Phycobilisome is the major light-harvesting complex in cyanobacteria and red alga. It consists of phycobiliproteins and their associated linker peptides which play key role in absorption and unidirectional transfer of light energy and the stability of the whole complex system, respectively. Former researches on the evolution among PBPs and linker peptides had mainly focused on the phylogenetic analysis and selective evolution. Coevolution is the change that the conformation of one residue is interrupted by mutation and a compensatory change selected for in its interacting partner. Here, coevolutionary analysis of allophycocyanin, phycocyanin, and phycoerythrin and covariation analysis of linker peptides were performed. Coevolution analyses reveal that these sites are significantly correlated, showing strong evidence of the functional and structural importance of interactions among these residues. According to interprotein coevolution analysis, less interaction was found between PBPs and linker peptides. Our results also revealed the correlations between the coevolution and adaptive selection in PBS were not directly related, but probably demonstrated by the sites coupled under physical-chemical interactions. 1. Introduction The process of photosynthesis is initiated by the absorption of light. In cyanobacteria and red algae, the main accessory light-harvesting complexes are comprised of the phycobilisomes (PBSs), which are attached to the cytoplasmic surface of the thylakoid membrane except Gloeobacter violaceus PCC7421 having no thylakoid membrane [1–6]. PBSs are composed of rods and a core and biochemically consist of phycobiliproteins (PBPs) and linker polypeptides, which are particularly superior subjects for the detailed analysis of structure and function due to their various components affected by growth conditions [2]. In view of the spectral properties as well as pigment compositions, allophycocyanin (APC), phycocyanin (PC), and phycoerythrin (PE) are the principal classes of PBPs in cyanobacteria. They consist of two different subunits, α and β, which exhibit high affinity for one another and associate into (α/β)-monomers to be organized as (α/β)3-trimers and (α/β)6-hexamers [7]. Different PBPs contain different kinds and different numbers of chromophores, covalently attached to the apoprotein by thioether bonds to cysteine residues. PC has three phycocyanobilin chromophores attached to the monomer through thioester linkages at the α84, β84, and β155 positions [8, 9]. In addition, unlike PBPs, most of the linker polypeptides do not bear
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