The GPCR repertoire in the demosponge Amphimedon queenslandica: insights into the GPCR system at the early divergence of animals
Tóm tắt
Từ khóa
Tài liệu tham khảo
Rask-Andersen M, Almen MS, Schioth HB: Trends in the exploitation of novel drug targets. Nat Rev Drug Discov. 2011, 10 (8): 579-590. 10.1038/nrd3478.
Lagerström MC, Schiöth HB: Structural diversity of G protein-coupled receptors and significance for drug discovery. Nat Rev Drug Discov. 2008, 7 (4): 339-357. 10.1038/nrd2518.
Schioth HB, Fredriksson R: The GRAFS classification system of G-protein coupled receptors in comparative perspective. Gen Comp Endocrinol. 2005, 142 (1–2): 94-101. 10.1016/j.ygcen.2004.12.018.
Fredriksson R, Lagerstrom MC, Lundin LG, Schioth HB: The G-protein-coupled receptors in the human genome form five main families. Phylogenetic analysis, paralogon groups, and fingerprints. Mol Pharmacol. 2003, 63 (6): 1256-1272. 10.1124/mol.63.6.1256.
Brody T, Cravchik A: Drosophila melanogaster G protein-coupled receptors. J Cell Biol. 2000, 150 (2): F83-F88. 10.1083/jcb.150.2.F83.
Krishnan A, Almen MS, Fredriksson R, Schioth HB: Remarkable similarities between the hemichordate (Saccoglossus kowalevskii) and vertebrate GPCR repertoire. Gene. 2013, 526 (2): 122-133. 10.1016/j.gene.2013.05.005.
Nordstrom KJ, Fredriksson R, Schioth HB: The amphioxus (Branchiostoma floridae) genome contains a highly diversified set of G protein-coupled receptors. BMC Evol Biol. 2008, 8: 9-10.1186/1471-2148-8-9.
Kamesh N, Aradhyam GK, Manoj N: The repertoire of G protein-coupled receptors in the sea squirt Ciona intestinalis. BMC Evol Biol. 2008, 8: 129-10.1186/1471-2148-8-129.
Krishnan A, Almén MS, Fredriksson R, Schiöth HB: The origin of GPCRs: identification of mammalian like Rhodopsin, Adhesion, Glutamate and Frizzled GPCRs in fungi. PLoS ONE. 2012, 7 (1): e29817-10.1371/journal.pone.0029817.
de Mendoza A, Sebe-Pedros A, Ruiz-Trillo I: The evolution of the GPCR signaling system in eukaryotes: modularity, conservation, and the transition to metazoan multicellularity. Genome Biol Evol. 2014, 6 (3): 606-619. 10.1093/gbe/evu038.
Srivastava M, Simakov O, Chapman J, Fahey B, Gauthier MEA, Mitros T, Richards GS, Conaco C, Dacre M, Hellsten U, Larroux C, Putnam NH, Stanke M, Adamska M, Darling A, Degnan SM, Oakley TH, Plachetzki DC, Zhai Y, Adamski M, Calcino A, Cummins SF, Goodstein DM, Harris C, Jackson DJ, Leys SP, Shu S, Woodcroft BJ, Vervoort M, Kosik KS, et al: The Amphimedon queenslandica genome and the evolution of animal complexity. Nature. 2010, 466 (7307): 720-726. 10.1038/nature09201.
Conaco C, Neveu P, Zhou H, Arcila ML, Degnan SM, Degnan BM, Kosik KS: Transcriptome profiling of the demosponge Amphimedon queenslandica reveals genome-wide events that accompany major life cycle transitions. BMC Genomics. 2012, 13: 209-10.1186/1471-2164-13-209.
Sakarya O, Armstrong KA, Adamska M, Adamski M, Wang IF, Tidor B, Degnan BM, Oakley TH, Kosik KS: A post-synaptic scaffold at the origin of the animal kingdom. PLoS One. 2007, 2 (6): e506-10.1371/journal.pone.0000506.
Adamska M, Larroux C, Adamski M, Green K, Lovas E, Koop D, Richards GS, Zwafink C, Degnan BM: Structure and expression of conserved Wnt pathway components in the demosponge Amphimedon queenslandica. Evol Dev. 2010, 12 (5): 494-518. 10.1111/j.1525-142X.2010.00435.x.
King N, Westbrook MJ, Young SL, Kuo A, Abedin M, Chapman J, Fairclough S, Hellsten U, Isogai Y, Letunic I, Marr M, Pincus D, Putnam N, Rokas A, Wright KJ, Zuzow R, Dirks W, Good M, Goodstein D, Lemons D, Li W, Lyons JB, Morris A, Nichols S, Richter DJ, Salamov A, Sequencing JG, Bork P, Lim WA, Manning G, et al: The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. Nature. 2008, 451 (7180): 783-788. 10.1038/nature06617.
Suga H, Chen Z, de Mendoza A, Sebe-Pedros A, Brown MW, Kramer E, Carr M, Kerner P, Vervoort M, Sanchez-Pons N, Torruella G, Derelle R, Manning G, Lang BF, Russ C, Haas BJ, Roger AJ, Nusbaum C, Ruiz-Trillo I: The Capsaspora genome reveals a complex unicellular prehistory of animals. Nat Commun. 2013, 4: 2325-10.1038/ncomms3325.
Srivastava M, Begovic E, Chapman J, Putnam NH, Hellsten U, Kawashima T, Kuo A, Mitros T, Salamov A, Carpenter ML, Signorovitch AY, Moreno MA, Kamm K, Grimwood J, Schmutz J, Shapiro H, Grigoriev IV, Buss LW, Schierwater B, Dellaporta SL, Rokhsar DS: The Trichoplax genome and the nature of placozoans. Nature. 2008, 454 (7207): 955-960. 10.1038/nature07191.
Nordstrom KJ, Sallman Almen M, Edstam MM, Fredriksson R, Schioth HB: Independent HHsearch, Needleman–Wunsch-based, and motif analyses reveal the overall hierarchy for most of the G protein-coupled receptor families. Mol Biol Evol. 2011, 28 (9): 2471-2480. 10.1093/molbev/msr061.
Degnan BM, Adamska M, Craigie A, Degnan SM, Fahey B, Gauthier M, Hooper JN, Larroux C, Leys SP, Lovas E, Richards GS: The demosponge amphimedon queenslandica: reconstructing the ancestral metazoan genome and deciphering the origin of animal multicellularity. CSH Protoc. 2008, 2008: pdb emo108-
Leys SP, Hill A: The physiology and molecular biology of sponge tissues. Adv Mar Biol. 2012, 62: 1-56. 10.1016/B978-0-12-394283-8.00001-1.
Fahey B, Degnan BM: Origin of animal epithelia: insights from the sponge genome. Evol Dev. 2010, 12 (6): 601-617. 10.1111/j.1525-142X.2010.00445.x.
Miller DJ, Ball EE: Animal evolution: the enigmatic phylum placozoa revisited. Curr Biol. 2005, 15 (1): R26-R28. 10.1016/j.cub.2004.12.016.
Technau U, Steele RE: Evolutionary crossroads in developmental biology: Cnidaria. Development. 2011, 138 (8): 1447-1458. 10.1242/dev.048959.
Watanabe H, Fujisawa T, Holstein TW: Cnidarians and the evolutionary origin of the nervous system. Dev Growth Differ. 2009, 51 (3): 167-183. 10.1111/j.1440-169X.2009.01103.x.
Harmar AJ: Family-B G-protein-coupled receptors. Genome Biol. 2001, 2 (12): REVIEWS3013-10.1186/gb-2001-2-12-reviews3013.
Nordström KJV, Lagerström MC, Wallér LMJ, Fredriksson R, Schiöth HB: The Secretin GPCRs Descended from the Family of Adhesion GPCRs. Mol Biol Evol. 2009, 26 (1): 71-84. 10.1093/molbev/msn228.
Cardoso JC, Pinto VC, Vieira FA, Clark MS, Power DM: Evolution of secretin family GPCR members in the metazoa. BMC Evol Biol. 2006, 6: 108-10.1186/1471-2148-6-108.
Fredriksson R, Schioth HB: The repertoire of G-protein-coupled receptors in fully sequenced genomes. Mol Pharmacol. 2005, 67 (5): 1414-1425. 10.1124/mol.104.009001.
Resnick D, Pearson A, Krieger M: The SRCR superfamily: a family reminiscent of the Ig superfamily. Trends Biochem Sci. 1994, 19 (1): 5-8. 10.1016/0968-0004(94)90165-1.
Sarrias MR, Gronlund J, Padilla O, Madsen J, Holmskov U, Lozano F: The Scavenger Receptor Cysteine-Rich (SRCR) domain: an ancient and highly conserved protein module of the innate immune system. Crit Rev Immunol. 2004, 24 (1): 1-37. 10.1615/CritRevImmunol.v24.i1.10.
Riesgo A, Farrar N, Windsor PJ, Giribet G, Leys SP: The analysis of eight transcriptomes from all poriferan classes reveals surprising genetic complexity in sponges. Mol Biol Evol. 2014, 31 (5): 1102-1120. 10.1093/molbev/msu057.
Martindale MQ: The evolution of metazoan axial properties. Nat Rev Genet. 2005, 6 (12): 917-927. 10.1038/nrg1725.
Muller WE: The origin of metazoan complexity: porifera as integrated animals. Integr Comp Biol. 2003, 43 (1): 3-10. 10.1093/icb/43.1.3.
Jekely G: Global view of the evolution and diversity of metazoan neuropeptide signaling. Proc Natl Acad Sci U S A. 2013, 110 (21): 8702-8707. 10.1073/pnas.1221833110.
Strotmann R, Schrock K, Boselt I, Staubert C, Russ A, Schoneberg T: Evolution of GPCR: change and continuity. Mol Cell Endocrinol. 2011, 331 (2): 170-178. 10.1016/j.mce.2010.07.012.
Mirabeau O, Joly JS: Molecular evolution of peptidergic signaling systems in bilaterians. Proc Natl Acad Sci U S A. 2013, 110 (22): E2028-E2037. 10.1073/pnas.1219956110.
Anctil M: Chemical transmission in the sea anemone Nematostella vectensis: a genomic perspective. Comp Biochem Physiol Part D Genomics Proteomics. 2009, 4 (4): 268-289. 10.1016/j.cbd.2009.07.001.
Ryan JF, Pang K, Schnitzler CE, Nguyen AD, Moreland RT, Simmons DK, Koch BJ, Francis WR, Havlak P, Smith SA, Putnam NH, Haddock SH, Dunn CW, Wolfsberg TG, Mullikin JC, Martindale MQ, Baxevanis AD: The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science. 2013, 342 (6164): 1242592-10.1126/science.1242592.
Holland LZ, Carvalho JE, Escriva H, Laudet V, Schubert M, Shimeld SM, Yu JK: Evolution of bilaterian central nervous systems: a single origin?. Evodevo. 2013, 4 (1): 27-10.1186/2041-9139-4-27.
Brooke NM, Holland PW: The evolution of multicellularity and early animal genomes. Curr Opin Genet Dev. 2003, 13 (6): 599-603. 10.1016/j.gde.2003.09.002.
Abedin M, King N: Diverse evolutionary paths to cell adhesion. Trends Cell Biol. 2010, 20 (12): 734-742. 10.1016/j.tcb.2010.08.002.
Ruiz-Trillo I, Burger G, Holland PW, King N, Lang BF, Roger AJ, Gray MW: The origins of multicellularity: a multi-taxon genome initiative. Trends Genet. 2007, 23 (3): 113-118. 10.1016/j.tig.2007.01.005.
Lange M, Norton W, Coolen M, Chaminade M, Merker S, Proft F, Schmitt A, Vernier P, Lesch KP, Bally-Cuif L: The ADHD-susceptibility gene lphn3.1 modulates dopaminergic neuron formation and locomotor activity during zebrafish development. Mol Psychiatry. 2012, 17 (9): 946-954. 10.1038/mp.2012.29.
Arcos-Burgos M, Jain M, Acosta MT, Shively S, Stanescu H, Wallis D, Domene S, Velez JI, Karkera JD, Balog J, Berg K, Kleta R, Gahl WA, Roessler E, Long R, Lie J, Pineda D, Londoño AC, Palacio JD, Arbelaez A, Lopera F, Elia J, Hakonarson H, Johansson S, Knappskog PM, Haavik J, Ribases M, Cormand B, Bayes M, Casas M, et al: A common variant of the latrophilin 3 gene, LPHN3, confers susceptibility to ADHD and predicts effectiveness of stimulant medication. Mol Psychiatry. 2010, 15 (11): 1053-1066. 10.1038/mp.2010.6.
Langenhan T, Aust G, Hamann J: Sticky signaling--adhesion class G protein-coupled receptors take the stage. Sci Signal. 2013, 6 (2): re3-
Silva JP, Lelianova VG, Ermolyuk YS, Vysokov N, Hitchen PG, Berninghausen O, Rahman MA, Zangrandi A, Fidalgo S, Tonevitsky AG, Dell A, Volynski KE, Ushkaryov YA: Latrophilin 1 and its endogenous ligand Lasso/teneurin-2 form a high-affinity transsynaptic receptor pair with signaling capabilities. Proc Natl Acad Sci U S A. 2011, 108 (29): 12113-12118. 10.1073/pnas.1019434108.
Boucard AA, Ko J, Sudhof TC: High affinity neurexin binding to cell adhesion G-protein-coupled receptor CIRL1/latrophilin-1 produces an intercellular adhesion complex. J Biol Chem. 2012, 287 (12): 9399-9413. 10.1074/jbc.M111.318659.
O’Sullivan ML, de Wit J, Savas JN, Comoletti D, Otto-Hitt S, Yates JR, Ghosh A: FLRT proteins are endogenous latrophilin ligands and regulate excitatory synapse development. Neuron. 2012, 73 (5): 903-910. 10.1016/j.neuron.2012.01.018.
van Roy F, Berx G: The cell-cell adhesion molecule E-cadherin. Cell Mol Life Sci. 2008, 65 (23): 3756-3788. 10.1007/s00018-008-8281-1.
Halbleib JM, Nelson WJ: Cadherins in development: cell adhesion, sorting, and tissue morphogenesis. Genes Dev. 2006, 20 (23): 3199-3214. 10.1101/gad.1486806.
Paavola KJ, Hall RA: Adhesion G protein-coupled receptors: signaling, pharmacology, and mechanisms of activation. Mol Pharmacol. 2012, 82 (5): 777-783. 10.1124/mol.112.080309.
DeLorey RWOaTM,: GABA Synthesis, Uptake and Release. 1999, Lippincott-Raven, Philadelphia, 6
Eichinger L, Pachebat JA, Glockner G, Rajandream MA, Sucgang R, Berriman M, Song J, Olsen R, Szafranski K, Xu Q, Tunggal B, Kummerfeld S, Madera M, Konfortov BA, Rivero F, Bankier AT, Lehmann R, Hamlin N, Davies R, Gaudet P, Fey P, Pilcher K, Chen G, Saunders D, Sodergren E, Davis P, Kerhornou A, Nie X, Hall N, Anjard C, et al: The genome of the social amoeba Dictyostelium discoideum. Nature. 2005, 435 (7038): 43-57. 10.1038/nature03481.
Prabhu Y, Muller R, Anjard C, Noegel AA: GrlJ, a Dictyostelium GABAB-like receptor with roles in post-aggregation development. BMC Dev Biol. 2007, 7: 44-10.1186/1471-213X-7-44.
Skerry TM, Genever PG: Glutamate signalling in non-neuronal tissues. Trends Pharmacol Sci. 2001, 22 (4): 174-181. 10.1016/S0165-6147(00)01642-4.
Elliott GRD, Leys SP: Evidence for glutamate, GABA and NO in coordinating behaviour in the sponge, Ephydatia muelleri (Demospongiae, Spongillidae). J Exp Biol. 2010, 213 (13): 2310-2321. 10.1242/jeb.039859.
Moroz LL, Kocot KM, Citarella MR, Dosung S, Norekian TP, Povolotskaya IS, Grigorenko AP, Dailey C, Berezikov E, Buckley KM, Ptitsyn A, Reshetov D, Mukherjee K, Moroz TP, Bobkova Y, Yu F, Kapitonov VV, Jurka J, Bobkov YV, Swore JJ, Girardo DO, Fodor A, Gusev F, Sanford R, Bruders R, Kittler E, Mills CE, Rast JP, Derelle R, Solovyev VV, et al: The ctenophore genome and the evolutionary origins of neural systems. Nature. 2014, 510 (7503): 109-114. 10.1038/nature13400.
Nedergaard M, Takano T, Hansen AJ: Beyond the role of glutamate as a neurotransmitter. Nat Rev Neurosci. 2002, 3 (9): 748-755. 10.1038/nrn916.
Niimura Y: On the origin and evolution of vertebrate olfactory receptor genes: comparative genome analysis among 23 chordate species. Genome Biol Evol. 2009, 1: 34-44. 10.1093/gbe/evp003.
Krishnan A, Almen MS, Fredriksson R, Schioth HB: Insights into the origin of nematode chemosensory GPCRs: putative orthologs of the Srw family are found across several phyla of protostomes. PLoS One. 2014, 9 (3): e93048-10.1371/journal.pone.0093048.
Nikitin M: Bioinformatic prediction of Trichoplax adhaerens regulatory peptides. Gen Comp Endocrinol 2014, pii: S0016-6480(14)00126-9.
Kersey PJ, Staines DM, Lawson D, Kulesha E, Derwent P, Humphrey JC, Hughes DS, Keenan S, Kerhornou A, Koscielny G, Langridge N, McDowall MD, Megy K, Maheswari U, Nuhn M, Paulini M, Pedro H, Toneva I, Wilson D, Yates A, Birney E: Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species. Nucleic Acids Res. 2012, 40 (Database issue): D91-D97. 10.1093/nar/gkr895.
Grigoriev IV, Nordberg H, Shabalov I, Aerts A, Cantor M, Goodstein D, Kuo A, Minovitsky S, Nikitin R, Ohm RA, Otillar R, Poliakov A, Ratnere I, Riley R, Smirnova T, Rokhsar D, Dubchak I: The genome portal of the Department of Energy Joint Genome Institute. Nucleic Acids Res. 2012, 40 (Database issue): D26-D32. 10.1093/nar/gkr947.
Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer ELL, Eddy SR, Bateman A, Finn RD: The Pfam protein families database. Nucleic Acids Res. 2011, 40 (D1): D290-D301. 10.1093/nar/gkr1065.
Eddy SR: Accelerated profile HMM searches. PLoS Comput Biol. 2011, 7 (10): e1002195-10.1371/journal.pcbi.1002195.
Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer ELL, Bateman A: The Pfam protein families database. Nucleic Acids Res. 2007, 36 (Database): D281-D288. 10.1093/nar/gkm960.
Käll L, Krogh A, Sonnhammer ELL: A combined transmembrane topology and signal peptide prediction method. J Mol Biol. 2004, 338 (5): 1027-1036. 10.1016/j.jmb.2004.03.016.
Tusnády GE, Simon I: The HMMTOP transmembrane topology prediction server. Bioinformatics. 2001, 17 (9): 849-850. 10.1093/bioinformatics/17.9.849.
Katoh K, Toh H: Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform. 2008, 9 (4): 286-298. 10.1093/bib/bbn013.
Ronquist F, Huelsenbeck JP: MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 2003, 19 (12): 1572-1574. 10.1093/bioinformatics/btg180.
Stamatakis A: RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 2006, 22 (21): 2688-2690. 10.1093/bioinformatics/btl446.
Darriba D, Taboada GL, Doallo R, Posada D: ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics. 2011, 27 (8): 1164-1165. 10.1093/bioinformatics/btr088.
Whelan S, Goldman N: A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol. 2001, 18 (5): 691-699. 10.1093/oxfordjournals.molbev.a003851.
Krishnan A, Dnyansagar R, Almén MS, Williams MJ, Fredriksson R, Narayanan M, Schiöth HB: Data from: The GPCR repertoire in the demosponge Amphimedon queenslandica: insights into the GPCR system at the early divergence of animals. Dryad Data Repository. doi: 10.5061/dryad.43t7r.