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In Silico Prediction and Functional Validation of ²⁸-Regulated Genes in Chlamydia and Escherichia coli ^,

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

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 Chlamydia 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 only, 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 Escherichia coli genome, we have predicted and functionally identified five previously unknown ²⁸-regulated genes in E. coli.

Published ahead of print on 22 September 2006.

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