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Journal of Bacteriology, December 2006, p. 8206-8212, Vol. 188, No. 23
0021-9193/06/$08.00+0     doi:10.1128/JB.01082-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

In Silico Prediction and Functional Validation of {sigma}28-Regulated Genes in Chlamydia and Escherichia coli{triangledown} ,{dagger}

Hilda Hiu Yin Yu,1,2 Dennis Kibler,1,4 and Ming Tan1,2,3*

Institute for Genomics and Bioinformatics,1 Department of Microbiology and Molecular Genetics,2 Department of Medicine, School of Medicine,3 Department of Computer Science, Donald Bren School of Information and Computer Science, University of California, Irvine, California 92697-40254

Received 21 July 2006/ Accepted 6 September 2006

{sigma}28 RNA polymerase is an alternative RNA polymerase that has been proposed to have a role in late developmental gene regulation in Chlamydia, but only a single target gene has been identified. To discover additional {sigma}28-dependent genes in the Chlamydia trachomatis genome, we applied bioinformatic methods using a probability weight matrix based on known {sigma}28 promoters in other bacteria and a second matrix based on a functional analysis of the {sigma}28 promoter. We tested 16 candidate {sigma}28 promoters predicted with these algorithms and found that 5 were active in a chlamydial {sigma}28 in vitro transcription assay. hctB, the known {sigma}28-regulated gene, is only expressed late in the chlamydial developmental cycle only, and two of the newly identified {sigma}28 target genes (tsp and tlyC_1) also have late expression profiles, providing support for {sigma}28 as a regulator of late gene expression. One of the other novel {sigma}28-regulated genes is dnaK, a known heat shock-responsive gene, suggesting that {sigma}28 RNA polymerase may be involved in the response to cellular stress. Our {sigma}28 prediction algorithm can be applied to other bacteria, and by performing a similar analysis on the Escherichia coli genome, we have predicted and functionally identified five previously unknown {sigma}28-regulated genes in E. coli.

* Corresponding author. Mailing address: B240, Med. Sci. I, Department of Microbiology and Molecular Genetics, University of California, Irvine, CA 92697-4025. Phone: (949) 824-3397. Fax: (949) 824-8598. E-mail: mingt{at}uci.edu.

{triangledown} Published ahead of print on 22 September 2006.

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

Journal of Bacteriology, December 2006, p. 8206-8212, Vol. 188, No. 23
0021-9193/06/$08.00+0     doi:10.1128/JB.01082-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.



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