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. 2016 Jul 11;2(7):e000061.
doi: 10.1099/mgen.0.000061. eCollection 2016 Jul.

Comparative genomics and evolution of transcriptional regulons in Proteobacteria

Semen A Leyn  1 , Inna A Suvorova  1 , Alexey E Kazakov  2 , Dmitry A Ravcheev  3 , Vita V Stepanova  1 , Pavel S Novichkov  2 , Dmitry A Rodionov  4   1
Affiliations

Comparative genomics and evolution of transcriptional regulons in Proteobacteria

Semen A Leyn et al. Microb Genom. .

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 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. 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.

Keywords: Proteobacteria; amino acid metabolism; comparative genomics; transcription factor.

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Figures

Fig. 1.
Fig. 1.
Taxonomic distribution of 33 studied TF regulons in four major classes of Proteobacteria. Circles include the number of TFs that are either taxonomic class-specific or shared between several classes.
Fig. 2.
Fig. 2.
Examples of motif changes in four orthologous groups of studied TFs. Conservative positions between motifs within groups are boxed with the same color.
Fig. 3.
Fig. 3.
Arginine metabolism and its regulation by ArgR in Proteobacteria.
Fig. 4.
Fig. 4.
Aromatic amino acid metabolism and its regulation by TyrR, TrpR and other transcription factors in Proteobacteria.
Fig. 5.
Fig. 5.
Hydroxyproline and proline utilization pathway and its regulation by HypR in Proteobacteria.
Fig. 6.
Fig. 6.
Histidine metabolism and its regulation by HutC in Proteobacteria.
See this image and copyright information in PMC

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Data Bibliography

    1. Leyn, S. A., Suvorova, I. A., Kazakov, A. E., Ravcheev, D. A., Stepanova, V. V., Novichkov, P. S. & Rodionov, D. A. RegPrecise 4.0. Collection of regulogs for transcription factor families in Proteobacteria. http://regprecise.lbl.gov/RegPrecise/project_proteobacteria.jsp (2016).

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