A hit map-based statistical method to predict best ligands for orphan olfactory receptors: Natural key odorants versus "lock Picks"

Methods in Molecular Biology

Volumn 1003, Issue , 2013, Pages 85-97

  Krautwurst, Dietmar ^a   Kotthoff, Matthias ^b  

^a DEUTSCHE FORSCHUNGSANSTALT FÜR LEBENSMITTELCHEMIE   (Germany)

^b FRAUNHOFER INSTITUTE FOR MOLECULAR BIOLOGY AND APPLIED ECOLOGY IME   (Germany)

Author keywords

Body odorants; Chemosensory receptors; Cognate odorant receptor frequency; Hit map; Key food odorants; Olfactory receptors; Phylogenetic dendrogram

Indexed keywords

LIGAND; ODORANT RECEPTOR; RECEPTOR; UNCLASSIFIED DRUG;

ANALYTICAL PARAMETERS; ARTICLE; BIOASSAY; CORRELATIONAL STUDY; HUMAN; NOMENCLATURE; NONHUMAN; OLFACTORY RECEPTOR; PHYLOGENY; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; SCREENING; STATISTICAL ANALYSIS; ANIMAL; BIOLOGY; CHEMISTRY; CLUSTER ANALYSIS; METABOLISM; METHODOLOGY; MOLECULAR EVOLUTION; MOUSE; ODOR; PROTEIN DATABASE; SEQUENCE HOMOLOGY; STATISTICS;

ANIMALS; BIOLOGICAL ASSAY; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; EVOLUTION, MOLECULAR; HUMANS; LIGANDS; MICE; ODORS; PHYLOGENY; PHYSICOCHEMICAL PROCESSES; RECEPTORS, ODORANT; SEQUENCE HOMOLOGY, AMINO ACID; STATISTICS AS TOPIC;

EID: 84884732538     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-377-0_6     Document Type: Article

References (72)

1. Buck L, Axel R (1991) A novel multigene family may encode odorant receptors: a molecular basis for odor recognition. Cell 65(1): 175-187
2. Levy NS, Bakalyar HA, Reed RR (1991) Signal transduction in olfactory neurons. J Steroid Biochem Mol Biol 39(4B):633-637
3. Dulac C, Axel R (1995) A novel family of genes encoding putative pheromone receptors in mammals. Cell 83(2):195-206
4. Rodriguez I et al (2000) A putative pheromone receptor gene expressed in human olfactory mucosa. Nat Genet 26(1):18-19
5. Rodriguez I, Mombaerts P (2002) Novel human vomeronasal receptor-like genes reveal species-speci fi c families. Curr Biol 12(12):R409-R411
6. Lewin AH (2006) Receptors of mammalian trace amines. AAPS J 8(1):E138-E145
7. Liberles SD (2009) Trace amine-associated receptors are olfactory receptors in vertebrates. Ann N Y Acad Sci 1170:168-172
8. Liberles SD, Buck LB (2006) A second class of chemosensory receptors in the olfactory epithelium. Nature 442(7103):645-650
9. HORDE (2011) The Human Olfactory Receptor Data Exploratorium (HORDE), The Weizmann Institute, http://bioportal.weizmann.ac.il/HORDE/
10. Malnic B, Godfrey PA, Buck LB (2004) The human olfactory receptor gene family. Proc Natl Acad Sci USA 101(8):2584-2589
11. Menashe I, Aloni R, Lancet D (2006) A probabilistic classi fi er for olfactory receptor pseudogenes. BMC Bioinformatics 7:393
12. Niimura Y, Nei M (2003) Evolution of olfactory receptor genes in the human genome. Proc Natl Acad Sci USA 100(21):12235-12240
13. Olender T et al (2004) The olfactory receptor universe-from whole genome analysis to structure and evolution. Genet Mol Res 3(4):545-553
14. Olender T, Lancet D, Nebert DW (2008) Update on the olfactory receptor (OR) gene superfamily. Hum Genomics 3(1):87-97
15. Zozulya S, Echeverri F, Nguyen T (2001) The human olfactory receptor repertoire. Genome Biol 2(6):RESEARCH0018
16. Glusman G et al (2000) The olfactory receptor gene superfamily: data mining, classi fi cation, and nomenclature. Mamm Genome 11(11): 1016-1023
17. Gilad Y, Lancet D (2003) Population differences in the human functional olfactory repertoire. Mol Biol Evol 20(3):307-314
18. Menashe I et al (2007) Genetic elucidation of human hyperosmia to isovaleric acid. PLoS Biol 5(11):2462-2468
19. Menashe I et al (2003) Different noses for different people. Nat Genet 34(2):143-144
20. Sharon D et al (2000) Identi fi cation and characterization of coding single-nucleotide polymorphisms within a human olfactory receptor gene cluster. Gene 260(1-2):87-94
21. Hayden S et al (2010) Ecological adaptation determines functional mammalian olfactory subgenomes. Genome Res 20(1):1-9
22. Grosch W (2001) Evaluation of the key odorants of foods by dilution experiments, aroma models and omission. Chem Senses 26(5): 533-545
23. Grosch W (2000) Speci fi city of the human nose in perceiving food odorants. In: Frontiers of fl avour science, Ninth Weurman fl avour research symposium. Deutsche Forschungsanstalt fuer Lebensmittelchemie, Garching
24. Wyart C et al (2007) Smelling a single component of male sweat alters levels of cortisol in women. J Neurosci 27(6):1261-1265
25. Doucet S et al (2007) The "smellscape" of mother's breast: effects of odor masking and selective unmasking on neonatal arousal, oral, and visual responses. Dev Psychobiol 49(2):129-138
26. Boulkroune N et al (2007) Repetitive olfactory exposure to the biologically signi fi cant steroid androstadienone causes a hedonic shift and gender dimorphic changes in olfactory-evoked potentials. Neuropsychopharmacology 24:24
27. Miller MC (2006) Human pheromones. Harv Ment Health Lett 23(5):8
28. Laska M, Wieser A, Salazar LT (2006) Sexspeci fi c differences in olfactory sensitivity for putative human pheromones in nonhuman primates. J Comp Psychol 120(2):106-112
29. Keller A et al (2007) Genetic variation in a human odorant receptor alters odour perception. Nature 449(7161):468-472
30. Shirokova E et al (2008) The human vomeronasal type-1 receptor family-detection of volatiles and cAMP signaling in HeLa/Olf cells. FASEB J 22(5):1416-1425
31. Krautwurst D (2008) Human olfactory receptor families and their odorants. Chem Biodivers 5(6):842-852
32. Shirokova E et al (2005) Identi fi cation of speci fi c ligands for orphan olfactory receptors. G protein-dependent agonism and antagonism of odorants. J Biol Chem 280(12): 11807-11815
33. NCBI (2011) National Center for Biotechnology Information, Gene search tool, Available from: http://www.ncbi.nlm.nih.gov/gene/
34. Tamura K et al (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28(10):2731-2739
35. Knudsen B et al. (2011) CLC Main Workbench 6.5, CLCbio
36. PubMed (2011) PubMed health, Available from: http://www.ncbi.nlm.nih.gov/ pubmedhealth/
37. SciFinder (2009) Chemistry research tool, Available from: https://scifinder.cas.org
38. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4(4): 406-425
39. Felsenstein J (1985) Con fi dence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791
40. Acree TE et al (1984) Food Chem. 14(4): 273-286
41. Rothe M, Thomas B (1963) Z. Lebensm.- Unters. Forsch. 119:302-310
42. Schieberle P (1995) New developments on methods for analysis of volatile fl avor compounds and their precursors. In: Gaonkar AG (ed) Characterization of food-emerging methods. Elsevier, Amsterdam, pp 403-433
43. Gallagher M et al (2008) Analyses of volatile organic compounds from human skin. Br J Dermatol 159(4):780-791
44. Hasegawa Y, Yabuki M, Matsukane M (2004) Identi fi cation of new odoriferous compounds in human axillary sweat. Chem Biodivers 1(12):2042-2050
45. Natsch A et al (2006) A broad diversity of volatile carboxylic acids, released by a bacterialaminoacylase from axilla secretions, as candidate molecules for the determination of human-body odor type. Chem Biodivers 3(1):1-20
46. Natsch A et al (2003) A speci fi c bacterial aminoacylase cleaves odorant precursors secreted in the human axilla. J Biol Chem 278(8): 5718-5727
47. Natsch A, Schmid J, Flachsmann F (2004) Identi fi cation of odoriferous sulfanylalkanols in human axilla secretions and their formation through cleavage of cysteine precursors by a C-S lyase isolated from axilla bacteria. Chem Biodivers 1(7):1058-1072
48. Zhang X, Firestein S (2002) The olfactory receptor gene superfamily of the mouse. Nat Neurosci 5(2):124-133
49. Tatusov RL, Koonin EV, Lipman DJ (1997) A genomic perspective on protein families. Science 278(5338):631-637
50. Schmiedeberg K et al (2007) Structural determinants of odorant recognition by the human olfactory receptors OR1A1 and OR1A2. J Struct Biol 159(3):400-412
51. Malnic B et al (1999) Combinatorial receptor codes for odors. Cell 96(5):713-723
52. Lapidot M et al (2001) Mouse-human orthology relationships in an olfactory receptor gene cluster. Genomics 71(3):296-306
53. Glusman G et al (2001) The complete human olfactory subgenome. Genome Res 11(5): 685-702
54. Jacquier V, Pick H, Vogel H (2006) Characterization of an extended receptive ligand repertoire of the human olfactory receptor OR17-40 comprising structurally related compounds. J Neurochem 97(2):537-544
55. Sanz G et al (2005) Comparison of odorant speci fi city of two human olfactory receptors from different phylogenetic classes and evidence for antagonism. Chem Senses 30(1):69-80
56. Spehr M et al (2003) Identi fi cation of a testicular odorant receptor mediating human sperm chemotaxis. Science 299(5615): 2054-2058
57. Wetzel CH et al (1999) Speci fi city and sensitivity of a human olfactory receptor functionally expressed in human embryonic kidney 293 cells and Xenopus Laevis oocytes. J Neurosci 19(17):7426-7433
58. Grosmaitre X et al (2009) SR1, a mouse odorant receptor with an unusually broad response pro fi le. J Neurosci 29(46):14545-14552
59. Grus WE, Zhang J (2008) Distinct evolutionary patterns between chemoreceptors of 2 vertebrate olfactory systems and the differential tuning hypothesis. Mol Biol Evol 25(8):1593-1601
60. Saito H et al (2009) Odor coding by a mammalian receptor repertoire. Sci Signal 2(60):ra9
61. Duan X et al (2012) Crucial role of copper in detection of metal-coordinating odorants. Proc Natl Acad Sci USA 109(9):3492-3497
62. Fujita Y et al (2007) Deorphanization of Dresden G protein-coupled receptor for an odorant receptor. J Recept Signal Transduct Res 27(4):323-334
63. Kajiya K et al (2001) Molecular bases of odor discrimination: reconstitution of olfactory receptors that recognize overlapping sets of odorants. J Neurosci 21(16):6018-6025
64. Kotthoff M, Schieberle P, Krautwurst D(2010) Human olfactory receptors for thiol key food odorants. In: 9th Wartburg symposium on fl avor chemistry & biology. Eisenach, Chair for Food Chemistry, Technische Universitaet Muenchen
65. Krautwurst D, Yau KW, Reed RR (1998) Identi fi cation of ligands for olfactory receptors by functional expression of a receptor library. Cell 95(7):917-926
66. Li YR, Matsunami H (2011) Activation state of the m3 muscarinic acetylcholine receptor modulates Mammalian odorant receptor signaling. Sci Signal 4(155):ra1
67. Saito H et al (2004) RTP family members induce functional expression of mammalian odorant receptors. Cell 119(5):679-691
68. Schmiedeberg K (2004) Molekulare klonierung, charakterisierung und struktur-funktionsbeziehungen von olfaktorischen rezeptoren für schlüsselaromastoffe, In: Mathematischnaturwissenschaftliche fakultät 2004, Universität Potsdam, Potsdam
69. Touhara K et al (1999) Functional identi fi cation and reconstitution of an odorant receptor in single olfactory neurons. Proc Natl Acad Sci USA 96(7):4040-4045
70. Olender S et al (2012) BMC Genomics 13:414
71. Wallrabenstein I (2013) PLoS One 8(2):e54950
72. Adipietro KA et al (2012) PLoS 8(7):p. e1002821