Evolution of the archaeal rhodopsins: Evolution rate changes by gene duplication and functional differentiation

Journal of Molecular Biology

Volumn 285, Issue 1, 1999, Pages 163-174

  Ihara, Kunio ^a   Umemura, Tohru ^a   Katagiri, Izumi ^a   Kitajima Ihara, Tomomi ^a   Sugiyama, Yasuo ^a   Kimura, Yoshiaki ^b   Mukohata, Yasuo ^a  

^a NAGOYA UNIVERSITY   (Japan)

^b BIOMOL ENG RESEARCH INSTITUTE   (Japan)

Author keywords

Bacteriorhodopsin; Gene duplication; Halobacteria; Halorhodopsin; Phylogenetic tree; Sensory rhodopsin

Indexed keywords

BACTERIORHODOPSIN; HALORHODOPSIN; RHODOPSIN;

AMINO ACID SEQUENCE; ARCHAEBACTERIUM; ARTICLE; DIFFERENTIATION; EVOLUTION; GENE DUPLICATION; HALOBACTERIUM; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; STRUCTURE ACTIVITY RELATION;

ARCHAEA; HALOBACTERIA; HALOBACTERIUM; HALOPHILIC ARCHAEON;

EID: 0033534585     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2286     Document Type: Article

References (60)

1. Bamberg E., Tittor J., Oesterhelt D. Light-driven proton or chloride pumping by halorhodopsin. Proc. Natl Acad. Sci. USA. 90:1993;639-643.
2. Blanck A., Oesterhelt D. The haloopsin gene II. Sequence primary structure of halorhodopsin and comparison with bacteriorhodopsin. EMBO J. 6:1987;265-273.
3. Blanck A., Oesterhelt D., Ferrando E., Schegk E. S., Lottspeich F. Primary structure of sensory rhodopsin I, a prokaryotic photoreceptor. EMBO J. 8:1989;3963-3971.
4. Blaurock A. E., Stoeckenius W. Structure of the purple membrane. Nature. 233:1971;152-155.
5. Bogomolni R. A., Spudich J. L. Identification of third rhodopsin-like pigment in phototactic Halobacterium halobium. Proc. Natl Acad. Sci. USA. 79:1982;6250-6254.
6. Bogomolni R. A., Stoeckenius W., Szundi I., Perozo E., Olson K. D., Spudich J. L. Removal of transducer HtrI allows electrogenic proton translocation by sensory rhodopsin I. Proc. Natl Acad. Sci. USA. 91:1994;10188-10192.
7. Danon A., Stoeckenius W. Photophosphorylation in Halobacteriumhalobium. Proc. Natl Acad. Sci. USA. 71:1974;1234-1238.
8. Der A., Szaraz S., Toth B. R., Tokaji Z., Keszthelyi L., Stoeckenius W. Alternative translocation of protons and halide ions by bacteriorhodopsin. Proc. Natl Acad. Sci. USA. 88:1991;4751-4755.
9. Doolittle R. F., Feng D. F., Tsang S., Cho G., Little E. Determining divergence times of the major kingdoms of living organisms with a protein clock. Science. 271:1996;470-477.
10. Dunn R., McCoy J., Simsek M., Majumdar A., Chang S. H., Rajbhandary U. L., Khorana H. G. The bacterio-rhodopsin gene. Proc. Natl Acad. Sci. USA. 78:1981;6744-6748.
11. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:1981;368-376.
12. Felsenstein J. PHYLIP-phylogeny Inference Package. 1993;Department of Genetics, University of Washington, Seattle.
13. Ferrando-May E., Krah M., Marwan W., Oesterhelt D. The methyl-accepting transducer protein HtrI is functionally associated with the photoreceptor sensory rhodopsin I in the archaeon Halobacteriumsalinarium. EMBO J. 12:1993;2999-3005.
14. Greenhalgh D. A., Farrens D. L., Subramaniam S., Khorana H. G. Hydrophobic amino acids in the retinal-binding pocket of bacteriorhodopsin. J. Biol. Chem. 268:1993;20305-20311.
15. Grigorieff N., Ceska T. A., Downing K. H., Baldwin J. M., Henderson R. Electron-crystallographic refinement of the structure of bacteriorhodopsin. J. Mol. Biol. 259:1996;393-421.
16. Henderson R., Baldwin J. M., Ceska T. A., Zemlin F., Beckmann E., Downing K. H. Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy. J. Mol. Biol. 213:1990;899-929.
17. Hoff W. D., Jung K. H., Spudich J. L. Molecular mechanism of photosignaling by archaeal sensory rhodopsins. Annu. Rev. Biophys. Biomol. Struct. 26:1997;223-258.
18. Jukes T. H., Cantor C. R. Evolution of protein molecules. Munro H. N. Mammalian Protein Metabolism. 1969;21-132 Academic Press, New York.
19. Kamekura M., Dyall S. M., Upasani V., Ventosa A., Kates M. Diversity of alkaliphilic halobacteria: proposals for transfer of Natronobacterium vacuolatum,Natronobacterium magadii , and Natronobacterium pharaonis to Halorubrum, Natrialba, andNatronomonas gen. nov., respectively, as Halorubrum vacuolatum comb. nov., Natrialba magadii comb. nov., and Natronomonas pharaonis comb. nov., respectively. Int. J. System. Bacteriol. 47:1997;853-857.
20. Kimura M. The Neutral Theory of Molecular Evolution. 1983;Cambridge University Press, Cambridge.
21. Kimura Y., Vassylyev D. G., Miyazawa A., Kidera A., Matsushima M., Mitsuoka K., Murata K., Hirai T., Fujiyoshi Y. Surface of bacteriorhodopsin revealed by high-resolution electron crystallography. Nature. 389:1997;206-211.
22. Kitajima T., Hirayama J., Ihara K., Sugiyama Y., Kamo N., Mukohata Y. Novel bacterial rhodopsins from Haloarcula vallismortis. Biochem. Biophys. Res. Commun. 220:1996;341-345.
23. Kuan G., Saier M. J. Phylogenetic relationships among bacteriorhodopsins. Res. Microbiol. 145:1994;273-285.
24. Kyte J., Doolittle R. F. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157:1982;105-132.
25. Lanyi J. K. Halorhodopsin: a light-driven electrogenic chloride transport system. Physiol. Rev. 70:1990;319-330.
26. Lanyi J. K. Mechanism of ion transport across membranes. Bacteriorhodopsin as a prototype for proton pumps. J. Biol. Chem. 272:1997;31209-31212.
27. Lanyi J. K., Duschl A., Hatfield G. W., May K., Oesterhelt D. The primary structure of a halorhodopsin from Natronobacterium pharaonis. Structural, functional and evolutionary implications for bacterial rhodopsins and halorhodopsins. J. Biol. Chem. 265:1990;1253-1260.
28. Larsen H. Halobacteriaceae. Krieg N. R. Bergey's Manual of Systematic Bacteriology. 1984;261-267 Williams & Wilkins, Baltimore.
29. Liang J., Edelsbrunner H., Fu P., Sundhakar P. V., Subramaniam S. Analytical shape computation of macromolecules: II. Inaccessible cavities in protein. Proteins: Struct. Funct. Genet. 33:1998;18-29.
30. Matsuno-Yagi A., Mukohata Y. Two possible roles of bacteriorhodopsin; a comparative study of strains of Halobacterium halobium differing in pigmentation. Biochem. Biophys. Res. Commun. 78:1977;237-243.
31. Mukohata Y. Comparative studies on ion pumps of the bacterial rhodopsin family. Biophys. Chem. 50:1994;191-201.
32. Mukohata Y., Matsuno-Yagi A., Kaji Y. Light-induced proton uptake and ATP synthesis by bacteriorhodopsin-depleted Halobacterium. Morishita H., Masui M. Saline Environment. 1980;31-38 Business Center Academic Society, Tokyo.
33. Mukohata Y., Sugiyama Y., Ihara K., Yoshida M. An Australian Halobacterium contains a novel proton pump retinal protein: archaerhodopsin. Biochem. Biophys. Res. Commun. 151:1988;1339-1345.
34. Nei M. Molecular Evolutionary Genetics. 1987;Colombia University Press, New York.
35. Ochman H., Wilson A. Evolution in bacteria: evidence for a universal rate in cellular genomes. J. Mol. Evol. 26:1987;74-86.
36. Oesterhelt D., Stoeckenius W. Rhodopsin-like protein from the purple membrane of Halobacterium halobium. Nature. 233:1971;149-152.
37. Otomo J., Urabe Y., Tomioka H., Sasabe H. The primary structures of helices A to G of three new bacteriorhodopsin-like retinal proteins. J. Gen. Microbiol. 138:1992;2389-2396.
38. Pardo L., Ballesteros J. A., Osman R., Weinstein H. On the use of the transmembrane domain of bacteriorhodopsin as a template for modeling the three-dimensional structure of guanine nucleotide-binding regulatory protein-coupled receptors. Proc. Natl Acad. Sci. USA. 89:1992;4009-4012.
39. Richards F. M. The interpretation of protein structures: total volume, group volume distributions and packing density. J. Mol. Biol. 82:1974;1-14.
40. Riesle J., Oesterhelt D., Dencher N. A., Heberle J. D38 is an essential part of the proton translocation pathway in bacteriorhodopsin. Biochemistry. 35:1996;6635-6643.
41. Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:1987;406-425.
42. Sambrook J., Fritsch E. F., Maniatis T. Molecular Cloning: A Laboratory Manual. 1989;Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
43. Sasaki J., Brown L. S., Chon Y. S., Kandori H., Maeda A., Needleman R., Lanyi J. K. Conversion of bacteriorhodopsin into a chloride ion pump. Science. 269:1995;73-75.
44. Schobert B., Lanyi J. K. Halorhodopsin is a light-driven chloride pump. J. Biol. Chem. 257:1982;10306-10313.
45. Schwartz R. M., Dayhoff M. O. Atlas of Protein Sequence and Structure. 1978;National Biomedical Research Foundation, Washington.
46. Seidel R., Scharf B., Gautel M., Kleine K., Oesterhelt D., Engelhard M. The primary structure of sensory rhodopsin II: a member of an additional retinal protein subgroup is coexpressed with its transducer, the halobacterial transducer of rhodopsin II. Proc. Natl Acad. Sci. USA. 92:1995;3036-3040.
47. Soppa J. Two hypotheses - one answer. Sequence comparison does not support an evolutionary link between halobacterial retinal proteins including bacteriorhodopsin and eukaryotic G-protein-coupled receptors. FEBS Letters. 342:1994;7-11.
48. Soppa J., Duschl J., Oesterhelt D. Bacterioopsin, haloopsin, and sensory opsin I of the halobacterial isolate Halobacterium sp. strain SG1: three new members of a growing family. J. Bacteriol. 175:1993;2720-2726.
49. Spudich E. N., Sundberg S. A., Manor D., Spudich J. L. Properties of a second sensory receptor protein in Halobacterium halobium phototaxis. Proteins: Struct. Funct. Genet. 1:1986;239-246.
50. Spudich J. L. Protein-protein interaction converts a proton pump into a sensory receptor. Cell. 79:1994;747-750.
51. Strimmer K., von Haeseler A. PUZZLE. 1997a;Zoological InstitutUniversitaet Muenchen, Muenchen.
52. Strimmer K., von Haeseler A. Likelihood-mapping: a simple method to visualize phylogenetic content of a sequence alignment. Proc. Natl Acad. Sci. USA. 94:1997b;6815-6819.
53. Sugiyama Y., Maeda M., Futai M., Mukohata Y. Isolation of a gene that encodes a new retinal protein, archaerhodopsin, from Halobacterium sp. aus-1. J. Biol. Chem. 264:1989;20859-20862.
54. -), and its coupled ATP formation. Biochim. Biophys. Acta. 1188:1994;287-292.
55. Takahashi T., Tomioka H., Kamo N., Kobatake Y. A photosystem other than PS370 also mediates the negative phototaxis of Halobacterium halobium. FEMS Microbiol. Letters. 28:1985;161-164.
56. Tateno M., Ihara K., Mukohata Y. The novel ion pump rhodopsins from Haloarcula form a family independent from both the bacteriorhodopsin and archaerhodopsin families/tribes. Arch. Biochem. Biophys. 315:1994;127-132.
57. Thompson J. D., Higgins D. G., Gibson T. J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl. Acids Res. 22:1994;4673-4680.
58. Tittor J., Haupts U., Haupts C., Oesterhelt D., Becker A., Bamberg E. Chloride and proton transport in bacteriorhodopsin mutant D85T: different modes of ion translocation in a retinal protein. J. Mol. Biol. 271:1997;405-416.
59. Tsuda M., Hazemoto N., Kondo M., Kamo N., Kobatake Y., Terayama Y. Two photocycles in Halobacterium halobium that lack bacteriorhodopsin. Biochem. Biophys. Res. Commun. 108:1982;970-976.
60. Zhang W., Brooun A., Mueller M. M., Alam M. The primary structures of the Archaeon Halobacterium salinarium blue light receptor sensory rhodopsin II and its transducer, a methyl-accepting protein. Proc. Natl Acad. Sci. USA. 93:1996;8230-8235.