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Title: Comparative genomics and evolution of transcriptional regulons in Proteobacteria

Journal Article · · Microbial Genomics
 [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)
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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.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1506255
Journal Information:
Microbial Genomics, Vol. 2, Issue 7; ISSN 2057-5858
Publisher:
Society for General MicrobiologyCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 16 works
Citation information provided by
Web of Science

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Cited By (2)

Regulation of Respiratory Pathways in Campylobacterota: A Review journal July 2019
TyrR is involved in the transcriptional regulation of biofilm formation and D-alanine catabolism in Azospirillum brasilense Sp7. journal February 2019

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
comparative genomics
transcription factor
amino acid metabolism
Proteobacteria