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Journal of Bacteriology, November 2004, p. 7796-7803, Vol. 186, No. 22
0021-9193/04/$08.00+0     DOI: 10.1128/JB.186.22.7796-7803.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

Global Transcriptome Analysis of the Heat Shock Response of Shewanella oneidensis{dagger} ,{ddagger}

Haichun Gao,1 Yue Wang,2 Xueduan Liu,1 Tingfen Yan,1 Liyou Wu,1 Eric Alm,2 Adam Arkin,2 Dorothea K. Thompson,1 and Jizhong Zhou1*

Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee,1 Departments of Bioengineering and Chemistry, University of California, Berkeley, Berkeley, California2

Received 15 January 2004/ Accepted 26 May 2004

Shewanella oneidensis is an important model organism for bioremediation studies because of its diverse respiratory capabilities. However, the genetic basis and regulatory mechanisms underlying the ability of S. oneidensis to survive and adapt to various environmentally relevant stresses is poorly understood. To define this organism's molecular response to elevated growth temperatures, temporal gene expression profiles were examined in cells subjected to heat stress by using whole-genome DNA microarrays for S. oneidensis. Approximately 15% (n = 711) of the total predicted S. oneidensis genes (n = 4,648) represented on the microarray were significantly up- or downregulated (P < 0.05) over a 25-min period after shift to the heat shock temperature. As expected, the majority of the genes that showed homology to known chaperones and heat shock proteins in other organisms were highly induced. In addition, a number of predicted genes, including those encoding enzymes in glycolysis and the pentose cycle, serine proteases, transcriptional regulators (MerR, LysR, and TetR families), histidine kinases, and hypothetical proteins were induced. Genes encoding membrane proteins were differentially expressed, suggesting that cells possibly alter their membrane composition or structure in response to variations in growth temperature. A substantial number of the genes encoding ribosomal proteins displayed downregulated coexpression patterns in response to heat stress, as did genes encoding prophage and flagellar proteins. Finally, a putative regulatory site with high conservation to the Escherichia coli {sigma}32-binding consensus sequence was identified upstream of a number of heat-inducible genes.

* Corresponding author. Mailing address: Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831. Phone: (865) 576-7544. Fax: (865) 576-8646. E-mail: zhouj{at}ornl.gov.

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

{ddagger} Presented in part at the 11th International Conference on Microbial Genomes, Durham, N.C., 28 September to 2 October 2003.

Journal of Bacteriology, November 2004, p. 7796-7803, Vol. 186, No. 22
0021-9193/04/$08.00+0     DOI: 10.1128/JB.186.22.7796-7803.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.



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