title: Evolutionary analysis of phycobiliproteins: implications for their structural and functional relationships.
abstract: Phycobiliproteins, together with linker polypeptides and various chromophores, are basic building blocks of phycobilisomes, a supramolecular complex with a light-harvesting function in cyanobacteria and red algae. Previous studies suggest that the different types of phycobiliproteins and the linker polypeptides originated from the same ancestor. Here we retrieve the phycobilisome-related genes from the well-annotated and even unfinished cyanobacteria genomes and find that many sites with elevated d(N)/d(S) ratios in different phycobiliprotein lineages are located in the chromophore-binding domain and the helical hairpin domains (X and Y). Covariation analyses also reveal that these sites are significantly correlated, showing strong evidence of the functional-structural importance of interactions among these residues. The potential selective pressure driving the diversification of phycobiliproteins may be related to the phycobiliprotein-chromophore microenvironment formation and the subunits interaction. Sites and genes identified here would provide targets for further research on the structural-functional role of these residues and energy transfer through the chromophores.
authors.affiliation: Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
authors.forename: Fangqing
authors.initials: F
authors.lastname: Zhao
authors.forename: Song
authors.initials: S
authors.lastname: Qin
mesh_terms: D019943:Amino Acid Substitution; D000458:Cyanobacteria / Q000235:genetics; D019143:Evolution, Molecular; D008958:Models, Molecular; D052979:Phycobiliproteins / Q000737:chemistry* / Q000235:genetics*; D045524:Phycobilisomes / Q000737:chemistry; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D012641:Selection, Genetic
chemical_list: D052979:Phycobiliproteins; D045524:Phycobilisomes