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Cyanobacteria respond to both light intensity and quality by adjusting the expression of many genes. In sub-optimal environmental conditions, sigma factors of the bacterial RNA polymerase play central regulatory roles by determining preferable promoters that the RNA polymerase holoenzyme binds to initiate transcription. Synechocystis sp. PCC 6803 genome encodes nine σ factors. The housekeeping σ factor, SigA, is essential for cell viability. Group 2 σ factors, SigB, SigC, SigD and SigE, are important for acclimation to different environmental conditions. Group 3 σ factors, SigF, SigG, SigH and SigI are structurally different and they have distinct roles in cell function. The ∆sigCDE strain (SigB is the only functional group 2 σ factor) lost light-saturated PSII activity in bright light more slowly than the control strain. The PSII repair cycle was as efficient in the ∆sigCDE strain as in the control strain, but the light-induced damage of PSII occurred more slowly in the ∆sigCDE strain. In isolated thylakoids, similar photoinhibition rates were measured for the ∆sigCDE and control strains, and biophysical measurements revealed that electron transfer reactions occurred similarly in both strains. This suggested that the resistance of the ∆sigCDE strain to photoinhibition is not due to differences in PSII properties, but some photo-protective mechanisms functioning very efficiently in the ∆sigCDE strain. Analysis of possible photoprotective mechanisms showed that few of them were upregulated in the ∆sigCDE strain while others were not. HPLC analysis revealed that the ∆sigCDE strain had a higher carotenoid content than the control strain. Specifically, the sigCDE strain had more myxoxanthophyll and zeaxanthin than the control strain while the amounts of echinenone and β-carotene were similar. Non-photochemical quenching, a mechanism that dissipates excitation energy of the phycobilisomes to heat, was higher in the sigCDE strain than in the control strain. Furthermore, the photoprotective flv4-sll2018-flv2 operon was up-regulated in the ∆sigCDE strain. No differences were detected in state transitions, IsiA protein, or in PSII charge recombination reactions.