title: Transcriptional and translational regulation by RNA thermometers, riboswitches and the sRNA DsrA in Escherichia coli O157:H7 Sakai under combined cold and osmotic stress adaptation.
abstract: The enteric pathogen Escherichia coli O157:H7 Sakai (EHEC) is able to grow at lower temperatures compared to commensal E. coli Growth at environmental conditions displays complex challenges different to those in a host. EHEC was grown at 37°C and at 14°C with 4% NaCl, a combination of cold and osmotic stress as present in the food chain. Comparison of RNAseq and RIBOseq data provided a snap shot of ongoing transcription and translation, differentiating transcriptional and post-transcriptional gene regulation, respectively. Indeed, cold and osmotic stress related genes are simultaneously regulated at both levels, but translational regulation clearly dominates. Special emphasis was given to genes regulated by RNA secondary structures in their 5'UTRs, such as RNA thermometers and riboswitches, or genes controlled by small RNAs encoded in trans The results reveal large differences in gene expression between short-time shock compared to adaptation in combined cold and osmotic stress. Whereas the majority of cold shock proteins, such as CspA, are translationally downregulated after adaptation, many osmotic stress genes are still significantly upregulated mainly translationally, but several also transcriptionally.
authors.affiliation: Chair for Microbial Ecology, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany.
authors.forename: Sarah Maria
authors.initials: SM
authors.lastname: Hücker
authors.affiliation: Chair for Data Analysis and Visualization, Department of Computer and Information Science, University of Konstanz, Box 78, 78457 Konstanz, Germany.
authors.forename: Svenja
authors.initials: S
authors.lastname: Simon
authors.affiliation: Chair for Microbial Ecology, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany.
authors.forename: Siegfried
authors.initials: S
authors.lastname: Scherer
authors.affiliation: Chair for Microbial Ecology, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany neuhaus@wzw.tum.de.
authors.forename: Klaus
authors.initials: K
authors.lastname: Neuhaus
mesh_terms: D000222:Adaptation, Physiological; D003080:Cold Temperature; D019453:Escherichia coli O157 / Q000235:genetics*; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D009690:Nucleic Acid Conformation; D009997:Osmotic Pressure; D014176:Protein Biosynthesis; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012330:RNA, Double-Stranded / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D058928:Riboswitch; D012965:Sodium Chloride / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D012329:RNA, Bacterial; D012330:RNA, Double-Stranded; D058928:Riboswitch; D012965:Sodium Chloride
keywords: EHEC; RIBOseq; RNA thermometer; cold stress adaptation; osmotic stress adaptation; riboswitch