title: Global Transcriptional Responses to Osmotic, Oxidative, and Imipenem Stress Conditions in Pseudomonas putida.
abstract: Bacteria cope with and adapt to stress by modulating gene expression in response to specific environmental cues. In this study, the transcriptional response ofPseudomonas putidaKT2440 to osmotic, oxidative, and imipenem stress conditions at two time points was investigated via identification of differentially expressed mRNAs and small RNAs (sRNAs). A total of 440 sRNA transcripts were detected, of which 10% correspond to previously annotated sRNAs, 40% to novel intergenic transcripts, and 50% to novel transcripts antisense to annotated genes. Each stress elicits a unique response as far as the extent and dynamics of the transcriptional changes. Nearly 200 protein-encoding genes exhibited significant changes in all stress types, implicating their participation in a general stress response. Almost half of the sRNA transcripts were differentially expressed under at least one condition, suggesting possible functional roles in the cellular response to stress conditions. The data show a larger fraction of differentially expressed sRNAs than of mRNAs with >5-fold expression changes. The work provides detailed insights into the mechanisms through whichP. putidaresponds to different stress conditions and increases understanding of bacterial adaptation in natural and industrial settings.IMPORTANCEThis study maps the complete transcriptional response ofP. putidaKT2440 to osmotic, oxidative, and imipenem stress conditions at short and long exposure times. Over 400 sRNA transcripts, consisting of both intergenic and antisense transcripts, were detected, increasing the number of identified sRNA transcripts in the strain by a factor of 10. Unique responses to each type of stress are documented, including both the extent and dynamics of the gene expression changes. The work adds rich detail to previous knowledge of stress response mechanisms due to the depth of the RNA sequencing data. Almost half of the sRNAs exhibit significant expression changes under at least one condition, suggesting their involvement in adaptation to stress conditions and identifying interesting candidates for further functional characterization.
authors.affiliation: The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
authors.forename: Klara
authors.initials: K
authors.lastname: Bojanovič
authors.affiliation: The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
authors.forename: Isotta
authors.initials: I
authors.lastname: D'Arrigo
authors.affiliation: The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark kalon@biosustain.dtu.dk.
authors.forename: Katherine S
authors.initials: KS
authors.lastname: Long
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial / Q000187:drug effects; D015378:Imipenem / Q000494:pharmacology*; D058977:Molecular Sequence Annotation; D009997:Osmotic Pressure; D018384:Oxidative Stress; D016958:Pseudomonas putida / Q000187:drug effects / Q000235:genetics* / Q000502:physiology*; D016372:RNA, Antisense / Q000235:genetics; D012329:RNA, Bacterial / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics; D058727:RNA, Small Untranslated / Q000235:genetics; D017423:Sequence Analysis, RNA
chemical_list: D000900:Anti-Bacterial Agents; D016372:RNA, Antisense; D012329:RNA, Bacterial; D012333:RNA, Messenger; D058727:RNA, Small Untranslated; D015378:Imipenem
keywords: KT2440; Pseudomonas putida; RNA-seq; antisense transcripts; differential expression; sRNA; transcriptomics