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The cyanobacterium Synechocystis sp. PCC 6803 possesses two leader peptidases, LepB1 (Sll0716) and LepB2 (Slr1377), responsible for the processing of signal peptide-containing proteins. Deletion of the gene for LepB1 results in an inability to grow photoautotrophically and an extreme light sensitivity. Here we show, using a combination of Blue Native/SDS-PAGE, Western blotting and iTRAQ analysis, that lack of LepB1 strongly affects the cell's ability to accumulate wild-type levels of both photosystem I (PSI) and cytochrome (Cyt) b6f complexes. The impaired assembly of PSI and Cyt b6f is considered to be caused by the no or slow processing of the integral subunits PsaF and Cyt f respectively. In particular, PsaF, one of the PSI subunits, was found incorporated into PSI in its unprocessed form, which could influence the assembly and/or stability of PSI. In contrast to these results, we found the amount of assembled photosystem II (PSII) unchanged, despite a slower processing of PsbO. Thus, imbalance in the ratios of PSI and Cyt b6f to photosystem II leads to an imbalanced photosynthetic electron flow up- and down-stream of the plastoquinone pool, resulting in the observed light sensitivity of the mutant. We conclude that LepB1 is the natural leader peptidase for PsaF, PsbO, and Cyt f. The maturation of PsbO and Cyt f can be partially performed by LepB2, whereas PsaF processing is completely dependent on LepB1. iTRAQ analysis also revealed a number of indirect effects accompanying the mutation, primarily a strong induction of the CydAB oxidase as well as a significant decrease in phycobiliproteins and chlorophyll/heme biosynthesis enzymes. The cyanobacterium Synechocystis sp. PCC 6803 possesses two leader peptidases, LepB1 (Sll0716) and LepB2 (Slr1377), responsible for the processing of signal peptide-containing proteins. Deletion of the gene for LepB1 results in an inability to grow photoautotrophically and an extreme light sensitivity. Here we show, using a combination of Blue Native/SDS-PAGE, Western blotting and iTRAQ analysis, that lack of LepB1 strongly affects the cell's ability to accumulate wild-type levels of both photosystem I (PSI) and cytochrome (Cyt) b6f complexes. The impaired assembly of PSI and Cyt b6f is considered to be caused by the no or slow processing of the integral subunits PsaF and Cyt f respectively. In particular, PsaF, one of the PSI subunits, was found incorporated into PSI in its unprocessed form, which could influence the assembly and/or stability of PSI. In contrast to these results, we found the amount of assembled photosystem II (PSII) unchanged, despite a slower processing of PsbO. Thus, imbalance in the ratios of PSI and Cyt b6f to photosystem II leads to an imbalanced photosynthetic electron flow up- and down-stream of the plastoquinone pool, resulting in the observed light sensitivity of the mutant. We conclude that LepB1 is the natural leader peptidase for PsaF, PsbO, and Cyt f. The maturation of PsbO and Cyt f can be partially performed by LepB2, whereas PsaF processing is completely dependent on LepB1. iTRAQ analysis also revealed a number of indirect effects accompanying the mutation, primarily a strong induction of the CydAB oxidase as well as a significant decrease in phycobiliproteins and chlorophyll/heme biosynthesis enzymes. Cyanobacteria comprise a diverse group of photoautotrophic prokaryotes with an oxygen evolving photosynthetic apparatus very similar to that of higher plants. Similarly to plant chloroplasts, they contain three different types of membranes, an outer membrane, a plasma membrane (PM), and a thylakoid membrane (TM). The thylakoid membrane is the site not only for photosynthesis but also the main site for respiration. The ultrastructure and organization of the membranes is however still under debate and mainly two different opinions prevail concerning the organization of plasma and thylakoid membranes. One is that the two membranes are continuous, making the periplasm and lumen a common compartment, the second that the membranes are completely separated (1Nierzwicki-Bauer S.A. Balkwill D.L. Stevens Jr., S.E. Three-dimensional ultrastructure of a unicellular cyanobacterium.J. Cell Biol. 1983; 97: 713-722Crossref PubMed Scopus (64) Google Scholar, 2Gantt E. Supramolecular membrane organization.in: Bryant D.A. The molecular biology of cyanobacteria. Kluwer Dordrecht, 1994: 119-138Crossref Google Scholar, 3Liberton M. Howard Berg R. Heuser J. Roth R. Pakrasi H.B. Ultrastructure of the membrane systems in the unicellular cyanobacterium Synechocystis sp. strain PCC 6803.Protoplasma. 2006; 227: 129-138Crossref PubMed Scopus (98) Google Scholar, 4van de Meene A.M. Hohmann-Marriott M.F. Vermaas The of the cyanobacterium Synechocystis sp. PCC 2006; PubMed Scopus Google Scholar, R. E. R. membrane and in J. PubMed Scopus Google Scholar, E. of and of a and thylakoid Cell Biol. PubMed Scopus Google Scholar, J. J. for membrane organization and in the cyanobacterium Synechocystis sp. PCC 6803 and PubMed Scopus Google Scholar, J. M. J. E. of the thylakoid membrane PubMed Scopus Google Scholar, de Meene A.M. Vermaas in thylakoid membrane are with photosystem I in Synechocystis sp. PCC PubMed Scopus Google The membrane organization the cyanobacterium the of a for the and of to the different membranes and of these in and the and J. and into membranes in and PubMed Scopus Google for the and systems to be by signal in prokaryotes and PubMed Scopus Google thylakoid and plasma membrane integral not signal into the membrane and integral in to the a of the M. is for membrane of subunits a and of the and of the PubMed Scopus Google Scholar, membrane the in and PubMed Scopus Google Scholar, J. de of the of on the membrane of E. using Biol. PubMed Scopus Google as for the photosystem II (PSII) E. of is for thylakoid in the cyanobacterium Synechocystis sp. Biol. 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