The PhaD regulator controls the simultaneous expression of the pha genes involved in polyhydroxyalkanoate metabolism and turnover in Pseudomonas putida KT2442

Environ Microbiol. 2010 Jun;12(6):1591-603. doi: 10.1111/j.1462-2920.2010.02199.x. Epub 2010 Apr 14.


The promoters of the pha gene cluster encoding the enzymes involved in the metabolism of polyhydroxyalkanoates (PHAs) in the model strain Pseudomonas putida KT2442 have been identified and compared. The pha locus is composed by five functional promoters upstream the phaC1, phaZ, phaC2, phaF and phaI genes (P(C1), P(Z), P(C2), P(F) and P(I) respectively). P(C1) and P(I) are the most active promoters of the pha cluster allowing the transcription of phaC1ZC2D and phaIF operons. All promoters with the sole exception of P(F) are carbon source-dependent. Their transcription profiles explain the simultaneous production of PHA depolymerase and synthases to maintain the metabolic balance and PHA turnover. Mutagenesis analyses demonstrated that PhaD, a TetR-like transcriptional regulator, behaves as a carbon source-dependent activator of the pha cluster. The phaD gene is mainly transcribed as part of the phaC1ZC2D transcription unit and controls its own transcription and that of phaIF operon. The ability of PhaD to bind the P(C1) and P(I) promoters was analysed by gel retardation and DNase I footprinting assays, demonstrating that PhaD interacts with a region of 25 bp at P(C1) promoter (named OPRc1) and a 29 bp region at P(I) promoter (named OPRi). These operators contain a single binding site formed by two inverted half sites of 6 bp separated by 8 bp which overlap the corresponding promoter boxes. The 3D model structure of PhaD activator predicts that the true effector might be a CoA-intermediate of fatty acid beta-oxidation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acetyl-CoA C-Acyltransferase* / chemistry
  • Acetyl-CoA C-Acyltransferase* / genetics
  • Acetyl-CoA C-Acyltransferase* / metabolism
  • Bacterial Proteins* / chemistry
  • Bacterial Proteins* / genetics
  • Bacterial Proteins* / metabolism
  • Base Sequence
  • Carbon / metabolism
  • Gene Expression Regulation, Bacterial*
  • Models, Molecular
  • Molecular Sequence Data
  • Multigene Family
  • Polyhydroxyalkanoates / metabolism*
  • Promoter Regions, Genetic
  • Protein Structure, Tertiary
  • Pseudomonas putida* / genetics
  • Pseudomonas putida* / metabolism
  • Regulatory Sequences, Nucleic Acid*


  • Bacterial Proteins
  • Polyhydroxyalkanoates
  • Carbon
  • Acetyl-CoA C-Acyltransferase
  • 3-oxoadipyl-coenzyme A thiolase