The phycobiliproteins of the unicellular cyanobacterium Synechocystis sp. strain BO 8402 and its derivative strain BO 9201 are compared. The biliproteins of strain BO 8402 are organized in paracrystalline inclusion bodies showing an intense autofluorescence in vivo. These protein-pigment aggregates have been isolated. The highly purified complexes contain phycocyanin with traces of phycoerythrin, corresponding linker polypeptides LR3PC and LR3PE (the latter in a small amount), and a unique colored polypeptide with an Mr of 55,000, designated L55. Allophycocyanin and the core linker polypeptides are absent. The substructure of the aggregates has been studied by electron microscopy. Physiological and genetic implications of the unusual pigment compositions of both strains are discussed.Phycobiliproteins are the major light-harvesting antennae of cyanobacteria and members of the families Rhodophyceae and Cryptophyceae (36,41). In cyanobacteria and members of the Rhodophyceae, they are assembled in phycobilisomeshigh-molecular-weight protein-pigment complexes with Mrs ranging from 5,000,000 to 20,000,000 (20). Phycobilisomes are connected with dimeric or tetrameric photosystem II complexes and localized along with rows of photosystem II particles at the protoplasmic surface of the thylakoid membranes (16,24). They have been characterized in numerous electronmicroscopical (28), spectroscopical (23), biochemical (19-22), genetic (8), and physiological (22, 39, 40) studies. Phycobilisomes consist of a core from which radiate 6 to 10 rods in a specific assembly classified as bundle shaped, hemidiscoidal, or hemiellipsoidal (21,42,44). The rods comprise either only phycocyanin or, in addition, phycoerythrin and, in some cases, phycoerythrocyanin (7), in ratios determined by genetic and environmental parameters (40). The biliproteins are joined by different linker polypeptides LRX that facilitate the sequential assembly and determine the different spectral properties of the subcomplexes (21). The substructure of the rods was postulated to be exclusively hexameric ((X)6 -LRX (19), but recent results indicate a partial assembly of trimeric biliprotein complexes forming hexameric stacks (32). The core is built up by a bi-or tricylindrical central pigment-linker complex, APCM, comprising allophycocyanin and two copies of the anchor polypeptide LCM. It serves as backbone of the phycobilisome and as a structural bridge to photosystem 11 (10,34,35 (33,34). However, the peripheral trimeric allophycocyanin complexes seem not essential for phycobilisome assembly (25,32). Energy is transferred from the outer chromophores of the rods to the terminal acceptors of the allophycocyanin core, allophycocyanin B and LCM (21). Further energy transmission to photosystem II is influenced by environmental factors (30, 40) and state transition processes (4).Synechocystis sp. strain BO 8402 was isolated from the prealpine Lake Constance (12). The strain is characterized by an intense red autofluorescence originating from a localized area within...