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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | null | J | null | Green Accepted | 10 | 509,882,600,018 | LONDON | Swiss Fed Inst Technol | Azizoglu, A;Stelling, J | 3034bk443e3q612p1s442q316z3m202t642527 | 1804 | Stelling, J | null | Azizoglu, A | 6 | Switzerland | 6 | Basel, Switzerland | 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 | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland;Swiss Fed Inst Technol, SIB Swiss Inst Bioinformat, CH-4058 Basel, Switzerland | 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 | null | 47 | Biochemistry & Molecular Biology | Swiss Fed Inst Technol | Switzerland | Azizoglu, Asli;Stelling, Jorg | Azizoglu, A;Stelling, J | BIOLOGICAL NOISE;DEGRADATION;DESIGN;EXPRESSION;HETEROGENEITY;REVEALS;STOCHASTICITY | Switzerland | null | Switzerland | 1 | null | BIOCHEMICAL SOCIETY TRANSACTIONS | null | 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. | joerg.stelling@bsse.ethz.ch | 2024-03-11
ER | We acknowledge financial support by the NCCR Molecular Systems Engineering funded by the Swiss National Science Foundation. | BIOLOGICAL NOISE;DEGRADATION;DESIGN;EXPRESSION;HETEROGENEITY;REVEALS;STOCHASTICITY | KG3ZR | 10.1042/BST20190295 | Azizoglu, A: Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland | 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 | Controlling cell-to-cell variability with synthetic gene circuits | 3 | null | null | Swiss Fed Inst Technol | Azizoglu, Asli | null | PORTLAND PRESS LTD | null | DEC | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland;Swiss Fed Inst Technol, SIB Swiss Inst Bioinformat, CH-4058 Basel, Switzerland | Basel, Switzerland | PORTLAND PRESS LTD | [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. | 0000-0002-2600-1322 | Stelling, J (corresponding author), Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland. | 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] | NCCR Molecular Systems Engineering - Swiss National Science Foundation | cell-to-cell;circuits;controlling;gene;synthetic;variability;with | 1 | WOS:000509882600018 | BIOCHEM SOC T | 1ST FLR, 10 QUEEN STREET PLACE, LONDON, ENGLAND | null | BIOLOGICAL NOISE;DEGRADATION;DESIGN;EXPRESSION;HETEROGENEITY;REVEALS;STOCHASTICITY | 2 | Azizoglu, Asli | 1 | 0300-5127 | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland;Swiss Fed Inst Technol, SIB Swiss Inst Bioinformat, CH-4058 Basel, Switzerland | Biochem. Soc. Trans. | 1470-8752 | null | 75 | Azizoglu, Asli;Stelling, Jorg | Azizoglu, Asli;Stelling, Jorg | NCCR Molecular Systems Engineering - Swiss National Science Foundation | 2,019 | null | controlling cell-to-cell variability;synthetic gene circuits | null | null | Stelling, Jorg | null | null | Swiss Fed Inst Technol | 2000;2001;2002;2003;2004;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017;2018;2019 | WOS | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland | Biochemistry & Molecular Biology | Stelling, J (corresponding author), Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland. | 31,803,907 | Azizoglu, Asli; Stelling, Jorg; | BIOLOGICAL NOISE;DEGRADATION;DESIGN;EXPRESSION;HETEROGENEITY;REVEALS;STOCHASTICITY | Azizoglu, Asli;Stelling, Jorg | ,;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 | Azizoglu, A;Stelling, J | Swiss Fed Inst Technol, Basel, Switzerland | 12 | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland | null | Review | Swiss Fed Inst Technol | 1795 | English | null | Swiss Fed Inst Technol | 2 | Swiss Fed Inst Technol, Basel, Switzerland | NCCR Molecular Systems Engineering - Swiss National Science Foundation | null |
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 | null | J | null | null | 8 | 503,917,900,004 | WASHINGTON | Homi Bhabha Natl Inst HBNI | Bagh, S;Bonnerjee, D;Mukhopadhyay, S | 545c2z6o1z191w37c51z571d2v4p1d4o1723f | 3020 | Bagh, S | null | Bonnerjee, D | null | India | 8 | Kolkata, India | 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 | Homi Bhabha Natl Inst, Biophys & Struct Genom Div, Saha Inst Nucl Phys, Block A-F,Sect 1, Kolkata 700064, India | 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 | null | 30 | Biochemistry & Molecular Biology;Chemistry | Homi Bhabha Natl Inst | India | Bagh, Sangram;Bonnerjee, Deepro;Mukhopadhyay, Sayak | Bagh, S;Bonnerjee, D;Mukhopadhyay, S | BINDING;BIOLOGY;ESCHERICHIA-COLI;EXPRESSION;PRINCIPLES;SPECIFICITY | India | mukhopadhyay, sayak | India | 1 | HJI-3440-2023 | BIOCONJUGATE CHEMISTRY | null | 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. | sangram.bagh@saha.ac.in | 2024-03-11
ER | 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. | ESCHERICHIA-COLI;BINDING;BIOLOGY;EXPRESSION;PRINCIPLES;SPECIFICITY | JX7NR | 10.1021/acs.bioconjchem.9b00517 | Bonnerjee, D: Homi Bhabha Natl Inst, Biophys & Struct Genom Div, Saha Inst Nucl Phys, Block A-F,Sect 1, Kolkata 700064, 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 | 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 | 8 | null | null | Homi Bhabha Natl Inst | Bagh, Sangram;Bonnerjee, Deepro;mukhopadhyay, sayak | null | AMER CHEMICAL SOC | null | DEC | Homi Bhabha Natl Inst, Biophys & Struct Genom Div, Saha Inst Nucl Phys, Block A-F,Sect 1, Kolkata 700064, India | Kolkata, India | AMER CHEMICAL SOC | [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. | 0000-0002-2172-6893;0000-0002-5736-0993;0000-0002-8565-0728 | Bagh, S (corresponding author), Homi Bhabha Natl Inst, Biophys & Struct Genom Div, Saha Inst Nucl Phys, Block A-F,Sect 1, Kolkata 700064, India. | 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] | Ramanujan Felowship (DST), Govt. of India;SERB [CRG/201B/001394];SINP intramural funding (Department of Atomic Energy, Govt. of India) | ,;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 | WOS:000503917900004 | BIOCONJUGATE CHEM | 1155 16TH ST, NW, WASHINGTON, DC 20036 USA | null | BINDING;BIOLOGY;ESCHERICHIA-COLI;EXPRESSION;PRINCIPLES;SPECIFICITY | 3 | Bonnerjee, Deepro | 0 | 1043-1802 | Homi Bhabha Natl Inst, Biophys & Struct Genom Div, Saha Inst Nucl Phys, Block A-F,Sect 1, Kolkata 700064, India | Bioconjugate Chem. | 1520-4812 | null | 29 | Bagh, Sangram;Bonnerjee, Deepro;Mukhopadhyay, Sayak | Bagh, Sangram;Bonnerjee, Deepro;Mukhopadhyay, Sayak | Ramanujan Felowship (DST), Govt. of India;SERB;SINP intramural funding (Department of Atomic Energy, Govt. of India) | 2,019 | 12 | 3-Input;3-Input-3-Output Synthetic Genetic Combinatorial Logic Circuit;Device Chemistry;Fabrication;Gate;Single Bacterial Cell | null | null | Bagh, Sangram | null | null | Homi Bhabha Natl Inst | 1997;2004;2005;2006;2007;2008;2009;2010;2012;2013;2014;2015;2016;2018;2019 | WOS | Homi Bhabha Natl Inst, Biophys & Struct Genom Div, Saha Inst Nucl Phys, Block A-F,Sect 1, Kolkata 700064, India | Biochemical Research Methods;Biochemistry & Molecular Biology;Chemistry, Multidisciplinary;Chemistry, Organic | Bagh, S (corresponding author), Homi Bhabha Natl Inst, Biophys & Struct Genom Div, Saha Inst Nucl Phys, Block A-F,Sect 1, Kolkata 700064, India. | 31,596,072 | Bonnerjee, Deepro; Mukhopadhyay, Sayak; Bagh, Sangram; | BINDING;BIOLOGY;ESCHERICHIA-COLI;EXPRESSION;PRINCIPLES;SPECIFICITY | Bagh, Sangram;Bonnerjee, Deepro;Mukhopadhyay, Sayak | ,;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 | Bagh, S;Bonnerjee, D;Mukhopadhyay, S | Homi Bhabha Natl Inst, Kolkata, India | 25 | Homi Bhabha Natl Inst, Biophys & Struct Genom Div, Saha Inst Nucl Phys, Block A-F,Sect 1, Kolkata 700064, India | null | Article | Homi Bhabha Natl Inst | 3013 | English | null | Homi Bhabha Natl Inst | 1 | Homi Bhabha Natl Inst, Kolkata, India | SINP intramural funding (Department of Atomic Energy, Govt. of India); SERB [CRG/201B/001394]; Ramanujan Felowship (DST), Govt. of India | CRG/201B/001394 |
<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 | null | J | null | Green Published, gold, Green Submitted | 13 | 511,651,300,003 | LONDON | Univ Groningen | Bovenberg, R A L;Büttel, Z;Driessen, A J M;Mózsik, L;Nygård, Y | 9601h2m696ay6g5g5a6t146m5p2c664a56b3s | null | Nygård, Y | null | Mózsik, L | null | Netherlands;Sweden | 14 | Delft, Netherlands.;Gothenburg, Sweden;Groningen, Netherlands. | 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 | 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 | 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 | null | 18 | Biotechnology & Applied Microbiology | Univ Groningen | Netherlands;Sweden | Bovenberg, Roel A L;Buttel, Zsofia;Driessen, Arnold J M;Mozsik, Laszlo;Nygard, Yvonne | Bovenberg, R A L;Büttel, Z;Driessen, A J M;Mózsik, L;Nygård, Y | CLUSTER;CORE PROMOTERS;EXPRESSION SYSTEM;ORGANIZATION;PARTS;PROTEIN;Q-SYSTEM;STRAIN;TET-ON | Netherlands;Sweden | Driessen, Arnold J.M.;Nygård, Yvonne | Netherlands | 2 | AAV-4877-2020;D-1876-2012 | MICROBIAL CELL FACTORIES | null | 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. | yvonne.nygard@chalmers.se | 2024-03-11
ER | 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). | 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 | KI9BI | 10.1186/s12934-019-1253-3 | Mózsik, L: Univ Groningen, Groningen Biomol Sci & Biotechnol Inst, Mol Microbiol, Nijenborgh 7, NL-9747 AG Groningen, Netherlands | 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 | Synthetic control devices for gene regulation in <i>Penicillium chrysogenum</i> | 13 | null | null | Chalmers Univ Technol;DSM Biotechnol Ctr;Univ Groningen | Buttel, Zsofia;Mozsik, Laszlo;Nygård, Yvonne | null | BMC | null | NOV 18 | 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 | Delft, Netherlands;Gothenburg, Sweden;Groningen, Netherlands | BMC | [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. | 0000-0001-5211-3873;0000-0001-6117-0343;0000-0003-0138-7553 | 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. | 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] | 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] | <i>Penicillium;chrysogenum</i>;control;devices;for;gene;in;regulation;synthetic | 3 | WOS:000511651300003 | MICROB CELL FACT | CAMPUS, 4 CRINAN ST, LONDON N1 9XW, ENGLAND | null | 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 | 5 | Mozsik, Laszlo | 0 | 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 | Microb. Cell. Fact. | 1475-2859 | null | 57 | Bovenberg, Roel A L;Buttel, Zsofia;Driessen, Arnold J M;Mozsik, Laszlo;Nygard, Yvonne | Bovenberg, Roel A L;Buttel, Zsofia;Driessen, Arnold J M;Mozsik, Laszlo;Nygard, Yvonne | 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 | 2,019 | 1 | <i>Penicillium chrysogenum</i>;gene regulation;synthetic control devices | Gene regulation;Hybrid transcription factor;Penicillium chrysogenum;Secondary metabolite production;Synthetic expression system;Synthetic gene cluster | 203 | Nygard, Yvonne | null | Gene regulation;Hybrid transcription factor;Penicillium chrysogenum;Secondary metabolite production;Synthetic expression system;Synthetic gene cluster | Chalmers Univ Technol;DSM Biotechnol Ctr;Univ Groningen | 1984;1985;1988;1991;1992;1999;2000;2003;2005;2006;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017;2018;2019 | WOS | Univ Groningen, Groningen Biomol Sci & Biotechnol Inst, Mol Microbiol, Nijenborgh 7, NL-9747 AG Groningen, Netherlands | Biotechnology & Applied Microbiology | 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. | 31,739,777 | Mozsik, Laszlo; Buttel, Zsofia; Bovenberg, Roel A. L.; Driessen, Arnold J. M.; Nygard, Yvonne; | CLUSTER;CORE PROMOTERS;EXPRESSION SYSTEM;ORGANIZATION;PARTS;PROTEIN;Q-SYSTEM;STRAINS;TET-ON | Bovenberg, Roel A L;Buttel, Zsofia;Driessen, Arnold J M;Mozsik, Laszlo;Nygard, Yvonne | (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 | Bovenberg, R A L;Büttel, Z;Driessen, A J M;Mózsik, L;Nygård, Y | Chalmers Univ Technol, Gothenburg, Sweden;DSM Biotechnol Ctr, Delft, Netherlands;Univ Groningen, Groningen, Netherlands | 7 | 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 | null | Article | Chalmers Univ Technol;DSM Biotechnol Ctr;Univ Groningen | null | English | null | Chalmers Univ Technol;DSM Biotechnol Ctr;Univ Groningen | 4 | Chalmers Univ Technol, Gothenburg, Sweden;DSM Biotechnol Ctr, Delft, Netherlands;Univ Groningen, Groningen, Netherlands | 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] | 607332;713482 |
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 | null | J | null | hybrid | 12 | 484,647,000,023 | OXFORD | Natl Univ Singapore | Chang, M W;Foo, J L;Ling, H;Xia, P F | 1s1f5j644g1t1r6l6f3p382v6n6d2p5f5g6e315p | null | Chang, M W;Foo, J L | null | Xia, P F | null | Singapore | 78 | Singapore, Singapore | 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 | 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 | 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 | null | 37 | Biotechnology & Applied Microbiology | Natl Univ Singapore | Singapore | Chang, Matthew Wook;Foo, Jee Loon;Ling, Hua;Xia, Peng-Fei | Chang, M W;Foo, J L;Ling, H;Xia, P F | CARBON-DIOXIDE;CLOSTRIDIUM-BEIJERINCKII;CRISPR-CAS SYSTEMS;DESIGN;DYNAMIC PATHWAY REGULATION;ENGINEERED BACTERIA;EXPRESSION;LACTOCOCCUS-LACTIS;STATE MACHINES;TOGGLE SWITCH | Singapore | Xia, Pengfei | Singapore | 1 | Q-3174-2019 | BIOTECHNOLOGY ADVANCES | null | 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. | bchcmw@nus.edu.sg;bchfjl@nus.edu.sg | 2024-03-11
ER | 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). | 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 | IW0JA | 10.1016/j.biotechadv.2019.04.015 | Xia, P F: Natl Univ Singapore, Dept Biochem, Yong Loo Lin Sch Med, 8 Med Dr, Singapore 117597, Singapore | 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 | Synthetic genetic circuits for programmable biological functionalities | 66 | null | null | Ctr Life Sci | Ling, Hua;Xia, Pengfei | null | PERGAMON-ELSEVIER SCIENCE LTD | null | NOV 1 | 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 | Singapore, Singapore | PERGAMON-ELSEVIER SCIENCE LTD | [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. | 0000-0001-5881-9834;0000-0002-0680-6422 | Foo, JL; Chang, MW (corresponding author), Ctr Life Sci, 28 Med Dr,02-07, Singapore 117456, Singapore. | 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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] | 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] | biological;circuits;for;functionalities;genetic;programmable;synthetic | 1 | WOS:000484647000023 | BIOTECHNOL ADV | THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND | null | 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 | 4 | Xia, Peng-Fei | 8 | 0734-9750 | 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 | Biotechnol. Adv. | 1873-1899 | null | 158 | Chang, Matthew Wook;Foo, Jee Loon;Ling, Hua;Xia, Peng-Fei | Chang, Matthew Wook;Foo, Jee Loon;Ling, Hua;Xia, Peng-Fei | 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 | 2,019 | 6 | programmable biological functionalities;synthetic genetic circuits | Genetic circuits;Genetic devices;Programmable functionalities | 107393 | Chang, Matthew Wook | null | Genetic circuits;genetic device;Programmable functionalities | Ctr Life Sci | 1999;2000;2002;2003;2004;2005;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017;2018;2019 | WOS | Natl Univ Singapore, Dept Biochem, Yong Loo Lin Sch Med, 8 Med Dr, Singapore 117597, Singapore | Biotechnology & Applied Microbiology | Foo, JL; Chang, MW (corresponding author), Ctr Life Sci, 28 Med Dr,02-07, Singapore 117456, Singapore. | 31,051,208 | Xia, Peng-Fei; Ling, Hua; Foo, Jee Loon; Chang, Matthew Wook; | CARBON-DIOXIDE;CLOSTRIDIUM-BEIJERINCKII;CRISPR-CAS SYSTEMS;DESIGN;DYNAMIC PATHWAY REGULATION;ENGINEERED BACTERIA;EXPRESSION;LACTOCOCCUS-LACTIS;STATE MACHINES;TOGGLE SWITCH | Chang, Matthew Wook;Foo, Jee Loon;Ling, Hua;Xia, Peng-Fei | ,;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 | Chang, M W;Foo, J L;Ling, H;Xia, P F | Natl Univ Singapore, Singapore, Singapore | 181 | Ctr Life Sci, 28 Med Dr,02-07, Singapore 117456, Singapore | null | Review | Natl Univ Singapore | null | English | null | Natl Univ Singapore | 2 | Natl Univ Singapore, Singapore, Singapore | 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] | ARO/2019/74459LS;DPRT/943/09/14;ICP1600012;MOE/2014/T2/2/128;SBP-P2;SBP-P7 |
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 | null | J | null | null | 8 | 484,758,500,008 | AMSTERDAM | Chinese Acad Sci | Dong, F;Gu, D C;Liao, Y Y;Wang, X W;Yang, Z Y;Zeng, L T | 2y4k4tm3l513w4x4k6w2r2c3c2i631b6d6g5q6k | null | Yang, Z Y | null | Zeng, L T | null | China | 37 | Guangdong, Peoples R China;Guangdong, Peoples R China. | 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 | 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 | 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 | null | 157 | Agriculture;Food Science & Technology | Chinese Acad Sci | China | Dong, Fang;Gu, Dachuan;Liao, Yinyin;Wang, Xuewen;Yang, Ziyin;Zeng, Lanting | Dong, F;Gu, D C;Liao, Y Y;Wang, X W;Yang, Z Y;Zeng, L T | GENE-EXPRESSION;LEAF;LEAVES;SALICYLIC-ACID;VOLATILE COMPOUNDS | China | Gu, Dachuan;Zeng, lanting | China | 1 | AAH-5092-2021;JAA-9491-2023 | POSTHARVEST BIOLOGY AND TECHNOLOGY | null | 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. | zyyang@scbg.ac.cn | 2024-03-11
ER | 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). | ABSCISIC-ACID;Aroma;Camellia sinensis;GENE-EXPRESSION;Jasmonic acid;LEAF;LEAVES;SALICYLIC-ACID;Tea;volatiles;VOLATILE COMPOUNDS | IW1VM | 10.1016/j.postharvbio.2019.110974 | 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 | 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 | Formation of and changes in phytohormone levels in response to stress during the manufacturing process of oolong tea (<i>Camellia sinensis</i>) | 32 | null | null | Chinese Acad Sci | null | null | ELSEVIER | null | NOV | 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 | Beijing, Peoples R China;Guangdong, Peoples R China | ELSEVIER | [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. | null | 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. | 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] | 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] | (<i>Camellia;and;changes;during;formation;in;levels;manufacturing;of;oolong;phytohormone;process;response;sinensis</i>);stress;tea;the;to | 3 | WOS:000484758500008 | POSTHARVEST BIOL TEC | RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS | null | Abscisic acid;Aroma;Camellia sinensis;GENE-EXPRESSION;Jasmonic acid;LEAF;LEAVES;SALICYLIC-ACID;Tea;Volatile;VOLATILE COMPOUNDS | 6 | Zeng, Lanting | 3 | 0925-5214 | 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 | Postharvest Biol. Technol. | 1873-2356 | null | 41 | Dong, Fang;Gu, Dachuan;Liao, Yinyin;Wang, Xuewen;Yang, Ziyin;Zeng, Lanting | Dong, Fang;Gu, Dachuan;Liao, Yinyin;Wang, Xuewen;Yang, Ziyin;Zeng, Lanting | 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 | 2,019 | null | formation;manufacturing process;oolong tea (<i>Camellia sinensis</i>);phytohormone levels;response | Abscisic acid;Aroma;Camellia sinensis;Jasmonic acid;Tea;Volatile | 110974 | Yang, Ziyin | null | Abscisic acid;Aroma;Camellia sinensis;Jasmonic acid;Tea;volatiles | Chinese Acad Sci | 1969;1990;1999;2002;2003;2005;2007;2008;2009;2010;2011;2013;2014;2015;2016;2017;2018;2019 | WOS | Chinese Acad Sci, Key Lab South China Agr Plant Mol Anal & Genet Im, 723 Xingke Rd, Guangzhou 510650, Guangdong, Peoples R China | Agronomy;Food Science & Technology;Horticulture | 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 | Zeng, Lanting; Wang, Xuewen; Liao, Yinyin; Gu, Dachuan; Dong, Fang; Yang, Ziyin; | GENE-EXPRESSION;LEAF;LEAVES;SALICYLIC-ACID;VOLATILE COMPOUNDS | Dong, Fang;Gu, Dachuan;Liao, Yinyin;Wang, Xuewen;Yang, Ziyin;Zeng, Lanting | (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 | Dong, F;Gu, D C;Liao, Y Y;Wang, X W;Yang, Z Y;Zeng, L T | Chinese Acad Sci, Guangdong, Peoples R China;Guangdong Food & Drug Vocat Coll, Guangdong, Peoples R China;Univ Chinese Acad Sci, Beijing, Peoples R China | 128 | 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 | null | Article | Chinese Acad Sci;Guangdong Food & Drug Vocat Coll;Univ Chinese Acad Sci | null | English | null | Chinese Acad Sci;Guangdong Food & Drug Vocat Coll;Univ Chinese Acad Sci | 5 | Chinese Acad Sci, Guangdong, Peoples R China;Guangdong Food & Drug Vocat Coll, Guangdong, Peoples R China;Univ Chinese Acad Sci, Beijing, Peoples R China | 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] | 2016A030306039;2018M640837;2018YFD1000601;31870684 |
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 | null | J | null | gold, Green Published | 15 | 491,306,200,009 | LONDON | Tsinghua Univ | Cao, Y B;Guo, Y K;Huang, H Y;Liao, W X;Liu, Q;Liu, Y Q;Lu, Y Y;Xie, Z | 2ord1n1sg3w630r1224242oy6q6o2a1d6r | null | Xie, Z | null | Huang, H Y | null | China | 63 | Beijing, Peoples R China;Beijing, Peoples R China. | 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 | 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 | 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 | null | 10 | Science & Technology - Other Topics | Tsinghua Univ | China | Cao, Yubing;Guo, Yakun;Huang, Huiya;Liao, Weixi;Liu, Qiang;Liu, Yiqi;Lu, Yinying;Xie, Zhen | Cao, Y B;Guo, Y K;Huang, H Y;Liao, W X;Liu, Q;Liu, Y Q;Lu, Y Y;Xie, Z | ALPHA;ANTIBODY;COLONY-STIMULATING FACTOR;DELIVERY;HEPATOCELLULAR-CARCINOMA;IDENTIFICATION;LIVER;REPLICATIVE ADENOVIRUS;VIRUS | China | Liu, Yiqi;Xie, Zhen | China | 1 | AAK-1630-2020;GPW-5925-2022 | NATURE COMMUNICATIONS | null | 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. | zhenxie@tsinghua.edu.cn | 2024-03-11
ER | 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. | ALPHA;ANTIBODIES;COLONY-STIMULATING FACTOR;DELIVERY;HEPATOCELLULAR-CARCINOMA;IDENTIFICATION;LIVER;REPLICATING ADENOVIRUS;virus | JF3SB | 10.1038/s41467-019-12794-2 | 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 | 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 | Oncolytic adenovirus programmed by synthetic gene circuit for cancer immunotherapy | 56 | null | null | Tsinghua Univ | null | null | NATURE PUBLISHING GROUP | null | OCT 22 | 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 | Beijing, Peoples R China | NATURE PUBLISHING GROUP | [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. 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Commun. | null | null | 48 | Cao, Yubing;Guo, Yakun;Huang, Huiya;Liao, Weixi;Liu, Qiang;Liu, Yiqi;Lu, Yinying;Xie, Zhen | Cao, Yubing;Guo, Yakun;Huang, Huiya;Liao, Weixi;Liu, Qiang;Liu, Yiqi;Lu, Yinying;Xie, Zhen | 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 | 2,019 | null | cancer immunotherapy;oncolytic adenovirus;synthetic gene circuit | null | 4801 | Xie, Zhen | null | null | Tsinghua Univ | 1993;1996;1998;1999;2000;2001;2003;2004;2006;2007;2008;2009;2011;2012;2013;2014;2015;2016;2017;2018 | WOS | Tsinghua Univ, MOE Key Lab Bioinformat, Ctr Synthet & Syst Biol, Dept Automat,Beijing Natl Res Ctr Informat Sci &, Beijing 100084, Peoples R China | Multidisciplinary Sciences | 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. | 31,641,136 | Huang, Huiya; Liu, Yiqi; Liao, Weixi; Cao, Yubing; Liu, Qiang; Guo, Yakun; Lu, Yinying; Xie, Zhen; | ALPHA;ANTIBODIES;COLONY-STIMULATING FACTOR;DELIVERY;HEPATOCELLULAR-CARCINOMA;IDENTIFICATION;LIVER;REPLICATING ADENOVIRUS;VIRUS | Cao, Yubing;Guo, Yakun;Huang, Huiya;Liao, Weixi;Liu, Qiang;Liu, Yiqi;Lu, Yinying;Xie, Zhen | ,;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 | Cao, Y B;Guo, Y K;Huang, H Y;Liao, W X;Liu, Q;Liu, Y Q;Lu, Y Y;Xie, Z | PLA Genaral Hosp, Beijing, Peoples R China;Syngentech Inc, Beijing, Peoples R China;Tsinghua Univ, Beijing, Peoples R China | 52 | 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 | Article | PLA Genaral Hosp;Syngentech Inc;Tsinghua Univ | null | English | null | PLA Genaral Hosp;Syngentech Inc;Tsinghua Univ | 4 | PLA Genaral Hosp, Beijing, Peoples R China;Syngentech Inc, Beijing, Peoples R China;Tsinghua Univ, Beijing, Peoples R China | 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. | 61721003 |
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 | null | J | null | null | 21 | 517,260,400,002 | BRISTOL | Univ Chicago | Dickinson, B C;Jones, K A;Zinkus-Boltz, J | 2y6601ymo634xq168f1q341j1w5461l4t | null | Dickinson, B C | null | Jones, K A | null | USA | 9 | Chicago, IL USA | 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 | Univ Chicago, Dept Chem, Chicago, IL 60637 USA | 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 | null | 3 | Materials Science;Physics;Science & Technology - Other Topics | Univ Chicago | USA | Dickinson, Bryan C;Jones, Krysten A;Zinkus-Boltz, Julia | Dickinson, B C;Jones, K A;Zinkus-Boltz, J | CONDITIONAL EXPRESSION;CRYSTAL-STRUCTURE;DIRECTED EVOLUTION;ENZYME PRODRUG THERAPY;GENE CIRCUITS;IN-VIVO;PROTEIN-PROTEIN INTERACTIONS;SPLIT-LUCIFERASE;STRUCTURAL BASIS;T7 RNA-POLYMERASE | USA | null | USA | 1 | null | NANO FUTURES | null | 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. | Dickinson@uchicago.edu | 2024-03-11
ER | 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. | 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 | KQ9SA | 10.1088/2399-1984/ab4b78 | Jones, K A: Univ Chicago, Dept Chem, Chicago, IL 60637 USA | 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 | Recent advances in developing and applying biosensors for synthetic biology | 7 | null | null | Univ Chicago | Jones, Krysten;Zinkus-Boltz, Julia | null | IOP PUBLISHING LTD | null | OCT | Univ Chicago, Dept Chem, Chicago, IL 60637 USA | Chicago, IL USA | IOP PUBLISHING LTD | [Jones, Krysten A.; Zinkus-Boltz, Julia; Dickinson, Bryan C.] Univ Chicago, Dept Chem, Chicago, IL 60637 USA. | 0000-0003-0028-5360;0000-0003-0711-5516 | Dickinson, BC (corresponding author), Univ Chicago, Dept Chem, Chicago, IL 60637 USA. | 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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] | National Cancer Institute of the National Institutes of Health [R21 CA217754];National Institute of Mental Health [RF1 MH114102];University of Chicago | advances;and;applying;biology;biosensors;developing;for;in;recent;synthetic | 1 | WOS:000517260400002 | NANO FUTURES | TEMPLE CIRCUS, TEMPLE WAY, BRISTOL BS1 6BE, ENGLAND | null | 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 | 3 | Jones, Krysten A | 6 | null | Univ Chicago, Dept Chem, Chicago, IL 60637 USA | Nano Futures | 2399-1984 | null | 271 | Dickinson, Bryan C;Jones, Krysten A;Zinkus-Boltz, Julia | Dickinson, Bryan C;Jones, Krysten A;Zinkus-Boltz, Julia | National Cancer Institute of the National Institutes of Health;National Institute of Mental Health;University of Chicago | 2,019 | 4 | biosensors;developing;recent advances;synthetic biology | biosensors;chemical biology;directed evolution;Synthetic biology | 042002 | Dickinson, Bryan C | null | Biosensor;chemical biology;directed evolution;Synthetic biology | Univ Chicago | 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 | WOS | Univ Chicago, Dept Chem, Chicago, IL 60637 USA | Materials Science, Multidisciplinary;Nanoscience & Nanotechnology;Physics, Applied | Dickinson, BC (corresponding author), Univ Chicago, Dept Chem, Chicago, IL 60637 USA. | null | Jones, Krysten A.; Zinkus-Boltz, Julia; Dickinson, Bryan C.; | CONDITIONAL EXPRESSION;CRYSTAL-STRUCTURE;DIRECTED EVOLUTION;ENZYME PRODRUG THERAPY;GENE CIRCUITS;IN-VIVO;PROTEIN-PROTEIN INTERACTIONS;SPLIT-LUCIFERASE;STRUCTURAL BASIS;T7 RNA-POLYMERASE | Dickinson, Bryan C;Jones, Krysten A;Zinkus-Boltz, Julia | ,;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 | Dickinson, B C;Jones, K A;Zinkus-Boltz, J | Univ Chicago, Chicago, IL USA | 55 | Univ Chicago, Dept Chem, Chicago, IL 60637 USA | null | Review | Univ Chicago | null | English | null | Univ Chicago | 1 | Univ Chicago, Chicago, IL USA | University of Chicago; National Institute of Mental Health [RF1 MH114102]; National Cancer Institute of the National Institutes of Health [R21 CA217754] | R21 CA217754;RF1 MH114102 |
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 | null | J | null | null | 7 | 496,872,800,005 | OXFORD | Kyoto Univ | Nakanishi, H;Saito, H | 4v1dh303h481x4h4d4182r5w60y3v4b105r45 | 22 | Saito, H | null | Nakanishi, H | null | Japan | 9 | Kyoto, Japan | 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 | Kyoto Univ, Ctr iPS Cell Res & Applicat CiRA, Sakyo Ku, 53 Kawahara Cho, Kyoto 6068507, Japan | 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 | null | 52 | Biochemistry & Molecular Biology;Biophysics | Kyoto Univ | Japan | Nakanishi, Hideyuki;Saito, Hirohide | Nakanishi, H;Saito, H | CELLS;LIN28 | Japan | Nakanishi, Hideyuki | Japan | 1 | Q-5855-2017 | CURRENT OPINION IN CHEMICAL BIOLOGY | null | 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. | hirohide.saito@cira.kyoto-u.ac.jp | 2024-03-11
ER | 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. | CELLS;LIN28 | JN4MH | 10.1016/j.cbpa.2019.04.013 | Nakanishi, H: Kyoto Univ, Ctr iPS Cell Res & Applicat CiRA, Sakyo Ku, 53 Kawahara Cho, Kyoto 6068507, Japan | 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 | Mammalian gene circuits with biomolecule-responsive RNA devices | 8 | null | null | Kyoto Univ | Nakanishi, Hideyuki | null | ELSEVIER SCI LTD | null | OCT | Kyoto Univ, Ctr iPS Cell Res & Applicat CiRA, Sakyo Ku, 53 Kawahara Cho, Kyoto 6068507, Japan | Kyoto, Japan | ELSEVIER SCI LTD | [Nakanishi, Hideyuki; Saito, Hirohide] Kyoto Univ, Ctr iPS Cell Res & Applicat CiRA, Sakyo Ku, 53 Kawahara Cho, Kyoto 6068507, Japan. | 0000-0003-1159-3676 | Saito, H (corresponding author), Kyoto Univ, Ctr iPS Cell Res & Applicat CiRA, Sakyo Ku, 53 Kawahara Cho, Kyoto 6068507, Japan. | 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] | Japan Society for the Promotion of Science (JSPS) KAKENHI [15H05722] | biomolecule-responsive;circuits;devices;gene;mammalian;RNA;with | 1 | WOS:000496872800005 | CURR OPIN CHEM BIOL | THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND | null | CELLS;LIN28 | 2 | Nakanishi, Hideyuki | 1 | 1367-5931 | Kyoto Univ, Ctr iPS Cell Res & Applicat CiRA, Sakyo Ku, 53 Kawahara Cho, Kyoto 6068507, Japan | Curr. Opin. Chem. Biol. | 1879-0402 | null | 25 | Nakanishi, Hideyuki;Saito, Hirohide | Nakanishi, Hideyuki;Saito, Hirohide | Japan Society for the Promotion of Science (JSPS) KAKENHI | 2,019 | null | biomolecule-responsive RNA devices;mammalian gene circuits | null | null | Saito, Hirohide | null | null | Kyoto Univ | 2001;2004;2005;2007;2010;2011;2012;2013;2015;2016;2017;2018 | WOS | Kyoto Univ, Ctr iPS Cell Res & Applicat CiRA, Sakyo Ku, 53 Kawahara Cho, Kyoto 6068507, Japan | Biochemistry & Molecular Biology;Biophysics | Saito, H (corresponding author), Kyoto Univ, Ctr iPS Cell Res & Applicat CiRA, Sakyo Ku, 53 Kawahara Cho, Kyoto 6068507, Japan. | 31,129,468 | Nakanishi, Hideyuki; Saito, Hirohide; | CELLS;LIN28 | Nakanishi, Hideyuki;Saito, Hirohide | ,;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 | Nakanishi, H;Saito, H | Kyoto Univ, Kyoto, Japan | 17 | Kyoto Univ, Ctr iPS Cell Res & Applicat CiRA, Sakyo Ku, 53 Kawahara Cho, Kyoto 6068507, Japan | null | Review | Kyoto Univ | 16 | English | null | Kyoto Univ | 1 | Kyoto Univ, Kyoto, Japan | Japan Society for the Promotion of Science (JSPS) KAKENHI [15H05722] | 15H05722 |
(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 | null | J | null | Green Published, Bronze, Green Submitted | 14 | 493,379,500,013 | CAMBRIDGE | 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 | 3s1s1ym1o2t5g53x2m32k3u3i31175b3cdc | null | de Greef, T F A;Maerkl, S J | null | van der Linden, A J | null | Netherlands;Switzerland | 8 | Eindhoven, Netherlands.;Lausanne, Switzerland;Nijmegen, Netherlands. | 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 | 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 | 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. | null | null | Science & Technology - Other Topics | Eindhoven Univ Technol | Netherlands;Switzerland | de Greef, Tom F A;Huck, Wilhelm T S;Maerkl, Sebastian J;Pieters, Pascal;Swank, Zoe;van der Linden, Ardjan J;Yelleswarapu, Maaruthy | de Greef, T F A;Huck, W T S;Maerkl, S J;Pieters, P;Swank, Z;van der Linden, A J;Yelleswarapu, M | CONSTRUCTION;CONTEXT;FREE PROTEIN-SYNTHESIS;NETWORKS;SYNTHETIC BIOLOGY | Netherlands;Switzerland | de Greef, Tom F. A.;Huck, Wilhelm T.S.;Maerkl, Sebastian J. J | Netherlands | 2 | B-1471-2012;C-5438-2008;I-8124-2014 | JOVE-JOURNAL OF VISUALIZED EXPERIMENTS | null | 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. | sebastian.maerkl@epfl.ch;t.f.a.d.greef@tue.nl | 2024-03-11
ER | 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. | Bioengineering;CONSTRUCTION;CONTEXT;FREE PROTEIN-SYNTHESIS;in vitro transcription and translation;Issue 152;micro-reactors;MICROFLUIDICS;NETWORKS;prolonged reactions;PROTEIN EXPRESSION;Synthetic biology | JI3PV | 10.3791/59655 | van der Linden, A J: Eindhoven Univ Technol, Dept Biomed Engn, Computat Biol Grp, Inst Complex Mol Syst, Eindhoven, Netherlands | (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 | A Multilayer Microfluidic Platform for the Conduction of Prolonged Cell-Free Gene Expression | 7 | null | null | Ecole Polytech Fed Lausanne;Eindhoven Univ Technol;Radboud Univ Nijmegen | Maerkl, Sebastian J. | null | JOURNAL OF VISUALIZED EXPERIMENTS | null | OCT | 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 | Eindhoven, Netherlands;Lausanne, Switzerland;Nijmegen, Netherlands | JOURNAL OF VISUALIZED EXPERIMENTS | [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. | 0000-0003-1917-5268 | 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. | 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 | 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] | a;Cell-Free;Conduction;expression;for;gene;Microfluidic;Multilayer;of;Platform;Prolonged;the | 3 | WOS:000493379500013 | JOVE-J VIS EXP | 1 ALEWIFE CENTER, STE 200, CAMBRIDGE, MA 02140 USA | null | Bioengineering;CONSTRUCTION;CONTEXT;FREE PROTEIN-SYNTHESIS;in vitro transcription and translation;Issue 152;micro-reactors;MICROFLUIDICS;NETWORKS;prolonged reactions;PROTEIN EXPRESSION;Synthetic biology | 7 | van der Linden, Ardjan J | 0 | 1940-087X | 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. | null | null | 49 | de Greef, Tom F A;Huck, Wilhelm T S;Maerkl, Sebastian J;Pieters, Pascal;Swank, Zoe;van der Linden, Ardjan J;Yelleswarapu, Maaruthy | de Greef, Tom F A;Huck, Wilhelm T S;Maerkl, Sebastian J;Pieters, Pascal;Swank, Zoe;van der Linden, Ardjan J;Yelleswarapu, Maaruthy | 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) | 2,019 | 152 | Conduction;Multilayer Microfluidic Platform;Prolonged Cell-Free Gene Expression | Bioengineering;in vitro transcription and translation;Issue 152;micro-reactors;Microfluidics;prolonged reactions;protein expression;Synthetic biology | e59655 | de Greef, Tom F A | null | Bioengineering;in vitro transcription and translation;Issue 152;micro-reactors;Microfluidics;prolonged reactions;protein expression;Synthetic biology | Ecole Polytech Fed Lausanne;Eindhoven Univ Technol;Radboud Univ Nijmegen | 1988;1999;2000;2001;2003;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017;2018;2019 | WOS | Eindhoven Univ Technol, Dept Biomed Engn, Computat Biol Grp, Inst Complex Mol Syst, Eindhoven, Netherlands | Multidisciplinary Sciences | 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. | 31,633,684 | van der Linden, Ardjan J.; Yelleswarapu, Maaruthy; Pieters, Pascal; Swank, Zoe; Huck, Wilhelm T. S.; Maerkl, Sebastian J.; de Greef, Tom F. A.; | CONSTRUCTION;CONTEXT;FREE PROTEIN-SYNTHESIS;NETWORKS;SYNTHETIC BIOLOGY | de Greef, Tom F A;Huck, Wilhelm T S;Maerkl, Sebastian J;Pieters, Pascal;Swank, Zoe;van der Linden, Ardjan J;Yelleswarapu, Maaruthy | (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 | de Greef, T F A;Huck, W T S;Maerkl, S J;Pieters, P;Swank, Z;van der Linden, A J;Yelleswarapu, M | Ecole Polytech Fed Lausanne, Lausanne, Switzerland;Eindhoven Univ Technol, Eindhoven, Netherlands;Radboud Univ Nijmegen, Nijmegen, Netherlands | 9 | 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 | Article | Ecole Polytech Fed Lausanne;Eindhoven Univ Technol;Radboud Univ Nijmegen | null | English | null | Ecole Polytech Fed Lausanne;Eindhoven Univ Technol;Radboud Univ Nijmegen | 3 | Ecole Polytech Fed Lausanne, Lausanne, Switzerland;Eindhoven Univ Technol, Eindhoven, Netherlands;Radboud Univ Nijmegen, Nijmegen, Netherlands | 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) | 024.001.035;024.003.013;200021_182019;677313 BioCircuit;723.016.003;723106;RGP0032/2015 |
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 | null | J | null | Green Published, gold | 8 | 484,596,900,008 | LONDON | MIT | Graham, D;Jun, T;Lu, T K;Müller, I E;Rubens, J R;Xavier, R | 5s640a1k66m5n3z6kg2gf6h395p5f6x5do | null | Lu, T K | null | Müller, I E | null | USA;USA.; | 26 | Cambridge, MA USA;Cambridge, MA USA. | 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 | 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 | 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 | null | 10 | Science & Technology - Other Topics | MIT | USA | Graham, Daniel;Jun, Tomi;Lu, Timothy K;Mueller, Isaak E;Rubens, Jacob R;Xavier, Ramnik | Graham, D;Jun, T;Lu, T K;Müller, I E;Rubens, J R;Xavier, R | COMBINATORIAL;DESIGN;ESCHERICHIA-COLI;EVOLUTION;HYDROGEN-PEROXIDE;REGULATORY NETWORKS;SOXR PROTEIN;SPECIFICITY;TALK;YEAST | USA | Jun, Tomi;Lu, Timothy K | USA | 1 | AAJ-4152-2020;G-4267-2012 | NATURE COMMUNICATIONS | null | 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. | timlu@mit.edu | 2024-03-11
ER | 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). | ESCHERICHIA-COLI;YEAST;COMBINATORIAL;DESIGN;EVOLUTION;HYDROGEN-PEROXIDE;REGULATORY NETWORKS;SOXR PROTEIN;SPECIFICITY;TALK | IV9PW | 10.1038/s41467-019-12021-y | Müller, I E: MIT, Dept Elect Engn & Comp Sci, Elect Res Lab, Synthet Biol Grp,Synthet Biol Ctr, Cambridge, MA 02139 USA | 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 | Gene networks that compensate for crosstalk with crosstalk | 21 | null | null | MIT | Jun, Tomi | null | NATURE PUBLISHING GROUP | null | SEP 6 | 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 | Boston, MA USA;Cambridge, MA USA;New York, NY USA | NATURE PUBLISHING GROUP | [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. | 0000-0002-2120-1704 | 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. | 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 | 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] | compensate;crosstalk;for;gene;networks;that;with | 5 | WOS:000484596900008 | NAT COMMUN | MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND | null | COMBINATORIAL;DESIGN;ESCHERICHIA-COLI;EVOLUTION;HYDROGEN-PEROXIDE;REGULATORY NETWORKS;SOXR PROTEIN;SPECIFICITY;TALK;YEAST | 6 | Mueller, Isaak E | 0 | 2041-1723 | 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 | Nat. Commun. | null | null | 69 | Graham, Daniel;Jun, Tomi;Lu, Timothy K;Mueller, Isaak E;Rubens, Jacob R;Xavier, Ramnik | Graham, Daniel;Jun, Tomi;Lu, Timothy K;Mueller, Isaak E;Rubens, Jacob R;Xavier, Ramnik | 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 | 2,019 | null | crosstalk;gene | null | 4028 | Lu, Timothy K | null | null | MIT | 1991;1996;1997;1998;1999;2002;2003;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016 | WOS | MIT, Dept Elect Engn & Comp Sci, Elect Res Lab, Synthet Biol Grp,Synthet Biol Ctr, Cambridge, MA 02139 USA | Multidisciplinary Sciences | 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. | 31,492,904 | Mueller, Isaak E.; Rubens, Jacob R.; Jun, Tomi; Graham, Daniel; Xavier, Ramnik; Lu, Timothy K.; | COMBINATORIAL;DESIGN;ESCHERICHIA-COLI;EVOLUTION;HYDROGEN-PEROXIDE;REGULATORY NETWORKS;SOXR PROTEIN;SPECIFICITY;TALK;YEAST | Graham, Daniel;Jun, Tomi;Lu, Timothy K;Mueller, Isaak E;Rubens, Jacob R;Xavier, Ramnik | (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 | Graham, D;Jun, T;Lu, T K;Müller, I E;Rubens, J R;Xavier, R | 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 | 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 | null | Article | Broad Inst;Dept Elect Engn & Comp Sci;Harvard MIT Hlth Sci & Technol Program;Massachusetts Gen Hosp;MIT;Mt Sinai Hosp | null | English | null | Broad Inst;Harvard MIT Hlth Sci & Technol Program;Massachusetts Gen Hosp;MIT;Mt Sinai Hosp | 8 | 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 | 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 | 1124247;1350625;1DP2OD008435;1P50GM098792;N000141310424 |
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 | null | J | null | null | 8 | 482,582,100,028 | SAN DIEGO | Kyushu Univ | Hamada, H;Hanai, T;Honjo, H;Iwasaki, K;Soma, Y;Tsuruno, K | 5v605b585f1z2i62rd4076h241de4iu3w47 | 275 | Hanai, T | null | Honjo, H | null | Japan | 43 | Fukuoka, Japan | 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 | 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 | 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 | null | 55 | Biotechnology & Applied Microbiology | Kyushu Univ | Japan | Hamada, Hiroyuki;Hanai, Taizo;Honjo, Hiroshi;Iwasaki, Kenshiro;Soma, Yuki;Tsuruno, Keigo | Hamada, H;Hanai, T;Honjo, H;Iwasaki, K;Soma, Y;Tsuruno, K | CELLOBIOSE;ESCHERICHIA-COLI;EXPRESSION;FLUX;ISOPROPANOL PRODUCTION;LYSIS;METABOLIC PATHWAY;SENSOR | Japan | Soma, Yuki | Japan | 1 | ABI-7016-2020 | METABOLIC ENGINEERING | null | 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. | taizo@brs.kyushu-u.ac.jp | 2024-03-11
ER | 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. | ESCHERICHIA-COLI;CELLOBIOSE;EXPRESSION;FLUX;ISOPROPANOL PRODUCTION;LYSIS;METABOLIC PATHWAYS;SENSOR | IT1BX | 10.1016/j.ymben.2019.08.007 | Honjo, H: Kyushu Univ, Grad Sch Syst Lifesci, Lab Bioinformat, Nishi Ku, 729 West Bldg 5,744 Motooka, Fukuoka, Fukuoka 8190395, Japan | 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 | Synthetic microbial consortium with specific roles designated by genetic circuits for cooperative chemical production | 36 | null | null | Kyushu Univ | Soma, Yuki | null | ACADEMIC PRESS INC ELSEVIER SCIENCE | null | SEP | 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 | Fukuoka, Japan | ACADEMIC PRESS INC ELSEVIER SCIENCE | [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. | 0000-0003-1083-6824 | Hanai, T (corresponding author), Kyushu Univ, Grad Sch Syst Lifesci, Lab Bioinformat, Nishi Ku, 729 West Bldg 5,744 Motooka, Fukuoka, Fukuoka 8190395, Japan. | 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] | Chemical Innovation Encouragement Prize from Japan Association for Chemical Innovation;JSPS KAKENHI [JP23119002, JP18K14065];Sumitomo Foundation | by;chemical;circuits;consortium;cooperative;designated;for;genetic;microbial;production;roles;specific;synthetic;with | 1 | WOS:000482582100028 | METAB ENG | 525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA | null | CELLOBIOSE;ESCHERICHIA-COLI;EXPRESSION;FLUX;ISOPROPANOL PRODUCTION;LYSIS;metabolic pathway;SENSOR | 6 | Honjo, Hiroshi | 9 | 1096-7176 | 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 | Metab. Eng. | 1096-7184 | null | 41 | Hamada, Hiroyuki;Hanai, Taizo;Honjo, Hiroshi;Iwasaki, Kenshiro;Soma, Yuki;Tsuruno, Keigo | Hamada, Hiroyuki;Hanai, Taizo;Honjo, Hiroshi;Iwasaki, Kenshiro;Soma, Yuki;Tsuruno, Keigo | Chemical Innovation Encouragement Prize from Japan Association for Chemical Innovation;JSPS KAKENHI;Sumitomo Foundation | 2,019 | null | cooperative chemical production;genetic circuits;specific roles;synthetic microbial consortium | null | null | Hanai, Taizo | null | null | Kyushu Univ | 1988;1996;2000;2001;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017;2018 | WOS | Kyushu Univ, Grad Sch Syst Lifesci, Lab Bioinformat, Nishi Ku, 729 West Bldg 5,744 Motooka, Fukuoka, Fukuoka 8190395, Japan | Biotechnology & Applied Microbiology | Hanai, T (corresponding author), Kyushu Univ, Grad Sch Syst Lifesci, Lab Bioinformat, Nishi Ku, 729 West Bldg 5,744 Motooka, Fukuoka, Fukuoka 8190395, Japan. | 31,401,244 | Honjo, Hiroshi; Iwasaki, Kenshiro; Soma, Yuki; Tsuruno, Keigo; Hamada, Hiroyuki; Hanai, Taizo; | CELLOBIOSE;ESCHERICHIA-COLI;EXPRESSION;FLUX;ISOPROPANOL PRODUCTION;LYSIS;METABOLIC PATHWAYS;SENSOR | Hamada, Hiroyuki;Hanai, Taizo;Honjo, Hiroshi;Iwasaki, Kenshiro;Soma, Yuki;Tsuruno, Keigo | ,;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 | Hamada, H;Hanai, T;Honjo, H;Iwasaki, K;Soma, Y;Tsuruno, K | Kyushu Univ, Fukuoka, Japan | 63 | Kyushu Univ, Grad Sch Syst Lifesci, Lab Bioinformat, Nishi Ku, 729 West Bldg 5,744 Motooka, Fukuoka, Fukuoka 8190395, Japan | null | Article | Kyushu Univ | 268 | English | null | Kyushu Univ | 2 | Kyushu Univ, Fukuoka, Japan | JSPS KAKENHI [JP23119002, JP18K14065]; Chemical Innovation Encouragement Prize from Japan Association for Chemical Innovation; Sumitomo Foundation | JP18K14065;JP23119002 |
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