Opsins and clusters of sensory G-protein-coupled receptors in the sea urchin genome

Developmental Biology

Volumn 300, Issue 1, 2006, Pages 461-475

  Raible, Florian ^a   Tessmar Raible, Kristin ^a   Arboleda, Enrique ^b   Kaller, Tobias ^a,c   Bork, Peer ^a   Arendt, Detlev ^a   Arnone, Maria I ^b  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b STAZIONE ZOOLOGICA ANTON DOHRN   (Italy)

^c FREIE UNIVERSITÄT BERLIN   (Germany)

Author keywords

Chemosensation; Gene cluster; Olfaction; Opsin; Pedicellariae, Tube feet; Rhodopsin type G protein coupled receptor (GPCR); Sea urchin; Surreal GPCR

Indexed keywords

G PROTEIN COUPLED RECEPTOR; OPSIN; RHODOPSIN;

ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; ECHINODERM; EXON; FISH GENETICS; GENE CLUSTER; GENE DUPLICATION; GENE EXPRESSION; GENE STRUCTURE; GENOME; NONHUMAN; OLFACTORY RECEPTOR; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FAMILY; SEA URCHIN; SENSORY NERVE CELL; SENSORY RECEPTOR; STIMULATION;

ANIMALIA; BILATERIA; ECHINODERMATA; ECHINOIDA; ECHINOIDEA; VERTEBRATA;

EID: 33751539851     PISSN: 00121606     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ydbio.2006.08.070     Document Type: Article

References (85)

1. Ache B.W., and Young J.M. Olfaction: diverse species, conserved principles. Neuron 48 (2005) 417-430
2. Agassiz A., and Clark H.L. Hawaiian and other Pacific Echini. Mus. Comp. Zool. (1907) 34
3. Aizenberg J., Tkachenko A., Weiner S., Addadi L., and Hendler G. Calcitic microlenses as part of the photoreceptor system in brittlestars. Nature 412 (2001) 819-822
4. 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
5. Arendt D. Evolution of eyes and photoreceptor cell types. Int. J. Dev. Biol. 47 (2003) 563-571
6. Arendt D., Tessmar K., de Campos-Baptista M.I., Dorresteijn A., and Wittbrodt J. Development of pigment-cup eyes in the polychaete Platynereis dumerilii and evolutionary conservation of larval eyes in Bilateria. Development 129 (2002) 1143-1154
7. Arendt D., Tessmar-Raible K., Snyman H., Dorresteijn A.W., and Wittbrodt J. Ciliary photoreceptors with a vertebrate-type opsin in an invertebrate brain. Science 306 (2004) 869-871
8. Barnes D.K.A., and Cook A.C. Quantifying behavioural determinants of the coastal European sea-urchin Paracentrotus lividus. Mar. Biol. 138 (2001) 1205-1212
9. Bermak J.C., Li M., Bullock C., and Zhou Q.-Y. Regulation of transport of the dopamine D1 receptor by a new membrane-associated ER protein. Nat. Cell Biol. 3 (2001) 492-498
10. Bjarnadóttir T.K., Fredriksson R., and Schiöth H.B. The gene repertoire and the common evolutionary history of glutamate, pheromone (V2R), taste and other related G protein-coupled receptors. Gene 362 (2005) 70-84
11. Blevins E., and Johnsen S. Spatial vision in the echinoid genus Echinometra. J. Exp. Biol. 207 (2004) 4249-4253
12. Bockaert J., Fagni L., Dumuis A., and Marin P. GPCR interacting proteins (GIP). Pharmacol. Ther. 103 (2004) 203-221
13. Bockaert J., and Pin J.P. Molecular tinkering of G protein-coupled receptors: an evolutionary success. EMBO J. 18 (1999) 1723-1729
14. Buck L., and Axel R. A novel multigene family may encode odorant receptors: a molecular basis for odor recognition. Cell 65 (1991) 175-187
15. Burke R.D. Development of pedicellariae in the pluteus larva of Lytechinus pictus (Echinodermata: Echinoidea). Can. J. Zool. 58 (1980) 1674-1682
16. Burke R.D., Angerer L.M., Elphick M., Humphrey R., Yaguchi G.W., Liang S., Kiyama S., Klein T., Brandhorst W.H., Rowe B.P., Wilson M., Mu K., Murray X., Mellott G., Hallböök D., Olinski F., and Thorndyke R. A genomic view of the sea urchin nervous system. Dev. Biol. 300 (2006) 434-460
17. Cameron R.A., Materna S.C., and Berney K. The Strongylocentrotus purpuratus genome: a comparative perspective. Dev. Biol. 300 (2006) 485-495
18. Campbell A.C. Observations on the activity of echinoid pedicellariae: I. Stem responses and their significance. Mar. Behav. Physiol. 2 (1973) 33-61
19. Campbell A.C. Observations on the activity of echinoid pedicellariae: II. Jaw responses of tridentate and ophiocephalous pedicellariae. Mar. Behav. Physiol. 3 (1974) 17-34
20. Campbell A.C. Observations on the activity of echinoid pedicellariae: III. Jaw responses of globiferous pedicellariae and their significance. Mar. Behav. Physiol. 4 (1976) 25-39
21. Campbell A.C. Form and function of pedicellariae. Echinoderm Stud. 1 (1983) 139-167
22. Clyne P.J., Warr C.G., Freeman M.R., Lessing D., Kim J., and Carlson J.R. A novel family of divergent seven-transmembrane proteins: candidate odorant receptors in Drosophila. Neuron 22 (1999) 327-338
23. Davidson E.H., and Erwin D.H. Gene regulatory networks and the evolution of animal body plans. Science 311 (2006) 796-800
24. de Hoon M.J., Imoto S., Nolan J., and Miyano S. Open source clustering software. Bioinformatics 20 (2004) 1453-1454
25. Delsuc F., Brinkmann H., Chourrout D., and Philippe H. Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature 439 (2006) 965-968
26. Döderlein L. Ueber "Krystallkörper" bei Seesternen. Denkschr. Med. Nat. Ges. Jena 8 (1898) 491-494
27. Dryer L. Evolution of odorant receptors. Bioessays 22 (2000) 803-810
28. Dubois P., and Ameye L. Regeneration of spines and pedicellariae in echinoderms: a review. Microsc. Res. Tech. 55 (2001) 427-437
29. Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32 (2004) 1792-1797
30. Finn R.D., Mistry J., Schuster-Böckler B., Griffiths-Jones S., Hollich V., Lassmann T., Moxon S., Marshall M., Khanna A., Durbin R., Eddy S.R., Sonnhammer E.L., and Bateman A. Pfam: clans, Web tools and services. Nucleic Acids Res. 34 (2006) D247-D251
31. Fredriksson R., and Schiöth H.B. The repertoire of G-protein-coupled receptors in fully sequenced genomes. Mol. Pharmacol. 67 (2005) 1414-1425
32. Gehring W., and Rosbash M. The coevolution of blue-light photoreception and circadian rhythms. J. Mol. Evol. 57 Suppl. 1 (2003) S286-S289
33. Geis H.L. Recent and fossil pedicellariae. J. Paleontol. 10 (1936) 427-448
34. Goldschmid A. Echinodermata. In: Westheide W., and Rieger R. (Eds). Spezielle Zoologie-Teil 1: Einzeller und Wirbellose Tiere (1996), Gustav Fischer Verlag, Stuttgart
35. Hamann O. Beiträge zur Histologie der Echinodermen. III. Anatomie und Histologie der Echiniden und Spatangiden (1887), Gustav Fischer, Jena
36. Hara-Nishimura I., Matsumoto T., Mori H., Nishimura M., Hara R., and Hara T. Cloning and nucleotide sequence of cDNA for retinochrome, retinal photoisomerase from the squid retina. FEBS Lett. 271 (1990) 106-110
37. Haude R. Evolutionary Reconstruction of Primitive (Spinate) Echinoid Pedicellariae (1998), Balkema, Rotterdam, London, UK
38. Hendler G., and Byrne M. Fine structure of the dorsal arm plate of Ophiocoma wendti: evidence for a photoreceptor system (Echinodermata Ophiuroidea). Zoomorphology 107 (1987) 261-272
39. Hill C.A., Fox A.N., Pitts R.J., Kent L.B., Tan P.L., Chrystal M.A., Cravchik A., Collins F.H., Robertson H.M., and Zwiebel L.J. G protein-coupled receptors in Anopheles gambiae. Science 298 (2002) 176-178
40. Hofmann K., and Stoffel W. TMbase-A database of membrane spanning protein segments. Biol. Chem. Hoppe Seyler 347 (1993) 166
41. Howard-Ashby M., Materna S.C., Brown C.T., Chen L., Cameron R.A., and Davidson E.H. Identification and characterization of homeobox transcription factor genes in S. purpuratus, and their expression in embryonic development. Dev. Biol. 300 (2006) 74-89
42. Johnsen S. Identification and localization of a possible rhodopsin in the echinoderms Asterias forbesi (Asteroidea) and Ophioderma brevispinum (Ophiuroidea). Biol. Bull. 193 (1997) 97-105
43. Kimura M. The Neutral Theory of Molecular Evolution (1983), Cambridge Univ. Press, Cambridge, U.K.
44. Kojima D., Terakita A., Ishikawa T., Tsukahara Y., Maeda A., and Shichida Y. A novel Go-mediated phototransduction cascade in scallop visual cells. J. Biol. Chem. 272 (1997) 22979-22982
45. Koyanagi M., Terakita A., Kubokawa K., and Shichida Y. Amphioxus homologs of Go-coupled rhodopsin and peropsin having 11-cis- and all-trans-retinals as their chromophores. FEBS Lett. 531 (2002) 525-528
46. Liberles S.D., and Buck L.B. A second class of chemosensory receptors in the olfactory epithelium. Nature 442 (2006) 645-650
47. Materna S.C., Howard-Ashby M., Gray R.F., and Davidson E.H. The C2H2 zinc finger genes of Strongylocentrotus purpuratus and their expression in embryonic development. Dev. Biol. 300 (2006) 108-120
48. Mathi S.K., Chan Y., Li X., and Wheeler M.B. Scanning of the glucagon-like peptide-1 receptor localizes G protein-activating determinants primarily to the N terminus of the third intracellular loop. Mol. Endocrinol. 11 (1997) 424-432
49. Millott N. Sensitivity to light and the reactions to changes in light intensity of the echinoid Diadema antillarum Philippi. Philos. Trans. R. Soc. B238 (1954) 187-220
50. Millott N. The photosensitivity of echinoids. Adv. Mar. Biol. 13 (1975) 1-52
51. Minokawa T., Rast J.P., Arenas-Mena C., Franco C.B., and Davidson E.H. Expression patterns of four different regulatory genes that function during sea urchin development. Gene Expr. Patterns 4 (2004) 449-456
52. Mortensen T. A Monograph of the Echinoidea (1943), C.A. Reitzel, Copenhagen
53. Mulder N.J., Apweiler R., Attwood T.K., Bairoch A., Bateman A., Binns D., Bradley P., Bork P., Bucher P., Cerutti L., Copley R., Courcelle E., Das U., Durbin R., Fleischmann W., Gough J., Haft D., Harte N., Hulo N., Kahn D., Kanapin A., Krestyaninova M., Lonsdale D., Lopez R., Letunic I., Madera M., Maslen J., McDowall J., Mitchell A., Nikolskaya A.N., Orchard S., Pagni M., Ponting C.P., Quevillon E., Selengut J., Sigrist C., Silventoinen J., Studholme V., Vaughan D.J., and Wu R. InterPro, progress and status in 2005. Nucleic Acids Res. 33 (2005) D201-D205
54. Nakashima Y., Kusakabe T., Kusakabe R., Terakita A., Shichida Y., and Tsuda M. Origin of the vertebrate visual cycle: genes encoding retinal photoisomerase and two putative visual cycle proteins are expressed in whole brain of a primitive chordate. J. Comp. Neurol. 460 (2003) 180-190
55. Nemer M., Rondinelli E., Infante D., and Infante A.A. Polyubiquitin RNA characteristics and conditional induction in sea urchin embryos. Dev. Biol. 145 (1991) 255-265
56. O'Connell M.G., Alender C.B., and Wood E.M. A Fine Structure Study of Venom Gland Cells in Globiferous pedicellariae from Strongylocentrotus purpuratus (Stimpson). J. Morph. 142 (1974) 411-432
57. Ohno S. Evolution by Gene Duplication (1970), Springer-Verlag, Heidelberg
58. Pennington J.T., and Emlet R.B. Ontogenetic and diel vertical migration of a planktonic echinoid larva, Dendraster excentricus (Eschscholtz): occurrence, causes, and probable consequences. J. Exp. Mar. Biol. Ecol. 104 (1986) 69-95
59. Peters B.H., and Campbell A.C. Morphology of the nervous and muscular systems in the heads of pedicellariae from the sea urchin Echinus esculentus L. J. Morphol. 193 (1987) 35-51
60. Phillips D.W. Chemical mediation of invertebrate defensive behaviors and the ability to distinguish between foraging and inactive predators. Marine Biology 49 (1978) 237-243
61. Pilpel Y., and Lancet D. The variable and conserved interfaces of modeled olfactory receptor proteins. Protein Sci. 8 (1999) 969-977
62. Pisut D.P. The Distance Chemosensory Behavior of the Sea Urchin Lytechinus variegatus (2004), Georgia Institute of Technology, Georgia
63. Raible F., and Arendt D. Metazoan evolution: some animals are more equal than others. Curr. Biol. 14 (2004) R106-R108
64. Ransick A., Rast J.P., Minokawa T., Calestani C., and Davidson E.H. New early zygotic regulators expressed in endomesoderm of sea urchin embryos discovered by differential array hybridization. Dev. Biol. 246 (2002) 132-147
65. Rast J.P., Amore G., Calestani C., Livi C.B., Ransick A., and Davidson E.H. Recovery of developmentally defined gene sets from high-density cDNA macroarrays. Dev. Biol. 228 (2000) 270-286
66. Rizzo F., Fernandez-Serra M., Squarzoni P., Archimandritis A., and Arnone M.I. Identification and developmental expression of the ets gene family in the sea urchin (Strongylocentrotus purpuratus). Dev. Biol. 300 (2006) 35-48
67. Rozen S., and Skaletsky H. Primer3 on the WWW for general users and for biologist programmers. Methods Mol. Biol. 132 (2000) 365-386
68. Rubin E., Shemesh Y., Cohen M., Elgavish S., Robertson H.M., and Bloch G. Molecular and phylogenetic analyses reveal mammalian-like clockwork in the honey bee (Apis mellifera) and shed new light on the molecular evolution of the circadian clock. Genome Res. 16 (2006) 1352-1365
69. Saldanha A.J. Java Treeview-extensible visualization of microarray data. Bioinformatics 20 (2004) 3246-3248
70. Samanta M.P., Tongprasit W., Istrail S., Cameron A., Tu Q., Davidson E.H., and Stolc V. A high-resolution transcriptome map of the sea urchin embryo. Science (2006) in press
71. Schiöth H.B., and Fredriksson R. The GRAFS classification system of G-protein coupled receptors in comparative perspective. Gen. Comp. Endocrinol. 142 (2005) 94-101
72. Schmidt H.A., Strimmer K., Vingron M., and von Haeseler A. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18 (2002) 502-504
73. Sea Urchin Sequencing Consortium. The sequence of the sea urchin genome. Science (2006) in press
74. Smith J.E. On the nervous system of the starfish Marthasterias glacialis (L.). Philos. Trans., B 227 (1937) 111-173
75. Smith J.E. Echinodermata. In: Bullock H., and Horridge A. (Eds). Structure and Function in the Nervous Systems of Invertebrates vol. 2 (1965), W. H. Freeman, San Francisco 1519-1558
76. Smith D.S., Brink D., and del Castillo J. Nerves in the spine of a sea urchin: a neglected division of the echinoderm nervous system. Proc. Natl. Acad. Sci. U. S. A. 82 (1985) 1555-1557
77. Snyder N., and Snyder H. Alarm response of Diadema antillarum. Science 168 (1970) 276-278
78. Terakita A. The opsins. Genome Biol. 6 (2005) 213
79. Thompson J.D., Higgins D.G., and Gibson T.J. 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 (1994) 4673-4680
80. Tu Q.C., Brown T., Davidson E.H., and Oliveri P. Sea urchin forkhead gene family: phylogeny and embryo expression. Dev. Biol. 300 (2006) 49-62
81. Vadas R.L. Preferential feeding: an optimization strategy in sea urchins. Ecol. Monogr. 47 (1977) 337-371
82. Waterston R.H., Lindblad-Toh K., Birney E., Rogers J., Abril J.F., Agarwal P., Agarwala R., Ainscough R., Alexandersson M., An P., Antonarakis S.E., Attwood J., Baertsch R., Bailey J., Barlow K., Beck S., Berry E., Birren B., Bloom T., Bork P., Botcherby M., Bray N., Brent M.R., Brown D.G., Brown S.D., Bult C., Burton J., Butler J., Campbell R.D., Carninci P., Cawley S., Chiaromonte F., Chinwalla A.T., Church D.M., Clamp M., Clee C., Collins F.S., Cook L.L., Copley R.R., Coulson A., Couronne O., Cuff J., Curwen V., Cutts T., Daly M., David R., Davies J., Delehaunty K.D., Deri J., Dermitzakis E.T., Dewey C., Dickens N.J., Diekhans M., Dodge S., Dubchak I., Dunn D.M., Eddy S.R., Elnitski L., Emes R.D., Eswara P., Eyras E., Felsenfeld A., Fewell G.A., Flicek P., Foley K., Frankel W.N., Fulton L.A., Fulton R.S., Furey T.S., Gage D., Gibbs R.A., Glusman G., Gnerre S., Goldman N., Goodstadt L., Grafham D., Graves T.A., Green E.D., Gregory S., Guigo R., Guyer M., Hardison R.C., Haussler D., Hayashizaki Y., Hillier L.W., Hinrichs A., Hlavina W., Holzer T., Hsu F., Hua A., Hubbard T., Hunt A., Jackson I., Jaffe D.B., Johnson L.S., Jones M., Jones T.A., Joy A., Kamal M., Karlsson E.K., et al. Initial sequencing and comparative analysis of the mouse genome. Nature 420 (2002) 520-562
83. Whittaker C.A., Bergeron K.F., Whittle J., Brandhorst B.P., Bourke R.D., and Hynes R.O. The echinoderm adhesome. Dev. Biol. 300 (2006) 252-266
84. Yang J., Lusk R., and Li W.H. Organismal complexity, protein complexity, and gene duplicability. Proc. Natl. Acad. Sci. U. S. A. 100 (2003) 15661-15665
85. Yoshida M. Photosensitivity (1966), Interscience, New York