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Originally published In Press as doi:10.1074/mcp.M500394-MCP200 on March 8, 2006.
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Molecular & Cellular Proteomics 5:1054-1071, 2006.
© 2006 by The American Society for Biochemistry and Molecular Biology, Inc.

Research

Molecular Dynamics of the Shewanella oneidensis Response to Chromate Stress*,S

Steven D. Brown{ddagger},§, Melissa R. Thompson§,¶,||,**, Nathan C. VerBerkmoes, Karuna Chourey{ddagger}, Manesh Shah{ddagger}{ddagger}, Jizhong Zhou{ddagger}, Robert L. Hettich,§§ and Dorothea K. Thompson{ddagger},¶¶,||||

From the {ddagger} Environmental Sciences Division, Chemical Sciences Division, and {ddagger}{ddagger} Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, || Graduate School of Genome Science and Technology, University of Tennessee-Oak Ridge National Laboratory, Tennessee 37830, and ¶¶ Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907

Temporal genomic profiling and whole-cell proteomic analyses were performed to characterize the dynamic molecular response of the metal-reducing bacterium Shewanella oneidensis MR-1 to an acute chromate shock. The complex dynamics of cellular processes demand the integration of methodologies that describe biological systems at the levels of regulation, gene and protein expression, and metabolite production. Genomic microarray analysis of the transcriptome dynamics of midexponential phase cells subjected to 1 mM potassium chromate (K2CrO4) at exposure time intervals of 5, 30, 60, and 90 min revealed 910 genes that were differentially expressed at one or more time points. Strongly induced genes included those encoding components of a TonB1 iron transport system (tonB1-exbB1-exbD1), hemin ATP-binding cassette transporters (hmuTUV), TonB-dependent receptors as well as sulfate transporters (cysP, cysW-2, and cysA-2), and enzymes involved in assimilative sulfur metabolism (cysC, cysN, cysD, cysH, cysI, and cysJ). Transcript levels for genes with annotated functions in DNA repair (lexA, recX, recA, recN, dinP, and umuD), cellular detoxification (so1756, so3585, and so3586), and two-component signal transduction systems (so2426) were also significantly up-regulated (p < 0.05) in Cr(VI)-exposed cells relative to untreated cells. By contrast, genes with functions linked to energy metabolism, particularly electron transport (e.g. so0902-03-04, mtrA, omcA, and omcB), showed dramatic temporal alterations in expression with the majority exhibiting repression. Differential proteomics based on multidimensional HPLC-MS/MS was used to complement the transcriptome data, resulting in comparable induction and repression patterns for a subset of corresponding proteins. In total, expression of 2,370 proteins were confidently verified with 624 (26%) of these annotated as hypothetical or conserved hypothetical proteins. The initial response of S. oneidensis to chromate shock appears to require a combination of different regulatory networks that involve genes with annotated functions in oxidative stress protection, detoxification, protein stress protection, iron and sulfur acquisition, and SOS-controlled DNA repair mechanisms.

§§ To whom correspondence for mass spectrometry and proteomics should be addressed: Chemical Sciences Division, Oak Ridge National Laboratory, P. O. Box 2008 MS-6131, Oak Ridge, TN 37831-6131. Tel.: 865-574-4968; Fax: 865-576-8559; E-mail: hettichrl{at}ornl.gov


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