHNOL;NUCLEIC ACIDS RES;PLOS ONE;PROTEIN EXPRES PURIF;VIRULENCE | Inouye, Satoshi;Suzuki, Takahiro | 2024-03-11
ER | Bryan, B J;Chin, J X;Donat, S;Enjalbert, B;Fath, S;Inouye, S;Puigbò, P;Qing, G L;Ruecker, O;Shao, N;Suzuki, T;Tannous, B A;Wille, T;Yarimizu, T | DX8HW | Kanagawa, Japan | 8 | null | 2 | null | 27,506,135 | Inouye, Satoshi;Suzuki, Takahiro | PROTEIN EXPRES PURIF | Aichi, Japan;Kanagawa, Japan |
Arter, M;Benenson, Y;Haefliger, B;Lapique, N;Schreiber, J | 10.15252/msb.20167265 | 899 | 111 RIVER ST, HOBOKEN 07030-5774, NJ USA | 1t1m1i364w2q1c362h484u65s4lf6c445k3d42 | Model-guided combinatorial optimization of complex synthetic gene networks | Swiss Fed Inst Technol | null | Benenson, Y (corresponding author), Swiss Fed Inst Technol, Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland. | null | Arter, Meret;Benenson, Yaakov;Haefliger, Benjamin;Lapique, Nicolas;Schreiber, Joerg | Biochemistry & Molecular Biology | Swiss National Science Foundation; NCCR "Molecular Systems Engineering"; ETH Zurich | WOS | Benenson, Y | Swiss Fed Inst Technol, Basel, Switzerland | 12 | Combinatorial;complex;gene;model-guided;networks;of;optimization;synthetic | 1 | Lapique, Nicolas | WILEY | Swiss Fed Inst Technol, Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland | Article | Swiss Fed Inst Technol | HOBOKEN | null | null | Swiss Fed Inst Technol | ETH Zurich;NCCR "Molecular Systems Engineering";Swiss National Science Foundation | Benenson, Y (corresponding author), Swiss Fed Inst Technol, Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland. | null | Arter, Meret;Benenson, Yaakov;Haefliger, Benjamin;Lapique, Nicolas;Schreiber, Joerg | 21 | 1 | 400,097,600,010 | ETH Zurich;NCCR "Molecular Systems Engineering";Swiss National Science Foundation | Switzerland | MOLECULAR SYSTEMS BIOLOGY | Switzerland | null | null | Swiss Fed Inst Technol, Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland | 1744-4292 | Arter, M;Benenson, Y;Haefliger, B;Lapique, N;Schreiber, J | DEC | kobi.benenson@bsse.ethz.ch | complex synthetic gene networks;model-guided combinatorial optimization | 5 | J | Biochemistry & Molecular Biology | AUTOMATED DESIGN;biosensor integration;biosensor reprogramming;combination;complex gene networks;complex synthetic gene networks;complex three-gene circuit;CONSTRUCTION;data;detailed mechanistic interrogation;directed evolution;diverse genetic building blocks;ESCHERICHIA-COLI;experimentation;expression;extensive prior knowledge;favorable parameter combinations;GENE;genetic diversity;high-throughput screening data;improved dynamic range;larger networks;library;library screening;LOGIC-CIRCUIT;long-standing challenge;MAMMALIAN-CELLS;miRNA inputs;miRNA sensor;MODEL;model validation;model-guided combinatorial optimization;model-guided generation;modeling;normal form circuits;novel proportional miRNA biosensor;phase space;predictive modeling;principle arbitrary logic;quantitative performance criteria;REGULATOR;RNA-BINDING PROTEINS;screening;search;sensor circuits;sensor genetic composition;Sensors;small number;specific genetic compositions;SPECIFICITIES;strategy;study;synthetic biology;Synthetic gene circuit;validated model | Schreiber, J | AUTOMATED DESIGN;CONSTRUCTION;directed evolution;ESCHERICHIA-COLI;EXPRESSION;library screening;LOGIC-CIRCUIT;MAMMALIAN-CELLS;miRNA sensor;modeling;REGULATOR;RNA-BINDING PROTEINS;SPECIFICITIES;Synthetic gene circuit | null | [Schreiber, Joerg; Arter, Meret; Lapique, Nicolas; Haefliger, Benjamin; Benenson, Yaakov] Swiss Fed Inst Technol, Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland. | This study is funded by Swiss National Science Foundation, NCCR "Molecular Systems Engineering" and ETH Zurich. We thank Urs Senn from the Liquid Automation Facility for the development of automated transfection protocols. We thank T. Horn, T. Lopes, and V. Jaggin for their help with flow cytometry; and N. Beerenwinkel, P. Mohammadi, and the members of Benenson laboratory for discussions. | biosensor integration;biosensor reprogramming;combination;complex gene networks;complex three-gene circuit;data;detailed mechanistic interrogation;diverse genetic building blocks;experimentation;extensive prior knowledge;favorable parameter combinations;gene;genetic diversity;high-throughput screening data;improved dynamic range;larger networks;library;long-standing challenge;miRNA inputs;model;model validation;model-guided generation;normal form circuits;novel proportional miRNA biosensor;phase space;predictive modeling;principle arbitrary logic;quantitative performance criteria;screening;search;sensor circuits;sensor genetic composition;sensors;small number;specific genetic compositions;strategy;study;synthetic biology;validated model | 10.1002/bit.10713;10.1002/jgm.314;10.1016/j.celrep.2016.07.061;10.1016/j.copbio.2009.08.007;10.1016/j.jbiotec.2016.01.005;10.1016/j.stem.2015.04.005;10.1021/acssynbio.5b00040;10.1038/35002125;10.1038/35002131;10.1038/msb.2008.62;10.1038/msb.2010.2;10.1038/nbt.1536;10.1038/nbt.1568;10.1038/nbt.2149;10.1038/nbt.2714;10.1038/nbt.3300;10.1038/nbt.3301;10.1038/nbt1307;10.1038/nchembio.1680;10.1038/nchembio.1736;10.1038/ncomms10709;10.1038/ncomms11163;10.1038/ncomms5729;10.1039/c2mb25483b;10.1042/BST0370918;10.1073/pnas.1120788109;10.1073/pnas.1203831109;10.1073/pnas.1205693109;10.1073/pnas.1422023112;10.1073/pnas.252535999;10.1073/pnas.89.12.5547;10.1074/jbc.M007690200;10.1093/bioinformatics/btm362;10.1093/nar/gkg595;10.1101/gr.089367.108;10.1126/science.1170160;10.1126/science.1205527;10.1126/science.aac7341;10.1146/annurev.biophys.36.040306.132600;10.1162/ARTL_a_00160;10.1371/journal.pbio.1001528;10.1371/journal.pone.0046688;10.1529/biophysj.104.044131;[10.1038/NMETH.2404, 10.1038/nmeth.2404];[10.1038/nnano.2010.135, 10.1038/NNANO.2010.135] | Swiss Fed Inst Technol | Arter, M;Benenson, Y;Haefliger, B;Lapique, N;Schreiber, J | Schreiber, J: Swiss Fed Inst Technol, Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland | null | null | 47 | null | Switzerland | Swiss Fed Inst Technol | Schreiber, Joerg | Green Published, gold | AUTOMATED DESIGN;CONSTRUCTION;DIRECTED EVOLUTION;ESCHERICHIA-COLI;EXPRESSION;LOGIC-CIRCUIT;MAMMALIAN-CELLS;REGULATOR;RNA-BINDING PROTEINS;SPECIFICITIES | Schreiber, Joerg; Arter, Meret; Lapique, Nicolas; Haefliger, Benjamin; Benenson, Yaakov; | null | Swiss Fed Inst Technol, Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland | Swiss Fed Inst Technol, Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland | null | library screening;miRNA sensor;modeling;Synthetic gene circuit | 12 | 1992;2000;2001;2002;2003;2004;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017 | 19 | Swiss Fed Inst Technol, Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland | Mol. Syst. Biol. | Benenson, Yaakov | WILEY | ,;a;access;and;applied;arbitrary;be;been;biology;biosensor;blocks;building;by;can;challenge;circuit;circuits;combination;combinations;complex;composition;compositions;constructing;criteria;data;detailed;diverse;diversity;dynamic;enabling;experimentation;extensive;facilitated;favorable;followed;for;form;from;further;gene;generate;generation;genetic;greatly;has;here;high-throughput;how;improved;in;including;initiate;inputs;integration;interrogation;into;knowledge;larger;library;logic;long-standing;mechanistic;miRNA;model;model-guided;modeling;networks;normal;novel;number;obtained;of;optimize;optimizing;order;parameter;performance;phase;predictive;principle;prior;proportional;quantitative;range;reprogramming;reveals;satisfy;screening;search;sensor;sensors;show;small;space;specific;strategy;study;successfully;synthetic;that;the;three-gene;to;uncover;used;using;validate;validated;validation;was;we;with;without | Swiss Fed Inst Technol | Constructing gene circuits that satisfy quantitative performance criteria has been a long-standing challenge in synthetic biology. Here, we show a strategy for optimizing a complex three-gene circuit, a novel proportional miRNA biosensor, using predictive modeling to initiate a search in the phase space of sensor genetic composition. We generate a library of sensor circuits using diverse genetic building blocks in order to access favorable parameter combinations and uncover specific genetic compositions with greatly improved dynamic range. The combination of high-throughput screening data and the data obtained from detailed mechanistic interrogation of a small number of sensors was used to validate the model. The validated model facilitated further experimentation, including biosensor reprogramming and biosensor integration into larger networks, enabling in principle arbitrary logic with miRNA inputs using normal form circuits. The study reveals how model-guided generation of genetic diversity followed by screening and model validation can be successfully applied to optimize performance of complex gene networks without extensive prior knowledge. | null | AUTOMATED DESIGN;CONSTRUCTION;DIRECTED EVOLUTION;ESCHERICHIA-COLI;EXPRESSION;LOGIC-CIRCUIT;MAMMALIAN-CELLS;REGULATORS;RNA-BINDING PROTEINS;SPECIFICITY | 2 | null | library screening;miRNA sensor;modeling;Synthetic gene circuit | 14 | ESCHERICHIA-COLI;AUTOMATED DESIGN;CONSTRUCTION;directed evolution;EXPRESSION;library screening;LOGIC-CIRCUIT;MAMMALIAN-CELLS;miRNA sensor;MODEL;REGULATOR;RNA-BINDING PROTEINS;SPECIFICITY;synthetic gene circuits | WOS:000400097600010 | Swiss Fed Inst Technol, Basel, Switzerland | Switzerland | 2,016 | null | 0000-0003-1217-8597 | null | null | English | null | ACS SYNTH BIOL;ANNU REV BIOPH BIOM;ARTIF LIFE;BIOCHEM SOC T;BIOINFORMATICS;BIOPHYS J;BIOTECHNOL BIOENG;CELL REP;CELL STEM CELL;CELL SYSTEM IN PRESS;CURR OPIN BIOTECH;GENOME RES;J BIOL CHEM;J BIOTECHNOL;J GENE MED;MOL BIOSYST;MOL SYST BIOL;NAT BIOTECHNOL;NAT CHEM BIOL;NAT COMMUN;NAT METHODS;NAT NANOTECHNOL;NAT STRUCT BIOL;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PLOS BIOL;PLOS ONE;SCIENCE | Arter, Meret;Benenson, Yaakov;Haefliger, Benjamin;Lapique, Nicolas;Schreiber, Joerg | 2024-03-11
ER | Alipanahi, B;Angelici, B;Batt, G;Beisel, C L;Benes, D;Carey, L B;Choi, Y;Egbert, R G;Ellefson, J W;Ellis, T;Elowitz, M B;Feng, X J;Folcher, M;Fux, C;Gardner, T S;Gossen, M;Haefliger, B;Haseltine, E L;Jeschek, M;Kudla, G;Lapique, N;Lee, I;Leisner, M;Li, Y Q;Lou, C B;Marchisio, M A;Miki, K;Mohammadi, P;Mutalik, V K;Nielsen, A A K;Orth, P;Prochazka, L;Rinaudo, K;Rodrigo, G;Salis, H M;Sayeg, M K;Schaerli, Y;Selcuklu, S D;Temme, K;Villaverde, A F;Weber, W;Wroblewska, L;Xie, Z;Yokobayashi, Y;Zhang, F Z;Zhou, T Y;Zuker, M | ET2JL | Basel, Switzerland | 22 | null | 1 | null | 28,031,353 | Arter, Meret;Benenson, Yaakov;Haefliger, Benjamin;Lapique, Nicolas;Schreiber, Joerg | MOL SYST BIOL | Basel, Switzerland |
Song, A G;Wang, N | 10.1109/TNNLS.2015.2495155 | null | 445 HOES LANE, PISCATAWAY, NJ 08855-4141 USA | 2v67t4b3bc6f6n2r6c54135k13k3q33q28i | Enhanced Logical Stochastic Resonance in Synthetic Genetic Networks | Southeast Univ | null | Wang, N (corresponding author), Southeast Univ, Sch Instrument Sci & Engn, Nanjing 210096, Jiangsu, Peoples R China. | null | Song, Aiguo;Wang, Nan | Computer Science, Artificial Intelligence;Computer Science, Hardware & Architecture;Computer Science, Theory & Methods;Engineering, Electrical & Electronic | National Science Foundation of China [61272379, 61325018] | WOS | Wang, N | Southeast Univ, Jiangsu, Peoples R China | 27 | enhanced;genetic;in;logical;networks;resonance;stochastic;synthetic | 1 | null | IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC | Southeast Univ, Sch Instrument Sci & Engn, Nanjing 210096, Jiangsu, Peoples R China | Article | Southeast Univ | PISCATAWAY | null | null | Southeast Univ | National Science Foundation of China | Wang, N (corresponding author), Southeast Univ, Sch Instrument Sci & Engn, Nanjing 210096, Jiangsu, Peoples R China. | 2739 | Song, Aiguo;Wang, Nan | 37 | 1 | 388,919,600,023 | National Science Foundation of China [61272379, 61325018] | China | IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS | China | null | null | Southeast Univ, Sch Instrument Sci & Engn, Nanjing 210096, Jiangsu, Peoples R China | 2162-237X | Song, A G;Wang, N | DEC | a.g.song@seu.edu.cn;wangnanseu@163.com | enhanced Logical Stochastic Resonance;synthetic genetic networks | 2 | J | Computer Science;Engineering | amplitude;background Gaussian noise;background noise;bacteriophage lambda;bistable system;brief;clear Set-Reset latch operation;concept;correct probability;decreases;desired logic operation;desired logic operation first increases;enhanced Logical Stochastic Resonance;frequency;genetic network;genetic regulatory network;increases;interplay;length;LOGICAL STOCHASTIC RESONANCE;lower;memory gates;moderate;NETWORK;noise strength;optimal plateau;output logic operation;point;required;robust Set-Reset latch operation;same time;Set-Reset latch;stability;stochastic resonance;synthetic gene network;synthetic genetic networks;unity | Wang, N | BISTABLE SYSTEM;genetic network;memory gates;STABILITY;stochastic resonance | 2736 | [Wang, Nan; Song, Aiguo] Southeast Univ, Sch Instrument Sci & Engn, Nanjing 210096, Jiangsu, Peoples R China. | This work was supported by the National Science Foundation of China under Grant 61272379 and Grant 61325018. | amplitude;background Gaussian noise;background noise;bacteriophage lambda;brief;clear Set-Reset latch operation;concept;correct probability;decreases;desired logic operation;desired logic operation first increases;frequency;genetic regulatory network;increases;interplay;length;logical stochastic resonance;lower;moderate;network;noise strength;optimal plateau;output logic operation;point;required;robust Set-Reset latch operation;same time;Set-Reset latch;synthetic gene network;unity | 10.1007/s11071-013-1136-9;10.1016/j.cnsns.2013.12.008;10.1016/j.physleta.2012.01.039;10.1038/35002125;10.1038/nature01257;10.1038/nature07389;10.1038/nbt1413;10.1063/1.1345702;10.1103/PhysRevE.84.055201;10.1103/PhysRevE.88.052721;10.1103/PhysRevLett.102.104101;10.1109/TCSI.2006.883882;10.1109/TCSII.2007.901631;10.1140/epjb/e2014-50193-2;10.1186/1754-1611-4-4;10.1209/0295-5075/93/18001;10.1209/0295-5075/93/50001;10.1371/journal.pone.0076032;10.7498/aps.62.190510 | Southeast Univ | Song, A G;Wang, N | Wang, N: Southeast Univ, Sch Instrument Sci & Engn, Nanjing 210096, Jiangsu, Peoples R China | null | 61272379;61325018 | 19 | null | China | Southeast Univ | Wang, Nan | null | BISTABLE SYSTEM;STABILITY | Wang, Nan; Song, Aiguo; | null | Southeast Univ, Sch Instrument Sci & Engn, Nanjing 210096, Jiangsu, Peoples R China | Southeast Univ, Sch Instrument Sci & Engn, Nanjing 210096, Jiangsu, Peoples R China | 2162-2388 | Genetic networks;memory gates;stochastic resonance | 12 | 2000;2001;2002;2006;2007;2008;2009;2010;2011;2012;2013;2014 | 26 | Southeast Univ, Sch Instrument Sci & Engn, Nanjing 210096, Jiangsu, Peoples R China | IEEE Trans. Neural Netw. Learn. Syst. | Song, Aiguo | IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC | ,;a;adding;addition;also;amplitude;and;applied;as;at;background;bacteriophage;be;brief;by;can;clear;concept;correct;decreases;derived;desired;easily;first;forcing;frequency;from;Gaussian;gene;genetic;getting;implement;in;increase;increases;indicate;interplay;is;lambda;latch;length;logic;logical;lower;may;moderate;morphed;network;noise;obtained;obtaining;of;only;operation;optimal;out;output;periodic;plateau;point;probability;regulatory;required;resonance;robust;same;Set-Reset;stochastic;strength;subjected;synthetic;than;that;the;then;this;time;to;tuning;unity;using;we;what;when | Southeast Univ | In this brief, the concept of logical stochastic resonance is applied to implement the Set-Reset latch in a synthetic gene network derived from a bacteriophage lambda. Clear Set-Reset latch operation is obtained when the network is only subjected to periodic forcing. The correct probability of obtaining the desired logic operation first increases to unity and then decreases as the amplitude of the periodic forcing increases. In addition, the output logic operation can be easily morphed by tuning the frequency and the amplitude of the periodic forcing. At the same time, we indicate that adding moderate periodic forcing to the background Gaussian noise may increase the length of the optimal plateau of getting the desired logic operation in genetic regulatory network. We also point out that robust Set-Reset latch operation can be obtained using the interplay of periodic forcing and background noise when the noise strength is lower than what is required. | null | BISTABLE SYSTEM;STABILITY | 2 | null | genetic network;memory gates;stochastic resonance | 4 | BISTABLE SYSTEM;Genetic networks;memory gates;STABILITY;stochastic resonance | WOS:000388919600023 | Southeast Univ, Jiangsu, Peoples R China | China | 2,016 | null | null | null | null | English | null | ACTA PHYS SIN-CH ED;CHAOS;COMMUN NONLINEAR SCI;EPL-EUROPHYS LETT;EUR PHYS J B;IEEE T CIRCUITS-I;IEEE T CIRCUITS-II;J Biol Eng;NAT BIOTECHNOL;NATURE;NONLINEAR DYNAM;PHYS LETT A;PHYS REV E;PHYS REV LETT;PLOS ONE | Song, Aiguo;Wang, Nan | 2024-03-11
ER | Ando, H;Canton, B;Dari, A;Elowitz, M B;Gupta, A;Hasty, J;Hellen, E H;Jin, X Q;Kohar, V;Li, C G;Murali, K;Nistala Goutam, J;Sharma, A;Stricker, J;Wang, N;Xu, Y | ED5VE | Jiangsu, Peoples R China | 27 | null | 1 | null | 26,571,540 | Song, Aiguo;Wang, Nan | IEEE T NEUR NET LEAR | Jiangsu, Peoples R China |
Gaytán, P;Roldán-Salgado, A;Sánchez-Barreto, C | 10.1016/j.gene.2016.07.026 | null | PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS | 5y106wu11264k402e3m4s5q3j494c23k1q2l50 | LanFP10-A, first functional fluorescent protein whose chromophore contains the elusive mutation G67A | Univ Nacl Autonoma Mexico | null | Gaytán, P (corresponding author), Univ Nacl Autonoma Mexico, Inst Biotechnol, Av Univ 2001, Cuernavaca 62210, Morelos, Mexico. | null | Gaytan, Paul;Roldan-Salgado, Abigail;Sanchez-Barreto, Celidee | Genetics & Heredity | null | WOS | Gaytán, P | Univ Nacl Autonoma Mexico, Morelos, Mexico | 592 | ,;chromophore;contains;elusive;first;fluorescent;functional;G67A;lanFP10-A;mutation;protein;the;whose | 1 | null | ELSEVIER SCIENCE BV | Univ Nacl Autonoma Mexico, Inst Biotechnol, Av Univ 2001, Cuernavaca 62210, Morelos, Mexico | Article | Univ Nacl Autonoma Mexico | AMSTERDAM | null | null | Univ Nacl Autonoma Mexico | null | Gaytán, P (corresponding author), Univ Nacl Autonoma Mexico, Inst Biotechnol, Av Univ 2001, Cuernavaca 62210, Morelos, Mexico. | 290 | Gaytan, Paul;Roldan-Salgado, Abigail;Sanchez-Barreto, Celidee | 19 | 1 | 384,387,600,007 | null | Mexico | GENE | Mexico | null | null | Univ Nacl Autonoma Mexico, Inst Biotechnol, Av Univ 2001, Cuernavaca 62210, Morelos, Mexico | 0378-1119 | Gaytán, P;Roldán-Salgado, A;Sánchez-Barreto, C | NOV 5 | paul@ibt.unam.mx | chromophore;elusive mutation G67A;first functional fluorescent protein;lanFP10-A | 3 | J | Genetics & Heredity | 1994;amino acid;Autofluorescent proteins;biosynthesis;Branchiostoma;C 2016 Elsevier B.V;chromophore;contrast;different reported chromophores;E. coli;elusive mutation G67A;entire protein family;first;first functional fluorescent protein;formation;functional yellow fluorescent protein;G67A mutation;GENE SYNTHESIS;genes encoding;Genetic reporters;genome;GFP FAMILY;GFP-like proteins;glycine 67 (Gly67);GREEN;Green Fluorescent Protein (GFP);heterologous systems;INTERMEDIATE;ISOMERIZATION;lancelet Branchiostoma floridae;lancelet genome;lanFP10-A;LanFP6-A;mutagenesis;mutants;natural autofluorescent proteins (AFPs);natural G67A mutation;natural protein;non-fluorescent;physicochemical properties;POSTTRANSLATIONAL CHEMISTRY;protein engineering;PROTEIN EXPRESSION;rights reserved;second GFP-like protein;synthetic gene encoding LanFP10-A;synthetic genes;twenty-two-year period;VARIANTS | Roldán-Salgado, A | Autofluorescent proteins;BIOSYNTHESIS;Branchiostoma;G67A mutation;GENE SYNTHESIS;Genetic reporters;GFP FAMILY;GFP-like proteins;GREEN;INTERMEDIATE;ISOMERIZATION;mutagenesis;MUTANTS;POSTTRANSLATIONAL CHEMISTRY;Protein engineering;PROTEIN EXPRESSION;Synthetic genes;VARIANTS | 281 | [Roldan-Salgado, Abigail; Sanchez-Barreto, Celidee; Gaytan, Paul] Univ Nacl Autonoma Mexico, Inst Biotechnol, Av Univ 2001, Cuernavaca 62210, Morelos, Mexico. | null | 1994;amino acid;contrast;different reported chromophores;E. coli;entire protein family;first;formation;functional yellow fluorescent protein;G67A mutation;genes encoding;genome;glycine 67 (Gly67);Green Fluorescent Protein (GFP);heterologous systems;lancelet Branchiostoma floridae;lancelet genome;LanFP10-A;LanFP6-A;natural autofluorescent proteins (AFPs);natural G67A mutation;natural protein;non-fluorescent;physicochemical properties;protein engineering;second GFP-like protein;synthetic gene encoding LanFP10-A;twenty-two-year period | 10.1002/pro.654;10.1016/0014-5793(79)80818-2;10.1016/0378-1119(89)90358-2;10.1016/0378-1119(95)00685-0;10.1016/j.bbrc.2005.04.166;10.1016/j.bios.2009.06.008;10.1016/j.chembiol.2008.07.009;10.1016/j.chemphys.2008.02.055;10.1016/j.gene.2009.07.003;10.1016/j.jbiotec.2006.01.015;10.1016/j.jmb.2012.01.044;10.1016/j.mimet.2015.08.005;10.1016/S0006-3495(97)78307-3;10.1016/S0960-9822(02)00450-5;10.1016/S1367-5931(03)00097-8;10.1021/bi0479205;10.1021/cr2001965;10.1021/ja0552693;10.1021/ja056635l;10.1021/ja2114568;10.1021/ja973019j;10.1021/sb3001326;10.1038/nature06967;10.1038/nbt0295-151;10.1038/NMETH1083;10.1039/b903641p;10.1039/b904023d;10.1073/pnas.2133463100;10.1073/pnas.91.26.12501;10.1073/pnas.97.22.11990;10.1074/jbc.M412327200;10.1074/jbc.M800599200;10.1093/nar/gnh058;10.1107/S0907444913004034;10.1134/S000629790903002X;10.1186/1471-2091-3-7;10.1186/1471-2148-9-77;10.1186/1745-6150-3-28;10.1371/journal.pone.0023513;10.2144/000113765;[10.1038/NMETH.2413, 10.1038/nmeth.2413] | Univ Nacl Autonoma Mexico | Gaytán, P;Roldán-Salgado, A;Sánchez-Barreto, C | Roldán-Salgado, A: Univ Nacl Autonoma Mexico, Inst Biotechnol, Av Univ 2001, Cuernavaca 62210, Morelos, Mexico | null | null | 42 | null | Mexico | Univ Nacl Autonoma Mexico | Roldan-Salgado, Abigail | null | BIOSYNTHESIS;GENE SYNTHESIS;GFP FAMILY;GREEN;INTERMEDIATE;ISOMERIZATION;MUTAGENESIS;MUTANTS;POSTTRANSLATIONAL CHEMISTRY;VARIANTS | Roldan-Salgado, Abigail; Sanchez-Barreto, Celidee; Gaytan, Paul; | null | Univ Nacl Autonoma Mexico, Inst Biotechnol, Av Univ 2001, Cuernavaca 62210, Morelos, Mexico | Univ Nacl Autonoma Mexico, Inst Biotechnol, Av Univ 2001, Cuernavaca 62210, Morelos, Mexico | 1879-0038 | Autofluorescent proteins;Branchiostoma;Protein engineering;G67A mutation;Genetic reporters;GFP-like proteins;protein expression;Synthetic gene | 2 | 1979;1981;1989;1994;1995;1996;1997;1998;2000;2002;2003;2004;2005;2006;2007;2008;2009;2011;2012;2013;2015 | 8 | Univ Nacl Autonoma Mexico, Inst Biotechnol, Av Univ 2001, Cuernavaca 62210, Morelos, Mexico | Gene | Gaytan, Paul | ELSEVIER SCIENCE BV | (AFPs);(GFP);(Gly67);,;1994;67;a;acid;also;amino;and;as;autofluorescent;been;Branchiostoma;by;chromophores;cloned;coli;containing;contains;contrast;demonstrate;different;E.;encoded;encoding;engineering;entire;essential;expressed;family;first;floridae;fluorescent;for;formation;found;functional;G67A;gene;genes;genome;GFP-like;glycine;green;has;have;heterologous;improve;in;is;lancelet;LanFP10-A;LanFP6-A;many;modified;mutation;natural;non-fluorescent;of;only;other;period;physicochemical;produces;properties;protein;proteins;regarded;reported;second;since;subsequently;successfully;synthetic;systems;that;the;their;this;throughout;to;twenty-two-year;was;we;when;work;yellow | Univ Nacl Autonoma Mexico | Since Green Fluorescent Protein (GFP) was first successfully expressed in heterologous systems in 1994, many genes encoding other natural autofluorescent proteins (AFPs) have been cloned and subsequently modified by protein engineering to improve their physicochemical properties. Throughout this twenty-two-year period, glycine 67 (Gly67) has been regarded as the only amino acid in the entire protein family that is essential for the formation of the different reported chromophores. In this work, we demonstrate that a synthetic gene encoding LanFP10-A, a natural protein encoded in the genome of the lancelet Branchiostoma floridae containing the G67A mutation, produces a heterologous, functional yellow fluorescent protein when expressed in E. coli. In contrast to LanFP10-A, LanFP6-A, a second GFP-like protein found in the lancelet genome that also contains the natural G67A mutation, was non-fluorescent. | null | BIOSYNTHESIS;GENE SYNTHESIS;GFP FAMILY;GREEN;INTERMEDIATE;ISOMERIZATION;MUTAGENESIS;MUTANTS;POSTTRANSLATIONAL CHEMISTRY;VARIANTS | 0 | null | Autofluorescent proteins;Branchiostoma;G67A mutation;Genetic reporters;GFP-like proteins;Protein engineering;protein expression;Synthetic genes | 10 | Autofluorescent proteins;BIOSYNTHESIS;Branchiostoma;Protein engineering;G67A mutation;GENE SYNTHESIS;Genetic reporters;GFP FAMILY;GFP-like proteins;GREEN;INTERMEDIATE;ISOMERIZATION;mutagenesis;MUTANTS;POSTTRANSLATIONAL CHEMISTRY;PROTEIN EXPRESSION;Synthetic gene;VARIANTS | WOS:000384387600007 | Univ Nacl Autonoma Mexico, Morelos, Mexico | Mexico | 2,016 | null | null | null | null | English | null | ACS SYNTH BIOL;ACTA CRYSTALLOGR D;BIO-TECHNOL;BIOCHEM BIOPH RES CO;BIOCHEMISTRY-MOSCOW+;BIOCHEMISTRY-US;BIOL DIRECT;BIOLUMINESCENCE CHEM;BIOPHYS J;BIOSENS BIOELECTRON;BIOTECHNIQUES;BMC BIOCHEM;BMC EVOL BIOL;CHEM BIOL;CHEM PHYS;CHEM REV;CHEM SOC REV;CURR BIOL;CURR OPIN CHEM BIOL;FEBS LETT;GENE;J AM CHEM SOC;J BIOL CHEM;J BIOTECHNOL;J MICROBIOL METH;J MOL BIOL;NAT METHODS;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PLOS ONE;PROTEIN SCI | Gaytan, Paul;Roldan-Salgado, Abigail;Sanchez-Barreto, Celidee | 2024-03-11
ER | Barondeau, D P;Baumann, D;Bomati, E K;Branchini, B R;Bravaya, K B;Bulina, M E;Chu, J;Cormack, B P;Craggs, T D;Delagrave, S;Gaytán, P;Gross, L A;Heim, R;Hein, R;Ho, S N;Lemay, N P;Li, G;Miyawaki, A;Pakhomov, A A;Patterson, G H;Pletnev, S;Pletneva, N V;Putnam, N H;Shaner, N C;Shcherbo, D;Shimomura, O;Sniegowski, J A;Stepanenko, O V;Subach, F V;Tejerizo, G T;Wang, Q;Ward W.W.;Wu, G;Young, L;Zimmer, M | DX4YS | Morelos, Mexico | 9 | null | 1 | null | 27,418,528 | Gaytan, Paul;Roldan-Salgado, Abigail;Sanchez-Barreto, Celidee | GENE | Morelos, Mexico |
Lord, N D;Paulsson, J;Potvin-Trottier, L;Vinnicombe, G | 10.1038/nature19841 | null | MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND | 4f6i253w7232695a4f353n6t6x685k614fxix | Synchronous long-term oscillations in a synthetic gene circuit | Harvard Med Sch | null | Paulsson, J (corresponding author), Harvard Med Sch, Dept Syst Biol, 200 Longwood Ave, Boston, MA 02115 USA. | null | Lord, Nathan D;Paulsson, Johan;Potvin-Trottier, Laurent;Vinnicombe, Glenn | Multidisciplinary Sciences | NSF [ECS-0335765, 1517372]; Natural Sciences and Engineering Research Council of Canada (NSERC); Fonds de recherche du Quebec - Nature et technologies; National Institutes of Health (NIH) [GM081563, GM095784]; Direct For Mathematical & Physical Scien; Division Of Mathematical Sciences [1517372] Funding Source: National Science Foundation | WOS | Paulsson, J | Harvard Med Sch, Boston, MA USA;Harvard Univ, Cambridge, MA USA;Univ Cambridge, Cambridge, England | 538 | a;circuit;gene;in;long-term;oscillations;synchronous;synthetic | 2 | Lord, Nathan;Potvin-Trottier, Laurent | NATURE PUBLISHING GROUP | Harvard Med Sch, Dept Syst Biol, 200 Longwood Ave, Boston, MA 02115 USA;Harvard Univ, Biophys Program, Cambridge, MA 02138 USA;Harvard Univ, Dept Mol & Cellular Biol, Cambridge, MA 02138 USA;Univ Cambridge, Dept Engn, Cambridge CB2 1PZ, England | Article | Harvard Med Sch | LONDON | null | null | Harvard Med Sch;Harvard Univ;Univ Cambridge | Direct For Mathematical & Physical Scien;Division Of Mathematical Sciences;Fonds de recherche du Quebec - Nature et technologies;National Institutes of Health (NIH);Natural Sciences and Engineering Research Council of Canada (NSERC);NSF | Paulsson, J (corresponding author), Harvard Med Sch, Dept Syst Biol, 200 Longwood Ave, Boston, MA 02115 USA. | + | Lord, Nathan D;Paulsson, Johan;Potvin-Trottier, Laurent;Vinnicombe, Glenn | 118 | 4 | 386,654,400,059 | Direct For Mathematical & Physical Scien;Division Of Mathematical Sciences [1517372] Funding Source: National Science Foundation;Fonds de recherche du Quebec - Nature et technologies;National Institutes of Health (NIH) [GM081563, GM095784];Natural Sciences and Engineering Research Council of Canada (NSERC);NSF [ECS-0335765, 1517372] | UK;USA | NATURE | USA | null | null | Harvard Med Sch, Dept Syst Biol, 200 Longwood Ave, Boston, MA 02115 USA | 0028-0836 | Lord, N D;Paulsson, J;Potvin-Trottier, L;Vinnicombe, G | OCT 27 | johan_paulsson@harvard.edu | synchronous long-term oscillations;synthetic gene circuit | 4 | J | Science & Technology - Other Topics | cells;circuit design;colonies;control loops;coupling;CYANOBACTERIA;error propagation;existing features;expression;first synthetic genetic oscillator;flasks;fluctuations;Genetic circuits;growth conditions;hundreds;importance;information losses;kept phase;modification;natural systems;NETWORK;noise;noise analyses;precision;principles;range;regular;repressilator(1);results;rivals natural systems;ROBUST;robust oscillations;simplest synthetic genetic networks;single cells;stochastic chemistry;streamlined circuits kept 14 generation periods;synchronous long-term oscillations;synthetic biology;Synthetic gene circuit;wide variety | Potvin-Trottier, L | CELLS;CYANOBACTERIA;EXPRESSION;FLUCTUATIONS;NETWORK;NOISE;ROBUST | 514 | [Potvin-Trottier, Laurent; Lord, Nathan D.; Paulsson, Johan] Harvard Med Sch, Dept Syst Biol, 200 Longwood Ave, Boston, MA 02115 USA. [Potvin-Trottier, Laurent] Harvard Univ, Biophys Program, Cambridge, MA 02138 USA. [Lord, Nathan D.] Harvard Univ, Dept Mol & Cellular Biol, Cambridge, MA 02138 USA. [Vinnicombe, Glenn] Univ Cambridge, Dept Engn, Cambridge CB2 1PZ, England. | We thank M. Elowitz for the repressilator plasmids, D. Landgraf for strains and plasmids, P. Cluzel for the fluorescent proteins, S. G. Megason and his laboratory for their microscope, R. Chait and M. Baym for the macroscope and C. Saenz for technical help on the microfluidics device. Some work was performed at the Harvard Medical School Microfluidics Facility and the Center for Nanoscale Systems, a member of the National Nanotechnology Infrastructure Network supported by NSF award ECS-0335765. L.P.-T. acknowledges fellowship support from the Natural Sciences and Engineering Research Council of Canada (NSERC) and the Fonds de recherche du Quebec - Nature et technologies. This work was supported by National Institutes of Health (NIH) grants (GM081563 and GM095784) and NSF award 1517372. | cells;circuit design;colonies;control loops;coupling;error propagation;existing features;first synthetic genetic oscillator;flasks;genetic circuits;growth conditions;hundreds;importance;information losses;kept phase;modification;natural systems;noise analyses;precision;principles;range;regular;repressilator(1);results;rivals natural systems;robust oscillations;simplest synthetic genetic networks;single cells;stochastic chemistry;streamlined circuits kept 14 generation periods;synthetic biology;wide variety | 10.1002/0471142727.mb1420s92;10.1016/j.cell.2009.04.048;10.1016/j.cell.2014.02.022;10.1016/j.cub.2010.04.045;10.1016/S0006-3495(00)76377-6;10.1017/S0033583501003663;10.1038/35002125;10.1038/nature02533;10.1038/nature03508;10.1038/nature06395;10.1038/nature07389;10.1038/nature07616;10.1038/nature08753;10.1038/nature09333;10.1038/nature12148;10.1038/nature12804;10.1038/nature13238;10.1073/pnas.092133899;10.1073/pnas.110057697;10.1103/PhysRevLett.94.218102;10.1126/science.1108451;10.1126/science.1172005;10.1126/science.1205369;10.1126/science.1230996;10.1126/science.1232758;10.1126/science.271.5251.990;10.1186/1752-0509-8-S4-S4;10.1371/journal.pone.0015179;10.2307/2006360, 10.2307/2006360];10.7554/eLife.09771 | Harvard Med Sch | Lord, N D;Paulsson, J;Potvin-Trottier, L;Vinnicombe, G | Potvin-Trottier, L: Harvard Med Sch, Dept Syst Biol, 200 Longwood Ave, Boston, MA 02115 USA | Potvin-Trottier, Laurent | 1517372;ECS-0335765;GM081563;GM095784 | 36 | null | USA | Harvard Med Sch;Harvard Univ;Univ Cambridge | Potvin-Trottier, Laurent | Green Submitted, Green Accepted | CELLS;CYANOBACTERIA;EXPRESSION;FLUCTUATIONS;NETWORK;NOISE;ROBUST | Potvin-Trottier, Laurent; Lord, Nathan D.; Vinnicombe, Glenn; Paulsson, Johan; | null | Harvard Med Sch, Dept Syst Biol, 200 Longwood Ave, Boston, MA 02115 USA;Harvard Univ, Biophys Program, Cambridge, MA 02138 USA;Harvard Univ, Dept Mol & Cellular Biol, Cambridge, MA 02138 USA;Univ Cambridge, Dept Engn, Cambridge CB2 1PZ, England | Harvard Med Sch, Dept Syst Biol, 200 Longwood Ave, Boston, MA 02115 USA;Harvard Univ, Biophys Program, Cambridge, MA 02138 USA;Harvard Univ, Dept Mol & Cellular Biol, Cambridge, MA 02138 USA;Univ Cambridge, Dept Engn, Cambridge CB2 1PZ, England | 1476-4687 | null | 7626 | 1926;1958;1968;1978;1996;1998;1999;2000;2001;2002;2004;2005;2007;2008;2009;2010;2011;2013;2014;2015 | 182 | Harvard Med Sch, Dept Syst Biol, 200 Longwood Ave, Boston, MA 02115 USA | Nature | Paulsson, Johan | NATURE PUBLISHING GROUP | ,;14;a;accurate;achieve;adding;allowing;analyses;and;any;are;between;biology;but;by;can;cells;chemistry;circuit;circuits;colonies;conditions;control;coupling;created;design;emphasize;engineered;error;even;existing;features;first;flasks;for;from;furthermore;generally;generation;generations;genetic;growth;here;highly;hundreds;importance;in;information;it;kept;less;loops;losses;modification;modify;natural;networks;noise;not;of;oscillate;oscillations;oscillator;our;over;perform;periods;phase;precision;principles;propagation;range;reduce;regular;removing;repressilator(1);results;revisit;rivals;robust;show;simplest;simply;single;some;sought;specifically;stochastic;streamlined;suggest;synchronously;synthetic;synthetically;systems;tasks;than;that;the;them;this;to;using;variety;we;wide;without | Harvard Med Sch | Synthetically engineered genetic circuits can perform a wide variety of tasks but are generally less accurate than natural systems. Here we revisit the first synthetic genetic oscillator, the repressilator(1), and modify it using principles from stochastic chemistry in single cells. Specifically, we sought to reduce error propagation and information losses, not by adding control loops, but by simply removing existing features. We show that this modification created highly regular and robust oscillations. Furthermore, some streamlined circuits kept 14 generation periods over a range of growth conditions and kept phase for hundreds of generations in single cells, allowing cells in flasks and colonies to oscillate synchronously without any coupling between them. Our results suggest that even the simplest synthetic genetic networks can achieve a precision that rivals natural systems, and emphasize the importance of noise analyses for circuit design in synthetic biology. | AAL-3122-2021 | CELLS;CYANOBACTERIA;EXPRESSION;FLUCTUATIONS;NETWORKS;NOISE;ROBUST | 3 | null | null | 16 | CELLS;CYANOBACTERIA;EXPRESSION;FLUCTUATIONS;NETWORKS;NOISE;ROBUST | WOS:000386654400059 | Harvard Med Sch, Boston, MA USA;Harvard Univ, Cambridge, MA USA;Univ Cambridge, Cambridge, England | UK;USA | 2,016 | null | 0000-0001-7876-2820;0000-0001-9553-2779 | null | null | English | null | APPL ENVIRON MICROB;BIOPHYS J;BMC SYST BIOL;CELL;CURR BIOL;Curr Protoc Mol Biol;Discrete-Time Signal Processing;ELIFE;INT TECHN COMM DAY H;MEASUREMENT POWER SP;NATURE;P NATL ACAD SCI USA;PHILOS MAG;PHYS REV LETT;PLOS ONE;Q REV BIOPHYS;SCIENCE;Spectral Analysis and its Applications | Lord, Nathan D;Paulsson, Johan;Potvin-Trottier, Laurent;Vinnicombe, Glenn | 2024-03-11
ER | Andersen, J B;Bell Jb.;Berg, O G;Blackman R. B.;Bonnet, J;Brewster, R C;Chabot, J R;Chait, R;Daniel, R;Danino, T;Edelstein Arthur;Elowitz, M B;Friedland, A E;Fung, E;Jenkins G. M.;Keiler, K C;Lestas, I;Mckane, A J;Mihalcescu, I;Mondragón-Palomino, O;Moriya, T;Nakajima, M;Niederholtmeyer, H;Norman, T M;Oppenheim A., V;Paulsson, J;Prindle, A;Stricker, J;Tabor, J J;Teng, S W;Tigges, M;Van Der Pol, B;Verdu S.;Vilar, J M G;Wang, P | EA5IY | Boston, MA USA | 233 | null | 3 | null | 27,732,583 | Lord, Nathan D;Paulsson, Johan;Potvin-Trottier, Laurent;Vinnicombe, Glenn | NATURE | Boston, MA USA;Cambridge, England;Cambridge, MA USA |
Brady, S F;Charlop-Powers, Z;Kang, H S | 10.1021/acssynbio.6b00080 | null | 1155 16TH ST, NW, WASHINGTON, DC 20036 USA | 28215455v6c4m4h4m315wc6c425w3051l2z1n | Multiplexed CRISPR/Cas9-and TAR-Mediated Promoter Engineering of Natural Product Biosynthetic Gene Clusters in Yeast | Rockefeller Univ | null | Brady, SF (corresponding author), Rockefeller Univ, Lab Genetically Encoded Small Mol, 1230 York Ave, New York, NY 10065 USA. | null | Brady, Sean F;Charlop-Powers, Zachary;Kang, Hahk-Soo | Biochemical Research Methods | NIH [U01 GM110714-1A1, AI110029] | WOS | Brady, S F | Konkuk Univ, Seoul, South Korea;Rockefeller Univ, New York, NY USA | 5 | biosynthetic;Clusters;CRISPR/Cas9-and;engineering;gene;in;multiplexed;natural;of;Product;Promoter;TAR-Mediated;yeast | 2 | Charlop-Powers, Zachary | AMER CHEMICAL SOC | Konkuk Univ, Dept Bioind Technol, Seoul 143701, South Korea;Rockefeller Univ, Lab Genetically Encoded Small Mol, 1230 York Ave, New York, NY 10065 USA | Article | Rockefeller Univ | WASHINGTON | null | null | Konkuk Univ;Rockefeller Univ | NIH | Brady, SF (corresponding author), Rockefeller Univ, Lab Genetically Encoded Small Mol, 1230 York Ave, New York, NY 10065 USA. | 1010 | Brady, Sean F;Charlop-Powers, Zachary;Kang, Hahk-Soo | 111 | 2 | 383,641,400,012 | NIH [U01 GM110714-1A1, AI110029] | South Korea;USA | ACS SYNTHETIC BIOLOGY | USA | null | null | Rockefeller Univ, Lab Genetically Encoded Small Mol, 1230 York Ave, New York, NY 10065 USA | 2161-5063 | Brady, S F;Charlop-Powers, Z;Kang, H S | SEP | sbrady@rockefeller.edu | multiplexed CRISPR/Cas9-and TAR-Mediated Promoter Engineering;Natural Product Biosynthetic Gene Clusters;Yeast | 3 | J | Biochemistry & Molecular Biology | activation;approach;bacterial genomes;biosynthetic gene;biosynthetic gene clusters;combines CRISPR/Cas9;CRISPR array;CRISPR plasmid;CRISPR-CAS SYSTEMS;CRISPR/Cas9;CRISPR/Cas9 system;discovery;DISRUPTION;DNA;DNA double-strand breaks;drug discovery;first application;gene clusters;generic method;growing collection;improved yeast-based promoter engineering platform (mCRISTAR);inefficiency;laboratory growth conditions;large gene clusters;major obstacle;mCRISTAR;metagenome;method;microbial genome;multiplex CRISPR;multiplex gene cluster refactoring;multiplexed CRISPR/Cas9-and TAR-Mediated Promoter Engineering;multiplexed promoter engineering;multiplexed replacement;Natural Product Biosynthetic Gene Clusters;natural product discovery;natural products;new paradigm;OLIGONUCLEOTIDES;projects;promoter engineering;promoter regions;promoters;resulting operon fragments;revealing chemistries;SACCHAROMYCES-CEREVISIAE;simple;single auxotrophic selection;single-marker multiplexed promoter engineering;synthetic gene cluster-specific promoter cassettes;TAR;transcriptional silence;use;yeast | Kang, H S | ACTIVATION;CRISPR-CAS SYSTEMS;CRISPR/Cas9;DISRUPTION;DRUG DISCOVERY;natural products;OLIGONUCLEOTIDES;promoter engineering;SACCHAROMYCES-CEREVISIAE;TAR | 1002 | [Kang, Hahk-Soo; Charlop-Powers, Zachary; Brady, Sean F.] Rockefeller Univ, Lab Genetically Encoded Small Mol, 1230 York Ave, New York, NY 10065 USA. [Kang, Hahk-Soo] Konkuk Univ, Dept Bioind Technol, Seoul 143701, South Korea. | This work was supported by NIH (U01 GM110714-1A1 and AI110029 to Z.C.-P.). | approach;bacterial genomes;biosynthetic gene;biosynthetic gene clusters;combines CRISPR/Cas9;CRISPR array;CRISPR plasmid;CRISPR/Cas9;CRISPR/Cas9 system;discovery;DNA;DNA double-strand breaks;first application;gene clusters;generic method;growing collection;improved yeast-based promoter engineering platform (mCRISTAR);inefficiency;laboratory growth conditions;large gene clusters;major obstacle;mCRISTAR;metagenome;method;microbial genome;multiplex CRISPR;multiplex gene cluster refactoring;multiplexed promoter engineering;multiplexed replacement;natural product biosynthetic gene clusters;natural product discovery;natural products;new paradigm;projects;promoter regions;promoters;resulting operon fragments;revealing chemistries;simple;single auxotrophic selection;single-marker multiplexed promoter engineering;synthetic gene cluster-specific promoter cassettes;TAR;transcriptional silence;use | 10.1002/bip.21450;10.1007/s00253-010-3018-0;10.1016/j.cell.2014.06.034;10.1016/j.ymben.2015.01.008;10.1016/S0076-6879(05)09019-1;10.1021/ja3093828;10.1021/sb400058n;10.1021/sb500255k;10.1038/522270a;10.1038/ja.2008.16;10.1038/nbt.2508;10.1038/nbt.2842;10.1038/ncomms3894;10.1038/nprot.2007.13;10.1038/nrd4510;10.1038/nrmicro3496;10.1042/BST20130164;10.1073/pnas.1507606112;10.1073/pnas.2036296100;10.1074/jbc.M413801200;10.1093/bioinformatics/btp163;10.1093/nar/gkt135;10.1126/science.1232033;10.1371/journal.pone.0005553 | Rockefeller Univ | Brady, S F;Charlop-Powers, Z;Kang, H S | Kang, H S: Rockefeller Univ, Lab Genetically Encoded Small Mol, 1230 York Ave, New York, NY 10065 USA | null | AI110029;U01 GM110714-1A1 | 25 | null | USA | Konkuk Univ;Rockefeller Univ | Kang, Hahk-Soo | Green Accepted | ACTIVATION;CRISPR-CAS SYSTEMS;DISRUPTION;DRUG DISCOVERY;OLIGONUCLEOTIDES;SACCHAROMYCES-CEREVISIAE | Kang, Hahk-Soo; Charlop-Powers, Zachary; Brady, Sean F.; | null | Konkuk Univ, Dept Bioind Technol, Seoul 143701, South Korea;Rockefeller Univ, Lab Genetically Encoded Small Mol, 1230 York Ave, New York, NY 10065 USA | Konkuk Univ, Dept Bioind Technol, Seoul 143701, South Korea;Rockefeller Univ, Lab Genetically Encoded Small Mol, 1230 York Ave, New York, NY 10065 USA | null | CRISPR/Cas9;promoter engineering;natural products;TAR | 9 | 1998;2003;2005;2006;2007;2009;2010;2011;2012;2013;2014;2015 | 71 | Rockefeller Univ, Lab Genetically Encoded Small Mol, 1230 York Ave, New York, NY 10065 USA | ACS Synth. Biol. | Brady, Sean F | AMER CHEMICAL SOC | (mCRISTAR);,;a;an;and;application;approach;are;array;as;auxotrophic;bacterial;biosynthetic;breaks;by;cassettes;chemistries;cluster;cluster-specific;clusters;collection;combines;conditions;construction;CRISPR;CRISPR/Cas9;describe;discovery;DNA;double-strand;emerged;enable;encoded;engineering;facilitate;first;for;found;fragments;from;gene;generic;genome;genomes;growing;growth;guide;has;here;highlights;implementing;improve;improved;in;induce;inefficiency;is;laboratory;large;major;mCRISTAR;metagenome;method;microbial;multiplex;multiplexed;natural;new;obstacle;of;operon;paradigm;plasmid;platform;product;products;projects;promoter;promoters;rapidly;reassembled;refactoring;regions;replacement;resulting;revealing;selection;sequencing;silence;simple;simplify;single;single-marker;synthetic;system;TAR;that;the;this;to;transcriptional;under;use;used;uses;using;we;will;yeast-based | Rockefeller Univ | The use of DNA sequencing to guide the discovery of natural products has emerged as a new paradigm for revealing chemistries encoded in bacterial genomes. A major obstacle to implementing this approach to natural product discovery is the transcriptional silence of biosynthetic gene clusters under laboratory growth conditions. Here we describe an improved yeast-based promoter engineering platform (mCRISTAR) that combines CRISPR/Cas9 and TAR to enable single-marker multiplexed promoter engineering of large gene clusters. mCRISTAR highlights the first application of the CRISPR/Cas9 system to multiplexed promoter engineering of natural product biosynthetic gene clusters. In this method, CRISPR/Cas9 is used to induce DNA double-strand breaks in promoter regions of biosynthetic gene clusters, and the resulting operon fragments are reassembled by TAR using synthetic gene cluster-specific promoter cassettes. mCRISTAR uses a CRISPR array to simplify the construction of a CRISPR plasmid for multiplex CRISPR and a single auxotrophic selection to improve the inefficiency of using a CRISPR array for multiplex gene cluster refactoring. mCRISTAR is a simple and generic method for multiplexed replacement of promoters in biosynthetic gene clusters that will facilitate the discovery of natural products from the rapidly growing collection of gene clusters found in microbial genome and metagenome sequencing projects. | null | ACTIVATION;CRISPR-CAS SYSTEMS;DISRUPTION;DRUG DISCOVERY;OLIGONUCLEOTIDES;SACCHAROMYCES-CEREVISIAE | 4 | null | CRISPR/Cas9;natural products;promoter engineering;TAR | 9 | SACCHAROMYCES-CEREVISIAE;ACTIVATION;CRISPR-Cas9;CRISPR-CAS SYSTEMS;DISRUPTION;DRUG DISCOVERY;promoter engineering;NATURAL-PRODUCTS;OLIGONUCLEOTIDES;TAR | WOS:000383641400012 | Konkuk Univ, Seoul, South Korea;Rockefeller Univ, New York, NY USA | South Korea;USA | 2,016 | null | 0000-0001-8816-4680 | null | null | English | null | ACS SYNTH BIOL;APPL MICROBIOL BIOT;BIOCHEM SOC T;BIOINFORMATICS;BIOPOLYMERS;CELL;J AM CHEM SOC;J ANTIBIOT;J BIOL CHEM;METAB ENG;METHOD ENZYMOL;NAT BIOTECHNOL;NAT COMMUN;NAT PROTOC;NAT REV DRUG DISCOV;NAT REV MICROBIOL;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PLOS ONE;SCIENCE;YEAST | Brady, Sean F;Charlop-Powers, Zachary;Kang, Hahk-Soo | 2024-03-11
ER | Bao, Z H;Brachmann, C B;Cimermancic, P;Cock, P J A;Demain, A L;Dicarlo, J E;Engler, C;Gietz, R D;Harvey, A L;Hong, H J;Jakounas, T;Jiang, W Y;Kallifidas, D;Karvelis, T;Kim, J H;Lok, C;Luo, Y Z;Mali, P;Montiel, D;Rutledge, P J;Sander, J D;Seghezzi, N;Shao, Z Y;Storici, F | DW4VP | New York, NY USA | 89 | null | 2 | null | 27,197,732 | Brady, Sean F;Charlop-Powers, Zachary;Kang, Hahk-Soo | ACS SYNTH BIOL | New York, NY USA;Seoul, South Korea |
Fontes, C M G A;Guerreiro, C I P D;Sequeira, A F;Vincentelli, R | 10.1007/s12033-016-9957-7 | null | 999 RIVERVIEW DRIVE SUITE 208, TOTOWA, NJ 07512 USA | 142m4z175226c5d1q3xnr003n1r4922693s | T7 Endonuclease I Mediates Error Correction in Artificial Gene Synthesis | Univ Lisbon | null | Fontes, CMGA (corresponding author), NZYTech Genes & Enzymes, Campus Lumiar,Estr Paco do Lumiar, P-1649038 Lisbon, Portugal.;Fontes, CMGA (corresponding author), Univ Lisbon, Fac Med Vet, CIISA, Ave Univ Tecn, P-1300477 Lisbon, Portugal. | null | Fontes, Carlos M G A;Guerreiro, Catarina I P D;Sequeira, Ana Filipa;Vincentelli, Renaud | Biochemistry & Molecular Biology;Biotechnology & Applied Microbiology | Fundacao para a Ciencia e a Tecnologia (Lisbon, Portugal); NZYTech [SFRH/BD/51602/2011] | WOS | Fontes, CMGA | Aix Marseille Univ, Marseille, France;NZYTech Genes & Enzymes, Lisbon, Portugal;Univ Lisbon, Lisbon, Portugal | 58 | Artificial;Correction;Endonuclease;Error;gene;I;in;Mediates;synthesis;t7 | 2 | Fontes, Carlos;Sequeira, Ana Filipa | HUMANA PRESS INC | Aix Marseille Univ, CNRS, AFMB, UMR 7257, Campus Luminy,163 Ave Luminy, F-13288 Marseille 09, France;NZYTech Genes & Enzymes, Campus Lumiar,Estr Paco do Lumiar, P-1649038 Lisbon, Portugal;Univ Lisbon, Fac Med Vet, CIISA, Ave Univ Tecn, P-1300477 Lisbon, Portugal;Univ Lisbon, Fac Med Vet, CIISA, Ave Univ Tecn, P-1300477 Lisbon, Portugal.; Fontes, CMGA (corresponding author), NZYTech Genes & Enzymes, Campus Lumiar,Estr Paco do Lumiar, P-1649038 Lisbon, Portugal | Article | NZYTech Genes & Enzymes;Univ Lisbon | TOTOWA | null | null | Aix Marseille Univ;Ave Univ Tecn;NZYTech Genes & Enzymes;Univ Lisbon | Fundacao para a Ciencia e a Tecnologia (Lisbon, Portugal);NZYTech | Fontes, CMGA (corresponding author), Univ Lisbon, Fac Med Vet, CIISA, Ave Univ Tecn, P-1300477 Lisbon, Portugal.; Fontes, CMGA (corresponding author), NZYTech Genes & Enzymes, Campus Lumiar,Estr Paco do Lumiar, P-1649038 Lisbon, Portugal. | 584 | Fontes, Carlos M G A;Guerreiro, Catarina I P D;Sequeira, Ana Filipa;Vincentelli, Renaud | 23 | 3 | 382,003,200,007 | Fundacao para a Ciencia e a Tecnologia (Lisbon, Portugal);NZYTech [SFRH/BD/51602/2011] | France;Portugal | MOLECULAR BIOTECHNOLOGY | Portugal | null | null | Univ Lisbon, Fac Med Vet, CIISA, Ave Univ Tecn, P-1300477 Lisbon, Portugal | 1073-6085 | Fontes, C M G A;Guerreiro, C I P D;Sequeira, A F;Vincentelli, R | SEP | cafontes@fmv.ulisboa.pt | Artificial Gene Synthesis;Error Correction;t7 Endonuclease | 4 | J | Biochemistry & Molecular Biology;Biotechnology & Applied Microbiology | 0.43 errors per 1 kb;ability;accurate production;Artificial Gene Synthesis;cleavage step (EMC);current gene synthesis protocols;data;de novo gene synthesis;deletions;different endonuclease enzymes;DNA;DNA strands;efficacy;eightfold relative;EMC;Enzyme mismatch cleavage (EMC);enzymes;Error Correction;error correction step;error frequency;error rate;Error removal;error-free synthetic genes;fidelity;gene assembly;GENE SYNTHESIS;gfp gene;green fluorescent protein;incorporation;incorrect impairments;insertions;integrated protocol;large scales;method;MISMATCH CLEAVAGE;mutation frequency;mutation removal;mutation-removal step;MUTATIONS;number;overall;overlapping oligonucleotides;PCR assembly;population;quality;removal;RESOLVASES;resulting artificial genes;sequence analysis;STRAND-SPECIFIC NUCLEASES;substitutions;synthetic genes;t7 Endonuclease;T7 endonuclease I;taken;template | Sequeira, A F | Enzyme mismatch cleavage (EMC);ENZYMES;Error removal;GENE SYNTHESIS;MISMATCH CLEAVAGE;REMOVAL;RESOLVASES;STRAND-SPECIFIC NUCLEASES;T7 endonuclease I | 573 | [Sequeira, Ana Filipa; Fontes, Carlos M. G. A.] Univ Lisbon, Fac Med Vet, CIISA, Ave Univ Tecn, P-1300477 Lisbon, Portugal. [Sequeira, Ana Filipa; Guerreiro, Catarina I. P. D.; Fontes, Carlos M. G. A.] NZYTech Genes & Enzymes, Campus Lumiar,Estr Paco do Lumiar, P-1649038 Lisbon, Portugal. [Vincentelli, Renaud] Aix Marseille Univ, CNRS, AFMB, UMR 7257, Campus Luminy,163 Ave Luminy, F-13288 Marseille 09, France. | Ana Filipa Sequeira was supported by Fundacao para a Ciencia e a Tecnologia (Lisbon, Portugal) and NZYTech through the individual fellowship SFRH/BD/51602/2011. | 0.43 errors per 1 kb;ability;accurate production;artificial gene synthesis;cleavage step (EMC);current gene synthesis protocols;data;de novo gene synthesis;deletions;different endonuclease enzymes;DNA;DNA strands;efficacy;eightfold relative;EMC;error correction step;error frequency;error rate;error-free synthetic genes;fidelity;gene assembly;gene synthesis;gfp gene;green fluorescent protein;incorporation;incorrect impairments;insertions;integrated protocol;large scales;method;mutation frequency;mutation removal;mutation-removal step;mutations;number;overall;overlapping oligonucleotides;PCR assembly;population;quality;resulting artificial genes;sequence analysis;substitutions;synthetic genes;T7 endonuclease;taken;template | 10.1002/elps.200700729;10.1002/elps.201100460;10.1006/jmbi.1997.1097;10.1007/s00253-012-4507-0;10.1016/j.jbiotec.2006.01.015;10.1016/j.tibtech.2011.10.002;10.1016/S0168-6445(02)00129-8;10.1021/bi992376z;10.1038/srep11302;10.1039/b822268c;10.1073/pnas.94.13.6847;10.1093/nar/28.18.3417;10.1093/nar/gkh599;10.1093/nar/gkr887;10.1093/nar/gku405;10.1093/nar/gnh160;10.1093/nar/gni058;10.1093/protein/gzu029;10.1101/SQB.1984.049.01.081;10.1111/1567-1364.12171;10.1385/MB:23:1:73;10.3389/fmicb.2014.00172;[10.1038/NMETH.2918, 10.1038/nmeth.2918] | Univ Lisbon | Fontes, C M G A;Guerreiro, C I P D;Sequeira, A F;Vincentelli, R | Sequeira, A F: Univ Lisbon, Fac Med Vet, CIISA, Ave Univ Tecn, P-1300477 Lisbon, Portugal | null | SFRH/BD/51602/2011 | 23 | null | Portugal | Aix Marseille Univ;NZYTech Genes & Enzymes;Univ Lisbon | Sequeira, Ana Filipa | null | ENZYMES;MISMATCH CLEAVAGE;REMOVAL;RESOLVASES;STRAND-SPECIFIC NUCLEASES | Sequeira, Ana Filipa; Guerreiro, Catarina I. P. D.; Vincentelli, Renaud; Fontes, Carlos M. G. A.; | null | Aix Marseille Univ, CNRS, AFMB, UMR 7257, Campus Luminy,163 Ave Luminy, F-13288 Marseille 09, France;NZYTech Genes & Enzymes, Campus Lumiar,Estr Paco do Lumiar, P-1649038 Lisbon, Portugal;Univ Lisbon, Fac Med Vet, CIISA, Ave Univ Tecn, P-1300477 Lisbon, Portugal | Aix Marseille Univ, CNRS, AFMB, UMR 7257, Campus Luminy,163 Ave Luminy, F-13288 Marseille 09, France;NZYTech Genes & Enzymes, Campus Lumiar,Estr Paco do Lumiar, P-1649038 Lisbon, Portugal;Univ Lisbon, Fac Med Vet, CIISA, Ave Univ Tecn, P-1300477 Lisbon, Portugal | 1559-0305 | Enzyme mismatch cleavage (EMC);Error removal;Gene synthesis;T7 endonuclease I | 8-9 | 1984;1997;2000;2003;2004;2005;2006;2008;2009;2012;2014;2015 | 7 | NZYTech Genes & Enzymes, Campus Lumiar,Estr Paco do Lumiar, P-1649038 Lisbon, Portugal;Univ Lisbon, Fac Med Vet, CIISA, Ave Univ Tecn, P-1300477 Lisbon, Portugal | Mol. Biotechnol. | Fontes, Carlos M G A | HUMANA PRESS INC | (EMC);,;0.43;1;a;ability;accumulated;accurate;an;analysed;analysis;and;artificial;artificially;as;assembly;associated;between;both;by;can;cleavage;cleave;correction;current;data;de;deletions;depends;different;diminished;DNA;effectively;efficacy;efficient;eightfold;EMC;encodes;endonuclease;enzymatic;enzymes;error;error-free;errors;fidelity;fluorescent;following;for;frequency;from;functional;gene;genes;gfp;green;here;I;impairments;improve;improved;in;including;incorporating;incorporation;incorrect;insertions;integrated;kb;large;largely;limits;method;mismatch;mismatches;mutation;mutation-removal;mutations;not;novo;number;of;oligonucleotides;on;overall;overlapping;PCR;per;population;presented;production;protein;protocol;protocols;quality;rate;recognize;reduced;relative;removal;remove;resulting;reveal;revealed;scales;sequence;small;specifically;step;strands;strongly;substitutions;synthesis;synthesized;synthetic;T7;taken;template;that;the;this;to;together;used;using;was;we;when;which;with | NZYTech Genes & Enzymes;Univ Lisbon | Efficacy of de novo gene synthesis largely depends on the quality of overlapping oligonucleotides used as template for PCR assembly. The error rate associated with current gene synthesis protocols limits the efficient and accurate production of synthetic genes, both in the small and large scales. Here, we analysed the ability of different endonuclease enzymes, which specifically recognize and cleave DNA mismatches resulting from incorrect impairments between DNA strands, to remove mutations accumulated in synthetic genes. The gfp gene, which encodes the green fluorescent protein, was artificially synthesized using an integrated protocol including an enzymatic mismatch cleavage step (EMC) following gene assembly. Functional and sequence analysis of resulting artificial genes revealed that number of deletions, insertions and substitutions was strongly reduced when T7 endonuclease I was used for mutation removal. This method diminished mutation frequency by eightfold relative to gene synthesis not incorporating an error correction step. Overall, EMC using T7 endonuclease I improved the population of error-free synthetic genes, resulting in an error frequency of 0.43 errors per 1 kb. Taken together, data presented here reveal that incorporation of a mutation-removal step including T7 endonuclease I can effectively improve the fidelity of artificial gene synthesis. | null | ENZYMES;MISMATCH CLEAVAGE;REMOVAL;RESOLVASE;STRAND-SPECIFIC NUCLEASES | 1 | null | Enzyme mismatch cleavage (EMC);Error removal;Gene synthesis;T7 endonuclease I | 12 | ENZYMES;Enzyme mismatch cleavage (EMC);Error removal;GENE SYNTHESIS;MISMATCH CLEAVAGE;REMOVAL;RESOLVASE;STRAND-SPECIFIC NUCLEASES;T7 endonuclease I | WOS:000382003200007 | Aix Marseille Univ, Marseille, France;NZYTech Genes & Enzymes, Lisbon, Portugal;Univ Lisbon, Lisbon, Portugal | France;Portugal | 2,016 | null | 0000-0001-8445-6221;0000-0002-1219-9753 | null | null | English | null | APPL MICROBIOL BIOT;BIOCHEMISTRY-US;COLD SPRING HARB SYM;ELECTROPHORESIS;FEMS MICROBIOL REV;FEMS YEAST RES;FRONT MICROBIOL;J BIOTECHNOL;J MOL BIOL;MOL BIOSYST;MOL BIOTECHNOL;NAT METHODS;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PROTEIN ENG DES SEL;SCI REP-UK;TRENDS BIOTECHNOL | Fontes, Carlos M G A;Guerreiro, Catarina I P D;Sequeira, Ana Filipa;Vincentelli, Renaud | 2024-03-11
ER | Aravind, L;Babon, J J;Carr, P A;Chao, R;Cheung, R C F;Currin, A;Demassy, B;Desai, N A;Fuhrmann, M;Huang, M C;Kosuri, S;Ma, S Y;Rosano, G L;Saaem, I;Smith, J;Tian, J D;Till, B J;Tsuji, T;Wan, W;White, M F;Wu, G;Yang, B;Zampini, M | DU1XG | Lisbon, Portugal;Lisbon, Portugal. | 11 | null | 3 | null | 27,334,914 | Fontes, Carlos M G A;Guerreiro, Catarina I P D;Sequeira, Ana Filipa;Vincentelli, Renaud | MOL BIOTECHNOL | Lisbon, Portugal;Marseille, France |
Bar-Ziv, R H;Morel, M;Nissim, L;Rotter, V;Shtrahman, R | 10.1073/pnas.1604391113 | null | 2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA | 1l1013p6d3k4g2c4r3g6r1x631m2k664r185r6d | Cellular heterogeneity mediates inherent sensitivity-specificity tradeoff in cancer targeting by synthetic circuits | Weizmann Inst Sci | null | Bar-Ziv, RH (corresponding author), Weizmann Inst Sci, Dept Mat & Interfaces, IL-76100 Rehovot, Israel.;Nissim, L (corresponding author), MIT, Synthet Biol Ctr, 77 Massachusetts Ave, Cambridge, MA 02139 USA. | null | Bar-Ziv, Roy H;Morel, Mathieu;Nissim, Lior;Rotter, Varda;Shtrahman, Roman | Multidisciplinary Sciences | null | WOS | Bar-Ziv, R H;Nissim, L | MIT, Cambridge, MA USA;Univ Paris, Paris, France;Weizmann Inst Sci, Rehovot, Israel | 113 | by;cancer;Cellular;circuits;heterogeneity;in;inherent;Mediates;sensitivity-specificity;synthetic;targeting;tradeoff | 3 | Morel, Mathieu;Nissim, Lior | NATL ACAD SCIENCES | MIT, Synthet Biol Ctr, 77 Massachusetts Ave, Cambridge, MA 02139 USA;Univ Paris 06, CNRS, Dept Chim,UMR PASTEUR 8640, Ecole Normale Super,Paris Sci & Lettres PSL Res U, F-75005 Paris, France;Univ Paris 06, CNRS, UMR PASTEUR 8640, Ecole Normale Super, F-75005 Paris, France;Weizmann Inst Sci, Dept Mat & Interfaces, IL-76100 Rehovot, Israel;Weizmann Inst Sci, Dept Mat & Interfaces, IL-76100 Rehovot, Israel.; Nissim, L (corresponding author), MIT, Synthet Biol Ctr, 77 Massachusetts Ave, Cambridge, MA 02139 USA;Weizmann Inst Sci, Dept Mol Cell Biol, IL-76100 Rehovot, Israel | Article | MIT;Weizmann Inst Sci | WASHINGTON | null | null | MIT;Synthet Biol Ctr;Univ Paris 06;Weizmann Inst Sci | null | Bar-Ziv, RH (corresponding author), Weizmann Inst Sci, Dept Mat & Interfaces, IL-76100 Rehovot, Israel.; Nissim, L (corresponding author), MIT, Synthet Biol Ctr, 77 Massachusetts Ave, Cambridge, MA 02139 USA. | 8138 | Bar-Ziv, Roy H;Morel, Mathieu;Nissim, Lior;Rotter, Varda;Shtrahman, Roman | 21 | 5 | 380,224,500,053 | null | France;Israel;USA | PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA | Israel;USA | null | null | Weizmann Inst Sci, Dept Mat & Interfaces, IL-76100 Rehovot, Israel | 0027-8424 | Bar-Ziv, R H;Morel, M;Nissim, L;Rotter, V;Shtrahman, R | JUL 19 | liorni@mit.edu;roy.bar-ziv@weizmann.ac.il | cancer;cellular heterogeneity;inherent sensitivity-specificity tradeoff;synthetic circuits | 5 | J | Science & Technology - Other Topics | activation threshold;analysis;background;BIOLOGY;CANCER;cancer cells;cancer gene therapy;cell-state targeting;cellular heterogeneity;cellular variability;CIRCUITS;combinatorial integration;computation;decision-making circuits;detrimental;enhanced specificity;error rates;escape;few cells;FRAMEWORK;gate acting;gate amplification gain;gene expression;GENERATION;heterogeneous cell populations;heterogeneous environment;inherent sensitivity-specificity tradeoff;inherent tradeoff;killing assay;light;mammalian synthetic biology;MAMMALIAN-CELLS;minimal loss;molecular parameters;multiple expression markers;normal ones;sensitivity;single-cell response function;specificity;synthetic circuits;synthetic circuits control specificity;synthetic gene circuits;SYSTEM;T-CELLS;target malignant state;tumor-mimicking cell-culture model;tunable logic;two promoters;unexplored;versatile means | Morel, M | BIOLOGY;cancer gene therapy;cell-state targeting;cellular heterogeneity;COMPUTATION;FRAMEWORK;GENERATION;mammalian synthetic biology;MAMMALIAN-CELLS;synthetic gene circuits;SYSTEM;T-CELLS | 8133 | [Morel, Mathieu; Shtrahman, Roman; Bar-Ziv, Roy H.] Weizmann Inst Sci, Dept Mat & Interfaces, IL-76100 Rehovot, Israel. [Morel, Mathieu] Univ Paris 06, CNRS, Dept Chim,UMR PASTEUR 8640, Ecole Normale Super,Paris Sci & Lettres PSL Res U, F-75005 Paris, France. [Morel, Mathieu] Univ Paris 06, CNRS, UMR PASTEUR 8640, Ecole Normale Super, F-75005 Paris, France. [Rotter, Varda] Weizmann Inst Sci, Dept Mol Cell Biol, IL-76100 Rehovot, Israel. [Nissim, Lior] MIT, Synthet Biol Ctr, 77 Massachusetts Ave, Cambridge, MA 02139 USA. | null | activation threshold;analysis;background;cancer;cancer cells;cellular variability;circuits;combinatorial integration;decision-making circuits;detrimental;enhanced specificity;error rates;escape;few cells;gate acting;gate amplification gain;gene expression;heterogeneous cell populations;heterogeneous environment;inherent tradeoff;killing assay;light;minimal loss;molecular parameters;multiple expression markers;normal ones;sensitivity;single-cell response function;specificity;synthetic circuits;synthetic circuits control specificity;synthetic gene circuits;target malignant state;tumor-mimicking cell-culture model;tunable logic;two promoters;unexplored;versatile means | 10.1002/bit.10655;10.1002/jmr.749;10.1007/s10875-012-9689-9;10.1007/s12079-011-0132-4;10.1016/j.cell.2012.05.045;10.1016/j.cell.2015.04.042;10.1016/j.cell.2016.01.011;10.1016/j.it.2015.06.004;10.1021/sb4000564;10.1038/msb.2010.99;10.1038/msb.2013.48;10.1038/msb4100173;10.1038/nature06915;10.1038/nature09326;10.1038/nature09565;10.1038/nature11149;10.1038/nature12148;10.1038/nature12624;10.1038/nbt.2287;10.1038/nbt.2459;10.1038/nbt.2877;10.1038/nrg3094;10.1038/nrm3738;10.1042/BJ20071193;10.1088/1478-3975/4/3/002;10.1093/nar/gks142;10.1126/science.1205527;10.1126/science.1232758;10.1126/scitranslmed.3009367;10.1128/JVI.72.11.8463-8471.1998;10.1148/radiology.143.1.7063747;10.1155/S1110724303209074;10.1158/0008-5472.CAN-04-3880;10.1158/0008-5472.CAN-09-2661;[10.1038/nchembio.1433, 10.1038/NCHEMBIO.1433];[10.1038/NMAT4497, 10.1038/nmat4497] | Weizmann Inst Sci | Bar-Ziv, R H;Morel, M;Nissim, L;Rotter, V;Shtrahman, R | Morel, M: Weizmann Inst Sci, Dept Mat & Interfaces, IL-76100 Rehovot, Israel | Morel, Mathieu | null | 38 | null | Israel | MIT;Univ Paris 06;Weizmann Inst Sci | Morel, Mathieu | Green Published, Bronze | BIOLOGY;COMPUTATION;FRAMEWORK;GENERATION;MAMMALIAN-CELLS;SYSTEM;T-CELLS | Morel, Mathieu; Shtrahman, Roman; Rotter, Varda; Nissim, Lior; Bar-Ziv, Roy H.; | null | MIT, Synthet Biol Ctr, 77 Massachusetts Ave, Cambridge, MA 02139 USA;Univ Paris 06, CNRS, Dept Chim,UMR PASTEUR 8640, Ecole Normale Super,Paris Sci & Lettres PSL Res U, F-75005 Paris, France;Univ Paris 06, CNRS, UMR PASTEUR 8640, Ecole Normale Super, F-75005 Paris, France;Weizmann Inst Sci, Dept Mat & Interfaces, IL-76100 Rehovot, Israel;Weizmann Inst Sci, Dept Mol Cell Biol, IL-76100 Rehovot, Israel | MIT, Synthet Biol Ctr, 77 Massachusetts Ave, Cambridge, MA 02139 USA;Univ Paris 06, CNRS, Dept Chim,UMR PASTEUR 8640, Ecole Normale Super,Paris Sci & Lettres PSL Res U, F-75005 Paris, France;Univ Paris 06, CNRS, UMR PASTEUR 8640, Ecole Normale Super, F-75005 Paris, France;Weizmann Inst Sci, Dept Mat & Interfaces, IL-76100 Rehovot, Israel;Weizmann Inst Sci, Dept Mol Cell Biol, IL-76100 Rehovot, Israel | null | cancer gene therapy;cell-state targeting;cellular heterogeneity;mammalian synthetic biology;Synthetic gene circuit | 29 | 1982;1998;1999;2003;2005;2007;2008;2010;2011;2012;2013;2014;2015;2016 | 18 | MIT, Synthet Biol Ctr, 77 Massachusetts Ave, Cambridge, MA 02139 USA;Weizmann Inst Sci, Dept Mat & Interfaces, IL-76100 Rehovot, Israel | Proc. Natl. Acad. Sci. U. S. A. | Bar-Ziv, Roy H | NATL ACAD SCIENCES | ,;a;acting;activation;also;amplification;an;analysis;and;are;as;assay;background;be;because;between;beyond;by;cancer;cell;cell-culture;cells;cellular;circuits;combinatorial;control;controlled;could;decision-making;detrimental;efficiently;emerging;enhanced;environment;error;escape;even;expression;far;few;function;gain;gate;gene;have;here;heterogeneous;highly;however;implement;in;inherent;integration;is;killing;light;logic;loss;malignant;Markers;means;measure;might;minimal;model;molecular;multiple;must;normal;of;on;ones;operating;optimized;our;parameters;populations;promoters;rates;remained;response;reveals;sensitive;sensitivity;show;single-cell;so;specificity;state;such;suggests;synthetic;target;that;the;this;threshold;to;tradeoff;tumor-mimicking;tunable;tuned;two;unexplored;variability;versatile;we;with | MIT;Weizmann Inst Sci | Synthetic gene circuits are emerging as a versatile means to target cancer with enhanced specificity by combinatorial integration of multiple expression markers. Such circuits must also be tuned to be highly sensitive because escape of even a few cells might be detrimental. However, the error rates of decision-making circuits in light of cellular variability in gene expression have so far remained unexplored. Here, we measure the single-cell response function of a tunable logic AND gate acting on two promoters in heterogeneous cell populations. Our analysis reveals an inherent tradeoff between specificity and sensitivity that is controlled by the AND gate amplification gain and activation threshold. We implement a tumor-mimicking cell-culture model of cancer cells emerging in a background of normal ones, and show that molecular parameters of the synthetic circuits control specificity and sensitivity in a killing assay. This suggests that, beyond the inherent tradeoff, synthetic circuits operating in a heterogeneous environment could be optimized to efficiently target malignant state with minimal loss of specificity. | A-9754-2016 | BIOLOGY;COMPUTATION;FRAMEWORK;GENERATION;MAMMALIAN-CELLS;SYSTEM;T-CELLS | 0 | null | cancer gene therapy;cell-state targeting;cellular heterogeneity;mammalian synthetic biology;synthetic gene circuits | 6 | BIOLOGY;CANCER GENE-THERAPY;cell-state targeting;cellular heterogeneity;COMPUTATION;FRAMEWORK;GENERATION;MAMMALIAN-CELLS;mammalian synthetic biology;synthetic gene circuits;SYSTEM;T-CELLS | WOS:000380224500053 | MIT, Cambridge, MA USA;Univ Paris, Paris, France;Weizmann Inst Sci, Rehovot, Israel | France;Israel;USA | 2,016 | null | 0000-0001-6495-4741;0000-0002-6284-1708 | null | null | English | null | ACS SYNTH BIOL;BIOCHEM J;BIOTECHNOL BIOENG;CANCER RES;CELL;J BIOMED BIOTECHNOL;J CELL COMMUN SIGNAL;J CLIN IMMUNOL;J MOL RECOGNIT;J VIROL;MOL SYST BIOL;NAT BIOTECHNOL;NAT CHEM BIOL;NAT MATER;NAT REV GENET;NAT REV MOL CELL BIO;NATURE;NUCLEIC ACIDS RES;PHYS BIOL;RADIOLOGY;SCI TRANSL MED;SCIENCE;TRENDS IMMUNOL | Bar-Ziv, Roy H;Morel, Mathieu;Nissim, Lior;Rotter, Varda;Shtrahman, Roman | 2024-03-11
ER | Anderson, J C;Ang, J;Ausländer, S;Bacchus, W;Barak, Y;Bonnet, J;Buganim, Y;Conde, J;Costello, J C;Daniel, R;Dull, T;Eldar, A;Gaber, R;Hanley, J A;Karpol, A;Kelm, J M;Khalil, A S;Kloss, C C;Lienert, F;Lohmueller, J J;Meacham, C E;Milyavsky, M;Nissim, L;Nyga, A;Robson, T;Roybal, K T;Rubsam, L Z;Russell, S J;Srivastava, S;Tamsir, A;Tanner, K;Van 'T Veer, L J;Weber, W;Wilkie, S;Xie, Z;Zomer, A | DR9NX | Cambridge, MA USA;Rehovot, Israel. | 26 | null | 3 | null | 27,385,823 | Bar-Ziv, Roy H;Morel, Mathieu;Nissim, Lior;Rotter, Varda;Shtrahman, Roman | P NATL ACAD SCI USA | Cambridge, MA USA;Paris, France;Rehovot, Israel |
Fleck, O;Freke, G;Hernandez, A D;Homma, T;Kis, Z;Krams, R;Lai, Z X;Pedrigi, R M;Rodin, T;Towhidi, L;Zafar, A | 10.1038/srep29643 | 29643 | HEIDELBERGER PLATZ 3, BERLIN, 14197, GERMANY | 3rej592m5t1t3805p1u443d5nq605d109w | Development of a synthetic gene network to modulate gene expression by mechanical forces | Imperial Coll London | null | Krams, R (corresponding author), Imperial Coll London, Dept Bioengn, Exhibit Rd, London SW7 2AZ, England. | null | Fleck, Oliver;Freke, Grace;Hernandez, Armando Del Rio;Homma, Takayuki;Kis, Zoltan;Krams, Rob;Lai, Zhangxing;Pedrigi, Ryan M;Rodin, Tania;Towhidi, Leila;Zafar, Asma | Multidisciplinary Sciences | British Hearth Foundation [RG/11/13/29055]; Department of Bioengineering, Imperial College London; British Heart Foundation [PG/15/49/31595, RG/11/13/29055] Funding Source: researchfish | WOS | Krams, R | Govt Coll Univ, Lahore, Pakistan;Imperial Coll London, London, England;Kyoto Univ, Kyoto, Japan;Natl Univ Singapore, Singapore, Singapore;UCL, London, England;Univ Cambridge, Cambridge, England | 6 | a;by;Development;expression;forces;gene;mechanical;modulate;network;of;synthetic;to | 4 | del Río Hernández, Armando E;Kis, Zoltan | NATURE PORTFOLIO | Govt Coll Univ, Govt Coll Univ, Katchery Rd, Lahore 54000, Pakistan;Imperial Coll London, Dept Bioengn, Exhibit Rd, London SW7 2AZ, England;Kyoto Univ, Inst Integrated Cell Mat Sci, Sakyo Ku, Yoshida Ushinomiya Cho, Kyoto 6068501, Japan;Natl Univ Singapore, Dept Biomed Engn, 4 Engn Dr 3, Singapore 117575, Singapore;Natl Univ Singapore, Dept Mech Engn, 9 Engn Dr 1, Singapore 117575, Singapore;UCL, Inst Child Hlth, 30 Guilford St, London WC1N 1EH, England;Univ Cambridge, Dept Engn, Trumpington St, Cambridge CB2 1PZ, England | Article | Imperial Coll London | BERLIN | null | null | Govt Coll Univ;Imperial Coll London;Kyoto Univ;Natl Univ Singapore;UCL;Univ Cambridge | British Heart Foundation;British Hearth Foundation;Department of Bioengineering, Imperial College London | Krams, R (corresponding author), Imperial Coll London, Dept Bioengn, Exhibit Rd, London SW7 2AZ, England. | null | Fleck, Oliver;Freke, Grace;Hernandez, Armando Del Rio;Homma, Takayuki;Kis, Zoltan;Krams, Rob;Lai, Zhangxing;Pedrigi, Ryan M;Rodin, Tania;Towhidi, Leila;Zafar, Asma | 13 | 7 | 379,392,100,001 | British Heart Foundation [PG/15/49/31595, RG/11/13/29055] Funding Source: researchfish;British Hearth Foundation [RG/11/13/29055];Department of Bioengineering, Imperial College London | Japan;Pakistan;Singapore;UK | SCIENTIFIC REPORTS | UK | null | null | Imperial Coll London, Dept Bioengn, Exhibit Rd, London SW7 2AZ, England | 2045-2322 | Fleck, O;Freke, G;Hernandez, A D;Homma, T;Kis, Z;Krams, R;Lai, Z X;Pedrigi, R M;Rodin, T;Towhidi, L;Zafar, A | JUL 12 | r.krams@imperial.ac.uk | development;gene expression;mechanical forces;synthetic gene network | 11 | J | Science & Technology - Other Topics | (mammalian) cells;60%;ACTING BRADYKININ-ANTAGONIST;activation;ASSAYS;atheroprotective transcription factor;ATHEROSCLEROSIS;B2 RECEPTOR;body;CELL-LINES;cells;development;electroporation;endothelial cell shear stress levels;ENDOTHELIAL SHEAR-STRESS;exposes cells;expression;first mammalian mechanosensitive synthetic gene network;FLOW;flow channel floor;flow setup;function;functional gene network;gene expression;gene network;gene network activation;gene network functionality;graded control;hard-to-transfect mammalian cells;high proportion;HOE-140;hybrid transfection procedure;increasing shear stress;KRUPPEL-LIKE FACTOR-2;length;little work;majority;mammalian antibiotic selection;mammalian cells;mechanical forces;mechanical stimuli;mechanosensor activity;MECHANOTRANSDUCTION;new approach mechanosyngenetics;plasmids replication;procedure takes 1 week;second electroporation;shear stress;shear stress magnitude;synthetic gene network;technique;WALL SHEAR | Kis, Z | ACTING BRADYKININ-ANTAGONIST;ATHEROSCLEROSIS;B2 RECEPTOR;CELL-LINES;ENDOTHELIAL SHEAR-STRESS;FLOW;HOE-140;KRUPPEL-LIKE FACTOR-2;MECHANOTRANSDUCTION;WALL SHEAR | null | [Kis, Zoltan; Rodin, Tania; Zafar, Asma; Lai, Zhangxing; Freke, Grace; Fleck, Oliver; Hernandez, Armando Del Rio; Towhidi, Leila; Pedrigi, Ryan M.; Homma, Takayuki; Krams, Rob] Imperial Coll London, Dept Bioengn, Exhibit Rd, London SW7 2AZ, England. [Zafar, Asma] Govt Coll Univ, Govt Coll Univ, Katchery Rd, Lahore 54000, Pakistan. [Lai, Zhangxing] Natl Univ Singapore, Dept Mech Engn, 9 Engn Dr 1, Singapore 117575, Singapore. [Lai, Zhangxing] Natl Univ Singapore, Dept Biomed Engn, 4 Engn Dr 3, Singapore 117575, Singapore. [Freke, Grace] UCL, Inst Child Hlth, 30 Guilford St, London WC1N 1EH, England. [Fleck, Oliver] Univ Cambridge, Dept Engn, Trumpington St, Cambridge CB2 1PZ, England. [Homma, Takayuki] Kyoto Univ, Inst Integrated Cell Mat Sci, Sakyo Ku, Yoshida Ushinomiya Cho, Kyoto 6068501, Japan. | Funding from British Hearth Foundation (RG/11/13/29055) and PhD Studentship (to Z.K.) from Department of Bioengineering, Imperial College London are gratefully acknowledged. | (mammalian) cells;60%;activation;assays;atheroprotective transcription factor;body;cells;electroporation;endothelial cell shear stress levels;exposes cells;expression;first mammalian mechanosensitive synthetic gene network;flow channel floor;flow setup;function;functional gene network;gene expression;gene network;gene network activation;gene network functionality;graded control;hard-to-transfect mammalian cells;high proportion;hybrid transfection procedure;increasing shear stress;length;little work;majority;mammalian antibiotic selection;mammalian cells;mechanical forces;mechanical stimuli;mechanosensor activity;new approach mechanosyngenetics;plasmids replication;procedure takes 1 week;second electroporation;shear stress;shear stress magnitude;technique | 10.1001/jama.282.21.2035;10.1002/0471142727.mb0903s62;10.1002/bit.22406;10.1007/s10439-005-8774-0;10.1007/s12033-007-0007-3;10.1016/0014-5793(90)80166-G;10.1016/0024-3205(94)00557-5;10.1016/j.bbamem.2006.10.021;10.1016/j.bios.2007.12.009;10.1016/j.cub.2014.04.027;10.1016/j.devcel.2005.12.006;10.1016/j.jacc.2007.02.059;10.1016/j.jbiomech.2014.03.031;10.1016/j.mvr.2004.08.002;10.1016/j.pbiomolbio.2014.06.009;10.1016/j.semcdb.2014.06.018;10.1016/j.ymeth.2003.11.009;10.1016/S0008-6363(98)00074-1;10.1016/S0014-2999(98)00165-4;10.1038/nrm2597;10.1038/sj.gt.3300867;10.1055/s-0037-1616937;10.1073/pnas.0607224103;10.1073/pnas.0710487105;10.1073/pnas.130192197;10.1073/pnas.1313364111;10.1073/pnas.88.17.7724;10.1073/pnas.89.12.5547;10.1074/jbc.271.50.32366;10.1074/jbc.M800362200;10.1084/jem.20031132;10.1089/ars.2010.3679;10.1093/cvr/cvt108;10.1097/CMR.0b013e3283390696;10.1097/HCO.0b013e3282f07548;10.1098/rspb.1971.0019;10.1098/rstb.2007.2128;10.1111/j.1365-2796.2006.01620.x;10.1111/j.1476-5381.1991.tb12248.x;10.1111/j.1476-5381.1991.tb12249.x;10.1111/j.1476-5381.1994.tb13130.x;10.1111/micc.12119;10.1128/MCB.20.18.6837-6848.2000;10.1136/gut.2010.220913;10.1146/annurev.bioeng.6.040803.140203;10.1152/physrev.00047.2009;10.1161/01.HYP.37.2.703;10.1161/01.RES.53.4.502;10.1161/ATVBAHA.114.303426;10.1161/CIRCULATIONAHA.104.525774;10.1161/CIRCULATIONAHA.105.590018;10.1161/CIRCULATIONAHA.110.005108;10.1172/JCI200215493;10.1177/1947603513495889;10.3791/50171 | Imperial Coll London | Fleck, O;Freke, G;Hernandez, A D;Homma, T;Kis, Z;Krams, R;Lai, Z X;Pedrigi, R M;Rodin, T;Towhidi, L;Zafar, A | Kis, Z: Imperial Coll London, Dept Bioengn, Exhibit Rd, London SW7 2AZ, England | del rio hernandez, armando e;del Río Hernández, Armando E;Kis, Zoltan | PG/15/49/31595;RG/11/13/29055 | 62 | null | UK | Govt Coll Univ;Imperial Coll London;Kyoto Univ;Natl Univ Singapore;UCL;Univ Cambridge | Kis, Zoltan | Green Published, Green Submitted, gold, Green Accepted | ACTING BRADYKININ-ANTAGONIST;ATHEROSCLEROSIS;B2 RECEPTOR;CELL-LINES;ENDOTHELIAL SHEAR-STRESS;FLOW;HOE-140;KRUPPEL-LIKE FACTOR-2;MECHANOTRANSDUCTION;WALL SHEAR | Kis, Zoltan; Rodin, Tania; Zafar, Asma; Lai, Zhangxing; Freke, Grace; Fleck, Oliver; Hernandez, Armando Del Rio; Towhidi, Leila; Pedrigi, Ryan M.; Homma, Takayuki; Krams, Rob; | null | Govt Coll Univ, Govt Coll Univ, Katchery Rd, Lahore 54000, Pakistan;Imperial Coll London, Dept Bioengn, Exhibit Rd, London SW7 2AZ, England;Kyoto Univ, Inst Integrated Cell Mat Sci, Sakyo Ku, Yoshida Ushinomiya Cho, Kyoto 6068501, Japan;Natl Univ Singapore, Dept Biomed Engn, 4 Engn Dr 3, Singapore 117575, Singapore;Natl Univ Singapore, Dept Mech Engn, 9 Engn Dr 1, Singapore 117575, Singapore;UCL, Inst Child Hlth, 30 Guilford St, London WC1N 1EH, England;Univ Cambridge, Dept Engn, Trumpington St, Cambridge CB2 1PZ, England | Govt Coll Univ, Govt Coll Univ, Katchery Rd, Lahore 54000, Pakistan;Imperial Coll London, Dept Bioengn, Exhibit Rd, London SW7 2AZ, England;Kyoto Univ, Inst Integrated Cell Mat Sci, Sakyo Ku, Yoshida Ushinomiya Cho, Kyoto 6068501, Japan;Natl Univ Singapore, Dept Biomed Engn, 4 Engn Dr 3, Singapore 117575, Singapore;Natl Univ Singapore, Dept Mech Engn, 9 Engn Dr 1, Singapore 117575, Singapore;UCL, Inst Child Hlth, 30 Guilford St, London WC1N 1EH, England;Univ Cambridge, Dept Engn, Trumpington St, Cambridge CB2 1PZ, England | null | null | null | 1971;1983;1990;1991;1992;1994;1996;1998;1999;2000;2001;2002;2003;2004;2005;2006;2007;2008;2009;2010;2011;2013;2014;2015 | 4 | Imperial Coll London, Dept Bioengn, Exhibit Rd, London SW7 2AZ, England | Sci Rep | Krams, Rob | NATURE PORTFOLIO | (mammalian);,;1;60%;a;activation;activity;address;allows;along;an;and;antibiotic;approach;are;as;assays;atheroprotective;been;body;but;by;call;cell;cells;channel;control;currently;develop;developed;directly;done;drive;easily;electroporation;endothelial;exposes;expression;factor;first;floor;flow;forces;function;functional;functionality;furthermore;gene;graded;hard-to-transfect;has;high;highly;hybrid;impossible;in;increasing;insert;into;involves;is;it;length;levels;linearly;little;logarithmically;magnitude;majority;mammalian;mechanical;mechanosensitive;mechanosensor;mechanosyngenetics;modular;modulate;monitor;needs;network;new;of;our;over;plasmids;procedure;proportion;replication;scalable;second;selection;sensitive;setup;shear;stimuli;stress;synthetic;takes;technique;test;that;the;these;this;to;transcription;transfection;use;varied;was;we;week;with;work;yielded | Imperial Coll London | The majority of (mammalian) cells in our body are sensitive to mechanical forces, but little work has been done to develop assays to monitor mechanosensor activity. Furthermore, it is currently impossible to use mechanosensor activity to drive gene expression. To address these needs, we developed the first mammalian mechanosensitive synthetic gene network to monitor endothelial cell shear stress levels and directly modulate expression of an atheroprotective transcription factor by shear stress. The technique is highly modular, easily scalable and allows graded control of gene expression by mechanical stimuli in hard-to-transfect mammalian cells. We call this new approach mechanosyngenetics. To insert the gene network into a high proportion of cells, a hybrid transfection procedure was developed that involves electroporation, plasmids replication in mammalian cells, mammalian antibiotic selection, a second electroporation and gene network activation. This procedure takes 1 week and yielded over 60% of cells with a functional gene network. To test gene network functionality, we developed a flow setup that exposes cells to linearly increasing shear stress along the length of the flow channel floor. Activation of the gene network varied logarithmically as a function of shear stress magnitude. | D-3555-2012;H-3611-2016;N-4262-2013 | ACTING BRADYKININ-ANTAGONIST;ATHEROSCLEROSIS;B2 RECEPTOR;CELL-LINES;ENDOTHELIAL SHEAR-STRESS;FLOW;HOE-140;KRUPPEL-LIKE FACTOR-2;MECHANOTRANSDUCTION;WALL SHEAR | 0 | null | null | 10 | ACTING BRADYKININ-ANTAGONIST;ATHEROSCLEROSIS;B2 RECEPTOR;CELL-LINES;ENDOTHELIAL SHEAR-STRESS;FLOW;HOE-140;KRUPPEL-LIKE FACTOR-2;MECHANOTRANSDUCTION;WALL SHEAR | WOS:000379392100001 | Govt Coll Univ, Lahore, Pakistan;Imperial Coll London, London, England;Kyoto Univ, Kyoto, Japan;Natl Univ Singapore, Singapore, Singapore;UCL, London, England;Univ Cambridge, Cambridge, England | Japan;Pakistan;Singapore;UK | 2,016 | null | 0000-0001-5062-8910;0000-0002-6598-8369 | null | null | English | null | ANN BIOMED ENG;ANNU REV BIOMED ENG;ANTIOXID REDOX SIGN;ARTERIOSCL THROM VAS;BBA-BIOMEMBRANES;BIORHEOLOGY;BIOSENS BIOELECTRON;BIOTECHNOL BIOENG;BRIT J PHARMACOL;CARDIOVASC RES;CARDIOVASCULAR DIS;CARTILAGE;CIRC RES;CIRCULATION;CURR BIOL;CURR OPIN CARDIOL;Curr Protoc Mol Biol;DEV CELL;EUR J PHARMACOL;FEBS LETT;GENE THER;GLOBAL STATUS REPORT ON VIOLENCE PREVENTION 2014;GUT;HAMOSTASEOLOGIE;HYPERTENSION;J AM COLL CARDIOL;J BIOL CHEM;J BIOMECH;J CLIN INVEST;J EXP MED;J INTERN MED;J TISSUE ENG REGENER;JAMA-J AM MED ASSOC;JOVE-J VIS EXP;LIFE SCI;MELANOMA RES;METHODS;MICROCIRCULATION;MICROVASC RES;MOL BIOTECHNOL;MOL CELL BIOL;NAT REV MOL CELL BIO;P NATL ACAD SCI USA;PFLUGERS ARCH EUROPE;PHILOS T R SOC B;PHYSIOL REV;PROC R SOC SER B-BIO;PROG BIOPHYS MOL BIO;SEMIN CELL DEV BIOL | Fleck, Oliver;Freke, Grace;Hernandez, Armando Del Rio;Homma, Takayuki;Kis, Zoltan;Krams, Rob;Lai, Zhangxing;Pedrigi, Ryan M;Rodin, Tania;Towhidi, Leila;Zafar, Asma | 2024-03-11
ER | Anishkin, A;Barnea, G;Bewick G. S.;Blaukat, A;Boon, R A;Buchmann, A;Buckwalter, J A;Carapuca, E;Caro, C G;Chachisvilis, M;Chatzizisis, Y S;Cheng, C;Chiu, J J;Davies, P F;Dengler, R;Duscher, D;Fedorchak, G R;Feletou, M;Fernandes, L;Frueh, J;Gomez-Martinez, M;Gossen, M;Gracia-Sancho, J;Gresch, O;Hock, F J;Jaalouk, D E;Kennard, M L;Kim, J A;Kinderlerer, A R;Kobilka, B K;Lechardeur, D;Majkut, S;Malek, A M;Mceachern, A E;Ng, C P;Nigro, P;Orr, A W;Pedrigi R. M.;Pedrigi, R M;Potter Huntington;Regoli, D;Roth, C M;Ruggiu A.;Samijo, S K;Schanstra, J P;Selvan, S R;Sen-Banerjee, S;Senbanerjee, S;Tarbell, J M;Urlinger, S;Volkers L.;White, C R;Who;Wirth, K;World Health Organization;Wragg, J W;Wu, W;Zarins, C K | DQ7MR | London, England | 4 | null | 6 | null | 27,404,994 | Fleck, Oliver;Freke, Grace;Hernandez, Armando Del Rio;Homma, Takayuki;Kis, Zoltan;Krams, Rob;Lai, Zhangxing;Pedrigi, Ryan M;Rodin, Tania;Towhidi, Leila;Zafar, Asma | SCI REP-UK | Cambridge, England;Kyoto, Japan;Lahore, Pakistan;London, England;Singapore, Singapore |
Balázsi, G;Bódi, Z;Charlebois, D A;Diao, J C;Nevozhay, D;Pál, C | 10.1021/acssynbio.5b00154 | null | 1155 16TH ST, NW, WASHINGTON, DC 20036 USA | 2t4149531y1f251u1jv4l2z5v5by6ey5333q | Efflux Pump Control Alters Synthetic Gene Circuit Function | Univ Texas MD Anderson Canc Ctr | null | Balázsi, G (corresponding author), SUNY Stony Brook, Dept Biomed Engn, Z-5281, Stony Brook, NY 11794 USA.;Balázsi, G (corresponding author), SUNY Stony Brook, Louis & Beatrice Laufer Ctr Phys & Quantitat Biol, Laufer Ctr 115C, Z-5252, Stony Brook, NY 11794 USA.;Balázsi, G (corresponding author), Univ Texas MD Anderson Canc Ctr, Dept Syst Biol, Unit 950, 7435 Fannin St, Houston, TX 77054 USA. | null | Balazsi, Gabor;Bodi, Zoltan;Charlebois, Daniel A;Diao, Junchen;Nevozhay, Dmitry;Pal, Csaba | Biochemical Research Methods | NIH Director's New Innovator Award Program [1DP2 OD006481-01]; Laufer Center for Physical AMP; Quantitative Biology; Lendiilet Program of the Hungarian Academy of Sciences; European Research Council [ERC-2007-StG]; University of Texas Graduate School of Biomedical Sciences at Houston; Ministry of Education and Science, Russian Federation [1326]; Natural Sciences and Engineering Research Council of Canada Postdoctoral Fellowship [PDF-453977-2014] | WOS | Balázsi, G | Far Eastern Fed Univ, Vladivostok, Russia;Hungarian Acad Sci, Szeged, Hungary;SUNY Stony Brook, Stony Brook, NY USA;Univ Texas MD Anderson Canc Ctr, Houston, TX USA | 5 | Alters;circuit;control;efflux;function;gene;Pump;synthetic | 3 | Balazsi, Gabor;Charlebois, Daniel | AMER CHEMICAL SOC | Far Eastern Fed Univ, Sch Biomed, 8 Sukhanova St, Vladivostok 690950, Russia;Hungarian Acad Sci, Biol Res Ctr, Inst Biochem, Temesvari Krt 62, H-6726 Szeged, Hungary;SUNY Stony Brook, Dept Biomed Engn, Z-5281, Stony Brook, NY 11794 USA;SUNY Stony Brook, Louis & Beatrice Laufer Ctr Phys & Quantitat Biol, Laufer Ctr 115C, Z-5252, Stony Brook, NY 11794 USA;Univ Texas MD Anderson Canc Ctr, Dept Syst Biol, Unit 950, 7435 Fannin St, Houston, TX 77054 USA;Univ Texas MD Anderson Canc Ctr, Dept Syst Biol, Unit 950, 7435 Fannin St, Houston, TX 77054 USA.; Balázsi, G (corresponding author), SUNY Stony Brook, Louis & Beatrice Laufer Ctr Phys & Quantitat Biol, Laufer Ctr 115C, Z-5252, Stony Brook, NY 11794 USA.; Balázsi, G (corresponding author), SUNY Stony Brook, Dept Biomed Engn, Z-5281, Stony Brook, NY 11794 USA | Article | Univ Texas MD Anderson Canc Ctr;SUNY Stony Brook | WASHINGTON | null | null | Far Eastern Fed Univ;Hungarian Acad Sci;SUNY Stony Brook;Univ Texas MD Anderson Canc Ctr | European Research Council;Laufer Center for Physical AMP;Lendiilet Program of the Hungarian Academy of Sciences;Ministry of Education and Science, Russian Federation;Natural Sciences and Engineering Research Council of Canada Postdoctoral Fellowship;NIH Director's New Innovator Award Program;Quantitative Biology;University of Texas Graduate School of Biomedical Sciences at Houston | Balázsi, G (corresponding author), Univ Texas MD Anderson Canc Ctr, Dept Syst Biol, Unit 950, 7435 Fannin St, Houston, TX 77054 USA.; Balázsi, G (corresponding author), SUNY Stony Brook, Louis & Beatrice Laufer Ctr Phys & Quantitat Biol, Laufer Ctr 115C, Z-5252, Stony Brook, NY 11794 USA.; Balázsi, G (corresponding author), SUNY Stony Brook, Dept Biomed Engn, Z-5281, Stony Brook, NY 11794 USA. | 631 | Balazsi, Gabor;Bodi, Zoltan;Charlebois, Daniel A;Diao, Junchen;Nevozhay, Dmitry;Pal, Csaba | 25 | 5 | 380,183,000,011 | European Research Council [ERC-2007-StG];Laufer Center for Physical AMP;Lendiilet Program of the Hungarian Academy of Sciences;Ministry of Education and Science, Russian Federation [1326];Natural Sciences and Engineering Research Council of Canada Postdoctoral Fellowship [PDF-453977-2014];NIH Director's New Innovator Award Program [1DP2 OD006481-01];Quantitative Biology;University of Texas Graduate School of Biomedical Sciences at Houston | Hungary;Russia;USA | ACS SYNTHETIC BIOLOGY | USA;USA.; | null | null | Univ Texas MD Anderson Canc Ctr, Dept Syst Biol, Unit 950, 7435 Fannin St, Houston, TX 77054 USA | 2161-5063 | Balázsi, G;Bódi, Z;Charlebois, D A;Diao, J C;Nevozhay, D;Pál, C | JUL | gabor.balazsi@stonybrook.edu | efflux Pump Control;synthetic gene circuit function | 6 | J | Biochemistry & Molecular Biology | ABC efflux pumps;ABC-TRANSPORTERS;altered dose-responses;another aspect;ATP-binding cassette (ABC) protein family;biofuels;BIOLOGY;Change;chemicals;controlled secretion;COUPLED CHEMICAL-REACTIONS;dose-responses;drive;DRUG-RESISTANCE;efflux;efflux pump;efflux Pump Control;efflux pump function;efflux pumps;expression;FEEDBACK;function;gene circuit dynamics;gene circuit function;Gene circuits;implicit feedback;inducer;intracellular inducer molecules;mathematical modeling;new biological systems;new circumstances;noise;one aspect;original gene circuits;overall;pdr5p;pharmaceuticals;poorly understood;predefined purposes;predictions;quantitative modeling;reduced regulator gene expression;Saccharomyces cerevisiae;SACCHAROMYCES-CEREVISIAE;SINGLE-CELL;stochastic simulation;synthetic biology aims;Synthetic gene circuit;synthetic gene circuit function;synthetic gene circuits;tetracycline family molecules;understanding synthetic gene circuit function;unexplained;used two synthetic gene circuits inducible;utility;will;yeast ABC pump (Pdr5p);YEAST-CELLS | Diao, J C | ABC-TRANSPORTERS;BIOLOGY;COUPLED CHEMICAL-REACTIONS;DRUG-RESISTANCE;efflux pump;EXPRESSION;FEEDBACK;NOISE;SACCHAROMYCES-CEREVISIAE;SINGLE-CELL;stochastic simulation;Synthetic gene circuit;YEAST-CELLS | 619 | [Diao, Junchen; Nevozhay, Dmitry; Balazsi, Gabor] Univ Texas MD Anderson Canc Ctr, Dept Syst Biol, Unit 950, 7435 Fannin St, Houston, TX 77054 USA. [Charlebois, Daniel A.; Balazsi, Gabor] SUNY Stony Brook, Louis & Beatrice Laufer Ctr Phys & Quantitat Biol, Laufer Ctr 115C, Z-5252, Stony Brook, NY 11794 USA. [Nevozhay, Dmitry] Far Eastern Fed Univ, Sch Biomed, 8 Sukhanova St, Vladivostok 690950, Russia. [Bodi, Zoltan; Pal, Csaba] Hungarian Acad Sci, Biol Res Ctr, Inst Biochem, Temesvari Krt 62, H-6726 Szeged, Hungary. [Balazsi, Gabor] SUNY Stony Brook, Dept Biomed Engn, Z-5281, Stony Brook, NY 11794 USA. | We thank W.-K. Huh for kindly sharing the PDR5::GFP fusion, and M. Bennett, M. Lorenz, G. May, T. F. Cooper and G. Peng for helpful discussions. This research was supported by the NIH Director's New Innovator Award Program (1DP2 OD006481-01) and by the Laufer Center for Physical & Quantitative Biology to GB; by the Lendiilet Program of the Hungarian Academy of Sciences, and the European Research Council (ERC-2007-StG) to CP; by the University of Texas Graduate School of Biomedical Sciences at Houston to JD; Program # 1326 of the Ministry of Education and Science, Russian Federation to DN; and by a Natural Sciences and Engineering Research Council of Canada Postdoctoral Fellowship [Grant no: PDF-453977-2014] to DC. | ABC efflux pumps;altered dose-responses;another aspect;ATP-binding cassette (ABC) protein family;biofuels;change;chemicals;controlled secretion;dose-responses;drive;efflux;efflux pump;efflux pump function;efflux pumps;expression;function;gene circuit dynamics;gene circuit function;gene circuits;implicit feedback;inducer;intracellular inducer molecules;mathematical modeling;new biological systems;new circumstances;one aspect;original gene circuits;overall;pdr5p;pharmaceuticals;poorly understood;predefined purposes;predictions;quantitative modeling;reduced regulator gene expression;Saccharomyces cerevisiae;synthetic biology aims;synthetic gene circuits;tetracycline family molecules;understanding synthetic gene circuit function;unexplained;used two synthetic gene circuits inducible;utility;will;yeast ABC pump (Pdr5p) | 10.1002/elps.200900244;10.1002/yea.320110408;10.1007/978-1-61779-086-7_5;10.1016/0021-9991(76)90041-3;10.1016/j.cell.2009.12.001;10.1016/j.cell.2014.02.039;10.1016/j.copbio.2014.01.001;10.1016/j.febslet.2009.10.071;10.1016/j.molcel.2006.11.003;10.1016/j.molcel.2014.04.022;10.1016/j.ymben.2015.11.005;10.1016/S0924-8579(03)00203-6;10.1021/bi100394j;10.1021/j100540a008;10.1021/sb300094q;10.1038/35002125;10.1038/35002131;10.1038/35014651;10.1038/msb.2011.21;10.1038/msb.2011.49;10.1038/msb4100081;10.1038/nature01546;10.1038/nature02026;10.1038/nature04785;10.1038/nature07389;10.1038/nature07616;10.1038/nature11516;10.1038/nbt.1536;10.1038/nbt.2510;10.1038/nbt1270;10.1038/ncb2085;10.1038/nchembio.1519;10.1038/nchembio.218;10.1038/ncomms2471;10.1038/ng869;10.1038/nrg2775;10.1038/nrg3227;10.1038/nrm2698;10.1073/pnas.0608451104;10.1073/pnas.0736140100;10.1073/pnas.0809901106;10.1074/jbc.271.49.31543;10.1074/jbc.M806446200;10.1089/mdr.1998.4.143;10.1093/nar/gkq091;10.1103/PhysRevE.89.052708;10.1126/science.1070919;10.1126/science.1205527;10.1126/science.1207084;10.1371/journal.pbio.0020137;10.1371/journal.pcbi.1000257;10.1371/journal.pcbi.1003229;10.3389/fmicb.2012.00360;[10.1038/NMETH.2926, 10.1038/nmeth.2926] | Univ Texas MD Anderson Canc Ctr | Balázsi, G;Bódi, Z;Charlebois, D A;Diao, J C;Nevozhay, D;Pál, C | Diao, J C: Univ Texas MD Anderson Canc Ctr, Dept Syst Biol, Unit 950, 7435 Fannin St, Houston, TX 77054 USA | Charlebois, Daniel;Nevozhay, Dmitry | 1326;1DP2 OD006481-01;ERC-2007-StG;PDF-453977-2014 | 55 | null | USA | Far Eastern Fed Univ;Hungarian Acad Sci;SUNY Stony Brook;Univ Texas MD Anderson Canc Ctr | Diao, Junchen | Green Accepted | ABC-TRANSPORTERS;BIOLOGY;COUPLED CHEMICAL-REACTIONS;DRUG-RESISTANCE;EXPRESSION;FEEDBACK;NOISE;SACCHAROMYCES-CEREVISIAE;SINGLE-CELL;YEAST-CELLS | Diao, Junchen; Charlebois, Daniel A.; Nevozhay, Dmitry; Bodi, Zoltan; Pal, Csaba; Balazsi, Gabor; | null | Far Eastern Fed Univ, Sch Biomed, 8 Sukhanova St, Vladivostok 690950, Russia;Hungarian Acad Sci, Biol Res Ctr, Inst Biochem, Temesvari Krt 62, H-6726 Szeged, Hungary;SUNY Stony Brook, Dept Biomed Engn, Z-5281, Stony Brook, NY 11794 USA;SUNY Stony Brook, Louis & Beatrice Laufer Ctr Phys & Quantitat Biol, Laufer Ctr 115C, Z-5252, Stony Brook, NY 11794 USA;Univ Texas MD Anderson Canc Ctr, Dept Syst Biol, Unit 950, 7435 Fannin St, Houston, TX 77054 USA | Far Eastern Fed Univ, Sch Biomed, 8 Sukhanova St, Vladivostok 690950, Russia;Hungarian Acad Sci, Biol Res Ctr, Inst Biochem, Temesvari Krt 62, H-6726 Szeged, Hungary;SUNY Stony Brook, Dept Biomed Engn, Z-5281, Stony Brook, NY 11794 USA;SUNY Stony Brook, Louis & Beatrice Laufer Ctr Phys & Quantitat Biol, Laufer Ctr 115C, Z-5252, Stony Brook, NY 11794 USA;Univ Texas MD Anderson Canc Ctr, Dept Syst Biol, Unit 950, 7435 Fannin St, Houston, TX 77054 USA | null | efflux pump;feedback;stochastic simulation;Synthetic gene circuit | 7 | 1976;1977;1995;1996;1998;2000;2001;2002;2003;2004;2006;2007;2008;2009;2010;2011;2012;2013;2014;2016 | 13 | SUNY Stony Brook, Dept Biomed Engn, Z-5281, Stony Brook, NY 11794 USA;SUNY Stony Brook, Louis & Beatrice Laufer Ctr Phys & Quantitat Biol, Laufer Ctr 115C, Z-5252, Stony Brook, NY 11794 USA;Univ Texas MD Anderson Canc Ctr, Dept Syst Biol, Unit 950, 7435 Fannin St, Houston, TX 77054 USA | ACS Synth. Biol. | Balazsi, Gabor | AMER CHEMICAL SOC | (ABC);(Pdr5p);,;a;ABC;achieve;addition;aims;also;alter;altered;an;and;another;are;as;aspect;ATP-binding;attributed;be;biofuels;biological;biology;by;can;cassette;cerevisiae;change;chemicals;circuit;circuits;circumstances;control;controlled;could;demonstrate;design;dose-responses;drive;dynamics;efflux;experimentally;explain;expression;family;feedback;for;from;fully;function;gene;here;highlight;how;however;implicit;in;indicated;inducer;inducible;intracellular;introduce;mathematical;modeling;molecules;new;of;one;or;original;other;out;overall;pdr5p;pharmaceuticals;poorly;predefined;predictions;protein;pump;pumping;pumps;purposes;quantitative;reduced;regulate;regulating;regulator;remained;Saccharomyces;secretion;substantially;such;synthetic;systems;tetracycline;that;the;these;this;to;two;understanding;understood;unexplained;used;utility;validated;ways;we;were;while;will;yeast | SUNY Stony Brook;Univ Texas MD Anderson Canc Ctr | Synthetic biology aims to design new biological systems for predefined purposes, such as the controlled secretion of biofuels, pharmaceuticals, or other chemicals. Synthetic gene circuits regulating an efflux pump from the ATP-binding cassette (ABC) protein family could achieve this. However, ABC efflux pumps can also drive out intracellular inducer molecules that control the gene circuits. This will introduce an implicit feedback that could alter gene circuit function in ways that are poorly understood. Here, we used two synthetic gene circuits inducible by tetracycline family molecules to regulate the expression of a yeast ABC pump (Pdr5p) that pumps out the inducer. Pdr5p altered the dose-responses of the original gene circuits substantially in Saccharomyces cerevisiae. While one aspect of the change could be attributed to the efflux pumping function of Pdr5p, another aspect remained unexplained. Quantitative modeling indicated that reduced regulator gene expression in addition to efflux pump function could fully explain the altered dose-responses. These predictions were validated experimentally. Overall, we highlight how efflux pumps can alter gene circuit dynamics and demonstrate the utility of mathematical modeling in understanding synthetic gene circuit function in new circumstances. | D-7251-2017;R-8264-2016 | ABC TRANSPORTER;BIOLOGY;COUPLED CHEMICAL-REACTIONS;DRUG-RESISTANCE;EXPRESSION;FEEDBACK;NOISE;SACCHAROMYCES-CEREVISIAE;SINGLE-CELL;YEAST-CELLS | 0 | null | efflux pump;feedback;stochastic simulation;Synthetic gene circuit | 13 | SACCHAROMYCES-CEREVISIAE;ABC TRANSPORTER;BIOLOGY;COUPLED CHEMICAL-REACTIONS;DRUG-RESISTANCE;EFFLUX PUMPS;EXPRESSION;FEEDBACK;NOISE;SINGLE-CELL;stochastic simulation;synthetic gene circuits;YEAST-CELLS | WOS:000380183000011 | Far Eastern Fed Univ, Vladivostok, Russia;Hungarian Acad Sci, Szeged, Hungary;SUNY Stony Brook, Stony Brook, NY USA;Univ Texas MD Anderson Canc Ctr, Houston, TX USA | Hungary;Russia;USA | 2,016 | null | 0000-0001-7426-1789;0000-0002-6865-5818 | null | null | English | null | ACS SYNTH BIOL;BIOCHEMISTRY-US;CELL;CURR OPIN BIOTECH;ELECTROPHORESIS;FEBS LETT;FRONT MICROBIOL;INT J ANTIMICROB AG;J BIOL CHEM;J COMPUT PHYS;J MOL MICROB BIOTECH;J PHYS CHEM-US;METAB ENG;METHODS MOL BIOL;MICROB DRUG RESIST;MOL CELL;MOL SYST BIOL;NAT BIOTECHNOL;NAT CELL BIOL;NAT CHEM BIOL;NAT COMMUN;NAT GENET;NAT METHODS;NAT REV GENET;NAT REV MOL CELL BIO;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PHYS REV E;PLOS BIOL;PLOS COMPUT BIOL;SCIENCE;YEAST | Balazsi, Gabor;Bodi, Zoltan;Charlebois, Daniel A;Diao, Junchen;Nevozhay, Dmitry;Pal, Csaba | 2024-03-11
ER | Airoldi, E M;Ananthaswamy, N;Becskei, A;Blake, W J;Bleris, L;Boyarskiy, S;Brophy, J A N;Charlebois, D A;Dublanche, Y;Dunlop, M J;Eldakak, A;Ellis, T;Elowitz, M B;Fraser, H B;Garcia-Bernardo, J;Gardner, T S;Gietz, R D;Gillespie, D T;Harrison, M E;Huh, W K;Ino, K;Khalil, A S;Klumpp, S;Kolaczkowski, M;Lage, H;Levy, S;Lu, P;Moon, T S;Murphy, K F;Nandagopal, N;Nevozhay, D;Newman, J R S;Nielsen, J;Nissim, L;Ozbudak, E M;Purnick, P E M;Rogers, B;Sauna, Z E;Simpson, M L;Siuti, P;Slusarczyk, A L;Stephanopoulos, G;Stricker, J;Tan, C;Tigges, M;Way, J C;Xie, Z | DR8XZ | Houston, TX USA.;Stony Brook, NY USA;Stony Brook, NY USA. | 16 | null | 4 | null | 27,111,147 | Balazsi, Gabor;Bodi, Zoltan;Charlebois, Daniel A;Diao, Junchen;Nevozhay, Dmitry;Pal, Csaba | ACS SYNTH BIOL | Houston, TX USA;Stony Brook, NY USA;Szeged, Hungary;Vladivostok, Russia |
Aycilar-Kucukgoze, I;Bovenberg, R A L;Gorochowski, T E;Ignatova, Z;Roubos, J A | 10.1021/acssynbio.6b00040 | null | 1155 16TH ST, NW, WASHINGTON, DC 20036 USA | 285k2r4f154l1o81m2cl2w2e580183h3y5u3s | A Minimal Model of Ribosome Allocation Dynamics Captures Trade-offs in Expression between Endogenous and Synthetic Genes | DSM Biotechnol Ctr | null | Gorochowski, TE (corresponding author), DSM Biotechnol Ctr, POB 1, NL-2600 MA Delft, Netherlands.;Gorochowski, TE (corresponding author), Univ Bristol, BrisSynBio, Life Sci Bldg,Tyndall Ave, Bristol BS8 1TQ, Avon, England. | null | Aycilar-Kucukgoze, Irem;Bovenberg, Roel A L;Gorochowski, Thomas E;Ignatova, Zoya;Roubos, Johannes A | Biochemical Research Methods | European Commission [289384]; BrisSynBio; BBSRC/EPSRC Synthetic Biology Research Centre [BB/L01386X/1]; Biotechnology and Biological Sciences Research Council [BB/L01386X/1] Funding Source: researchfish; BBSRC [BB/L01386X/1] Funding Source: UKRI | WOS | Gorochowski, T E | DSM Biotechnol Ctr, Delft, Netherlands;Univ Bristol, Avon, England;Univ Groningen, Groningen, Netherlands;Univ Hamburg, Hamburg, Germany;Univ Potsdam, Potsdam, Germany | 5 | a;Allocation;and;between;Captures;dynamics;Endogenous;expression;genes;in;Minimal;model;of;Ribosome;synthetic;Trade-offs | 3 | Avcilar Kucukgoze, Irem;Gorochowski, Thomas;Ignatova, Zoya | AMER CHEMICAL SOC | DSM Biotechnol Ctr, POB 1, NL-2600 MA Delft, Netherlands;DSM Biotechnol Ctr, POB 1, NL-2600 MA Delft, Netherlands.; Gorochowski, TE (corresponding author), Univ Bristol, BrisSynBio, Life Sci Bldg,Tyndall Ave, Bristol BS8 1TQ, Avon, England;Univ Bristol, BrisSynBio, Life Sci Bldg,Tyndall Ave, Bristol BS8 1TQ, Avon, England;Univ Groningen, Groningen Biomol Sci & Biotechnol Inst, Synthet Biol & Cell Engn, NL-9747 AG Groningen, Netherlands;Univ Hamburg, Dept Chem, Biochem & Mol Biol, D-20146 Hamburg, Germany;Univ Potsdam, Inst Biochem & Biol, Biochem, D-14476 Potsdam, Germany | Article | DSM Biotechnol Ctr;Univ Bristol | WASHINGTON | null | null | DSM Biotechnol Ctr;Univ Bristol;Univ Groningen;Univ Hamburg;Univ Potsdam | BBSRC;BBSRC/EPSRC Synthetic Biology Research Centre;Biotechnology and Biological Sciences Research Council;BrisSynBio;European Commission | Gorochowski, TE (corresponding author), DSM Biotechnol Ctr, POB 1, NL-2600 MA Delft, Netherlands.; Gorochowski, TE (corresponding author), Univ Bristol, BrisSynBio, Life Sci Bldg,Tyndall Ave, Bristol BS8 1TQ, Avon, England. | 720 | Aycilar-Kucukgoze, Irem;Bovenberg, Roel A L;Gorochowski, Thomas E;Ignatova, Zoya;Roubos, Johannes A | 18 | 5 | 380,183,000,020 | BBSRC [BB/L01386X/1] Funding Source: UKRI;BBSRC/EPSRC Synthetic Biology Research Centre [BB/L01386X/1];Biotechnology and Biological Sciences Research Council [BB/L01386X/1] Funding Source: researchfish;BrisSynBio;European Commission [289384] | Germany;Netherlands;UK | ACS SYNTHETIC BIOLOGY | Netherlands;UK | null | null | DSM Biotechnol Ctr, POB 1, NL-2600 MA Delft, Netherlands | 2161-5063 | Aycilar-Kucukgoze, I;Bovenberg, R A L;Gorochowski, T E;Ignatova, Z;Roubos, J A | JUL | thomas.gorochowski@bristol.ac.uk | expression;Minimal Model;Ribosome Allocation Dynamics Captures Trade-offs;Synthetic Genes | 5 | J | Biochemistry & Molecular Biology | additional ambient stress;burden;cell;cell physiology;cells;cellular growth;cellular resources;CIRCUITS;CODON USAGE;competition;CONSEQUENCES;considered;covering transcript abundance;demands;efficient heterologous expression;elongation time;ENDOGENOUS GENES;environmental stress;ESCHERICHIA-COLI;executing orthogonal genetic circuits;exposure;expression;finite set;genome;growth;guiding principles;host chassis;indirect interactions;intriguingly;largest proportion;maintenance;match experimental shifts;Minimal Model;model-predicted changes;optimization;parameters;places;processes;protein biosynthesis;protein synthesis resources;protein translation;PROTEIN-SYNTHESIS;redistribution;resource allocation;resources;responses;results;ribosome allocation;ribosome allocation dynamics;Ribosome Allocation Dynamics Captures Trade-offs;shared translational resources;simple model;SURVIVAL;synthetic;synthetic biology;synthetic circuits;Synthetic gene expression;synthetic genes;synthetic protein expression rate;systems biology;three key variables;tractable nature;transcript levels;translation;translation initiation rate;translation times;versatile tool | Gorochowski, T E | CIRCUITS;CODON USAGE;CONSEQUENCES;ESCHERICHIA-COLI;GENOME;GROWTH;OPTIMIZATION;protein biosynthesis;PROTEIN-SYNTHESIS;RESPONSES;Synthetic biology;systems biology;TRANSLATION | 710 | [Gorochowski, Thomas E.; Bovenberg, Roel A. L.; Roubos, Johannes A.] DSM Biotechnol Ctr, POB 1, NL-2600 MA Delft, Netherlands. [Gorochowski, Thomas E.] Univ Bristol, BrisSynBio, Life Sci Bldg,Tyndall Ave, Bristol BS8 1TQ, Avon, England. [Aycilar-Kucukgoze, Irem; Ignatova, Zoya] Univ Potsdam, Inst Biochem & Biol, Biochem, D-14476 Potsdam, Germany. [Bovenberg, Roel A. L.] Univ Groningen, Groningen Biomol Sci & Biotechnol Inst, Synthet Biol & Cell Engn, NL-9747 AG Groningen, Netherlands. [Ignatova, Zoya] Univ Hamburg, Dept Chem, Biochem & Mol Biol, D-20146 Hamburg, Germany. | All authors were supported by European Commission-funded Marie-Curie Actions Initial Training Network for Integrated Cellular Homeostasis (NICHE) Project 289384. T.E.G. was additionally supported by BrisSynBio, a BBSRC/EPSRC Synthetic Biology Research Centre (BB/L01386X/1). | additional ambient stress;burden;cell;cell physiology;cells;cellular growth;cellular resources;competition;considered;covering transcript abundance;demands;efficient heterologous expression;elongation time;endogenous genes;environmental stress;executing orthogonal genetic circuits;exposure;finite set;guiding principles;host chassis;indirect interactions;intriguingly;largest proportion;maintenance;match experimental shifts;minimal model;model-predicted changes;parameters;places;processes;protein synthesis resources;protein translation;redistribution;resource allocation;resources;results;ribosome allocation;ribosome allocation dynamics;shared translational resources;simple model;survival;synthetic;synthetic biology;synthetic circuits;synthetic gene expression;synthetic protein expression rate;three key variables;tractable nature;transcript levels;translation;translation initiation rate;translation times;versatile tool | 10.1002/(SICI)1097-0290(19991020)65:2<151::AID-BIT4>3.0.CO;2-V;10.1006/jmbi.1993.1319;10.1007/978-88-470-0784-0_3];10.1007/s10955-011-0183-1;10.1016/0958-1669(95)80082-4;10.1016/j.bpj.2013.04.049;10.1016/j.bpj.2013.12.010;10.1016/j.bpj.2015.06.034;10.1016/j.cell.2014.02.033;10.1016/j.jmb.2008.06.068;10.1016/S0168-1656(00)00365-5;10.1016/S0958-1669(96)80051-6;10.1021/sb4001245;10.1038/msb.2011.94;10.1038/msb.2013.32;10.1038/nature08753;10.1038/nature10965;10.1038/nbt1172;10.1038/nrg2398;10.1038/nrg2899;10.1038/nrm1618;10.1073/pnas.0503858102;10.1073/pnas.0802190105;10.1073/pnas.1416533112;10.1093/bioinformatics/bts185;10.1093/gbe/evt174;10.1093/nar/gkt602;10.1093/nar/gkv1280;10.1093/nar/gkv199;10.1103/PhysRevLett.108.018102;10.1126/science.1170160;10.1126/science.1192588;10.1126/science.1241934;10.1128/JB.01990-07;10.1128/jb.177.6.1497-1504.1995;10.1128/JB.180.17.4704-4710.1998;10.1146/annurev.micro.61.080706.093440;10.1186/1475-2859-8-31;10.1371/journal.pcbi.1002127;10.1371/journal.pgen.1004392;10.1371/journal.pone.0127039;10.1385/MB:34:3:355;10.15252/msb.20145697;10.15252/msb.20156178;[10.1038/nmeth.2403, 10.1038/NMETH.2403];[10.1038/NMETH.2404, 10.1038/nmeth.2404];[10.1038/NMETH.2926, 10.1038/nmeth.2926];[10.1038/NMETH.3339, 10.1038/nmeth.3339] | DSM Biotechnol Ctr | Aycilar-Kucukgoze, I;Bovenberg, R A L;Gorochowski, T E;Ignatova, Z;Roubos, J A | Gorochowski, T E: DSM Biotechnol Ctr, POB 1, NL-2600 MA Delft, Netherlands | Gorochowski, Thomas | 289384;BB/L01386X/1 | 51 | null | Netherlands | DSM Biotechnol Ctr;Univ Bristol;Univ Groningen;Univ Hamburg;Univ Potsdam | Gorochowski, Thomas E | Green Published, hybrid | CIRCUITS;CODON USAGE;CONSEQUENCES;ESCHERICHIA-COLI;GENOME;GROWTH;OPTIMIZATION;PROTEIN-SYNTHESIS;RESPONSES;TRANSLATION | Gorochowski, Thomas E.; Aycilar-Kucukgoze, Irem; Bovenberg, Roel A. L.; Roubos, Johannes A.; Ignatova, Zoya; | null | DSM Biotechnol Ctr, POB 1, NL-2600 MA Delft, Netherlands;Univ Bristol, BrisSynBio, Life Sci Bldg,Tyndall Ave, Bristol BS8 1TQ, Avon, England;Univ Groningen, Groningen Biomol Sci & Biotechnol Inst, Synthet Biol & Cell Engn, NL-9747 AG Groningen, Netherlands;Univ Hamburg, Dept Chem, Biochem & Mol Biol, D-20146 Hamburg, Germany;Univ Potsdam, Inst Biochem & Biol, Biochem, D-14476 Potsdam, Germany | DSM Biotechnol Ctr, POB 1, NL-2600 MA Delft, Netherlands;Univ Bristol, BrisSynBio, Life Sci Bldg,Tyndall Ave, Bristol BS8 1TQ, Avon, England;Univ Groningen, Groningen Biomol Sci & Biotechnol Inst, Synthet Biol & Cell Engn, NL-9747 AG Groningen, Netherlands;Univ Hamburg, Dept Chem, Biochem & Mol Biol, D-20146 Hamburg, Germany;Univ Potsdam, Inst Biochem & Biol, Biochem, D-14476 Potsdam, Germany | null | protein biosynthesis;Synthetic biology;systems biology;translation | 7 | 1925;1993;1995;1996;1998;1999;2001;2004;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016 | 79 | DSM Biotechnol Ctr, POB 1, NL-2600 MA Delft, Netherlands;Univ Bristol, BrisSynBio, Life Sci Bldg,Tyndall Ave, Bristol BS8 1TQ, Avon, England | ACS Synth. Biol. | Ignatova, Zoya | AMER CHEMICAL SOC | ,;a;able;abundance;accurately;across;additional;after;allocation;also;ambient;among;and;arise;be;because;between;biology;burden;can;captures;capturing;cell;cells;cellular;changes;chassis;circuits;closely;competition;considered;construct;contain;contains;covering;critically;dedicated;demands;demonstrate;design;develop;distributed;dynamics;efficient;elongation;endogenous;ensure;environmental;executing;experimental;exploits;exploring;exposure;expressing;expression;faced;faithfully;finite;for;further;gene;genes;genetic;growth;guiding;here;heterologous;host;in;indirect;infer;initiation;interactions;intriguingly;is;it;key;largest;levels;maintenance;makes;many;match;minimal;model;model-predicted;must;nature;of;often;on;Orthogonal;our;parameters;physiology;places;principles;processes;proportion;protein;rarely;rate;redistribution;related;required;resource;resources;results;Ribosome;set;shared;shifts;show;simple;stress;survival;synthesis;synthetic;that;the;their;them;these;this;three;time;times;to;together;tool;tractable;transcript;translation;translational;variables;versatile;we;when;with;yet | DSM Biotechnol Ctr;Univ Bristol | Cells contain a finite set of resources that must be distributed across many processes to ensure survival. Among them, the largest proportion of cellular resources is dedicated to protein translation. Synthetic biology often exploits these resources in executing orthogonal genetic circuits, yet the burden this places on the cell is rarely considered. Here, we develop a minimal model of ribosome allocation dynamics capturing the demands on translation when expressing a synthetic construct together with endogenous genes required for the maintenance of cell physiology. Critically, it contains three key variables related to design parameters of the synthetic construct covering transcript abundance, translation initiation rate, and elongation time. We show that model-predicted changes in ribosome allocation closely match experimental shifts in synthetic protein expression rate and cellular growth. Intriguingly, the model is also able to accurately infer transcript levels and translation times after further exposure to additional ambient stress. Our results demonstrate that a simple model of resource allocation faithfully captures the redistribution of protein synthesis resources when faced with the burden of synthetic gene expression and environmental stress. The tractable nature of the model makes it a versatile tool for exploring the guiding principles of efficient heterologous expression and the indirect interactions that can arise between synthetic circuits and their host chassis because of competition for shared translational resources. | JPA-4825-2023 | CIRCUITS;CODON USAGE;CONSEQUENCES;ESCHERICHIA-COLI;GENOME;GROWTH;OPTIMIZATION;PROTEIN-SYNTHESIS;RESPONSES;TRANSLATION | 0 | null | protein biosynthesis;Synthetic biology;systems biology;translation | 11 | ESCHERICHIA-COLI;CIRCUITS;CODON USAGE;CONSEQUENCES;GENOME;GROWTH;OPTIMIZATION;protein biosynthesis;PROTEIN-SYNTHESIS;RESPONSES;Synthetic biology;systems biology;TRANSLATION | WOS:000380183000020 | DSM Biotechnol Ctr, Delft, Netherlands;Univ Bristol, Avon, England;Univ Groningen, Groningen, Netherlands;Univ Hamburg, Hamburg, Germany;Univ Potsdam, Potsdam, Germany | Germany;Netherlands;UK | 2,016 | null | 0000-0002-9478-8825;0000-0003-1702-786X;0009-0006-7615-2969 | null | null | English | null | ACS SYNTH BIOL;ANNU REV MICROBIOL;BIOINFORMATICS;BIOPHYS J;BIOTECHNOL BIOENG;CELL;CURR OPIN BIOTECH;ESCHERICHIA COLI SAL;GENOME BIOL EVOL;J BACTERIOL;J BIOTECHNOL;J MOL BIOL;J STAT PHYS;MICROB CELL FACT;MOL BIOTECHNOL;MOL SYST BIOL;NAT BIOTECHNOL;NAT METHODS;NAT REV GENET;NAT REV MOL CELL BIO;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PHYS REV LETT;PHYSL STRESS RESPONS;PLOS COMPUT BIOL;PLOS GENET;PLOS ONE;SCIENCE;SCIENTIFICA ACTA;Z PHYS | Aycilar-Kucukgoze, Irem;Bovenberg, Roel A L;Gorochowski, Thomas E;Ignatova, Zoya;Roubos, Johannes A | 2024-03-11
ER | [Anonymous];Basan, M;Bentele, K;Bratsun, D;Bremer H.;Brophy, J A N;Carbonell-Ballestero, M;Carpousis, A J;Ceroni, F;Chevance, F F V;Cookson, N A;Danino, T;Dong, H J;Enfors, S O;Farewell, A;Geertsma, E R;Goodman, D B;Gorochowski, T E;Gunasekera, T S;Gyorgy, A;Hess, A K;Holcik, M;Hui, S;Kane, J F;Kensy, F;Kudla, G;Lara, A R;Li, G W;Lsing E.;López-Maury, L;Marzuoli A.;Mather, W H;Mitarai, N;Mutalik, V K;Nuñez, P A;Plotkin, J B;Pédelacq, J D;Reuveni, S;Rondelez, Y;Schweder, T;Scott, M;Vind, J;Weickert, M J;Weisse, A Y;Wohlgemuth, S E;Zavala, E;Zia, R K P;Zur, H | DR8XZ | Avon, England;Delft, Netherlands. | 90 | null | 5 | null | 27,112,032 | Aycilar-Kucukgoze, Irem;Bovenberg, Roel A L;Gorochowski, Thomas E;Ignatova, Zoya;Roubos, Johannes A | ACS SYNTH BIOL | Avon, England;Delft, Netherlands;Groningen, Netherlands;Hamburg, Germany;Potsdam, Germany |
Cleto, S;Jusiak, B;Lu, T K;Perez-Piñera, P | 10.1016/j.tibtech.2015.12.014 | null | 84 THEOBALDS RD, LONDON WC1X 8RR, ENGLAND | s5f3l3e3y4e354v633e5q3u6a6h675nu1s6s37 | Engineering Synthetic Gene Circuits in Living Cells with CRISPR Technology | MIT | null | Lu, TK (corresponding author), MIT, Dept Elect Engn & Comp Sci, Cambridge, MA 02139 USA.;Lu, TK (corresponding author), MIT, Elect Res Lab, Synthet Biol Ctr, Dept Biol Engn, Cambridge, MA 02139 USA. | null | Cleto, Sara;Jusiak, Barbara;Lu, Timothy K;Perez-Pinera, Pablo | Biotechnology & Applied Microbiology | null | WOS | Lu, T K | MIT, Cambridge, MA USA;Univ Illinois, Urbana, IL USA | 34 | Cells;circuits;CRISPR;engineering;gene;in;living;synthetic;technology;with | 1 | Cleto, Sara;Perez-Pinera, Pablo | ELSEVIER SCIENCE LONDON | MIT, Dept Elect Engn & Comp Sci, Cambridge, MA 02139 USA;MIT, Elect Res Lab, Synthet Biol Ctr, Dept Biol Engn, Cambridge, MA 02139 USA;MIT, Elect Res Lab, Synthet Biol Ctr, Dept Biol Engn, Cambridge, MA 02139 USA.; Lu, TK (corresponding author), MIT, Dept Elect Engn & Comp Sci, Cambridge, MA 02139 USA;Univ Illinois, Dept Bioengn, Urbana, IL USA | Review | MIT | LONDON | null | null | Elect Res Lab;MIT;Univ Illinois | null | Lu, TK (corresponding author), MIT, Elect Res Lab, Synthet Biol Ctr, Dept Biol Engn, Cambridge, MA 02139 USA.; Lu, TK (corresponding author), MIT, Dept Elect Engn & Comp Sci, Cambridge, MA 02139 USA. | 547 | Cleto, Sara;Jusiak, Barbara;Lu, Timothy K;Perez-Pinera, Pablo | 88 | 3 | 378,961,700,006 | null | USA | TRENDS IN BIOTECHNOLOGY | USA;USA.; | null | null | MIT, Elect Res Lab, Synthet Biol Ctr, Dept Biol Engn, Cambridge, MA 02139 USA | 0167-7799 | Cleto, S;Jusiak, B;Lu, T K;Perez-Piñera, P | JUL | tim@lugroup.org | CRISPR technology;engineering Synthetic Gene Circuits;living cells | 4 | J | Biotechnology & Applied Microbiology | ability;activation;basic research purposes;biomedical applications;CAS SYSTEMS;COMBINATORIAL GENETICS;control cell behavior;CRISPR;CRISPR technology;CRISPR-mediated gene regulation;designing synthetic TFs;effective synthetic transcription factors (TFs);efficient gene circuits;ENDOGENOUS GENES;engineering synthetic gene circuits;FINGER TRANSCRIPTION FACTORS;future;heterologous host cells;interspaced short palindromic repeat (CRISPR) system;living cells;logic gates;MAMMALIAN-CELLS;offers unprecedented ease;one;potential;programmable;prokaryotic;recent advances;REPRESSOR PROTEINS;RNA;sequence-specific;synthetic biology;synthetic gene circuits;TARGETING DNA;transcriptional regulation;transcriptional regulatory devices | Jusiak, B | ACTIVATION;CAS SYSTEMS;COMBINATORIAL GENETICS;ENDOGENOUS GENES;FINGER TRANSCRIPTION FACTORS;logic gates;MAMMALIAN-CELLS;REPRESSOR PROTEINS;RNA;TARGETING DNA | 535 | [Jusiak, Barbara; Cleto, Sara; Lu, Timothy K.] MIT, Elect Res Lab, Synthet Biol Ctr, Dept Biol Engn, Cambridge, MA 02139 USA. [Jusiak, Barbara; Cleto, Sara; Lu, Timothy K.] MIT, Dept Elect Engn & Comp Sci, Cambridge, MA 02139 USA. [Perez-Pinera, Pablo] Univ Illinois, Dept Bioengn, Urbana, IL USA. | null | ability;basic research purposes;biomedical applications;control cell behavior;CRISPR;CRISPR-mediated gene regulation;designing synthetic TFs;effective synthetic transcription factors (TFs);efficient gene circuits;future;heterologous host cells;interspaced short palindromic repeat (CRISPR) system;offers unprecedented ease;one;potential;programmable;prokaryotic;recent advances;sequence-specific;synthetic biology;synthetic gene circuits;transcriptional regulation;transcriptional regulatory devices | 10.1016/j.cbpa.2013.10.006;10.1016/j.cell.2007.05.045;10.1016/j.cell.2009.04.048;10.1016/j.cell.2012.05.045;10.1016/j.cell.2013.02.022;10.1016/j.cell.2013.06.044;10.1016/j.cell.2014.05.010;10.1016/j.cell.2014.09.029;10.1016/j.cell.2014.09.039;10.1016/j.cell.2014.11.052;10.1016/j.cels.2015.06.001;10.1016/j.chembiol.2014.12.011;10.1016/j.gene.2011.06.015;10.1016/j.molcel.2014.04.022;10.1016/j.pbi.2010.04.010;10.1016/j.stemcr.2013.07.002;10.1016/j.ymben.2011.10.003;10.1021/ja3065667;10.1021/sb400081r;10.1021/sb400114p;10.1038/35002131;10.1038/cr.2013.122;10.1038/gt.2008.96;10.1038/nature02491;10.1038/nature03461;10.1038/nature03556;10.1038/nature07389;10.1038/nature08753;10.1038/nature09886;10.1038/nature11149;10.1038/nature11516;10.1038/nature12148;10.1038/nature12466;10.1038/nature13769;10.1038/nature14136;10.1038/nbt.1536;10.1038/nbt.1755;10.1038/nbt.1775;10.1038/nbt.2351;10.1038/nbt.2508;10.1038/nbt.2510;10.1038/nbt.2623;10.1038/nbt.2673;10.1038/nbt.2675;10.1038/nbt.2842;10.1038/nbt.3011;10.1038/nbt.3199;10.1038/nbt.3326;10.1038/nbt0202-135;10.1038/nchembio.1753;10.1038/ncomms1516;10.1038/ncomms5408;10.1038/ncomms6393;10.1038/nrg2775;10.1038/nrm3738;10.1073/pnas.040552697;10.1073/pnas.1400093111;10.1073/pnas.91.10.4509;10.1073/pnas.94.11.5525;10.1074/jbc.M005108200;10.1093/emboj/cdg619;10.1093/nar/gks142;10.1093/nar/gkt135;10.1093/nar/gkt520;10.1093/nar/gku749;10.1099/mic.0.023960-0;10.1111/jipb.12152;10.1126/science.1138140;10.1126/science.1165771;10.1126/science.1172005;10.1126/science.1225829;10.1126/science.1232033;10.1126/science.1256272;10.1186/gb-2003-4-10-231;10.1371/journal.pone.0033279;10.15252/msb.20145735;10.1534/genetics.110.120717;10.4161/rna.23764;[10.1038/nmeth.2184, 10.1038/NMETH.2184];[10.1038/nmeth.2598, 10.1038/NMETH.2598];[10.1038/nmeth.2600, 10.1038/NMETH.2600];[10.1038/NMETH.2681, 10.1038/nmeth.2681];[10.1038/NMETH.2926, 10.1038/nmeth.2926];[10.1038/NMETH.2969, 10.1038/nmeth.2969];[10.1038/NMETH.3312, 10.1038/nmeth.3312];[10.1038/NMETH.3433, 10.1038/nmeth.3433];[10.1146/annurev.bioeng-071811-150118, 10.1146/annurev-bioeng-071811-150118] | MIT | Cleto, S;Jusiak, B;Lu, T K;Perez-Piñera, P | Jusiak, B: MIT, Elect Res Lab, Synthet Biol Ctr, Dept Biol Engn, Cambridge, MA 02139 USA | Lu, Timothy K | null | 87 | null | USA | MIT;Univ Illinois | Jusiak, Barbara | Bronze | ACTIVATION;CAS SYSTEMS;COMBINATORIAL GENETICS;ENDOGENOUS GENES;FINGER TRANSCRIPTION FACTORS;LOGIC GATES;MAMMALIAN-CELLS;REPRESSOR PROTEINS;RNA;TARGETING DNA | Jusiak, Barbara; Cleto, Sara; Perez-Pinera, Pablo; Lu, Timothy K.; | null | MIT, Dept Elect Engn & Comp Sci, Cambridge, MA 02139 USA;MIT, Elect Res Lab, Synthet Biol Ctr, Dept Biol Engn, Cambridge, MA 02139 USA;Univ Illinois, Dept Bioengn, Urbana, IL USA | MIT, Dept Elect Engn & Comp Sci, Cambridge, MA 02139 USA;MIT, Elect Res Lab, Synthet Biol Ctr, Dept Biol Engn, Cambridge, MA 02139 USA;Univ Illinois, Dept Bioengn, Urbana, IL USA | 1879-3096 | null | 7 | 1994;1997;2000;2002;2003;2004;2005;2007;2008;2009;2010;2011;2012;2013;2014;2015 | 85 | MIT, Dept Elect Engn & Comp Sci, Cambridge, MA 02139 USA;MIT, Elect Res Lab, Synthet Biol Ctr, Dept Biol Engn, Cambridge, MA 02139 USA | Trends Biotechnol. | Lu, Timothy K | ELSEVIER SCIENCE LONDON | (CRISPR);(TFs);,;ability;advances;and;applications;availability;basic;be;behavior;biology;biomedical;both;build;can;cell;cells;circuits;clustered;complex;control;CRISPR;CRISPR-mediated;depends;designing;devices;discuss;ease;effective;efficient;factors;for;future;gene;goals;harnessed;heterologous;host;how;in;increasingly;interspaced;is;of;offer;offers;on;one;palindromic;potential;programmable;prokaryotic;purposes;recent;recently;regularly;regulation;regulatory;repeat;research;review;sequence-specific;short;synthetic;system;TFs;that;the;to;transcription;transcriptional;unprecedented;used;various;we | MIT | One of the goals of synthetic biology is to build regulatory circuits that control cell behavior, for both basic research purposes and biomedical applications. The ability to build transcriptional regulatory devices depends on the availability of programmable, sequence-specific, and effective synthetic transcription factors (TFs). The prokaryotic clustered regularly interspaced short palindromic repeat (CRISPR) system, recently harnessed for transcriptional regulation in various heterologous host cells, offers unprecedented ease in designing synthetic TFs. We review how CRISPR can be used to build synthetic gene circuits and discuss recent advances in CRISPR-mediated gene regulation that offer the potential to build increasingly complex, programmable, and efficient gene circuits in the future. | G-4267-2012 | ACTIVATION;CAS SYSTEMS;COMBINATORIAL GENETICS;ENDOGENOUS GENES;FINGER TRANSCRIPTION FACTORS;LOGIC GATES;MAMMALIAN-CELLS;REPRESSOR PROTEINS;RNA;TARGET DNA | 2 | null | null | 13 | ACTIVATION;CAS SYSTEMS;COMBINATORIAL GENETICS;ENDOGENOUS GENES;FINGER TRANSCRIPTION FACTORS;logic gates;MAMMALIAN-CELLS;REPRESSOR PROTEINS;RNA;TARGET DNA | WOS:000378961700006 | MIT, Cambridge, MA USA;Univ Illinois, Urbana, IL USA | USA | 2,016 | null | 0000-0002-9167-0004;0000-0003-1273-0142 | null | null | English | null | ACS SYNTH BIOL;ANNU REV BIOMED ENG;CELL;CELL RES;CELL SYST;CHEM BIOL;CURR OPIN CHEM BIOL;CURR OPIN PLANT BIOL;EMBO J;GENE;GENE THER;GENETICS;GENOME BIOL;J AM CHEM SOC;J BIOL CHEM;J INTEGR PLANT BIOL;METAB ENG;MICROBIOL-SGM;MOL CELL;MOL SYST BIOL;NAT BIOTECHNOL;NAT CHEM BIOL;NAT COMMUN;NAT METHODS;NAT REV GENET;NAT REV MOL CELL BIO;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PLOS ONE;RNA BIOL;SCIENCE;STEM CELL REP | Cleto, Sara;Jusiak, Barbara;Lu, Timothy K;Perez-Pinera, Pablo | 2024-03-11
ER | Ausländer, D;Ausländer, S;Bacchus, W;Barrangou, R;Basu, S;Beerli, R R;Bikard, D;Blount, B A;Bogdanove, A J;Boyle, P M;Brophy, J A N;Chavez, A;Cheng, A A;Cheng, A W;Christian, M;Citorik, R J;Daniel, R;Danino, T;Deans, T L;Deltcheva, E;Dicarlo, J E;Ellis, T;Esvelt, K M;Farzadfard, F;Friedland, A E;Fu, Y F;Gao, Y B;Gardner, T S;Gilbert, L A;Hilton, I B;Hsu, P D;Jiang, W Y;Jinek, M;Kabadi, A M;Khalil, A S;Kiani, S;Konermann, S;Lienert, F;Liu, C C;Liu, Q;Liu, Y C;Lohmueller, J J;Maeder, M L;Magnenat, L;Mali, P;Margolin, J F;Marraffini, L A;Mercer, A C;Miller, J C;Mimee, M;Mittler, G;Mojica, F J M;Moon, T S;Nielsen, A A;Nihongaki, Y;Nissim, L;O'Connell, M R;Orioli, A;Pattanayak, V;Perez-Pinera, P;Polstein, L R;Qi, L S;Sander, J D;Shah, S A;Shechner, D M;Siuti, P;Stricker, J;Tabor, J J;Tanenbaum, M E;Urnov, F D;Urrutia, R;Wang, B J;Wong, A S L;Ye, H F;You, L C;Zalatan, J G;Zhang, F;Zhang, Z H | DQ1LE | Cambridge, MA USA;Cambridge, MA USA. | 109 | null | 2 | null | 26,809,780 | Cleto, Sara;Jusiak, Barbara;Lu, Timothy K;Perez-Pinera, Pablo | TRENDS BIOTECHNOL | Cambridge, MA USA;Urbana, IL USA |
Beuron, F;Herdewijn, P;Holliger, P;Morris, E P;Peak-Chew, S Y;Taylor, A I | 10.1002/cbic.201600136 | null | POSTFACH 101161, 69451 WEINHEIM, GERMANY | 6g3s1o5v196c1w6t1ch59556r1s3m23315a6hs | Nanostructures from Synthetic Genetic Polymers | MRC | null | Taylor, AI (corresponding author), Concordia Univ, Dept Biol, Ctr Appl Synthet Biol, 7141 Rue Sherbrooke, Montreal, PQ H4B 1R6, Canada.;Taylor, AI; Holliger, P (corresponding author), MRC, Mol Biol Lab, Francis Crick Ave, Cambridge CB2 0QH, England. | null | Beuron, Fabienne;Herdewijn, Piet;Holliger, Philipp;Morris, Edward P;Peak-Chew, Sew-Yeu;Taylor, Alexander I | Biochemistry & Molecular Biology;Chemistry, Medicinal | Medical Research Council [U105178804]; European Science Foundation (ESF); Biotechnology and Biological Sciences Research Council [09-EuroSYNBIO-OP-013, INTENSIFY BB/M005623/1]; Cancer Research UK [C12209A16749]; MRC [MC_U105178804] Funding Source: UKRI; Cancer Research UK [16749] Funding Source: researchfish; Medical Research Council [MC_U105178804] Funding Source: researchfish | WOS | Holliger, P;Taylor, A I | Concordia Univ, Montreal PQ, Canada;Inst Canc Res, London, England;Katholieke Univ Leuven, Leuven, Belgium;MRC, Cambridge, England;Univ Evry, Evry, France | 17 | From;genetic;nanostructures;Polymers;synthetic | 4 | Herdewijn, Piet;Morris, Edward | WILEY-V C H VERLAG GMBH | Concordia Univ, Dept Biol, Ctr Appl Synthet Biol, 7141 Rue Sherbrooke, Montreal, PQ H4B 1R6, Canada;Inst Canc Res, Chester Beatty Labs, Div Struct Biol, 237 Fulham Rd, London SW3 6JB, England;Katholieke Univ Leuven, Rega Inst, Minderbroedersstr 10, B-3000 Leuven, Belgium;MRC, Mol Biol Lab, Francis Crick Ave, Cambridge CB2 0QH, England;P (corresponding author), MRC, Mol Biol Lab, Francis Crick Ave, Cambridge CB2 0QH, England.; Taylor, AI (corresponding author), Concordia Univ, Dept Biol, Ctr Appl Synthet Biol, 7141 Rue Sherbrooke, Montreal, PQ H4B 1R6, Canada;Univ Evry, Inst Syst & Synthet Biol, 5 Rue Henri Desbrueres, F-91030 Evry, France | Article | Concordia Univ;MRC | WEINHEIM | null | null | Concordia Univ;Inst Canc Res;Katholieke Univ Leuven;Mol Biol Lab;MRC;Univ Evry | Biotechnology and Biological Sciences Research Council;Cancer Research UK;European Science Foundation (ESF);Medical Research Council;MRC | Taylor, AI; Holliger, P (corresponding author), MRC, Mol Biol Lab, Francis Crick Ave, Cambridge CB2 0QH, England.; Taylor, AI (corresponding author), Concordia Univ, Dept Biol, Ctr Appl Synthet Biol, 7141 Rue Sherbrooke, Montreal, PQ H4B 1R6, Canada. | 1110 | Beuron, Fabienne;Herdewijn, Piet;Holliger, Philipp;Morris, Edward P;Peak-Chew, Sew-Yeu;Taylor, Alexander I | 51 | 5 | 379,156,400,009 | Biotechnology and Biological Sciences Research Council [09-EuroSYNBIO-OP-013, INTENSIFY BB/M005623/1];Cancer Research UK [16749] Funding Source: researchfish;Cancer Research UK [C12209A16749];European Science Foundation (ESF);Medical Research Council [MC_U105178804] Funding Source: researchfish;Medical Research Council [U105178804];MRC [MC_U105178804] Funding Source: UKRI | Belgium;Canada;France;UK | CHEMBIOCHEM | Canada;UK | null | null | MRC, Mol Biol Lab, Francis Crick Ave, Cambridge CB2 0QH, England | 1439-4227 | Beuron, F;Herdewijn, P;Holliger, P;Morris, E P;Peak-Chew, S Y;Taylor, A I | JUN 16 | alex.taylor@concordia.ca;ph1@mrc-lmb.cam.ac.uk | nanostructures;Synthetic Genetic Polymers | 6 | J | Biochemistry & Molecular Biology;Pharmacology & Pharmacy | 2-fluoroarabino nucleic acids (FANA);600kDa all-FANA octahedron;70kDa tetrahedra;alternative building blocks;assembly;CAGE;chemical biology;chemical scope;cyclohexene nucleic acids (CeNA);DELIVERY;DNA;DNA nanotechnology;electron microscopy;enhanced biostability;evolution;expanded range;four different XNA chemistries (2-fluro-2-deoxy-ribofuranose nucleic acid (2F-RNA);hexitol nucleic acids (HNA);implications;increasing complexity;materials;mixed designs;moderate chemical diversity;nano-objects;nanoscale objects;nanostructures;natural nucleic acids;nature;NUCLEIC-ACIDS;physicochemical properties;PNA;potential applications;programmable nanostructure assembly;results;RNA;scope;self-assembly;STRUCTURAL DNA NANOTECHNOLOGY;synthetic genetic polymers;SYSTEM;therapy;visualised;xeno nucleic acids (XNAs) | Taylor, A I | CAGE;chemical biology;DELIVERY;DNA nanotechnology;electron microscopy;EVOLUTION;NUCLEIC-ACIDS;PNA;RNA;self-assembly;STRUCTURAL DNA NANOTECHNOLOGY;SYSTEM;THERAPY;xeno nucleic acids (XNAs) | 1107 | [Taylor, Alexander I.; Peak-Chew, Sew-Yeu; Holliger, Philipp] MRC, Mol Biol Lab, Francis Crick Ave, Cambridge CB2 0QH, England. [Taylor, Alexander I.] Concordia Univ, Dept Biol, Ctr Appl Synthet Biol, 7141 Rue Sherbrooke, Montreal, PQ H4B 1R6, Canada. [Beuron, Fabienne; Morris, Edward P.] Inst Canc Res, Chester Beatty Labs, Div Struct Biol, 237 Fulham Rd, London SW3 6JB, England. [Herdewijn, Piet] Katholieke Univ Leuven, Rega Inst, Minderbroedersstr 10, B-3000 Leuven, Belgium. [Herdewijn, Piet] Univ Evry, Inst Syst & Synthet Biol, 5 Rue Henri Desbrueres, F-91030 Evry, France. | This work was supported by the Medical Research Council (program no. U105178804 to P.H.) and by grants from the European Science Foundation (ESF) and the Biotechnology and Biological Sciences Research Council (09-EuroSYNBIO-OP-013 and INTENSIFY BB/M005623/1 to A.I.T.) and Cancer Research UK (C12209A16749 to E.P.M.) We would like to thank Christos Savva, Xiao-Chen Bai, and Sjores Scheres (MRC Laboratory of Molecular Biology) and Richard Berry (University of Oxford) for useful discussions and advice. | 2-fluoroarabino nucleic acids (FANA);600kDa all-FANA octahedron;70kDa tetrahedra;alternative building blocks;assembly;chemical scope;cyclohexene nucleic acids (CeNA);DNA;electron microscopy;enhanced biostability;expanded range;four different XNA chemistries (2-fluro-2-deoxy-ribofuranose nucleic acid (2F-RNA);hexitol nucleic acids (HNA);implications;increasing complexity;materials;mixed designs;moderate chemical diversity;nano-objects;nanoscale objects;natural nucleic acids;nature;physicochemical properties;potential applications;programmable nanostructure assembly;results;RNA;scope;synthetic genetic polymers;visualised;xeno nucleic acids (XNAs) | 10.1002/ANGE.200603392;10.1002/anie.200603392;10.1002/anie.201500561;10.1002/anie.201507375;10.1002/cbdv.200900185;10.1016/0022-5193(82)90002-9;10.1016/j.cbpa.2010.08.002;10.1016/j.cbpa.2014.09.022;10.1016/j.cell.2012.12.024;10.1016/j.cell.2014.03.008;10.1016/j.chembiol.2014.07.008;10.1021/ar500076k;10.1021/ja505101a;10.1021/nl304147f;10.1021/nl502385k;10.1021/nl901265n;10.1021/nn1024658;10.1021/nn2005574;10.1021/nn3022662;10.1021/nn503513p;10.1038/am.2013.22;10.1038/nature02307;10.1038/nature04586;10.1038/nature13982;10.1038/nsmb.2815;10.1039/b402293a;10.1039/b917661f;10.1039/c2cc36358e;10.1039/c2cc37556g;10.1073/pnas.1120964109;10.1088/0953-8984/24/16/164203;10.1093/nar/gkq1270;10.1093/nar/gks672;10.1093/nar/gkt808;10.1093/nar/gku617;10.1093/nar/gkv1057;10.1093/nar/gkv1472;10.1126/science.1104686;10.1126/science.1214081;10.1126/science.1217622;10.1126/science.1225624;10.1126/science.1227268;10.1126/science.1260901;10.1126/science.289.5481.920;10.3390/molecules200917645;10.4161/1949095X.2014.992181;[10.1038/NCHEM.1241, 10.1038/nchem.1241];[10.1038/nnano.2011.187, 10.1038/NNANO.2011.187];[10.1038/nnano.2014.100, 10.1038/NNANO.2014.100];[10.1038/nnano.2014.58, 10.1038/NNANO.2014.58];[10.1038/NNANO.2015.180, 10.1038/nnano.2015.180] | MRC | Beuron, F;Herdewijn, P;Holliger, P;Morris, E P;Peak-Chew, S Y;Taylor, A I | Taylor, A I: MRC, Mol Biol Lab, Francis Crick Ave, Cambridge CB2 0QH, England | null | 09-EuroSYNBIO-OP-013;16749;C12209A16749;INTENSIFY BB/M005623/1;MC_U105178804;U105178804 | 54 | null | UK | Concordia Univ;Inst Canc Res;Katholieke Univ Leuven;MRC;Univ Evry | Taylor, Alexander I | Green Published, hybrid | CAGE;DELIVERY;EVOLUTION;NUCLEIC-ACIDS;PNA;RNA;STRUCTURAL DNA NANOTECHNOLOGY;SYSTEM;THERAPY | Taylor, Alexander I.; Beuron, Fabienne; Peak-Chew, Sew-Yeu; Morris, Edward P.; Herdewijn, Piet; Holliger, Philipp; | null | Concordia Univ, Dept Biol, Ctr Appl Synthet Biol, 7141 Rue Sherbrooke, Montreal, PQ H4B 1R6, Canada;Inst Canc Res, Chester Beatty Labs, Div Struct Biol, 237 Fulham Rd, London SW3 6JB, England;Katholieke Univ Leuven, Rega Inst, Minderbroedersstr 10, B-3000 Leuven, Belgium;MRC, Mol Biol Lab, Francis Crick Ave, Cambridge CB2 0QH, England;Univ Evry, Inst Syst & Synthet Biol, 5 Rue Henri Desbrueres, F-91030 Evry, France | Concordia Univ, Dept Biol, Ctr Appl Synthet Biol, 7141 Rue Sherbrooke, Montreal, PQ H4B 1R6, Canada;Inst Canc Res, Chester Beatty Labs, Div Struct Biol, 237 Fulham Rd, London SW3 6JB, England;Katholieke Univ Leuven, Rega Inst, Minderbroedersstr 10, B-3000 Leuven, Belgium;MRC, Mol Biol Lab, Francis Crick Ave, Cambridge CB2 0QH, England;Univ Evry, Inst Syst & Synthet Biol, 5 Rue Henri Desbrueres, F-91030 Evry, France | 1439-7633 | chemical biology;DNA nanotechnology;electron microscopy;self-assembly;xeno nucleic acids (XNAs) | 12 | 1982;2000;2004;2006;2009;2010;2011;2012;2013;2014;2015;2016 | 42 | Concordia Univ, Dept Biol, Ctr Appl Synthet Biol, 7141 Rue Sherbrooke, Montreal, PQ H4B 1R6, Canada;MRC, Mol Biol Lab, Francis Crick Ave, Cambridge CB2 0QH, England | ChemBioChem | Holliger, Philipp | WILEY-V C H VERLAG GMBH | (2-fluro-2-deoxy-ribofuranose;(2F-RNA);(CeNA);(FANA);(HNA);(XNAs);,;2-fluoroarabino;600kDa;70kDa;:;a;acid;acids;all-FANA;also;alternative;an;and;applications;approximate;as;assembly;be;beyond;biostability;blocks;building;by;called;can;chemical;chemistries;complexity;constructed;construction;could;cyclohexene;describe;design;designs;different;diversity;DNA;elaborated;electron;enhanced;entirely;expanded;expanding;explore;extend;for;found;four;from;genetic;here;hexitol;however;implications;in;including;increasing;made;materials;microscopy;mixed;moderate;nano-objects;nanoscale;nanostructure;natural;nature;not;nucleic;objects;octahedron;of;or;our;physicochemical;polymers;potential;programmable;properties;range;results;RNA;scope;specifically;structural;synthetic;tetrahedra;the;to;visualised;we;well;with;xeno;XNA | Concordia Univ;MRC | Nanoscale objects of increasing complexity can be constructed from DNA or RNA. However, the scope of potential applications could be enhanced by expanding beyond the moderate chemical diversity of natural nucleic acids. Here, we explore the construction of nano-objects made entirely from alternative building blocks: synthetic genetic polymers not found in nature, also called xeno nucleic acids (XNAs). Specifically, we describe assembly of 70kDa tetrahedra elaborated in four different XNA chemistries (2-fluro-2-deoxy-ribofuranose nucleic acid (2F-RNA), 2-fluoroarabino nucleic acids (FANA), hexitol nucleic acids (HNA), and cyclohexene nucleic acids (CeNA)), as well as mixed designs, and a approximate to 600kDa all-FANA octahedron, visualised by electron microscopy. Our results extend the chemical scope for programmable nanostructure assembly, with implications for the design of nano-objects and materials with an expanded range of structural and physicochemical properties, including enhanced biostability. | null | CAGES;DELIVERY;EVOLUTION;NUCLEIC-ACIDS;PNA;RNA;STRUCTURAL DNA NANOTECHNOLOGY;SYSTEM;THERAPY | 2 | null | chemical biology;DNA nanotechnology;electron microscopy;self-assembly;xeno nucleic acids (XNAs) | 4 | CAGES;chemical biology;DELIVERY;DNA nanotechnology;ELECTRON-MICROSCOPY;EVOLUTION;NUCLEIC-ACIDS;PNA;RNA;self-assembly;STRUCTURAL DNA NANOTECHNOLOGY;SYSTEM;THERAPY;xeno nucleic acids (XNAs) | WOS:000379156400009 | Concordia Univ, Montreal PQ, Canada;Inst Canc Res, London, England;Katholieke Univ Leuven, Leuven, Belgium;MRC, Cambridge, England;Univ Evry, Evry, France | Belgium;Canada;France;UK | 2,016 | null | 0000-0003-3544-0041;0000-0003-3589-8503 | null | null | English | null | ACCOUNTS CHEM RES;ACS NANO;ANGEW CHEM;ANGEW CHEM INT EDIT;Artif DNA PNA XNA;CELL;CHEM BIODIVERS;CHEM BIOL;CHEM COMMUN;CURR OPIN CHEM BIOL;J AM CHEM SOC;J PHYS-CONDENS MAT;J THEOR BIOL;MOLECULES;NANO LETT;NAT CHEM;NAT NANOTECHNOL;NAT STRUCT MOL BIOL;NATURE;NPG ASIA MATER;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;SCIENCE | Beuron, Fabienne;Herdewijn, Piet;Holliger, Philipp;Morris, Edward P;Peak-Chew, Sew-Yeu;Taylor, Alexander I | 2024-03-11
ER | Afonin, K A;Amir, Y;Anosova, I;Breaker, R R;Burns, J R;Cassinelli, V;Cech, T R;Chworos, A;Conway, J W;Cozens, C;Douglas, S M;Erben C.M.;Erben, C M;Ferreira-Bravo, I A;Fica, S M;Flory Justin, D;Fu, J L;Goodman, R P;Grabow, W W;Hahn, J;Herdewijn, P;Jones, M R;Kato, T;Ke, Y G;Keum, J W;Langecker, M;Liu, J;Lo, P K;Martín-Pintado, N;Nissen, P;Pallan, P S;Pedersen, R O;Pei, H;Peters, J P;Pinheiro, A V;Pinheiro, V B;Rothemund, P W K;Sachdeva, G;Seeman, N C;Serganov, A;Shih, W M;Stern, A;Surana, S;Taylor, A I;Walsh, A S;Wilds C. J.;Yamazaki, T;Yu, H Y;Zhang, F;Zhao, Y X;Zuo H.;Zuo, H | DQ4EJ | Cambridge, England.;Montreal PQ, Canada | 46 | null | 5 | null | 26,992,063 | Beuron, Fabienne;Herdewijn, Piet;Holliger, Philipp;Morris, Edward P;Peak-Chew, Sew-Yeu;Taylor, Alexander I | CHEMBIOCHEM | Cambridge, England;Evry, France;Leuven, Belgium;London, England;Montreal PQ, Canada |
Ang, K S;Kyriakopoulos, S;Lee, D Y;Li, W | 10.1016/j.ymeth.2016.01.016 | null | 525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA | 4h4h5t49t2h1k5g651ja6x3g2y5h54m1b2z1w | Multi-omics data driven analysis establishes reference codon biases for synthetic gene design in microbial and mammalian cells | Natl Univ Singapore | null | Lee, DY (corresponding author), Natl Univ Singapore, Dept Chem & Biomol Engn, 4 Engn Dr 4, Singapore 117585, Singapore. | null | Ang, Kok Siong;Kyriakopoulos, Sarantos;Lee, Dong-Yup;Li, Wei | Biochemical Research Methods;Biochemistry & Molecular Biology | National University of Singapore; National Research Foundation of Singapore [NRF2013-THE001-035]; Biomedical Research Council of A*STAR (Agency for Science, Technology and Research), Singapore; Next-Generation BioGreen 21 Program (SSAC), Rural Development Administration, Republic of Korea [PJ01109405] | WOS | Lee, D Y | ASTAR, Singapore, Singapore;Natl Univ Singapore, Singapore, Singapore;Sangon Biotech Shanghai Co Ltd, Shanghai, Peoples R China | 102 | Analysis;and;biases;Cells;codon;data;design;driven;establishes;for;gene;in;mammalian;microbial;multi-omics;reference;synthetic | 2 | Lee, Dong-Yup | ACADEMIC PRESS INC ELSEVIER SCIENCE | ASTAR, Bioproc Technol Inst, 20 Biopolis Way,06-01 Ctr, Singapore 138668, Singapore;Natl Univ Singapore, Dept Chem & Biomol Engn, 4 Engn Dr 4, Singapore 117585, Singapore;Natl Univ Singapore, Inst Life Sci, NUS Synthet Biol Clin & Technol Innovat SynCTI, 28 Med Dr, Singapore 117456, Singapore;Sangon Biotech Shanghai Co Ltd, 698 Xiangmin Rd, Shanghai 201611, Peoples R China | Article | Natl Univ Singapore | SAN DIEGO | null | null | ASTAR;Natl Univ Singapore;Sangon Biotech Shanghai Co Ltd | Biomedical Research Council of A*STAR (Agency for Science, Technology and Research), Singapore;National Research Foundation of Singapore;National University of Singapore;Next-Generation BioGreen 21 Program (SSAC), Rural Development Administration, Republic of Korea | Lee, DY (corresponding author), Natl Univ Singapore, Dept Chem & Biomol Engn, 4 Engn Dr 4, Singapore 117585, Singapore. | 35 | Ang, Kok Siong;Kyriakopoulos, Sarantos;Lee, Dong-Yup;Li, Wei | 10 | 4 | 377,316,200,005 | Biomedical Research Council of A*STAR (Agency for Science, Technology and Research), Singapore;National Research Foundation of Singapore [NRF2013-THE001-035];National University of Singapore;Next-Generation BioGreen 21 Program (SSAC), Rural Development Administration, Republic of Korea [PJ01109405] | China;Singapore | METHODS | Singapore | null | null | Natl Univ Singapore, Dept Chem & Biomol Engn, 4 Engn Dr 4, Singapore 117585, Singapore | 1046-2023 | Ang, K S;Kyriakopoulos, S;Lee, D Y;Li, W | JUN 1 | cheld@nus.edu.sg | mammalian cells;multi-omics data driven analysis;reference codon biases;synthetic gene design | 4 | J | Biochemistry & Molecular Biology | -omics specific codon biases;-omics subsets;abundant proteins;analyzed multi-omics data;available genomic;C 2016 Elsevier Inc;CARBON-SOURCES;CC;Chinese hamster ovary (CHO) cells;CHO cells;codon;codon bias patterns;codon context (CC);Codon optimization;codon pair frequencies;correlation;different input codon biases;effect;ENHANCED EXPRESSION;Escherichia coli;ESCHERICHIA-COLI;expressed transcripts;expression;general lack;genome sequence;HAMSTER OVARY CELLS;HIGH-LEVEL EXPRESSION;host dependent;human IFN gamma sequence;ICU;improved heterologous gene design;individual codon;individual codon usage (ICU) design parameters;mammalian cells;mammalian expression hosts;Microbial and mammalian hosts;microbial cells;mRNA;Multi-omics data;multi-omics data driven analysis;one cluster;Pichia pastoris;PICHIA-PASTORIS;principal component analysis;protein expression levels;proteomic;PROTEOMIC ANALYSIS;RECOMBINANT PROTEIN-PRODUCTION;Reference codon bias;reference codon biases;reference codon usage biases;results;rights reserved;robust design parameter;Saccharomyces cerevisiae;SACCHAROMYCES-CEREVISIAE;SEQUENCES;silico case study;similar codon bias patterns;study;subsets;Synthetic gene design;transcriptomic;translatomic data;via | Ang, K S | CARBON-SOURCES;Codon optimization;ENHANCED EXPRESSION;ESCHERICHIA-COLI;GENOME SEQUENCE;HAMSTER OVARY CELLS;HIGH-LEVEL EXPRESSION;Microbial and mammalian hosts;Multi-omics data;PICHIA-PASTORIS;PROTEOMIC ANALYSIS;RECOMBINANT PROTEIN-PRODUCTION;Reference codon bias;SACCHAROMYCES-CEREVISIAE;Synthetic gene design | 26 | [Ang, Kok Siong; Lee, Dong-Yup] Natl Univ Singapore, Dept Chem & Biomol Engn, 4 Engn Dr 4, Singapore 117585, Singapore. [Ang, Kok Siong; Lee, Dong-Yup] Natl Univ Singapore, Inst Life Sci, NUS Synthet Biol Clin & Technol Innovat SynCTI, 28 Med Dr, Singapore 117456, Singapore. [Kyriakopoulos, Sarantos; Lee, Dong-Yup] ASTAR, Bioproc Technol Inst, 20 Biopolis Way,06-01 Ctr, Singapore 138668, Singapore. [Li, Wei] Sangon Biotech Shanghai Co Ltd, 698 Xiangmin Rd, Shanghai 201611, Peoples R China. | This work was supported by the National University of Singapore, the National Research Foundation of Singapore (NRF2013-THE001-035), Biomedical Research Council of A*STAR (Agency for Science, Technology and Research), Singapore, and a grant from the Next-Generation BioGreen 21 Program (SSAC, No. PJ01109405), Rural Development Administration, Republic of Korea. | -omics specific codon biases;-omics subsets;abundant proteins;analyzed multi-omics data;available genomic;CC;Chinese hamster ovary (CHO) cells;CHO cells;codon;codon bias patterns;codon context (CC);codon optimization;codon pair frequencies;correlation;different input codon biases;effect;Escherichia coli;expressed transcripts;expression;general lack;host dependent;human IFN gamma sequence;ICU;improved heterologous gene design;individual codon;individual codon usage (ICU) design parameters;mammalian expression hosts;microbial cells;mRNA;one cluster;Pichia pastoris;principal component analysis;protein expression levels;proteomic;reference codon usage biases;results;robust design parameter;Saccharomyces cerevisiae;sequences;silico case study;similar codon bias patterns;study;subsets;synthetic gene design;transcriptomic;translatomic data;via | 10.1002/pmic.201400267;10.1007/s00253-012-4540-z;10.1007/s00253-014-6079-7;10.1007/s00449-014-1333-z;10.1007/s10295-013-1341-z;10.1007/s10529-012-1097-y;10.1007/s11693-010-9062-3;10.1016/j.cell.2014.02.033;10.1016/j.ejps.2012.11.016;10.1016/j.enzmictec.2015.04.008;10.1016/j.febslet.2009.10.036;10.1016/j.jbiotec.2013.07.010;10.1016/j.jbiotec.2013.07.011;10.1016/j.jtbi.2013.11.022;10.1016/j.molcel.2015.05.035;10.1016/j.pep.2013.12.006;10.1021/pr300476w;10.1038/nature02046;10.1038/nbt.1544;10.1038/nbt.1932;10.1073/pnas.1120799109;10.1074/mcp.M113.029165;10.1093/bioinformatics/btl117;10.1093/nar/gkj405;10.1098/rsif.2008.0520.focus;10.1128/JB.00034-09;10.1134/S0003683814090051;10.1186/1471-2164-13-738;10.1186/1475-2859-10-15;10.1186/1752-0509-6-134;10.1186/1752-0509-8-33;10.1186/s12864-015-1393-8;10.1186/s12896-015-0177-1;10.1371/journal.pgen.1004734;10.1371/journal.pone.0123288;10.1534/g3.113.008995 | Natl Univ Singapore | Ang, K S;Kyriakopoulos, S;Lee, D Y;Li, W | Ang, K S: Natl Univ Singapore, Dept Chem & Biomol Engn, 4 Engn Dr 4, Singapore 117585, Singapore | Ang, Kok Siong;Lee, Dong-Yup | NRF2013-THE001-035;PJ01109405 | 36 | null | Singapore | ASTAR;Natl Univ Singapore;Sangon Biotech Shanghai Co Ltd | Ang, Kok Siong | null | CARBON-SOURCES;ENHANCED EXPRESSION;ESCHERICHIA-COLI;GENOME SEQUENCE;HAMSTER OVARY CELLS;HIGH-LEVEL EXPRESSION;PICHIA-PASTORIS;PROTEOMIC ANALYSIS;RECOMBINANT PROTEIN-PRODUCTION;SACCHAROMYCES-CEREVISIAE | Ang, Kok Siong; Kyriakopoulos, Sarantos; Li, Wei; Lee, Dong-Yup; | null | ASTAR, Bioproc Technol Inst, 20 Biopolis Way,06-01 Ctr, Singapore 138668, Singapore;Natl Univ Singapore, Dept Chem & Biomol Engn, 4 Engn Dr 4, Singapore 117585, Singapore;Natl Univ Singapore, Inst Life Sci, NUS Synthet Biol Clin & Technol Innovat SynCTI, 28 Med Dr, Singapore 117456, Singapore;Sangon Biotech Shanghai Co Ltd, 698 Xiangmin Rd, Shanghai 201611, Peoples R China | ASTAR, Bioproc Technol Inst, 20 Biopolis Way,06-01 Ctr, Singapore 138668, Singapore;Natl Univ Singapore, Dept Chem & Biomol Engn, 4 Engn Dr 4, Singapore 117585, Singapore;Natl Univ Singapore, Inst Life Sci, NUS Synthet Biol Clin & Technol Innovat SynCTI, 28 Med Dr, Singapore 117456, Singapore;Sangon Biotech Shanghai Co Ltd, 698 Xiangmin Rd, Shanghai 201611, Peoples R China | 1095-9130 | Codon optimization;Microbial and mammalian hosts;Multi-omics data;Reference codon bias;Synthetic gene design | null | 2003;2006;2009;2010;2011;2012;2013;2014;2015 | 16 | Natl Univ Singapore, Dept Chem & Biomol Engn, 4 Engn Dr 4, Singapore 117585, Singapore | Methods | Lee, Dong-Yup | ACADEMIC PRESS INC ELSEVIER SCIENCE | (CC);(CHO);(ICU);,;-omics;abundant;among;analysis;analyzed;and;are;available;between;bias;biases;by;case;CC;cells;cerevisiae;Chinese;CHO;cluster;clustering;codon;coli;compared;compiled;component;context;correlation;data;dependent;derive;design;despite;different;distinguishable;effect;efficiently;Escherichia;establish;expressed;expression;for;forming;frequencies;further;gamma;gene;general;generated;genomic;hamster;heterologous;hierarchical;highly;host;hosts;however;human;ICU;IFN;improved;in;indicated;individual;input;interestingly;investigated;is;lack;levels;mammalian;microbial;more;mRNA;multi-omics;not;of;on;one;optimization;optimized;our;ovary;pair;parameter;parameters;pastoris;patterns;Pichia;principal;protein;proteins;proteomic;publicly;reference;results;robust;Saccharomyces;sequence;sequences;silico;similar;specific;specifically;study;subsets;supported;synthetic;than;that;the;their;then;thereof;this;thus;to;transcriptomic;transcripts;translated;translatomic;usage;using;various;via;we;were | Natl Univ Singapore | In this study, we analyzed multi-omics data and subsets thereof to establish reference codon usage biases for codon optimization in synthetic gene design. Specifically, publicly available genomic, transcriptomic, proteomic and translatomic data for microbial and mammalian expression hosts, Escherichia coli, Saccharomyces cerevisiae, Pichia pastoris and Chinese hamster ovary (CHO) cells, were compiled to derive their individual codon and codon pair frequencies. Then, host dependent and -omics specific codon biases were generated and compared by principal component analysis and hierarchical clustering. Interestingly, our results indicated the similar codon bias patterns of the highly expressed transcripts, highly abundant proteins, and efficiently translated mRNA in microbial cells, despite the general lack of correlation between mRNA and protein expression levels. However, for CHO cells, the codon bias patterns among various -omics subsets are not distinguishable, forming one cluster. Thus, we further investigated the effect of different input codon biases on codon optimized sequences using the codon context (CC) and individual codon usage (ICU) design parameters, via in silico case study on the expression of human IFN gamma sequence in CHO cells. The results supported that CC is more robust design parameter than ICU for improved heterologous gene design. | D-6650-2011;M-2674-2019 | CARBON-SOURCES;ENHANCED EXPRESSION;ESCHERICHIA-COLI;GENOME SEQUENCE;HAMSTER OVARY CELLS;HIGH-LEVEL EXPRESSION;PICHIA-PASTORIS;PROTEOMIC ANALYSIS;RECOMBINANT PROTEIN-PRODUCTION;SACCHAROMYCES-CEREVISIAE | 0 | null | Codon optimization;Microbial and mammalian hosts;Multi-omics data;Reference codon bias;Synthetic gene design | 10 | ESCHERICHIA-COLI;SACCHAROMYCES-CEREVISIAE;CARBON-SOURCES;Codon optimization;ENHANCED EXPRESSION;GENOME SEQUENCE;HAMSTER OVARY CELLS;HIGH-LEVEL EXPRESSION;Microbial and mammalian hosts;Multi-omics data;Pichia pastoris;PROTEOMIC ANALYSIS;RECOMBINANT PROTEIN-PRODUCTION;Reference codon bias;Synthetic gene design | WOS:000377316200005 | ASTAR, Singapore, Singapore;Natl Univ Singapore, Singapore, Singapore;Sangon Biotech Shanghai Co Ltd, Shanghai, Peoples R China | China;Singapore | 2,016 | null | 0000-0003-0901-708X | null | null | English | null | APPL BIOCHEM MICRO+;APPL MICROBIOL BIOT;BIOINFORMATICS;BIOPROC BIOSYST ENG;BIOTECHNOL LETT;BMC BIOTECHNOL;BMC GENOMICS;BMC SYST BIOL;CELL;ENZYME MICROB TECH;EUR J PHARM SCI;FEBS LETT;J BACTERIOL;J BIOTECHNOL;J IND MICROBIOL BIOT;J PROTEOME RES;J R SOC INTERFACE;J THEOR BIOL;MICROB CELL FACT;MOL CELL;MOL CELL PROTEOMICS;NAT BIOTECHNOL;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PLOS GENET;PLOS ONE;PROTEIN EXPRES PURIF;PROTEOMICS;Syst Synth Biol | Ang, Kok Siong;Kyriakopoulos, Sarantos;Lee, Dong-Yup;Li, Wei | 2024-03-11
ER | Adhikari, H;Ata Ö;Baycin-Hizal, D;Bin Pek, H;Chung, B K S;Courtes, F C;De Schutter, K;Engel, S R;Gerashchenko, M V;Ghaemmaghami, S;He, M;Kim, H J;Krug, K;Lanza, A M;Lewis, N E;Li, G W;Liang, S L;Liu, G L;Liu, X W;Lu, X M;Maier, T;Menzella, H G;Prielhofer, R;Quax, T E F;Raab David;Renuse, S;Riley, M;Sarantos, K;Shukurov, R R;Snajder, M;Suzuki, R;Tu, Y B;Wei, W;Welch, M;Xu, X | DN8GC | Singapore, Singapore | 16 | null | 3 | null | 26,850,284 | Ang, Kok Siong;Kyriakopoulos, Sarantos;Lee, Dong-Yup;Li, Wei | METHODS | Shanghai, Peoples R China;Singapore, Singapore |
Glyzin, S D;Kolesov, A Y;Rozov, N K | 10.1134/S0040577916060106 | null | 233 SPRING ST, NEW YORK, NY 10013-1578 USA | 255f1172432t13f5i6z252u3h10j4x5j126r3h | BUFFERING IN CYCLIC GENE NETWORKS | Demidov Yaroslavl State Univ | null | Glyzin, SD (corresponding author), Demidov Yaroslavl State Univ, Yaroslavl, Russia. | null | Glyzin, S D;Kolesov, A Yu;Rozov, N Kh | Physics, Mathematical;Physics, Multidisciplinary | Russian Foundation for Basic Research [15-01-04066_a]; Russian State Research Task [2014/258, 1875] | WOS | Glyzin, S D | Demidov Yaroslavl State Univ, Yaroslavl, Russia;Lomonosov Moscow State Univ, Moscow, Russia | 187 | BUFFERING;CYCLIC;gene;in;networks | 1 | Glyzin, Sergey;Rozov, Nicolai;Rozov, Nikolai | MAIK NAUKA/INTERPERIODICA/SPRINGER | Demidov Yaroslavl State Univ, Yaroslavl, Russia;Lomonosov Moscow State Univ, Moscow, Russia | Article | Demidov Yaroslavl State Univ | NEW YORK | null | null | Demidov Yaroslavl State Univ;Lomonosov Moscow State Univ | Russian Foundation for Basic Research;Russian State Research Task | Glyzin, SD (corresponding author), Demidov Yaroslavl State Univ, Yaroslavl, Russia. | 951 | Glyzin, S D;Kolesov, A Yu;Rozov, N Kh | 3 | 2 | 379,309,300,010 | Russian Foundation for Basic Research [15-01-04066_a];Russian State Research Task [2014/258, 1875] | Russia | THEORETICAL AND MATHEMATICAL PHYSICS | Russia | null | null | Demidov Yaroslavl State Univ, Yaroslavl, Russia | 0040-5779 | Glyzin, S D;Kolesov, A Y;Rozov, N K | JUN | fpo.mgu@mail.ru;glyzin@uniyar.ac.ru;kolesov@uniyar.ac.ru | BUFFERING;CYCLIC GENE NETWORKS | 3 | J | Physics | appropriate choice;artificial gene network;artificial oscillating gene networks;asymptotic behavior;buffering;CHAINS;cyclic chain of unidirectionally coupled equations;cyclic chains;CYCLIC GENE NETWORKS;given finite number;mathematical models;parameters;phenomenon;RELAXATION SELF-OSCILLATIONS;so-called traveling waves;special type;stability;stable periodic motions;SYSTEM;traveling wave;unidirectionally coupled delay differential-difference equations | Glyzin, S D | artificial gene network;asymptotic behavior;buffering;CHAINS;cyclic chain of unidirectionally coupled equations;RELAXATION SELF-OSCILLATIONS;STABILITY;traveling wave | 935 | [Glyzin, S. D.; Kolesov, A. Yu.] Demidov Yaroslavl State Univ, Yaroslavl, Russia. [Rozov, N. Kh.] Lomonosov Moscow State Univ, Moscow, Russia. | This research was supported by the Russian Foundation for Basic Research (Grant No. 15-01-04066_a) and the Russian State Research Task No. 2014/258 (Project No. 1875). | appropriate choice;artificial oscillating gene networks;cyclic chains;given finite number;mathematical models;parameters;phenomenon;so-called traveling waves;special type;stable periodic motions;system;unidirectionally coupled delay differential-difference equations | 10.1007/s11232-013-0041-1;10.1038/35002125;10.1070/IM2013v077n02ABEH002636;10.1070/IM2014v078n04ABEH002704;10.1103/PhysRevE.81.066206;10.1134/S0012266111070020;10.1134/S0012266113100017;10.1134/S0965542510120031;10.1142/S0218127409025237 | Demidov Yaroslavl State Univ | Glyzin, S D;Kolesov, A Y;Rozov, N K | Glyzin, S D: Demidov Yaroslavl State Univ, Yaroslavl, Russia | Glyzin, Sergey;Kolesov, Andrei Yu.;Kolesov, Andrey;Rozov, Nicolai | 15-01-04066_a;1875;2014/258 | 15 | null | Russia | Demidov Yaroslavl State Univ;Lomonosov Moscow State Univ | Glyzin, S D | null | CHAINS;RELAXATION SELF-OSCILLATIONS | Glyzin, S. D.; Kolesov, A. Yu.; Rozov, N. Kh.; | null | Demidov Yaroslavl State Univ, Yaroslavl, Russia;Lomonosov Moscow State Univ, Moscow, Russia | Demidov Yaroslavl State Univ, Yaroslavl, Russia;Lomonosov Moscow State Univ, Moscow, Russia | 1573-9333 | artificial gene network;asymptotic behavior;buffering;cyclic chain of unidirectionally coupled equations;stability;traveling wave | 3 | 1952;1997;2000;2003;2004;2009;2010;2011;2013;2014 | 4 | Demidov Yaroslavl State Univ, Yaroslavl, Russia | Theor. Math. Phys. | Rozov, N Kh | MAIK NAUKA/INTERPERIODICA/SPRINGER | ,;:;a;an;any;appropriate;are;artificial;buffering;chains;choice;coexist;consider;coupled;cyclic;delay;differential-difference;equations;establish;finite;for;gene;given;in;is;mathematical;models;motions;networks;number;of;oscillating;parameters;periodic;phenomenon;realized;so-called;special;stable;system;that;the;these;traveling;type;unidirectionally;waves;we | Demidov Yaroslavl State Univ | We consider cyclic chains of unidirectionally coupled delay differential-difference equations that are mathematical models of artificial oscillating gene networks. We establish that the buffering phenomenon is realized in these system for an appropriate choice of the parameters: any given finite number of stable periodic motions of a special type, the so-called traveling waves, coexist. | A-7646-2018;AAU-2535-2020;ABC-6838-2021;B-2224-2013 | CHAIN;RELAXATION SELF-OSCILLATIONS | 0 | null | artificial gene network;asymptotic behavior;buffering;cyclic chain of unidirectionally coupled equations;stability;traveling wave | 17 | artificial gene network;asymptotic behavior;buffering;CHAIN;cyclic chain of unidirectionally coupled equations;RELAXATION SELF-OSCILLATIONS;STABILITY;traveling waves | WOS:000379309300010 | Demidov Yaroslavl State Univ, Yaroslavl, Russia;Lomonosov Moscow State Univ, Moscow, Russia | Russia | 2,016 | null | 0000-0001-8585-298X;0000-0002-6403-4061;0000-0002-9330-549X | null | null | English | null | COMP MATH MATH PHYS;COMP MATH MATH PHYS+;DIFF EQUAT+;INT J BIFURCAT CHAOS;IZV MATH+;NATURE;P STEKLOV I MATH;PHYS REV E;SIB ZH IND MAT;THEOR MATH PHYS+ | Glyzin, S D;Kolesov, A Yu;Rozov, N Kh | 2024-03-11
ER | Buse, O;Demidenko G.V.;Elowitz, M B;Fadeev, S I;Glyzin, S D;Kolesov A. Yu.;Kolesov, A Y;Likhoshvai V.A.;Tikhonov Andreinikolaevich;Volokitin, E P | DQ6IY | Yaroslavl, Russia | 4 | null | 2 | null | null | Glyzin, S D;Kolesov, A Yu;Rozov, N Kh | THEOR MATH PHYS+ | Moscow, Russia;Yaroslavl, Russia |