An olfactory receptor pseudogene whose function emerged in humans: A case study in the evolution of structure-function in GPCRs

Journal of Structural and Functional Genomics

Volumn 9, Issue 1-4, 2008, Pages 29-40

  Lai, Peter C ^a   Bahl, Gautam ^b   Gremigni, Maryse ^c   Matarazzo, Valery ^c   Clot Faybesse, Olivier ^c   Ronin, Catherine ^c   Crasto, Chiquito J ^d,e  

^a Bard College at Simon's Rock   (United States)

^b WAYNE STATE UNIVERSITY   (United States)

^c AIX MARSEILLE UNIVERSITÉ   (France)

^d YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^e UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

Author keywords

Computational modeling; Docking; Functional pseudogene; Olfactory receptors

Indexed keywords

COMPLEMENTARY DNA; GTP BINDING PROTEIN COUPLED RECEPTOR; RECEPTOR; UNCLASSIFIED DRUG;

ARTICLE; BIOINFORMATICS; GENOME ANALYSIS; GENOMICS; MATHEMATICAL MODEL; NUCLEOTIDE SEQUENCE; OLFACTORY RECEPTOR PSEUDOGENE; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN MODIFICATION; PROTEIN STRUCTURE; PSEUDOGENE; SEQUENCE ANALYSIS;

AMINO ACID SEQUENCE; BASE SEQUENCE; CLONING, MOLECULAR; COMPUTATIONAL BIOLOGY; DATABASES AS TOPIC; DNA, COMPLEMENTARY; EVOLUTION, MOLECULAR; HUMANS; MARKOV CHAINS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; PSEUDOGENES; RECEPTORS, G-PROTEIN-COUPLED; RECEPTORS, ODORANT;

MAMMALIA;

EID: 57249095884     PISSN: 1345711X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10969-008-9043-x     Document Type: Article

References (62)

1. TH Ji M Grossmann I Ji 1998 G protein-coupled receptors. I. Diversity of receptor-ligand interactions J Biol Chem 273 17299 17302
2. G Muller 2000 Towards 3D structures of G protein-coupled receptors: a multidisciplinary approach Curr Med Chem 7 861 888
3. N King CT Hittinger SB Carroll 2003 Evolution of key cell signaling and adhesion protein families predates animal origins Science 301 361 363
4. P Mombaerts 1999 Molecular biology of odorant receptors in vertebrates Annu Rev Neurosci 22 487 509
5. T Abaffy A Malhotra CW Luetje 2007 The molecular basis for ligand specificity in a mouse olfactory receptor: a network of functionally important residues J Biol Chem 282 1216 1224
6. T Bozza P Feinstein C Zheng P Mombaerts 2002 Odorant receptor expression defines functional units in the mouse olfactory system J Neurosci 22 3033 3043
7. RC Bruch RD Rulli 1988 Ligand binding specificity of a neutral l-amino acid olfactory receptor Comp Biochem Physiol B 91 535 540
8. S Katada T Hirokawa Y Oka M Suwa K Touhara 2005 Structural basis for a broad but selective ligand spectrum of a mouse olfactory receptor: mapping the odorant-binding site J Neurosci 25 1806 1815
9. B Malnic J Hirono T Sato LB Buck 1999 Combinatorial receptor codes for odors Cell 96 713 723
10. P Mombaerts 2004 Odorant receptor gene choice in olfactory sensory neurons: the one receptor-one neuron hypothesis revisited Curr Opin Neurobiol 14 31 36
11. P Mombaerts 1996 Targeting olfaction Curr Opin Neurobiol 6 481 486
12. Y Oka M Omura H Kataoka K Touhara 2004 Olfactory receptor antagonism between odorants EMBO J 23 120 126
13. A Rothman P Feinstein J Hirota P Mombaerts 2005 The promoter of the mouse odorant receptor gene M71 Mol Cell Neurosci 28 535 546
14. K Touhara 2002 Odor discrimination by G protein-coupled olfactory receptors Microsc Res Tech 58 135 141
15. K Touhara S Sengoku K Inaki A Tsuboi J Hirono T Sato H Sakano T Haga 1999 Functional identification and reconstitution of an odorant receptor in single olfactory neurons Proc Natl Acad Sci USA 96 4040 4045
16. LB Buck 1996 Information coding in the vertebrate olfactory system Annu Rev Neurosci 19 517 544
17. Shepherd GM (1995) Toward a molecular basis for sensory perception. In: Gazzaniga MS, Bizzi E (eds) The cognitive neurosciences. MIT Press, Cambridge, pp 105-137
18. G Glusman I Yanai I Rubin D Lancet 2001 The complete human olfactory subgenome Genome Res 11 685 702
19. B Malnic PA Godfrey LB Buck 2004 The human olfactory receptor gene family Proc Natl Acad Sci USA 101 2584 2589
20. Y Niimura M Nei 2003 Evolution of olfactory receptor genes in the human genome Proc Natl Acad Sci USA 100 12235 12240
21. Zozulya S, Echeverri F, Nguyen T (2001) The human olfactory receptor repertoire. Genome Biol 2:RESEARCH0018
22. P Quignon M Giraud M Rimbault P Lavigne S Tacher E Morin E Retout AS Valin K Lindblad-Toh J Nicolas F Galibert 2005 The dog and rat olfactory receptor repertoires Genome Biol 6 R83
23. JM Young BM Shykind RP Lane L Tonnes-Priddy JA Ross M Walker EM Williams BJ Trask 2003 Odorant receptor expressed sequence tags demonstrate olfactory expression of over 400 genes, extensive alternate splicing and unequal expression levels Genome Biol 4 R71
24. X Zhang S Firestein 2002 The olfactory receptor gene superfamily of the mouse Nat Neurosci 5 124 133
25. Y Niimura M Nei 2005 Comparative evolutionary analysis of olfactory receptor gene clusters between humans and mice Gene 346 13 21
26. Y Niimura M Nei 2007 Extensive gains and losses of olfactory receptor genes in mammalian evolution PLoS ONE 2 e708
27. D Sharon G Glusman Y Pilpel M Khen F Gruetzner T Haaf D Lancet 1999 Primate evolution of an olfactory receptor cluster: diversification by gene conversion and recent emergence of pseudogenes Genomics 61 24 36
28. I Menashe O Man D Lancet Y Gilad 2002 Population differences in haplotype structure within a human olfactory receptor gene cluster Hum Mol Genet 11 1381 1390
29. V Matarazzo O Clot-Faybesse B Marcet G Guiraudie-Capraz B Atanasova G Devauchelle M Cerutti P Etievant C Ronin 2005 Functional characterization of two human olfactory receptors expressed in the baculovirus Sf9 insect cell system Chem Senses 30 195 207
30. T Imai M Suzuki H Sakano 2006 Odorant receptor-derived cAMP signals direct axonal targeting Science 314 657 661
31. T Fuchs G Glusman S Horn-Saban D Lancet Y Pilpel 2001 The human olfactory subgenome: from sequence to structure and evolution Hum Genet 108 1 13
32. I Visiers JA Ballesteros H Weinstein 2002 Three-dimensional representations of G protein-coupled receptor structures and mechanisms Methods Enzymol 343 329 371
33. GE Tusnady I Simon 2001 The HMMTOP transmembrane topology prediction server Bioinformatics 17 849 850
34. Moller S, Vilo J, Croning MD (2001) Prediction of the coupling specificity of G protein coupled receptors to their G proteins. Bioinformatics 17(Suppl 1):S174-S181
35. RC Araneda AD Kini S Firestein 2000 The molecular receptive range of an odorant receptor Nat Neurosci 3 1248 1255
36. PC Lai MS Singer CJ Crasto 2005 Structural activation pathways from dynamic olfactory receptor-odorant interactions Chem Senses 30 781 792
37. MS Singer 2000 Analysis of the molecular basis for octanal interactions in the expressed rat 17 olfactory receptor Chem Senses 25 155 165
38. B John A Sali 2003 Comparative protein structure modeling by iterative alignment, model building and model assessment Nucleic Acids Res 31 3982 3992
39. W Pirovano KA Feenstra J Heringa 2008 PRALINETM: a strategy for improved multiple alignment of transmembrane proteins Bioinformatics 24 492 497
40. WB Floriano S Hall N Vaidehi U Kim D Drayna WA Goddard III 2006 Modeling the human PTC bitter-taste receptor interactions with bitter tastants J Mol Model 12 931 941
41. WB Floriano N Vaidehi WA Goddard III 2004 Making sense of olfaction through predictions of the 3-D structure and function of olfactory receptors Chem Senses 29 269 290
42. WB Floriano N Vaidehi WA Goddard MS Singer III GM Shepherd 2000 Molecular mechanisms underlying differential odor responses of a mouse olfactory receptor Proc Natl Acad Sci USA 97 10712 10716
43. WB Floriano N Vaidehi G Zamanakos WA Goddard III 2004 HierVLS hierarchical docking protocol for virtual ligand screening of large-molecule databases J Med Chem 47 56 71
44. PL Freddolino MY Kalani N Vaidehi WB Floriano SE Hall RJ Trabanino VW Kam WA Goddard III 2004 Predicted 3D structure for the human beta 2 adrenergic receptor and its binding site for agonists and antagonists Proc Natl Acad Sci USA 101 2736 2741
45. SE Hall WB Floriano N Vaidehi WA Goddard III 2004 Predicted 3-D structures for mouse I7 and rat I7 olfactory receptors and comparison of predicted odor recognition profiles with experiment Chem Senses 29 595 616
46. O Man Y Gilad D Lancet 2004 Prediction of the odorant binding site of olfactory receptor proteins by human-mouse comparisons Protein Sci 13 240 254
47. MS Singer GM Shepherd 1994 Molecular modeling of ligand-receptor interactions in the OR5 olfactory receptor Neuroreport 5 1297 1300
48. N Vaidehi WB Floriano R Trabanino SE Hall P Freddolino EJ Choi G Zamanakos WA Goddard III 2002 Prediction of structure and function of G protein-coupled receptors Proc Natl Acad Sci USA 99 12622 12627
49. K Melen A Krogh G von Heijne 2003 Reliability measures for membrane protein topology prediction algorithms J Mol Biol 327 735 744
50. T Okada 2004 X-ray crystallographic studies for ligand-protein interaction changes in rhodopsin Biochem Soc Trans 32 738 741
51. DA Gschwend AC Good ID Kuntz 1996 Molecular docking towards drug discovery J Mol Recognit 9 175 186
52. DA Gschwend ID Kuntz 1996 Orientational sampling and rigid-body minimization in molecular docking revisited: on-the-fly optimization and degeneracy removal J Comput Aided Mol Des 10 123 132
53. FM Richards 1977 Areas, volumes, packing and protein structure Annu Rev Biophys Bioeng 6 151 176
54. L Buck R Axel 1991 A novel multigene family may encode odorant receptors: a molecular basis for odor recognition Cell 65 175 187
55. M Burger JA Burger RC Hoch Z Oades H Takamori IU Schraufstatter 1999 Point mutation causing constitutive signaling of CXCR2 leads to transforming activity similar to Kaposi's sarcoma herpesvirus-G protein-coupled receptor J Immunol 163 2017 2022
56. A Scheer F Fanelli T Costa PG De Benedetti S Cotecchia 1996 Constitutively active mutants of the alpha 1B-adrenergic receptor: role of highly conserved polar amino acids in receptor activation EMBO J 15 3566 3578
57. R Benton S Sachse SW Michnick LB Vosshall 2006 Atypical membrane topology and heteromeric function of Drosophila odorant receptors in vivo PLoS Biol 4 e20
58. JM Otaki S Firestein 2001 Length analyses of mammalian G-protein-coupled receptors J Theor Biol 211 77 100
59. T Olender E Feldmesser T Atarot M Eisenstein D Lancet 2004 The olfactory receptor universe-from whole genome analysis to structure and evolution Genet Mol Res 3 545 553
60. S Yohannan S Faham D Yang JP Whitelegge JU Bowie 2004 The evolution of transmembrane helix kinks and the structural diversity of G protein-coupled receptors Proc Natl Acad Sci USA 101 959 963
61. S Katada K Touhara 2004 A molecular basis for odorant recognition: olfactory receptor pharmacology Nippon Yakurigaku Zasshi 124 201 209
62. A Krebs C Villa PC Edwards GF Schertler 1998 Characterisation of an improved two-dimensional p22121 crystal from bovine rhodopsin J Mol Biol 282 991 1003