A "holistic" kinesin phylogeny reveals new kinesin families and predicts protein functions

Molecular Biology of the Cell

Volumn 17, Issue 4, 2006, Pages 1734-1743

  Wickstead, Bill ^a   Gull, Keith ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

KINESIN; KINESIN 16; KINESIN 17; KINESIN 2; KINESIN 9; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARABIDOPSIS; ARTICLE; BAYES THEOREM; CAENORHABDITIS ELEGANS; CELL LINEAGE; CHLAMYDOMONAS REINHARDTII; CILIATE; CRYPTOSPORIDIUM PARVUM; DIATOM; DICTYOSTELIUM DISCOIDEUM; DROSOPHILA MELANOGASTER; ENCEPHALITOZOON CUNICULI; ENTAMOEBA HISTOLYTICA; EUKARYOTE; EUKARYOTIC FLAGELLUM; GENE SEQUENCE; GIARDIA LAMBLIA; HOMO SAPIENS; HUMAN; LEISHMANIA MAJOR; METAZOON; MOLECULAR EVOLUTION; NONHUMAN; PARALOGY; PHYLOGENY; PHYLUM; PLASMODIUM FALCIPARUM; PREDICTION; PRIORITY JOURNAL; PROBABILITY; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN LOCALIZATION; RED ALGA; RELIABILITY; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES POMBE; SEQUENCE ANALYSIS; THEILERIA ANNULATA; TRYPANOSOMA BRUCEI; YEAST; ANIMAL; BIOLOGY; CLASSIFICATION; PHYSIOLOGY;

EUKARYOTA;

ANIMALS; BAYES THEOREM; COMPUTATIONAL BIOLOGY; HUMANS; KINESIN; MARKOV CHAINS; PHYLOGENY;

EID: 33745338902     PISSN: 10591524     EISSN: None     Source Type: Journal    
DOI: 10.1091/mbc.E05-11-1090     Document Type: Article

References (58)

1. Abrahamsen, M. S., et al. (2004). Complete genome sequence of the apicomplexan Cryptosporidium parvum. Science 304, 441-445.
2. Adams, M. D., et al. (2000). The genome sequence of Drosophila melanogaster. Science 287, 2185-2195.
3. Arabidopsis Genome Initiative. (2000). Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796-815.
4. Armbrust, E. V., et al. (2004). The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. Science 306, 79-86.
5. Baldauf, S. L. (2003). Phytogeny for the faint of heart: a tutorial. Trends Genet. 19, 345-351.
6. Bateman, A., et al. (2004). The Pfam protein families database. Nucleic Acids Res. 32, D138-D141.
7. Bergsten, J. (2005). A review of long-branch attraction. Cladistics 21, 163-193.
8. Bernstein, M., Beech, P. L., Katz, S. G., and Rosenbaum, J. L. (1994). A new kinesin-like protein (Klp1) localized to a single microtubule of the Chlamydomonas flagellum. J. Cell Biol. 125, 1313-1326.
9. Berriman, M., et al. (2005). The genome of the African trypanosome Trypanosama brucei. Science 309, 416-422.
10. Betley, J. N., Heinrich, B., Vernos, I., Sardet, C., Prodon, F., and Deshler, J. O. (2004). Kinesin II mediates Vg1 mRNA transport in Xenopus oocytes. Curr. Biol. 14, 219-224.
11. Briggs, L. J., Davidge, J. A., Wickstead, B., Ginger, M. L., and Gull, K. (2004). More than one way to build a flagellum: comparative genomics of parasitic protozoa. Curr. Biol. 14, R611-R612.
12. Case, R. B., Pierce, D. W., HomBooher, N., Hart, C. L., and Vale, R. D. (1997). The directional preference of kinesin motors is specified by an element outside of the motor catalytic domain. Cell 90, 959-966.
13. Cavalier-Smith, T. (2004). Only six kingdoms of life. Proc. R. Soc. Lond., Ser. B Biol. Sci. 271, 1251-1262.
14. Dagenbach, E. M., and Endow, S. A. (2004). A new kinesin tree. J. Cell Sci. 117, 3-7.
15. Douzery, E. J. P., Snell, E. A., Bapteste, E., Delsuc, F., and Philippe, H. (2004). The timing of eukaryotic evolution: does a relaxed molecular clock reconcile proteins and fossils? Proc. Nat. Acad. Sci. USA 101, 15386-15391.
16. Eichinger, L., et al. (2005). The genome of the social amoeba Dictyostelium discoideum. Nature 435, 43-57.
17. Endow, S. A., and Waligora, K. W. (1998). Determinants of kinesin motor polarity. Science 281, 1200-1202.
18. Fan, J., and Beck, K. A. (2004). A role for the spectrin superfamily member Syne-1 and kinesin II in cytokinesis. J. Cell Sci. 117, 619-629.
19. Galtier, N. (2001). Maximum-likelihood phylogenetic analysis under a covarion-like model. Mol. Biol. Evol. 18, 866-873.
20. Gardner, M. J., et al. (2002). Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419, 498-511.
21. Goffeau, A., et al. (1996). Life with 6000 genes. Science 274, 546-&.
22. Goodson, H. V., Kang, S. J., and Endow, S. A. (1994). Molecular phylogeny of the kinesin family of microtubule motor proteins. J. Cell Sci. 107, 1875-1884.
23. Hirokawa, N., Noda, Y., and Okada, Y. (1998). Kinesin and dynein superfamily proteins in organelle transport and cell division. Curr. Opin. Cell Biol. 10, 60-73.
24. Hirokawa, N., and Takemura, R. (2004). Kinesin superfamily proteins and their various functions and dynamics. Exp. Cell Res. 301, 50-59.
25. Holder, M., and Lewis, P. O. (2003). Phylogeny estimation: traditional and Bayesian approaches. Nat. Rev. Genet. 4, 275-284.
26. Huelsenbeck, J. P., Larger, B., Miller, R. E., and Ronquist, F. (2002). Potential applications and pitfalls of Bayesian inference of phylogeny. Syst. Biol. 51, 673-688.
27. Ivens, A. C., et al. (2005). The genome of the kinetoplastid parasite Leishmania major. Science 309, 436-442.
28. Katinka, M. D., et al. (2001). Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi. Nature 414, 450-453.
29. Katoh, M. (2005). Characterization of KIF12 gene in silico. Oncol. Rep. 13, 367-370.
30. Kim, A. J., and Endow, S. A. (2000). A kinesin family tree. J. Cell Sci. 113, 3681-3682.
31. Kollmar, M., and Glockner, G. (2003). Identification and phylogenetic analysis of Dictyostelium discoideum kinesin proteins. BMC Genomics 4, 47.
32. Krogh, A., Brown, M., Mian, I. S., Sjolander, K., and Haussler, D. (1994). Hidden Markov models in computational biology: applications to protein modeling. J. Mol. Biol. 235, 1501-1531.
33. Lander, E. S., et al. (2001). Initial sequencing and analysis of the human genome. Nature 409, 860-921.
34. Lawrence, C. J., et al. (2004). A standardized kinesin nomenclature. J. Cell Biol. 167, 19-22.
35. Lawrence, C. J., Malmberg, R. L., Muszynski, M. G., and Dawe, R. K. (2002). Maximum likelihood methods reveal conservation of function among closely related kinesin families. J. Mol. Evol. 54, 42-53.
36. Lawrence, C. J., Morris, N. R., Meagher, R. B., and Dawe, R. K. (2001). Dyneins have run their course in plant lineage. Traffic 2, 362-363.
37. Le Bot, N., Antony, C., White, J., Karsenti, E., and Vernos, I. (1998). Role of Xk1p3, a subunit of the Xenopus kinesin II heterotrimeric complex, in membrane transport between the endoplasmic reticulum and the Golgi apparatus. J. Cell Biol. 143, 1559-1573.
38. Letunic, I., Copley, R. R., Schmidt, S., Ciccarelli, F. D., Doerks, T., Schultz, J., Ponting, C. P., and Bork, P. (2004). SMART 4.0, towards genomic data integration. Nucleic Acids Res. 32, D142-D144.
39. Loftus, B., et al. (2005). The genome of the protist parasite Entamoeba histolytica. Nature 433, 865-868.
40. Marszalek, J. R., and Goldstein, L. S. B. (2000). Understanding the functions of kinesin-II. Biochim. Biophys. Acta Mol. Cell Res. 1496, 142-150.
41. Matsuzaki, M., et al. (2004). Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D. Nature 428, 653-657.
42. Miki, H., Okada, Y., and Hirokawa, N. (2005). Analysis of the kinesin superfamily: insights into structure and function. Trends Cell Biol. 15, 465-476.
43. Moore, J. D., and Endow, S. A. (1996). Kinesin proteins: a phylum of motors for microtubule-based motility. Bioessays 18, 207-219.
44. Mrug, M., Li, R. H., Cui, X. Q., Schoeb, T. R., Churchill, G. A., and Guay-Woodford, L. M. (2005). Kinesin family member 12 is a candidate polycystic kidney disease modifier in the cpk mouse. J. Am. Soc. Nephrol. 16, 905-916.
45. Pain, A., et al. (2005). Genome of the host-cell transforming parasite Theileria annulata compared with T. parva. Science 309, 131-133.
46. Richards, T. A., and Cavalier-Smith, T. (2005). Myosin domain evolution and the primary divergence of eukaryotes. Nature 436, 1113-1118.
47. Rogers, S. L., Tint, I. S., Fanapour, P. C., and Gelfand, V. I. (1997). Regulated bidirectional motility of melanophore pigment granules along microtubules in vitro. Proc. Natl. Acad. Sci. USA 94, 3720-3725.
48. Ronquist, F., and Huelsenbeck, J. P. (2003). MrBayes 3, Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572-1574.
49. Siddiqui, S. S. (2002). Metazoan motor models: kinesin superfamily in C. elegans. Traffic 3, 20-28.
50. Simpson, A. G. B., and Roger, A. J. (2004). The real 'kingdoms' of eukaryotes. Curr. Biol. 14, R693-R696.
51. Sisson, J. C., Ho, K. S., Suyama, K., and Scott, M. P. (1997). Costal2, a novel kinesin related protein in the hedgehog signaling pathway. Cell 90, 235-245.
52. Swofford, D. L. (1998). Phylogenetic analysis using parsimony (*and other methods), Sunderland, MA: Sinauer.
53. The C. elegans Sequencing Consortium. (1998). Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282, 2012-2018.
54. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F., and Higgins, D. G. (1997). The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24, 4876-4882.
55. Tuma, M. C., Zill, A., Le Bot, N., Vernos, I., and Gelfand, V. (1998). Heterotrimeric kinesin II is the microtubule motor protein responsible for pigment dispersion in Xenopus melanophores. J. Cell Biol. 143, 1547-1558.
56. Whelan, S., and Goldman, N. (2001). A general empirical model of protein evolution derived from multiple protein families using a maximum likelihood approach. Mol. Biol. Evol. 18, 691-699.
57. Wood, V., et al. (2002). The genome sequence of Schizosaccharomyces pombe. Nature 415, 871-880.
58. Yokoyama, R., O'Toole, E., Ghosh, S., and Mitchell, D. R. (2004). Regulation of flagellar dynein activity by a central pair kinesin. Proc. Natl. Acad. Sci. USA 101, 17398-17403.