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Functional Genomics of Stress Response in Pseudomonas putida KT2440

Oleg N. Reva,^1,2, Christian Weinel,^1,, Miryam Weinel,^1, Kerstin Böhm,¹ Diana Stjepandic,³ Jörg D. Hoheisel,³ and Burkhard Tümmler^1*

Klinische Forschergruppe, OE 6711, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, D-30623 Hannover, Germany,¹ Institute of Microbiology and Virology, Zabolotnogo 154, 03143, Kiev, Ukraine,² Functional Genome Analysis, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 506, D-69120 Heidelberg, Germany³

Received 19 January 2006/ Accepted 15 March 2006

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°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°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.

O.N.R., C.W., and M.W. contributed equally to this work.

Present address: BASF Aktiengesellschaft, Computational Chemistry and Biology GVC/C-A30, 67056 Ludwigshafen, Germany.

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