Cautionary Notes on the Use of Arabinose- and Rhamnose-Inducible Expression Vectors in Pseudomonas aeruginosa

J Bacteriol. 2021 Jul 22;203(16):e0022421. doi: 10.1128/JB.00224-21. Epub 2021 Jul 22.


The Pseudomonas aeruginosa virulence factor regulator (Vfr) is a cyclic AMP (cAMP)-responsive transcription factor homologous to the Escherichia coli cAMP receptor protein (CRP). Unlike CRP, which plays a central role in E. coli energy metabolism and catabolite repression, Vfr is primarily involved in the control of P. aeruginosa virulence factor expression. Expression of the Vfr regulon is controlled at the level of vfr transcription, Vfr translation, cAMP synthesis, and cAMP degradation. While investigating mechanisms that regulate Vfr translation, we placed vfr transcription under the control of the rhaBp rhamnose-inducible promoter system (designated PRha) and found that PRha promoter activity was highly dependent upon vfr. Vfr dependence was also observed for the araBp arabinose-inducible promoter (designated PBAD). The observation of Vfr dependence was not entirely unexpected. Both promoters are derived from E. coli, where maximal promoter activity is dependent upon CRP. Like CRP, we found that Vfr directly binds to promoter probes derived from the PRha and PBAD promoters in vitro. Because Vfr-cAMP activity is highly integrated into numerous global regulatory systems, including c-di-GMP signaling, the Gac/Rsm system, MucA/AlgU/AlgZR signaling, and Hfq/sRNAs, the potential exists for significant variability in PRha and PBAD promoter activity in a variety of genetic backgrounds, and use of these promoter systems in P. aeruginosa should be employed with caution. IMPORTANCE Heterologous gene expression and complementation constitute a valuable and widely utilized tool in bacterial genetics. The arabinose-inducible ParaBAD (PBAD) and rhamnose-inducible PrhaBAD (PRha) promoter systems are commonly used in P. aeruginosa genetics and prized for the tight control and dynamic expression ranges that can be achieved. In this study, we demonstrate that the activity of both promoters is dependent upon the cAMP-dependent transcription factor Vfr. While this poses an obvious problem for use in a vfr mutant background, the issue is more pervasive, considering that vfr transcription/synthesis and cAMP homeostasis are highly integrated into the cellular physiology of the organism and influenced by numerous global regulatory systems. Fortunately, the synthetic PTac promoter is not subject to Vfr regulatory control.

Keywords: Pseudomonas aeruginosa; Vfr; arabinose; cyclic AMP; rhamnose.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Arabinose / metabolism*
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Catabolite Repression
  • Cyclic AMP Receptor Protein / genetics
  • Cyclic AMP Receptor Protein / metabolism
  • Gene Expression Regulation, Bacterial*
  • Genetic Vectors / genetics
  • Genetic Vectors / metabolism
  • Promoter Regions, Genetic
  • Pseudomonas aeruginosa / genetics
  • Pseudomonas aeruginosa / metabolism*
  • Regulon
  • Rhamnose / metabolism*
  • Transcription Factors / genetics
  • Transcription Factors / metabolism
  • Virulence Factors / genetics
  • Virulence Factors / metabolism


  • Bacterial Proteins
  • Cyclic AMP Receptor Protein
  • Transcription Factors
  • Vfr protein, Pseudomonas aeruginosa
  • Virulence Factors
  • Arabinose
  • Rhamnose