Comparative genomics of CytR, an unusual member of the LacI family of transcription factors

PLoS One. 2012;7(9):e44194. doi: 10.1371/journal.pone.0044194. Epub 2012 Sep 24.

Abstract

CytR is a transcription regulator from the LacI family, present in some gamma-proteobacteria including Escherichia coli and known not only for its cellular role, control of transport and utilization of nucleosides, but for a number of unusual structural properties. The present study addressed three related problems: structure of CytR-binding sites and motifs, their evolutionary conservation, and identification of new members of the CytR regulon. While the majority of CytR-binding sites are imperfect inverted repeats situated between binding sites for another transcription factor, CRP, other architectures were observed, in particular, direct repeats. While the similarity between sites for different genes in one genome is rather low, and hence the consensus motif is weak, there is high conservation of orthologous sites in different genomes (mainly in the Enterobacteriales) arguing for the presence of specific CytR-DNA contacts. On larger evolutionary distances candidate CytR sites may migrate but the approximate distance between flanking CRP sites tends to be conserved, which demonstrates that the overall structure of the CRP-CytR-DNA complex is gene-specific. The analysis yielded candidate CytR-binding sites for orthologs of known regulon members in less studied genomes of the Enterobacteriales and Vibrionales and identified a new candidate member of the CytR regulon, encoding a transporter named NupT (YcdZ).

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Binding Sites
  • Escherichia coli / classification
  • Escherichia coli / genetics*
  • Escherichia coli / metabolism
  • Escherichia coli Proteins / genetics*
  • Escherichia coli Proteins / metabolism
  • Evolution, Molecular
  • Gene Expression Regulation, Bacterial
  • Genomics*
  • Lac Repressors / genetics*
  • Lac Repressors / metabolism
  • Molecular Sequence Data
  • Operator Regions, Genetic
  • Phylogeny
  • Protein Binding
  • Repressor Proteins / genetics*
  • Repressor Proteins / metabolism
  • Sequence Alignment
  • Transcription Factors / genetics*
  • Transcription Factors / metabolism

Substances

  • CytR protein, E coli
  • Escherichia coli Proteins
  • Lac Repressors
  • LacI protein, E coli
  • Repressor Proteins
  • Transcription Factors

Grant support

This study was partially supported by the Ministry of Education and Science of Russia via contract 07.514.11.4007, the Russian Foundation of Basic Research via grant 10-04-00431, and the Russian Academy of Sciences via the Program in Molecular and Cellular Biology. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.