The polypeptide composition and spectral properties of three photosystem 11 (PSII) deficient mutants of the cyanobacterium Synechocystis 6803 have been determined. The levels of the 43 and 47 kilodalton chlorophyll-binding proteins and the reaction center component D2 are affected differently in each mutant; the 33 kD polypeptide of the oxygen-evolving complex is found at wild-type levels in all three. The 43 and 47 kilodalton proteins are implicated as important elements in the assembly and/or stability of the PSII reaction center, although the loss of one of these polypeptides does not lead to the loss of all PSII proteins. Low temperature fluorescence emission spectra of wild-type cells reveal chlorophyll-attributable peaks at 687 (PSII), 696 (PSII), and 725 (photosystem 1) nanometers. All three mutants retain the 725 nanometer fluorescence but lack the 696 nanometer peak. This suggests that the latter fluorescence arises from PSII reaction center chlorophyll or results from interactions among functional PSII components in vivo. Cells that contain the 43 kilodalton and lack the 47 kilodalton protein, retain the 687 fluorescence; furthermore, in as much as this fluorescence is absent from cells without the 43 kilodalton protein, the 687 nanometer peak is judged to emanate from the 43 kilodalton chlorophyll-protein. A new peak, probably previously obscured, is revealed at 691 nanometers in cells that retain the 47 kilodalton protein but lack the 43 kilodalton polypeptide, suggesting that emission near 691 nanometers can be attributed to the 47 kilodalton polypeptide. Membrane-bound phycobilisomes are retained in these cells as is coupled-energy transfer between phycocyanin and allophycocyanin. Energy transfer to photosystem I by way of phycocyanin excitation proceeds as in wild-type cells despite the absence of certain PSII components.Light energy absorbed by the accessory pigments associated with PSII is transferred to the PSII reaction center leading to charge separation and the release of molecular oxygen. These processes-light absorption, charge separation, and oxygen evolution-occur in three spatially distinct but functionally interdependent complexes. In cyanobacteria, light is gathered principally by phycobilisomes, well-studied supramolecular complexes composed of repeated units of several chromophore-conjugated phycobiliproteins and 'colorless' polypeptides (3,30 (15,20,26, and see below), however, little evidence has been obtained for the existence of counterparts to the chloroplast 16 and 23 kD proteins (26).Two major Chl-fluorescence emission maxima seen at 77 K have been associated with PSII preparations of chloroplasts (4,22). A peak at 685 nm (F685) has alternatively been identified with a fluorescence emission peak exhibited by the isolated 43 kD Chl-binding protein (17) and, more recently, it has been attributed to the back reaction of P680+ and pheophytin-(1, 24). A second maximum at 695 nm (F695) has been ascribed to the 47 kD Chl-containing protein (5,17,22,23,29), as well as to pheo...