Pivotal roles for the receiver domain in the mechanism of action of the response regulator RamR of Streptomyces coelicolor

J Mol Biol. 2005 Sep 2;351(5):1030-47. doi: 10.1016/j.jmb.2005.06.053.

Abstract

The response regulator RamR activates expression of the ramCSAB operon, the source of the morphogenetic peptide SapB, and is therefore important for morphogenesis of the bacterium Streptomyces coelicolor. Like most response regulators, RamR consists of an amino-terminal receiver domain and a carboxy-terminal DNA binding domain. Four of five highly conserved active site residues known to be important in other response regulators are present in RamR: D12, D56 (the predicted site of phosphorylation), T84 and K105. Here, we show that in spite of this, RamR did not demonstrate an ability to autophosphorylate in vitro in the presence of small molecule phosphodonors. The unphosphorylated protein behaved as a dimer and bound cooperatively to three sites in the ramC promoter, one with very high affinity and two with lower affinity. On its own, the RamR DNA binding domain could not bind DNA but was able to interfere with the action of full length RamR in a manner suggesting direct protein-protein contact. Surprisingly, substitution of residues D12 or T84 had no effect on RamR function in vivo. In contrast, D56A and K105A substitutions caused defects in both dimer formation and DNA binding while the more conservative substitution, D56N permitted dimer formation but not DNA binding. L102 in RamR corresponds to a well-conserved tyrosine (or aromatic) residue that is important for function in the other response regulators. While a L102Y variant, which introduced the aromatic side-chain usually found at this position, functioned normally, L102A and L102W substitutions blocked RamR function in vivo. We show that these substitutions specifically impaired cooperative DNA binding by RamR at the lower affinity recognition sequences. The biochemical properties of RamR therefore differ markedly from those of other well-characterized response regulators.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / metabolism
  • Binding Sites
  • Binding, Competitive
  • Blotting, Western
  • Chromatography, Gel
  • Chromatography, Liquid
  • DNA / chemistry
  • DNA-Binding Proteins / chemistry*
  • DNA-Binding Proteins / metabolism
  • Dimerization
  • Dose-Response Relationship, Drug
  • Gene Expression Regulation, Bacterial
  • Genetic Complementation Test
  • Genotype
  • Kinetics
  • Mass Spectrometry
  • Models, Genetic
  • Molecular Conformation
  • Molecular Sequence Data
  • Muramidase
  • Mutation
  • Nucleic Acid Conformation
  • Operon
  • Phosphorylation
  • Plasmids / metabolism
  • Promoter Regions, Genetic
  • Protein Binding
  • Protein Structure, Tertiary
  • Streptomyces coelicolor / metabolism*
  • Transcription Factors / chemistry*
  • Transcription Factors / metabolism
  • Transcriptional Activation

Substances

  • Bacterial Proteins
  • DNA-Binding Proteins
  • RamR protein, Streptomyces
  • Transcription Factors
  • DNA
  • Muramidase