The omega subunit of the RNA polymerase core directs transcription efficiency in cyanobacteria

Nucleic Acids Res. 2014 Apr;42(7):4606-14. doi: 10.1093/nar/gku084. Epub 2014 Jan 29.


The eubacterial RNA polymerase core, a transcription machinery performing DNA-dependent RNA polymerization, consists of two α subunits and β, β' and ω subunits. An additional σ subunit is recruited for promoter recognition and transcription initiation. Cyanobacteria, a group of eubacteria characterized by oxygenic photosynthesis, have a unique composition of the RNA polymerase (RNAP) core due to splitting of the β' subunit to N-terminal γ and C-terminal β' subunits. The physiological roles of the small ω subunit of RNAP, encoded by the rpoZ gene, are not yet completely understood in any bacteria. We found that although ω is non-essential in cyanobacteria, it has a major impact on the overall gene expression pattern. In ΔrpoZ strain, recruitment of the primary σ factor into the RNAP holoenzyme is inefficient, which causes downregulation of highly expressed genes and upregulation of many low-expression genes. Especially, genes encoding proteins of photosynthetic carbon concentrating and carbon fixing complexes were down, and the ΔrpoZ mutant showed low light-saturated photosynthetic activity and accumulated photoprotective carotenoids and α-tocopherol. The results indicate that the ω subunit facilitates the association of the primary σ factor with the RNAP core, thereby allowing efficient transcription of highly expressed genes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / genetics
  • Cyanobacteria / enzymology*
  • DNA-Directed RNA Polymerases / genetics
  • DNA-Directed RNA Polymerases / physiology*
  • Fimbriae, Bacterial / genetics
  • Gene Deletion
  • Gene Expression Regulation, Bacterial
  • Heat-Shock Proteins / genetics
  • Synechocystis / genetics
  • Transcription, Genetic*


  • Bacterial Proteins
  • Heat-Shock Proteins
  • HspA protein, bacteria
  • RNA polymerase omega subunit
  • DNA-Directed RNA Polymerases