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Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation
BACKGROUND: The SOS response is an almost ubiquitous response of cells to genotoxic stresses. The full complement of genes in the SOS regulon for Vibrio species has only been addressed through bioinformatic analyses predicting LexA binding box consensus and in vitro validation. Here, we perform whol...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5963079/ https://www.ncbi.nlm.nih.gov/pubmed/29783948 http://dx.doi.org/10.1186/s12864-018-4716-8 |
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author | Krin, Evelyne Pierlé, Sebastian Aguilar Sismeiro, Odile Jagla, Bernd Dillies, Marie-Agnès Varet, Hugo Irazoki, Oihane Campoy, Susana Rouy, Zoé Cruveiller, Stéphane Médigue, Claudine Coppée, Jean-Yves Mazel, Didier |
author_facet | Krin, Evelyne Pierlé, Sebastian Aguilar Sismeiro, Odile Jagla, Bernd Dillies, Marie-Agnès Varet, Hugo Irazoki, Oihane Campoy, Susana Rouy, Zoé Cruveiller, Stéphane Médigue, Claudine Coppée, Jean-Yves Mazel, Didier |
author_sort | Krin, Evelyne |
collection | PubMed |
description | BACKGROUND: The SOS response is an almost ubiquitous response of cells to genotoxic stresses. The full complement of genes in the SOS regulon for Vibrio species has only been addressed through bioinformatic analyses predicting LexA binding box consensus and in vitro validation. Here, we perform whole transcriptome sequencing from Vibrio cholerae treated with mitomycin C as an SOS inducer to characterize the SOS regulon and other pathways affected by this treatment. RESULTS: Comprehensive transcriptional profiling allowed us to define the full landscape of promoters and transcripts active in V. cholerae. We performed extensive transcription start site (TSS) mapping as well as detection/quantification of the coding and non-coding RNA (ncRNA) repertoire in strain N16961. To improve TSS detection, we developed a new technique to treat RNA extracted from cells grown in various conditions. This allowed for identification of 3078 TSSs with an average 5’UTR of 116 nucleotides, and peak distribution between 16 and 64 nucleotides; as well as 629 ncRNAs. Mitomycin C treatment induced transcription of 737 genes and 28 ncRNAs at least 2 fold, while it repressed 231 genes and 17 ncRNAs. Data analysis revealed that in addition to the core genes known to integrate the SOS regulon, several metabolic pathways were induced. This study allowed for expansion of the Vibrio SOS regulon, as twelve genes (ubiEJB, tatABC, smpA, cep, VC0091, VC1190, VC1369–1370) were found to be co-induced with their adjacent canonical SOS regulon gene(s), through transcriptional read-through. Characterization of UV and mitomycin C susceptibility for mutants of these newly identified SOS regulon genes and other highly induced genes and ncRNAs confirmed their role in DNA damage rescue and protection. CONCLUSIONS: We show that genotoxic stress induces a pervasive transcriptional response, affecting almost 20% of the V. cholerae genes. We also demonstrate that the SOS regulon is larger than previously known, and its syntenic organization is conserved among Vibrio species. Furthermore, this specific co-localization is found in other γ-proteobacteria for genes recN-smpA and rmuC-tatABC, suggesting SOS regulon conservation in this phylum. Finally, we comment on the limitations of widespread NGS approaches for identification of all RNA species in bacteria. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-018-4716-8) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-5963079 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-59630792018-06-25 Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation Krin, Evelyne Pierlé, Sebastian Aguilar Sismeiro, Odile Jagla, Bernd Dillies, Marie-Agnès Varet, Hugo Irazoki, Oihane Campoy, Susana Rouy, Zoé Cruveiller, Stéphane Médigue, Claudine Coppée, Jean-Yves Mazel, Didier BMC Genomics Research Article BACKGROUND: The SOS response is an almost ubiquitous response of cells to genotoxic stresses. The full complement of genes in the SOS regulon for Vibrio species has only been addressed through bioinformatic analyses predicting LexA binding box consensus and in vitro validation. Here, we perform whole transcriptome sequencing from Vibrio cholerae treated with mitomycin C as an SOS inducer to characterize the SOS regulon and other pathways affected by this treatment. RESULTS: Comprehensive transcriptional profiling allowed us to define the full landscape of promoters and transcripts active in V. cholerae. We performed extensive transcription start site (TSS) mapping as well as detection/quantification of the coding and non-coding RNA (ncRNA) repertoire in strain N16961. To improve TSS detection, we developed a new technique to treat RNA extracted from cells grown in various conditions. This allowed for identification of 3078 TSSs with an average 5’UTR of 116 nucleotides, and peak distribution between 16 and 64 nucleotides; as well as 629 ncRNAs. Mitomycin C treatment induced transcription of 737 genes and 28 ncRNAs at least 2 fold, while it repressed 231 genes and 17 ncRNAs. Data analysis revealed that in addition to the core genes known to integrate the SOS regulon, several metabolic pathways were induced. This study allowed for expansion of the Vibrio SOS regulon, as twelve genes (ubiEJB, tatABC, smpA, cep, VC0091, VC1190, VC1369–1370) were found to be co-induced with their adjacent canonical SOS regulon gene(s), through transcriptional read-through. Characterization of UV and mitomycin C susceptibility for mutants of these newly identified SOS regulon genes and other highly induced genes and ncRNAs confirmed their role in DNA damage rescue and protection. CONCLUSIONS: We show that genotoxic stress induces a pervasive transcriptional response, affecting almost 20% of the V. cholerae genes. We also demonstrate that the SOS regulon is larger than previously known, and its syntenic organization is conserved among Vibrio species. Furthermore, this specific co-localization is found in other γ-proteobacteria for genes recN-smpA and rmuC-tatABC, suggesting SOS regulon conservation in this phylum. Finally, we comment on the limitations of widespread NGS approaches for identification of all RNA species in bacteria. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-018-4716-8) contains supplementary material, which is available to authorized users. BioMed Central 2018-05-21 /pmc/articles/PMC5963079/ /pubmed/29783948 http://dx.doi.org/10.1186/s12864-018-4716-8 Text en © The Author(s). 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Krin, Evelyne Pierlé, Sebastian Aguilar Sismeiro, Odile Jagla, Bernd Dillies, Marie-Agnès Varet, Hugo Irazoki, Oihane Campoy, Susana Rouy, Zoé Cruveiller, Stéphane Médigue, Claudine Coppée, Jean-Yves Mazel, Didier Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation |
title | Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation |
title_full | Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation |
title_fullStr | Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation |
title_full_unstemmed | Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation |
title_short | Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation |
title_sort | expansion of the sos regulon of vibrio cholerae through extensive transcriptome analysis and experimental validation |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5963079/ https://www.ncbi.nlm.nih.gov/pubmed/29783948 http://dx.doi.org/10.1186/s12864-018-4716-8 |
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