Eukaryotic and eubacterial contributions to the establishment of plastid proteome estimated by large-scale phylogenetic analyses.

Plastids including chloroplasts arose from a cyanobacterial endosymbiont and have retained their own genome, but the size has been reduced to less than one-tenth of the original bacterial genome. Over time, genes essential to plastid function have been transferred from the ancestral plastid genome to the nucleus, and the gene products are now targeted into the plastid from the host cytosol. However, phylogenetic analyses have suggested that the functions of certain original proteins encoded by the endosymbiont genome have been replaced by nucleus-encoded proteins of noncyanobacterial origin and that several proteins have been newly added to maintain and control plastids. In order to evaluate the rate and origin of noncyanobacterial proteins that have contributed to the establishment of the plastid proteome, we performed phylogenetic analyses of plastid-targeted proteins that are shared by the red alga Cyanidioschyzon merolae (455 proteins) and the Viridiplanta Arabidopsis thaliana (744 proteins). Our results show that approximately 40% of the plastid proteome common to red algae and green plants originated from genes of both the ancestral eukaryotic host and various lineages of bacteria (eubacteria) other than cyanobacteria. The replacement or addition of components was frequently observed for most of the plastid functions except for the light reaction of photosynthesis and the translation and degradation of proteins in the plastid. These results suggest that a considerable amount of bacterial metagenomic material, as well as the genomes of the host and the endosymbiont, has contributed to the establishment of the plastid before the split of the red and green algae.