Expanding the RpoS/σS-network by RNA sequencing and identification of σS-controlled small RNAs in Salmonella
| Autor: | Marc Monot, Odile Sismeiro, Corinne Lévi-Meyrueis, Bernd Jagla, Véronique Monteil, Bruno Dupuy, Françoise Norel, Jean-Yves Coppée, Marie-Agnès Dillies |
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| Přispěvatelé: | Université Paris-Sud - Paris 11 (UP11), Génétique Moléculaire, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Transcriptome et Epigénome (PF2), Institut Pasteur [Paris], Pathogénèse des Bactéries Anaérobies / Pathogenesis of Bacterial Anaerobes (PBA (U-Pasteur_6)), Institut Pasteur [Paris]-Université Paris Diderot - Paris 7 (UPD7), This work was supported by the French National Research Agency (ANR- 11-BSV3-009 to FN) and by grants from the Institut Pasteur and the Centre National de la Recherche Scientifique., ANR-11-BSV3-0009,SIGMADAPT,Rôle de SigmaS dans la compétitivité et l'adaptation des bactéries à l'environnement(2011), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP), Institut Pasteur [Paris] (IP)-Université Paris Diderot - Paris 7 (UPD7) |
| Jazyk: | angličtina |
| Rok vydání: | 2014 |
| Předmět: |
Salmonella typhimurium
Respiratory chain Biochemistry chemistry.chemical_compound Sigma factor Salmonella RNA polymerase Microbial Physiology Molecular Cell Biology Transcriptional regulation MESH: Sequence Analysis RNA Gene Regulatory Networks Bacterial Physiology 2. Zero hunger Regulation of gene expression Genetics Escherichia Coli Multidisciplinary Systems Biology Microbial Growth and Development MESH: Sigma Factor Genomics MESH: RNA Small Untranslated Functional Genomics Bacterial Pathogens RNA Bacterial Medical Microbiology Prokaryotic Models Medicine MESH: RNA Bacterial Transcriptome Analysis Research Article Evolutionary Processes Science DNA transcription Sigma Factor Biology Research and Analysis Methods Microbiology MESH: Genetic Loci Molecular Genetics MESH: Gene Expression Profiling Model Organisms Gene Gram Negative Bacteria Microbial Pathogens Microbial Metabolism Evolutionary Biology Biology and life sciences Sequence Analysis RNA Gene Expression Profiling RNA Computational Biology Bacteriology MESH: Salmonella typhimurium [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry Molecular Biology/Molecular biology Cell Biology RNA stability Genome Analysis Organismal Evolution Gene regulation chemistry Genetic Loci Microbial Evolution RNA Small Untranslated Gene expression Gene Function Genome Expression Analysis rpoS Developmental Biology |
| Zdroj: | PLoS ONE PLoS ONE, Public Library of Science, 2014, 9 (5), pp.e96918. ⟨10.1371/journal.pone.0096918⟩ PLoS ONE, Vol 9, Iss 5, p e96918 (2014) PLoS ONE, 2014, 9 (5), pp.e96918. ⟨10.1371/journal.pone.0096918⟩ |
| ISSN: | 1932-6203 |
| DOI: | 10.1371/journal.pone.0096918⟩ |
| Popis: | International audience; The RpoS/σS sigma subunit of RNA polymerase (RNAP) controls a global adaptive response that allows many Gram-negative bacteria to survive starvation and various stresses. σS also contributes to biofilm formation and virulence of the food-borne pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium). In this study, we used directional RNA-sequencing and complementary assays to explore the σS-dependent transcriptome of S. Typhimurium during late stationary phase in rich medium. This study confirms the large regulatory scope of σS and provides insights into the physiological functions of σS in Salmonella. Extensive regulation by σS of genes involved in metabolism and membrane composition, and down-regulation of the respiratory chain functions, were important features of the σS effects on gene transcription that might confer fitness advantages to bacterial cells and/or populations under starving conditions. As an example, we show that arginine catabolism confers a competitive fitness advantage in stationary phase. This study also provides a firm basis for future studies to address molecular mechanisms of indirect regulation of gene expression by σS. Importantly, the σS-controlled downstream network includes small RNAs that might endow σS with post-transcriptional regulatory functions. Of these, four (RyhB-1/RyhB-2, SdsR, SraL) were known to be controlled by σS and deletion of the sdsR locus had a competitive fitness cost in stationary phase. The σS-dependent control of seven additional sRNAs was confirmed in Northern experiments. These findings will inspire future studies to investigate molecular mechanisms and the physiological impact of post-transcriptional regulation by σS. |
| Databáze: | OpenAIRE |
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