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Characterization of the Escherichia coli σ(S) core regulon by Chromatin Immunoprecipitation-sequencing (ChIP-seq) analysis.

  • Peano C Institute of Biomedical Technologies, National Research Council (ITB-CNR), Segrate (MI), Italy.
  • Wolf J EAWAG, Swiss Federal Institute for Environmental Science and Technology, Dübendorf, Switzerland.
  • Demol J Lab. Adaptation et Pathogénie des Micro-organismes (LAPM), Univ. Grenoble Alpes, F-38000 Grenoble, France.
  • Rossi E Department of Biosciences, Università degli Studi di Milano, Milan, Italy.
  • Petiti L Institute of Biomedical Technologies, National Research Council (ITB-CNR), Segrate (MI), Italy.
  • De Bellis G Institute of Biomedical Technologies, National Research Council (ITB-CNR), Segrate (MI), Italy.
  • Geiselmann J Lab. Adaptation et Pathogénie des Micro-organismes (LAPM), Univ. Grenoble Alpes, F-38000 Grenoble, France.
  • Egli T EAWAG, Swiss Federal Institute for Environmental Science and Technology, Dübendorf, Switzerland.
  • Lacour S Lab. Adaptation et Pathogénie des Micro-organismes (LAPM), Univ. Grenoble Alpes, F-38000 Grenoble, France.
  • Landini P Department of Biosciences, Università degli Studi di Milano, Milan, Italy.
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  • 2015-05-29
Published in:
  • Scientific reports. - 2015
Binding Sites
Chromatin Immunoprecipitation
Escherichia coli
Gene Expression Regulation, Bacterial
Promoter Regions, Genetic
RNA, Untranslated
Sigma Factor
Transcription, Genetic
English 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 σ(S)-associated RNA polymerase form (Eσ(S)) during transition from exponential to stationary phase. We identified 63 binding sites for Eσ(S) 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 σ(S)-encoding rpoS gene. Eσ(S) binding did not always correlate with an increase in transcription level, suggesting that, at some σ(S)-dependent promoters, Eσ(S) might remain poised in a pre-initiation state upon binding. A large fraction of Eσ(S)-binding sites corresponded to promoters recognized by RNA polymerase associated with σ(70) or other σ factors, suggesting a considerable overlap in promoter recognition between different forms of RNA polymerase. In particular, Eσ(S) 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 Eσ(S) in the regulation of non coding RNAs, such as OmrA/B, RyeA/B and SibC.
Language
  • English
Open access status
gold
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Persistent URL
https://fredi.hepvs.ch/global/documents/99581
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