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Peano C, Wolf J, Demol J, Rossi E, Petiti L, De Bellis G, Geiselmann J, Egli T, Lacour S, Landini P. Characterization of the Escherichia coli σ(S) core regulon by Chromatin Immunoprecipitation-sequencing (ChIP-seq) analysis. Sci Rep 2015; 5:10469. [PMID: 26020590 PMCID: PMC4447067 DOI: 10.1038/srep10469] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 04/15/2015] [Indexed: 11/29/2022] Open
Abstract
In bacteria, selective promoter recognition by RNA polymerase is achieved by its association with σ factors, accessory subunits able to direct RNA polymerase “core enzyme” (E) to different promoter sequences. Using Chromatin Immunoprecipitation-sequencing (ChIP-seq), we searched for promoters bound by the σS-associated RNA polymerase form (EσS) during transition from exponential to stationary phase. We identified 63 binding sites for EσS overlapping known or putative promoters, often located upstream of genes (encoding either ORFs or non-coding RNAs) showing at least some degree of dependence on the σS-encoding rpoS gene. EσS binding did not always correlate with an increase in transcription level, suggesting that, at some σS-dependent promoters, EσS might remain poised in a pre-initiation state upon binding. A large fraction of EσS-binding sites corresponded to promoters recognized by RNA polymerase associated with σ70 or other σ factors, suggesting a considerable overlap in promoter recognition between different forms of RNA polymerase. In particular, EσS appears to contribute significantly to transcription of genes encoding proteins involved in LPS biosynthesis and in cell surface composition. Finally, our results highlight a direct role of EσS in the regulation of non coding RNAs, such as OmrA/B, RyeA/B and SibC.
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Affiliation(s)
- Clelia Peano
- Institute of Biomedical Technologies, National Research Council (ITB-CNR), Segrate (MI), Italy
| | - Johannes Wolf
- EAWAG, Swiss Federal Institute for Environmental Science and Technology, Dübendorf, Switzerland
| | - Julien Demol
- Lab. Adaptation et Pathogénie des Micro-organismes (LAPM), Univ. Grenoble Alpes, F-38000 Grenoble, France.,UMR 5163, Centre National de Recherche Scientifique (CNRS), Grenoble, France
| | - Elio Rossi
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Luca Petiti
- Institute of Biomedical Technologies, National Research Council (ITB-CNR), Segrate (MI), Italy
| | - Gianluca De Bellis
- Institute of Biomedical Technologies, National Research Council (ITB-CNR), Segrate (MI), Italy
| | - Johannes Geiselmann
- Lab. Adaptation et Pathogénie des Micro-organismes (LAPM), Univ. Grenoble Alpes, F-38000 Grenoble, France.,UMR 5163, Centre National de Recherche Scientifique (CNRS), Grenoble, France
| | - Thomas Egli
- EAWAG, Swiss Federal Institute for Environmental Science and Technology, Dübendorf, Switzerland
| | - Stephan Lacour
- Lab. Adaptation et Pathogénie des Micro-organismes (LAPM), Univ. Grenoble Alpes, F-38000 Grenoble, France.,UMR 5163, Centre National de Recherche Scientifique (CNRS), Grenoble, France
| | - Paolo Landini
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
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Landini P, Egli T, Wolf J, Lacour S. sigmaS, a major player in the response to environmental stresses in Escherichia coli: role, regulation and mechanisms of promoter recognition. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:1-13. [PMID: 24596257 DOI: 10.1111/1758-2229.12112] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 09/12/2013] [Indexed: 06/03/2023]
Abstract
Bacterial cells often face hostile environmental conditions, to which they adapt by activation of stress responses. In Escherichia coli, environmental stresses resulting in significant reduction in growth rate stimulate the expression of the rpoS gene, encoding the alternative σ factor σ(S). The σ(S) protein associates with RNA polymerase, and through transcription of genes belonging to the rpoS regulon allows the activation of a 'general stress response', which protects the bacterial cell from harmful environmental conditions. Each step of this process is finely tuned in order to cater to the needs of the bacterial cell: in particular, selective promoter recognition by σ(S) is achieved through small deviations from a common consensus DNA sequence for both σ(S) and the housekeeping σ(70). Recognition of specific DNA elements by σ(S) is integrated with the effects of environmental signals and the interaction with regulatory proteins, in what represents a fascinating example of multifactorial regulation of gene expression. In this report, we discuss the function of the rpoS gene in the general stress response, and review the current knowledge on regulation of rpoS expression and on promoter recognition by σ(S).
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Affiliation(s)
- Paolo Landini
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
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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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