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

The eubacterial RNA polymerase core, a transcription machinery performing DNA-dependent RNA polymerization, consists of two alpha subunits and beta, beta' and omega subunits. An additional Sigma 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 beta' subunit to N-terminal gamma and C-terminal beta' subunits. The physiological roles of the small omega subunit of RNAP, encoded by the rpoZ gene, are not yet completely understood in any bacteria. We found that although omega is non-essential in cyanobacteria, it has a major impact on the overall gene expression pattern. In delta rpoZ strain, recruitment of the primary Sigma 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 delta rpoZ mutant showed low light-saturated photosynthetic activity and accumulated photoprotective carotenoids and alpha-tocopherol. The results indicate that the omega subunit facilitates the association of the primary Sigma factor with the RNAP core, thereby allowing efficient transcription of highly expressed genes.