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Photosynthetic organisms are capable of redistributing the absorbed light energy between photosystems I (PSI) and II (PSII), which is accompanied by short-term modifications in the photosynthetic apparatus known as “state transitions”. In order to understand how activity of PSI and PSII is regulated during state transitions in cyanobacteria, we studied photosynthetic parameters of photosystems in Synechocystis PCC 6803 wild type (WT) and its mutants deficient in oxidases (Ox-) or succinate dehydrogenase (SDH-). After dark adaptation Ox- mutant, lacking the oxidation agents, is expected to have reduced PQ pool, while in SDH- mutant the PQ pool would be more oxidized due to partial inhibition of the respiratory chain electron carriers. We found that the PQ pool was indeed reduced in Ox- mutant and oxidized in SDH- mutant, indicating different states of the photosynthetic apparatus in these mutants. Analysis of the variable fluorescence and 77K fluorescence emission spectra revealed that after dark adaptation WT and SDH- mutant were in State 1, while the Ox- mutant was in State 2. When compared to State 1, State 2 was characterized by ~1.5 times lower photochemical activity of PSII and 4 times slower rates of Qa reoxidation, indicating inhibition of the electron transport on the acceptor side of PSII. On the other hand, in State 2 we observed evidence of high activity of cyclic electron transfer around PSI (high rate of P700 reduction and the low level of P700 oxidation). Illumination with continuous light 1 (440 nm) allowed oxidation of the PQ pool in the Ox- mutant, thus promoting it to State 1. As in WT and SDH- mutant, Ox- mutant in State 1 was characterized by high variable fluorescence and fast rates of Qa reoxidation, indicating acceleration of linear electron transport, as well as lower activity of cyclic electron transport around PS1. Thus, we show that PSII of cyanobacteria has a higher photosynthetic activity in State 1, while it is partially inactivated in State 2. We suggest that this process is controlled by the redox state of PQ in cyanobacteria through enhancement/inhibition of electron transport on the acceptor side of PSII.