A kinome of 2600 in the ciliate Paramecium tetraurelia

FEBS Letters

Volumn 583, Issue 22, 2009, Pages 3589-3592

  Bemm, Felix ^a   Schwarz, Roland ^a   Förster, Frank ^a   Schultz, Jörg ^a  

^a Biocenter ^*  (Germany)

Author keywords

Domain; Genome; Kinase; Sequence analysis

Indexed keywords

CALCIUM CALMODULIN DEPENDENT PROTEIN KINASE; PROTEIN KINASE;

ARTICLE; CILIATE; CONTROLLED STUDY; EMBEDDING; GENETIC ANALYSIS; MOLECULAR MECHANICS; NONHUMAN; PARAMECIUM TETRAURELIA; PHYLOGENETIC TREE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FAMILY; REGULATORY MECHANISM;

ANIMALS; BINDING SITES; COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; GENOME, PROTOZOAN; HUMANS; PARAMECIUM TETRAURELIA; PHYLOGENY; PROTEIN KINASES; PROTOZOAN PROTEINS;

CILIOPHORA; EUKARYOTA; PARAMECIUM TETRAURELIA;

EID: 72049131815     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.febslet.2009.10.029     Document Type: Article

References (30)

1. Hunter T., and Plowman G.D. The protein kinases of budding yeast: six score and more. Trends Biochem. Sci. 22 (1997) 18-22
2. Hunter T. A thousand and one protein kinases. Cell 50 (1987) 823-829
3. Hunter T. 1001 protein kinases redux-towards 2000. Semin. Cell Biol. 5 (1994) 367-376
4. Manning G., Whyte D.B., Martinez R., Hunter T., and Sudarsanam S. The protein kinase complement of the human genome. Science 298 (2002) 1912-1934
5. Eisen J.A., Coyne R.S., Wu M., Wu D., Thiagarajan M., Wortman J.R., Badger J.H., Ren Q., Amedeo P., Jones K.M., Tallon L.J., Delcher A.L., Salzberg S.L., Silva J.C., Haas B.J., Majoros W.H., Farzad M., Carlton J.M., Smith R.K., Garg J., Pearlman R.E., Karrer K.M., Sun L., Manning G., Elde N.C., Turkewitz A.P., Asai D.J., Wilkes D.E., Wang Y., Cai H., Collins K., Stewart B.A., Lee S.R., Wilamowska K., Weinberg Z., Ruzzo W.L., Wloga D., Gaertig J., Frankel J., Tsao C.-C., Gorovsky M.A., Keeling P.J., Waller R.F., Patron N.J., Cherry J.M., Stover N.A., Krieger C.J., del Toro C., Ryder H.F., Williamson S.C., Barbeau R.A., Hamilton E.P., and Orias E. Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biol. 4 (2006) e286
6. Plattner H. My favorite cell-Paramecium. Bioessays 24 (2002) 649-658
7. Plattner H., and Kissmehl R. Molecular aspects of membrane trafficking in paramecium. Int. Rev. Cytol. 232 (2003) 185-216
8. Aury J.-M., Jaillon O., Duret L., Noel B., Jubin C., Porcel B.M., Ségurens B., Daubin V., Anthouard V., Aiach N., Arnaiz O., Billaut A., Beisson J., Blanc I., Bouhouche K., Câmara F., Duharcourt S., Guigo R., Gogendeau D., Katinka M., Keller A.-M., Kissmehl R., Klotz C., Koll F., Le Mouël A., Lepère G., Malinsky S., Nowacki M., Nowak J.K., Plattner H., Poulain J., Ruiz F., Serrano V., Zagulski M., Dessen P., Bétermier M., Weissenbach J., Scarpelli C., Schächter V., Sperling L., Meyer E., Cohen J., and Wincker P. Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. Nature 444 (2006) 171-178
9. Krupa A., Abhinandan K.R., and Srinivasan N. KinG: a database of protein kinases in genomes. Nucleic Acids Res. 32 (2004) D153-D155
10. Arnaiz O., Cain S., Cohen J., and Sperling L. ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data. Nucleic Acids Res. 35 (2007) D439-D444
11. Letunic I., Doerks T., and Bork P. SMART 6: recent updates and new developments. Nucleic Acids Res. 37 (2009) D229-D232
12. Durbin R. Biological Sequence Analysis. Probabilistic Models of Proteins and Nucleic Acids (2007), Cambridge Univ. Press, Cambridge
13. Martin D.M.A., Miranda-Saavedra D., and Barton G.J. Kinomer v. 1.0: a database of systematically classified eukaryotic protein kinases. Nucleic Acids Res. 37 (2009) D244-D250
14. Schultz J., Doerks T., Ponting C.P., Copley R.R., and Bork P. More than 1,000 putative new human signalling proteins revealed by EST data mining. Nat. Genet. 25 (2000) 201-204
15. Finn R.D., Tate J., Mistry J., Coggill P.C., Sammut S.J., Hotz H.-R., Ceric G., Forslund K., Eddy S.R., Sonnhammer E.L.L., and Bateman A. The Pfam protein families database. Nucleic Acids Res. 36 (2008) D281-D288
16. Lupas A., van Dyke M., and Stock J. Predicting coiled coils from protein sequences. Science 252 (1991) 1162-1164
17. Golub G.H., and VanLoan C.F. Matrix Computations (1996), Johns Hopkins Univ. Press, Baltimore
18. Shawe-Taylor J., and Cristianini N. Kernel Methods for Pattern Analysis (2006), Cambridge University Press, Cambridge
19. Schölkopf B., and Smola A.J. Learning with Kernels. Support Vector Machines, Regularization, Optimization, and Beyond (2002), MIT Press, Cambridge, MA
20. Higham N.J. Computing a nearest symmetric positive semidefinite matrix. Linear Algebra Appl. 103 (1988) 103-118
21. Pils B., and Schultz J. Inactive enzyme-homologues find new function in regulatory processes. J. Mol. Biol. 340 (2004) 399-404
22. Hanks S.K., Quinn A.M., and Hunter T. The protein kinase family: conserved features and deduced phylogeny of the catalytic domains. Science 241 (1988) 42-52
23. Fok A.K., Aihara M.S., Ishida M., and Allen R.D. Calmodulin localization and its effects on endocytic and phagocytic membrane trafficking in Paramecium multimicronucleatum. J. Eukaryot. Microbiol. 55 (2008) 481-491
24. Maihle N.J., Dedman J.R., Means A.R., Chafouleas J.G., and Satir B.H. Presence and indirect immunofluorescent localization of calmodulin in Paramecium tetraurelia. J. Cell Biol. 89 (1981) 695-699
25. Emes R.D., Goodstadt L., Winter E.E., and Ponting C.P. Comparison of the genomes of human and mouse lays the foundation of genome zoology. Hum. Mol. Genet. 12 (2003) 701-709
26. Sonnhammer, E.L., Heijne, G. von and Krogh, A. (1998) A hidden Markov model for predicting transmembrane helices in protein sequences. In Proceedings/... International Conference on Intelligent Systems for Molecular Biology; ISMB. International Conference on Intelligent Systems for Molecular Biology, Vol. 6, pp. 175-182.
27. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17 (2000) 540-552
28. Desper R., and Gascuel O. Theoretical foundation of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting. Mol. Biol. Evol. 21 (2004) 587-598
29. Jaillon O., Bouhouche K., Gout J.-F., Aury J.-M., Noel B., Saudemont B., Nowacki M., Serrano V., Porcel B.M., Ségurens B., Le Mouël A., Lepère G., Schächter V., Bétermier M., Cohen J., Wincker P., Sperling L., Duret L., and Meyer E. Translational control of intron splicing in eukaryotes. Nature 451 (2008) 359-362
30. Letunic I., and Bork P. Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23 (2007) 127-128