In silico prediction and functional validation of σ28- regulated genes in Chlamydia and Escherichia coli

Abstract

σ28 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 σ28-dependent genes in the Chlamydia trachomatis genome, we applied bioinformatic methods using a probability weight matrix based on known σ28 promoters in other bacteria and a second matrix based on a functional analysis of the σ28 promoter. We tested 16 candidate σ28 promoters predicted with these algorithms and found that 5 were active in a chlamydial σ28 in vitro transcription assay. hctB, the known σ28-regulated gene, is only expressed late in the chlamydial developmental cycle only, and two of the newly identified σ28 target genes (tsp and tlyC_1) also have late expression profiles, providing support for σ28 as a regulator of late gene expression. One of the other novel σ28- regulated genes is dnaK, a known heat shock-responsive gene, suggesting that σ28 RNA polymerase may be involved in the response to cellular stress. Our σ28 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 σ28-regulated genes in E. coli. Copyright © 2006, American Society for Microbiology. All Rights Reserved.