1
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Stringer AM, Fitzgerald DM, Wade JT. Mapping the Escherichia coli DnaA-binding landscape reveals a preference for binding pairs of closely spaced DNA sites. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001474. [PMID: 39012340 PMCID: PMC11317965 DOI: 10.1099/mic.0.001474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/14/2024] [Indexed: 07/17/2024]
Abstract
DnaA is a widely conserved DNA-binding protein that is essential for the initiation of DNA replication in many bacterial species, including Escherichia coli. Cooperative binding of ATP-bound DnaA to multiple 9mer sites ('DnaA boxes') at the origin of replication results in local unwinding of the DNA and recruitment of the replication machinery. DnaA also functions as a transcription regulator by binding to DNA sites upstream of target genes. Previous studies have identified many sites of direct positive and negative regulation by E. coli DnaA. Here, we use a ChIP-seq to map the E. coli DnaA-binding landscape. Our data reveal a compact regulon for DnaA that coordinates the initiation of DNA replication with expression of genes associated with nucleotide synthesis, replication, DNA repair and RNA metabolism. We also show that DnaA binds preferentially to pairs of DnaA boxes spaced 2 or 3 bp apart. Mutation of either the upstream or downstream site in a pair disrupts DnaA binding, as does altering the spacing between sites. We conclude that binding of DnaA at almost all target sites requires a dimer of DnaA, with each subunit making critical contacts with a DnaA box.
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Affiliation(s)
- Anne M. Stringer
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Devon M. Fitzgerald
- Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, 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, SUNY, Albany, New York, USA
- RNA Institute, University at Albany, SUNY, Albany, New York, USA
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2
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Qiu GW, Zheng WC, Yang HM, Wang YY, Qi X, Huang D, Dai GZ, Shi H, Price NM, Qiu BS. Phosphorus deficiency alleviates iron limitation in Synechocystis cyanobacteria through direct PhoB-mediated gene regulation. Nat Commun 2024; 15:4426. [PMID: 38789507 PMCID: PMC11126600 DOI: 10.1038/s41467-024-48847-4] [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: 09/14/2023] [Accepted: 05/14/2024] [Indexed: 05/26/2024] Open
Abstract
Iron and phosphorus are essential nutrients that exist at low concentrations in surface waters and may be co-limiting resources for phytoplankton growth. Here, we show that phosphorus deficiency increases the growth of iron-limited cyanobacteria (Synechocystis sp. PCC 6803) through a PhoB-mediated regulatory network. We find that PhoB, in addition to its well-recognized role in controlling phosphate homeostasis, also regulates key metabolic processes crucial for iron-limited cyanobacteria, including ROS detoxification and iron uptake. Transcript abundances of PhoB-targeted genes are enriched in samples from phosphorus-depleted seawater, and a conserved PhoB-binding site is widely present in the promoters of the target genes, suggesting that the PhoB-mediated regulation may be highly conserved. Our findings provide molecular insights into the responses of cyanobacteria to simultaneous iron/phosphorus nutrient limitation.
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Affiliation(s)
- Guo-Wei Qiu
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Wen-Can Zheng
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Hao-Ming Yang
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Yu-Ying Wang
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Xing Qi
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Da Huang
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Guo-Zheng Dai
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Huazhong Shi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA
| | - Neil M Price
- Department of Biology, McGill University, 1205 Docteur Penfield, Montreal, Québec, H3A 1B1, Canada
| | - Bao-Sheng Qiu
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China.
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3
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Ghosh T, Jahangirnejad S, Chauvier A, Stringer AM, Korepanov AP, Côté JP, Wade JT, Lafontaine DA. Direct and indirect control of Rho-dependent transcription termination by the Escherichia coli lysC riboswitch. RNA (NEW YORK, N.Y.) 2024; 30:381-391. [PMID: 38253429 PMCID: PMC10946432 DOI: 10.1261/rna.079779.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024]
Abstract
Bacterial riboswitches are molecular structures that play a crucial role in controlling gene expression to maintain cellular balance. The Escherichia coli lysC riboswitch has been previously shown to regulate gene expression through translation initiation and mRNA decay. Recent research suggests that lysC gene expression is also influenced by Rho-dependent transcription termination. Through a series of in silico, in vitro, and in vivo experiments, we provide experimental evidence that the lysC riboswitch directly and indirectly modulates Rho transcription termination. Our study demonstrates that Rho-dependent transcription termination plays a significant role in the cotranscriptional regulation of lysC expression. Together with previous studies, our work suggests that lysC expression is governed by a lysine-sensing riboswitch that regulates translation initiation, transcription termination, and mRNA degradation. Notably, both Rho and RNase E target the same region of the RNA molecule, implying that RNase E may degrade Rho-terminated transcripts, providing a means to selectively eliminate these incomplete messenger RNAs. Overall, this study sheds light on the complex regulatory mechanisms used by bacterial riboswitches, emphasizing the role of transcription termination in the control of gene expression and mRNA stability.
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Affiliation(s)
- Tithi Ghosh
- Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec, Canada J1K 2R1
| | - Shirin Jahangirnejad
- Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec, Canada J1K 2R1
| | - Adrien Chauvier
- Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec, Canada J1K 2R1
| | - Anne M Stringer
- Wadsworth Center, New York State Department of Health, Albany, New York 12208, USA
| | - Alexey P Korepanov
- Expression Génétique Microbienne, UMR8261 CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Jean Phillippe Côté
- Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec, Canada J1K 2R1
| | - Joseph T Wade
- Wadsworth Center, New York State Department of Health, Albany, New York 12208, USA
- Department of Biomedical Sciences, University at Albany, Albany, New York 12201, USA
| | - Daniel A Lafontaine
- Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec, Canada J1K 2R1
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4
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Tsukimi T, Obana N, Shigemori S, Arakawa K, Miyauchi E, Yang J, Song I, Ashino Y, Wakayama M, Soga T, Tomita M, Ohno H, Mori H, Fukuda S. Genetic mutation in Escherichia coli genome during adaptation to the murine intestine is optimized for the host diet. mSystems 2024; 9:e0112323. [PMID: 38205998 PMCID: PMC10878103 DOI: 10.1128/msystems.01123-23] [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: 10/23/2023] [Accepted: 11/15/2023] [Indexed: 01/12/2024] Open
Abstract
Mammalian gut microbes colonize the intestinal tract of their host and adapt to establish a microbial ecosystem. The host diet changes the nutrient profile of the intestine and has a high impact on microbiota composition. Genetic mutations in Escherichia coli, a prevalent species in the human gut, allow for adaptation to the mammalian intestine, as reported in previous studies. However, the extent of colonization fitness in the intestine elevated by genetic mutation and the effects of diet change on these mutations in E. coli are still poorly known. Here, we show that notable mutations in sugar metabolism-related genes (gatC, araC, and malI) were detected in the E. coli K-12 genome just 2 weeks after colonization in the germ-free mouse intestine. In addition to elevated fitness by deletion of gatC, as previously reported, deletion of araC and malI also elevated E. coli fitness in the murine intestine in a host diet-dependent manner. In vitro cultures of medium containing nutrients abundant in the intestine (e.g., galactose, N-acetylglucosamine, and asparagine) also showed increased E. coli fitness after deletion of the genes-of-interest associated with their metabolism. Furthermore, the host diet was found to influence the developmental trajectory of gene mutations in E. coli. Taken together, we suggest that genetic mutations in E. coli are selected in response to the intestinal environment, which facilitates efficient utilization of nutrients abundant in the intestine under laboratory conditions. Our study offers some insight into the possible adaptation mechanisms of gut microbes.IMPORTANCEThe gut microbiota is closely associated with human health and is greatly impacted by the host diet. Bacteria such as Escherichia coli live in the gut all throughout the life of a human host and adapt to the intestinal environment. Adaptive mutations in E. coli are reported to enhance fitness in the mammalian intestine, but to what extent is still poorly known. It is also unknown whether the host diet affects what genes are mutated and to what extent fitness is affected. This study suggests that genetic mutations in the E. coli K-12 strain are selected in response to the intestinal environment and facilitate efficient utilization of abundant nutrients in the germ-free mouse intestine. Our study provides a better understanding of these intestinal adaptation mechanisms of gut microbes.
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Affiliation(s)
- Tomoya Tsukimi
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Nozomu Obana
- Transborder Medical Research Center, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Suguru Shigemori
- Transborder Medical Research Center, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - Eiji Miyauchi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan
| | - Jiayue Yang
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Isaiah Song
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Yujin Ashino
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Masataka Wakayama
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - Hiroshi Ohno
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Hirotada Mori
- Graduate School of Biological Science, Nara Institute of Science and Technology, Ikoma, Japan
- Institute of Animal Sciences, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Shinji Fukuda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
- Transborder Medical Research Center, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
- Gut Environmental Design Group, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Japan
- Laboratory for Regenerative Microbiology, Juntendo University Graduate School of Medicine, Tokyo, Japan
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Keegan NR, Colón Torres NJ, Stringer AM, Prager LI, Brockley MW, McManaman CL, Wade JT, Paczkowski JE. Promoter selectivity of the RhlR quorum-sensing transcription factor receptor in Pseudomonas aeruginosa is coordinated by distinct and overlapping dependencies on C4-homoserine lactone and PqsE. PLoS Genet 2023; 19:e1010900. [PMID: 38064526 PMCID: PMC10732425 DOI: 10.1371/journal.pgen.1010900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 12/20/2023] [Accepted: 11/21/2023] [Indexed: 12/21/2023] Open
Abstract
Quorum sensing is a mechanism of bacterial cell-cell communication that relies on the production and detection of small molecule autoinducers, which facilitate the synchronous expression of genes involved in group behaviors, such as virulence factor production and biofilm formation. The Pseudomonas aeruginosa quorum sensing network consists of multiple interconnected transcriptional regulators, with the transcription factor, RhlR, acting as one of the main drivers of quorum sensing behaviors. RhlR is a LuxR-type transcription factor that regulates its target genes when bound to its cognate autoinducer, C4-homoserine lactone, which is synthesized by RhlI. RhlR function is also regulated by the metallo-β-hydrolase enzyme, PqsE. We recently showed that PqsE binds RhlR to alter its affinity for promoter DNA, a new mechanism of quorum-sensing receptor activation. Here, we perform ChIP-seq analyses of RhlR to map the binding of RhlR across the P. aeruginosa genome, and to determine the impact of C4-homoserine lactone and PqsE on RhlR binding to different sites across the P. aeruginosa genome. We identify 40 RhlR binding sites, all but three of which are associated with genes known to be regulated by RhlR. C4-homoserine lactone is required for maximal binding of RhlR to many of its DNA sites. Moreover, C4-homoserine lactone is required for maximal RhlR-dependent transcription activation from all sites, regardless of whether it impacts RhlR binding to DNA. PqsE is required for maximal binding of RhlR to many DNA sites, with similar effects on RhlR-dependent transcription activation from those sites. However, the effects of PqsE on RhlR specificity are distinct from those of C4-homoserine lactone, and PqsE is sufficient for RhlR binding to some DNA sites in the absence of C4-homoserine lactone. Together, C4-homoserine lactone and PqsE are required for RhlR binding at the large majority of its DNA sites. Thus, our work reveals three distinct modes of activation by RhlR: i) when RhlR is unbound by autoinducer but bound by PqsE, ii) when RhlR is bound by autoinducer but not bound by PqsE, and iii) when RhlR is bound by both autoinducer and PqsE, establishing a stepwise mechanism for the progression of the RhlR-RhlI-PqsE quorum sensing pathway in P. aeruginosa.
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Affiliation(s)
- Nicholas R. Keegan
- Department of Biomedical Sciences, University at Albany, School of Public Health, Albany, New York, United States of America
| | - Nathalie J. Colón Torres
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Anne M. Stringer
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Lia I. Prager
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
- Department of Biological Sciences, University at Albany, Albany, New York, United States of America
| | - Matthew W. Brockley
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
- Department of Biological Sciences, University at Albany, Albany, New York, United States of America
| | - Charity L. McManaman
- Department of Biomedical Sciences, University at Albany, School of Public Health, Albany, New York, United States of America
| | - Joseph T. Wade
- Department of Biomedical Sciences, University at Albany, School of Public Health, Albany, New York, United States of America
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Jon E. Paczkowski
- Department of Biomedical Sciences, University at Albany, School of Public Health, Albany, New York, United States of America
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [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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Drousiotis K, Herman R, Hawkhead J, Leech A, Wilkinson A, Thomas GH. Characterization of the l-arabinofuranose-specific GafABCD ABC transporter essential for l-arabinose-dependent growth of the lignocellulose-degrading bacterium Shewanella sp. ANA-3. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001308. [PMID: 36920280 PMCID: PMC10191376 DOI: 10.1099/mic.0.001308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 02/07/2023] [Indexed: 03/16/2023]
Abstract
Microbes that have evolved to live on lignocellulosic biomass face unique challenges in the effective and efficient use of this material as food. The bacterium Shewanella sp. ANA-3 has the potential to utilize arabinan and arabinoxylan, and uptake of the monosaccharide, l-arabinose, derived from these polymers, is known to be mediated by a single ABC transporter. We demonstrate that the substrate binding protein of this system, GafASw, binds specifically to l-arabinofuranose, which is the rare furanose form of l-arabinose found in lignocellulosic biomass. The structure of GafASw was resolved to 1.7 Å and comparison to Escherichia coli YtfQ (GafAEc) revealed binding site adaptations that confer specificity for furanose over pyranose forms of monosaccharides, while selecting arabinose over another related monosaccharide, galactose. The discovery of a bacterium with a natural predilection for a sugar found abundantly in certain lignocellulosic materials suggests an intimate connection in the enzymatic release and uptake of the sugar, perhaps to prevent other microbes scavenging this nutrient before it mutarotates to l-arabinopyranose. This biological discovery also provides a clear route to engineer more efficient utilization of plant biomass components in industrial biotechnology.
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Affiliation(s)
| | - Reyme Herman
- Department of Biology, University of York, PO Box 373, York, UK
| | - Judith Hawkhead
- Department of Biology, University of York, PO Box 373, York, UK
| | - Andrew Leech
- Biology Technology Facility, University of York, PO Box 373, York. YO10 5YW, UK
| | - Anthony Wilkinson
- Department of Chemistry, York Structural Biology Laboratory, University of York, PO Box 373, York. YO10 5YW, UK
| | - Gavin H. Thomas
- Department of Biology, University of York, PO Box 373, York, UK
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8
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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] [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.,Corresponding author:
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9
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Ohlendorf R, Möglich A. Light-regulated gene expression in Bacteria: Fundamentals, advances, and perspectives. Front Bioeng Biotechnol 2022; 10:1029403. [PMID: 36312534 PMCID: PMC9614035 DOI: 10.3389/fbioe.2022.1029403] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 09/29/2022] [Indexed: 11/13/2022] Open
Abstract
Numerous photoreceptors and genetic circuits emerged over the past two decades and now enable the light-dependent i.e., optogenetic, regulation of gene expression in bacteria. Prompted by light cues in the near-ultraviolet to near-infrared region of the electromagnetic spectrum, gene expression can be up- or downregulated stringently, reversibly, non-invasively, and with precision in space and time. Here, we survey the underlying principles, available options, and prominent examples of optogenetically regulated gene expression in bacteria. While transcription initiation and elongation remain most important for optogenetic intervention, other processes e.g., translation and downstream events, were also rendered light-dependent. The optogenetic control of bacterial expression predominantly employs but three fundamental strategies: light-sensitive two-component systems, oligomerization reactions, and second-messenger signaling. Certain optogenetic circuits moved beyond the proof-of-principle and stood the test of practice. They enable unprecedented applications in three major areas. First, light-dependent expression underpins novel concepts and strategies for enhanced yields in microbial production processes. Second, light-responsive bacteria can be optogenetically stimulated while residing within the bodies of animals, thus prompting the secretion of compounds that grant health benefits to the animal host. Third, optogenetics allows the generation of precisely structured, novel biomaterials. These applications jointly testify to the maturity of the optogenetic approach and serve as blueprints bound to inspire and template innovative use cases of light-regulated gene expression in bacteria. Researchers pursuing these lines can choose from an ever-growing, versatile, and efficient toolkit of optogenetic circuits.
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Affiliation(s)
- Robert Ohlendorf
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Andreas Möglich
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany
- Bayreuth Center for Biochemistry and Molecular Biology, Universität Bayreuth, Bayreuth, Germany
- North-Bavarian NMR Center, Universität Bayreuth, Bayreuth, Germany
- *Correspondence: Andreas Möglich,
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10
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Abstract
Dickeya dadantii is a phytopathogenic bacterium that causes soft rot in a wide range of plant hosts worldwide and a model organism for studying virulence gene regulation. The present study provides a comprehensive and annotated transcriptomic map of D. dadantii obtained by a computational method combining five independent transcriptomic data sets: (i) paired-end RNA sequencing (RNA-seq) data for a precise reconstruction of the RNA landscape; (ii) DNA microarray data providing transcriptional responses to a broad variety of environmental conditions; (iii) long-read Nanopore native RNA-seq data for isoform-level transcriptome validation and determination of transcription termination sites; (iv) differential RNA sequencing (dRNA-seq) data for the precise mapping of transcription start sites; (v) in planta DNA microarray data for a comparison of gene expression profiles between in vitro experiments and the early stages of plant infection. Our results show that transcription units sometimes coincide with predicted operons but are generally longer, most of them comprising internal promoters and terminators that generate alternative transcripts of variable gene composition. We characterize the occurrence of transcriptional read-through at terminators, which might play a basal regulation role and explain the extent of transcription beyond the scale of operons. We finally highlight the presence of noncontiguous operons and excludons in the D. dadantii genome, novel genomic arrangements that might contribute to the basal coordination of transcription. The highlighted transcriptional organization may allow D. dadantii to finely adjust its gene expression program for a rapid adaptation to fast-changing environments.
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11
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Putzeys L, Boon M, Lammens EM, Kuznedelov K, Severinov K, Lavigne R. Development of ONT-cappable-seq to unravel the transcriptional landscape of Pseudomonas phages. Comput Struct Biotechnol J 2022; 20:2624-2638. [PMID: 35685363 PMCID: PMC9163698 DOI: 10.1016/j.csbj.2022.05.034] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/16/2022] [Accepted: 05/16/2022] [Indexed: 11/28/2022] Open
Affiliation(s)
- Leena Putzeys
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | - Maarten Boon
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | - Eveline-Marie Lammens
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | | | | | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
- Corresponding author.
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12
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Vasicek EM, O'Neal L, Parsek MR, Fitch J, White P, Gunn JS. L-Arabinose Transport and Metabolism in Salmonella Influences Biofilm Formation. Front Cell Infect Microbiol 2021; 11:698146. [PMID: 34368016 PMCID: PMC8341724 DOI: 10.3389/fcimb.2021.698146] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/21/2021] [Indexed: 11/28/2022] Open
Abstract
L-arabinose inducible promoters are commonly used in gene expression analysis. However, nutrient source and availability also play a role in biofilm formation; therefore, L-arabinose metabolism could impact biofilm development. In this study we examined the impact of L-arabinose on Salmonella enterica serovar Typhimurium (S. Typhimurium) biofilm formation. Using mutants impaired for the transport and metabolism of L-arabinose, we showed that L-arabinose metabolism negatively impacts S. Typhimurium biofilm formation in vitro. When L-arabinose metabolism is abrogated, biofilm formation returned to baseline levels. However, without the ability to import extracellular L-arabinose, biofilm formation significantly increased. Using RNA-Seq we identified several gene families involved in these different phenotypes including curli expression, amino acid synthesis, and L-arabinose metabolism. Several individual candidate genes were tested for their involvement in the L-arabinose-mediated biofilm phenotypes, but most played no significant role. Interestingly, in the presence of L-arabinose the diguanylate cyclase gene adrA was downregulated in wild type S. Typhimurium. Meanwhile cyaA, encoding an adenylate cyclase, was downregulated in an L-arabinose transport mutant. Using an IPTG-inducible plasmid to deplete c-di-GMP via vieA expression, we were able to abolish the increased biofilm phenotype seen in the transport mutant. However, the mechanism by which the L-arabinose import mutant forms significantly larger biofilms remains to be determined. Regardless, these data suggest that L-arabinose metabolism influences intracellular c-di-GMP levels and therefore biofilm formation. These findings are important when considering the use of an L-arabinose inducible promoter in biofilm conditions.
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Affiliation(s)
- Erin M Vasicek
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, OH, United States.,Infectious Diseases Institute, The Ohio State University, Columbus, OH, United States.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States
| | - Lindsey O'Neal
- Department of Microbiology, University of Washington, Seattle, WA, United States
| | - Matthew R Parsek
- Department of Microbiology, University of Washington, Seattle, WA, United States
| | - James Fitch
- The Institute for Genomic Medicine, The Research Institute at Nationwide Children's Hospital, Columbus, OH, United States
| | - Peter White
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States.,The Institute for Genomic Medicine, The Research Institute at Nationwide Children's Hospital, Columbus, OH, United States
| | - John S Gunn
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, OH, United States.,Infectious Diseases Institute, The Ohio State University, Columbus, OH, United States.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States
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13
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Matilla MA, Ortega Á, Krell T. The role of solute binding proteins in signal transduction. Comput Struct Biotechnol J 2021; 19:1786-1805. [PMID: 33897981 PMCID: PMC8050422 DOI: 10.1016/j.csbj.2021.03.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/22/2021] [Accepted: 03/22/2021] [Indexed: 12/13/2022] Open
Abstract
The solute binding proteins (SBPs) of prokaryotes are present in the extracytosolic space. Although their primary function is providing substrates to transporters, SBPs also stimulate different signaling proteins, including chemoreceptors, sensor kinases, diguanylate cyclases/phosphodiesterases and Ser/Thr kinases, thereby causing a wide range of responses. While relatively few such systems have been identified, several pieces of evidence suggest that SBP-mediated receptor activation is a widespread mechanism. (1) These systems have been identified in Gram-positive and Gram-negative bacteria and archaea. (2) There is a structural diversity in the receptor domains that bind SBPs. (3) SBPs belonging to thirteen different families interact with receptor ligand binding domains (LBDs). (4) For the two most abundant receptor LBD families, dCache and four-helix-bundle, there are different modes of interaction with SBPs. (5) SBP-stimulated receptors carry out many different functions. The advantage of SBP-mediated receptor stimulation is attributed to a strict control of SBP levels, which allows a precise adjustment of the systeḿs sensitivity. We have compiled information on the effect of ligands on the transcript/protein levels of their cognate SBPs. In 87 % of the cases analysed, ligands altered SBP expression levels. The nature of the regulatory effect depended on the ligand family. Whereas inorganic ligands typically downregulate SBP expression, an upregulation was observed in response to most sugars and organic acids. A major unknown is the role that SBPs play in signaling and in receptor stimulation. This review attempts to summarize what is known and to present new information to narrow this gap in knowledge.
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Affiliation(s)
- Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, Granada 18008, Spain
| | - Álvaro Ortega
- Department of Biochemistry and Molecular Biology 'B' and Immunology, Faculty of Chemistry, University of Murcia, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, Granada 18008, Spain
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14
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Adhikari S, Erill I, Curtis PD. Transcriptional rewiring of the GcrA/CcrM bacterial epigenetic regulatory system in closely related bacteria. PLoS Genet 2021; 17:e1009433. [PMID: 33705385 PMCID: PMC7987155 DOI: 10.1371/journal.pgen.1009433] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 03/23/2021] [Accepted: 02/19/2021] [Indexed: 01/14/2023] Open
Abstract
Transcriptional rewiring is the regulation of different target genes by orthologous regulators in different organisms. While this phenomenon has been observed, it has not been extensively studied, particularly in core regulatory systems. Several global cell cycle regulators are conserved in the Alphaproteobacteria, providing an excellent model to study this phenomenon. First characterized in Caulobacter crescentus, GcrA and CcrM compose a DNA methylation-based regulatory system that helps coordinate the complex life cycle of this organism. These regulators are well-conserved across Alphaproteobacteria, but the extent to which their regulatory targets are conserved is not known. In this study, the regulatory targets of GcrA and CcrM were analyzed by SMRT-seq, RNA-seq, and ChIP-seq technologies in the Alphaproteobacterium Brevundimonas subvibrioides, and then compared to those of its close relative C. crescentus that inhabits the same environment. Although the regulators themselves are highly conserved, the genes they regulate are vastly different. GcrA directly regulates 204 genes in C. crescentus, and though B. subvibrioides has orthologs to 147 of those genes, only 48 genes retained GcrA binding in their promoter regions. Additionally, only 12 of those 48 genes demonstrated significant transcriptional change in a gcrA mutant, suggesting extensive transcriptional rewiring between these organisms. Similarly, out of hundreds of genes CcrM regulates in each of these organisms, only 2 genes were found in common. When multiple Alphaproteobacterial genomes were analyzed bioinformatically for potential GcrA regulatory targets, the regulation of genes involved in DNA replication and cell division was well conserved across the Caulobacterales but not outside this order. This work suggests that significant transcriptional rewiring can occur in cell cycle regulatory systems even over short evolutionary distances. The degree to which genetic or physiological systems evolve over evolutionary distance is often untested. One can assume that the same system in different organisms will change very little if 1) the evolutionary distance between the organisms is small, 2) the systems perform critical functions, and 3) the organisms have been under similar selective pressures (i.e. the organisms inhabited the same ecological niche). The Alphaproteobacteria offer an excellent opportunity to test this assertion as several critical global transcriptional regulators are conserved throughout this clade. In this study, the regulons of two such global regulators, GcrA and CcrM, in two closely related Alphaproteobacteria that inhabit the same ecological niche were compared and it was found that they regulate vastly different genes. In many cases, genes were present in both organisms, but targeted by a regulator in one organism and not in the other. These results suggest that significant transcriptional rewiring can occur even in a core regulatory system over small evolutionary distances and indicate that conservation of genes and genetic regulators may not be a complete indicator of their physiological function in an organism.
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Affiliation(s)
- Satish Adhikari
- Department of Biology, University of Mississippi, University, Mississippi, United States of America
| | - Ivan Erill
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, United States of America
| | - Patrick D. Curtis
- Department of Biology, University of Mississippi, University, Mississippi, United States of America
- * E-mail:
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15
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Regulatory Cross Talk between Motility and Interbacterial Communication in Salmonella enterica Serovar Typhimurium. J Bacteriol 2021; 203:JB.00510-20. [PMID: 33257526 DOI: 10.1128/jb.00510-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 11/23/2020] [Indexed: 01/29/2023] Open
Abstract
FliA is a broadly conserved σ factor that directs transcription of genes involved in flagellar motility. We previously identified FliA-transcribed genes in Escherichia coli and Salmonella enterica serovar Typhimurium, and we showed that E. coli FliA transcribes many unstable, noncoding RNAs from intragenic promoters. Here, we show that FliA in S Typhimurium also directs the transcription of large numbers of unstable, noncoding RNAs from intragenic promoters, and we identify two previously unreported FliA-transcribed protein-coding genes. One of these genes, sdiA, encodes a transcription factor that responds to quorum-sensing signals produced by other bacteria. We show that FliA-dependent transcription of sdiA is required for SdiA activity, highlighting a regulatory link between flagellar motility and intercellular communication.IMPORTANCE Initiation of bacterial transcription requires association of a σ factor with the core RNA polymerase to facilitate sequence-specific recognition of promoter elements. FliA is a widely conserved σ factor that directs transcription of genes involved in flagellar motility. We previously showed that Escherichia coli FliA transcribes many unstable, noncoding RNAs from promoters within genes. Here, we demonstrate the same phenomenon in Salmonella Typhimurium. We also show that S Typhimurium FliA directs transcription of the sdiA gene, which encodes a transcription factor that responds to quorum-sensing signals produced by other bacteria. FliA-dependent transcription of sdiA is required for transcriptional control of SdiA target genes, highlighting a regulatory link between flagellar motility and intercellular communication.
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16
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Adams PP, Baniulyte G, Esnault C, Chegireddy K, Singh N, Monge M, Dale RK, Storz G, Wade JT. Regulatory roles of Escherichia coli 5' UTR and ORF-internal RNAs detected by 3' end mapping. eLife 2021; 10:62438. [PMID: 33460557 PMCID: PMC7815308 DOI: 10.7554/elife.62438] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 11/26/2020] [Indexed: 02/06/2023] Open
Abstract
Many bacterial genes are regulated by RNA elements in their 5´ untranslated regions (UTRs). However, the full complement of these elements is not known even in the model bacterium Escherichia coli. Using complementary RNA-sequencing approaches, we detected large numbers of 3´ ends in 5´ UTRs and open reading frames (ORFs), suggesting extensive regulation by premature transcription termination. We documented regulation for multiple transcripts, including spermidine induction involving Rho and translation of an upstream ORF for an mRNA encoding a spermidine efflux pump. In addition to discovering novel sites of regulation, we detected short, stable RNA fragments derived from 5´ UTRs and sequences internal to ORFs. Characterization of three of these transcripts, including an RNA internal to an essential cell division gene, revealed that they have independent functions as sRNA sponges. Thus, these data uncover an abundance of cis- and trans-acting RNA regulators in bacterial 5´ UTRs and internal to ORFs. In most organisms, specific segments of a cell’s genetic information are copied to form single-stranded molecules of various sizes and purposes. Each of these RNA molecules, as they are known, is constructed as a chain that starts at the 5´ end and terminates at the 3´ end. Certain RNAs carry the information present in a gene, which provides the instructions that a cell needs to build proteins. Some, however, are ‘non-coding’ and instead act to fine-tune the activity of other RNAs. These regulatory RNAs can be separate from the RNAs they control, or they can be embedded in the very sequences they regulate; new evidence also shows that certain regulatory RNAs can act in both ways. Many regulatory RNAs are yet to be catalogued, even in simple, well-studied species such as the bacterium Escherichia coli. Here, Adams et al. aimed to better characterize the regulatory RNAs present in E. coli by mapping out the 3´ ends of every RNA molecule in the bacterium. This revealed many new regulatory RNAs and offered insights into where these sequences are located. For instance, the results show that several of these RNAs were embedded within RNA produced from larger genes. Some were nested in coding RNAs, and were parts of a longer RNA sequence that is adjacent to the protein coding segment. Others, however, were present within the instructions that code for a protein. The work by Adams et al. reveals that regulatory RNAs can be located in unexpected places, and provides a method for identifying them. This can be applied to other types of bacteria, in particular in species with few known RNA regulators.
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Affiliation(s)
- Philip P Adams
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, United States.,Postdoctoral Research Associate Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, United States
| | - Gabriele Baniulyte
- Wadsworth Center, New York State Department of Health, Albany, United States
| | - Caroline Esnault
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, United States
| | - Kavya Chegireddy
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, United States
| | - Navjot Singh
- Wadsworth Center, New York State Department of Health, Albany, United States
| | - Molly Monge
- Wadsworth Center, New York State Department of Health, Albany, United States
| | - Ryan K Dale
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, United States
| | - Gisela Storz
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, United States
| | - Joseph T Wade
- Wadsworth Center, New York State Department of Health, Albany, United States.,Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, United States
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17
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Kravchenko U, Gogoleva N, Kalubaka N, Kruk A, Diubo Y, Gogolev Y, Nikolaichik Y. The PhoPQ Two-Component System Is the Major Regulator of Cell Surface Properties, Stress Responses and Plant-Derived Substrate Utilisation During Development of Pectobacterium versatile-Host Plant Pathosystems. Front Microbiol 2021; 11:621391. [PMID: 33519782 PMCID: PMC7843439 DOI: 10.3389/fmicb.2020.621391] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/24/2020] [Indexed: 11/19/2022] Open
Abstract
Pectobacterium versatile (formerly P. carotovorum) is a recently defined species of soft rot enterobacteria capable of infecting many plant hosts and damaging different tissues. Complex transcriptional regulation of virulence properties can be expected for such a versatile pathogen. However, the relevant information is available only for related species and is rather limited. The PhoPQ two-component system, originally described in pectobacteria as PehRS, was previously shown to regulate a single gene, pehA. Using an insertional phoP mutant of Pectobacterium versatile (earlier-P. carotovorum), we demonstrate that PhoP regulates at least 115 genes with a majority of them specific for pectobacteria. The functions performed by PhoP-controlled genes include degradation, transport and metabolism of plant-derived carbon sources (polygalacturonate, arabinose-containing polysaccharides and citrate), modification of bacterial cell envelope and stress resistance. We also demonstrated PhoP involvement in establishing the order of plant cell wall decomposition and utilisation of the corresponding breakdown products. Based on experimental data and in silico analysis, we defined a PhoP binding site motif and provided proof for its universality in enteric bacteria. Scanning P. versatile genome for the locations of this motif suggested a much larger PhoP regulon enriched with the genes important for a plant pathogen, which makes PhoP a global virulence regulator. Potential PhoP targets include many regulatory genes and PhoP control over one of them, expI, was confirmed experimentally, highlighting the link between the PhoPQ two-component and quorum sensing systems. High concentrations of calcium and magnesium ions were found to abolish the PhoPQ-dependent transcription activation but did not relieve repression. Reduced PhoP expression and minimisation of PhoP dependence of regulon members' expression in P. versatile cells isolated from potato tuber tissues suggest that PhoPQ system is a key switch of expression levels of multiple virulence-related genes fine-tuned to control the development of P. versatile-host plant pathosystem.
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Affiliation(s)
- Uljana Kravchenko
- Department of Molecular Biology, Belarusian State University, Minsk, Belarus
| | - Natalia Gogoleva
- Federal Research Center “Kazan Scientific Center of RAS”, Kazan Institute of Biochemistry and Biophysics, Kazan, Russia
- Laboratory of Extreme Biology, Kazan Federal University Institute of Fundamental Medicine and Biology, Kazan, Russia
| | - Nastassia Kalubaka
- Department of Molecular Biology, Belarusian State University, Minsk, Belarus
| | - Alla Kruk
- Department of Molecular Biology, Belarusian State University, Minsk, Belarus
| | - Yuliya Diubo
- Department of Molecular Biology, Belarusian State University, Minsk, Belarus
| | - Yuri Gogolev
- Federal Research Center “Kazan Scientific Center of RAS”, Kazan Institute of Biochemistry and Biophysics, Kazan, Russia
- Department of Biochemistry, Biotechnology and Pharmacology, Kazan Federal University Institute of Fundamental Medicine and Biology, Kazan, Russia
| | - Yevgeny Nikolaichik
- Department of Molecular Biology, Belarusian State University, Minsk, Belarus
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18
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Genome-wide Identification of DNA-protein Interaction to Reconstruct Bacterial Transcription Regulatory Network. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-020-0030-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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19
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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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20
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Stringer AM, Baniulyte G, Lasek-Nesselquist E, Seed KD, Wade JT. Transcription termination and antitermination of bacterial CRISPR arrays. eLife 2020; 9:e58182. [PMID: 33124980 PMCID: PMC7665894 DOI: 10.7554/elife.58182] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 10/29/2020] [Indexed: 12/11/2022] Open
Abstract
A hallmark of CRISPR-Cas immunity systems is the CRISPR array, a genomic locus consisting of short, repeated sequences ('repeats') interspersed with short, variable sequences ('spacers'). CRISPR arrays are transcribed and processed into individual CRISPR RNAs that each include a single spacer, and direct Cas proteins to complementary sequences in invading nucleic acid. Most bacterial CRISPR array transcripts are unusually long for untranslated RNA, suggesting the existence of mechanisms to prevent premature transcription termination by Rho, a conserved bacterial transcription termination factor that rapidly terminates untranslated RNA. We show that Rho can prematurely terminate transcription of bacterial CRISPR arrays, and we identify a widespread antitermination mechanism that antagonizes Rho to facilitate complete transcription of CRISPR arrays. Thus, our data highlight the importance of transcription termination and antitermination in the evolution of bacterial CRISPR-Cas systems.
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Affiliation(s)
- Anne M Stringer
- Wadsworth Center, New York State Department of HealthAlbanyUnited States
| | - Gabriele Baniulyte
- Department of Biomedical Sciences, School of Public Health, University at AlbanyAlbanyUnited States
| | | | - Kimberley D Seed
- Department of Plant and Microbial Biology, University of California, BerkeleyBerkeleyUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Joseph T Wade
- Wadsworth Center, New York State Department of HealthAlbanyUnited States
- Department of Biomedical Sciences, School of Public Health, University at AlbanyAlbanyUnited States
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21
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Golder T, Mukhopadhyay AK, Koley H, Nandy RK. Nonmetabolizable Arabinose Inhibits Vibrio cholerae Growth in M9 Medium with Gluconate as the Sole Carbon Source. Jpn J Infect Dis 2020; 73:343-348. [PMID: 32350213 DOI: 10.7883/yoken.jjid.2019.304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The serogroups O1 and O139 of the marine bacterium Vibrio cholerae are responsible for causing cholera in humans. The pentose sugar arabinose is nonmetabolizable by the pathogen and is present in environmental niches as well as in the human intestine. In this study, arabinose-mediated V. cholerae growth interference was assessed in M9 minimal medium containing gluconate as the sole carbon source in the light of Entner-Doudoroff (ED) pathway, an obligatory metabolic route for gluconate utilization. V. cholerae O1 and O139 strains failed to grow in the presence of ≥ 0.3% arabinose in M9 with 0.2% gluconate, but there was no growth inhibition in the presence of arabinose in M9 with 0.2% glucose. Transcriptional analysis of edd and eda, the genes constituting the ED pathway, showed ~100- and ~17-fold increases, respectively, in M9-gluconate. Minor increases of ~4- and ~2-fold for edd and eda, respectively, were noted in AKI medium supplemented with 0.5% arabinose. The observed arabinose-mediated growth inhibition can contribute toward deepening the understanding of altered phenotypes, if any, via complementation/expression studies in V. cholerae with pBAD vectors and arabinose as an inducer.
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Affiliation(s)
- Taniya Golder
- ICMR-National Institute of Cholera and Enteric Diseases (NICED), India
| | | | - Hemanta Koley
- ICMR-National Institute of Cholera and Enteric Diseases (NICED), India
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22
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Baranova DE, Willsey GG, Levinson KJ, Smith C, Wade J, Mantis NJ. Transcriptional profiling of Vibrio cholerae O1 following exposure to human anti- lipopolysaccharide monoclonal antibodies. Pathog Dis 2020; 78:ftaa029. [PMID: 32589220 PMCID: PMC7371154 DOI: 10.1093/femspd/ftaa029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 06/22/2020] [Indexed: 02/04/2023] Open
Abstract
Following an episode of cholera, a rapidly dehydrating, watery diarrhea caused by the Gram-negative bacterium, Vibrio cholerae O1, humans mount a robust anti-lipopolysaccharide (LPS) antibody response that is associated with immunity to subsequent re-infection. In neonatal mouse and rabbit models of cholera, passively administered anti-LPS polyclonal and monoclonal (MAb) antibodies reduce V. cholerae colonization of the intestinal epithelia by inhibiting bacterial motility and promoting vibrio agglutination. Here we demonstrate that human anti-LPS IgG MAbs also arrest V. cholerae motility and induce bacterial paralysis. A subset of those MAbs also triggered V. cholerae to secrete an extracellular matrix (ECM). To identify changes in gene expression that accompany antibody exposure and that may account for motility arrest and ECM production, we subjected V. cholerae O1 El Tor to RNA-seq analysis after treatment with ZAC-3 IgG, a high affinity MAb directed against the core/lipid A region of LPS. We identified > 160 genes whose expression was altered following ZAC-3 IgG treatment, although canonical outer membrane stress regulons were not among them. ompS (VCA1028), a porin associated with virulence and indirectly regulated by ToxT, and norR (VCA0182), a σ54-dependent transcription factor involved in late stages of infection, were two upregulated genes worth noting.
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Affiliation(s)
- Danielle E Baranova
- Department of Biomedical Sciences, University at Albany, 1400 Washington Ave, Albany NY 12222
- Division of Infectious Diseases, Wadsworth Center, NYS Department of Health, 120 New Scotland Ave, Albany NY 12208
| | - Graham G Willsey
- Division of Infectious Diseases, Wadsworth Center, NYS Department of Health, 120 New Scotland Ave, Albany NY 12208
| | - Kara J Levinson
- Department of Biomedical Sciences, University at Albany, 1400 Washington Ave, Albany NY 12222
- Division of Infectious Diseases, Wadsworth Center, NYS Department of Health, 120 New Scotland Ave, Albany NY 12208
| | - Carol Smith
- Division of Molecular Genetics, Wadsworth Center, NYS Department of Health, 120 New Scotland Ave, Albany NY 12208
| | - Joseph Wade
- Department of Biomedical Sciences, University at Albany, 1400 Washington Ave, Albany NY 12222
- Division of Molecular Genetics, Wadsworth Center, NYS Department of Health, 120 New Scotland Ave, Albany NY 12208
| | - Nicholas J Mantis
- Department of Biomedical Sciences, University at Albany, 1400 Washington Ave, Albany NY 12222
- Division of Infectious Diseases, Wadsworth Center, NYS Department of Health, 120 New Scotland Ave, Albany NY 12208
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23
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Šmídová K, Ziková A, Pospíšil J, Schwarz M, Bobek J, Vohradsky J. DNA mapping and kinetic modeling of the HrdB regulon in Streptomyces coelicolor. Nucleic Acids Res 2019; 47:621-633. [PMID: 30371884 PMCID: PMC6344877 DOI: 10.1093/nar/gky1018] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 10/11/2018] [Indexed: 02/06/2023] Open
Abstract
HrdB in streptomycetes is a principal sigma factor whose deletion is lethal. This is also the reason why its regulon has not been investigated so far. To overcome experimental obstacles, for investigating the HrdB regulon, we constructed a strain whose HrdB protein was tagged by an HA epitope. ChIP-seq experiment, done in 3 repeats, identified 2137 protein-coding genes organized in 337 operons, 75 small RNAs, 62 tRNAs, 6 rRNAs and 3 miscellaneous RNAs. Subsequent kinetic modeling of regulation of protein-coding genes with HrdB alone and with a complex of HrdB and a transcriptional cofactor RbpA, using gene expression time series, identified 1694 genes that were under their direct control. When using the HrdB-RbpA complex in the model, an increase of the model fidelity was found for 322 genes. Functional analysis revealed that HrdB controls the majority of gene groups essential for the primary metabolism and the vegetative growth. Particularly, almost all ribosomal protein-coding genes were found in the HrdB regulon. Analysis of promoter binding sites revealed binding motif at the -10 region and suggested the possible role of mono- or di-nucleotides upstream of the -10 element.
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Affiliation(s)
- Klára Šmídová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, 14220 Prague, Czechia
- First Faculty of Medicine, Institute of Immunology and Microbiology, Charles University, 12800 Prague, Czechia
| | - Alice Ziková
- Institute of Microbiology, Academy of Sciences of the Czech Republic, 14220 Prague, Czechia
| | - Jiří Pospíšil
- Institute of Microbiology, Academy of Sciences of the Czech Republic, 14220 Prague, Czechia
| | - Marek Schwarz
- Institute of Microbiology, Academy of Sciences of the Czech Republic, 14220 Prague, Czechia
| | - Jan Bobek
- First Faculty of Medicine, Institute of Immunology and Microbiology, Charles University, 12800 Prague, Czechia
- Chemistry Department, Faculty of Science, J. E. Purkinje University, 40096 Ústí nad Labem, Czechia
| | - Jiri Vohradsky
- Institute of Microbiology, Academy of Sciences of the Czech Republic, 14220 Prague, Czechia
- To whom correspondence should be addressed. Tel: +420 241 062 513;
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24
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SmpB down-regulates proton-motive force for the persister tolerance to aminoglycosides in Aeromonas veronii. Biochem Biophys Res Commun 2018; 507:407-413. [PMID: 30449596 DOI: 10.1016/j.bbrc.2018.11.052] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 11/09/2018] [Indexed: 11/21/2022]
Abstract
Bacterial persisters comprise a small fraction of phenotypically heterogeneous variants with transient capability for survival when exposed to high concentrations of antibiotic. In aquatic pathogenic bacteria Aeromonas veronii, Small Protein B (SmpB), the core factor of trans-translation system, was identified as a new persistence-related gene. The SmpB deletion exhibited a higher susceptibility and lower persister cell formation under aminoglycosides antibiotics pressure compared with wild type. The transcriptional and translational activities of smpB gene were significantly enhanced by the gentamicin challenge in exponential phase, but not changed in stationary phase. The transcriptomic analysis revealed that the smpB deletion stimulated the production of proton-motive force (PMF). The cell survival induced by carbonyl cyanide m-chlorophenyl hydrazone (CCCP) further verified that SmpB variation affected the quantities of PMF. Taken together, these results uncovered a novel mechanism of persister formation mediated by SmpB under aminoglycosides treatments.
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25
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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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26
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Yan B, Boitano M, Clark TA, Ettwiller L. SMRT-Cappable-seq reveals complex operon variants in bacteria. Nat Commun 2018; 9:3676. [PMID: 30201986 PMCID: PMC6131387 DOI: 10.1038/s41467-018-05997-6] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 08/07/2018] [Indexed: 11/22/2022] Open
Abstract
Current methods for genome-wide analysis of gene expression require fragmentation of original transcripts into small fragments for short-read sequencing. In bacteria, the resulting fragmented information hides operon complexity. Additionally, in vivo processing of transcripts confounds the accurate identification of the 5' and 3' ends of operons. Here we develop a methodology called SMRT-Cappable-seq that combines the isolation of un-fragmented primary transcripts with single-molecule long read sequencing. Applied to E. coli, this technology results in an accurate definition of the transcriptome with 34% of known operons from RegulonDB being extended by at least one gene. Furthermore, 40% of transcription termination sites have read-through that alters the gene content of the operons. As a result, most of the bacterial genes are present in multiple operon variants reminiscent of eukaryotic splicing. By providing such granularity in the operon structure, this study represents an important resource for the study of prokaryotic gene network and regulation.
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Affiliation(s)
- Bo Yan
- New England Biolabs Inc., 240 County Road, Ipswich, MA, 01938, USA
| | | | - Tyson A Clark
- PacBio, 1305 O'Brien Drive, Menlo Park, CA, 94025, USA
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27
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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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28
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Determining the Specificity of Cascade Binding, Interference, and Primed Adaptation In Vivo in the Escherichia coli Type I-E CRISPR-Cas System. mBio 2018; 9:mBio.02100-17. [PMID: 29666291 PMCID: PMC5904413 DOI: 10.1128/mbio.02100-17] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In clustered regularly interspaced short palindromic repeat (CRISPR)-Cas (CRISPR-associated) immunity systems, short CRISPR RNAs (crRNAs) are bound by Cas proteins, and these complexes target invading nucleic acid molecules for degradation in a process known as interference. In type I CRISPR-Cas systems, the Cas protein complex that binds DNA is known as Cascade. Association of Cascade with target DNA can also lead to acquisition of new immunity elements in a process known as primed adaptation. Here, we assess the specificity determinants for Cascade-DNA interaction, interference, and primed adaptation in vivo, for the type I-E system of Escherichia coli Remarkably, as few as 5 bp of crRNA-DNA are sufficient for association of Cascade with a DNA target. Consequently, a single crRNA promotes Cascade association with numerous off-target sites, and the endogenous E. coli crRNAs direct Cascade binding to >100 chromosomal sites. In contrast to the low specificity of Cascade-DNA interactions, >18 bp are required for both interference and primed adaptation. Hence, Cascade binding to suboptimal, off-target sites is inert. Our data support a model in which the initial Cascade association with DNA targets requires only limited sequence complementarity at the crRNA 5' end whereas recruitment and/or activation of the Cas3 nuclease, a prerequisite for interference and primed adaptation, requires extensive base pairing.IMPORTANCE Many bacterial and archaeal species encode CRISPR-Cas immunity systems that protect against invasion by foreign DNA. In the Escherichia coli CRISPR-Cas system, a protein complex, Cascade, binds 61-nucleotide (nt) CRISPR RNAs (crRNAs). The Cascade complex is directed to invading DNA molecules through base pairing between the crRNA and target DNA. This leads to recruitment of the Cas3 nuclease, which destroys the invading DNA molecule and promotes acquisition of new immunity elements. We made the first in vivo measurements of Cascade binding to DNA targets. Thus, we show that Cascade binding to DNA is highly promiscuous; endogenous E. coli crRNAs can direct Cascade binding to >100 chromosomal locations. In contrast, we show that targeted degradation and acquisition of new immunity elements require highly specific association of Cascade with DNA, limiting CRISPR-Cas function to the appropriate targets.
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29
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Candelli T, Challal D, Briand JB, Boulay J, Porrua O, Colin J, Libri D. High-resolution transcription maps reveal the widespread impact of roadblock termination in yeast. EMBO J 2018; 37:embj.201797490. [PMID: 29351914 DOI: 10.15252/embj.201797490] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 12/14/2017] [Accepted: 12/15/2017] [Indexed: 01/04/2023] Open
Abstract
Transcription termination delimits transcription units but also plays important roles in limiting pervasive transcription. We have previously shown that transcription termination occurs when elongating RNA polymerase II (RNAPII) collides with the DNA-bound general transcription factor Reb1. We demonstrate here that many different DNA-binding proteins can induce termination by a similar roadblock (RB) mechanism. We generated high-resolution transcription maps by the direct detection of RNAPII upon nuclear depletion of two essential RB factors or when the canonical termination pathways for coding and non-coding RNAs are defective. We show that RB termination occurs genomewide and functions independently of (and redundantly with) the main transcription termination pathways. We provide evidence that transcriptional readthrough at canonical terminators is a significant source of pervasive transcription, which is controlled to a large extent by RB termination. Finally, we demonstrate the occurrence of RB termination around centromeres and tRNA genes, which we suggest shields these regions from RNAPII to preserve their functional integrity.
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Affiliation(s)
- Tito Candelli
- Institut Jacques Monod, CNRS, UMR 7592, Univ Paris Diderot, Paris, France.,Ecole doctorale Structure et Dynamique des Systèmes Vivants, Université Paris Saclay, Gif sur Yvette, France
| | - Drice Challal
- Institut Jacques Monod, CNRS, UMR 7592, Univ Paris Diderot, Paris, France.,Ecole doctorale Structure et Dynamique des Systèmes Vivants, Université Paris Saclay, Gif sur Yvette, France
| | - Jean-Baptiste Briand
- Institut Jacques Monod, CNRS, UMR 7592, Univ Paris Diderot, Paris, France.,Ecole doctorale Structure et Dynamique des Systèmes Vivants, Université Paris Saclay, Gif sur Yvette, France
| | - Jocelyne Boulay
- Institut de Biologie Intégrative de la Cellule (I2BC), CNRS, UMR 9198, Univ Paris-Saclay, Centre Energie Atomique, Gif sur Yvette, France
| | - Odil Porrua
- Institut Jacques Monod, CNRS, UMR 7592, Univ Paris Diderot, Paris, France
| | - Jessie Colin
- Institut Jacques Monod, CNRS, UMR 7592, Univ Paris Diderot, Paris, France
| | - Domenico Libri
- Institut Jacques Monod, CNRS, UMR 7592, Univ Paris Diderot, Paris, France
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30
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Baniulyte G, Singh N, Benoit C, Johnson R, Ferguson R, Paramo M, Stringer AM, Scott A, Lapierre P, Wade JT. Identification of regulatory targets for the bacterial Nus factor complex. Nat Commun 2017; 8:2027. [PMID: 29229908 PMCID: PMC5725501 DOI: 10.1038/s41467-017-02124-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 11/08/2017] [Indexed: 11/21/2022] Open
Abstract
Nus factors are broadly conserved across bacterial species, and are often essential for viability. A complex of five Nus factors (NusB, NusE, NusA, NusG and SuhB) is considered to be a dedicated regulator of ribosomal RNA folding, and has been shown to prevent Rho-dependent transcription termination. Here, we identify an additional cellular function for the Nus factor complex in Escherichia coli: repression of the Nus factor-encoding gene, suhB. This repression occurs primarily by translation inhibition, followed by Rho-dependent transcription termination. Thus, the Nus factor complex can prevent or promote Rho activity depending on the gene context. Conservation of putative NusB/E binding sites upstream of Nus factor genes suggests that Nus factor autoregulation occurs in many bacterial species. Additionally, many putative NusB/E binding sites are also found upstream of other genes in diverse species, and we demonstrate Nus factor regulation of one such gene in Citrobacter koseri. We conclude that Nus factors have an evolutionarily widespread regulatory function beyond ribosomal RNA, and that they are often autoregulatory.
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Affiliation(s)
- Gabriele Baniulyte
- Wadsworth Center, New York State Department of Health, Albany, NY, 12208, USA
- Department of Biomedical Sciences, School of Public Health, University at Albany, Rensselaer, NY, 12144, USA
| | - Navjot Singh
- Wadsworth Center, New York State Department of Health, Albany, NY, 12208, USA
| | - Courtney Benoit
- Wadsworth Center, New York State Department of Health, Albany, NY, 12208, USA
| | - Richard Johnson
- Wadsworth Center, New York State Department of Health, Albany, NY, 12208, USA
- Department of Biomedical Sciences, School of Public Health, University at Albany, Rensselaer, NY, 12144, USA
| | - Robert Ferguson
- Wadsworth Center, New York State Department of Health, Albany, NY, 12208, USA
| | - Mauricio Paramo
- Wadsworth Center, New York State Department of Health, Albany, NY, 12208, USA
| | - Anne M Stringer
- Wadsworth Center, New York State Department of Health, Albany, NY, 12208, USA
| | - Ashley Scott
- Wadsworth Center, New York State Department of Health, Albany, NY, 12208, USA
| | - Pascal Lapierre
- Wadsworth Center, New York State Department of Health, Albany, NY, 12208, USA
| | - Joseph T Wade
- Wadsworth Center, New York State Department of Health, Albany, NY, 12208, USA.
- Department of Biomedical Sciences, School of Public Health, University at Albany, Rensselaer, NY, 12144, USA.
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31
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Bastet L, Chauvier A, Singh N, Lussier A, Lamontagne AM, Prévost K, Massé E, Wade JT, Lafontaine DA. Translational control and Rho-dependent transcription termination are intimately linked in riboswitch regulation. Nucleic Acids Res 2017; 45:7474-7486. [PMID: 28520932 PMCID: PMC5499598 DOI: 10.1093/nar/gkx434] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 05/01/2017] [Accepted: 05/09/2017] [Indexed: 12/21/2022] Open
Abstract
Riboswitches are regulatory elements that control gene expression by altering RNA structure upon the binding of specific metabolites. Although Bacillus subtilis riboswitches have been shown to control premature transcription termination, less is known about regulatory mechanisms employed by Escherichia coli riboswitches, which are predicted to regulate mostly at the level of translation initiation. Here, we present experimental evidence suggesting that the majority of known E. coli riboswitches control transcription termination by using the Rho transcription factor. In the case of the thiamin pyrophosphate-dependent thiM riboswitch, we find that Rho-dependent transcription termination is triggered as a consequence of translation repression. Using in vitro and in vivo assays, we show that the Rho-mediated regulation relies on RNA target elements located at the beginning of thiM coding region. Gene reporter assays indicate that relocating Rho target elements to a different gene induces transcription termination, demonstrating that such elements are modular domains controlling Rho. Our work provides strong evidence that translationally regulating riboswitches also regulate mRNA levels through an indirect control mechanism ensuring tight control of gene expression.
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Affiliation(s)
- Laurène Bastet
- Department of Biology, Faculty of Sciences, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada
| | - Adrien Chauvier
- Department of Biology, Faculty of Sciences, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada
| | - Navjot Singh
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Antony Lussier
- Department of Biology, Faculty of Sciences, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada
| | - Anne-Marie Lamontagne
- Department of Biology, Faculty of Sciences, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada
| | - Karine Prévost
- Department of Biochemistry, Faculty of Medicine and Health Sciences, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec J1E 4K8, Canada
| | - Eric Massé
- Department of Biochemistry, Faculty of Medicine and Health Sciences, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec J1E 4K8, Canada
| | - Joseph T. Wade
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
- Department of Biomedical Sciences, University at Albany, Albany, NY 12201, USA
| | - Daniel A. Lafontaine
- Department of Biology, Faculty of Sciences, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada
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32
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van Rossum T, Muras A, Baur MJ, Creutzburg SC, van der Oost J, Kengen SW. A growth- and bioluminescence-based bioreporter for the in vivo detection of novel biocatalysts. Microb Biotechnol 2017; 10:625-641. [PMID: 28393499 PMCID: PMC5404197 DOI: 10.1111/1751-7915.12612] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 01/10/2017] [Accepted: 01/13/2017] [Indexed: 11/28/2022] Open
Abstract
The use of bioreporters in high-throughput screening for small molecules is generally laborious and/or expensive. The technology can be simplified by coupling the generation of a desired compound to cell survival, causing only positive cells to stay in the pool of generated variants. Here, a dual selection/screening system was developed for the in vivo detection of novel biocatalysts. The sensor part of the system is based on the transcriptional regulator AraC, which controls expression of both a selection reporter (LeuB or KmR; enabling growth) for rapid reduction of the initially large library size and a screening reporter (LuxCDABE; causing bioluminescence) for further quantification of the positive variants. Of four developed systems, the best system was the medium copy system with KmR as selection reporter. As a proof of principle, the system was tested for the selection of cells expressing an l-arabinose isomerase derived from mesophilic Escherichia coli or thermophilic Geobacillus thermodenitrificans. A more than a millionfold enrichment of cells with l-arabinose isomerase activity was demonstrated by selection and exclusion of false positives by screening. This dual selection/screening system is an important step towards an improved detection method for small molecules, and thereby for finding novel biocatalysts.
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Affiliation(s)
- Teunke van Rossum
- Laboratory of MicrobiologyWageningen University and ResearchStippeneng 46708WE WageningenThe Netherlands
| | - Aleksandra Muras
- Laboratory of MicrobiologyWageningen University and ResearchStippeneng 46708WE WageningenThe Netherlands
| | - Marco J.J. Baur
- Laboratory of MicrobiologyWageningen University and ResearchStippeneng 46708WE WageningenThe Netherlands
| | - Sjoerd C.A. Creutzburg
- Laboratory of MicrobiologyWageningen University and ResearchStippeneng 46708WE WageningenThe Netherlands
| | - John van der Oost
- Laboratory of MicrobiologyWageningen University and ResearchStippeneng 46708WE WageningenThe Netherlands
| | - Servé W.M. Kengen
- Laboratory of MicrobiologyWageningen University and ResearchStippeneng 46708WE WageningenThe Netherlands
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33
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Horizontally acquired AT-rich genes in Escherichia coli cause toxicity by sequestering RNA polymerase. Nat Microbiol 2017; 2:16249. [PMID: 28067866 DOI: 10.1038/nmicrobiol.2016.249] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 11/08/2016] [Indexed: 11/09/2022]
Abstract
Horizontal gene transfer permits rapid dissemination of genetic elements between individuals in bacterial populations. Transmitted DNA sequences may encode favourable traits. However, if the acquired DNA has an atypical base composition, it can reduce host fitness. Consequently, bacteria have evolved strategies to minimize the harmful effects of foreign genes. Most notably, xenogeneic silencing proteins bind incoming DNA that has a higher AT content than the host genome. An enduring question has been why such sequences are deleterious. Here, we showed that the toxicity of AT-rich DNA in Escherichia coli frequently results from constitutive transcription initiation within the coding regions of genes. Left unchecked, this causes titration of RNA polymerase and a global downshift in host gene expression. Accordingly, a mutation in RNA polymerase that diminished the impact of AT-rich DNA on host fitness reduced transcription from constitutive, but not activator-dependent, promoters.
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34
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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: 56] [Impact Index Per Article: 8.0] [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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Qian Z, Trostel A, Lewis DEA, Lee SJ, He X, Stringer AM, Wade JT, Schneider TD, Durfee T, Adhya S. Genome-Wide Transcriptional Regulation and Chromosome Structural Arrangement by GalR in E. coli. Front Mol Biosci 2016; 3:74. [PMID: 27900321 PMCID: PMC5110547 DOI: 10.3389/fmolb.2016.00074] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 10/26/2016] [Indexed: 11/13/2022] Open
Abstract
The regulatory protein, GalR, is known for controlling transcription of genes related to D-galactose metabolism in Escherichia coli. Here, using a combination of experimental and bioinformatic approaches, we identify novel GalR binding sites upstream of several genes whose function is not directly related to D-galactose metabolism. Moreover, we do not observe regulation of these genes by GalR under standard growth conditions. Thus, our data indicate a broader regulatory role for GalR, and suggest that regulation by GalR is modulated by other factors. Surprisingly, we detect regulation of 158 transcripts by GalR, with few regulated genes being associated with a nearby GalR binding site. Based on our earlier observation of long-range interactions between distally bound GalR dimers, we propose that GalR indirectly regulates the transcription of many genes by inducing large-scale restructuring of the chromosome.
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Affiliation(s)
- Zhong Qian
- Laboratory of Molecular Biology, National Institutes of Health, National Cancer Institute Bethesda, MD, USA
| | - Andrei Trostel
- Laboratory of Molecular Biology, National Institutes of Health, National Cancer Institute Bethesda, MD, USA
| | - Dale E A Lewis
- Laboratory of Molecular Biology, National Institutes of Health, National Cancer Institute Bethesda, MD, USA
| | - Sang Jun Lee
- Microbiomics and Immunity Research Center, Korea Research Institute of Bioscience and Biotechnology Daejeon, Korea
| | - Ximiao He
- Laboratory of Metabolism, National Institutes of Health, National Cancer Institute Bethesda, MD, USA
| | - Anne M Stringer
- Wadsworth Center, New York State Department of Health Albany, NY, USA
| | - Joseph T Wade
- Wadsworth Center, New York State Department of HealthAlbany, NY, USA; Department of Biomedical Sciences, School of Public Health, University of AlbanyAlbany, NY, USA
| | - Thomas D Schneider
- Gene Regulation and Chromosome Biology Laboratory, National Institutes of Health, National Cancer Institute, Center for Cancer Research Frederick, MD, USA
| | | | - Sankar Adhya
- Laboratory of Molecular Biology, National Institutes of Health, National Cancer Institute Bethesda, MD, USA
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Smith C, Stringer AM, Mao C, Palumbo MJ, Wade JT. Mapping the Regulatory Network for Salmonella enterica Serovar Typhimurium Invasion. mBio 2016; 7:e01024-16. [PMID: 27601571 PMCID: PMC5013294 DOI: 10.1128/mbio.01024-16] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 08/10/2016] [Indexed: 12/20/2022] Open
Abstract
UNLABELLED Salmonella enterica pathogenicity island 1 (SPI-1) encodes proteins required for invasion of gut epithelial cells. The timing of invasion is tightly controlled by a complex regulatory network. The transcription factor (TF) HilD is the master regulator of this process and senses environmental signals associated with invasion. HilD activates transcription of genes within and outside SPI-1, including six other TFs. Thus, the transcriptional program associated with host cell invasion is controlled by at least 7 TFs. However, very few of the regulatory targets are known for these TFs, and the extent of the regulatory network is unclear. In this study, we used complementary genomic approaches to map the direct regulatory targets of all 7 TFs. Our data reveal a highly complex and interconnected network that includes many previously undescribed regulatory targets. Moreover, the network extends well beyond the 7 TFs, due to the inclusion of many additional TFs and noncoding RNAs. By comparing gene expression profiles of regulatory targets for the 7 TFs, we identified many uncharacterized genes that are likely to play direct roles in invasion. We also uncovered cross talk between SPI-1 regulation and other regulatory pathways, which, in turn, identified gene clusters that likely share related functions. Our data are freely available through an intuitive online browser and represent a valuable resource for the bacterial research community. IMPORTANCE Invasion of epithelial cells is an early step during infection by Salmonella enterica and requires secretion of specific proteins into host cells via a type III secretion system (T3SS). Most T3SS-associated proteins required for invasion are encoded in a horizontally acquired genomic locus known as Salmonella pathogenicity island 1 (SPI-1). Multiple regulators respond to environmental signals to ensure appropriate timing of SPI-1 gene expression. In particular, there are seven transcription regulators that are known to be involved in coordinating expression of SPI-1 genes. We have used complementary genome-scale approaches to map the gene targets of these seven regulators. Our data reveal a highly complex and interconnected regulatory network that includes many previously undescribed target genes. Moreover, our data functionally implicate many uncharacterized genes in the invasion process and reveal cross talk between SPI-1 regulation and other regulatory pathways. All datasets are freely available through an intuitive online browser.
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Affiliation(s)
- Carol Smith
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Anne M Stringer
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Chunhong Mao
- Biocomplexity Institute of Virginia Tech, Virginia Tech, Blacksburg, Virginia, USA
| | - Michael J Palumbo
- 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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Liu H, Wang K, Lindås AC, Peeters E. The genome-scale DNA-binding profile of BarR, a β-alanine responsive transcription factor in the archaeon Sulfolobus acidocaldarius. BMC Genomics 2016; 17:569. [PMID: 27502941 PMCID: PMC4977709 DOI: 10.1186/s12864-016-2890-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Accepted: 07/06/2016] [Indexed: 01/09/2023] Open
Abstract
Background The Leucine-responsive Regulatory Protein (Lrp) family is a widespread family of regulatory transcription factors in prokaryotes. BarR is an Lrp-like transcription factor in the model archaeon Sulfolobus acidocaldarius that activates the expression of a β-alanine aminotransferase gene, which is involved in β-alanine degradation. In contrast to classical Lrp-like transcription factors, BarR is not responsive to any of the α-amino acids but interacts specifically with β-alanine. Besides the juxtaposed β-alanine aminotransferase gene, other regulatory targets of BarR have not yet been identified although β-alanine is the precursor of coenzyme A and thus an important central metabolite. The aim of this study is to extend the knowledge of the DNA-binding characteristics of BarR and of its corresponding regulon from a local to a genome-wide perspective. Results We characterized the genome-wide binding profile of BarR using chromatin immunoprecipation combined with high-throughput sequencing (ChIP-seq). This revealed 21 genomic binding loci. High-enrichment binding regions were validated to interact with purified BarR protein in vitro using electrophoretic mobility shift assays and almost all targets were also shown to harbour a conserved semi-palindromic binding motif. Only a small subset of enriched genomic sites are located in intergenic regions at a relative short distance to a promoter, and qRT-PCR analysis demonstrated that only one additional operon is under activation of BarR, namely the glutamine synthase operon. The latter is also a target of other Lrp-like transcription factors. Detailed inspection of the BarR ChIP-seq profile at the β-alanine aminotransferase promoter region in combination with binding motif predictions indicate that the operator structure is more complicated than previously anticipated, consisting of multiple (major and auxiliary) operators. Conclusions BarR has a limited regulon, and includes also glutamine synthase genes besides the previously characterized β-alanine aminotransferase. Regulation of glutamine synthase is suggestive of a link between β-alanine and α-amino acid metabolism in S. acidocaldarius. Furthermore, this work reveals that the BarR regulon overlaps with that of other Lrp-like regulators. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2890-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Han Liu
- Department of Bio-Engineering Sciences, Research Group of Microbiology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium
| | - Kun Wang
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius v. 20C, SE-10691, Stockholm, Sweden
| | - Ann-Christin Lindås
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius v. 20C, SE-10691, Stockholm, Sweden
| | - Eveline Peeters
- Department of Bio-Engineering Sciences, Research Group of Microbiology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium.
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38
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Sanfilippo JE, Nguyen AA, Karty JA, Shukla A, Schluchter WM, Garczarek L, Partensky F, Kehoe DM. Self-regulating genomic island encoding tandem regulators confers chromatic acclimation to marine Synechococcus. Proc Natl Acad Sci U S A 2016; 113:6077-82. [PMID: 27152022 PMCID: PMC4889380 DOI: 10.1073/pnas.1600625113] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The evolutionary success of marine Synechococcus, the second-most abundant phototrophic group in the marine environment, is partly attributable to this group's ability to use the entire visible spectrum of light for photosynthesis. This group possesses a remarkable diversity of light-harvesting pigments, and most of the group's members are orange and pink because of their use of phycourobilin and phycoerythrobilin chromophores, which are attached to antennae proteins called phycoerythrins. Many strains can alter phycoerythrin chromophore ratios to optimize photon capture in changing blue-green environments using type IV chromatic acclimation (CA4). Although CA4 is common in most marine Synechococcus lineages, the regulation of this process remains unexplored. Here, we show that a widely distributed genomic island encoding tandem master regulators named FciA (for type four chromatic acclimation island) and FciB plays a central role in controlling CA4. FciA and FciB have diametric effects on CA4. Interruption of fciA causes a constitutive green light phenotype, and interruption of fciB causes a constitutive blue light phenotype. These proteins regulate all of the molecular responses occurring during CA4, and the proteins' activity is apparently regulated posttranscriptionally, although their cellular ratio appears to be critical for establishing the set point for the blue-green switch in ecologically relevant light environments. Surprisingly, FciA and FciB coregulate only three genes within the Synechococcus genome, all located within the same genomic island as fciA and fciB These findings, along with the widespread distribution of strains possessing this island, suggest that horizontal transfer of a small, self-regulating DNA region has conferred CA4 capability to marine Synechococcus throughout many oceanic areas.
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Affiliation(s)
| | - Adam A Nguyen
- Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148; Department of Chemistry, University of New Orleans, New Orleans, LA 70148
| | - Jonathan A Karty
- Mass Spectrometry Facility, Department of Chemistry, Indiana University, Bloomington, IN 47405
| | - Animesh Shukla
- Department of Biology, Indiana University, Bloomington, IN 47405
| | - Wendy M Schluchter
- Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148; Department of Chemistry, University of New Orleans, New Orleans, LA 70148
| | - Laurence Garczarek
- Sorbonne Universités, Université Pierre et Marie Curie University Paris 06, CNRS, UMR 7144, Station Biologique, Plankton Group, 29688 Roscoff, France
| | - Frédéric Partensky
- Sorbonne Universités, Université Pierre et Marie Curie University Paris 06, CNRS, UMR 7144, Station Biologique, Plankton Group, 29688 Roscoff, France
| | - David M Kehoe
- Department of Biology, Indiana University, Bloomington, IN 47405; Indiana Molecular Biology Institute, Indiana University, Bloomington, IN 47405
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Abstract
UNLABELLED A complex of highly conserved proteins consisting of NusB, NusE, NusA, and NusG is required for robust expression of rRNA in Escherichia coli. This complex is proposed to prevent Rho-dependent transcription termination by a process known as "antitermination." The mechanism of this antitermination in rRNA is poorly understood but requires association of NusB and NusE with a specific RNA sequence in rRNA known as BoxA. Here, we identify a novel member of the rRNA antitermination machinery: the inositol monophosphatase SuhB. We show that SuhB associates with elongating RNA polymerase (RNAP) at rRNA in a NusB-dependent manner. Although we show that SuhB is required for BoxA-mediated antitermination in a reporter system, our data indicate that the major function of the NusB/E/A/G/SuhB complex is not to prevent Rho-dependent termination of rRNA but rather to promote correct rRNA maturation. This occurs through formation of a SuhB-mediated loop between NusB/E/BoxA and RNAP/NusA/G. Thus, we have reassigned the function of these proteins at rRNA and identified another key player in this complex. IMPORTANCE As RNA polymerase transcribes the rRNA operons in E. coli, it complexes with a set of proteins called Nus that confer enhanced rates of transcription elongation, correct folding of rRNA, and rRNA assembly with ribosomal proteins to generate a fully functional ribosome. Four Nus proteins were previously known, NusA, NusB, NusE, and NusG; here, we discover and describe a fifth, SuhB, that is an essential component of this complex. We demonstrate that the main function of this SuhB-containing complex is not to prevent premature transcription termination within the rRNA operon, as had been long claimed, but to enable rRNA maturation and a functional ribosome fully competent for translation.
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40
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Abstract
Y. pestis exhibits dramatically different traits of pathogenicity and transmission, albeit their close genetic relationship with its ancestor-Y. pseudotuberculosis, a self-limiting gastroenteric pathogen. Y. pestis is evolved into a deadly pathogen and transmitted to mammals and/or human beings by infected flea biting or directly contacting with the infected animals. Various kinds of environmental changes are implicated into its complex life cycle and pathogenesis. Dynamic regulation of gene expression is critical for environmental adaptation or survival, primarily reflected by genetic regulation mediated by transcriptional factors and small regulatory RNAs at the transcriptional and posttranscriptional level, respectively. The effects of genetic regulation have been shown to profoundly influence Y. pestis physiology and pathogenesis such as stress resistance, biofilm formation, intracellular survival, and replication. In this chapter, we mainly summarize the progresses on popular methods of genetic regulation and on regulatory patterns and consequences of many key transcriptional and posttranscriptional regulators, with a particular emphasis on how genetic regulation influences the biofilm and virulence of Y. pestis.
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Wang J, Rennie W, Liu C, Carmack CS, Prévost K, Caron MP, Massé E, Ding Y, Wade JT. Identification of bacterial sRNA regulatory targets using ribosome profiling. Nucleic Acids Res 2015; 43:10308-20. [PMID: 26546513 PMCID: PMC4666370 DOI: 10.1093/nar/gkv1158] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 10/19/2015] [Indexed: 12/30/2022] Open
Abstract
Bacteria express large numbers of non-coding, regulatory RNAs known as ‘small RNAs’ (sRNAs). sRNAs typically regulate expression of multiple target messenger RNAs (mRNAs) through base-pairing interactions. sRNA:mRNA base-pairing often results in altered mRNA stability and/or altered translation initiation. Computational identification of sRNA targets is challenging due to the requirement for only short regions of base-pairing that can accommodate mismatches. Experimental approaches have been applied to identify sRNA targets on a genomic scale, but these focus only on those targets regulated at the level of mRNA stability. Here, we utilize ribosome profiling (Ribo-seq) to experimentally identify regulatory targets of the Escherichia coli sRNA RyhB. We not only validate a majority of known RyhB targets using the Ribo-seq approach, but also discover many novel ones. We further confirm regulation of a selection of known and novel targets using targeted reporter assays. By mutating nucleotides in the mRNA of a newly discovered target, we demonstrate direct regulation of this target by RyhB. Moreover, we show that Ribo-seq distinguishes between mRNAs regulated at the level of RNA stability and those regulated at the level of translation. Thus, Ribo-seq represents a powerful approach for genome-scale identification of sRNA targets.
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Affiliation(s)
- Jing Wang
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - William Rennie
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Chaochun Liu
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Charles S Carmack
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Karine Prévost
- RNA Group, Department of Biochemistry, University of Sherbrooke, Sherbrooke, Quebec, J1H 5N4, Canada
| | - Marie-Pier Caron
- RNA Group, Department of Biochemistry, University of Sherbrooke, Sherbrooke, Quebec, J1H 5N4, Canada
| | - Eric Massé
- RNA Group, Department of Biochemistry, University of Sherbrooke, Sherbrooke, Quebec, J1H 5N4, Canada
| | - Ye Ding
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA Department of Biomedical Sciences, University at Albany, Albany, NY 12201, USA
| | - Joseph T Wade
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA Department of Biomedical Sciences, University at Albany, Albany, NY 12201, USA
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Jain D, Narayanan N, Nair DT. Plasticity in Repressor-DNA Interactions Neutralizes Loss of Symmetry in Bipartite Operators. J Biol Chem 2015; 291:1235-42. [PMID: 26511320 DOI: 10.1074/jbc.m115.689695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Indexed: 11/06/2022] Open
Abstract
Transcription factor-DNA interactions are central to gene regulation. Many transcription factors regulate multiple target genes and can bind sequences that do not conform strictly to the consensus. To understand the structural mechanism utilized by the transcription regulators to bind diverse target sequences, we have employed the repressor AraR from Bacillus subtilis as a model system. AraR is known to bind to eight different operator sites in the bacterial genome. Although there are differences in the sequences of four of these operators, ORE1, ORX1, ORA1, and ORR3, the AraR-DNA binding domain (AraR-DBD) as well as full-length AraR unexpectedly binds to each of these sequences with similar affinities as measured by fluorescence anisotropy experiments. We have determined crystal structures of AraR-DBD in complex with two different natural operators ORE1 and ORX1 up to 2.07 and 1.97 Å resolution, respectively. These structures were compared with the previously reported structures of AraR-DBD bound to two other natural operators (ORA1 and ORR3). Interactions of two molecules of AraR-DBD with the symmetric operator, ORE1, are identical, but their interaction with the non-symmetric operator ORX1 results in breakdown of the symmetry in protein-DNA interactions. The novel interactions observed are accompanied by local conformational change in the DNA. ChIP-sequencing (ChIP-Seq) data on other transcription factors has shown that they can bind to diverse targets, and hence the plasticity exhibited by AraR may be a general phenomenon. The ability of transcription factors to form alternate interactions may be important for employment in new functions and evolution of novel regulatory circuits.
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Affiliation(s)
- Deepti Jain
- From the Transcription Regulation Lab and the National Centre for Biological Sciences (NCBS-TIFR), UAS-GKVK Campus, Bellary Road, Bangalore 560065, and
| | - Naveen Narayanan
- the National Centre for Biological Sciences (NCBS-TIFR), UAS-GKVK Campus, Bellary Road, Bangalore 560065, and the Genomic Integrity and Plasticity Lab, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Bhankri Village, Faridabad 121001, Manipal University, Manipal, 576104 Karnataka, India
| | - Deepak T Nair
- the National Centre for Biological Sciences (NCBS-TIFR), UAS-GKVK Campus, Bellary Road, Bangalore 560065, and the Genomic Integrity and Plasticity Lab, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Bhankri Village, Faridabad 121001
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Barquist L, Vogel J. Accelerating Discovery and Functional Analysis of Small RNAs with New Technologies. Annu Rev Genet 2015; 49:367-94. [PMID: 26473381 DOI: 10.1146/annurev-genet-112414-054804] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Over the past decade, bacterial small RNAs (sRNAs) have gone from a biological curiosity to being recognized as a major class of regulatory molecules. High-throughput methods for sampling the transcriptional output of bacterial cells demonstrate that sRNAs are universal features of bacterial transcriptomes, are plentiful, and appear to vary extensively over evolutionary time. With ever more bacteria coming under study, the question becomes how can we accelerate the discovery and functional characterization of sRNAs in diverse organisms. New technologies built on high-throughput sequencing are emerging that can rapidly provide global insight into the numbers and functions of sRNAs in bacteria of interest, providing information that can shape hypotheses and guide research. In this review, we describe recent developments in transcriptomics (RNA-seq) and functional genomics that we expect to help us develop an integrated, systems-level view of sRNA biology in bacteria.
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Affiliation(s)
- Lars Barquist
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany; ,
| | - Jörg Vogel
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany; ,
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44
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OperomeDB: A Database of Condition-Specific Transcription Units in Prokaryotic Genomes. BIOMED RESEARCH INTERNATIONAL 2015; 2015:318217. [PMID: 26543854 PMCID: PMC4620388 DOI: 10.1155/2015/318217] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 03/02/2015] [Indexed: 12/30/2022]
Abstract
Background. In prokaryotic organisms, a substantial fraction of adjacent genes are organized into operons—codirectionally organized genes in prokaryotic genomes with the presence of a common promoter and terminator. Although several available operon databases provide information with varying levels of reliability, very few resources provide experimentally supported results. Therefore, we believe that the biological community could benefit from having a new operon prediction database with operons predicted using next-generation RNA-seq datasets. Description. We present operomeDB, a database which provides an ensemble of all the predicted operons for bacterial genomes using available RNA-sequencing datasets across a wide range of experimental conditions. Although several studies have recently confirmed that prokaryotic operon structure is dynamic with significant alterations across environmental and experimental conditions, there are no comprehensive databases for studying such variations across prokaryotic transcriptomes. Currently our database contains nine bacterial organisms and 168 transcriptomes for which we predicted operons. User interface is simple and easy to use, in terms of visualization, downloading, and querying of data. In addition, because of its ability to load custom datasets, users can also compare their datasets with publicly available transcriptomic data of an organism. Conclusion. OperomeDB as a database should not only aid experimental groups working on transcriptome analysis of specific organisms but also enable studies related to computational and comparative operomics.
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45
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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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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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47
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Knapp GS, Lyubetskaya A, Peterson MW, Gomes ALC, Ma Z, Galagan JE, McDonough KA. Role of intragenic binding of cAMP responsive protein (CRP) in regulation of the succinate dehydrogenase genes Rv0249c-Rv0247c in TB complex mycobacteria. Nucleic Acids Res 2015; 43:5377-93. [PMID: 25940627 PMCID: PMC4477654 DOI: 10.1093/nar/gkv420] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Accepted: 04/19/2015] [Indexed: 11/14/2022] Open
Abstract
Bacterial pathogens adapt to changing environments within their hosts, and the signaling molecule adenosine 3', 5'-cyclic monophosphate (cAMP) facilitates this process. In this study, we characterized in vivo DNA binding and gene regulation by the cAMP-responsive protein CRP in M. bovis BCG as a model for tuberculosis (TB)-complex bacteria. Chromatin immunoprecipitation followed by deep-sequencing (ChIP-seq) showed that CRP associates with ∼900 DNA binding regions, most of which occur within genes. The most highly enriched binding region was upstream of a putative copper transporter gene (ctpB), and crp-deleted bacteria showed increased sensitivity to copper toxicity. Detailed mutational analysis of four CRP binding sites upstream of the virulence-associated Rv0249c-Rv0247c succinate dehydrogenase genes demonstrated that CRP directly regulates Rv0249c-Rv0247c expression from two promoters, one of which requires sequences intragenic to Rv0250c for maximum expression. The high percentage of intragenic CRP binding sites and our demonstration that these intragenic DNA sequences significantly contribute to biologically relevant gene expression greatly expand the genome space that must be considered for gene regulatory analyses in mycobacteria. These findings also have practical implications for an important bacterial pathogen in which identification of mutations that affect expression of drug target-related genes is widely used for rapid drug resistance screening.
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Affiliation(s)
- Gwendowlyn S Knapp
- 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
| | | | | | - Zhuo Ma
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, PO Box 22002, Albany, NY 12201-2002, USA
| | - James E Galagan
- Bioinformatics Program, Boston University, Boston, MA 02215, USA Department of Biomedical Engineering, Boston, MA 02215, USA Department of Microbiology, Boston University, Boston, MA 02215, USA
| | - Kathleen A McDonough
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, PO Box 22002, Albany, NY 12201-2002, USA Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY 12201, USA
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48
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Abstract
Protein-DNA interactions are central to many basic biological processes, including transcription regulation, DNA replication, and DNA repair. Chromatin Immunoprecipitation (ChIP) is used to determine the position and strength of protein-DNA interactions in vivo. Coupling ChIP with microarrays (ChIP-chip), and more recently with deep sequencing (ChIP-seq), has allowed genome-wide profiling of DNA binding events in vivo. In this chapter we outline the steps to generate ChIP-seq libraries from bacterial samples and briefly discuss basic analysis of the data.
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Affiliation(s)
- Richard P Bonocora
- Division of Genetics, Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, NY, 12208, USA,
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Wade JT. Mapping Transcription Regulatory Networks with ChIP-seq and RNA-seq. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 883:119-34. [PMID: 26621465 DOI: 10.1007/978-3-319-23603-2_7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Bacterial genomes encode numerous transcription factors, DNA-binding proteins that regulate transcription initiation. Identifying the regulatory targets of transcription factors is a major challenge of systems biology. Here I describe the use of two genome-scale approaches, ChIP-seq and RNA-seq, that are used to map transcription factor regulons. ChIP-seq maps the association of transcription factors with DNA, and RNA-seq determines changes in RNA levels associated with transcription factor perturbation. I discuss the strengths and weaknesses of these and related approaches, and I describe how ChIP-seq and RNA-seq can be combined to map individual transcription factor regulons and entire regulatory networks.
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Affiliation(s)
- Joseph T Wade
- New York State Department of Health, Wadsworth Center, Albany, NY, 12208, USA.
- Department of Biomedical Sciences, University at Albany, Albany, NY, 12201, USA.
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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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