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Title: Comparative genomics of transcriptional regulation of methionine metabolism in proteobacteria

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.
Authors:
 [1] ;  [1] ;  [2] ;  [3] ;  [4] ;  [5] ;  [6] ;  [7]
  1. Russian Academy of Sciences, Moscow (Russia). A.A. Kharkevich Institute for Information Transmission Problems.
  2. Moscow State Univ., Moscow (Russia). Faculty of Bioengineering and Bioinformatics.
  3. Comprehensive School, Moscow (Russia)
  4. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  5. Russian Academy of Sciences, Moscow (Russia). A.A. Kharkevich Institute for Information Transmission Problems; Moscow State Univ., Moscow (Russia). Faculty of Bioengineering and Bioinformatics.
  6. Russian Academy of Sciences, Moscow (Russia). A.A. Kharkevich Institute for Information Transmission Problems; Sanford-Burnham Medical Research Inst., La Jolla, CA (United States)
  7. Univ. of Groningen (Netherlands)
Publication Date:
OSTI Identifier:
1212374
Grant/Contract Number:
AC02-05CH11231
Type:
Accepted Manuscript
Journal Name:
PLoS ONE
Additional Journal Information:
Journal Volume: 9; Journal Issue: 11; Journal ID: ISSN 1932-6203
Publisher:
Public Library of Science
Research Org:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES regulons; methionine; gene regulation; genome evolution; genomic databases; biosynthesis; regulator genes; comparative genomics