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J. Bacteriol. doi:10.1128/JB.01082-06
Copyright (c) 2006, American Society for Microbiology and/or the Listed Authors/Institutions. All Rights Reserved.

In silico prediction and functional validation of s²⁸-regulated genes in Chlamydia and E. coli

Institute for Genomics and Bioinformatics, Department of Microbiology and Molecular Genetics and Department of Medicine, School of Medicine, and Department of Computer Science, Donald Bren School of Information and Computer Science, University of California, Irvine, CA 92697-4025

^* To whom correspondence should be addressed. Email: mingt{at}uci.edu.

	Abstract

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

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