Functional genomics of stress response in Pseudomonas putida KT2440

Abstract

The metabolically versatile soil bacterium Pseudomonas putida has to cope with numerous abiotic stresses in its habitats. The stress responses of P. putida KT2440 to 4 degrees C, pH 4.5, 0.8 M urea, and 45 mM sodium benzoate were analyzed by determining the global mRNA expression profiles and screening for stress-intolerant nonauxotrophic Tn5 transposon mutants. In 392 regulated genes or operons, 36 gene regions were differentially expressed by more than 2.5-fold, and 32 genes in 23 operons were found to be indispensable for growth during exposure to one of the abiotic stresses. The transcriptomes of the responses to urea, benzoate, and 4 degrees C correlated positively with each other but negatively with the transcriptome of the mineral acid response. The CbrAB sensor kinase, the cysteine synthase CysM, PcnB and VacB, which control mRNA stability, and BipA, which exerts transcript-specific translational control, were essential to cope with cold stress. The cyo operon was required to cope with acid stress. A functional PhoP, PtsP, RelA/SpoT modulon, and adhesion protein LapA were necessary for growth in the presence of urea, and the outer membrane proteins OmlA and FepA and the phosphate transporter PstBACS were indispensable for growth in the presence of benzoate. A lipid A acyltransferase (PP0063) was a mandatory component of the stress responses to cold, mineral acid, and benzoate. Adaptation of the membrane barrier, uptake of phosphate, maintenance of the intracellular pH and redox status, and translational control of metabolism are key mechanisms of the response of P. putida to abiotic stresses.

FIG. 1.

Chromosomal map positions of stress response genes. Circle 1 (outermost circle) to circle 4 indicate expression of chromosomal loci that are up-regulated (red circles) and down-regulated (open circles) by >2.5-fold upon exposure to stress conditions. Circle 1, organic acid stress (45 mM sodium benzoate); circle 2, chaotropic stress (0.8 M urea); circle 3, cold stress (growth at 4°C); circle 4, acid stress (growth at pH 4.5 [HCl]). The positions of the STM-disrupted genes are indicated in the innermost circle.

FIG. 2.

Roles and cellular localization of the indispensable nonredundant key elements of the P. putida KT2440 response to abiotic stresses.