RegPrecise 3.0--a resource for genome-scale exploration of transcriptional regulation in bacteria.

Background: Genome-scale prediction of gene regulation and reconstruction of transcriptional regulatory networks in prokaryotes is one of the critical tasks of modern genomics. Bacteria from different taxonomic groups, whose lifestyles and natural environments are substantially different, possess highly diverged transcriptional regulatory networks. The comparative genomics approaches are useful for in silico reconstruction of bacterial regulons and networks operated by both transcription factors (TFs) and RNA regulatory elements (riboswitches).

Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus.

Background: Genome-scale prediction of gene regulation and reconstruction of transcriptional regulatory networks in bacteria is one of the critical tasks of modern genomics. The Shewanella genus is comprised of metabolically versatile gamma-proteobacteria, whose lifestyles and natural environments are substantially different from Escherichia coli and other model bacterial species. The comparative genomics approaches and computational identification of regulatory sites are useful for the in silico reconstruction of transcriptional regulatory networks in bacteria.

Transcriptional regulation of the methionine and cysteine transport and metabolism in streptococci.

In streptococci, unlike other Firmicutes, methionine biosynthesis is controlled by protein transcription factors, rather than regulatory RNAs. It was observed that most available streptococcal genomes contain orthologs of two transcriptional regulators of the LysR family: MtaR/MetR and CmbR/FhuR. Comparative genomics techniques were applied to identify two binding motifs occurring upstream of genes involved in metabolism and transport of methionine and cysteine and satisfying the LysR family requirements.

Comparative genomics of transcriptional regulation in yeasts and its application to identification of a candidate alpha-isopropylmalate transporter.

Conservation rates in non-protein-coding regions of five yeast genomes of the genus Saccharomyces were analyzed using multiple whole-genome alignments. This analysis confirmed previously shown decrease in conservation rates observed immediately upstream of the translation start point and downstream of the stop-codon. Further, there was a sharp conservation peak in the upstream regions likely related to the core promoter (-35 bp to +35 bp around TSS) and a conservation peak downstream of the stop-codon whose function is not yet clear.