ArticleScientific reports2015
Characterization of the Escherichia coli σ(S) core regulon by Chromatin Immunoprecipitation-sequencing (ChIP-seq) analysis.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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39 citing papers in PubMed, 68 citations in OpenAlex.
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- Twin Small RNAs and Divergent Fates: The Expansive Regulatory Networks of OmrA and OmrB.International journal of molecular sciences · 2025Review
- Control of iron acquisition by multiple small RNAs unravels a new role for transcriptional terminator loops in gene regulation.Nucleic acids research · 2024Article
- An Optimized Method for Reconstruction of Transcriptional Regulatory Networks in Bacteria Using ChIP-exo and RNA-seq Datasets.Journal of microbiology (Seoul, Korea) · 2024Article
- GnuR Represses the Expression of Glucose and Gluconate Catabolism in Pseudomonas putida KT2440.Microbial biotechnology · 2024Article
- RpoS and the bacterial general stress response.Microbiology and molecular biology reviews : MMBR · 2024Review
- A negative feedback loop is critical for recovery of RpoS after stress in Escherichia coli.PLoS genetics · 2024Article
- Mutations upstream fromJournal of bacteriology · 2024Article
- A negative feedback loop is critical for recovery of RpoS after stress inbioRxiv : the preprint server for biology · 2023Article
- BosR and PlzA reciprocally regulate RpoS function to sustain Borrelia burgdorferi in ticks and mammals.The Journal of clinical investigation · 2023Article
- proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms.Nucleic acids research · 2022Article
- Bacterial toxin-antitoxin modules: classification, functions, and association with persistence.Current research in microbial sciences · 2021Review
- Insertion of prpoD_rpoS fragment enhances expression of recombinant protein by dps auto-inducible promoter in Escherichia coli.Molecular biology reports · 2021Article
- Function, Evolution, and Composition of the RpoS Regulon inFrontiers in microbiology · 2020Review
- Diversity inFrontiers in microbiology · 2020Review
- Spatial organization of RNA polymerase and its relationship with transcription inProceedings of the National Academy of Sciences of the United States of America · 2019Article
- BINDER: computationally inferring a gene regulatory network for Mycobacterium abscessus.BMC bioinformatics · 2019Article
- Trouble is coming: Signaling pathways that regulate general stress responses in bacteria.The Journal of biological chemistry · 2019Review
Corrections and comments
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Authors and funding
10 authors at 5 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
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 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.
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