The cyanobacterium Synechocystis sp. PCC 6803 contains four members of the FtsH protease family. One of these, FtsH (slr0228), has been implicated recently in the repair of photodamaged photosystem II (PSII) complexes. We have demonstrated here, using a combination of blue native PAGE, radiolabeling, and immunoblotting, that FtsH (slr0228) is required for selective replacement of the D1 reaction center subunit in both wild type PSII complexes and in PSII subcomplexes lacking the PSII chlorophyll a-binding subunit CP43. To test whether FtsH (slr0228) has a more general role in protein quality control in vivo, we have studied the synthesis and degradation of PSII subunits in wild type and in defined insertion and missense mutants incapable of proper assembly of the PSII holoenzyme. We discovered that, when the gene encoding FtsH (slr0228) was disrupted in these strains, the overall level of assembly intermediates and unassembled PSII proteins markedly increased. Pulse-chase experiments showed that this was due to reduced rates of degradation in vivo. Importantly, analysis of epitope-tagged and green fluorescent protein-tagged strains revealed that slr0228 was present in the thylakoid and not the cytoplasmic membrane. Overall, our results show that FtsH (slr0228) plays an important role in controlling the removal of PSII subunits from the thylakoid membrane and is not restricted to selective D1 turnover.All cellular organisms possess quality control mechanisms to prevent the accumulation of unwanted proteins (1). Of current interest are the processes by which damaged and unassembled proteins are removed from the thylakoid membrane, which is the location of the protein complexes involved in oxygenic photosynthetic electron transport in cyanobacteria and chloroplasts (2). Side reactions associated with the light reactions of photosynthesis lead to the production of a variety of potentially hazardous molecules (e.g. reactive oxygen species) that can oxidize components, such as amino acid side chains and pigment cofactors (3). Ultimately, unless the damage is repaired, there is a net reduction in photosynthetic performance known as photoinhibition (for review see Ref. 4). As yet, the repair pathways and, more generally, the quality control processes involved in the assembly of the thylakoid membrane protein complexes and removal of aberrant proteins remain poorly understood.One component that is especially prone to photodamage is the photosystem II (PSII) 2 complex, which is composed of over 25 membrane and peripheral proteins and is responsible for the light-driven oxidation of water and reduction of plastoquinone (5). The D1 protein, together with the homologous D2 protein, binds the cofactors involved in electron transfer through the complex (6). The D1 subunit is also the chief target for light-induced damage in PSII and undergoes rapid synthesis and degradation in the light to maintain PSII activity in what is termed the PSII repair cycle (4).Although the precise mechanism of PSII repair is unknown, recent work ha...