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 oxidative, osmotic, and membrane 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% are novel intergenic transcripts and 50% are 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. Overall design: 21 samples were analyzed. There were 6 tested conditions compared to the control. Each of them has 3 biological replicas. Osmotic stress (NaCl), oxidative stress (H2O2) and membrane (IP-imipenem)stress T1 (7 min) and T2 (60 min) after the compound addition = 3 conditions x 2 time points x 3 bio replicas + 3 bio replicas of the control (T0-before the addtion of the compound).