title: In silico prediction and functional validation of sigma28-regulated genes in Chlamydia and Escherichia coli.
abstract: 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.
authors.affiliation: Institute for Genomics and Bioinformatics, University of California, Irvine, California 92697-4025, USA.
authors.forename: Hilda Hiu Yin
authors.initials: HH
authors.lastname: Yu
authors.forename: Dennis
authors.initials: D
authors.lastname: Kibler
authors.forename: Ming
authors.initials: M
authors.lastname: Tan
mesh_terms: D000465:Algorithms; D001425:Bacterial Outer Membrane Proteins / Q000235:genetics; D001483:Base Sequence; D002692:Chlamydia trachomatis / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D012321:DNA-Directed RNA Polymerases / Q000235:genetics*; D048168:Escherichia coli K12 / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial; D006360:Heat-Shock Proteins / Q000235:genetics; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic; D014158:Transcription, Genetic
chemical_list: D001425:Bacterial Outer Membrane Proteins; D006360:Heat-Shock Proteins; C062222:dnak protein, Chlamydia trachomatis; C403898:RNA polymerase sigma(28); D012321:DNA-Directed RNA Polymerases