Phosphate control over nitrogen metabolism in Streptomyces coelicolor: direct and indirect negative control of glnR, glnA, glnII and amtB expression by the response regulator PhoP

Nucleic Acids Res. 2009 Jun;37(10):3230-42. doi: 10.1093/nar/gkp162. Epub 2009 Mar 24.


Bacterial growth requires equilibrated concentration of C, N and P sources. This work shows a phosphate control over the nitrogen metabolism in the model actinomycete Streptomyces coelicolor. Phosphate control of metabolism in Streptomyces is exerted by the two component system PhoR-PhoP. The response regulator PhoP binds to well-known PHO boxes composed of direct repeat units (DRus). PhoP binds to the glnR promoter, encoding the major nitrogen regulator as shown by EMSA studies, but not to the glnRII promoter under identical experimental conditions. PhoP also binds to the promoters of glnA and glnII encoding two glutamine synthetases, and to the promoter of the amtB-glnK-glnD operon, encoding an ammonium transporter and two putative nitrogen sensing/regulatory proteins. Footprinting analyses revealed that the PhoP-binding sequence overlaps the GlnR boxes in both glnA and glnII. 'Information theory' quantitative analyses of base conservation allowed us to establish the structure of the PhoP-binding regions in the glnR, glnA, glnII and amtB genes. Expression studies using luxAB as reporter showed that PhoP represses the above mentioned nitrogen metabolism genes. A mutant deleted in PhoP showed increased expression of the nitrogen metabolism genes. The possible conservation of phosphate control over nitrogen metabolism in other microorganisms is discussed.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism*
  • Binding Sites
  • Cation Transport Proteins / genetics
  • Gene Expression Regulation, Bacterial*
  • Glutamate-Ammonia Ligase / genetics
  • Nitrogen / metabolism*
  • Operator Regions, Genetic
  • Operon
  • Phosphates / metabolism
  • Promoter Regions, Genetic
  • Repressor Proteins / metabolism*
  • Streptomyces coelicolor / genetics*
  • Streptomyces coelicolor / metabolism*
  • Trans-Activators / genetics
  • Trans-Activators / metabolism
  • Transcription, Genetic


  • Bacterial Proteins
  • Cation Transport Proteins
  • GlnR protein, Streptomyces coelicolor
  • Phosphates
  • Repressor Proteins
  • Trans-Activators
  • PhoP protein, Bacteria
  • glutamine synthetase I
  • Glutamate-Ammonia Ligase
  • Nitrogen