DksA represses ribosomal gene transcription in Pseudomonas aeruginosa by interacting with RNA polymerase on ribosomal promoters

Mol Microbiol. 2005 May;56(4):1087-102. doi: 10.1111/j.1365-2958.2005.04597.x.

Abstract

In Escherichia coli transcription of ribosomal RNA (rRNA) is regulated by the H-NS and Fis proteins, as well as by the small signal molecule ppGpp and the initiating nucleotides. During amino acid starvation, the concentration of ppGpp increases, and binding of this alarmone to RNA polymerase (RNAP) leads to inhibition of rRNA transcription, a regulatory event called stringent response. Here we show that in Pseudomonas aeruginosa DksA, a protein with pleiotropic effects, is a negative regulator of rRNA transcription both during exponential growth and stringent conditions. A dksA mutant overexpresses rRNA, without being affected in the production of ppGpp. Cell-fractionation and chromosome immunoprecipitation experiments demonstrate that DksA is associated with DNA, in particular with promoters of ribosomal genes in vivo. The binding to rRNA promoters specifically increases during stringent response, and correlates with the binding of RNAP to these regions. Moreover DksA can be copurified with RNAP subunits in vivo. DNA band shift experiments show that DksA, in synergy with ppGpp, increases the binding of RNAP to ribosomal promoters. Therefore DksA might be a new regulator of rRNA transcription in P. aeruginosa.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / genetics
  • Bacterial Proteins / isolation & purification
  • Bacterial Proteins / metabolism*
  • DNA, Bacterial
  • DNA-Directed RNA Polymerases / chemistry
  • DNA-Directed RNA Polymerases / metabolism*
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism
  • Gene Expression Regulation, Bacterial*
  • Promoter Regions, Genetic*
  • Protein Subunits / genetics
  • Protein Subunits / isolation & purification
  • Protein Subunits / metabolism
  • Pseudomonas aeruginosa* / genetics
  • Pseudomonas aeruginosa* / metabolism
  • RNA, Ribosomal / genetics
  • RNA, Ribosomal / metabolism*
  • Transcription, Genetic*

Substances

  • Bacterial Proteins
  • DNA, Bacterial
  • Escherichia coli Proteins
  • Protein Subunits
  • RNA, Ribosomal
  • dksA protein, E coli
  • DNA-Directed RNA Polymerases