Evolution of the phycobiliproteins.

Amino acid sequence alignments and phylogenetic analyses have been used to examine the relationships among 100 phycobiliprotein sequences. The alignments revealed a number of highly conserved amino acid residues that are involved in chromophore attachment and conformation, alpha-beta interactions and phycobilisome assembly. The phylogenetic analysis confirmed that the phycobiliprotein subfamilies, previously classified by their biochemical and spectroscopic properties, also formed coherent evolutionary groups. The alpha and beta subunits formed two distinct evolutionary lines that originate from a common ancestor. The pattern of divergence among the alpha subfamilies was identical to that of the beta subfamilies, strongly suggesting that the alpha and beta subunits of each phycobiliprotein type have coevolved. The phylogenetic data support a monophyletic separation of the eukaryotic sequences from the extant cyanobacterial sequences. The eukaryotic phycoerythrins appeared more closely related to the marine Synechococcus phycoerythrins than to the other cyanobacterial phycoerythrins. The cryptophyte phycobiliproteins formed a monophyletic group within the rhodophyte lineage. In conjunction with other phylogenetic markers, the analysis of additional phycobiliprotein sequences may help to further resolve the relationships among phycobiliprotein-containing organisms.