title: The evolutionary relationship between microbial rhodopsins and metazoan rhodopsins.
abstract: Rhodopsins are photoreceptive proteins with seven-transmembrane alpha-helices and a covalently bound retinal. Based on their protein sequences, rhodopsins can be classified into microbial rhodopsins and metazoan rhodopsins. Because there is no clearly detectable sequence identity between these two groups, their evolutionary relationship was difficult to decide. Through ancestral state inference, we found that microbial rhodopsins and metazoan rhodopsins are divergently related in their seven-transmembrane domains. Our result proposes that they are homologous proteins and metazoan rhodopsins originated from microbial rhodopsins. Structure alignment shows that microbial rhodopsins and metazoan rhodopsins share a remarkable structural homology while the position of retinal-binding lysine is different between them. It suggests that the function of photoreception was once lost during the evolution of rhodopsin genes. This result explains why there is no clearly detectable sequence similarity between the two rhodopsin groups: after losing the photoreception function, rhodopsin gene was freed from the functional constraint and the process of divergence could quickly change its original sequence beyond recognition.
authors.affiliation: State Key Laboratory of Genetic Engineering, Ministry of Education, School of Life Sciences, Fudan University, Shanghai 200433, China.
authors.forename: Libing
authors.initials: L
authors.lastname: Shen
authors.forename: Chao
authors.initials: C
authors.lastname: Chen
authors.forename: Hongxiang
authors.initials: H
authors.lastname: Zheng
authors.forename: Li
authors.initials: L
authors.lastname: Jin
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000378:metabolism*; D030541:Databases, Genetic; D019143:Evolution, Molecular; D014644:Genetic Variation; D006801:Humans; D008239:Lysine / Q000235:genetics / Q000378:metabolism; D008969:Molecular Sequence Data; D009154:Mutation; D010802:Phylogeny; D011485:Protein Binding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012243:Rhodopsin / Q000145:classification / Q000235:genetics / Q000378:metabolism*; D025604:Rhodopsins, Microbial / Q000145:classification / Q000235:genetics / Q000378:metabolism*; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid
chemical_list: D025604:Rhodopsins, Microbial; D012243:Rhodopsin; D008239:Lysine