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Lévi-Meyrueis C, Monteil V, Sismeiro O, Dillies MA, Kolb A, Monot M, Dupuy B, Duarte SS, Jagla B, Coppée JY, Beraud M, Norel F. Repressor activity of the RpoS/σS-dependent RNA polymerase requires DNA binding. Nucleic Acids Res 2015; 43:1456-68. [PMID: 25578965 PMCID: PMC4330354 DOI: 10.1093/nar/gku1379] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The RpoS/σ(S) sigma subunit of RNA polymerase (RNAP) activates transcription of stationary phase genes in many Gram-negative bacteria and controls adaptive functions, including stress resistance, biofilm formation and virulence. In this study, we address an important but poorly understood aspect of σ(S)-dependent control, that of a repressor. Negative regulation by σ(S) has been proposed to result largely from competition between σ(S) and other σ factors for binding to a limited amount of core RNAP (E). To assess whether σ(S) binding to E alone results in significant downregulation of gene expression by other σ factors, we characterized an rpoS mutant of Salmonella enterica serovar Typhimurium producing a σ(S) protein proficient for Eσ(S) complex formation but deficient in promoter DNA binding. Genome expression profiling and physiological assays revealed that this mutant was defective for negative regulation, indicating that gene repression by σ(S) requires its binding to DNA. Although the mechanisms of repression by σ(S) are likely specific to individual genes and environmental conditions, the study of transcription downregulation of the succinate dehydrogenase operon suggests that σ competition at the promoter DNA level plays an important role in gene repression by Eσ(S).
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Affiliation(s)
- Corinne Lévi-Meyrueis
- Institut Pasteur, Laboratoire Systèmes Macromoléculaires et Signalisation, Département de Microbiologie, rue du Docteur Roux, 75015 Paris, France CNRS ERL3526, rue du Docteur Roux, 75015 Paris, France Université Paris Sud XI, 15, rue Georges Clémenceau, 91405 Orsay Cedex, France
| | - Véronique Monteil
- Institut Pasteur, Laboratoire Systèmes Macromoléculaires et Signalisation, Département de Microbiologie, rue du Docteur Roux, 75015 Paris, France CNRS ERL3526, rue du Docteur Roux, 75015 Paris, France
| | - Odile Sismeiro
- Institut Pasteur, Plate-forme Transcriptome et Epigénome, Département Génomes et génétique, rue du Docteur Roux, 75015 Paris, France
| | - Marie-Agnès Dillies
- Institut Pasteur, Plate-forme Transcriptome et Epigénome, Département Génomes et génétique, rue du Docteur Roux, 75015 Paris, France
| | - Annie Kolb
- Institut Pasteur, Laboratoire Systèmes Macromoléculaires et Signalisation, Département de Microbiologie, rue du Docteur Roux, 75015 Paris, France CNRS ERL3526, rue du Docteur Roux, 75015 Paris, France
| | - Marc Monot
- Institut Pasteur, Laboratoire Pathogenèse des bactéries anaérobies, Département de Microbiologie, rue du Docteur Roux, 75015 Paris, France
| | - Bruno Dupuy
- Institut Pasteur, Laboratoire Pathogenèse des bactéries anaérobies, Département de Microbiologie, rue du Docteur Roux, 75015 Paris, France
| | - Sara Serradas Duarte
- Institut Pasteur, Laboratoire Systèmes Macromoléculaires et Signalisation, Département de Microbiologie, rue du Docteur Roux, 75015 Paris, France CNRS ERL3526, rue du Docteur Roux, 75015 Paris, France
| | - Bernd Jagla
- Institut Pasteur, Plate-forme Transcriptome et Epigénome, Département Génomes et génétique, rue du Docteur Roux, 75015 Paris, France
| | - Jean-Yves Coppée
- Institut Pasteur, Plate-forme Transcriptome et Epigénome, Département Génomes et génétique, rue du Docteur Roux, 75015 Paris, France
| | - Mélanie Beraud
- Institut Pasteur, Laboratoire Systèmes Macromoléculaires et Signalisation, Département de Microbiologie, rue du Docteur Roux, 75015 Paris, France CNRS ERL3526, rue du Docteur Roux, 75015 Paris, France Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris, rue du Docteur Roux, 75015 Paris, France
| | - Françoise Norel
- Institut Pasteur, Laboratoire Systèmes Macromoléculaires et Signalisation, Département de Microbiologie, rue du Docteur Roux, 75015 Paris, France CNRS ERL3526, rue du Docteur Roux, 75015 Paris, France
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Fröhlich KS, Papenfort K, Berger AA, Vogel J. A conserved RpoS-dependent small RNA controls the synthesis of major porin OmpD. Nucleic Acids Res 2011; 40:3623-40. [PMID: 22180532 PMCID: PMC3333887 DOI: 10.1093/nar/gkr1156] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
A remarkable feature of many small non-coding RNAs (sRNAs) of Escherichia coli and Salmonella is their accumulation in the stationary phase of bacterial growth. Several stress response regulators and sigma factors have been reported to direct the transcription of stationary phase-specific sRNAs, but a widely conserved sRNA gene that is controlled by the major stationary phase and stress sigma factor, σ(S) (RpoS), has remained elusive. We have studied in Salmonella the conserved SdsR sRNA, previously known as RyeB, one of the most abundant stationary phase-specific sRNAs in E. coli. Alignments of the sdsR promoter region and genetic analysis strongly suggest that this sRNA gene is selectively transcribed by σ(S). We show that SdsR down-regulates the synthesis of the major Salmonella porin OmpD by Hfq-dependent base pairing; SdsR thus represents the fourth sRNA to regulate this major outer membrane porin. Similar to the InvR, MicC and RybB sRNAs, SdsR recognizes the ompD mRNA in the coding sequence, suggesting that this mRNA may be primarily targeted downstream of the start codon. The SdsR-binding site in ompD was localized by 3'-RACE, an experimental approach that promises to be of use in predicting other sRNA-target interactions in bacteria.
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Affiliation(s)
- Kathrin S Fröhlich
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany
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Koo BM, Rhodius VA, Nonaka G, deHaseth PL, Gross CA. Reduced capacity of alternative sigmas to melt promoters ensures stringent promoter recognition. Genes Dev 2009; 23:2426-36. [PMID: 19833768 DOI: 10.1101/gad.1843709] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In bacteria, multiple sigmas direct RNA polymerase to distinct sets of promoters. Housekeeping sigmas direct transcription from thousands of promoters, whereas most alternative sigmas are more selective, recognizing more highly conserved promoter motifs. For sigma(32) and sigma(28), two Escherichia coli Group 3 sigmas, altering a few residues in Region 2.3, the portion of sigma implicated in promoter melting, to those universally conserved in housekeeping sigmas relaxed their stringent promoter requirements and significantly enhanced melting of suboptimal promoters. All Group 3 sigmas and the more divergent Group 4 sigmas have nonconserved amino acids at these positions and rarely transcribe >100 promoters. We suggest that the balance of "melting" and "recognition" functions of sigmas is critical to setting the stringency of promoter recognition. Divergent sigmas may generally use a nonoptimal Region 2.3 to increase promoter stringency, enabling them to mount a focused response to altered conditions.
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Affiliation(s)
- Byoung-Mo Koo
- Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, California 94158, USA
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Osiriphun Y, Wongtrakoongate P, Sanongkiet S, Suriyaphol P, Thongboonkerd V, Tungpradabkul S. Identification and Characterization of RpoS Regulon and RpoS-Dependent Promoters in Burkholderia pseudomallei. J Proteome Res 2009; 8:3118-31. [DOI: 10.1021/pr900066h] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yupaporn Osiriphun
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand, Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand, and Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Patompon Wongtrakoongate
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand, Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand, and Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Sucharat Sanongkiet
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand, Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand, and Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Prapat Suriyaphol
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand, Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand, and Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Visith Thongboonkerd
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand, Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand, and Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Sumalee Tungpradabkul
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand, Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand, and Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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5
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Yan B, Núñez C, Ueki T, Esteve-Núñez A, Puljic M, Adkins RM, Methé BA, Lovley DR, Krushkal J. Computational prediction of RpoS and RpoD regulatory sites in Geobacter sulfurreducens using sequence and gene expression information. Gene 2006; 384:73-95. [PMID: 17014972 DOI: 10.1016/j.gene.2006.06.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2006] [Revised: 06/11/2006] [Accepted: 06/29/2006] [Indexed: 11/18/2022]
Abstract
RpoS, the sigma S subunit of RNA polymerase, is vital during the growth and survival of Geobacter sulfurreducens under conditions typically encountered in its native subsurface environments. We investigated the conservation of sites that may be important for RpoS function in G. sulfurreducens. We also employed sequence information and expression microarray data to predict G. sulfurreducens genome sites that may be related to RpoS regulation. Hierarchical clustering identified three clusters of significantly downregulated genes in the rpoS deletion mutant. The search for conserved overrepresented motifs in co-regulated operons identified likely -35 and -10 promoter elements upstream of a number of functionally important G. sulfurreducens operons that were downregulated in the rpoS deletion mutant. Putative -35/-10 promoter elements were also identified in the G. sulfurreducens genome using sequence similarity searches to matrices of -35/-10 promoter elements found in G. sulfurreducens and in Escherichia coli. Due to a sufficient degree of sequence similarity between -35/-10 promoter elements for RpoS, RpoD, and other sigma factors, both the sequence similarity searches and the search for conserved overrepresented motifs using microarray data may identify promoter elements for both RpoS and other sigma factors.
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Affiliation(s)
- Bin Yan
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
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Niedziela-Majka A, Heyduk T. Escherichia coli RNA polymerase contacts outside the -10 promoter element are not essential for promoter melting. J Biol Chem 2005; 280:38219-27. [PMID: 16169843 DOI: 10.1074/jbc.m507984200] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We examined the relative affinity of model promoter constructs for binding Escherichia coli RNA polymerase (RNAP) holoenzyme. Model promoter constructs were designed to mimic DNA structures characteristic for different steps of transcription initiation. DNA duplexes in which a chemical cross-link was introduced just downstream from -10 hexamer to prevent DNA melting upon RNAP binding were used to mimic RNAP-promoter contacts in a closed complex. Fork junction DNA molecules with double-stranded/single-stranded junction between -11 and -10 position were used to study interactions of RNA polymerase with DNA in open complex. The -35 and -10 promoter regions were found to be equally important for the initial RNAP binding. The recognition of -35 promoter region was independent of structural context of the model promoter fragment. In contrast, free energy of RNAP binding to -10 hexamer was highly dependent on DNA structure. The relative importance of -10 region for sequence-specific interaction with the polymerase was the lowest for constructs mimicking closed complex and the highest for the constructs mimicking open complex. The relative importance of region -10 was also dependent on the presence of -35 consensus element indicating a communication between different DNA binding determinants of polymerase during open complex formation. Short double-stranded promoter fragments comprising only -35 and -10 or only -10 consensus elements underwent melting in a complex with polymerase indicating that the core of promoter melting activity of the polymerase is localized to a very small subset of all promoter-polymerase contacts.
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Affiliation(s)
- Anita Niedziela-Majka
- Edward A. Doisy Department of Biochemistry and Molecular Biology, St. Louis University Medical School, St. Louis, Missouri 63104, USA
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Weber H, Polen T, Heuveling J, Wendisch VF, Hengge R. Genome-wide analysis of the general stress response network in Escherichia coli: sigmaS-dependent genes, promoters, and sigma factor selectivity. J Bacteriol 2005; 187:1591-603. [PMID: 15716429 PMCID: PMC1063999 DOI: 10.1128/jb.187.5.1591-1603.2005] [Citation(s) in RCA: 600] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The sigmaS (or RpoS) subunit of RNA polymerase is the master regulator of the general stress response in Escherichia coli. While nearly absent in rapidly growing cells, sigmaS is strongly induced during entry into stationary phase and/or many other stress conditions and is essential for the expression of multiple stress resistances. Genome-wide expression profiling data presented here indicate that up to 10% of the E. coli genes are under direct or indirect control of sigmaS and that sigmaS should be considered a second vegetative sigma factor with a major impact not only on stress tolerance but on the entire cell physiology under nonoptimal growth conditions. This large data set allowed us to unequivocally identify a sigmaS consensus promoter in silico. Moreover, our results suggest that sigmaS-dependent genes represent a regulatory network with complex internal control (as exemplified by the acid resistance genes). This network also exhibits extensive regulatory overlaps with other global regulons (e.g., the cyclic AMP receptor protein regulon). In addition, the global regulatory protein Lrp was found to affect sigmaS and/or sigma70 selectivity of many promoters. These observations indicate that certain modules of the sigmaS-dependent general stress response can be temporarily recruited by stress-specific regulons, which are controlled by other stress-responsive regulators that act together with sigma70 RNA polymerase. Thus, not only the expression of genes within a regulatory network but also the architecture of the network itself can be subject to regulation.
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Affiliation(s)
- Harald Weber
- Institut für Biologie, Mikrobiologie, Freie Universität Berlin, Königin-Luise-Str. 12-16a, 14195 Berlin, Germany
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8
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Lee SJ, Gralla JD. Osmo-regulation of bacterial transcription via poised RNA polymerase. Mol Cell 2004; 14:153-62. [PMID: 15099515 DOI: 10.1016/s1097-2765(04)00202-3] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2003] [Revised: 02/27/2004] [Accepted: 03/08/2004] [Indexed: 11/30/2022]
Abstract
Adaptation to high-salt environments is critical for the survival of a wide range of cells, especially for pathogenic bacteria that colonize the animal gut and urinary tract. The adaptation strategy involves production of the salt potassium glutamate, which induces a specific gene expression program that produces electro-neutral osmolytes while inhibiting general sigma(70) transcription. These data show that in Escherichia coli potassium glutamate stimulates transcription by disengaging inhibitory polymerase interactions at a sigma(38) promoter. These occur in an upstream region that is marked by an osmotic shock promoter DNA consensus sequence. The disruption activates a poised RNA polymerase to transcribe. This transcription program leads to the production of osmolytes that are shown to have only minor effects on transcription and therefore help to restore normal cell function. An osmotic shock gene expression cycle is discussed.
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Affiliation(s)
- Shun Jin Lee
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, P.O. Box 951569, Los Angeles, CA 90095, USA
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Subbarayan PR, Sarkar M. Escherichia coli rpoS gene has an internal secondary translation initiation region. Biochem Biophys Res Commun 2004; 313:294-9. [PMID: 14684159 DOI: 10.1016/j.bbrc.2003.11.132] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Sigma S (sigma(s)) encoded by rpoS in Escherichia coli is a stationary phase specific sigma subunit of the RNA polymerase holoenzyme. Widespread among the E. coli K12 strains is an amber mutation that prematurely terminates sigma(s). These rpoSAm mutants would be expected to show no sigma(s) activity. However, suppressor free rpoSAm mutants retain an intermediate catalase activity, a sigma S controlled function. By analyzing the sequence of the rpoS gene we hypothesize that a 277 amino acids long delta1-53 sigma(s) of about 30 kDa can be translated from an internal secondary translation initiation region (STIR, AGGGAGN11GUG) that is located downstream of the amber codon. By cloning this rpoSAm gene, following the expression, function, and N-terminal sequence of this mutant protein, we report the presence of a functional internal STIR in E. coli rpoS, from where a truncated but nevertheless functional form of sigma(s) can be synthesized.
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Fenton MS, Gralla JD. Roles for inhibitory interactions in the use of the -10 promoter element by sigma 70 holoenzyme. J Biol Chem 2003; 278:39669-74. [PMID: 12902332 DOI: 10.1074/jbc.m307412200] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A panel of seven -10 region DNA mutants was tested for holoenzyme binding against a panel of 13 region 2 mutants of sigma 70. No patterns were noticed that would indicate unique interactions between individual amino acids and individual -10 region bases. Instead, certain amino acid substitutions led to increased holoenzyme binding to DNA, implying that the wild type interactions are associated with an inhibitory component. These inhibitory interactions were stronger on DNA containing non-consensus sequences, like those of typical promoters. In addition, the DNA segment downstream from the -10 element was also inhibitory to binding when in duplex form but stimulated binding when in single strand form. Overall, the data suggest that -10 region duplex recognition and melting have a large component of overcoming unfavorable protein:DNA base interactions, particularly when the bases are non-consensus, and that this contributes to setting physiologically appropriate variations in transcription rate.
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Affiliation(s)
- Mike S Fenton
- Department of Chemistry and Biochemistry and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, 90095-1569, USA
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