Bacteriorhodopsins (BRs) are known as an alternative system of the photosynthesis to produce energy from sunlight in prokaryotes. A lot of BR sequences have been reported so far, however, information regarding their evolutionary history is still less. To analyze their evolution in details, we performed the comprehensive survey of BR genes using about 39,000 prokaryotes complete genomes registered in RefSeq database, and surprisingly, found only about 220 species possessing BR genes in their genomes. BRs are only found in Halobacteria species in archaea. Most of Halobacteria species have two or three BRs in their genomes. On the other hand, BRs were detected in a wide range of species in eu-bacteria while they have only one copy of BR gene in their genomes in general.
Phylogenetic analysis of BRs showed seven large clusters in the resultant tree. Four of them were composed of archaeal BRs while the remaining three composed of eu-bacterial BRs (E1-E3). Each eu-bacterial cluster contains branchings between largely different taxonomic groups. These results suggest that BRs have moved from archaea to eubacteria and then prevail into a wide range of eu-bacteria by lots of horizontal gene transfer [HGT] events. Next we investigated distributions of BRs using metagenomes from various environments. BRs were found in shallow aquatic environments in general. Archaeal BRs were only detected in high salinity and shallow water environments. Although eu-bacterial E1 and E2 BRs were found in most of shallow aquatic environments, E2 BRs were well detected in fresh water environments. E3 BRs were not found from any metagenomes tested, however, the BRs were found in genomes of strains isolated from plant bodies or rhizosphere. These results suggest that BRs might be related to environmental adaptation in prokaryotes.