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 of KT2440 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 which responds to different stress conditions and increases understanding of bacterial adaptation in natural and industrial settings. This study maps the complete transcriptional response of KT2440 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.

Characterization and Salt Response in Recurrent Halotolerant Exiguobacterium sp. SH31 Isolated From Sediments of Salar de Huasco, Chilean Altiplano

“…A recent report indicates that the salt concentration is dependent on motility in a pigment halotolerant Vibrio strain isolated from Salar de Atacama, but motility was inhibited in higher salt concentrations (150 g/l NaCl; Gallardo et al, 2016 ). Substantial energy is needed for flagellar biosynthesis and bacteria are able to inhibit certain processes in response to stress, motility was reduced, and biofilm formation was seen in SH31 ( Figure 4 ) a general bacterial response to osmotic stress found in diverse organisms, as it was shown in Pseudomonas putida ( Bojanovič et al, 2017 ). Some factors that induce biofilm maturation, including in Pseudomonas and Shewanella , are changes in oxygen or carbon substrate concentration, pH, or other chemical parameters ( Gjermansen et al, 2005 ).…”

“…Finally, genes related to biofilm ( pgaC ), cell chemotaxis ( bdlA ), and signaling ( luxS ) were induced in the NaCl conditions; on the contrary, ywqC or tkm (capsule/biofilm) was found to be significantly decreased in the 25 g/l condition and was not changed in 50 g/l of NaCl. It has been found that many of the reactions related to biofilm formation are upregulated in response to salinity ( Bojanovič et al, 2017 ). LuxS is a signaling protein that mediates quorum sensing between certain species, as well as biofilm formation and motility.…”

Predominance of deterministic microbial community dynamics in salterns exposed to different light intensities

“…The low‐irradiation community, when exposed to high light, rapidly showed gene shifts that were reflective of the community changes due to environmental stress. We especially detected an increase in abundance of genes related to osmotic stress, which tend to be accompanied by reactions related to oxidative stress in bacterial cells (Botsford and Lewis, ; Bojanovič et al ., ). Genes related to the biosynthesis of compounds such as glutathione that can hamper oxidative damage under osmotic stress (Smirnova and Oktyabrsky, ), and ergothioneine, an amino acid with antioxidant and cytoprotective capabilities against cellular stressors (Cheah and Halliwell, ), were also detected in increased abundances.…”

Gross transcriptomic analysis of Pseudomonas putida for diagnosing environmental shifts

“…Such profiles not only expose global physiological responses, but also pinpoint the roles of distinct genes that can then be separately studied. Without surprise, Pseudomonas putida has not been alien to such technical and conceptual developments and a suite of transcriptomes of this bacterium have been published in recent years with different methods for inspecting the responses of this microorganism to different physicochemical settings (Yuste et al ., ; Kim et al ., , ; La Rosa et al ., ; Bojanovic et al ., ; Molina‐Santiago et al ., ). However, such experiments were run by different laboratories with diverse RNA extraction and preparation methods, and with different data analysis and representation tools, and thus make comparisons challenging.…”