Rhodopsin Molecular Evolution in Mammals Inhabiting Low Light Environments

Zhao, Huabin; Ru, Binghua; Teeling, Emma C.; Faulkes, Christopher G.; Zhang, Shuyi; Rossiter, Stephen J.

Yet even without spectral shifts, our sliding window analyses indicate that most amino acid replacements in the mammal rhodopsin gene are concentrated in several key domains, pointing to functional significance. Extracellular domain I comprises just six amino acids and includes the replacement V104I that is seen in the leopard seal, Weddell seal, the high-duty-cycle bats, western longfingered bat, Sowerby's beaked whale and Cape dune mole rat. However, it is unlikely that this site confers any spectral shift [17] . The transmembrane helix VII spans 21 amino acids and has accumulated numerous non-synonymous substitutions including I286T that was only recorded in the leopard and Weddell seal, S297A only in the harp, harbor and ringed seal, and S297G in the bearded seal. Other replacements (A292S, S298A and S299A) were shared across phylogentically distant several taxa. Of these, A292S is a critical site replacement, S298A and S299A are unlikely to cause spectral-tuning, while the spectral properties of replacements at positions 286 and 297 are not clear [17] . Indeed, transmembrane and extracellular domains often interact with ligands [50] and, in G-protein-coupled receptors in general, appear to bind small molecules [51, 52] and larger ligands [50, [53] [54] . However, no such interactions between ligands and extracellular domains have been documented in rhodopsin specifically. Consequently, unless these replacements have some unknown adaptive significance for rhodopsin function, such as in phototransduction, then it is not possible to dismiss some degree of neutral variation.