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Response of Desulfovibrio vulgaris to Alkaline Stress ^,

Sergey Stolyar,^1,10* Qiang He,^6,10, Marcin P. Joachimiak,^2,10 Zhili He,¹⁰ Zamin Koo Yang,^4,10 Sharon E. Borglin,^9,10 Dominique C. Joyner,^9,10 Katherine Huang,^2,10 Eric Alm,^7,10 Terry C. Hazen,^9,10 Jizhong Zhou,^4,8,10 Judy D. Wall,^5,10 Adam P. Arkin,^2,3,10 and David A. Stahl^1,10

Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington,¹ Physical Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley, California,² Department of Bioengineering, University of California, Berkeley, California,³ Oak Ridge National Laboratory, Oak Ridge, Tennessee,⁴ Department of Biochemistry, University of Missouri-Columbia, Columbia, Missouri,⁵ Department of Civil and Environmental Engineering, Temple University, Philadelphia, Pennsylvania,⁶ Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts,⁷ Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma,⁸ Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, California,⁹ Virtual Institute for Microbial Stress and Survival^,,¹⁰

Received 21 February 2007/ Accepted 10 September 2007

The response of exponentially growing Desulfovibrio vulgaris Hildenborough to pH 10 stress was studied using oligonucleotide microarrays and a study set of mutants with genes suggested by microarray data to be involved in the alkaline stress response deleted. The data showed that the response of D. vulgaris to increased pH is generally similar to that of Escherichia coli but is apparently controlled by unique regulatory circuits since the alternative sigma factors (sigma S and sigma E) contributing to this stress response in E. coli appear to be absent in D. vulgaris. Genes previously reported to be up-regulated in E. coli were up-regulated in D. vulgaris; these genes included three ATPase genes and a tryptophan synthase gene. Transcription of chaperone and protease genes (encoding ATP-dependent Clp and La proteases and DnaK) was also elevated in D. vulgaris. As in E. coli, genes involved in flagellum synthesis were down-regulated. The transcriptional data also identified regulators, distinct from sigma S and sigma E, that are likely part of a D. vulgaris Hildenborough-specific stress response system. Characterization of a study set of mutants with genes implicated in alkaline stress response deleted confirmed that there was protective involvement of the sodium/proton antiporter NhaC-2, tryptophanase A, and two putative regulators/histidine kinases (DVU0331 and DVU2580).

Published ahead of print on 5 October 2007.

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Present address: Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN.