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The Scientific World Journal
Volume 2013 (2013), Article ID 435651, 10 pages
http://dx.doi.org/10.1155/2013/435651
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.

Linked References

  1. K. Nakanishi, “11-cis-retinal, a molecule uniquely suited for vision,” Pure and Applied Chemistry, vol. 63, pp. 161–170, 1991. View at Publisher · View at Google Scholar
  2. J. L. Spudich, C. S. Yang, K. H. Jung, and E. N. Spudich, “Retinylidene proteins: structures and functions from archaea to humans,” Annual Review of Cell and Developmental Biology, vol. 16, pp. 365–392, 2000. View at Publisher · View at Google Scholar · View at Scopus
  3. B. Schobert and J. K. Lanyi, “Halorhodopsin is a light-driven chloride pump,” Journal of Biological Chemistry, vol. 257, no. 17, pp. 10306–10313, 1982. View at Google Scholar · View at Scopus
  4. O. Beja, L. Aravind, E. V. Koonin et al., “Bacterial rhodopsin: evidence for a new type of phototrophy in the sea,” Science, vol. 289, no. 5486, pp. 1902–1906, 2000. View at Publisher · View at Google Scholar · View at Scopus
  5. O. A. Sineshchekov, K. H. Jung, and J. L. Spudich, “Two rhodopsins mediate phototaxis to low- and high-intensity light in Chlamydomonas reinhardtii,” Proceedings of the National Academy of Sciences of the United States of America, vol. 99, no. 13, pp. 8689–8694, 2002. View at Publisher · View at Google Scholar · View at Scopus
  6. K. H. Jung, V. D. Trivedi, and J. L. Spudich, “Demonstration of a sensory rhodopsin in eubacteria,” Molecular Microbiology, vol. 47, no. 6, pp. 1513–1522, 2003. View at Publisher · View at Google Scholar · View at Scopus
  7. A. Terakita, “The opsins,” Genome Biology, vol. 6, no. 3, article 213, 2005. View at Publisher · View at Google Scholar · View at Scopus
  8. S. A. Waschuk, A. G. Bezerra, L. Shi, and L. S. Brown, “Leptosphaeria rhodopsin: bacteriorhodopsin-like proton pump from a eukaryote,” Proceedings of the National Academy of Sciences of the United States of America, vol. 102, no. 19, pp. 6879–6883, 2005. View at Publisher · View at Google Scholar · View at Scopus
  9. D. Arendt, K. Tessmar-Raible, H. Snyman, A. W. Dorresteijn, and J. Wittbrodf, “Ciliary photoreceptors with a vertebrate-type opsin in an invertebrate brain,” Science, vol. 306, no. 5697, pp. 869–871, 2004. View at Publisher · View at Google Scholar · View at Scopus
  10. M. Koyanagi, K. Kubokawa, H. Tsukamoto, Y. Shichida, and A. Terakita, “Cephalochordate melanopsin: evolutionary linkage between invertebrate visual cells and vertebrate photosensitive retinal ganglion cells,” Current Biology, vol. 15, no. 11, pp. 1065–1069, 2005. View at Publisher · View at Google Scholar · View at Scopus
  11. M. Koyanagi and A. Terakita, “Gq-coupled rhodopsin subfamily composed of invertebrate visual pigment and melanopsin,” Photochemistry and Photobiology, vol. 84, no. 4, pp. 1024–1030, 2008. View at Publisher · View at Google Scholar · View at Scopus
  12. I. Provencio, G. Jiang, W. J. De Grip, W. Pär Hayes, and M. D. Rollag, “Melanopsin: an opsin in melanophores, brain, and eye,” Proceedings of the National Academy of Sciences of the United States of America, vol. 95, no. 1, pp. 340–345, 1998. View at Publisher · View at Google Scholar · View at Scopus
  13. E. E. Tarttelin, J. Bellingham, M. W. Hankins, R. G. Foster, and R. J. Lucas, “Neuropsin (Opn5): a novel opsin identified in mammalian neural tissue,” FEBS Letters, vol. 554, no. 3, pp. 410–416, 2003. View at Publisher · View at Google Scholar · View at Scopus
  14. S. Blackshaw and S. H. Snyder, “Encephalopsin: a novel mammalian extraretinal opsin discretely localized in the brain,” Journal of Neuroscience, vol. 19, no. 10, pp. 3681–3690, 1999. View at Google Scholar · View at Scopus
  15. M. Jiang, S. Pandey, and H. K. W. Fong, “An opsin homologue in the retina and pigment epithelium,” Investigative Ophthalmology and Visual Science, vol. 34, no. 13, pp. 3669–3678, 1993. View at Google Scholar · View at Scopus
  16. D. Shen, M. Jiang, W. Hao, L. Tao, M. Salazar, and H. K. W. Fong, “A human opsin-related gene that encodes a retinaldehyde-binding protein,” Biochemistry, vol. 33, no. 44, pp. 13117–13125, 1994. View at Google Scholar · View at Scopus
  17. H. Sun, D. J. Gilbert, N. G. Copeland, N. A. Jenkins, and J. Nathans, “Peropsin, a novel visual pigment-like protein located in the apical microvilli of the retinal pigment epithelium,” Proceedings of the National Academy of Sciences of the United States of America, vol. 94, no. 18, pp. 9893–9898, 1997. View at Publisher · View at Google Scholar · View at Scopus
  18. M. Max, P. J. McKinnon, K. J. Seidenman et al., “Pineal opsin: a nonvisual opsin expressed in chick pineal,” Science, vol. 267, no. 5203, pp. 1502–1506, 1995. View at Google Scholar · View at Scopus
  19. S. Blackshaw and S. H. Snyder, “Parapinopsin, a novel catfish opsin localized to the parapineal organ, defines a new gene family,” Journal of Neuroscience, vol. 17, no. 21, pp. 8083–8092, 1997. View at Google Scholar · View at Scopus
  20. A. R. Philp, J. M. Garcia-Fernandez, B. G. Soni, R. J. Lucas, J. Bellingham, and R. G. Foster, “Vertebrate ancient (VA) opsin and extraretinal photoreception in the Atlantic salmon (Salmo salar),” Journal of Experimental Biology, vol. 203, no. 12, pp. 1925–1936, 2000. View at Google Scholar · View at Scopus
  21. P. Moutsaki, D. Whitmore, J. Bellingham, K. Sakamoto, Z. K. David-Gray, and R. G. Foster, “Teleost multiple tissue (tmt) opsin: a candidate photopigment regulating the peripheral clocks of zebrafish?” Molecular Brain Research, vol. 112, no. 1-2, pp. 135–145, 2003. View at Publisher · View at Google Scholar · View at Scopus
  22. W. R. Pearson, “Protein sequence comparison and Protein evolution,” Tutorial, ISMB2000, 2001.
  23. M. O. Dayhoff, R. M. Schwartz, and B. C. Orcutt, “A model of evolutionary change in proteins,” Atlas of Protein Sequence and Structure, vol. 5, no. 3, pp. 345–352, 1978. View at Google Scholar
  24. W. M. Fitch, “Distinguishing homologous from analogous proteins,” Systematic zoology, vol. 19, no. 2, pp. 99–113, 1970. View at Google Scholar · View at Scopus
  25. D. Lawson, P. Arensburger, P. Atkinson et al., “VectorBase: a data resource for invertebrate vector genomics,” Nucleic Acids Research, vol. 37, no. 1, pp. D583–D587, 2009. View at Publisher · View at Google Scholar · View at Scopus
  26. S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, “Basic local alignment search tool,” Journal of Molecular Biology, vol. 215, no. 3, pp. 403–410, 1990. View at Publisher · View at Google Scholar · View at Scopus
  27. W. R. Pearson and D. J. Lipman, “Improved tools for biological sequence comparison,” Proceedings of the National Academy of Sciences of the United States of America, vol. 85, no. 8, pp. 2444–2448, 1988. View at Google Scholar · View at Scopus
  28. R. C. Edgar, “MUSCLE: multiple sequence alignment with high accuracy and high throughput,” Nucleic Acids Research, vol. 32, no. 5, pp. 1792–1797, 2004. View at Publisher · View at Google Scholar · View at Scopus
  29. C. Guda, S. Lu, E. D. Scheeff, P. E. Bourne, and I. N. Shindyalov, “CE-MC: a multiple protein structure alignment server,” Nucleic Acids Research, vol. 32, pp. W100–W103, 2004. View at Publisher · View at Google Scholar · View at Scopus
  30. F. Abascal, R. Zardoya, and D. Posada, “ProtTest: selection of best-fit models of protein evolution,” Bioinformatics, vol. 21, no. 9, pp. 2104–2105, 2005. View at Publisher · View at Google Scholar · View at Scopus
  31. K. Tamura, D. Peterson, N. Peterson, G. Stecher, M. Nei, and S. Kumar, “MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods,” Molecular Biology and Evolution, vol. 28, no. 10, pp. 2731–2739, 2011. View at Publisher · View at Google Scholar
  32. S. Guindon, J. F. Dufayard, V. Lefort, M. Anisimova, W. Hordijk, and O. Gascuel, “New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0,” Systematic Biology, vol. 59, no. 3, pp. 307–321, 2010. View at Publisher · View at Google Scholar · View at Scopus
  33. M. Anisimova and O. Gascuel, “Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative,” Systematic Biology, vol. 55, no. 4, pp. 539–552, 2006. View at Publisher · View at Google Scholar · View at Scopus
  34. J. P. Huelsenbeck and F. Ronquist, “MRBAYES: bayesian inference of phylogenetic trees,” Bioinformatics, vol. 17, no. 8, pp. 754–755, 2001. View at Google Scholar · View at Scopus
  35. J. Felsenstein, “Phylogeny Inference Package (PHYLIP),” Version 3.5., University of Washington, Seattle, Wash, USA, 1993.
  36. R. F. Doolittle, “Convergent evolution: the need to be explicit,” Trends in Biochemical Sciences, vol. 19, no. 1, pp. 15–18, 1994. View at Publisher · View at Google Scholar · View at Scopus
  37. H. Luecke, B. Schobert, H. T. Richter, J. P. Cartailler, and J. K. Lanyi, “Structure of bacteriorhodopsin at 1.55 A resolution,” Journal of Molecular Biology, vol. 291, no. 4, pp. 899–911, 1999. View at Publisher · View at Google Scholar · View at Scopus
  38. K. Edman, A. Royant, P. Nollert et al., “Early structural rearrangements in the photocycle of an integral membrane sensory receptor,” Structure, vol. 10, no. 4, pp. 473–482, 2002. View at Publisher · View at Google Scholar · View at Scopus
  39. T. Okada, M. Sugihara, A. N. Bondar, M. Elstner, P. Entel, and V. Buss, “The retinal conformation and its environment in rhodopsin in light of a new 2.2 A crystal structure,” Journal of Molecular Biology, vol. 342, no. 2, pp. 571–583, 2004. View at Publisher · View at Google Scholar · View at Scopus
  40. L. Vogeley, O. A. Sineshchekov, V. D. Trivedi, J. Sasaki, J. L. Spudich, and H. Luecke, “Anabaena sensory rhodopsin: a photochromic color sensor at 2.0 A,” Science, vol. 306, no. 5700, pp. 1390–1393, 2004. View at Publisher · View at Google Scholar · View at Scopus
  41. M. Murakami and T. Kouyama, “Crystal structure of squid rhodopsin,” Nature, vol. 453, no. 7193, pp. 363–367, 2008. View at Publisher · View at Google Scholar · View at Scopus
  42. M. Nei, X. Gu, and T. Sitnikova, “Evolution by the birth-and-death process in multigene families of the vertebrate immune system,” Proceedings of the National Academy of Sciences of the United States of America, vol. 94, pp. 7799–7806, 1997. View at Publisher · View at Google Scholar
  43. A. H. Knoll and S. B. Carroll, “Early animal evolution: emerging views from comparative biology and geology,” Science, vol. 284, no. 5423, pp. 2129–2137, 1999. View at Publisher · View at Google Scholar · View at Scopus
  44. X. Gu, “Early metazoan divergence was about 830 million years ago,” Journal of Molecular Evolution, vol. 47, no. 3, pp. 369–371, 1998. View at Publisher · View at Google Scholar · View at Scopus
  45. T. Marti, S. J. Rosselet, H. Otto, M. P. Heyn, and H. G. Khorana, “The retinylidene Schiff base counterion in bacteriorhodopsin,” Journal of Biological Chemistry, vol. 266, no. 28, pp. 18674–18683, 1991. View at Google Scholar · View at Scopus
  46. H. Luecke, B. Schobert, J. Stagno et al., “Crystallographic structure of xanthorhodopsin, the light-driven proton pump with a dual chromophore,” Proceedings of the National Academy of Sciences of the United States of America, vol. 105, no. 43, pp. 16561–16565, 2008. View at Publisher · View at Google Scholar · View at Scopus
  47. L. Bofkin and N. Goldman, “Variation in evolutionary processes at different codon positions,” Molecular Biology and Evolution, vol. 24, no. 2, pp. 513–521, 2007. View at Publisher · View at Google Scholar · View at Scopus
  48. V. Katritch, V. Cherezov, and R. C. Stevens, “Diversity and modularity of G protein-coupled receptor structures,” Trends in Pharmacological Sciences, vol. 33, no. 1, pp. 17–27, 2012. View at Publisher · View at Google Scholar
  49. K. J. Nordström, M. Sällman Almén, M. M. Edstam, R. Fredriksson, and H. B. Schiöth, “Independent HHsearch, Needleman—Wunsch-based, and motif analyses reveal the overall hierarchy for most of the G protein-coupled receptor families,” Molecular Biology and Evolution, vol. 28, no. 9, pp. 2471–2480, 2011. View at Publisher · View at Google Scholar