Reference : Comparative genomics and evolution of transcriptional regulons in Proteobacteria
Scientific journals : Article
Life sciences : Biochemistry, biophysics & molecular biology
Computational Sciences
http://hdl.handle.net/10993/27628
Comparative genomics and evolution of transcriptional regulons in Proteobacteria
English
Leyn, Semen [A.A.Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences]
Suvorova, Inna [A.A.Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences]
Kazakov, Alexey [Lawrence Berkeley National Laboratory]
Ravcheev, Dmitry mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
Stepanova, Vita [A.A.Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences]
Novichkov, Pavel [Lawrence Berkeley National Laboratory]
Rodionov, Dmitry [A.A.Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences > > > ; Sanford-Burnham-Prebys Medical Discovery Institute]
19-Apr-2016
Microbial Genomics
Yes
International
[en] 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 of Proteobacteria. Overall, we predict over 10,600 TF binding sites and identified more than 15,600 target genes for 1,896 TFs constituting the studied orthologous groups of regulators. These include a set of orthologs for 21 metabolism-associated TFs from Escherichia coli and/or Shewanella that are conserved in five or more taxonomic groups and several additional TFs that represent non-orthologous substitutions of the metabolic regulators in some lineages of Proteobacteria. 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. The detailed analysis of ArgR, TyrR, TrpR, HutC, HypR and other amino acid-specific regulons demonstrated remarkable differences in regulatory strategies used by various lineages of Proteobacteria. The obtained genomic collection of in silico reconstructed TF regulons contains a large number of new regulatory interactions that awaits future experimental validation. It provides a framework for future evolutionary studies of transcriptional regulatory networks in Bacteria. It can be also used for functional annotation of putative metabolic transporters and enzymes that are abundant in the reconstructed regulons.
http://hdl.handle.net/10993/27628

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