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Title: Comparative genomics and evolution of transcriptional regulons in Proteobacteria

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 of Proteobacteria. 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 from Esc herichia 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. 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 await future experimental validation. The collection provides a framework for future evolutionary studies of transcriptional regulatory networks in Bacteria. It canmore » be also used for functional annotation of putative metabolic transporters and enzymes that are abundant in the reconstructed regulons.« less

Authors:
 [1];  [1];  [2];  [3];  [1];  [2];  [4]
  1. Russian Academy of Sciences (RAS), Moscow (Russian Federation)
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  3. Luxembourg Centre for System Biomedicine, Esch-Belval (Luxembourg)
  4. ​Sanford-Burnham-Prebys Medical Discovery Inst., La Jolla, CA (United States); Russian Academy of Sciences (RAS), Moscow (Russian Federation)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1506255
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Microbial Genomics
Additional Journal Information:
Journal Volume: 2; Journal Issue: 7; Journal ID: ISSN 2057-5858
Publisher:
Society for General Microbiology
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; comparative genomics; transcription factor; amino acid metabolism; Proteobacteria

Citation Formats

Leyn, Semen A., Suvorova, Inna A., Kazakov, Alexey E., Ravcheev, Dmitry A., Stepanova, Vita V., Novichkov, Pavel S., and Rodionov, Dmitry A. Comparative genomics and evolution of transcriptional regulons in Proteobacteria. United States: N. p., 2016. Web. doi:10.1099/mgen.0.000061.
Leyn, Semen A., Suvorova, Inna A., Kazakov, Alexey E., Ravcheev, Dmitry A., Stepanova, Vita V., Novichkov, Pavel S., & Rodionov, Dmitry A. Comparative genomics and evolution of transcriptional regulons in Proteobacteria. United States. doi:10.1099/mgen.0.000061.
Leyn, Semen A., Suvorova, Inna A., Kazakov, Alexey E., Ravcheev, Dmitry A., Stepanova, Vita V., Novichkov, Pavel S., and Rodionov, Dmitry A. Mon . "Comparative genomics and evolution of transcriptional regulons in Proteobacteria". United States. doi:10.1099/mgen.0.000061. https://www.osti.gov/servlets/purl/1506255.
@article{osti_1506255,
title = {Comparative genomics and evolution of transcriptional regulons in Proteobacteria},
author = {Leyn, Semen A. and Suvorova, Inna A. and Kazakov, Alexey E. and Ravcheev, Dmitry A. and Stepanova, Vita V. and Novichkov, Pavel S. and Rodionov, Dmitry A.},
abstractNote = {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 1896 TFs constituting the studied orthologous groups of regulators. These include a set of orthologues for 21 metabolism-associated TFs from Esc herichia 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. 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 await future experimental validation. The collection 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.},
doi = {10.1099/mgen.0.000061},
journal = {Microbial Genomics},
number = 7,
volume = 2,
place = {United States},
year = {2016},
month = {7}
}

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