We have studied the process of charge stabilization and recombination in various engineered strains of Synechocystis 6803 in which either the whole D1 protein of the Photosystem II reaction center was replaced by the D1′ product of the psbA1 gene, or prominent point mutations of D1′ were introduced into the normal D1. Both the up-shifted thermoluminescence peak positions and increased time constants of flash-induced chlorophyll fluorescence components, that can be assigned to charge recombination, indicated that the energetic stabilization of the S2QA− and S2QB− charge pairs is increased in D1′ containing Photosystem II. Similar stabilization of S2QA− was induced by the Phe186Leu, Phe186Ala and Phe186LeuPro162Ser substitutions in the normal D1 protein. However, these replacements also affected the function of the QA
− QB two-electron gate by slowing down the QA to QB electron transfer step and decreasing the redox gap between QA and QB. We conclude that in the D1′-containing PSII centers and in the Phe186 mutants, Em(S2/S1) is decreased by 20–25 mV. In the Phe186 mutants, this affect is accompanied by a 40–50 mV decrease of Em(QB/QB−), which provides an example of pronounced long-range influence of PSII donor side modifications on the QA
− QB binding region. However, this acceptor side effect is compensated by the other substitutions of the D1′ protein, which restores efficient electron flow between QA and QB, indicating that D1′-containing PSII centers might have a physiological function under certain environmental conditions.
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