bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diversification of Paralogous α-Isopropylmalate Synthases by Modulation of Feedback Control and Hetero-Oligomerization in Saccharomyces cerevisiae
Authors: López Geovani , Quezada Héctor , Duhne Mariana , González James , Lezama Mijail , El-Hafidi Mohammed , Colón Maritrini , Martínez de la Escalera Ximena , Flores-Villegas Mirelle Citlali , Scazzocchio Claudio , DeLuna Alexander , González Alicia 
Published: April 2015

ABSTRACT

Production of α-isopropylmalate (α-IPM) is critical for leucine biosynthesis and for the global control of metabolism. The budding yeast
Saccharomyces cerevisiae
has two paralogous genes,
LEU4
and
LEU9
, that encode α-IPM synthase (α-IPMS) isozymes. Little is known about the biochemical differences between these two α-IPMS isoenzymes. Here, we show that the Leu4 homodimer is a leucine-sensitive isoform, while the Leu9 homodimer is resistant to such feedback inhibition. The
leu4
Δ mutant, which expresses only the feedback-resistant Leu9 homodimer, grows slowly with either glucose or ethanol and accumulates elevated pools of leucine; this phenotype is alleviated by the addition of leucine. Transformation of the
leu4
Δ mutant with a centromeric plasmid carrying
LEU4
restored the wild-type phenotype. Bimolecular fluorescent complementation analysis showed that Leu4-Leu9 heterodimeric isozymes are formed
in vivo
. Purification and kinetic analysis showed that the hetero-oligomeric isozyme has a distinct leucine sensitivity behavior. Determination of α-IPMS activity in ethanol-grown cultures showed that α-IPM biosynthesis and growth under these respiratory conditions depend on the feedback-sensitive Leu4 homodimer. We conclude that retention and further diversification of two yeast α-IPMSs have resulted in a specific regulatory system that controls the leucine–α-IPM biosynthetic pathway by selective feedback sensitivity of homomeric and heterodimeric isoforms.
Cryptococcus Strains with Different Pathogenic Potentials Have Diverse Protein Secretomes
Authors: Campbell Leona T. , Simonin Anna R. , Chen Cuilan , Ferdous Jannatul , Padula Matthew P. , Harry Elizabeth , Hofer Markus , Campbell Iain L. , Carter Dee A. 
Published: April 2015

ABSTRACT

Secreted proteins are the frontline between the host and pathogen. In mammalian hosts, secreted proteins enable invasive infection and can modulate the host immune response. Cryptococcosis, caused by pathogenic
Cryptococcus
species, begins when inhaled infectious propagules establish to produce pulmonary infection, which, if not resolved, can disseminate to the central nervous system to cause meningoencephalitis. Strains of
Cryptococcus
species differ in their capacity to cause disease, and the mechanisms underlying this are not well understood. To investigate the role of secreted proteins in disease, we determined the secretome for three genome strains of
Cryptococcus
species, including a hypovirulent and a hypervirulent strain of
C. gattii
and a virulent strain of
C. neoformans
. Sixty-seven unique proteins were identified, with different numbers and types of proteins secreted by each strain. The secretomes of the virulent strains were largely limited to proteolytic and hydrolytic enzymes, while the hypovirulent strain had a diverse secretome, including non-conventionally secreted canonical cytosolic and immunogenic proteins that have been implicated in virulence. The hypovirulent strain cannot establish pulmonary infection in a mouse model, but strains of this genotype have caused human meningitis. To directly test brain infection, we used intracranial inoculation and found that the hypovirulent strain was substantially more invasive than its hypervirulent counterpart. We suggest that immunogenic proteins secreted by this strain invoke a host response that limits pulmonary infection but that there can be invasive growth and damage if infection reaches the brain. Given their known role in virulence, it is possible that non-conventionally secreted proteins mediate this process.
Draft Genome Sequence of Bioactive-Compound-Producing Cyanobacterium Tolypothrix campylonemoides Strain VB511288
Authors: Das Subhadeep , Singh Deeksha , Madduluri Madhavi , Chandrababunaidu Mathu Malar , Gupta Akash , Adhikary Siba Prasad , Tripathy Sucheta 
Published: April 2015

ABSTRACT
We report here the draft genome sequence of Tolypothrix campylonemoides VB511288, isolated from building facades in Santiniketan, India. The members of this genus produce several compounds of commercial importance. The draft assembly is 10,627,177 bases in 135 scaffolds, and it contains 7,886 protein-coding genes, 994 pseudogenes, 18 rRNA genes, and 76 tRNA genes.
Genome Sequence of Magnetospirillum magnetotacticum Strain MS-1
Authors: Smalley Matthew D. , Marinov Georgi K. , Bertani L. Elizabeth , DeSalvo Gilberto 
Published: April 2015

ABSTRACT

Here, we report the genome sequence of
Magnetospirillum magnetotacticum
strain MS-1, which consists of of 36 contigs and 4,136 protein-coding genes.
Whole-Genome Shotgun Sequence of the Keratinolytic Bacterium Lysobacter sp. A03, Isolated from the Antarctic Environment
Authors: Pereira Jamile Queiroz , Ambrosini Adriana , Sant’Anna Fernando Hayashi , Tadra-Sfeir Michele , Faoro Helisson , Pedrosa Fábio Oliveira , Souza Emanuel Maltempi , Brandelli Adriano , Passaglia Luciane M. P. 
Published: April 2015

ABSTRACT
Lysobacter sp. strain A03 is a protease-producing bacterium isolated from decomposing-penguin feathers collected in the Antarctic environment. This strain has the ability to degrade keratin at low temperatures. The A03 genome sequence provides the possibility of finding new genes with biotechnological potential to better understand its cold-adaptation mechanism and survival in cold environments.
Genome of Rhizobium sp. UR51a, Isolated from Rice Cropped in Southern Brazilian Fields
Authors: de Souza Rocheli , Sant’Anna Fernando Hayashi , Ambrosini Adriana , Tadra-Sfeir Michele , Faoro Helisson , Pedrosa Fabio Oliveira , Souza Emanuel Maltempi , Passaglia Luciane M. P. 
Published: April 2015

ABSTRACT
Rhizobium sp. UR51a is a Gram-negative bacterium isolated from roots of rice plants, and it presents plant growth-promoting abilities. The nutrient uptake in rice plants inoculated with UR51a was satisfactory. The genome of strain UR51a is composed of 5,233,443-bp and harbors 5,079 coding sequences.
Transcriptional Analysis of the MrpJ Network: Modulation of Diverse Virulence-Associated Genes and Direct Regulation of
mrp
Fimbrial and
flhDC
Flagellar Operons in Proteus mirabilis
Authors: Bode Nadine J. , Debnath Irina , Kuan Lisa , Schulfer Anjelique , Ty Maureen , Pearson Melanie M. 
Published: April 2015

ABSTRACT

The enteric bacterium
Proteus mirabilis
is associated with a significant number of catheter-associated urinary tract infections (UTIs). Strict regulation of the antagonistic processes of adhesion and motility, mediated by fimbriae and flagella, respectively, is essential for disease progression. Previously, the transcriptional regulator MrpJ, which is encoded by the
mrp
fimbrial operon, has been shown to repress both swimming and swarming motility. Here we show that MrpJ affects an array of cellular processes beyond adherence and motility. Microarray analysis found that expression of
mrpJ
mimicking levels observed during UTIs leads to differential expression of 217 genes related to, among other functions, bacterial virulence, type VI secretion, and metabolism. We probed the molecular mechanism of transcriptional regulation by MrpJ using transcriptional reporters and chromatin immunoprecipitation (ChIP). Binding of MrpJ to two virulence-associated target gene promoters, the promoters of the flagellar master regulator
flhDC
and
mrp
itself, appears to be affected by the condensation state of the native chromosome, although both targets share a direct MrpJ binding site proximal to the transcriptional start. Furthermore, an
mrpJ
deletion mutant colonized the bladders of mice at significantly lower levels in a transurethral model of infection. Additionally, we observed that
mrpJ
is widely conserved in a collection of recent clinical isolates. Altogether, these findings support a role of MrpJ as a global regulator of
P. mirabilis
virulence.
Resources for Genetic and Genomic Analysis of Emerging Pathogen Acinetobacter baumannii
Authors: Gallagher Larry A. , Ramage Elizabeth , Weiss Eli J. , Radey Matthew , Hayden Hillary S. , Held Kiara G. , Huse Holly K. , Zurawski Daniel V. , Brittnacher Mitchell J. , Manoil Colin 
Published: April 2015

ABSTRACT

Acinetobacter baumannii
is a Gram-negative bacterial pathogen notorious for causing serious nosocomial infections that resist antibiotic therapy. Research to identify factors responsible for the pathogen's success has been limited by the resources available for genome-scale experimental studies. This report describes the development of several such resources for
A. baumannii
strain AB5075, a recently characterized wound isolate that is multidrug resistant and displays robust virulence in animal models. We report the completion and annotation of the genome sequence, the construction of a comprehensive ordered transposon mutant library, the extension of high-coverage transposon mutant pool sequencing (Tn-seq) to the strain, and the identification of the genes essential for growth on nutrient-rich agar. These resources should facilitate large-scale genetic analysis of virulence, resistance, and other clinically relevant traits that make
A. baumannii
a formidable public health threat.

IMPORTANCE
Acinetobacter baumannii
is one of six bacterial pathogens primarily responsible for antibiotic-resistant infections that have become the scourge of health care facilities worldwide. Eliminating such infections requires a deeper understanding of the factors that enable the pathogen to persist in hospital environments, establish infections, and resist antibiotics. We present a set of resources that should accelerate genome-scale genetic characterization of these traits for a reference isolate of
A. baumannii
that is highly virulent and representative of current outbreak strains.
Biosynthesis of the Common Polysaccharide Antigen of Pseudomonas aeruginosa PAO1: Characterization and Role of GDP-
d
-Rhamnose:GlcNAc/GalNAc-Diphosphate-Lipid α1,3-
d
-Rhamnosyltransferase WbpZ
Authors: Wang Shuo , Hao Youai , Lam Joseph S. , Vlahakis Jason Z. , Szarek Walter A. , Vinnikova Anna , Veselovsky Vladimir V. , Brockhausen Inka 
Published: April 2015

ABSTRACT

The opportunistic pathogen
Pseudomonas aeruginosa
produces two major cell surface lipopolysaccharides, characterized by distinct O antigens, called common polysaccharide antigen (CPA) and O-specific antigen (OSA). CPA contains a polymer of
d
-rhamnose (
d
-Rha) in α1-2 and α1-3 linkages. Three putative glycosyltransferase genes,
wbpX
,
wbpY
, and
wbpZ
, are part of the CPA biosynthesis cluster. To characterize the enzymatic function of the
wbpZ
gene product, we chemically synthesized the donor substrate GDP-
d
-Rha and enzymatically synthesized GDP-
d
-[
3
H]Rha. Using nuclear magnetic resonance (NMR) spectroscopy, we showed that WbpZ transferred one
d
-Rha residue from GDP-
d
-Rha in α1-3 linkage to both GlcNAc- and GalNAc-diphosphate-lipid acceptor substrates. WbpZ is also capable of transferring
d
-mannose (
d
-Man) to these acceptors. Therefore, WbpZ has a relaxed specificity with respect to both acceptor and donor substrates. The diphosphate group of the acceptor, however, is required for activity. WbpZ does not require divalent metal ion for activity and exhibits an unusually high pH optimum of 9. WbpZ from PAO1 is therefore a GDP-
d
-Rha:GlcNAc/GalNAc-diphosphate-lipid α1,3-
d
-rhamnosyltransferase that has significant activity of GDP-
d
-Man:GlcNAc/GalNAc-diphosphate-lipid α1,3-
d
-mannosyltransferase. We used site-directed mutagenesis to replace the Asp residues of the two DXD motifs with Ala. Neither of the mutant constructs of
wbpZ
(D172A or D254A) could be used to rescue CPA biosynthesis in the Δ
wbpZ
knockout mutant in a complementation assay. This suggested that D172 and D254 are essential for WbpZ function. This work is the first detailed characterization study of a
d
-Rha-transferase and a critical step in the development of CPA synthesis inhibitors.

IMPORTANCE
This is the first characterization of a
d
-rhamnosyltransferase and shows that it is essential in
Pseudomonas aeruginosa
for the synthesis of the common polysaccharide antigen.
Rho Kinase Inhibitors Block Melanoma Cell Migration and Inhibit Metastasis
Authors: Sadok Amine , McCarthy Afshan , Caldwell John , Collins Ian , Garrett Michelle D. , Yeo Maggie , Hooper Steven , Sahai Erik , Kuemper Sandra , Mardakheh Faraz K. , Marshall Christopher J. 
Published: April 2015

Abstract
There is an urgent need to identify new therapeutic opportunities for metastatic melanoma. Fragment-based screening has led to the discovery of orally available, ATP-competitive AKT kinase inhibitors, AT13148 and CCT129254. These compounds also inhibit the Rho-kinases ROCK 1 and ROCK 2 and we show they potently inhibit ROCK activity in melanoma cells in culture and in vivo. Treatment of melanoma cells with CCT129254 or AT13148 dramatically reduces cell invasion, impairing both “amoeboid-like” and mesenchymal-like modes of invasion in culture. Intravital imaging shows that CCT129254 or AT13148 treatment reduces the motility of melanoma cells in vivo. CCT129254 inhibits melanoma metastasis when administered 2 days after orthotopic intradermal injection of the cells, or when treatment starts after metastases have arisen. Mechanistically, our data suggest that inhibition of ROCK reduces the ability of melanoma cells to efficiently colonize the lungs. These results suggest that these novel inhibitors of ROCK may be beneficial in the treatment of metastasis. Cancer Res; 75(11); 2272–84. ©2015 AACR.
Effective Eradication of Glioblastoma Stem Cells by Local Application of an AC133/CD133-Specific T-cell–Engaging Antibody and CD8 T Cells
Authors: Prasad Shruthi , Gaedicke Simone , Machein Marcia , Mittler Gerhard , Braun Friederike , Hettich Michael , Firat Elke , Klingner Kerstin , Schüler Julia , Wider Dagmar , Wäsch Ralph M. , Herold-Mende Christel , Elsässer-Beile Ursula , Niedermann Gabriele 
Published: April 2015

Abstract
Cancer stem cells (CSC) drive tumorigenesis and contribute to genotoxic therapy resistance, diffuse infiltrative invasion, and immunosuppression, which are key factors for the incurability of glioblastoma multiforme (GBM). The AC133 epitope of CD133 is an important CSC marker for GBM and other tumor entities. Here, we report the development and preclinical evaluation of a recombinant AC133×CD3 bispecific antibody (bsAb) that redirects human polyclonal T cells to AC133+ GBM stem cells (GBM-SC), inducing their strong targeted lysis. This novel bsAb prevented the outgrowth of AC133-positive subcutaneous GBM xenografts. Moreover, upon intracerebral infusion along with the local application of human CD8+ T cells, it exhibited potent activity in prophylactic and treatment models of orthotopic GBM-SC–derived invasive brain tumors. In contrast, normal hematopoietic stem cells, some of which are AC133-positive, were virtually unaffected at bsAb concentrations effective against GBM-SCs and retained their colony-forming abilities. In conclusion, our data demonstrate the high activity of this new bsAb against patient-derived AC133-positive GBM-SCs in models of local therapy of highly invasive GBM. Cancer Res; 75(11); 2166–76. ©2015 AACR.
Leptin–STAT3–G9a Signaling Promotes Obesity-Mediated Breast Cancer Progression
Authors: Chang Chao-Ching , Wu Meng-Ju , Yang Jer-Yen , Camarillo Ignacio G. , Chang Chun-Ju 
Published: April 2015

Abstract
Obesity has been linked to breast cancer progression but the underlying mechanisms remain obscure. Here we report how leptin, an obesity-associated adipokine, regulates a transcriptional pathway to silence a genetic program of epithelial homeostasis in breast cancer stem–like cells (CSC) that promotes malignant progression. Using genome-wide ChIP-seq and RNA expression profiling, we defined a role for activated STAT3 and G9a histone methyltransferase in epigenetic silencing of miR-200c, which promotes the formation of breast CSCs defined by elevated cell surface levels of the leptin receptor (OBRhi). Inhibiting the STAT3/G9a pathway restored expression of miR-200c, which in turn reversed the CSC phenotype to a more differentiated epithelial phenotype. In a rat model of breast cancer driven by diet-induced obesity, STAT3 blockade suppressed the CSC-like OBRhi population and abrogated tumor progression. Together, our results show how targeting STAT3-G9a signaling regulates CSC plasticity during obesity-related breast cancer progression, suggesting a novel therapeutic paradigm to suppress CSC pools and limit breast malignancy. Cancer Res; 75(11); 2375–86. ©2015 AACR.
Global Transcriptional Changes Following Statin Treatment in Breast Cancer
Authors: Bjarnadottir Olöf , Kimbung Siker , Johansson Ida , Veerla Srinivas , Jönsson Mats , Bendahl Pär-Ola , Grabau Dorthe , Hedenfalk Ingrid , Borgquist Signe 
Published: April 2015

Abstract
Background: Statins purportedly exert antitumoral effects, but the underlying mechanisms are currently not fully elucidated. The aim of this study was to explore potential statin-induced effects on global gene expression profiles in primary breast cancer.
Experimental Design: This window-of-opportunity phase II trial enrolled 50 newly diagnosed breast cancer patients prescribed atorvastatin (80 mg/day) for 2 weeks presurgically. Pre- and posttreatment tumor samples were analyzed using Significance Analysis of Microarrays (SAM) to identify differentially expressed genes. Similarly, SAM and gene ontology analyses were applied to gene expression data derived from atorvastatin-treated breast cancer cell lines (MCF7, BT474, SKBR3, and MDAMB231) comparing treated and untreated cells. The Systematic Motif Analysis Retrieval Tool (SMART) was used to identify enriched transcription factor-binding sites. Literature Vector Analysis (LitVAn) identified gene module functionality, and pathway analysis was performed using GeneGo Pathways Software (MetaCore; https://portal.genego.com/).
Results: Comparative analysis of gene expression profiles in paired clinical samples revealed 407 significantly differentially expressed genes (FDR = 0); 32 upregulated and 375 downregulated genes. Restricted filtration (fold change ≥1.49) resulted in 21 upregulated and 46 downregulated genes. Significantly upregulated genes included DUSP1, RHOB1, GADD45B, and RGS1. Pooled results from gene ontology, LitVAn and SMART analyses identified statin-induced effects on the apoptotic and MAPK pathways among others. Comparative analyses of gene expression profiles in breast cancer cell lines showed significant upregulation of the mevalonate and proapoptotic pathways following atorvastatin treatment.
Conclusions: We report potential statin-induced changes in global tumor gene expression profiles, indicating MAPK pathway inhibition and proapoptotic events. Clin Cancer Res; 21(15); 3402–11. ©2015 AACR.
A Novel Anti-CD22 Anthracycline-Based Antibody–Drug Conjugate (ADC) That Overcomes Resistance to Auristatin-Based ADCs
Authors: Yu Shang-Fan , Zheng Bing , Go MaryAnn , Lau Jeff , Spencer Susan , Raab Helga , Soriano Robert , Jhunjhunwala Suchit , Cohen Robert , Caruso Michele , Polakis Paul , Flygare John , Polson Andrew G. 
Published: April 2015

Abstract
Purpose: We are interested in identifying mechanisms of resistance to the current generation of antibody–drug conjugates (ADC) and developing ADCs that can overcome this resistance.
Experimental Design: Pinatuzumab vedotin (anti-CD22-vc-MMAE) and polatuzumab vedotin (anti-CD79b-vc-MMAE) are ADCs that contain the microtubule inhibitor monomethyl auristatin E (MMAE) attached to the antibody by the protease-cleavable linker maleimidocaproyl-valine-citrulline-p-aminobenzoyloxycarbonyl (MC-vc-PAB). Early clinical trial data suggest that these ADCs have promising efficacy for the treatment of non-Hodgkin lymphoma (NHL); however, some patients do not respond or become resistant to the ADCs. Anthracyclines are very effective in NHL, but ADCs containing the anthracycline doxorubicin were not clinically efficacious probably due to the low drug potency and inadequate linker technology. The anthracycline analogue PNU-159682 is thousands of times more cytotoxic than doxorubicin, so we used it to develop a new class of ADCs. We used the same MC-vc-PAB linker and antibody in pinatuzumab vedotin but replaced the MMAE with a derivative of PNU-159682 to make anti-CD22-NMS249 and tested it for in vivo efficacy in xenograft tumors resistant to MMAE-based ADCs.
Results: We derived cell lines from in vivo xenograft tumors that were made resistant to anti-CD22-vc-MMAE and anti-CD79b-vc-MMAE. We identified P-gp (ABCB1/MDR1) as the major driver of resistance to the vc-MMAE–based conjugates. Anti-CD22-NMS249 was at least as effective as anti-CD22-vc-MMAE in xenograft models of the parental cell lines and maintained its efficacy in the resistant cell lines.
Conclusions: These studies provide proof of concept for an anthracycline-based ADC that could be used to treat B-cell malignancies that are resistant to vc-MMAE conjugates. Clin Cancer Res; 21(14); 3298–306. ©2015 AACR.
Biological Activities of RUNX1 Mutants Predict Secondary Acute Leukemia Transformation from Chronic Myelomonocytic Leukemia and Myelodysplastic Syndromes
Authors: Tsai Shu-Chun , Shih Lee-Yung , Liang Sung-Tzu , Huang Ying-Jung , Kuo Ming-Chung , Huang Chein-Fuang , Shih Yu-Shu , Lin Tung-Huei , Chiu Ming-Chun , Liang Der-Cherng 
Published: April 2015

Abstract
Purpose: Transcription factor RUNX1 is essential for normal hematopoiesis. High mutation frequencies of RUNX1 gene in chronic myelomonocytic leukemia (CMML) and myelodysplastic syndromes (MDS) have been described, whereas the biologic significances of the mutations were not investigated. Here, we aimed to correlate the biologic activities of the RUNX1 mutants with the clinical outcomes of patients.
Experimental Design: We examined the mutational status of RUNX1 in 143 MDS and 84 CMML patients. Then, we studied the DNA and CBFβ binding abilities of all the RUNX1 mutants identified by using electrophoretic mobility shift assay and co-immunoprecipitation assay, and also determined their activities on target C-FMS gene induction by Western blotting and luciferase reporter assay. Using luciferase reporter assay, the relative biologic activities of each RUNX1 mutant could be quantified and correlated with the patient outcomes by statistical analyses.
Results: We observed that most RUNX1 mutants had reduced abilities in DNA binding, CBFβ heterodimerization, and C-FMS gene induction. The relative biologic activities of RUNX1 mutants were grouped into high- and low-activity mutations. Correlation of the activities of RUNX1 mutants with the clinical outcomes revealed that patients harboring lower activities of RUNX1 mutants had a higher risk and shorter time to secondary acute myeloid leukemia transformation in MDS and CMML. In multivariate analysis, low RUNX1 activity remained an independent predictor for secondary acute myeloid leukemia–free survival in MDS patients.
Conclusions: The biologic activity rather than the mutational status of RUNX1 might be an indicator in predicting outcome of patients with MDS and CMML. Clin Cancer Res; 21(15); 3541–51. ©2015 AACR.