title: Comparative genomics of transcriptional regulation of methionine metabolism in Proteobacteria.
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.
authors.affiliation: A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.
authors.forename: Semen A
authors.initials: SA
authors.lastname: Leyn
authors.affiliation: A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.
authors.forename: Inna A
authors.initials: IA
authors.lastname: Suvorova
authors.affiliation: Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia.
authors.forename: Tatiana D
authors.initials: TD
authors.lastname: Kholina
authors.affiliation: Comprehensive School 463, Moscow, Russia.
authors.forename: Sofia S
authors.initials: SS
authors.lastname: Sherstneva
authors.affiliation: Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.
authors.forename: Pavel S
authors.initials: PS
authors.lastname: Novichkov
authors.affiliation: A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia; Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia.
authors.forename: Mikhail S
authors.initials: MS
authors.lastname: Gelfand
authors.affiliation: A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia; Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America.
authors.forename: Dmitry A
authors.initials: DA
authors.lastname: Rodionov
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism; D055028:Comparative Genomic Hybridization; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D008715:Methionine / Q000378:metabolism*; D020560:Proteobacteria / Q000235:genetics* / Q000378:metabolism; D050436:Regulatory Elements, Transcriptional; D058928:Riboswitch / Q000502:physiology; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D058928:Riboswitch; D014157:Transcription Factors; D008715:Methionine