Inorganic carbon levels regulate growth via SigC signaling cascade in cyanobacteria

Cyanobacterial growth depends on inorganic carbon (Ci; CO₂ and bicarbonate) concentration, but mechanism(s) adjusting photosynthesis and growth according to Ci remain unclear. ΔrpoZ cells lacking the ω subunit of the RNA polymerase (RNAP) show a unique high-CO₂ lethal phenotype in Synechocystis sp. PCC 6803. Bioinformatics, biochemical and 3D modeling studies were used to reveal how suppressor mutations rescue ΔrpoZ cells in 3% CO₂. Suppressor mutations were mapped to the ssr1600 gene. Ssr1600 was shown to function as an anti-σ factor antagonist. The Slr1861 protein was identified as an anti-σ factor and as an Ssr1600 kinase. The Slr1861/Ssr1600 pair was shown to control the formation of RNAP-SigC holoenzyme using a phosphorylation-controlled partner-switching mechanism. In high CO₂, excess formation of growth-limiting RNAP-SigC holoenzyme in ΔrpoZ reduces the expression of cell wall synthesis, photosynthetic and nutrient uptake genes, leading to low photosynthesis activity and cell lysis. In the suppressor mutants, drastically decreased Ssr1600 levels lowered the amounts of RNAP-SigC holoenzyme to similar levels as in the control strain, returning an almost normal transcriptome composition, photosynthesis and growth. The results indicate that SigC, Slr1861 and Ssr1600 proteins form a growth-regulating signaling cascade in cyanobacteria, which connects growth to environmental Ci levels.