Evolutionary expansion of the Ras switch regulatory module in eukaryotes

Nucleic Acids Research

Volumn 39, Issue 13, 2011, Pages 5526-5537

  Díez, Diego ^a,b   Sánchez Jiménez, Francisca ^c   Ranea, Juan A G ^c  

^a KYOTO UNIVERSITY   (Japan)

^b INSTITUTO DE INVESTIGACIONES BIOMÉDICAS ALBERTO SOLS   (Spain)

^c UNIVERSITY OF MÁLAGA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

GUANINE NUCLEOTIDE EXCHANGE FACTOR; GUANOSINE TRIPHOSPHATASE ACTIVATING PROTEIN; RAS PROTEIN;

ALTERNATIVE RNA SPLICING; ARTICLE; CLADISTICS; CONTROLLED STUDY; EUKARYOTE; GENE DUPLICATION; GENETIC MODEL; GENETIC VARIABILITY; GENOME SIZE; MAMMAL; MOLECULAR EVOLUTION; MULTIGENE FAMILY; ORTHOLOGY; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN LOCALIZATION;

ALTERNATIVE SPLICING; ANIMALS; EVOLUTION, MOLECULAR; GENETIC VARIATION; HUMANS; MAMMALS; PHYLOGENY; PROTEIN STRUCTURE, TERTIARY; RAS GTPASE-ACTIVATING PROTEINS; RAS GUANINE NUCLEOTIDE EXCHANGE FACTORS; RAS PROTEINS;

EUKARYOTA; EUTELEOSTOMI; MAMMALIA;

EID: 80052204526     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr154     Document Type: Article

References (50)

1. Brambilla, R., Gnesutta, N., Minichiello, L., White, G., Roylance, A.J., Herron, C.E., Ramsey, M., Wolfer, D.P., Cestari, V., Rossi-Arnaud, C. et al. (1997) A role for the Ras signalling pathway in synaptic transmission and long-term memory. Nature, 390, 281-286.
2. Manabe, T., Aiba, A., Yamada, A., Ichise, T., Sakagami, H., Kondo, H. and Katsuki, M. (2000) Regulation of long-term potentiation by H-Ras through NMDA receptor phosphorylation. J. Neurosci., 20, 2504-2511. (Pubitemid 30220337)
3. Bos, J.L. (1989) Ras oncogenes in human cancer: a review. Cancer Res., 49, 4682-4689. (Pubitemid 19213607)
4. Downward, J. (2003) Targeting RAS signalling pathways in cancer therapy. Nat. Rev. Cancer, 3, 11-22. (Pubitemid 37328883)
5. Colicelli, J. (2004) Human RAS superfamily proteins and related GTPases. Sci. STKE, 2004, RE13.
6. Xiao, G.H., Shoarinejad, F., Jin, F., Golemis, E.A. and Yeung, R.S. (1997) The tuberous sclerosis 2 gene product, tuberin, functions as a Rab5 GTPase activating protein (GAP) in modulating endocytosis. J. Biol. Chem., 272, 6097-6100. (Pubitemid 27118073)
7. Hu, K.Q. and Settleman, J. (1997) Tandem SH2 binding sites mediate the RasGAP-RhoGAP interaction: a conformational mechanism for SH3 domain regulation. EMBO J., 16, 473-483. (Pubitemid 27067777)
8. Burbelo, P.D., Miyamoto, S., Utani, A., Brill, S., Yamada, K.M., Hall, A. and Yamada, Y. (1995) p190-B, a new member of the Rho GAP family, and Rho are induced to cluster after integrin cross-linking. J. Biol. Chem., 270, 30919-30926. (Pubitemid 26012175)
9. Bos, J.L., Rehmann, H. and Wittinghofer, A. (2007) GEFs and GAPs: critical elements in the control of small G proteins. Cell, 129, 865-877. (Pubitemid 46802708)
10. Garcia-Ranea, J.A. and Valencia, A. (1998) Distribution and functional diversification of the ras superfamily in Saccharomyces cerevisiae. FEBS Lett., 434, 219-225. (Pubitemid 29052229)
11. Vernoud, V., Horton, A.C., Yang, Z. and Nielsen, E. (2003) Analysis of the small GTPase gene superfamily of Arabidopsis. Plant Physiol., 131, 1191-1208. (Pubitemid 36405305)
12. Bernards, A. (2003) GAPs galore! A survey of putative Ras superfamily GTPase activating proteins in man and Drosophila. Biochim. Biophys. Acta, 1603, 47-82. (Pubitemid 36262941)
13. Bernards, A. (2006) Ras superfamily and interacting proteins database. Methods Enzymol., 407, 1-9.
14. Hubbard, T., Andrews, D., Caccamo, M., Cameron, G., Chen, Y., Clamp, M., Clarke, L., Coates, G., Cox, T., Cunningham, F. et al. (2005) Ensembl 2005. Nucleic Acids Res., 33, D447-D453. (Pubitemid 40207913)
15. Donoghue, P.C. and Benton, M.J. (2007) Rocks and clocks: calibrating the Tree of Life using fossils and molecules. Trends Ecol. Evol., 22, 424-431. (Pubitemid 47058779)
16. Blair Hedges, S. and Kumar, S. (2003) Genomic clocks and evolutionary timescales. Trends Genet., 19, 200-206. (Pubitemid 36398422)
17. Hedges, S.B. (2002) The origin and evolution of model organisms. Nat. Rev. Genet., 3, 838-849. (Pubitemid 35303516)
18. Eddy, S.R. (1998) Profile hidden Markov models. Bioinformatics, 14, 755-763. (Pubitemid 28552108)
19. R Development Core Team. (2005) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
20. Thompson, J.D., Higgins, D.G. and 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. (Pubitemid 24354800)
21. Howe, K., Bateman, A. and Durbin, R. (2002) QuickTree: building huge Neighbour-Joining trees of protein sequences. Bioinformatics, 18, 1546-1547. (Pubitemid 35422615)
22. Chevenet, F., Brun, C., Banuls, A.L., Jacq, B. and Christen, R. (2006) TreeDyn: towards dynamic graphics and annotations for analyses of trees. BMC Bioinformatics, 7, 439.
23. Koscielny, G., Le Texier, V., Gopalakrishnan, C., Kumanduri, V., Riethoven, J.J., Nardone, F., Stanley, E., Fallsehr, C., Hofmann, O., Kull, M. et al. (2009) ASTD: The Alternative Splicing and Transcript Diversity database. Genomics, 93, 213-220.
24. The Arabidopsis Genome Initiative. (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408, 796-815.
25. Ohno, S. (1970) Evolution by Gene Duplication. Springer, London.
26. Wilkins, A. and Insall, R.H. (2001) Small GTPases in Dictyostelium: lessons from a social amoeba. Trends Genet., 17, 41-48. (Pubitemid 32332979)
27. Maruoka, H., Konno, D., Hori, K. and Sobue, K. (2005) Collaboration of PSD-Zip70 with its binding partner, SPAR, in dendritic spine maturity. J. Neurosci., 25, 1421-1430. (Pubitemid 40250718)
28. Li, Z., McNulty, D.E., Marler, K.J., Lim, L., Hall, C., Annan, R.S. and Sacks, D.B. (2005) IQGAP1 promotes neurite outgrowth in a phosphorylation- dependent manner. J. Biol. Chem., 280, 13871-13878. (Pubitemid 40517286)
29. Briggs, M.W. and Sacks, D.B. (2003) IQGAP proteins are integral components of cytoskeletal regulation. EMBO Rep., 4, 571-574. (Pubitemid 36939947)
30. Briggs, M.W. and Sacks, D.B. (2003) IQGAP1 as signal integrator: Ca2+, calmodulin, Cdc42 and the cytoskeleton. FEBS Lett., 542, 7-11. (Pubitemid 36555704)
31. Rumbaugh, G., Adams, J.P., Kim, J.H. and Huganir, R.L. (2006) SynGAP regulates synaptic strength and mitogen-activated protein kinases in cultured neurons. Proc. Natl Acad. Sci. USA, 103, 4344-4351.
32. Yang, S.N., Huang, C.B., Yang, C.H., Lai, M.C., Chen, W.F., Wang, C.L., Wu, C.L. and Huang, L.T. (2004) Impaired SynGAP expression and long-term spatial learning and memory in hippocampal CA1 area from rats previously exposed to perinatal hypoxia-induced insults: beneficial effects of A68930. Neurosci. Lett., 371, 73-78.
33. Zhang, J., Guo, J., Dzhagalov, I. and He, Y.W. (2005) An essential function for the calcium-promoted Ras inactivator in Fcgamma receptor-mediated phagocytosis. Nat. Immunol., 6, 911-919. (Pubitemid 43090446)
34. Ebinu, J.O., Stang, S.L., Teixeira, C., Bottorff, D.A., Hooton, J., Blumberg, P.M., Barry, M., Bleakley, R.C., Ostergaard, H.L. and Stone, J.C. (2000) RasGRP links T-cell receptor signaling to Ras. Blood, 95, 3199-3203. (Pubitemid 30321173)
35. Pasvolsky, R., Feigelson, S.W., Kilic, S.S., Simon, A.J., Tal-Lapidot, G., Grabovsky, V., Crittenden, J.R., Amariglio, N., Safran, M., Graybiel, A.M. et al. (2007) A LAD-III syndrome is associated with defective expression of the Rap-1 activator CalDAG-GEFI in lymphocytes, neutrophils, and platelets. J. Exp. Med., 204, 1571-1582. (Pubitemid 47048024)
36. Correll, R.N., Pang, C., Niedowicz, D.M., Finlin, B.S. and Andres, D.A. (2008) The RGK family of GTP-binding proteins: regulators of voltage-dependent calcium channels and cytoskeleton remodeling. Cell. Signal., 20, 292-300.
37. Takahashi, K., Mitsui, K. and Yamanaka, S. (2003) Role of ERas in promoting tumour-like properties in mouse embryonic stem cells. Nature, 423, 541-545. (Pubitemid 36648578)
38. Kawasaki, H., Springett, G.M., Toki, S., Canales, J.J., Harlan, P., Blumenstiel, J.P., Chen, E.J., Bany, I.A., Mochizuki, N., Ashbacher, A. et al. (1998) A Rap guanine nucleotide exchange factor enriched highly in the basal ganglia. Proc. Natl Acad. Sci. USA, 95, 13278-13283. (Pubitemid 28509562)
39. Ichiba, T., Hoshi, Y., Eto, Y., Tajima, N. and Kuraishi, Y. (1999) Characterization of GFR, a novel guanine nucleotide exchange factor for Rap1. FEBS Lett., 457, 85-89. (Pubitemid 29387414)
40. Jefferson, J.A. and Shankland, S.J. (2007) Familial nephrotic syndrome: PLCE1 enters the fray. Nephrol. Dial. Transplant, 22, 1849-1852. (Pubitemid 47244751)
41. Mees, A., Rock, R., Ciccarelli, F.D., Leberfinger, C.B., Borawski, J.M., Bork, P., Wiese, S., Gessler, M. and Kerkhoff, E. (2005) Very-KIND is a novel nervous system specific guanine nucleotide exchange factor for Ras GTPases. Gene Expr. Patterns, 6, 79-85. (Pubitemid 41819234)
42. Huang, J., Furuya, A. and Furuichi, T. (2007) Very-KIND, a KIND domain containing RasGEF, controls dendrite growth by linking Ras small GTPases and MAP2. J. Cell Biol., 179, 539-552. (Pubitemid 350074796)
43. Benton, M.J. and Donoghue, P.C. (2007) Paleontological evidence to date the tree of life. Mol. Biol. Evol., 24, 26-53. (Pubitemid 46026279)
44. Gough, J. (2005) Convergent evolution of domain architectures (is rare). Bioinformatics, 21, 1464-1471. (Pubitemid 40552751)
45. Sharp, P.A. (1987) Splicing of messenger RNA precursors. Science, 235, 766-771. (Pubitemid 17028328)
46. Modrek, B. and Lee, C.J. (2003) Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss. Nat. Genet., 34, 177-180. (Pubitemid 36666928)
47. Bernards, A., Haase, V.H., Murthy, A.E., Menon, A., Hannigan, G.E. and Gusella, J.F. (1992) Complete human NF1 cDNA sequence: two alternatively spliced mRNAs and absence of expression in a neuroblastoma line. DNA Cell Biol., 11, 727-734. (Pubitemid 23001677)
48. Guil, S., de La Iglesia, N., Fernandez-Larrea, J., Cifuentes, D., Ferrer, J.C., Guinovart, J.J. and Bach-Elias, M. (2003) Alternative splicing of the human proto-oncogene c-H-ras renders a new Ras family protein that trafficks to cytoplasm and nucleus. Cancer Res., 63, 5178-5187. (Pubitemid 37139824)
49. Kopelman, N.M., Lancet, D. and Yanai, I. (2005) Alternative splicing and gene duplication are inversely correlated evolutionary mechanisms. Nat. Genet., 37, 588-589. (Pubitemid 40770412)
50. Bernards, A. and Settleman, J. (2007) GEFs in growth factor signaling. Growth Factors, 25, 355-361. (Pubitemid 351194034)