Global Transcriptional Responses to Osmotic, Oxidative, and Imipenem Stress Conditions in Pseudomonas putida

Bacteria cope with and adapt to stress by modulating gene expression in response to specific environmental cues. In this study the transcriptional response of Pseudomonas putida KT2440 to osmotic, oxidative, and imipenem stress conditions at two time points was investigated via identification of differentially expressed mRNAs and sRNAs. A total of 440 small RNA transcripts were detected, where 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 in at least one condition, suggesting possible functional roles in the cellular response to stress conditions. The data show a higher fraction of differentially expressed sRNAs with greater than 5-fold expression changes compared with mRNAs. The work provides detailed insights into the mechanisms through which P. putida responds to different stress conditions and increases understanding of bacterial adaptation in natural and industrial settings. Importance This study maps the complete transcriptional response of P. putida KT2440 to osmotic, oxidative and imipenem stress conditions at short and long exposure times. Over 400 small RNA transcripts are detected, consisting of both intergenic and antisense transcripts, increasing the number of identified sRNA transcripts in the strain by a factor of ten. 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 in at least one condition, suggesting their involvement in adaptation to stress conditions and identifying interesting candidates for further functional characterization.