Evolution of the archaeal rhodopsins: Evolution rate changes by gene duplication and functional differentiation

The amino acid sequences of 25 archaeal retinal proteins from 13 different strains of extreme halophiles were analyzed to establish their molecular ph ylogenetic relationship. On the basis of amino acid sequence similarity, th ese proteins apparently formed a distinct family designated as the archaeal rhodopsin family (ARF), which was not related to other known proteins, inc luding G protein-coupled receptors. The archaeal rhodopsin family was furth er divided into four clusters with different functions; H+ pump (bacteriorh odopsin), Cl- pump (halorhodopsin), and two kinds of sensor (sensory rhodop sin and phoborhodopsin). These four rhodopsin clusters seemed to have occur red by gene duplication(s) before the generic speciation of halophilic arch aea, based on phylogenetic analysis. Therefore, the degrees of differences in amino acid sequences within each cluster simply reflected the divergent evolution of halophilic archaea. By comparing the branch lengths after spec iation points of the reconstituted tree, we calculated the relative evoluti on rates of the four archaeal rhodopsins barteriorhodopsin:halorhodopsin:se nsory rhodopsin: phoborhodopsin to be 5:4:3:10. From these values, the degr ees of functional and structural restriction of each protein can be inferre d. The branching topology of four clusters grouped bacteriorhodopsin and ha lorhodopsin versus sensory rhodopsin and phoborhodopsin by likelihood mappi ng. Using bacteriorhodopsin (and halorhodopsin) as an outgroup, the gene du plication point of sensory rhodopsin/phoborhodopsin was determined. By calc ulating the branch lengths between the gene duplication point and each halo philic archaea speciation point, we could speculate upon the relative evolu tion rate of pre-sensory rhodopsin and pre-phoborhodopsin. The evolution ra te of pre-sensory rhodopsin was fivefold faster than that of pre-phoborhodo psin, which suggests that the original function of the ancestral sensor was similar to that of phoborhodopsin, and that sensory rhodopsin evolved from pre-sensory rhodopsin by the accumulation of mutations. The changes in evo lution rate by gene duplication and functional differentiation were demonst rated in the archaeal rhodopsin family using the gene duplication date and halobacterial speciation date as common time stamps. (C) 1999 Academic Pres s.