Phylogenomic and structural modeling analyses of the PsbP superfamily reveal multiple small segment additions in the evolution of photosystem II-associated PsbP protein in green plants

PsbP is a thylakoid lumen protein involved in oxygen evolution in photosystem II (PSII) in green plants. Genomic analysis identified a number of PsbP homologs in plants, algae, and cyanobacteria. To analyze the transition of cyanobacterial PsbO/U/V complex to PsbO/P/Q complex in green plants, the evolutionary history of the PsbP superfamily was reconstructed. Phylogenetic analyses suggested that PsbP homologs be classified into eight major families (A–H), which were also characterized by specific insertion/deletion of short segments, as found by sequence alignment and homology modeling. Family A represented authentic PsbP proteins involved in oxygen evolution. The cyanobacterial PsbP and plant/algal PPL (Family H), having the simplest structure, should be considered as the root of all other families of PsbP, which subsequently gained various short, family-specific structural motifs during diversification of PsbP families. Interestingly, segments specific to Family A proteins were found arranged as a ring surrounding the modeled Arabidopsis PsbP protein. These results suggest that Family A-specific additions of short segments played a decisive role in the transition of PsbO/U/V to PsbO/P/Q complex in green plants.