Gene duplication in early vertebrates results in tissue-specific subfunctionalized adaptor proteins: CASP and GRASP

Journal of Molecular Evolution

Volumn 67, Issue 2, 2008, Pages 168-178

  MacNeil, Adam J ^a   McEachern, Lori A ^a   Pohajdak, Bill ^a  

^a DALHOUSIE UNIVERSITY   (Canada)

Author keywords

Adaptor protein; Cytohesin; Gene duplication; Nuclear receptor 4A; Paralogue; PDZ domain protein; PDZ binding motif; Protein family; Subfunctionalization; Vertebrate

Indexed keywords

ADAPTOR PROTEIN; AMINO ACID; CASP PROTEIN; GRASP PROTEIN; PDZ PROTEIN;

ADAPTIVE IMMUNITY; ARTICLE; BRAIN; COMPARATIVE STUDY; CONTROLLED STUDY; EXON; FISH; GENE DUPLICATION; GENE LOCUS; GENE MUTATION; GENE STRUCTURE; GENETIC CONSERVATION; HUMAN; MOLECULAR EVOLUTION; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PROTEIN BINDING; PROTEIN MOTIF; PROTEIN STRUCTURE; RAT; SPECIES; VERTEBRATE;

AMINO ACID SEQUENCE; ANIMALS; CARRIER PROTEINS; GENE DUPLICATION; GENOME; HUMANS; MEMBRANE PROTEINS; MOLECULAR SEQUENCE DATA; ORGAN SPECIFICITY; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; VERTEBRATES;

BRANCHIOSTOMA LANCEOLATUM; CHORDATA; VERTEBRATA;

EID: 50249154770     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-008-9136-y     Document Type: Article

References (36)

1. Boehm T, Hofer S, Winklehner P, Kellersch B, Geiger C, Trockenbacher A, Neyer S, Fiegl H, Ebner S, Ivarsson L, Schneider R, Kremmer E, Heufler C, Kolanus W (2003) Attenuation of cell adhesion in lymphocytes is regulated by CYTIP, a protein which mediates signal complex sequestration. EMBO J 22:1014-1024
2. Christoffels A, Koh EG, Chia JM, Brenner S, Aparicio S, Venkatesh B (2004) Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes. Mol Biol Evol 21:1146-1151
3. Cooper MD, Alder MN (2006) The evolution of adaptive immune systems. Cell 124:815-822
4. Coppola V, Barrick CA, Bobisse S, Rodriguez-Galan MC, Pivetta M, Reynolds D, Howard OM, Palko ME, Esteban PF, Young HA, Rosato A, Tessarollo L (2006) The scaffold protein Cybr is required for cytokine-modulated trafficking of leukocytes in vivo. Mol Cell Biol 26:5249-5258
5. Esteban PF, Yoon HY, Becker J, Dorsey SG, Caprari P, Palko ME, Coppola V, Saragovi HU, Randazzo PA, Tessarollo L (2006) A kinase-deficient TrkC receptor isoform activates Arf6-Rac1 signaling through the scaffold protein tamalin. J Cell Biol 173:291-299
6. Force A, Lynch M, Pickett FB, Amores A, Yan YL, Postlethwait J (1999) Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151:1531-1545
7. Holland PW, Garcia-Fernandez J, Williams NA, Sidow A (1994) Gene duplications and the origins of vertebrate development. Dev Suppl:125-133
8. Hughes AL, Piontkivska H (2005) DNA repeat arrays in chicken and human genomes and the adaptive evolution of avian genome size. BMC Evol Biol 5:12
9. Hung AY, Sheng M (2002) PDZ domains: structural modules for protein complex assembly. J Biol Chem 277:5699-702
10. Jaillon O, Aury JM, Brunet F, Petit JL, Stange-Thomann N, Mauceli E, Bouneau L, Fischer C, Ozouf-Costaz C, Bernot A, Nicaud S, Jaffe D, Fisher S, Lutfalla G, Dossat C, Segurens B, Dasilva C, Salanoubat M, Levy M, Boudet N, Castellano S, Anthouard V, Jubin C, Castelli V, Katinka M, Vacherie B, Biemont C, Skalli Z, Cattolico L, Poulain J, De Berardinis V, Cruaud C, Duprat S, Brottier P, Coutanceau JP, Gouzy J, Parra G, Lardier G, Chapple C, McKernan KJ, McEwan P, Bosak S, Kellis M, Volff JN, Guigo R, Zody MC, Mesirov J, Lindblad-Toh K, Birren B, Nusbaum C, Kahn D, Robinson-Rechavi M, Laudet V, Schachter V, Quetier F, Saurin W, Scarpelli C, Wincker P, Lander ES, Weissenbach J, Roest Crollius H (2004) Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431:946-957
11. Jelen F, Oleksy A, Smietana K, Otlewski J (2003) PDZ domains-common players in the cell signaling. Acta Biochim Pol 50:985-1017
12. Jemth P, Gianni S (2007) PDZ domains: folding and binding. Biochemistry 46:8701-8708
13. Joubert L, Hanson B, Barthet G, Sebben M, Claeysen S, Hong W, Marin P, Dumuis A, Bockaert J (2004) New sorting nexin (SNX27) and NHERF specifically interact with the 5-HT4a receptor splice variant: roles in receptor targeting. J Cell Sci 117:5367-5379
14. Kapsimali M, Bourrat F, Vernier P (2001) Distribution of the orphan nuclear receptor Nurr1 in medaka (Oryzias latipes): cues to the definition of homologous cell groups in the vertebrate brain. J Comp Neurol 431:276-292
15. Kent WJ (2002) BLAT-the BLAST-like alignment tool. Genome Res 12:656-664
16. Kimura K, Kitano J, Nakajima Y, Nakanishi S (2004) Hyperpolarization- activated, cyclic nucleotide-gated HCN2 cation channel forms a protein assembly with multiple neuronal scaffold proteins in distinct modes of protein-protein interaction. Genes Cells 9:631-640
17. Kitano J, Kimura K, Yamazaki Y, Soda T, Shigemoto R, Nakajima Y, Nakanishi S (2002) Tamalin, a PDZ domain-containing protein, links a protein complex formation of group 1 metabotropic glutamate receptors and the guanine nucleotide exchange factor cytohesins. J Neurosci 22:1280-1289
18. Kitano J, Yamazaki Y, Kimura K, Masukado T, Nakajima Y, Nakanishi S (2003) Tamalin is a scaffold protein that interacts with multiple neuronal proteins in distinct modes of protein-protein association. J Biol Chem 278:14762-14768
19. Lynch M, Conery JS (2000) The evolutionary fate and consequences of duplicate genes. Science 290:1151-1155
20. Lynch M, Force A (2000) The probability of duplicate gene preservation by subfunctionalization. Genetics 154:459-473
21. MacNeil AJ, Mansour M, Pohajdak B (2007) Sorting nexin 27 interacts with the Cytohesin associated scaffolding protein (CASP) in lymphocytes. Biochem Biophys Res Commun 359:848-853
22. Malmberg EK, Andersson CX, Gentzsch M, Chen JH, Mengos A, Cui L, Hansson GC, Riordan JR (2004) Bcr (breakpoint cluster region) protein binds to PDZ-domains of scaffold protein PDZK1 and vesicle coat protein Mint3. J Cell Sci 117:5535-5541
23. Mansour M, Lee SY, Pohajdak B (2002) The N-terminal coiled coil domain of the cytohesin/ARNO family of guanine nucleotide exchange factors interacts with the scaffolding protein CASP. J Biol Chem 277:32302-32309
24. Nevrivy DJ, Peterson VJ, Avram D, Ishmael JE, Hansen SG, Dowell P, Hruby DE, Dawson MI, Leid M (2000) Interaction of GRASP, a protein encoded by a novel retinoic acid-induced gene, with members of the cytohesin family of guanine nucleotide exchange factors. J Biol Chem 275:16827-16836
25. Nourry C, Grant SG, Borg JP (2003) PDZ domain proteins: plug and play! Sci STKE 2003:RE7
26. Nowak MA, Boerlijst MC, Cooke J, Smith JM (1997) Evolution of genetic redundancy. Nature 388:167-171
27. Ogawa M, Miyakawa T, Nakamura K, Kitano J, Furushima K, Kiyonari H, Nakayama R, Nakao K, Moriyoshi K, Nakanishi S (2007) Altered sensitivities to morphine and cocaine in scaffold protein tamalin knockout mice. Proc Natl Acad Sci USA 104:14789-14794
28. Osorio J, Retaux S (2008) The lamprey in evolutionary studies. Dev Genes Evol 218:221-235
29. Page RD (1996) TreeView: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12:357-358
30. Pancer Z, Cooper MD (2006) The evolution of adaptive immunity. Annu Rev Immunol 24:497-518
31. Pegan S, Tan J, Huang A, Slesinger PA, Riek R, Choe S (2007) NMR studies of interactions between C-terminal tail of Kir2.1 channel and PDZ1, 2 domains of PSD95. Biochemistry 46:5315-5322
32. Sidow A (1996) Gen(om)e duplications in the evolution of early vertebrates. Curr Opin Genet Dev 6:715-722
33. Stamatakis A, Ludwig T, Meier H (2005) RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 21:456-463
34. Sugi T, Oyama T, Muto T, Nakanishi S, Morikawa K, Jingami H (2007) Crystal structures of autoinhibitory PDZ domain of Tamalin: implications for metabotropic glutamate receptor trafficking regulation. EMBO J 26:2192-2205
35. Tang P, Cheng TP, Agnello D, Wu CY, Hissong BD, Watford WT, Ahn HJ, Galon J, Moss J, Vaughan M, O'Shea JJ, Gadina M (2002) Cybr, a cytokine-inducible protein that binds cytohesin-1 and regulates its activity. Proc Natl Acad Sci USA 99:2625-2629
36. Watford WT, Li D, Agnello D, Durant L, Yamaoka K, Yao ZJ, Ahn HJ, Cheng TP, Hofmann SR, Cogliati T, Chen A, Hissong BD, Husa MR, Schwartzberg P, O'Shea JJ, Gadina M (2006) Cytohesin binder and regulator (Cybr) is not essential for T- and dendritic-cell activation and differentiation. Mol Cell Biol 26:6623-6632