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Research Paper

Evolution of the Ras-like small GTPases and their regulators

Pages 4-16 | Received 29 Sep 2010, Accepted 09 Feb 2011, Published online: 01 Jan 2011

References

  • Wennerberg K, Rossman KL, Der CJ. The Ras superfamily at a glance. J Cell Sci 2005; 118:843 - 846; http://dx.doi.org/10.1242/jcs.01660
  • Yutin N, Wolf MY, Wolf YI, Koonin EV. The origins of phagocytosis and eukaryogenesis. Biology direct 2009; 4:9; http://dx.doi.org/10.1186/1745-6150-4-9
  • Jékely G. Small GTPases and the evolution of the eukaryotic cell. BioEssays 2003; 25:1129 - 1138; http://dx.doi.org/10.1002/bies.10353
  • Brighouse A, Dacks JB, Field MC. Rab protein evolution and the history of the eukaryotic endomembrane system. Cell Mol Life Sci 2010; 1:17; http://dx.doi.org/10.1007/s00018-010-0436-1
  • Boureux A, Vignal E, Faure S, Fort P. Evolution of the Rho family of ras-like GTPases in eukaryotes. Mol Biol Evol 2007; 24:203 - 216; http://dx.doi.org/10.1093/molbev/msl145
  • Elias M, Patron NJ, Keeling PJ. The RAB family GTPase Rab1A from Plasmodium falciparum defines a unique paralog shared by chromalveolates and rhizaria. J Eukaryot Microbiol 56:348 - 356; http://dx.doi.org/10.1111/j.1550-7408.2009.00408.x
  • Bos JL, Rehmann H, Wittinghofer A. GEFs and GAPs: critical elements in the control of small G proteins. Cell 2007; 129:865 - 877; http://dx.doi.org/10.1016/j.cell.2007.05.018
  • Dam TJP van, Rehmann H, Bos JL, Snel B. Phylogeny of the CDC25 homology domain reveals rapid differentiation of Ras pathways between early animals and fungi. Cell Signal 2009; 21:1579 - 1585; http://dx.doi.org/10.1016/j.cellsig.2009.06.004
  • Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 2002; 30:3059 - 3066; http://dx.doi.org/10.1093/nar/gkf436
  • Stamatakis A, Ludwig T, Meier H. RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 2005; 21:456 - 463; http://dx.doi.org/10.1093/bioinformatics/bti191
  • Gridley S, Chavez JA, Lane WS, Lienhard GE. Adipocytes contain a novel complex similar to the tuberous sclerosis complex. Cell Signal 2006; 18:1626 - 1632; http://dx.doi.org/10.1016/j.cellsig.2006.01.002
  • Shirakawa R, Fukai S, Kawato M, Higashi T, Kondo H, Ikeda T, et al. Tuberous sclerosis tumor suppressor complex-like complexes act as GTPase-activating proteins for Ral GTPases. J Biol Chem 2009; 284:21580 - 21588; http://dx.doi.org/10.1074/jbc.M109.012112
  • Scrima A, Thomas C, Deaconescu D, Wittinghofer A. The Rap-RapGAP complex: GTP hydrolysis without catalytic glutamine and arginine residues. EMBO J 2008; 27:1145 - 1153; http://dx.doi.org/10.1038/emboj.2008.30
  • Chen XQ. The Myotonic Dystrophy Kinase-related Cdc42-binding Kinase Is Involved in the Regulation of Neurite Outgrowth in PC12 Cells. J Biol Chem 1999; 274:19901 - 19905; http://dx.doi.org/10.1074/jbc.274.28.19901
  • Lodhi IJ, Chiang SH, Chang L, Vollenweider D, Watson RT, Inoue M, et al. Gapex-5, a Rab31 guanine nucleotide exchange factor that regulates Glut4 trafficking in adipocytes. Cell Metab 2007; 5:59 - 72; http://dx.doi.org/10.1016/j.cmet.2006.12.006
  • Sato M, Sato K, Fonarev P, Huang CJ, Liou W, Grant BD. Caenorhabditis elegans RME-6 is a novel regulator of RAB-5 at the clathrin-coated pit. Nat Cell Biol 2005; 7:559 - 569; http://dx.doi.org/10.1038/ncb1261
  • Hunker CM, Galvis A, Kruk I, Giambini H, Veisaga ML, Barbieri MA. Rab5-activating protein 6, a novel endosomal protein with a role in endocytosis. Biochem Bioph Res Co 2006; 340:967 - 975; http://dx.doi.org/10.1016/j.bbrc.2005.12.099
  • Hart MJ, Callow MG, Souza B, Polakis P. IQGAP1, a calmodulin-binding protein with a rasGAP-related domain, is a potential effector for cdc42Hs. EMBO J 1996; 15:2997 - 3005
  • Brill S, Li S, Lyman C, Church D, Wasmuth J, Weissbach L, et al. The Ras GTPase-activating-protein-related human protein IQGAP2 harbors a potential actin binding domain and interacts with calmodulin and Rho family GTPases. Mol Cell Biol 1996; 16:4869 - 4878
  • Osman MA. Iqg1p, a Yeast Homologue of the Mammalian IQGAPs, Mediates Cdc42p Effects on the Actin Cytoskeleton. J Cell Biol 1998; 142:443 - 455; http://dx.doi.org/10.1083/jcb.142.2.443
  • Imai Y, Miyake S, Hughes DA, Yamamoto M. Identification of a GTPase-activating protein homolog in Schizosaccharomyces pombe. Mol Cell Biol 1991; 11:3088 - 3094
  • Johannessen CM, Reczek EE, James MF, Brems H, Legius E, Cichowski K. The NF1 tumor suppressor critically regulates TSC2 and mTOR. P Natl Acad Sci USA 2005; 102:8573 - 8578; http://dx.doi.org/10.1073/pnas.0503224102
  • Park HO, Chant J, Herskowitz I. BUD2 encodes a GTPase-activating protein for Bud1/Rsr1 necessary for proper bud-site selection in yeast. Nature 1993; 365:269 - 274; http://dx.doi.org/10.1038/365269a0
  • Krapivinsky G, Medina I, Krapivinsky L, Gapon S, Clapham DE. SynGAP-MUPP1-CaMKII synaptic complexes regulate p38 MAP kinase activity and NMDA receptor-dependent synaptic AMPA receptor potentiation. Neuron 2004; 43:563 - 574; http://dx.doi.org/10.1016/j.neuron.2004.08.003
  • Kupzig S, Deaconescu D, Bouyoucef D, Walker SA, Liu Q, Polte CL, et al. GAP1 family members constitute bifunctional Ras and Rap GTPase-activating proteins. J Biol Chem 2006; 281:9891 - 9900; http://dx.doi.org/10.1074/jbc.M512802200
  • Pena V, Hothorn M, Eberth A, Kaschau N, Parret A, Gremer L, et al. The C2 domain of SynGAP is essential for stimulation of the Rap GTPase reaction. EMBO Rep 2008; 9:350 - 355; http://dx.doi.org/10.1038/embor.2008.20
  • Bos JL. Linking Rap to cell adhesion. Curr Opin Cell Biol 2005; 17:123 - 128; http://dx.doi.org/10.1016/j.ceb.2005.02.009
  • Bos JL. ras oncogenes in human cancer: a review. Cancer Res 1989; 49:4682 - 4689
  • Colicelli J. Human RAS superfamily proteins and related GTPases. Science STKE 2004; 13; http://dx.doi.org/10.1126/stke.2502004re13
  • Cox AD, Der CJ. Ras history. Small GTPases 2010; 1:2 - 27; http://dx.doi.org/10.4161/sgtp.1.1.12178
  • Karnoub AE, Weinberg RA. Ras oncogenes: split personalities. Nat Rev Mol Cell Bio 2008; 9:517 - 531; http://dx.doi.org/10.1038/nrm2438
  • Drivas GT, Palmieri S, D'Eustachio P, Rush MG. Evolutionary grouping of the RAS-protein family. Biochem Bioph Res Co 1991; 176:1130 - 1135; http://dx.doi.org/10.1016/0006-291X(91)90402-S
  • Valencia A, Chardin P, Wittinghofer A, Sander C. The ras protein family: evolutionary tree and role of conserved amino acids. Biochemistry 1991; 30:4637 - 4648
  • Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, et al. The Pfam protein families database. Nucleic Acids Res 2008; 36:281 - 288; http://dx.doi.org/10.1093/nar/gkm960
  • Guindon S, Gascuel O. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003; 52:696 - 704; http://dx.doi.org/10.1080/10635150390235520
  • Moskalenko S, Henry DO, Rosse C, Mirey G, Camonis JH, White MA. The exocyst is a Ral effector complex. Nat Cell Biol 2002; 4:66 - 72; http://dx.doi.org/10.1038/ncb728
  • Lipschutz JH, Mostov KE. Exocytosis: the many masters of the exocyst. Curr Biol 2002; 12:212 - 214; http://dx.doi.org/10.1016/S0960-9822(02)00753-4
  • Kitayama H, Sugimoto Y, Matsuzaki T, Ikawa Y, Noda M. A ras-related gene with transformation suppressor activity. Cell 1989; 56:77 - 84; http://dx.doi.org/10.1016/0092-8674(89)90985-9
  • Fritz-Laylin LK, Prochnik SE, Ginger ML, Dacks JB, Carpenter ML, Field MC, et al. The Genome of Naegleria gruberi Illuminates Early Eukaryotic Versatility. Cell 2010; 140:631 - 642; http://dx.doi.org/10.1016/j.cell.2010.01.032
  • Wullschleger S, Loewith R, Hall MN. TOR signaling in growth and metabolism. Cell 2006; 124:471 - 484; http://dx.doi.org/10.1016/j.cell.2006.01.016
  • Inoki K, Ouyang H, Zhu T, Lindvall C, Wang Y, Zhang X, et al. TSC2 integrates Wnt and energy signals via a coordinated phosphorylation by AMPK and GSK3 to regulate cell growth. Cell 2006; 126:955 - 968; http://dx.doi.org/10.1016/j.cell.2006.06.055
  • Inoki K, Zhu T, Guan KL. TSC2 Mediates Cellular Energy Response to Control Cell Growth and Survival. Cell 2003; 115:577 - 590; http://dx.doi.org/10.1016/S0092-8674(03)00929-2
  • Garami A, Zwartkruis FJT, Nobukuni T, Joaquin M, Roccio M, Stocker H, et al. Insulin Activation of Rheb, a Mediator of mTOR/S6K/4E-BP Signaling, Is Inhibited by TSC1 and 2. Mol Cell 2003; 11:1457 - 1466; http://dx.doi.org/10.1016/S1097-2765(03)00220-X
  • Douzery EJP, Snell EA, Bapteste E, Delsuc F, Philippe H. The timing of eukaryotic evolution: does a relaxed molecular clock reconcile proteins and fossils?. P Natl Acad Sci USA 2004; 101:15386 - 15391; http://dx.doi.org/10.1073/pnas.0403984101
  • Aspuria PJ, Tamanoi F. The Rheb family of GTPbinding proteins. Cell Signal 2004; 16:1105 - 1112; http://dx.doi.org/10.1016/j.cellsig.2004.03.019
  • Hubbard TJ, Aken BL, Ayling S, Ballester B, Beal K, Bragin E, et al. Ensembl 2009. Nucleic Acids Res 2009; 37:690 - 697; http://dx.doi.org/10.1093/nar/gkn828
  • Eddy SR. Profile hidden Markov models. Bioinformatics 1998; 14:755 - 763; http://dx.doi.org/10.1093/bioinformatics/14.9.755
  • Howe K, Bateman A, Durbin R. QuickTree: building huge Neighbour-Joining trees of protein sequences. Bioinformatics 2002; 18:1546 - 1547; http://dx.doi.org/10.1093/bioinformatics/18.11.1546
  • Huson D, Richter D, Rausch C, Dezulian T, Franz M, Rupp R. Dendroscope: An interactive viewer for large phylogenetic trees. BMC bioinformatics 2007; 8:460; http://dx.doi.org/10.1186/1471-2105-8-460
  • Letunic I, Bork P. Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 2007; 23:127 - 128; http://dx.doi.org/10.1093/bioinformatics/btl529
  • Roger AJ, Hug LA. The origin and diversification of eukaryotes: problems with molecular phylogenetics and molecular clock estimation. Philos T Roy Soc B 2006; 361:1039 - 1054; http://dx.doi.org/10.1098/rstb.2006.1845