Identification of cryptochrome DASH from vertebrates

Genes to Cells

Volumn 9, Issue 5, 2004, Pages 479-495

  Daiyasu, Hiromi ^a   Ishikawa, Tomoko ^a   Kuma, Kei Ichi ^a   Iwai, Shigenori ^b   Todo, Takeshi ^a   Toh, Hiroyuki ^a  

^a KYOTO UNIVERSITY   (Japan)

^b OSAKA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; CRYPTOCHROME; CRYPTOCHROME DASH; DEOXYRIBODIPYRIMIDINE PHOTOLYASE; FOLIC ACID; QUERCETIN; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; AMPHIBIA; ANIMAL CELL; ARTICLE; BACTERIOPLANKTON; CONTROLLED STUDY; DNA SEQUENCE; ENZYME ACTIVITY; EXPRESSED SEQUENCE TAG; FISH; FUNGUS; GENETIC CODE; MOLECULAR CLONING; NEUROSPORA CRASSA; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN FAMILY; PROTEIN PURIFICATION; SEQUENCE DATABASE; VERTEBRATE; XENOPUS LAEVIS; ZEBRA FISH;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; CLONING, MOLECULAR; COMPUTATIONAL BIOLOGY; DEOXYRIBODIPYRIMIDINE PHOTO-LYASE; EVOLUTION, MOLECULAR; EXPRESSED SEQUENCE TAGS; FLAVOPROTEINS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE HOMOLOGY, AMINO ACID; VERTEBRATES; XENOPUS LAEVIS; XENOPUS PROTEINS; ZEBRAFISH; ZEBRAFISH PROTEINS;

AMPHIBIA; ARABIDOPSIS; ARABIDOPSIS THALIANA; DANIO RERIO; FUNGI; NEUROSPORA; NEUROSPORA CRASSA; SYNECHOCYSTIS; SYNECHOCYSTIS SP.; SYNECHOCYSTIS SP. PCC 6803; VERTEBRATA; VIBRIO; VIBRIO CHOLERAE; XENOPUS LAEVIS;

EID: 2942657138     PISSN: 13569597     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1356-9597.2004.00738.x     Document Type: Article

References (54)

1. Adachi, J. & Hasegawa, M. (1996) MOLPHY (Programs for Molecular Phylogenetics), 2.3b3. Tokyo: Institute of Statistical Mathematics.
2. Ahmad, M. & Cashmore, A.R. (1993) HY4 gene of A. thaliana encodes a protein with characteristics of a blue-light photo-receptor. Nature 366, 162-166.
3. Altschul, S.F., Madden, T.L., Schaffer, A.A., et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acids Res. 25, 3389-3402.
4. Aubert, C., Vos, M.H., Mathis, P, Eker, A.P. & Brettel, K. (2000) Intraprotein radical transfer during photoactivation of DNA photolyase. Nature 405, 586-590.
5. Brudler, R., Hitomi, K., Daiyasu, H., et al. (2003) Identification of a new cryptochrome class. Structure, function, and evolution. Mol. Cell 11, 59-67.
6. Cashmore, A.R., Jarillo, J.A., Wu, Y.J. & Liu, D. (1999) Cryptochromes: blue light receptors for plants and animals. Science 284, 760-765.
7. Daiyasu, H. & Toh, H. (2000) Molecular evolution of the myeloperoxidase family. J. Mol. Evol. 51, 433-445.
8. Dehal, P., Satou, Y., Campbell, R.K., et al. (2002) The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science 298, 2157-2167.
9. Dunlap, J.C. (1999) Molecular bases for circadian clocks. Cell 96, 271-290.
10. Felsenstein, J. (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17, 368-376.
11. Felsenstein, J. (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.
12. Felsenstein, J. (1993) PHYLIP (phylogeny inference package), Version 3.5c. Seattle: Department of Genetics. University of Washington.
13. Felsenstein, J. (1996) Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods. Methods Enzymol. 266, 418-427.
14. Frohman, M.A., Dush, M.K. & Martin, G.R. (1988) Rapid production of full-length cDNAs from rare transcripts: amplification using a single gene-specific oligonucleotide primer. Proc. Natl. Acad. Sci. USA 85, 8998-9002.
15. Froy, O., Chang, D.C. & Reppert, S.M. (2002) Redox potential: differential roles in dCRY and mCRY1 functions. Curr. Biol. 12, 147-152.
16. Galagan, J.E., Calvo, S.E., Borkovich, K.A., et al. (2003) The genome sequence of the filamentous fungus Neurospora crassa. Nature 422, 859-868.
17. Gardner, M.J., Hall, N., Fung, E., et al. (2002) Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419, 498-511.
18. Griffin, E.A. Jr, Staknis, D. & Weitz, C.J. (1999) Light-independent role of CRY1 and CRY2 in the mammalian circadian clock. Science 286, 768-771.
19. Hirayama, J., Fukuda, I., Ishikawa, T., Kobayashi, Y. & Todo, T. (2003) New role of zCRY and zPER2 as regulators of sub-cellular distributions of zCLOCK and zBMAL proteins. Nucleic Acids Res. 31, 935-943.
20. Hitomi, K., Kim, S.T., Iwai, S., et al. (1997) Binding and catalytic properties of Xenopus (6-4) photolyase. J. Biol. Chem. 272, 32591-32598.
21. Hitomi, K., Okamoto, K., Daiyasu, H., et al. (2000) Bacterial cryptochrome and photolyase: characterization of two photolyase-like genes of Synechocystis sp. PCC6803. Nucleic Acids Res. 28, 2353-2362.
22. Ishikawa, T., Hirayama, J., Kobayashi, Y. & Todo, T. (2002) Zebrafish CRY represses transcription mediated by CLOCK-BMAL heterodimer without inhibiting its binding to DNA. Genes Cells 7, 1073-1086.
23. Johnson, J.L., Hamm-Alvarez, S., Payne, G., Sancar, G.B., Rajagopalan, K.V. & Sancar, A. (1988) Identification of the second chromophore of Escherichia coli and yeast DNA photolyases as 5,10-methenyltetrahydrofolate. Proc. Natl. Acad. Sci. USA 85, 2046-2050.
24. Jones, D.T., Taylor, W.R. & Thornton, J.M. (1992) The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8, 275-282.
25. Kanai, S., Kikuno, R., Toh, H., Ryo, H. & Todo, T. (1997) Molecular evolution of the photolyase-blue-light photoreceptor family. J. Mol. Evol. 45, 535-548.
26. Kato, T. Jr, Todo, T., Ayaki, H., et al. (1994) Cloning of a marsupial DNA photolyase gene and the lack of related nucleotide sequences in placental mammals. Nucl. Acids Res. 22, 4119-4124.
27. Kleine, T., Lockhart, P. & Batschauer, A. (2003) An Arabidopsis protein closely related to Synechocystis cryptochrome is targeted to organelles. Plant J. 35, 93-103.
28. Kobayashi, Y., Ishikawa, T., Hirayama, J., et al. (2000) Molecular analysis of zebrafish photolyase/cryptochrome family: two types of cryptochromes present in zebrafish. Genes Cells 5, 725-738.
29. Komori, H., Masui, R., Kuramitsu, S., et al. (2001) Crystal structure of thermostable DNA photolyase: pyrimidine-dimer recognition mechanism. Proc. Natl. Acad. Sci. USA 98, 13560-13565.
30. Kume, K., Zylka, M.J., Sriram, S., et al. (1999) mCRY1 and mCRY2 are essential components of the negative limb of the circadian clock feedback loop. Cell 98, 193-205.
31. Lee, K., Dunlap, J.C. & Loros, J.J. (2003) Roles for WHITE COLLAR-1 in circadian and general photoperception in Neurospora crassa. Genetics 163, 103-114.
32. Li, Y.F. & Sancar, A. (1990) Active site of Escherichia coli DNA photolyase: mutations at Trp277 alter the selectivity of the enzyme without affecting the quantum yield of photorepair. Biochemistry 29, 5698-5706.
33. Loros, J.J. & Dunlap, J.C. (2001) Genetic and molecular analysis of circadian rhythms in Neurospora. Annu. Rev. Physiol. 63, 757-794.
34. Martin, W., Rujan, T., Richly, E., et al. (2002) Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proc. Natl. Acad. Sci. USA 99, 12246-12251.
35. Miki, K., Tamada, T., Nishida, H., et al. (1993) Crystallization and preliminary X-ray diffraction studies of photolyase (photo-reactivating enzyme) from the cyanobacterium. Anacystis nidulans. J. Mol. Biol. 233, 167-169.
36. Murzin, A.G., Brenner, S.E., Hubbard, T. & Chothia, C. (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540.
37. Page, R.D. (1996) Tree View: an application to display phylogenetic trees on personal computers. Comput. Appl. Biosci. 12, 357-358.
38. Park, H.W., Kim, S.T., Sancar, A. & Deisenhofer, J. (1995) Crystal structure of DNA photolyase from Fscherichia coli. Science 268, 1866-1872.
39. Rachael, A., Simon, B., Karen, B., et al. (1998) Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282, 2012-2018.
40. Rosato, E., Codd, V, Mazzotta, G., et al. (2001) Light-dependent interaction between Drosophila CRY and the clock protein PER mediated by the carboxy terminus of CRY. Curr. Biol. 11, 909-917.
41. Saitou, N. & Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425.
42. Sancar, A. (1994) Structure and function of DNA photolyase. Biochemistry 33, 2-9.
43. Sancar, G.B. (1990) DNA photolyases: physical properties, action mechanism, and roles in dark repair. Mutat. Res. 236, 147-160.
44. Taylor, W.R. & Orengo, C.A. (1989) Protein structure alignment. J. Mol. Biol. 208, 1-22.
45. Thompson, J.D., Higgins, D.G. & Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680.
46. Todo, T. (1999) Functional diversity of the DNA photolyase/ blue light receptor family. Mutat. Res. 434, 89-97.
47. Todo, T., Kim, S.T., Hitomi, K., et al. (1997) Flavin adenine dinucleotide as a chromophore of the Xenopus (6-4) photolyase. Nucl. Acids Res. 25, 764-768.
48. Todo, T., Ryo, H., Takemori, H., et al. (1994) High-level expression of the photorepair gene in Drosophila ovary and its evolutionary implications. Mutat. Res. 315, 213-228.
49. Todo, T., Ryo, H., Yamamoto, K., et al. (1996) Similarity among the Drosophila (6-4) photolyase, a human photolyase homolog, and the DNA photolyase-blue-light photoreceptor family. Science 272, 109-112.
50. Todo, T., Takemori, H., Ryo, H., et al. (1993) A new photo-reactivating enzyme that specifically repairs ultraviolet light-induced (6-4),photoproducts. Nature 361, 371-374.
51. Toh, H. (1997) Introduction of a distance cut-off into structural alignment by the double dynamic programming algorithm. Comput. Appl. Biosci. 13, 387-396.
52. Van Gelder, R.N., Herzog, E.D., Schwartz, W.J. & Taghert, P.H. (2003) Circadian rhythms: in the loop at last. Science 300, 1534-1535.
53. Worthington, E.N., Kavakli, I.H., Berrocal-Tito, G., Bondo, B.E. & Sancar, A. (2003) Purification and characterization of three members of the photolyase/cryptochrome family blue-light photoreceptors from Vibrio cholerae. J. Biol. Chem. 278, 39143-39154.
54. Yasui, A., Eker, A.P., Yasuhira, S., et al. (1994) A new class of DNA photolyases present in various organisms including aplacental mammals. EMBO J. 13, 6143-6151.