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Journal of Bacteriology, February 2006, p. 1633-1642, Vol. 188, No. 4
0021-9193/06/$08.00+0     doi:10.1128/JB.188.4.1633-1642.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Transcriptome Profiling of Shewanella oneidensis Gene Expression following Exposure to Acidic and Alkaline pH

Adam B. Leaphart,^1,, Dorothea K. Thompson,^1,2,* Katherine Huang,^2,3 Eric Alm,^2,3 Xiu-Feng Wan,⁴ Adam Arkin,^2,3,5 Steven D. Brown,¹ Liyou Wu,¹ Tingfen Yan,¹ Xueduan Liu,¹ Gene S. Wickham,¹ and Jizhong Zhou^1,2

Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831,¹ Virtual Institute for Microbial Stress and Survival, Lawrence Berkeley National Laboratory, Berkeley, California,² Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720,³ Department of Microbiology, Miami University, Oxford, Ohio 45056,⁴ Department of Bioengineering, University of California, Berkeley, California 94720⁵

Received 5 August 2005/ Accepted 15 November 2005

The molecular response of Shewanella oneidensis MR-1 to variations in extracellular pH was investigated based on genomewide gene expression profiling. Microarray analysis revealed that cells elicited both general and specific transcriptome responses when challenged with environmental acid (pH 4) or base (pH 10) conditions over a 60-min period. Global responses included the differential expression of genes functionally linked to amino acid metabolism, transcriptional regulation and signal transduction, transport, cell membrane structure, and oxidative stress protection. Response to acid stress included the elevated expression of genes encoding glycogen biosynthetic enzymes, phosphate transporters, and the RNA polymerase sigma-38 factor (rpoS), whereas the molecular response to alkaline pH was characterized by upregulation of nhaA and nhaR, which are predicted to encode an Na⁺/H⁺ antiporter and transcriptional activator, respectively, as well as sulfate transport and sulfur metabolism genes. Collectively, these results suggest that S. oneidensis modulates multiple transporters, cell envelope components, and pathways of amino acid consumption and central intermediary metabolism as part of its transcriptome response to changing external pH conditions.

Supplemental material for this article may be found at http://jb.asm.org/.

These authors contributed equally to this work.

Present address: Clemson Veterinary Diagnostic Center, P.O. Box 102406, Columbia, SC 29224-2406.

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