Comparative genomics of transcriptional regulation of methionine metabolism in Proteobacteria

PLoS One. 2014 Nov 20;9(11):e113714. doi: 10.1371/journal.pone.0113714. eCollection 2014.

Abstract

Methionine metabolism and uptake genes in Proteobacteria are controlled by a variety of RNA and DNA regulatory systems. We have applied comparative genomics to reconstruct regulons for three known transcription factors, MetJ, MetR, and SahR, and three known riboswitch motifs, SAH, SAM-SAH, and SAM_alpha, in ∼ 200 genomes from 22 taxonomic groups of Proteobacteria. We also identified two novel regulons: a SahR-like transcription factor SamR controlling various methionine biosynthesis genes in the Xanthomonadales group, and a potential RNA regulatory element with terminator-antiterminator mechanism controlling the metX or metZ genes in beta-proteobacteria. For each analyzed regulator we identified the core, taxon-specific and genome-specific regulon members. By analyzing the distribution of these regulators in bacterial genomes and by comparing their regulon contents we elucidated possible evolutionary scenarios for the regulation of the methionine metabolism genes in Proteobacteria.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Bacterial Proteins / metabolism
  • Comparative Genomic Hybridization
  • Gene Expression Regulation, Bacterial
  • Genome, Bacterial*
  • Methionine / metabolism*
  • Proteobacteria / genetics*
  • Proteobacteria / metabolism
  • Regulatory Elements, Transcriptional
  • Riboswitch / physiology
  • Transcription Factors / metabolism

Substances

  • Bacterial Proteins
  • Riboswitch
  • Transcription Factors
  • Methionine

Grants and funding

This research was supported by the Russian Science Foundation via grants 14-14-00289 (to S.A.L and D.A.R.) and 14-24-00155 (to I.A.S. and M.S.G.). This research was also partially supported by the Genomic Science Program (GSP), Office of Biological and Environmental Research (OBER), and U.S. Department of Energy (DOE), and is a contribution of the Pacific Northwest National Laboratory (PNNL) Foundational Scientific Focus Area. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.