Halobacterial rhodopsins

Following the discovery of the bacteriorhodopsin proton pump in Halobacteri um halobium (salinarum), not only the halorhodopsin halide pump and two pho tosensor rhodopsins (sensory rhodopsin and phoborhodopsin) in the same spec ies, but also homologs of these four rhodopsins in strains of other genera of Halobacteriaceae have been reported. Twenty-eight full (and partial) seq uences of the genomic DNA of these rhodopsins have been analyzed. The deduc ed amino acid sequences have led to new strategies and tactics for understa nding bacterial rhodopsins on a comparative basis, as summarized briefly in this article. The data discussed include (i) alignment of the sequences to qualify/characterize the conserved residues; (ii) assignment of residues t hat cause differences in function(s)/properties; and (iii) phylogeny of the halobacterial rhodopsins to suggest their evolutionary paths. The four kin ds of rhodopsin in each strain are assumed, on the basis of their genera-sp ecific distributions, to have arisen by at least two gene-duplication proce sses during evolution prior to generic speciation, The first duplication of the rhodopsin ancestor gene yielded two genes, each of which was duplicate d again to give four genes in the ancestor halobacterium. The bacterium car rying four rhodopsin genes, after accumulating mutations, became ready for generic speciation and the delivery of four rhodopsins to each species. The original rhodopsin ancestor is speculated to be closest to the proton pump (bacteriorhodopsin).