The TyrR transcription factor regulates the divergent akr-ipdC operons of Enterobacter cloacae UW5

PLoS One. 2015 Mar 26;10(3):e0121241. doi: 10.1371/journal.pone.0121241. eCollection 2015.

Abstract

The TyrR transcription factor regulates genes involved in the uptake and biosynthesis of aromatic amino acids in Enterobacteriaceae. Genes may be positively or negatively regulated depending on the presence or absence of each aromatic amino acid, all three of which function as cofactors for TyrR. In this report we detail the transcriptional control of two divergently transcribed genes, akr and ipdC, by TyrR, elucidated by promoter fusion expression assays and electrophoretic mobility shift assays to assess protein-DNA interactions. Expression of both genes was shown to be controlled by TyrR via interactions with two TyrR boxes located within the akr-ipdC intergenic region. Expression of ipdC required TyrR bound to the proximal strong box, and is strongly induced by phenylalanine, and to a lesser extent by tryptophan and tyrosine. Down-regulation of akr was reliant on interactions with the weak box, and may also require a second, as yet unidentified protein for further repression. Tyrosine enhanced repression of akr. Electrophoretic mobility shift assays demonstrated that TyrR interacts with both the strong and weak boxes, and that binding of the weak box in vitro requires an intact adjacent strong box. While the strong box shows a high degree of conservation with the TyrR binding site consensus sequence, the weak box has atypical spacing of the two half sites comprising the palindromic arms. Site-directed mutagenesis demonstrated sequence-specific interaction between TyrR and the weak box. This is the first report of TyrR-controlled expression of two divergent protein-coding genes, transcribed from independent promoters. Moreover, the identification of a predicted aldo-keto reductase as a member of the TyrR regulon further extends the function of the TyrR regulon.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acids, Aromatic / metabolism
  • Bacterial Proteins / genetics*
  • Bacterial Proteins / metabolism*
  • Base Sequence
  • Binding Sites
  • Chromosome Mapping
  • Enterobacter cloacae / genetics*
  • Enterobacter cloacae / metabolism*
  • Gene Expression
  • Gene Expression Regulation, Bacterial*
  • Gene Order
  • Genes, Reporter
  • Molecular Sequence Data
  • Mutagenesis, Site-Directed
  • Operon*
  • Promoter Regions, Genetic
  • Protein Binding
  • Sequence Alignment
  • Transcription Factors / metabolism*
  • Transcription Initiation Site

Substances

  • Amino Acids, Aromatic
  • Bacterial Proteins
  • Transcription Factors

Grants and funding

This study was supported by a Discovery Grant to C.L.P. and a Post-Graduate Scholarship D to T.J.D.C. from the Natural Sciences and Engineering Research Council of Canada (NSERC). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.