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Fu X, Wan X, Memon AA, Fan XY, Sun Q, Chen H, Yao Y, Deng Z, Ma J, Ma W. Regulatory role of Mycobacterium tuberculosis MtrA on dormancy/resuscitation revealed by a novel target gene-mining strategy. Front Microbiol 2024; 15:1415554. [PMID: 38952446 PMCID: PMC11215152 DOI: 10.3389/fmicb.2024.1415554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 05/28/2024] [Indexed: 07/03/2024] Open
Abstract
Introduction The unique dormancy of Mycobacterium tuberculosis plays a significant role in the major clinical treatment challenge of tuberculosis, such as its long treatment cycle, antibiotic resistance, immune escape, and high latent infection rate. Methods To determine the function of MtrA, the only essential response regulator, one strategy was developed to establish its regulatory network according to high-quality genome-wide binding sites. Results and discussion The complex modulation mechanisms were implied by the strong bias distribution of MtrA binding sites in the noncoding regions, and 32.7% of the binding sites were located inside the target genes. The functions of 288 potential MtrA target genes predicted according to 294 confirmed binding sites were highly diverse, and DNA replication and damage repair, lipid metabolism, cell wall component biosynthesis, cell wall assembly, and cell division were the predominant pathways. Among the 53 pathways shared between dormancy/resuscitation and persistence, which accounted for 81.5% and 93.0% of the total number of pathways, respectively, MtrA regulatory genes were identified not only in 73.6% of their mutual pathways, but also in 75.4% of the pathways related to dormancy/resuscitation and persistence respectively. These results suggested the pivotal roles of MtrA in regulating dormancy/resuscitation and the apparent relationship between dormancy/resuscitation and persistence. Furthermore, the finding that 32.6% of the MtrA regulons were essential in vivo and/or in vitro for M. tuberculosis provided new insight into its indispensability. The findings mentioned above indicated that MtrA is a novel promising therapeutic target for tuberculosis treatment since the crucial function of MtrA may be a point of weakness for M. tuberculosis.
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Affiliation(s)
- Xiang Fu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoyu Wan
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, Shanghai, China
| | - Aadil Ahmed Memon
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiao-Yong Fan
- Shanghai Public Health Clinical Center, Shanghai Institute of Infectious Diseases and Biosecurity, Fudan University, Shanghai, China
| | - Qiuhong Sun
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, Shanghai, China
| | - Haifeng Chen
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yufeng Yao
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jian Ma
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, Shanghai, China
| | - Wei Ma
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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Lally P, Gómez-Romero L, Tierrafría VH, Aquino P, Rioualen C, Zhang X, Kim S, Baniulyte G, Plitnick J, Smith C, Babu M, Collado-Vides J, Wade JT, Galagan JE. Predictive Biophysical Neural Network Modeling of a Compendium of in vivo Transcription Factor DNA Binding Profiles for Escherichia coli. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.23.594371. [PMID: 38826350 PMCID: PMC11142182 DOI: 10.1101/2024.05.23.594371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
The DNA binding of most Escherichia coli Transcription Factors (TFs) has not been comprehensively mapped, and few have models that can quantitatively predict binding affinity. We report the global mapping of in vivo DNA binding for 139 E. coli TFs using ChIP-Seq. We used these data to train BoltzNet, a novel neural network that predicts TF binding energy from DNA sequence. BoltzNet mirrors a quantitative biophysical model and provides directly interpretable predictions genome-wide at nucleotide resolution. We used BoltzNet to quantitatively design novel binding sites, which we validated with biophysical experiments on purified protein. We have generated models for 125 TFs that provide insight into global features of TF binding, including clustering of sites, the role of accessory bases, the relevance of weak sites, and the background affinity of the genome. Our paper provides new paradigms for studying TF-DNA binding and for the development of biophysically motivated neural networks.
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Affiliation(s)
- Patrick Lally
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215
| | - Laura Gómez-Romero
- Instituto Nacional de Medicina Genómica, Periférico Sur 4809, Arenal Tepepan, Ciudad de México 14610, México
- Escuela de Medicina y Ciencias de la Salud, Tecnológico de Monterrey, Ciudad de México, México
| | - Víctor H. Tierrafría
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, México
| | - Patricia Aquino
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215
| | - Claire Rioualen
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, México
| | - Xiaoman Zhang
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215
| | - Sunyoung Kim
- Department of Biochemistry, University of Regina, Regina, Saskatchewan, SK S4S 0A2, Canada
| | | | - Jonathan Plitnick
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Carol Smith
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Mohan Babu
- Department of Biochemistry, University of Regina, Regina, Saskatchewan, SK S4S 0A2, Canada
| | - Julio Collado-Vides
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, México
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Joseph T. Wade
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
- Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY, USA
| | - James E. Galagan
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215
- Bioinformatics Program, Boston University, 24 Cummington Mall, Boston, MA 02215
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3
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Coutte L, Antoine R, Slupek S, Locht C. Combined transcriptomic and ChIPseq analyses of the Bordetella pertussis RisA regulon. mSystems 2024; 9:e0095123. [PMID: 38470037 PMCID: PMC11019879 DOI: 10.1128/msystems.00951-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 02/19/2024] [Indexed: 03/13/2024] Open
Abstract
The regulation of Bordetella pertussis virulence is mediated by the two-component system BvgA/S, which activates the transcription of virulence-activated genes (vags). In the avirulent phase, the vags are not expressed, but instead, virulence-repressed genes (vrgs) are expressed, under the control of another two-component system, RisA/K. Here, we combined transcriptomic and chromatin immunoprecipitation sequencing (ChIPseq) data to examine the RisA/K regulon. We performed RNAseq analyses of RisA-deficient and RisA-phosphoablative B. pertussis mutants cultivated in virulent and avirulent conditions. We confirmed that the expression of most vrgs is regulated by phosphorylated RisA. However, the expression of some, including those involved in flagellum biosynthesis and chemotaxis, requires RisA independently of phosphorylation. Many RisA-regulated genes encode proteins with regulatory functions, suggesting multiple RisA regulation cascades. By ChIPseq analyses, we identified 430 RisA-binding sites, 208 within promoter regions, 201 within open reading frames, and 21 in non-coding regions. RisA binding was demonstrated in the promoter regions of most vrgs and, surprisingly, of some vags, as well as for other genes not identified as vags or vrgs. Unexpectedly, many genes, including some vags, like prn, brpL, bipA, and cyaA, contain a BvgA-binding site and a RisA-binding site, which increases the complexity of the RisAK/BvgAS network in B. pertussis virulence regulation.IMPORTANCEThe expression of virulence-activated genes (vags) of Bordetella pertussis, the etiological agent of whooping cough, is under the transcriptional control of the two-component system BvgA/S, which allows the bacterium to switch between virulent and avirulent phases. In addition, the more recently identified two-component system RisA/K is required for the expression of B. pertussis genes, collectively named vrgs, that are repressed during the virulent phase but activated during the avirulent phase. We have characterized the RisA/K regulon by combined transcriptomic and chromatin immunoprecipitation sequencing analyses. We identified more than 400 RisA-binding sites. Many of them are localized in promoter regions, especially vrgs, but some were found within open reading frames and in non-coding regions. Surprisingly, RisA-binding sites were also found in promoter regions of some vags, illustrating the previously underappreciated complexity of virulence regulation in B. pertussis.
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Affiliation(s)
- Loïc Coutte
- U1019–UMR9017, University of Lille, CNRS, Inserm, CHU Lille, CIIL-Center for Infection and Immunity of Lille, Institut Pasteur de Lille, Lille, France
| | - Rudy Antoine
- U1019–UMR9017, University of Lille, CNRS, Inserm, CHU Lille, CIIL-Center for Infection and Immunity of Lille, Institut Pasteur de Lille, Lille, France
| | - Stephanie Slupek
- U1019–UMR9017, University of Lille, CNRS, Inserm, CHU Lille, CIIL-Center for Infection and Immunity of Lille, Institut Pasteur de Lille, Lille, France
| | - Camille Locht
- U1019–UMR9017, University of Lille, CNRS, Inserm, CHU Lille, CIIL-Center for Infection and Immunity of Lille, Institut Pasteur de Lille, Lille, France
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4
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Fitzgerald DM, Stringer AM, Smith C, Lapierre P, Wade JT. Genome-Wide Mapping of the Escherichia coli PhoB Regulon Reveals Many Transcriptionally Inert, Intragenic Binding Sites. mBio 2023; 14:e0253522. [PMID: 37067422 PMCID: PMC10294691 DOI: 10.1128/mbio.02535-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 03/23/2023] [Indexed: 04/18/2023] Open
Abstract
Genome-scale analyses have revealed many transcription factor binding sites within, rather than upstream of, genes, raising questions as to the function of these binding sites. Here, we use complementary approaches to map the regulon of the Escherichia coli transcription factor PhoB, a response regulator that controls transcription of genes involved in phosphate homeostasis. Strikingly, the majority of PhoB binding sites are located within genes, but these intragenic sites are not associated with detectable transcription regulation and are not evolutionarily conserved. Many intragenic PhoB sites are located in regions bound by H-NS, likely due to shared sequence preferences of PhoB and H-NS. However, these PhoB binding sites are not associated with transcription regulation even in the absence of H-NS. We propose that for many transcription factors, including PhoB, binding sites not associated with promoter sequences are transcriptionally inert and hence are tolerated as genomic "noise." IMPORTANCE Recent studies have revealed large numbers of transcription factor binding sites within the genes of bacteria. The function, if any, of the vast majority of these binding sites has not been investigated. Here, we map the binding of the transcription factor PhoB across the Escherichia coli genome, revealing that the majority of PhoB binding sites are within genes. We show that PhoB binding sites within genes are not associated with regulation of the overlapping genes. Indeed, our data suggest that bacteria tolerate the presence of large numbers of nonregulatory, intragenic binding sites for transcription factors and that these binding sites are not under selective pressure.
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Affiliation(s)
- Devon M. Fitzgerald
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, USA
| | - Anne M. Stringer
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Carol Smith
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Pascal Lapierre
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Joseph T. Wade
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, USA
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5
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Fitzgerald D, Stringer A, Smith C, Lapierre P, Wade JT. Genome-wide mapping of the Escherichia coli PhoB regulon reveals many transcriptionally inert, intragenic binding sites. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.07.527549. [PMID: 36798257 PMCID: PMC9934606 DOI: 10.1101/2023.02.07.527549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Genome-scale analyses have revealed many transcription factor binding sites within, rather than upstream of genes, raising questions as to the function of these binding sites. Here, we use complementary approaches to map the regulon of the Escherichia coli transcription factor PhoB, a response regulator that controls transcription of genes involved in phosphate homeostasis. Strikingly, the majority of PhoB binding sites are located within genes, but these intragenic sites are not associated with detectable transcription regulation and are not evolutionarily conserved. Many intragenic PhoB sites are located in regions bound by H-NS, likely due to shared sequence preferences of PhoB and H-NS. However, these PhoB binding sites are not associated with transcription regulation even in the absence of H-NS. We propose that for many transcription factors, including PhoB, binding sites not associated with promoter sequences are transcriptionally inert, and hence are tolerated as genomic "noise". IMPORTANCE Recent studies have revealed large numbers of transcription factor binding sites within the genes of bacteria. The function, if any, of the vast majority of these binding sites has not been investigated. Here, we map the binding of the transcription factor PhoB across the Escherichia coli genome, revealing that the majority of PhoB binding sites are within genes. We show that PhoB binding sites within genes are not associated with regulation of the overlapping genes. Indeed, our data suggest that bacteria tolerate the presence of large numbers of non-regulatory, intragenic binding sites for transcription factors, and that these binding sites are not under selective pressure.
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Affiliation(s)
- Devon Fitzgerald
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, USA
| | - Anne Stringer
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Carol Smith
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Pascal Lapierre
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Joseph T. Wade
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, USA
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6
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Li P, Wang X, Smith C, Shi Y, Wade JT, Sun W. Dissecting psa Locus Regulation in Yersinia pestis. J Bacteriol 2021; 203:e0023721. [PMID: 34280001 PMCID: PMC8425409 DOI: 10.1128/jb.00237-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 07/12/2021] [Indexed: 11/20/2022] Open
Abstract
The pH 6 antigen (PsaA) of Yersinia pestis is a virulence factor that is expressed in response to high temperature (37°C) and low pH (6.0). Previous studies have implicated the PsaE and PsaF regulators in the temperature- and pH-dependent regulation of psaA. Here, we show that PsaE levels are themselves controlled by pH and temperature, explaining the regulation of psaA. We identify hundreds of binding sites for PsaE across the Y. pestis genome, with the majority of binding sites located in intergenic regions bound by the nucleoid-associated protein H-NS. However, we detect direct regulation of only two transcripts by PsaE, likely due to displacement of H-NS from the corresponding promoter regions; our data suggest that most PsaE binding sites are nonregulatory or that they require additional environmental cues. We also identify the precise binding sites for PsaE that are required for temperature- and pH-dependent regulation of psaA and psaE. Thus, our data reveal the critical role that PsaE plays in the regulation of psaA and suggest that PsaE may have many additional regulatory targets. IMPORTANCE Y. pestis, the etiologic agent of plague, has been responsible for high mortality in several epidemics throughout human history. The plague bacillus has been used as a biological weapon during human history and is currently one of the most likely biological threats. PsaA and PsaE appear to play important roles during Y. pestis infection. Understanding their regulation by environmental cues would facilitate a solution to impede Y. pestis infection.
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Affiliation(s)
- Peng Li
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, New York, USA
| | - Xiuran Wang
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, New York, USA
| | - Carol Smith
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Yixin Shi
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Joseph T. Wade
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Department of Biomedical Sciences, School of Public Health University at Albany, Rensselaer, New York, USA
| | - Wei Sun
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, New York, USA
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7
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Li X, Jiang X, Xu M, Fang Y, Wang Y, Sun G, Guo J. Identification of stress-responsive transcription factors with protein-bound Escherichia coli genomic DNA libraries. AMB Express 2020; 10:199. [PMID: 33140118 PMCID: PMC7606416 DOI: 10.1186/s13568-020-01133-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 10/18/2020] [Indexed: 11/10/2022] Open
Abstract
Bacteria promoters along with operators are crucial elements in the control of gene expression in microbes in response to environmental stress changes. A genome-wide promoter DNA regulatory library is in demand to be developed for a microbe reporter method to monitor the existence of any given environmental stress substance. In this study, we utilized Escherichia coli (E. coli) as a model system for the preparation of both cell lysates and genomic DNA fragments. Through enriching protein-bound DNA fragments to construct luciferase reporter libraries, we found that, of 280 clones collected and sequenced, 131 clones contained either the promoter-35 and -10 conservative sequences and/or an operator transcription factor binding sites (TFBS) region. To demonstrate the functionality of the identified clones, five of 131 clones containing LexA binding sequence have been demonstrated to be induced in response to mitomycin C treatment. To evaluate our libraries as a functional screening library, 80 randomly picked up clones were cultured and treated with and without MMC, where two clones were shown to have greater than twofold induction. In addition, two arsenite-responsive clones were identified from 90 clones, one having the well-known ArsR and another having the osmotically inducible lipoprotein (OsmE1). The newly discovered osmE1 has been quantitatively validated to be induced by arsenite treatment with real-time PCR in a dose response and time course manner. This enriching protein-bound DNA luciferase reporter libraries and functional screening facilitate the identification of stress-responsive transcriptional factors in microbes. We developed functional libraries containing E. coli genomic-wide protein-bound DNA as enhancers/operators to regulate downstream luciferase in response to stress.
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8
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Mejía-Almonte C, Busby SJW, Wade JT, van Helden J, Arkin AP, Stormo GD, Eilbeck K, Palsson BO, Galagan JE, Collado-Vides J. Redefining fundamental concepts of transcription initiation in bacteria. Nat Rev Genet 2020; 21:699-714. [PMID: 32665585 PMCID: PMC7990032 DOI: 10.1038/s41576-020-0254-8] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2020] [Indexed: 12/15/2022]
Abstract
Despite enormous progress in understanding the fundamentals of bacterial gene regulation, our knowledge remains limited when compared with the number of bacterial genomes and regulatory systems to be discovered. Derived from a small number of initial studies, classic definitions for concepts of gene regulation have evolved as the number of characterized promoters has increased. Together with discoveries made using new technologies, this knowledge has led to revised generalizations and principles. In this Expert Recommendation, we suggest precise, updated definitions that support a logical, consistent conceptual framework of bacterial gene regulation, focusing on transcription initiation. The resulting concepts can be formalized by ontologies for computational modelling, laying the foundation for improved bioinformatics tools, knowledge-based resources and scientific communication. Thus, this work will help researchers construct better predictive models, with different formalisms, that will be useful in engineering, synthetic biology, microbiology and genetics.
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Affiliation(s)
- Citlalli Mejía-Almonte
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Morelos, Cuernavaca, México
| | | | - Joseph T Wade
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Jacques van Helden
- Aix-Marseille University, INSERM UMR S 1090, Theory and Approaches of Genome Complexity (TAGC), Marseille, France
- CNRS, Institut Français de Bioinformatique, IFB-core, UMS 3601, Evry, France
| | - Adam P Arkin
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Gary D Stormo
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Karen Eilbeck
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - James E Galagan
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Julio Collado-Vides
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Morelos, Cuernavaca, México.
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.
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Abstract
Bordetella pertussis, the etiological agent of whooping cough, remains a major global health problem. Despite the global usage of whole-cell vaccines since the 1950s and of acellular vaccines in the 1990s, it still is one of the most prevalent vaccine-preventable diseases in industrialized countries. Virulence of B. pertussis is controlled by BvgA/S, a two-component system responsible for upregulation of virulence-activated genes (vags) and downregulation of virulence-repressed genes (vrgs). By transcriptome sequencing (RNAseq) analyses, we identified more than 270 vags or vrgs, and chromatin immunoprecipitation sequencing (ChIPseq) analyses revealed 148 BvgA-binding sites, 91 within putative promoter regions, 52 within open reading frames, and 5 in noncoding regions. Some vags, such as dnt and fhaL, do not contain a BvgA-binding site, suggesting indirect regulation. In contrast, several vrgs and some genes not identified by RNAseq analyses under laboratory conditions contain strong BvgA-binding sites, indicating previously unappreciated complexities of BvgA/S biology. Bordetella pertussis regulates the production of its virulence factors by the two-component system BvgAS. In the virulence phase, BvgS phosphorylates BvgA, which then activates the transcription of virulence-activated genes (vags). In the avirulence phase, such as during growth in the presence of MgSO4, BvgA is not phosphorylated and the vags are not expressed. Instead, a set of virulence-repressed genes (vrgs) is expressed. Here, we performed transcriptome sequencing (RNAseq) analyses on B. pertussis cultivated with or without MgSO4 and on a BvgA-deficient Tohama I derivative. We observed that 146 genes were less expressed under modulating conditions or in the BvgA-deficient strain than under the nonmodulating condition, while 130 genes were more expressed. Some of the genes code for proteins with regulatory functions, suggesting a BvgA/S regulation cascade. To determine which genes are directly regulated by BvgA, we performed chromatin immunoprecipitation sequencing (ChIPseq) analyses. We identified 148 BvgA-binding sites, 91 within putative promoter regions, 52 within open reading frames, and 5 in noncoding regions. Among the former, 32 are in BvgA-regulated putative promoter regions. Some vags, such as dnt and fhaL, contain no BvgA-binding site, suggesting indirect BvgA regulation. Unexpectedly, BvgA also bound to some vrg putative promoter regions. Together, these observations indicate an unrecognized complexity of BvgA/S biology. IMPORTANCEBordetella pertussis, the etiological agent of whooping cough, remains a major global health problem. Despite the global usage of whole-cell vaccines since the 1950s and of acellular vaccines in the 1990s, it still is one of the most prevalent vaccine-preventable diseases in industrialized countries. Virulence of B. pertussis is controlled by BvgA/S, a two-component system responsible for upregulation of virulence-activated genes (vags) and downregulation of virulence-repressed genes (vrgs). By transcriptome sequencing (RNAseq) analyses, we identified more than 270 vags or vrgs, and chromatin immunoprecipitation sequencing (ChIPseq) analyses revealed 148 BvgA-binding sites, 91 within putative promoter regions, 52 within open reading frames, and 5 in noncoding regions. Some vags, such as dnt and fhaL, do not contain a BvgA-binding site, suggesting indirect regulation. In contrast, several vrgs and some genes not identified by RNAseq analyses under laboratory conditions contain strong BvgA-binding sites, indicating previously unappreciated complexities of BvgA/S biology.
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10
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Grazon C, Baer RC, Kuzmanović U, Nguyen T, Chen M, Zamani M, Chern M, Aquino P, Zhang X, Lecommandoux S, Fan A, Cabodi M, Klapperich C, Grinstaff MW, Dennis AM, Galagan JE. A progesterone biosensor derived from microbial screening. Nat Commun 2020; 11:1276. [PMID: 32152281 PMCID: PMC7062782 DOI: 10.1038/s41467-020-14942-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 02/03/2020] [Indexed: 01/08/2023] Open
Abstract
Bacteria are an enormous and largely untapped reservoir of biosensing proteins. We describe an approach to identify and isolate bacterial allosteric transcription factors (aTFs) that recognize a target analyte and to develop these TFs into biosensor devices. Our approach utilizes a combination of genomic screens and functional assays to identify and isolate biosensing TFs, and a quantum-dot Förster Resonance Energy Transfer (FRET) strategy for transducing analyte recognition into real-time quantitative measurements. We use this approach to identify a progesterone-sensing bacterial aTF and to develop this TF into an optical sensor for progesterone. The sensor detects progesterone in artificial urine with sufficient sensitivity and specificity for clinical use, while being compatible with an inexpensive and portable electronic reader for point-of-care applications. Our results provide proof-of-concept for a paradigm of microbially-derived biosensors adaptable to inexpensive, real-time sensor devices.
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Affiliation(s)
- Chloé Grazon
- Department of Chemistry, Boston University, Boston, MA, 02215, USA
- University Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, F-33600, Pessac, France
| | - R C Baer
- Department of Microbiology, Boston University, Boston, MA, 02118, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, 02118, USA
| | - Uroš Kuzmanović
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Thuy Nguyen
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Mingfu Chen
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Marjon Zamani
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Margaret Chern
- Division of Materials Science and Engineering, Boston University, Boston, MA, 02215, USA
| | - Patricia Aquino
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Xiaoman Zhang
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | | | - Andy Fan
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Mario Cabodi
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Catherine Klapperich
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
- Division of Materials Science and Engineering, Boston University, Boston, MA, 02215, USA
| | - Mark W Grinstaff
- Department of Chemistry, Boston University, Boston, MA, 02215, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
- Division of Materials Science and Engineering, Boston University, Boston, MA, 02215, USA
| | - Allison M Dennis
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
- Division of Materials Science and Engineering, Boston University, Boston, MA, 02215, USA
| | - James E Galagan
- Department of Microbiology, Boston University, Boston, MA, 02118, USA.
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, 02118, USA.
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA.
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11
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Thöming JG, Tomasch J, Preusse M, Koska M, Grahl N, Pohl S, Willger SD, Kaever V, Müsken M, Häussler S. Parallel evolutionary paths to produce more than one Pseudomonas aeruginosa biofilm phenotype. NPJ Biofilms Microbiomes 2020; 6:2. [PMID: 31934344 PMCID: PMC6954232 DOI: 10.1038/s41522-019-0113-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 12/16/2019] [Indexed: 01/28/2023] Open
Abstract
Studying parallel evolution of similar traits in independent within-species lineages provides an opportunity to address evolutionary predictability of molecular changes underlying adaptation. In this study, we monitored biofilm forming capabilities, motility, and virulence phenotypes of a plethora of phylogenetically diverse clinical isolates of the opportunistic pathogen Pseudomonas aeruginosa. We also recorded biofilm-specific and planktonic transcriptional responses. We found that P. aeruginosa isolates could be stratified based on the production of distinct organismal traits. Three major biofilm phenotypes, which shared motility and virulence phenotypes, were produced repeatedly in several isolates, indicating that the phenotypes evolved via parallel or convergent evolution. Of note, while we found a restricted general response to the biofilm environment, the individual groups of biofilm phenotypes reproduced biofilm transcriptional profiles that included the expression of well-known biofilm features, such as surface adhesive structures and extracellular matrix components. Our results provide insights into distinct ways to make a biofilm and indicate that genetic adaptations can modulate multiple pathways for biofilm development that are followed by several independent clinical isolates. Uncovering core regulatory pathways that drive biofilm-associated growth and tolerance towards environmental stressors promises to give clues to host and environmental interactions and could provide useful targets for new clinical interventions.
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Affiliation(s)
- Janne G. Thöming
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
- Department of Clinical Microbiology, Copenhagen University Hospital – Rigshospitalet, Copenhagen, Denmark
| | - Jürgen Tomasch
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Matthias Preusse
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Michal Koska
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Nora Grahl
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sarah Pohl
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sven D. Willger
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Volkhard Kaever
- Research Core Unit Metabolomics and Institute of Pharmacology, Hannover Medical School, Hannover, Germany
| | - Mathias Müsken
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Susanne Häussler
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
- Department of Clinical Microbiology, Copenhagen University Hospital – Rigshospitalet, Copenhagen, Denmark
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
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12
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Rioualen C, Charbonnier-Khamvongsa L, Collado-Vides J, van Helden J. Integrating Bacterial ChIP-seq and RNA-seq Data With SnakeChunks. CURRENT PROTOCOLS IN BIOINFORMATICS 2019; 66:e72. [PMID: 30786165 PMCID: PMC7302399 DOI: 10.1002/cpbi.72] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Next-generation sequencing (NGS) is becoming a routine approach in most domains of the life sciences. To ensure reproducibility of results, there is a crucial need to improve the automation of NGS data processing and enable forthcoming studies relying on big datasets. Although user-friendly interfaces now exist, there remains a strong need for accessible solutions that allow experimental biologists to analyze and explore their results in an autonomous and flexible way. The protocols here describe a modular system that enable a user to compose and fine-tune workflows based on SnakeChunks, a library of rules for the Snakemake workflow engine. They are illustrated using a study combining ChIP-seq and RNA-seq to identify target genes of the global transcription factor FNR in Escherichia coli, which has the advantage that results can be compared with the most up-to-date collection of existing knowledge about transcriptional regulation in this model organism, extracted from the RegulonDB database. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Claire Rioualen
- Aix-Marseille University, INSERM, Laboratory of Theory and Approaches of Genome Complexity (TAGC), Marseille, France
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Lucie Charbonnier-Khamvongsa
- Aix-Marseille University, INSERM, Laboratory of Theory and Approaches of Genome Complexity (TAGC), Marseille, France
| | - Julio Collado-Vides
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts
| | - Jacques van Helden
- Aix-Marseille University, INSERM, Laboratory of Theory and Approaches of Genome Complexity (TAGC), Marseille, France
- Institut Français de Bioinformatique (IFB), UMS 3601-CNRS, Université Paris-Saclay, Orsay, France
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13
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MrpJ Directly Regulates Proteus mirabilis Virulence Factors, Including Fimbriae and Type VI Secretion, during Urinary Tract Infection. Infect Immun 2018; 86:IAI.00388-18. [PMID: 30082479 DOI: 10.1128/iai.00388-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 07/30/2018] [Indexed: 12/18/2022] Open
Abstract
Proteus mirabilis is a leading cause of catheter-associated urinary tract infections (CAUTIs) and urolithiasis. The transcriptional regulator MrpJ inversely modulates two critical aspects of P. mirabilis UTI progression: fimbria-mediated attachment and flagellum-mediated motility. Transcriptome data indicated a network of virulence-associated genes under MrpJ's control. Here, we identify the direct gene regulon of MrpJ and its contribution to P. mirabilis pathogenesis, leading to the discovery of novel virulence targets. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) was used for the first time in a CAUTI pathogen to probe for in vivo direct targets of MrpJ. Selected MrpJ-regulated genes were mutated and assessed for their contribution to UTI using a mouse model. ChIP-seq revealed a palindromic MrpJ binding sequence and 78 MrpJ-bound regions, including binding sites upstream of genes involved in motility, fimbriae, and a type VI secretion system (T6SS). A combinatorial mutation approach established the contribution of three fimbriae (fim8A, fim14A, and pmpA) to UTI and a new pathogenic role for the T6SS in UTI progression. In conclusion, this study (i) establishes the direct gene regulon and an MrpJ consensus binding site and (ii) led to the discovery of new virulence genes in P. mirabilis UTI, which could be targeted for therapeutic intervention of CAUTI.
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14
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Promoter Boundaries for the luxCDABE and betIBA-proXWV Operons in Vibrio harveyi Defined by the Method Rapid Arbitrary PCR Insertion Libraries (RAIL). J Bacteriol 2018. [PMID: 29531178 DOI: 10.1128/jb.00724-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Experimental studies of transcriptional regulation in bacteria require the ability to precisely measure changes in gene expression, often accomplished through the use of reporter genes. However, the boundaries of promoter sequences required for transcription are often unknown, thus complicating the construction of reporters and genetic analysis of transcriptional regulation. Here, we analyze reporter libraries to define the promoter boundaries of the luxCDABE bioluminescence operon and the betIBA-proXWV osmotic stress operon in Vibrio harveyi We describe a new method called rapid arbitrary PCR insertion libraries (RAIL) that combines the power of arbitrary PCR and isothermal DNA assembly to rapidly clone promoter fragments of various lengths upstream of reporter genes to generate large libraries. To demonstrate the versatility and efficiency of RAIL, we analyzed the promoters driving expression of the luxCDABE and betIBA-proXWV operons and created libraries of DNA fragments from these loci fused to fluorescent reporters. Using flow cytometry sorting and deep sequencing, we identified the DNA regions necessary and sufficient for maximum gene expression for each promoter. These analyses uncovered previously unknown regulatory sequences and validated known transcription factor binding sites. We applied this high-throughput method to gfp, mCherry, and lacZ reporters and multiple promoters in V. harveyi We anticipate that the RAIL method will be easily applicable to other model systems for genetic, molecular, and cell biological applications.IMPORTANCE Gene reporter constructs have long been essential tools for studying gene regulation in bacteria, particularly following the recent advent of fluorescent gene reporters. We developed a new method that enables efficient construction of promoter fusions to reporter genes to study gene regulation. We demonstrate the versatility of this technique in the model bacterium Vibrio harveyi by constructing promoter libraries for three bacterial promoters using three reporter genes. These libraries can be used to determine the DNA sequences required for gene expression, revealing regulatory elements in promoters. This method is applicable to various model systems and reporter genes for assaying gene expression.
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15
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Fitzgerald DM, Smith C, Lapierre P, Wade JT. The evolutionary impact of intragenic FliA promoters in proteobacteria. Mol Microbiol 2018; 108:361-378. [PMID: 29476659 PMCID: PMC5943157 DOI: 10.1111/mmi.13941] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2018] [Indexed: 12/12/2022]
Abstract
In Escherichia coli, one sigma factor recognizes the majority of promoters, and six 'alternative' sigma factors recognize specific subsets of promoters. The alternative sigma factor FliA (σ28 ) recognizes promoters upstream of many flagellar genes. We previously showed that most E. coli FliA binding sites are located inside genes. However, it was unclear whether these intragenic binding sites represent active promoters. Here, we construct and assay transcriptional promoter-lacZ fusions for all 52 putative FliA promoters previously identified by ChIP-seq. These experiments, coupled with integrative analysis of published genome-scale transcriptional datasets, strongly suggest that most intragenic FliA binding sites are active promoters that transcribe highly unstable RNAs. Additionally, we show that widespread intragenic FliA-dependent transcription may be a conserved phenomenon, but that specific promoters are not themselves conserved. We conclude that intragenic FliA-dependent promoters and the resulting RNAs are unlikely to have important regulatory functions. Nonetheless, one intragenic FliA promoter is broadly conserved and constrains evolution of the overlapping protein-coding gene. Thus, our data indicate that intragenic regulatory elements can influence bacterial protein evolution and suggest that the impact of intragenic regulatory sequences on genome evolution should be considered more broadly.
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Affiliation(s)
- Devon M. Fitzgerald
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, USA
| | - Carol Smith
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Pascal Lapierre
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Joseph T. Wade
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, USA
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
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16
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Validating regulatory predictions from diverse bacteria with mutant fitness data. PLoS One 2017; 12:e0178258. [PMID: 28542589 PMCID: PMC5443562 DOI: 10.1371/journal.pone.0178258] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 04/27/2017] [Indexed: 11/26/2022] Open
Abstract
Although transcriptional regulation is fundamental to understanding bacterial physiology, the targets of most bacterial transcription factors are not known. Comparative genomics has been used to identify likely targets of some of these transcription factors, but these predictions typically lack experimental support. Here, we used mutant fitness data, which measures the importance of each gene for a bacterium’s growth across many conditions, to test regulatory predictions from RegPrecise, a curated collection of comparative genomics predictions. Because characterized transcription factors often have correlated fitness with one of their targets (either positively or negatively), correlated fitness patterns provide support for the comparative genomics predictions. At a false discovery rate of 3%, we identified significant cofitness for at least one target of 158 TFs in 107 ortholog groups and from 24 bacteria. Thus, high-throughput genetics can be used to identify a high-confidence subset of the sequence-based regulatory predictions.
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17
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Aquino P, Honda B, Jaini S, Lyubetskaya A, Hosur K, Chiu JG, Ekladious I, Hu D, Jin L, Sayeg MK, Stettner AI, Wang J, Wong BG, Wong WS, Alexander SL, Ba C, Bensussen SI, Bernstein DB, Braff D, Cha S, Cheng DI, Cho JH, Chou K, Chuang J, Gastler DE, Grasso DJ, Greifenberger JS, Guo C, Hawes AK, Israni DV, Jain SR, Kim J, Lei J, Li H, Li D, Li Q, Mancuso CP, Mao N, Masud SF, Meisel CL, Mi J, Nykyforchyn CS, Park M, Peterson HM, Ramirez AK, Reynolds DS, Rim NG, Saffie JC, Su H, Su WR, Su Y, Sun M, Thommes MM, Tu T, Varongchayakul N, Wagner TE, Weinberg BH, Yang R, Yaroslavsky A, Yoon C, Zhao Y, Zollinger AJ, Stringer AM, Foster JW, Wade J, Raman S, Broude N, Wong WW, Galagan JE. Coordinated regulation of acid resistance in Escherichia coli. BMC SYSTEMS BIOLOGY 2017; 11:1. [PMID: 28061857 PMCID: PMC5217608 DOI: 10.1186/s12918-016-0376-y] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 12/07/2016] [Indexed: 12/29/2022]
Abstract
Background Enteric Escherichia coli survives the highly acidic environment of the stomach through multiple acid resistance (AR) mechanisms. The most effective system, AR2, decarboxylates externally-derived glutamate to remove cytoplasmic protons and excrete GABA. The first described system, AR1, does not require an external amino acid. Its mechanism has not been determined. The regulation of the multiple AR systems and their coordination with broader cellular metabolism has not been fully explored. Results We utilized a combination of ChIP-Seq and gene expression analysis to experimentally map the regulatory interactions of four TFs: nac, ntrC, ompR, and csiR. Our data identified all previously in vivo confirmed direct interactions and revealed several others previously inferred from gene expression data. Our data demonstrate that nac and csiR directly modulate AR, and leads to a regulatory network model in which all four TFs participate in coordinating acid resistance, glutamate metabolism, and nitrogen metabolism. This model predicts a novel mechanism for AR1 by which the decarboxylation enzymes of AR2 are used with internally derived glutamate. This hypothesis makes several testable predictions that we confirmed experimentally. Conclusions Our data suggest that the regulatory network underlying AR is complex and deeply interconnected with the regulation of GABA and glutamate metabolism, nitrogen metabolism. These connections underlie and experimentally validated model of AR1 in which the decarboxylation enzymes of AR2 are used with internally derived glutamate. Electronic supplementary material The online version of this article (doi:10.1186/s12918-016-0376-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Patricia Aquino
- Department of Biomedical Engineering, Boston University, Boston, USA.,BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Brent Honda
- Department of Biomedical Engineering, Boston University, Boston, USA
| | - Suma Jaini
- Department of Biomedical Engineering, Boston University, Boston, USA
| | | | - Krutika Hosur
- Department of Biomedical Engineering, Boston University, Boston, USA.,BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Joanna G Chiu
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Iriny Ekladious
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Dongjian Hu
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Lin Jin
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Marianna K Sayeg
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Arion I Stettner
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Julia Wang
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Brandon G Wong
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Winnie S Wong
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | | | - Cong Ba
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Seth I Bensussen
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - David B Bernstein
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Dana Braff
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Susie Cha
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Daniel I Cheng
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Jang Hwan Cho
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Kenny Chou
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - James Chuang
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Daniel E Gastler
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Daniel J Grasso
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | | | - Chen Guo
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Anna K Hawes
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Divya V Israni
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Saloni R Jain
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Jessica Kim
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Junyu Lei
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Hao Li
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - David Li
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Qian Li
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | | | - Ning Mao
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Salwa F Masud
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Cari L Meisel
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Jing Mi
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | | | - Minhee Park
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Hannah M Peterson
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Alfred K Ramirez
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Daniel S Reynolds
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Nae Gyune Rim
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Jared C Saffie
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Hang Su
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Wendell R Su
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Yaqing Su
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Meng Sun
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Meghan M Thommes
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Tao Tu
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | | | - Tyler E Wagner
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | | | - Rouhui Yang
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | | | - Christine Yoon
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Yanyu Zhao
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | | | - Anne M Stringer
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - John W Foster
- Department of Microbiology and Immunology, University of South Alabama College of Medicine, Mobile, AL, 36688, USA
| | - Joseph Wade
- Wadsworth Center, New York State Department of Health, Albany, NY, USA.,Department of Biomedical Sciences, University at Albany, Albany, NY, USA
| | - Sahadaven Raman
- Department of Microbiology and Immunology, University of South Alabama College of Medicine, Mobile, AL, 36688, USA
| | - Natasha Broude
- Department of Biomedical Engineering, Boston University, Boston, USA
| | - Wilson W Wong
- Department of Biomedical Engineering, Boston University, Boston, USA
| | - James E Galagan
- Department of Biomedical Engineering, Boston University, Boston, USA. .,Bioinformatics program, Boston University, Boston, USA. .,National Emerging Infectious Diseases Laboratory, Boston University, Boston, USA.
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18
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Dekhang R, Wu C, Smith KM, Lamb TM, Peterson M, Bredeweg EL, Ibarra O, Emerson JM, Karunarathna N, Lyubetskaya A, Azizi E, Hurley JM, Dunlap JC, Galagan JE, Freitag M, Sachs MS, Bell-Pedersen D. The Neurospora Transcription Factor ADV-1 Transduces Light Signals and Temporal Information to Control Rhythmic Expression of Genes Involved in Cell Fusion. G3 (BETHESDA, MD.) 2017; 7:129-142. [PMID: 27856696 PMCID: PMC5217103 DOI: 10.1534/g3.116.034298] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 11/01/2016] [Indexed: 12/20/2022]
Abstract
Light and the circadian clock have a profound effect on the biology of organisms through the regulation of large sets of genes. Toward understanding how light and the circadian clock regulate gene expression, we used genome-wide approaches to identify the direct and indirect targets of the light-responsive and clock-controlled transcription factor ADV-1 in Neurospora crassa A large proportion of ADV-1 targets were found to be light- and/or clock-controlled, and enriched for genes involved in development, metabolism, cell growth, and cell fusion. We show that ADV-1 is necessary for transducing light and/or temporal information to its immediate downstream targets, including controlling rhythms in genes critical to somatic cell fusion. However, while ADV-1 targets are altered in predictable ways in Δadv-1 cells in response to light, this is not always the case for rhythmic target gene expression. These data suggest that a complex regulatory network downstream of ADV-1 functions to generate distinct temporal dynamics of target gene expression relative to the central clock mechanism.
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Affiliation(s)
- Rigzin Dekhang
- Department of Biology, Texas A&M University, College Station, Texas 77843
| | - Cheng Wu
- Department of Biology, Texas A&M University, College Station, Texas 77843
| | - Kristina M Smith
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
| | - Teresa M Lamb
- Department of Biology, Texas A&M University, College Station, Texas 77843
| | | | - Erin L Bredeweg
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
| | - Oneida Ibarra
- Department of Biology, Texas A&M University, College Station, Texas 77843
| | - Jillian M Emerson
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755
| | | | | | - Elham Azizi
- Bioinformatics Program, Boston University, Massachusetts 02215
| | - Jennifer M Hurley
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Jay C Dunlap
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755
| | - James E Galagan
- Bioinformatics Program, Boston University, Massachusetts 02215
- National Emerging Infectious Diseases Laboratories, Boston University, Massachusetts 02118
- Department of Microbiology, Boston University, Massachusetts 02215
- Department of Biomedical Engineering, Boston University, Massachusetts 02215
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
| | - Matthew S Sachs
- Department of Biology, Texas A&M University, College Station, Texas 77843
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19
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Li CW, Lee YL, Chen BS. Genetic-and-Epigenetic Interspecies Networks for Cross-Talk Mechanisms in Human Macrophages and Dendritic Cells during MTB Infection. Front Cell Infect Microbiol 2016; 6:124. [PMID: 27803888 PMCID: PMC5067469 DOI: 10.3389/fcimb.2016.00124] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 09/22/2016] [Indexed: 12/29/2022] Open
Abstract
Tuberculosis is caused by Mycobacterium tuberculosis (Mtb) infection. Mtb is one of the oldest human pathogens, and evolves mechanisms implied in human evolution. The lungs are the first organ exposed to aerosol-transmitted Mtb during gaseous exchange. Therefore, the guards of the immune system in the lungs, such as macrophages (Mϕs) and dendritic cells (DCs), are the most important defense against Mtb infection. There have been several studies discussing the functions of Mϕs and DCs during Mtb infection, but the genome-wide pathways and networks are still incomplete. Furthermore, the immune response induced by Mϕs and DCs varies. Therefore, we analyzed the cross-talk genome-wide genetic-and-epigenetic interspecies networks (GWGEINs) between Mϕs vs. Mtb and DCs vs. Mtb to determine the varying mechanisms of both the host and pathogen as it relates to Mϕs and DCs during early Mtb infection. First, we performed database mining to construct candidate cross-talk GWGEIN between human cells and Mtb. Then we constructed dynamic models to characterize the molecular mechanisms, including intraspecies gene/microRNA (miRNA) regulation networks (GRNs), intraspecies protein-protein interaction networks (PPINs), and the interspecies PPIN of the cross-talk GWGEIN. We applied a system identification method and a system order detection scheme to dynamic models to identify the real cross-talk GWGEINs using the microarray data of Mϕs, DCs and Mtb. After identifying the real cross-talk GWGEINs, the principal network projection (PNP) method was employed to construct host-pathogen core networks (HPCNs) between Mϕs vs. Mtb and DCs vs. Mtb during infection process. Thus, we investigated the underlying cross-talk mechanisms between the host and the pathogen to determine how the pathogen counteracts host defense mechanisms in Mϕs and DCs during Mtb H37Rv early infection. Based on our findings, we propose Rv1675c as a potential drug target because of its important defensive role in Mϕs. Furthermore, the membrane essential proteins v1098c, and Rv1696 (or cytoplasm for Rv0667), in Mtb could also be potential drug targets because of their important roles in Mtb survival in both cell types. We also propose the drugs Lopinavir, TMC207, ATSM, and GTSM as potential therapeutic treatments for Mtb infection since they target the above potential drug targets.
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Affiliation(s)
- Cheng-Wei Li
- Laboratory of Control and Systems Biology, National Tsing Hua University Hsinchu, Taiwan
| | - Yun-Lin Lee
- Laboratory of Control and Systems Biology, National Tsing Hua University Hsinchu, Taiwan
| | - Bor-Sen Chen
- Laboratory of Control and Systems Biology, National Tsing Hua University Hsinchu, Taiwan
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20
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Gomes ALC, Wang HH. The Role of Genome Accessibility in Transcription Factor Binding in Bacteria. PLoS Comput Biol 2016; 12:e1004891. [PMID: 27104615 PMCID: PMC4841574 DOI: 10.1371/journal.pcbi.1004891] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 03/31/2016] [Indexed: 02/01/2023] Open
Abstract
ChIP-seq enables genome-scale identification of regulatory regions that govern gene expression. However, the biological insights generated from ChIP-seq analysis have been limited to predictions of binding sites and cooperative interactions. Furthermore, ChIP-seq data often poorly correlate with in vitro measurements or predicted motifs, highlighting that binding affinity alone is insufficient to explain transcription factor (TF)-binding in vivo. One possibility is that binding sites are not equally accessible across the genome. A more comprehensive biophysical representation of TF-binding is required to improve our ability to understand, predict, and alter gene expression. Here, we show that genome accessibility is a key parameter that impacts TF-binding in bacteria. We developed a thermodynamic model that parameterizes ChIP-seq coverage in terms of genome accessibility and binding affinity. The role of genome accessibility is validated using a large-scale ChIP-seq dataset of the M. tuberculosis regulatory network. We find that accounting for genome accessibility led to a model that explains 63% of the ChIP-seq profile variance, while a model based in motif score alone explains only 35% of the variance. Moreover, our framework enables de novo ChIP-seq peak prediction and is useful for inferring TF-binding peaks in new experimental conditions by reducing the need for additional experiments. We observe that the genome is more accessible in intergenic regions, and that increased accessibility is positively correlated with gene expression and anti-correlated with distance to the origin of replication. Our biophysically motivated model provides a more comprehensive description of TF-binding in vivo from first principles towards a better representation of gene regulation in silico, with promising applications in systems biology.
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Affiliation(s)
- Antonio L. C. Gomes
- Department of Systems Biology, Columbia University, New York, New York, United States of America
| | - Harris H. Wang
- Department of Systems Biology, Columbia University, New York, New York, United States of America
- Department of Pathology and Cell Biology, Columbia University, New York, New York, United States of America
- * E-mail:
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21
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Sharp JD, Singh AK, Park ST, Lyubetskaya A, Peterson MW, Gomes ALC, Potluri LP, Raman S, Galagan JE, Husson RN. Comprehensive Definition of the SigH Regulon of Mycobacterium tuberculosis Reveals Transcriptional Control of Diverse Stress Responses. PLoS One 2016; 11:e0152145. [PMID: 27003599 PMCID: PMC4803200 DOI: 10.1371/journal.pone.0152145] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 03/09/2016] [Indexed: 11/24/2022] Open
Abstract
Expression of SigH, one of 12 Mycobacterium tuberculosis alternative sigma factors, is induced by heat, oxidative and nitric oxide stresses. SigH activation has been shown to increase expression of several genes, including genes involved in maintaining redox equilibrium and in protein degradation. However, few of these are known to be directly regulated by SigH. The goal of this project is to comprehensively define the Mycobacterium tuberculosis genes and operons that are directly controlled by SigH in order to gain insight into the role of SigH in regulating M. tuberculosis physiology. We used ChIP-Seq to identify in vivo SigH binding sites throughout the M. tuberculosis genome, followed by quantification of SigH-dependent expression of genes linked to these sites and identification of SigH-regulated promoters. We identified 69 SigH binding sites, which are located both in intergenic regions and within annotated coding sequences in the annotated M. tuberculosis genome. 41 binding sites were linked to genes that showed greater expression following heat stress in a SigH-dependent manner. We identified several genes not previously known to be regulated by SigH, including genes involved in DNA repair, cysteine biosynthesis, translation, and genes of unknown function. Experimental and computational analysis of SigH-regulated promoter sequences within these binding sites identified strong consensus -35 and -10 promoter sequences, but with tolerance for non-consensus bases at specific positions. This comprehensive identification and validation of SigH-regulated genes demonstrates an extended SigH regulon that controls an unexpectedly broad range of stress response functions.
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Affiliation(s)
- Jared D. Sharp
- Division of Infectious Diseases, Boston Children’s Hospital and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, United States of America
| | - Atul K. Singh
- Division of Infectious Diseases, Boston Children’s Hospital and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, United States of America
| | - Sang Tae Park
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts 02118, United States of America
| | - Anna Lyubetskaya
- Bioinformatics Program, Boston University, Boston, Massachusetts 02215, United States of America
| | - Matthew W. Peterson
- Department of Microbiology, Boston University, Boston, Massachusetts 02215, United States of America
| | - Antonio L. C. Gomes
- Bioinformatics Program, Boston University, Boston, Massachusetts 02215, United States of America
| | - Lakshmi-Prasad Potluri
- Division of Infectious Diseases, Boston Children’s Hospital and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, United States of America
| | - Sahadevan Raman
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts 02118, United States of America
| | - James E. Galagan
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts 02118, United States of America
- Bioinformatics Program, Boston University, Boston, Massachusetts 02215, United States of America
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States of America
- Department of Microbiology, Boston University, Boston, Massachusetts 02215, United States of America
| | - Robert N. Husson
- Division of Infectious Diseases, Boston Children’s Hospital and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, United States of America
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22
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Wu W, Sun X, Gao Y, Jiang J, Cui Z, Ge B, Wu H, Zhang L, Li Y. Genome-Wide De Novo Prediction of Cis-Regulatory Binding Sites in Mycobacterium tuberculosis H37Rv. PLoS One 2016; 11:e0148965. [PMID: 26886880 PMCID: PMC4757040 DOI: 10.1371/journal.pone.0148965] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 01/26/2016] [Indexed: 12/03/2022] Open
Abstract
The transcription regulatory system of Mycobacterium tuberculosis (M. tb) remains incompletely understood. In this study, we have applied the eGLECLUBS algorithm to a group of related prokaryotic genomes for de novo genome-wide prediction of cis-regulatory binding sites (CRBSs) in M. tb H37Rv. The top 250 clusters from our prediction recovered 83.3% (50/60) of all known CRBSs in extracted inter-operonic sequences of this strain. We further demonstrated that the integration of our prediction results with the ChIP-Seq datasets is very effective in identifying true binding sites of TFs. Using electrophoretic mobility shift assays and real-time RT-PCR, we experimentally verified our prediction of CRBSs for Rv0081, an important transcription factor thought to be involved in regulation of M. tb under hypoxia.
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Affiliation(s)
- Wei Wu
- State Key Lab of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, College of Life Sciences, Fudan University, Shanghai, PR China
| | - Xian Sun
- State Key Lab of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, College of Life Sciences, Fudan University, Shanghai, PR China
| | - Yun Gao
- State Key Lab of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, College of Life Sciences, Fudan University, Shanghai, PR China
| | - Jun Jiang
- State Key Lab of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, College of Life Sciences, Fudan University, Shanghai, PR China
| | - Zhenling Cui
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Medical School, Tongji University, Shanghai, China
| | - Baoxue Ge
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Medical School, Tongji University, Shanghai, China
| | - Hai Wu
- State Key Lab of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, College of Life Sciences, Fudan University, Shanghai, PR China
| | - Lu Zhang
- State Key Lab of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, College of Life Sciences, Fudan University, Shanghai, PR China
- * E-mail: ;
| | - Yao Li
- State Key Lab of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, College of Life Sciences, Fudan University, Shanghai, PR China
- * E-mail: ;
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Abstract
Transcription factors (TFs) play a central role in regulating gene expression in all bacteria. Yet until recently, studies of TF binding were limited to a small number of factors at a few genomic locations. Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) provides the ability to map binding sites globally for TFs, and the scalability of the technology enables the ability to map binding sites for every DNA binding protein in a prokaryotic organism. We have developed a protocol for ChIP-Seq tailored for use with mycobacteria and an analysis pipeline for processing the resulting data. The protocol and pipeline have been used to map over 100 TFs from Mycobacterium tuberculosis, as well as numerous TFs from related mycobacteria and other bacteria. The resulting data provide evidence that the long-accepted spatial relationship between TF binding site, promoter motif, and the corresponding regulated gene may be too simple a paradigm, failing to adequately capture the variety of TF binding sites found in prokaryotes. In this article we describe the protocol and analysis pipeline, the validation of these methods, and the results of applying these methods to M. tuberculosis.
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Abstract
Twenty years ago, the publication of the first bacterial genome sequence, from Haemophilus influenzae, shook the world of bacteriology. In this Timeline, we review the first two decades of bacterial genome sequencing, which have been marked by three revolutions: whole-genome shotgun sequencing, high-throughput sequencing and single-molecule long-read sequencing. We summarize the social history of sequencing and its impact on our understanding of the biology, diversity and evolution of bacteria, while also highlighting spin-offs and translational impact in the clinic. We look forward to a 'sequencing singularity', where sequencing becomes the method of choice for as-yet unthinkable applications in bacteriology and beyond.
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Affiliation(s)
- Nicholas J Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Mark J Pallen
- Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
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25
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Bonocora RP, Smith C, Lapierre P, Wade JT. Genome-Scale Mapping of Escherichia coli σ54 Reveals Widespread, Conserved Intragenic Binding. PLoS Genet 2015; 11:e1005552. [PMID: 26425847 PMCID: PMC4591121 DOI: 10.1371/journal.pgen.1005552] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 09/03/2015] [Indexed: 11/18/2022] Open
Abstract
Bacterial RNA polymerases must associate with a σ factor to bind promoter DNA and initiate transcription. There are two families of σ factor: the σ70 family and the σ54 family. Members of the σ54 family are distinct in their ability to bind promoter DNA sequences, in the context of RNA polymerase holoenzyme, in a transcriptionally inactive state. Here, we map the genome-wide association of Escherichia coli σ54, the archetypal member of the σ54 family. Thus, we vastly expand the list of known σ54 binding sites to 135. Moreover, we estimate that there are more than 250 σ54 sites in total. Strikingly, the majority of σ54 binding sites are located inside genes. The location and orientation of intragenic σ54 binding sites is non-random, and many intragenic σ54 binding sites are conserved. We conclude that many intragenic σ54 binding sites are likely to be functional. Consistent with this assertion, we identify three conserved, intragenic σ54 promoters that drive transcription of mRNAs with unusually long 5ʹ UTRs. Bacterial RNA polymerases must associate with a σ factor to bind to promoter DNA sequences upstream of genes and initiate transcription. There are two families of σ factor: σ70 and σ54. Members of the σ54 family are distinct from members of the σ70 family in their ability to bind promoter DNA sequences, in association with RNA polymerase, in a transcriptionally inactive state. We have determined positions in the Escherichia coli genome that are bound by σ54, the archetypal member of the σ54 family. Surprisingly, we identified 135 binding sites for σ54, a huge increase over the number of previously described sites. Our data suggest that there are more than 250 σ54 sites in total. Strikingly, most σ54 binding sites are located inside genes, whereas only one intragenic σ54 binding site has previously been described. The location and orientation of intragenic σ54 binding sites is non-random, and many intragenic σ54 binding sites are conserved in other bacterial species. We conclude that many intragenic σ54 binding sites are likely to be functional. Consistent with this notion, we identify three σ54 promoters in E. coli that are located inside genes but drive transcription of unusual mRNAs for the neighboring genes.
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Affiliation(s)
- Richard P. Bonocora
- Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Carol Smith
- Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Pascal Lapierre
- Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Joseph T. Wade
- Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, United States of America
- * E-mail:
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26
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Ranganathan S, Bai G, Lyubetskaya A, Knapp GS, Peterson MW, Gazdik M, C Gomes AL, Galagan JE, McDonough KA. Characterization of a cAMP responsive transcription factor, Cmr (Rv1675c), in TB complex mycobacteria reveals overlap with the DosR (DevR) dormancy regulon. Nucleic Acids Res 2015; 44:134-51. [PMID: 26358810 PMCID: PMC4705688 DOI: 10.1093/nar/gkv889] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 08/26/2015] [Indexed: 12/17/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) Cmr (Rv1675c) is a CRP/FNR family transcription factor known to be responsive to cAMP levels and during macrophage infections. However, Cmr's DNA binding properties, cellular targets and overall role in tuberculosis (TB) complex bacteria have not been characterized. In this study, we used experimental and computational approaches to characterize Cmr's DNA binding properties and identify a putative regulon. Cmr binds a 16-bp palindromic site that includes four highly conserved nucleotides that are required for DNA binding. A total of 368 binding sites, distributed in clusters among ∼200 binding regions throughout the Mycobacterium bovis BCG genome, were identified using ChIP-seq. One of the most enriched Cmr binding sites was located upstream of the cmr promoter, and we demonstrated that expression of cmr is autoregulated. cAMP affected Cmr binding at a subset of DNA loci in vivo and in vitro, including multiple sites adjacent to members of the DosR (DevR) dormancy regulon. Our findings of cooperative binding of Cmr to these DNA regions and the regulation by Cmr of the DosR-regulated virulence gene Rv2623 demonstrate the complexity of Cmr-mediated gene regulation and suggest a role for Cmr in the biology of persistent TB infection.
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Affiliation(s)
- Sridevi Ranganathan
- Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany, NY 12201, USA
| | - Guangchun Bai
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, PO Box 22002, Albany, NY 12201-2002, USA
| | - Anna Lyubetskaya
- Bioinformatics Program, Boston University, Boston, MA 02215, USA
| | - Gwendowlyn S Knapp
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, PO Box 22002, Albany, NY 12201-2002, USA
| | | | - Michaela Gazdik
- Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany, NY 12201, USA
| | | | - James E Galagan
- Bioinformatics Program, Boston University, Boston, MA 02215, USA Department of Microbiology, Boston University, Boston, MA 02215, USA Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA
| | - Kathleen A McDonough
- Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany, NY 12201, USA Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, PO Box 22002, Albany, NY 12201-2002, USA
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27
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Myers KS, Park DM, Beauchene NA, Kiley PJ. Defining bacterial regulons using ChIP-seq. Methods 2015; 86:80-8. [PMID: 26032817 DOI: 10.1016/j.ymeth.2015.05.022] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 05/22/2015] [Accepted: 05/23/2015] [Indexed: 11/28/2022] Open
Abstract
Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is a powerful method that identifies protein-DNA binding sites in vivo. Recent studies have illustrated the value of ChIP-seq in studying transcription factor binding in various bacterial species under a variety of growth conditions. These results show that in addition to identifying binding sites, correlation of ChIP-seq data with expression data can reveal important information about bacterial regulons and regulatory networks. In this chapter, we provide an overview of the current state of knowledge about ChIP-seq methodology in bacteria, from sample preparation to raw data analysis. We also describe visualization and various bioinformatic analyses of processed ChIP-seq data.
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Affiliation(s)
- Kevin S Myers
- Laboratory of Genetics, University of Wisconsin - Madison, Madison, WI 53706, USA; Great Lakes Bioenergy Research Center, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Dan M Park
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Nicole A Beauchene
- Department of Biomolecular Chemistry, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Patricia J Kiley
- Department of Biomolecular Chemistry, University of Wisconsin - Madison, Madison, WI 53706, USA; Great Lakes Bioenergy Research Center, University of Wisconsin - Madison, Madison, WI 53706, USA.
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28
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Li J, Overall CC, Nakayasu ES, Kidwai AS, Jones MB, Johnson RC, Nguyen NT, McDermott JE, Ansong C, Heffron F, Cambronne ED, Adkins JN. Analysis of the Salmonella regulatory network suggests involvement of SsrB and H-NS in σ(E)-regulated SPI-2 gene expression. Front Microbiol 2015; 6:27. [PMID: 25713562 PMCID: PMC4322710 DOI: 10.3389/fmicb.2015.00027] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 01/08/2015] [Indexed: 02/04/2023] Open
Abstract
The extracytoplasmic functioning sigma factor σE is known to play an essential role for Salmonella enterica serovar Typhimurium to survive and proliferate in macrophages and mice. However, its regulatory network is not well-characterized, especially during infection. Here we used microarray to identify genes regulated by σE in Salmonella grown in three conditions: a nutrient-rich condition and two others that mimic early and late intracellular infection. We found that in each condition σE regulated different sets of genes, and notably, several global regulators. When comparing nutrient-rich and infection-like conditions, large changes were observed in the expression of genes involved in Salmonella pathogenesis island (SPI)-1 type-three secretion system (TTSS), SPI-2 TTSS, protein synthesis, and stress responses. In total, the expression of 58% of Salmonella genes was affected by σE in at least one of the three conditions. An important finding is that σE up-regulates SPI-2 genes, which are essential for Salmonella intracellular survival, by up-regulating SPI-2 activator ssrB expression at the early stage of infection and down-regulating SPI-2 repressor hns expression at a later stage. Moreover, σE is capable of countering the silencing of H-NS, releasing the expression of SPI-2 genes. This connection between σE and SPI-2 genes, combined with the global regulatory effect of σE, may account for the lethality of rpoE-deficient Salmonella in murine infection.
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Affiliation(s)
- Jie Li
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University Portland, OR, USA
| | - Christopher C Overall
- Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA
| | - Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA
| | - Afshan S Kidwai
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University Portland, OR, USA
| | - Marcus B Jones
- Department of Infectious Diseases, J. Craig Venter Institute Rockville, MD, USA
| | - Rudd C Johnson
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University Portland, OR, USA
| | - Nhu T Nguyen
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University Portland, OR, USA
| | - Jason E McDermott
- Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA
| | - Charles Ansong
- Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA
| | - Fred Heffron
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University Portland, OR, USA
| | - Eric D Cambronne
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University Portland, OR, USA
| | - Joshua N Adkins
- Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA
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29
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Fitzgerald DM, Bonocora RP, Wade JT. Comprehensive mapping of the Escherichia coli flagellar regulatory network. PLoS Genet 2014; 10:e1004649. [PMID: 25275371 PMCID: PMC4183435 DOI: 10.1371/journal.pgen.1004649] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 08/03/2014] [Indexed: 12/14/2022] Open
Abstract
Flagellar synthesis is a highly regulated process in all motile bacteria. In Escherichia coli and related species, the transcription factor FlhDC is the master regulator of a multi-tiered transcription network. FlhDC activates transcription of a number of genes, including some flagellar genes and the gene encoding the alternative Sigma factor FliA. Genes whose expression is required late in flagellar assembly are primarily transcribed by FliA, imparting temporal regulation of transcription and coupling expression to flagellar assembly. In this study, we use ChIP-seq and RNA-seq to comprehensively map the E. coli FlhDC and FliA regulons. We define a surprisingly restricted FlhDC regulon, including two novel regulated targets and two binding sites not associated with detectable regulation of surrounding genes. In contrast, we greatly expand the known FliA regulon. Surprisingly, 30 of the 52 FliA binding sites are located inside genes. Two of these intragenic promoters are associated with detectable noncoding RNAs, while the others either produce highly unstable RNAs or are inactive under these conditions. Together, our data redefine the E. coli flagellar regulatory network, and provide new insight into the temporal orchestration of gene expression that coordinates the flagellar assembly process. Flagella are surface-associated appendages that propel bacteria and are involved in diverse functions such as chemotaxis, surface attachment, and host cell invasion. Flagella are incredibly complex macromolecular machines that are energetically costly to produce, assemble, and power. Flagellar production is tightly regulated and flagellar components are only synthesized when flagellar motility is advantageous. Regulation also ensures that flagellar components are produced in roughly the same order in which they are needed, increasing efficiency of the assembly process. The transcriptional regulation of flagellar genes has been studied extensively in the model organism Escherichia coli; however, many questions remain. We have used an unbiased, genome-wide approach to comprehensively identify all of the binding sites and regulatory targets for the two key regulators of flagellar synthesis, FlhDC and FliA. Our results redefine the flagellar regulatory network, and suggest that FliA binds many sites that are not associated with productive transcription. This work is important because it suggests possible new functions for FliA outside of the transcription of canonical mRNAs, and it provides new insight into the temporal orchestration of gene expression that coordinates the flagellar assembly process.
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Affiliation(s)
- Devon M. Fitzgerald
- Department of Biomedical Sciences, University at Albany, Albany, New York, United States of America
| | - Richard P. Bonocora
- Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Joseph T. Wade
- Department of Biomedical Sciences, University at Albany, Albany, New York, United States of America
- Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
- * E-mail:
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30
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Haning K, Cho SH, Contreras LM. Small RNAs in mycobacteria: an unfolding story. Front Cell Infect Microbiol 2014; 4:96. [PMID: 25105095 PMCID: PMC4109619 DOI: 10.3389/fcimb.2014.00096] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 07/03/2014] [Indexed: 01/10/2023] Open
Abstract
Mycobacteria represent a class of powerful pathogens, including those causing tuberculosis and leprosy, which continue to be worldwide health challenges. In the last 20 years, an abundance of non-coding, small RNAs (sRNAs) have been discovered in model bacteria and gained significant attention as regulators of cellular responses, including pathogenesis. Naturally, a search in mycobacteria followed, revealing over 200 sRNAs thus far. Characterization of these sRNAs is only beginning, but differential expression under environmental stresses suggests relevance to mycobacterial pathogenesis. This review provides a comprehensive overview of the current knowledge of sRNAs in mycobacteria, including historical perspective and techniques used for identification and characterization.
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Affiliation(s)
- Katie Haning
- McKetta Department of Chemical Engineering, Cockrell School of Engineering, The University of Texas at AustinAustin, TX, USA
| | - Seung Hee Cho
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at AustinAustin, TX, USA
| | - Lydia M. Contreras
- McKetta Department of Chemical Engineering, Cockrell School of Engineering, The University of Texas at AustinAustin, TX, USA
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at AustinAustin, TX, USA
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31
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Kahramanoglou C, Cortes T, Matange N, Hunt DM, Visweswariah SS, Young DB, Buxton RS. Genomic mapping of cAMP receptor protein (CRP Mt) in Mycobacterium tuberculosis: relation to transcriptional start sites and the role of CRPMt as a transcription factor. Nucleic Acids Res 2014; 42:8320-9. [PMID: 24957601 PMCID: PMC4117774 DOI: 10.1093/nar/gku548] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Chromatin immunoprecipitation identified 191 binding sites of Mycobacterium tuberculosis cAMP receptor protein (CRPMt) at endogenous expression levels using a specific α-CRPMt antibody. Under these native conditions an equal distribution between intragenic and intergenic locations was observed. CRPMt binding overlapped a palindromic consensus sequence. Analysis by RNA sequencing revealed widespread changes in transcriptional profile in a mutant strain lacking CRPMt during exponential growth, and in response to nutrient starvation. Differential expression of genes with a CRPMt-binding site represented only a minor portion of this transcriptional reprogramming with ∼19% of those representing transcriptional regulators potentially controlled by CRPMt. The subset of genes that are differentially expressed in the deletion mutant under both culture conditions conformed to a pattern resembling canonical CRP regulation in Escherichia coli, with binding close to the transcriptional start site associated with repression and upstream binding with activation. CRPMt can function as a classical transcription factor in M. tuberculosis, though this occurs at only a subset of CRPMt-binding sites.
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Affiliation(s)
- Christina Kahramanoglou
- Division of Mycobacterial Research, MRC National Institute for Medical Research, Mill Hill, London, NW7 1AA, UK
| | - Teresa Cortes
- Division of Mycobacterial Research, MRC National Institute for Medical Research, Mill Hill, London, NW7 1AA, UK
| | - Nishad Matange
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore 560012, India
| | - Debbie M Hunt
- Division of Mycobacterial Research, MRC National Institute for Medical Research, Mill Hill, London, NW7 1AA, UK
| | - Sandhya S Visweswariah
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore 560012, India
| | - Douglas B Young
- Division of Mycobacterial Research, MRC National Institute for Medical Research, Mill Hill, London, NW7 1AA, UK Centre for Molecular Bacteriology and Infection, Imperial College London, SW7 2AZ, UK
| | - Roger S Buxton
- Division of Mycobacterial Research, MRC National Institute for Medical Research, Mill Hill, London, NW7 1AA, UK
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Jones CJ, Newsom D, Kelly B, Irie Y, Jennings LK, Xu B, Limoli DH, Harrison JJ, Parsek MR, White P, Wozniak DJ. ChIP-Seq and RNA-Seq reveal an AmrZ-mediated mechanism for cyclic di-GMP synthesis and biofilm development by Pseudomonas aeruginosa. PLoS Pathog 2014; 10:e1003984. [PMID: 24603766 PMCID: PMC3946381 DOI: 10.1371/journal.ppat.1003984] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2013] [Accepted: 01/23/2014] [Indexed: 11/28/2022] Open
Abstract
The transcription factor AmrZ regulates genes important for P. aeruginosa virulence, including type IV pili, extracellular polysaccharides, and the flagellum; however, the global effect of AmrZ on gene expression remains unknown, and therefore, AmrZ may directly regulate many additional genes that are crucial for infection. Compared to the wild type strain, a ΔamrZ mutant exhibits a rugose colony phenotype, which is commonly observed in variants that accumulate the intracellular second messenger cyclic diguanylate (c-di-GMP). Cyclic di-GMP is produced by diguanylate cyclases (DGC) and degraded by phosphodiesterases (PDE). We hypothesized that AmrZ limits the intracellular accumulation of c-di-GMP through transcriptional repression of gene(s) encoding a DGC. In support of this, we observed elevated c-di-GMP in the ΔamrZ mutant compared to the wild type strain. Consistent with other strains that accumulate c-di-GMP, when grown as a biofilm, the ΔamrZ mutant formed larger microcolonies than the wild-type strain. This enhanced biofilm formation was abrogated by expression of a PDE. To identify potential target DGCs, a ChIP-Seq was performed and identified regions of the genome that are bound by AmrZ. RNA-Seq experiments revealed the entire AmrZ regulon, and characterized AmrZ as an activator or repressor at each binding site. We identified an AmrZ-repressed DGC-encoding gene (PA4843) from this cohort, which we named AmrZ dependent cyclase A (adcA). PAO1 overexpressing adcA accumulates 29-fold more c-di-GMP than the wild type strain, confirming the cyclase activity of AdcA. In biofilm reactors, a ΔamrZ ΔadcA double mutant formed smaller microcolonies than the single ΔamrZ mutant, indicating adcA is responsible for the hyper biofilm phenotype of the ΔamrZ mutant. This study combined the techniques of ChIP-Seq and RNA-Seq to define the comprehensive regulon of a bifunctional transcriptional regulator. Moreover, we identified a c-di-GMP mediated mechanism for AmrZ regulation of biofilm formation and chronicity. Pathogenic bacteria such as Pseudomonas aeruginosa utilize a wide variety of systems to sense and respond to the changing conditions during an infection. When a stress is sensed, signals are transmitted to impact expression of many genes that allow the bacterium to adapt to the changing conditions. AmrZ is a protein that regulates production of several virulence-associated gene products, though we predicted that its role in virulence was more expansive than previously described. Transcription factors such as AmrZ often affect the expression of a gene by binding and promoting or inhibiting expression of the target gene. Two global techniques were utilized to determine where AmrZ binds in the genome, and what effect AmrZ has once bound. This approach revealed that AmrZ represses the production of a signaling molecule called cyclic diguanylate, which is known to induce the formation of difficult to treat communities of bacteria called biofilms. This study also identified many novel targets of AmrZ to promote future studies of this regulator. Collectively, these data can be utilized to develop treatments to inhibit biofilm formation during devastating chronic infections.
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Affiliation(s)
- Christopher J. Jones
- Department of Microbiology and Environmental Toxicology, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Infection and Immunity and Center for Microbial Interface Biology, Ohio State University, Columbus, Ohio, United States of America
| | - David Newsom
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, United States of America
| | - Benjamin Kelly
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, United States of America
| | - Yasuhiko Irie
- Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom
| | - Laura K. Jennings
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Binjie Xu
- Department of Microbiology, Ohio State University, Columbus, Ohio, United States of America
| | - Dominique H. Limoli
- Department of Infection and Immunity and Center for Microbial Interface Biology, Ohio State University, Columbus, Ohio, United States of America
| | - Joe J. Harrison
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Matthew R. Parsek
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Peter White
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, United States of America
| | - Daniel J. Wozniak
- Department of Microbiology and Environmental Toxicology, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Microbiology, Ohio State University, Columbus, Ohio, United States of America
- * E-mail:
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Picossi S, Flores E, Herrero A. ChIP analysis unravels an exceptionally wide distribution of DNA binding sites for the NtcA transcription factor in a heterocyst-forming cyanobacterium. BMC Genomics 2014; 15:22. [PMID: 24417914 PMCID: PMC3898017 DOI: 10.1186/1471-2164-15-22] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 12/26/2013] [Indexed: 11/20/2022] Open
Abstract
Background The CRP-family transcription factor NtcA, universally found in cyanobacteria, was initially discovered as a regulator operating N control. It responds to the N regime signaled by the internal 2-oxoglutarate levels, an indicator of the C to N balance of the cells. Canonical NtcA-activated promoters bear an NtcA-consensus binding site (GTAN8TAC) centered at about 41.5 nucleotides upstream from the transcription start point. In strains of the Anabaena/Nostoc genera NtcA is pivotal for the differentiation of heterocysts in response to N stress. Results In this study, we have used chromatin immunoprecipitation followed by high-throughput sequencing to identify the whole catalog of NtcA-binding sites in cells of the filamentous, heterocyst-forming cyanobacterium Anabaena sp. PCC 7120 three hours after the withdrawal of combined N. NtcA has been found to bind to 2,424 DNA regions in the genome of Anabaena, which have been ascribed to 2,153 genes. Interestingly, only a small proportion of those genes are involved in N assimilation and metabolism, and 65% of the binding regions were located intragenically. Conclusions The distribution of NtcA-binding sites identified here reveals the largest bacterial regulon described to date. Our results show that NtcA has a much wider role in the physiology of the cell than it has been previously thought, acting both as a global transcriptional regulator and possibly also as a factor influencing the superstructure of the chromosome (and plasmids).
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Affiliation(s)
- Silvia Picossi
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Américo Vespucio 49, Seville E-41092, Spain.
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Nguyen-Duc T, van Oeffelen L, Song N, Hassanzadeh-Ghassabeh G, Muyldermans S, Charlier D, Peeters E. The genome-wide binding profile of the Sulfolobus solfataricus transcription factor Ss-LrpB shows binding events beyond direct transcription regulation. BMC Genomics 2013; 14:828. [PMID: 24274039 PMCID: PMC4046817 DOI: 10.1186/1471-2164-14-828] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 11/15/2013] [Indexed: 11/18/2022] Open
Abstract
Background Gene regulatory processes are largely resulting from binding of transcription factors to specific genomic targets. Leucine-responsive Regulatory Protein (Lrp) is a prevalent transcription factor family in prokaryotes, however, little information is available on biological functions of these proteins in archaea. Here, we study genome-wide binding of the Lrp-like transcription factor Ss-LrpB from Sulfolobus solfataricus. Results Chromatin immunoprecipitation in combination with DNA microarray analysis (ChIP-chip) has revealed that Ss-LrpB interacts with 36 additional loci besides the four previously identified local targets. Only a subset of the newly identified binding targets, concentrated in a highly variable IS-dense genomic region, is also bound in vitro by pure Ss-LrpB. There is no clear relationship between the in vitro measured DNA-binding specificity of Ss-LrpB and the in vivo association suggesting a limited permissivity of the crenarchaeal chromatin for transcription factor binding. Of 37 identified binding regions, 29 are co-bound by LysM, another Lrp-like transcription factor in S. solfataricus. Comparative gene expression analysis in an Ss-lrpB mutant strain shows no significant Ss-LrpB-mediated regulation for most targeted genes, with exception of the CRISPR B cluster, which is activated by Ss-LrpB through binding to a specific motif in the leader region. Conclusions The genome-wide binding profile presented here implies that Ss-LrpB is associated at additional genomic binding sites besides the local gene targets, but acts as a specific transcription regulator in the tested growth conditions. Moreover, we have provided evidence that two Lrp-like transcription factors in S. solfataricus, Ss-LrpB and LysM, interact in vivo. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-14-828) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | - Eveline Peeters
- Research group of Microbiology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.
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Tsai CH, Baranowski C, Livny J, McDonough KA, Wade JT, Contreras LM. Identification of novel sRNAs in mycobacterial species. PLoS One 2013; 8:e79411. [PMID: 24244498 PMCID: PMC3828370 DOI: 10.1371/journal.pone.0079411] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 09/28/2013] [Indexed: 01/29/2023] Open
Abstract
Bacterial small RNAs (sRNAs) are short transcripts that typically do not encode proteins and often act as regulators of gene expression through a variety of mechanisms. Regulatory sRNAs have been identified in many species, including Mycobacterium tuberculosis, the causative agent of tuberculosis. Here, we use a computational algorithm to predict sRNA candidates in the mycobacterial species M. smegmatis and M. bovis BCG and confirmed the expression of many sRNAs using Northern blotting. Thus, we have identified 17 and 23 novel sRNAs in M. smegmatis and M. bovis BCG, respectively. We have also applied a high-throughput technique (Deep-RACE) to map the 5' and 3' ends of many of these sRNAs and identified potential regulators of sRNAs by analysis of existing ChIP-seq datasets. The sRNAs identified in this work likely contribute to the unique biology of mycobacteria.
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Affiliation(s)
- Chen-Hsun Tsai
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, United States of America
| | - Catherine Baranowski
- Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Jonathan Livny
- Channing Laboratory, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Kathleen A. McDonough
- Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
- Department of Biomedical Sciences, University at Albany, SUNY, Albany, New York, United States of America
| | - Joseph T. Wade
- Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
- Department of Biomedical Sciences, University at Albany, SUNY, Albany, New York, United States of America
| | - Lydia M. Contreras
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, United States of America
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The Mycobacterium tuberculosis regulatory network and hypoxia. Nature 2013; 499:178-83. [PMID: 23823726 DOI: 10.1038/nature12337] [Citation(s) in RCA: 327] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Accepted: 05/23/2013] [Indexed: 12/26/2022]
Abstract
We have taken the first steps towards a complete reconstruction of the Mycobacterium tuberculosis regulatory network based on ChIP-Seq and combined this reconstruction with system-wide profiling of messenger RNAs, proteins, metabolites and lipids during hypoxia and re-aeration. Adaptations to hypoxia are thought to have a prominent role in M. tuberculosis pathogenesis. Using ChIP-Seq combined with expression data from the induction of the same factors, we have reconstructed a draft regulatory network based on 50 transcription factors. This network model revealed a direct interconnection between the hypoxic response, lipid catabolism, lipid anabolism and the production of cell wall lipids. As a validation of this model, in response to oxygen availability we observe substantial alterations in lipid content and changes in gene expression and metabolites in corresponding metabolic pathways. The regulatory network reveals transcription factors underlying these changes, allows us to computationally predict expression changes, and indicates that Rv0081 is a regulatory hub.
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