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The Scientific World Journal
Volume 2013 (2013), Article ID 435651, 10 pages
Research Article

The Evolutionary Relationship between Microbial Rhodopsins and Metazoan Rhodopsins

State Key Laboratory of Genetic Engineering and Key Laboratory of Contemporary Anthropology of Ministry of Education, School of Life Sciences, Fudan University, Shanghai 200433, China

Received 15 November 2012; Accepted 16 December 2012

Academic Editors: L. Han, X. Li, Z. Su, and X. Xu

Copyright © 2013 Libing Shen et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


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.