title: Comparative genomics and evolution of transcriptional regulons inProteobacteria.
abstract: Comparative genomics approaches are broadly used for analysis of transcriptional regulation in bacterial genomes. In this work, we identified binding sites and reconstructed regulons for 33 orthologous groups of transcription factors (TFs) in 196 reference genomes from 21 taxonomic groups ofProteobacteria. Overall, we predict over 10 600 TF binding sites and identified more than 15 600 target genes for 1896 TFs constituting the studied orthologous groups of regulators. These include a set of orthologues for 21 metabolism-associated TFs fromEscherichia coliand/orShewanellathat are conserved in five or more taxonomic groups and several additional TFs that represent non-orthologous substitutions of the metabolic regulators in some lineages ofProteobacteria. By comparing gene contents of the reconstructed regulons, we identified the core, taxonomy-specific and genome-specific TF regulon members and classified them by their metabolic functions. Detailed analysis of ArgR, TyrR, TrpR, HutC, HypR and other amino-acid-specific regulons demonstrated remarkable differences in regulatory strategies used by various lineages ofProteobacteria. The obtained genomic collection ofin silicoreconstructed TF regulons contains a large number of new regulatory interactions that await future experimental validation. The collection provides a framework for future evolutionary studies of transcriptional regulatory networks inBacteria. It can be also used for functional annotation of putative metabolic transporters and enzymes that are abundant in the reconstructed regulons.
authors.affiliation: 1​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: 1​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: 2​Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Alexey E
authors.initials: AE
authors.lastname: Kazakov
authors.affiliation: 3​Luxembourg Centre for System Biomedicine, Esch-Belval, Luxembourg.
authors.forename: Dmitry A
authors.initials: DA
authors.lastname: Ravcheev
authors.affiliation: 1​A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.
authors.forename: Vita V
authors.initials: VV
authors.lastname: Stepanova
authors.affiliation: 2​Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Pavel S
authors.initials: PS
authors.lastname: Novichkov
authors.affiliation: 4​Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.|1​A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.
authors.forename: Dmitry A
authors.initials: DA
authors.lastname: Rodionov
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D001665:Binding Sites / Q000235:genetics; D019143:Evolution, Molecular; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D023281:Genomics; D010802:Phylogeny; D020560:Proteobacteria / Q000145:classification / Q000235:genetics*; D018085:Regulon / Q000235:genetics*
chemical_list: D001426:Bacterial Proteins
keywords: Proteobacteria; amino acid metabolism; comparative genomics; transcription factor