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Genomewide Gene Expression Analysis of Response of Desulfovibrio vulgaris to High pH

Abstract

High pH can often be encountered in natural environments by microorganisms. As a part of the DOE Genomics:GTL initiative evaluating the use of microbial stress response to monitor the status of environmental systems, we studied the effect of exposure to high alkaline (pH10) media on exponentially growing Desulfovibrio vulgaris Hildenborough (DvH) cells. Any given gram-negative bacterium under high pH stress is challenged by mainly three factors: intracellular alkalinized pH, diminished membrane potential and misfolded degrading proteins. To maintain viability in this stressful state, the cell could transport protons or acids into the cell, synthesize compounds that acidify the cytoplasm, increase protein folding, or increase degradation of denatured proteins. In our experiments, several genes reported to be upregulated in E. coli at high pH were also upregulated in DvH. These include three ATPase genes and a tryptophan synthase gene. As in E. coli, genes involved inflagella synthesis were downregulated during pH 10 stress. DvH also upregulated chaperone and protease genes such as an ATP-dependent Clp protease, an ATP-dependent protease La, and dnaK. Some energy production genes were consistently downregulated at high pH. These include pyruvate carboxylase, desulfoferrodoxin, and ferredoxin II. Finally, the microarray data revealed a potential DvH specific pH homeostasis mechanism. In DvH but not other deltaproteobacteria or E. coli, the antiporter nhaC and a putative L-aspartate oxidase gene are adjacent in the genome and likely to be in the same operon. Both of these genes were upregulated in D. vulgaris during high pH stress. Thus, part of the DvH response to high pH stress appears to involve coupling pumping of protons into the cell with conversion of L-aspartate to oxaloacetate which is likely to increase the acidity of the cell. The effect of several mutations on resistance to high pH will be reported.

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