Lineage-specific expansions provide genomic complexity among sea urchin GTPases

Developmental Biology

Volumn 300, Issue 1, 2006, Pages 165-179

  Beane, Wendy S ^a   Voronina, Ekaterina ^b   Wessel, Gary M ^b   McClay, David R ^a  

^a DUKE UNIVERSITY   (United States)

^b BROWN UNIVERSITY   (United States)

Author keywords

Dynamin; Echinoderm; G protein; Galpha; Gene duplication; Phylogenomics; Ras GTPase; Rho; Signal recognition particle receptor; SRP; Translation

Indexed keywords

DYNAMIN; GUANINE NUCLEOTIDE BINDING PROTEIN; GUANOSINE TRIPHOSPHATASE; RAS PROTEIN;

ARTICLE; BIOSYNTHESIS; CIONA INTESTINALIS; CONTROLLED STUDY; DROSOPHILA; GENE DUPLICATION; GENE EXPRESSION; GENE NUMBER; GENOME; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; PROTEIN ANALYSIS; SEA URCHIN; STRONGYLOCENTROTUS; UROCHORDATA; VERTEBRATE;

CIONA; ECHINODERMATA; ECHINOIDEA; PROTOSTOMIA; STRONGYLOCENTROTUS PURPURATUS; VERTEBRATA;

EID: 34248143563     PISSN: 00121606     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ydbio.2006.08.046     Document Type: Article

References (138)

1. Abbott C.M., and Proud C.G. Translation factors: in sickness and in health. Trends Biochem. Sci. 29 (2004) 25-31
2. Abramow-Newerly M., Roy A.A., Nunn C., and Chidiac P. RGS proteins have a signalling complex: interactions between RGS proteins and GPCRs, effectors, and auxiliary proteins. Cell Signal 18 (2006) 579-591
3. Adami C. What is complexity?. Bioessays 24 (2002) 1085-1094
4. Adjei A.A. Blocking oncogenic Ras signaling for cancer therapy. J. Natl. Cancer Inst. 93 (2001) 1062-1074
5. Ali B.R., and Seabra M.C. Targeting of Rab GTPases to cellular membranes. Biochem. Soc. Trans. 33 (2005) 652-656
6. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 (1997) 3389-3402
7. Asano K., Clayton J., Shalev A., and Hinnebusch A.G. A multifactor complex of eukaryotic initiation factors, eIF1, eIF2, eIF3, eIF5, and initiator tRNA(Met) is an important translation initiation intermediate in vivo. Genes Dev. 14 (2000) 2534-2546
8. Aspenstrom P., Fransson A., and Saras J. Rho GTPases have diverse effects on the organization of the actin filament system. Biochem. J. 377 (2004) 327-337
9. Bateman A., Coin L., Durbin R., Finn R.D., Hollich V., Griffiths-Jones S., Khanna A., Marshall M., Moxon S., Sonnhammer E.L., Studholme D.J., Yeats C., and Eddy S.R. The Pfam protein families database. Nucleic Acids Res. 32 (2004) D138-D141
10. Beane W.S., Gross J.M., and McClay D.R. RhoA regulates initiation of invagination, but not convergent extension, during sea urchin gastrulation. Dev. Biol. 292 (2006) 213-225
11. Bement W.M., Benink H.A., and von Dassow G. A microtubule-dependent zone of active RhoA during cleavage plane specification. J. Cell Biol. 170 (2005) 91-101
12. Birney E., Andrews D., Caccamo M., Chen Y., Clarke L., Coates G., Cox T., Cunningham F., Curwen V., Cutts T., Down T., Durbin R., Fernandez-Suarez X.M., Flicek P., Graf S., Hammond M., Herrero J., Howe K., Iyer V., Jekosch K., Kahari A., Kasprzyk A., Keefe D., Kokocinski F., Kulesha E., London D., Longden I., Melsopp C., Meidl P., Overduin B., Parker A., Proctor G., Prlic A., Rae M., Rios D., Redmond S., Schuster M., Sealy I., Searle S., Severin J., Slater G., Smedley D., Smith J., Stabenau A., Stalker J., Trevanion S., Ureta-Vidal A., Vogel J., White S., Woodwark C., and Hubbard T.J. Ensembl 2006. Nucleic Acids Res. 34 (2006) D556-D561
13. Blake J.A., Eppig J.T., Bult C.J., Kadin J.A., and Richardson J.E. The Mouse Genome Database (MGD): updates and enhancements. Nucleic Acids Res. 34 (2006) D562-D567
14. Blattner F.R., Plunkett III G., Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., and Shao Y. The complete genome sequence of Escherichia coli K-12. Science 277 (1997) 1453-1474
15. Bos J.L. All in the family? New insights and questions regarding interconnectivity of Ras, Rap1 and Ral. EMBO J. 17 (1992) 6776-6782
16. Bradham C.A., Foltz K.R., Beane W.S., Arnone M.I., Rizzo F., Coffman J.A., Mushegian A., Goel M., Morales J., Geneviere A.-M., Lapraz F., Robertson A.J., Kelkar H., Loza-Coll M., Townley I.K., Raisch M., Roux M.M., Lepage T., Gache C., McClay D.R., and Manning G. The sea urchin kinome: a first look. Dev. Biol. (2006)
17. Brooks J.M., and Wessel G.M. The major yolk protein of sea urchins is endocytosed by a dynamin-dependent mechanism. Biol. Reprod. 71 (2004) 705-713
18. Browne G.J., and Proud C.G. Regulation of peptide-chain elongation in mammalian cells. Eur. J. Biochem. 269 (2002) 5360-5368
19. Burd C.G., Strochlic T.I., and Gangi Setty S.R. Arf-like GTPases: not so Arf-like after all. Trends Cell Biol. 14 (2004) 687-694
20. Byrum C.A., Walton K.D., Robertson A.J., Carbonneau S., Thomason R.T., Coffman J.A., and McClay D.R. Protein tyrosine and serine-threonine phosphatases in the sea urchin, Strongylocentrotus purpuratus: identification and potential functions. Dev. Biol. (2006)
21. Carroll S.B., Grenier J.K., and Weatherbee S.D. From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design (2005), Blackwell, Malden, MA 105-113
22. Conner S., and Wessel G.M. Rab3 mediates cortical granule exocytosis in the sea urchin egg. Dev. Biol. 203 (1998) 334-344
23. Conner S.D., and Wessel G.M. A rab3 homolog in sea urchin functions in cell division. FASEB J. 14 (2000) 1559-1566
24. Conner S.D., and Wessel G.M. Syntaxin, VAMP, and Rab3 are selectively expressed during sea urchin embryogenesis. Mol. Reprod. Dev. 58 (2001) 22-29
25. Consortium I.H.G.S. Finishing the euchromatic sequence of the human genome. Nature 431 (2004) 931-945
26. Corpet F. Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res. 16 (1988) 10881-10890
27. Covian-Nares F., Martinez-Cadena G., Lopez-Godinez J., Voronina E., Wessel G.M., and Garcia-Soto J. A Rho-signaling pathway mediates cortical granule translocation in the sea urchin oocyte. Mech. Dev. 121 (2004) 225-235
28. Croce J.C., Wu S.-Y., Byrum C.A., Xu R., Duloquin L., Wikramanayake A.H., Gache C., and McClay D.R. A genome-wide survey of the evolutionarily conserved Wnt pathways in the sea urchin Strongylocentrotus purpuratus. Dev. Biol. (2006)
29. Danino D., and Hinshaw J.E. Dynamin family of mechanoenzymes. Curr. Opin. Cell Biol. 13 (2001) 454-460
30. Das S., Ghosh R., and Maitra U. Eukaryotic translation initiation factor 5 functions as a GTPase-activating protein. J. Biol. Chem. 276 (2001) 6720-6726
31. Debant A., Serra-Pages C., Seipel K., O'Brien S., Tang M., Park S.H., and Streuli M. The multidomain protein Trio binds the LAR transmembrane tyrosine phosphatase, contains a protein kinase domain, and has separate rac-specific and rho-specific guanine nucleotide exchange factor domains. Proc. Natl. Acad. Sci. U. S. A. 93 (1996) 5466-5471
32. DerMardirossian C., and Bokoch G.M. GDIs: central regulatory molecules in Rho GTPase activation. Trends Cell Biol. 15 (2005) 356-363
33. Drysdale R.A., and Crosby M.A. FlyBase: genes and gene models. Nucleic Acids Res. 33 (2005) D390-D395
34. Dubois T., Paleotti O., Mironov A.A., Fraisier V., Stradal T.E., De Matteis M.A., Franco M., and Chavrier P. Golgi-localized GAP for Cdc42 functions downstream of ARF1 to control Arp2/3 complex and F-actin dynamics. Nat. Cell Biol. 7 (2005) 353-364
35. Egea P.F., Stroud R.M., and Walter P. Targeting proteins to membranes: structure of the signal recognition particle. Curr. Opin. Struct. Biol. 15 (2005) 213-220
36. Ehrhardt A., Ehrhardt G.R., Guo X., and Schrader J.W. Ras and relatives-Job sharing and networking keep an old family together. Exp. Hematol. 30 (2002) 1089-1106
37. Ehrhardt A., David M.D., Ehrhardt G.R., and Schrader J.W. Distinct mechanisms determine the patterns of differential activation of H-Ras, N-Ras, K-Ras 4B, and M-Ras by receptors for growth factors or antigen. Mol. Cell. Biol. 24 (2004) 6311-6323
38. Erwin D.H., and Davidson E.H. The last common bilaterian ancestor. Development 129 (2002) 3021-3032
39. Farfel Z., Bourne H.R., and Iiri T. The expanding spectrum of G protein diseases. N. Engl. J. Med. 340 (1999) 1012-1020
40. Finlin B.S., Gau C.L., Murphy G.A., Shao H., Kimel T., Seitz R.S., Chiu Y.F., Botstein D., Brown P.O., Der C.J., Tamanoi F., Andres D.A., and Perou C.M. RERG is a novel ras-related, estrogen-regulated and growth-inhibitory gene in breast cancer. J. Biol. Chem. 276 (2001) 42259-42267
41. Fitzpatrick D.A., O'Halloran D.M., and Burnell A.M. Multiple lineage specific expansions within the guanylyl cyclase gene family. BMC Evol. Biol. 6 (2006) 26
42. Frolova L., Le Goff X., Zhouravleva G., Davydova E., Philippe M., and Kisselev L. Eukaryotic polypeptide chain release factor eRF3 is an eRF1- and ribosome-dependent guanosine triphosphatase. RNA 2 (1996) 334-341
43. Gaspar N.J., Kinzy T.G., Scherer B.J., Humbelin M., Hershey J.W., and Merrick W.C. Translation initiation factor eIF-2. Cloning and expression of the human cDNA encoding the gamma-subunit. J. Biol. Chem. 269 (1994) 3415-3422
44. Goody R.S., Rak A., and Alexandrov K. The structural and mechanistic basis for recycling of Rab proteins between membrane compartments. Cell. Mol. Life Sci. 62 (2005) 1657-1670
45. Gross S.R., and Kinzy T.G. Translation elongation factor 1A is essential for regulation of the actin cytoskeleton and cell morphology. Nat. Struct. Mol. Biol. 12 (2005) 772-778
46. Guo X., Stratton L., and Schrader J.W. Expression of activated M-Ras in hemopoietic stem cells initiates leukemogenic transformation, immortalization and preferential generation of mast cells. Oncogene (2006)
47. Hacker U., and Perrimon N. DRhoGEF2 encodes a member of the Dbl family of oncogenes and controls cell shape changes during gastrulation in Drosophila. Genes Dev. 12 (1998) 274-284
48. Hamaguchi M., Meth J.L., von Klitzing C., Wei W., Esposito D., Rodgers L., Walsh T., Welcsh P., King M.C., and Wigler M.H. DBC2, a candidate for a tumor suppressor gene involved in breast cancer. Proc. Natl. Acad. Sci. U. S. A. 99 (2002) 13647-13652
49. Hancock J.M. Gene factories, microfunctionalization and the evolution of gene families. Trends Genet. 21 (2005) 591-595
50. Hoffman G.R., and Cerione R.A. Signaling to the Rho GTPases: networking with the DH domain. FEBS Lett. 513 (2002) 85-91
51. Hollmann M.W., Strumper D., Herroeder S., and Durieux M.E. Receptors, G proteins, and their interactions. Anesthesiology 103 (2005) 1066-1078
52. Huelsenbeck J.P., Ronquist F., Nielsen R., and Bollback J.P. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294 (2001) 2310-2314
53. Hughes A.L. Gene duplication and the origin of novel proteins. Proc. Natl. Acad. Sci. U. S. A. 102 (2005) 8791-8792
54. Inge-Vechtomov S., Zhouravleva G., and Philippe M. Eukaryotic release factors (eRFs) history. Biol. Cell 95 (2003) 195-209
55. Jaffe A.B., and Hall A. Rho GTPases: biochemistry and biology. Annu. Rev. Cell Dev. Biol. 21 (2005) 247-269
56. Jenna S., and Lamarche-Vane N. The superfamily of Rho GTP-ase activating proteins. Rho GTPases (2004), Landes Biosciences, Georgetown, TX 68-95
57. Jordens I., Marsman M., Kuijl C., and Neefjes J. Rab proteins, connecting transport and vesicle fusion. Traffic 6 (2005) 1070-1077
58. Kahn R.A., Volpicelli-Daley L., Bowzard B., Shrivastava-Ranjan P., Li Y., Zhou C., and Cunningham L. Arf family GTPases: roles in membrane traffic and microtubule dynamics. Biochem. Soc. Trans. 33 (2005) 1269-1272
59. Kapp L.D., and Lorsch J.R. The molecular mechanics of eukaryotic translation. Annu. Rev. Biochem. 73 (2004) 657-704
60. Keenan R.J., Freymann D.M., Stroud R.M., and Walter P. The signal recognition particle. Annu. Rev. Biochem. 70 (2001) 755-775
61. Kelly K. The RGK family: a regulatory tail of small GTP-binding proteins. Trends Cell Biol. 15 (2005) 640-643
62. Kimmelman A., Tolkacheva T., Lorenzi M.V., Osada M., and Chan A.M. Identification and characterization of R-ras3: a novel member of the RAS gene family with a non-ubiquitous pattern of tissue distribution. Oncogene 15 (1997) 2675-2685
63. Kjeldgaard M., Nyborg J., and Clark B.F. The GTP binding motif: variations on a theme. FASEB J. 10 (1996) 1347-1368
64. Kuriyama R., Savereide P., Lefebvre P., and Dasgupta S. The predicted amino acid sequence of a centrosphere protein in dividing sea urchin eggs is similar to elongation factor (EF-1 alpha). J. Cell Sci. 95 Pt. 2 (1990) 231-236
65. Lamberti A., Caraglia M., Longo O., Marra M., Abbruzzese A., and Arcari P. The translation elongation factor 1A in tumorigenesis, signal transduction and apoptosis: review article. Amino Acids 26 (2004) 443-448
66. Larhammar D., Lundin L.G., and Hallbook F. The human Hox-bearing chromosome regions did arise by block or chromosome (or even genome) duplications. Genome Res. 12 (2002) 1910-1920
67. Leaf D.S., and Blum L.D. Analysis of rab10 localization in sea urchin embryonic cells by three-dimensional reconstruction. Exp. Cell Res. 243 (1998) 39-49
68. LeBlanc J.M., and Infante A.A. Association of 7 SL RNA and an SRP-like particle with polysomes and endoplasmic reticulum in the developing sea urchin embryo. Dev. Biol. 132 (1989) 139-152
69. LeBlanc J.M., and Infante A.A. Sea urchin small RNA ribonucleoprotein particles: identification, synthesis, and subcellular localization during early embryonic development. Mol. Reprod. Dev. 31 (1992) 96-105
70. Lee J.H., Pestova T.V., Shin B.S., Cao C., Choi S.K., and Dever T.E. Initiation factor eIF5B catalyzes second GTP-dependent step in eukaryotic translation initiation. Proc. Natl. Acad. Sci. U. S. A. 99 (2002) 16689-16694
71. Lepage T., Lapraz F., Rottinger E., Duboc V., Range R., Duloquin L., Walton K., Wu S.-Y., Bradham C., Wittaker C., Loza M.A., Hibino T., Wilson K., Poustka A., McClay D., Angerer L., and Gache C. Genes for receptors tyrosine kinases and TGF signalling pathways encoded in the sea urchin genome. Dev. Biol. (2006)
72. Lespinet O., Wolf Y.I., Koonin E.V., and Aravind L. The role of lineage-specific gene family expansion in the evolution of eukaryotes. Genome Res. 12 (2002) 1048-1059
73. Lim R.Y., Aebi U., and Stoffler D. From the trap to the basket: getting to the bottom of the nuclear pore complex. Chromosoma 115 (2006) 15-26
74. Lin C.Y., Li C.C., Huang P.H., and Lee F.J. A developmentally regulated ARF-like 5 protein (ARL5), localized to nuclei and nucleoli, interacts with heterochromatin protein 1. J. Cell Sci. 115 (2002) 4433-4445
75. Londei P. Evolution of translational initiation: new insights from the archaea. FEMS Microbiol. Rev. 29 (2005) 185-200
76. Luirink J., and Sinning I. SRP-mediated protein targeting: structure and function revisited. Biochim. Biophys. Acta 1694 (2004) 17-35
77. Maddison D.R., and Maddison W.P. MacClade 4: Analysis of Phylogeny and Character Evolution (2000), Sinauer Associates, Sunderland, MA
78. Malumbres M., and Barbacid M. RAS oncogenes: the first 30 years. Nat. Rev., Cancer 3 (2003) 459-465
79. Manzo S., Martinez-Cadena G., Lopez-Godinez J., Pedraza-Reyes M., and Garcia-Soto J. A Rho GTPase controls the rate of protein synthesis in the sea urchin egg. Biochem. Biophys. Res. Commun. 310 (2003) 685-690
80. Marchler-Bauer A., Anderson J.B., Cherukuri P.F., DeWeese-Scott C., Geer L.Y., Gwadz M., He S., Hurwitz D.I., Jackson J.D., Ke Z., Lanczycki C.J., Liebert C.A., Liu C., Lu F., Marchler G.H., Mullokandov M., Shoemaker B.A., Simonyan V., Song J.S., Thiessen P.A., Yamashita R.A., Yin J.J., Zhang D., and Bryant S.H. CDD: a Conserved Domain Database for protein classification. Nucleic Acids Res. 33 (2005) D192-D196
81. Marinissen M.J., Chiariello M., and Gutkind J.S. Regulation of gene expression by the small GTPase Rho through the ERK6 (p38 gamma) MAP kinase pathway. Genes Dev. 15 (2001) 535-553
82. Marlow F., Topczewski J., Sepich D., and Solnica-Krezel L. Zebrafish Rho kinase 2 acts downstream of Wnt11 to mediate cell polarity and effective convergence and extension movements. Curr. Biol. 12 (2002) 876-884
83. McCudden C.R., Hains M.D., Kimple R.J., Siderovski D.P., and Willard F.S. G-protein signaling: back to the future. Cell. Mol. Life Sci. 62 (2005) 551-577
84. Meller N., Merlot S., and Guda C. CZH proteins: a new family of Rho-GEFs. J. Cell Sci. 118 (2005) 4937-4946
85. Michaelson D., Ali W., Chiu V.K., Bergo M., Silletti J., Wright L., Young S.G., and Philips M. Postprenylation CAAX processing is required for proper localization of Ras but not Rho GTPases. Mol. Biol. Cell 16 (2005) 1606-1616
86. Morales J., Mulner-Lorillon O., Cosson B., Morin E., Belle R., Bradham C.A., Beane W.S., and Cormier P. Translational control genes in the sea urchin genome. Dev. Biol. (2006)
87. Nagai K., Oubridge C., Kuglstatter A., Menichelli E., Isel C., and Jovine L. Structure, function and evolution of the signal recognition particle. EMBO J. 22 (2003) 3479-3485
88. Namekawa M., Ribai P., Nelson I., Forlani S., Fellmann F., Goizet C., Depienne C., Stevanin G., Ruberg M., Durr A., and Brice A. SPG3A is the most frequent cause of hereditary spastic paraplegia with onset before age 10 years. Neurology 66 (2006) 112-114
89. Nishimura Y., and Mabuchi I. An IQGAP-like protein is involved in actin assembly together with Cdc42 in the sea urchin egg. Cell. Motil. Cytoskelet. 56 (2003) 207-218
90. Nishimura Y., Nakano K., and Mabuchi I. Localization of Rho GTPase in sea urchin eggs. FEBS Lett. 441 (1998) 121-126
91. Novoselov V.V., Alexandrova E.M., Ermakova G.V., and Zaraisky A.G. Expression zones of three novel genes abut the developing anterior neural plate of Xenopus embryo. Gene Expression Patterns 3 (2003) 225-230
92. Ohta K., Toriyama M., Miyazaki M., Murofushi H., Hosoda S., Endo S., and Sakai H. The mitotic apparatus-associated 51-kDa protein from sea urchin eggs is a GTP-binding protein and is immunologically related to yeast polypeptide elongation factor 1 alpha. J. Biol. Chem. 265 (1990) 3240-3247
93. Ohta K., Sato C., Matsuda T., Toriyama M., Vacquier V.D., Lennarz W.J., and Kitajima K. Co-localization of receptor and transducer proteins in the glycosphingolipid-enriched, low density, detergent-insoluble membrane fraction of sea urchin sperm. Glycoconj. J. 17 (2000) 205-214
94. Paduch M., Jelen F., and Otlewski J. Structure of small G proteins and their regulators. Acta Biochim. Pol. 48 (2001) 829-850
95. Peri S., Navarro J.D., Amanchy R., Kristiansen T.Z., Jonnalagadda C.K., Surendranath V., Niranjan V., Muthusamy B., Gandhi T.K., Gronborg M., Ibarrola N., Deshpande N., Shanker K., Shivashankar H.N., Rashmi B.P., Ramya M.A., Zhao Z., Chandrika K.N., Padma N., Harsha H.C., Yatish A.J., Kavitha M.P., Menezes M., Choudhury D.R., Suresh S., Ghosh N., Saravana R., Chandran S., Krishna S., Joy M., Anand S.K., Madavan V., Joseph A., Wong G.W., Schiemann W.P., Constantinescu S.N., Huang L., Khosravi-Far R., Steen H., Tewari M., Ghaffari S., Blobe G.C., Dang C.V., Garcia J.G., Pevsner J., Jensen O.N., Roepstorff P., Deshpande K.S., Chinnaiyan A.M., Hamosh A., Chakravarti A., and Pandey A. Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res. 13 (2003) 2363-2371
96. Philips A., Blein M., Robert A., Chambon J.P., Baghdiguian S., Weill M., and Fort P. Ascidians as a vertebrate-like model organism for physiological studies of Rho GTPase signaling. Biol. Cell 95 5 (2003) 295-302
97. Phillips R.B. Adaptive evolution or genetic drift? Does genome complexity produce organismal complexity?. Heredity 93 (2004) 122-123
98. Pool M.R. Signal recognition particles in chloroplasts, bacteria, yeast and mammals (review). Mol. Membr. Biol. 22 (2005) 3-15
99. Praefcke G.J., and McMahon H.T. The dynamin superfamily: universal membrane tubulation and fission molecules?. Nat. Rev., Mol. Cell Biol. 5 (2004) 133-147
100. Proud C.G. eIF2 and the control of cell physiology. Semin. Cell Dev. Biol. 16 (2005) 3-12
101. Raible F., Tessmar-Raible K., Arboleda E., Kaller T., Bork P., Arendt D., and Arnone M.I. Opsins and clusters of sensory G-protein coupled receptors in the sea urchin genome. Dev. Biol. (2006)
102. Ramos S., Khademi F., Somesh B.P., and Rivero F. Genomic organization and expression profile of the small GTPases of the RhoBTB family in human and mouse. Gene 298 (2002) 147-157
103. Reams A.B., and Neidle E.L. Selection for gene clustering by tandem duplication. Annu. Rev. Microbiol. 58 (2004) 119-142
104. Romisch K., Miller F.W., Dobberstein B., and High S. Human autoantibodies against the 54 kDa protein of the signal recognition particle block function at multiple stages. Arthritis Res. Ther. 8 (2006) R39
105. Ronquist F., and Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
106. Rosenblad M.A., Gorodkin J., Knudsen B., Zwieb C., and Samuelsson T. SRPDB: signal recognition particle database. Nucleic Acids Res. 31 (2003) 363-364
107. Rossman K.L., Der C.J., and Sondek J. GEF means go: turning on RHO GTPases with guanine nucleotide-exchange factors. Nat. Rev., Mol. Cell Biol. 6 (2005) 167-180
108. Sahai E., and Marshall C.J. RHO-GTPases and cancer. Nat. Rev., Cancer 2 (2002) 133-142
109. Salas-Marco J., and Bedwell D.M. GTP hydrolysis by eRF3 facilitates stop codon decoding during eukaryotic translation termination. Mol. Cell. Biol. 24 (2004) 7769-7778
110. Samanta, M.P., Tongprasit, W., Istrail, S., Cameron, A., Tu, Q., Davidson, E.H., and Stolc, V. (2006). A high-resolution transcriptome map of the sea urchin embryo.
111. Scheffzek K., and Ahmadian M.R. GTPase activating proteins: structural and functional insights 18 years after discovery. Cell. Mol. Life Sci. 62 (2005) 3014-3038
112. Seabra M.C., and Wasmeier C. Controlling the location and activation of Rab GTPases. Curr. Opin. Cell Biol. 16 (2004) 451-457
113. Siderovski D.P., and Willard F.S. The GAPs, GEFs, and GDIs of heterotrimeric G-protein alpha subunits. Int. J. Biol. Sci. 1 (2005) 51-66
114. Sonnhammer E.L., and Koonin E.V. Orthology, paralogy and proposed classification for paralog subtypes. Trends Genet. 18 (2002) 619-620
115. Spiegel A.M., and Weinstein L.S. Inherited diseases involving g proteins and G protein-coupled receptors. Annu. Rev. Med. 55 (2004) 27-39
116. Stamatakis A., Ludwig T., and Meier H. RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 21 (2005) 456-463
117. Stenmark H., and Olkkonen V.M. The Rab GTPase family. Genome Biol. 2 (2001) (REVIEWS3007)
118. Stochaj U., and Rother K.L. Nucleocytoplasmic trafficking of proteins: with or without Ran?. BioEssays 21 (1999) 579-589
119. Su Z.J., Hahn C.N., Goodall G.J., Reck N.M., Leske A.F., Davy A., Kremmidiotis G., Vadas M.A., and Gamble J.R. A vascular cell-restricted RhoGAP, p73RhoGAP, is a key regulator of angiogenesis. Proc. Natl. Acad. Sci. U. S. A. 101 (2004) 12212-12217
120. Swofford D.L. PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods) (1998), Sinauer Associates, Sunderland, MA
121. Tahinci E., and Symes K. Distinct functions of Rho and Rac are required for convergent extension during Xenopus gastrulation. Dev. Biol. 259 (2003) 318-335
122. Taylor J.S., and Raes J. Duplication and divergence: the evolution of new genes and old ideas. Annu. Rev. Genet. 38 (2004) 615-643
123. Tereshina M.B., Zaraisky A.G., and Novoselov V.V. Ras-dva, a member of novel family of small GTPases, is required for the anterior ectoderm patterning in the Xenopus laevis embryo. Development 133 (2006) 485-494
124. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25 (1997) 4876-4882
125. Thoms S., and Erdmann R. Dynamin-related proteins and Pex11 proteins in peroxisome division and proliferation. FEBS J. 272 (2005) 5169-5181
126. Vestal D.J. The guanylate-binding proteins (GBPs): proinflammatory cytokine-induced members of the dynamin superfamily with unique GTPase activity. J. Interferon Cytokine Res. 25 (2005) 435-443
127. 2+ release at fertilization in the sea urchin. J. Cell Sci. 117 (2004) 5995-6005
128. Voronina E., and Wessel G.M. Regulatory contribution of heterotrimeric G-proteins to oocyte maturation in the sea urchin. Mech. Dev. 121 (2004) 247-259
129. Votruba M., Aijaz S., and Moore A.T. A review of primary hereditary optic neuropathies. J. Inherited Metab. Dis. 26 (2003) 209-227
130. Walton K.D., Croce J.C., Glenn T.D., Wu S.-Y., and McClay D.R. Genomics and expression profiles of the Hedgehog and Notch signaling pathways in sea urchin development. Dev. Biol. (2006)
131. Wennerberg K., Rossman K.L., and Der C.J. The Ras superfamily at a glance. J. Cell Sci. 118 (2005) 843-846
132. Wettschureck N., and Offermanns S. Mammalian G proteins and their cell type specific functions. Physiol. Rev. 85 (2005) 1159-1204
133. Whitehead I.P. Rho family guanine nucleotide exchange factors. Rho GTPases (2004), Landes Biosciences, Georgetown, TX 46-67
134. Wilkins A., Ping Q., and Carpenter C.L. RhoBTB2 is a substrate of the mammalian Cul3 ubiquitin ligase complex. Genes Dev. 18 (2004) 856-861
135. Williams D.D., Price N.T., Loughlin A.J., and Proud C.G. Characterization of the mammalian initiation factor eIF2B complex as a GDP dissociation stimulator protein. J. Biol. Chem. 276 (2001) 24697-24703
136. Wistow G., Bernstein S.L., Ray S., Wyatt M.K., Behal A., Touchman J.W., Bouffard G., Smith D., and Peterson K. Expressed sequence tag analysis of adult human iris for the NEIBank project: steroid-response factors and similarities with retinal pigment epithelium. Mol. Vision 8 (2002) 185-195
137. Zong H., Kaibuchi K., and Quilliam L.A. The insert region of RhoA is essential for Rho kinase activation and cellular transformation. Mol. Cell. Biol. 21 (2001) 5287-5298
138. Zuk P.A., and Elferink L.A. Rab15 differentially regulates early endocytic trafficking. J. Biol. Chem. 275 (2000) 26754-26764