This thesis focuses on the functional and structural characterization of FtsH proteases in Synechocystis PCC 6803. One of the aims was to determine localization and subunit organization of FtsH homologues in Synechocystis cells using GST and GFP tagged FtsH derivatives. The main result of the thesis is identification of two FtsH hetero-oligomeric complexes and one homo-oligomeric complex in Synechocystis cells. The large part of the thesis is aimed at establishing the role of the first hetero-oligomeric complex, FtsH2/FtsH3, in quality control of Photosystem II and at identification of a mechanism, how its substrate proteins D1 and D2 are recognized. Another part is dedicated to characterization of the second hetero-oligomeric complex, FtsH1/FtsH3, which consists of two essential FtsH homologues and which is here identified as an important regulatory element in maintaining iron homeostasis.