Skip to main content

Databases in SenseLab for the Genomics, Proteomics, and Function of Olfactory Receptors

  • Protocol
  • First Online:
Olfactory Receptors

Abstract

We present here, the salient aspects of three databases: Olfactory Receptor Database (ORDB) is a repository of genomics and proteomics information of ORs; OdorDB stores information related to odorous compounds, specifically identifying those that have been shown to interact with olfactory rectors; and OdorModelDB disseminates information related to computational models of olfactory receptors (ORs). The data stored among these databases is integrated. Presented in this chapter are descriptions of these resources, which are part of the SenseLab suite of databases, a discussion of the computational infrastructure that enhances the efficacy of information storage, retrieval, dissemination, and automated data population from external sources.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Buck L, Axel R (1991) A novel multigene family may encode odorant receptors: a molecular basis for odor recognition. Cell 65:175–187

    Article  PubMed  CAS  Google Scholar 

  2. Beets MG (1970) The molecular parameters of olfactory response. Pharmacol Rev 22:1–34

    PubMed  CAS  Google Scholar 

  3. Mateson JF (1954) The olfactory area and the olfactory receptor process. Ann N Y Acad Sci 58:83–95

    Article  PubMed  CAS  Google Scholar 

  4. Mombaerts P (2004) Love at first smell–the 2004 Nobel Prize in physiology or medicine. N Engl J Med 351:2579–2580

    Article  PubMed  CAS  Google Scholar 

  5. Zhang X, Firestein S (2002) The olfactory receptor gene superfamily of the mouse. Nat Neurosci 5:124–133

    PubMed  CAS  Google Scholar 

  6. Sharon D, Glusman G, Pilpel Y, Horn-Saban S, Lancet D (1998) Genome dynamics, ­evolution, and protein modeling in the ­olfactory receptor gene superfamily. Ann N Y Acad Sci 855:182–193

    Article  PubMed  CAS  Google Scholar 

  7. Glusman G, Bahar A, Sharon D, Pilpel Y, White J, Lancet D (2000) The olfactory receptor gene superfamily: data mining, classification, and nomenclature. Mamm Genome 11:1016–1023

    Article  PubMed  CAS  Google Scholar 

  8. Glusman G, Yanai I, Rubin I, Lancet D (2001) The complete human olfactory subgenome. Genome Res 11:685–702

    Article  PubMed  CAS  Google Scholar 

  9. Gilad Y, Man O, Glusman G (2005) A comparison of the human and chimpanzee olfactory receptor gene repertoires. Genome Res 15:224–230

    Article  PubMed  CAS  Google Scholar 

  10. Crasto C, Singer MS, Shepherd GM (2001) The olfactory receptor family album. Genome Biol 2:REVIEWS1027

    Article  PubMed  CAS  Google Scholar 

  11. Crasto C, Marenco L, Miller P, Shepherd G (2002) Olfactory receptor database: a metadata-driven automated population from sources of gene and protein sequences. Nucleic Acids Res 30:354–360

    Article  PubMed  CAS  Google Scholar 

  12. Crasto CJ, Marenco LN, Liu N, Morse TM, Cheung KH, Lai PC, Bahl G, Masiar P, Lam HY, Lim E, Chen H, Nadkarni P, Migliore M, Miller PL, Shepherd GM (2007) SenseLab: new developments in disseminating neuroscience information. Brief Bioinform 8:150–162

    Article  PubMed  CAS  Google Scholar 

  13. Healy MD, Smith JE, Singer MS, Nadkarni PM, Skoufos E, Miller PL, Shepherd GM (1997) Olfactory receptor database (ORDB): a resource for sharing and analyzing published and unpublished data. Chem Senses 22:321–326

    Article  PubMed  CAS  Google Scholar 

  14. Shepherd GM, Mirsky JS, Healy MD, Singer MS, Skoufos E, Hines MS, Nadkarni PM, Miller PL (1998) The human brain project: neuroinformatics tools for integrating, searching and modeling multidisciplinary neuroscience data. Trends Neurosci 21:460–468

    Article  PubMed  CAS  Google Scholar 

  15. Skoufos E, Healy MD, Singer MS, Nadkarni PM, Miller PL, Shepherd GM (1999) Olfactory receptor database: a database of the largest eukaryotic gene family. Nucleic Acids Res 27:343–345

    Article  PubMed  CAS  Google Scholar 

  16. Skoufos E, Marenco L, Nadkarni PM, Miller PL, Shepherd GM (2000) Olfactory receptor database: a sensory chemoreceptor resource. Nucleic Acids Res 28:341–343

    Article  PubMed  CAS  Google Scholar 

  17. Osterhammel P, Terkildsen K, Zilstorff K (1969) Electro-olfactograms in man. J Laryngol Otol 83:731–733

    Article  PubMed  CAS  Google Scholar 

  18. Hummel T, Knecht M, Kobal G (1996) Peripherally obtained electrophysiological responses to olfactory stimulation in man: electro-olfactograms exhibit a smaller degree of desensitization compared with subjective intensity estimates. Brain Res 717:160–164

    Article  PubMed  CAS  Google Scholar 

  19. Scott JW, Scott-Johnson PE (2002) The electroolfactogram: a review of its history and uses. Microsc Res Tech 58:152–160

    Article  PubMed  Google Scholar 

  20. Knecht M, Hummel T (2004) Recording of the human electro-olfactogram. Physiol Behav 83:13–19

    PubMed  CAS  Google Scholar 

  21. Shirokova E, Schmiedeberg K, Bedner P, Niessen H, Willecke K, Raguse JD, Meyerhof W, Krautwurst D (2005) Identification of specific ligands for orphan olfactory receptors. G protein-dependent agonism and antagonism of odorants. J Biol Chem 280:11807–11815

    Article  PubMed  CAS  Google Scholar 

  22. Matarazzo V, Clot-Faybesse O, Marcet B, Guiraudie-Capraz G, Atanasova B, Devauchelle G, Cerutti M, Etievant P, Ronin C (2005) Functional characterization of two human olfactory receptors expressed in the baculovirus Sf9 insect cell system. Chem Senses 30:195–207

    Article  PubMed  CAS  Google Scholar 

  23. Doengi M, Hirnet D, Coulon P, Pape HC, Deitmer JW, Lohr C (2009) GABA uptake-dependent Ca(2+) signaling in developing olfactory bulb astrocytes. Proc Natl Acad Sci USA 106:17570–17575

    Article  PubMed  CAS  Google Scholar 

  24. Murmu MS, Stinnakre J, Real E, Martin JR (2011) Calcium-stores mediate adaptation in axon terminals of olfactory receptor neurons in Drosophila. BMC Neurosci 12:105

    Article  PubMed  CAS  Google Scholar 

  25. Tsuboi A, Imai T, Kato HK, Matsumoto H, Igarashi KM, Suzuki M, Mori K, Sakano H (2011) Two highly homologous mouse odorant receptors encoded by tandemly-linked MOR29A and MOR29B genes respond differently to phenyl ethers. Eur J Neurosci 33:205–213

    Article  PubMed  Google Scholar 

  26. Breer H (1993) Olfactory receptor cells: recognition and transduction of chemical signals. Cytotechnology 11:13–16

    Article  PubMed  CAS  Google Scholar 

  27. Singer MS, Shepherd GM (1994) Molecular modeling of ligand-receptor interactions in the OR5 olfactory receptor. Neuroreport 5:1297–1300

    Article  PubMed  CAS  Google Scholar 

  28. Singer MS (2000) Analysis of the molecular basis for octanal interactions in the expressed rat 17 olfactory receptor. Chem Senses 25:155–165

    Article  PubMed  CAS  Google Scholar 

  29. Floriano WB, Vaidehi N, Goddard WA 3rd, Singer MS, Shepherd GM (2000) Molecular mechanisms underlying differential odor responses of a mouse olfactory receptor. Proc Natl Acad Sci USA 97:10712–10716

    Article  PubMed  CAS  Google Scholar 

  30. Zhao H, Ivic L, Otaki JM, Hashimoto M, Mikoshiba K, Firestein S (1998) Functional expression of a mammalian odorant receptor. Science 279:237–242

    Article  PubMed  CAS  Google Scholar 

  31. Araneda RC, Kini AD, Firestein S (2000) The molecular receptive range of an odorant receptor. Nat Neurosci 3:1248–1255

    Article  PubMed  CAS  Google Scholar 

  32. Bozza T, Feinstein P, Zheng C, Mombaerts P (2002) Odorant receptor expression defines functional units in the mouse olfactory system. J Neurosci 22:3033–3043

    PubMed  CAS  Google Scholar 

  33. Luu P, Acher F, Bertrand HO, Fan J, Ngai J (2004) Molecular determinants of ligand selectivity in a vertebrate odorant receptor. J Neurosci 24:10128–10137

    Article  PubMed  CAS  Google Scholar 

  34. Chase J, Touhara K, Prestwich GD, Schal C, Blomquist GJ (1992) Biosynthesis and endocrine control of the production of the German cockroach sex pheromone 3,11-dimethylnonacosan-2-one. Proc Natl Acad Sci USA 89:6050–6054

    Article  PubMed  CAS  Google Scholar 

  35. Touhara K, Sengoku S, Inaki K, Tsuboi A, Hirono J, Sato T, Sakano H, Haga T (1999) Functional identification and reconstitution of an odorant receptor in single olfactory neurons. Proc Natl Acad Sci USA 96:4040–4045

    Article  PubMed  CAS  Google Scholar 

  36. Touhara K (2001) Functional cloning and reconstitution of vertebrate odorant receptors. Life Sci 68:2199–2206

    Article  PubMed  CAS  Google Scholar 

  37. Touhara K (2002) Odor discrimination by G protein-coupled olfactory receptors. Microsc Res Tech 58:135–141

    Article  PubMed  CAS  Google Scholar 

  38. Katada S, Nakagawa T, Kataoka H, Touhara K (2003) Odorant response assays for a heterologously expressed olfactory receptor. Biochem Biophys Res Commun 305:964–969

    Article  PubMed  CAS  Google Scholar 

  39. Oka Y, Nakamura A, Watanabe H, Touhara K (2004) An odorant derivative as an antagonist for an olfactory receptor. Chem Senses 29:815–822

    Article  PubMed  CAS  Google Scholar 

  40. Oka Y, Omura M, Kataoka H, Touhara K (2004) Olfactory receptor antagonism between odorants. EMBO J 23:120–126

    Article  PubMed  CAS  Google Scholar 

  41. Oka Y, Katada S, Omura M, Suwa M, Yoshihara Y, Touhara K (2006) Odorant receptor map in the mouse olfactory bulb: in vivo sensitivity and specificity of receptor-defined glomeruli. Neuron 52:857–869

    Article  PubMed  CAS  Google Scholar 

  42. Touhara K (2007) Deorphanizing vertebrate olfactory receptors: recent advances in odorant-response assays. Neurochem Int 51:132–139

    Article  PubMed  CAS  Google Scholar 

  43. Schmiedeberg K, Shirokova E, Weber HP, Schilling B, Meyerhof W, Krautwurst D (2007) Structural determinants of odorant recognition by the human olfactory receptors OR1A1 and OR1A2. J Struct Biol 159:400–412

    Article  PubMed  CAS  Google Scholar 

  44. Grosmaitre X, Fuss SH, Lee AC, Adipietro KA, Matsunami H, Mombaerts P, Ma M (2009) SR1, a mouse odorant receptor with an unusually broad response profile. J Neurosci 29:14545–14552

    Article  PubMed  CAS  Google Scholar 

  45. Nara K, Saraiva LR, Ye X, Buck LB (2011) A large-scale analysis of odor coding in the olfactory epithelium. J Neurosci 31:9179–9191

    Article  PubMed  CAS  Google Scholar 

  46. Muller G (2000) Towards 3D structures of G protein-coupled receptors: a multidisciplinary approach. Curr Med Chem 7:861–888

    Article  PubMed  CAS  Google Scholar 

  47. Lai PC, Bahl G, Gremigni M, Matarazzo V, Clot-Faybesse O, Ronin C, Crasto CJ (2008) An olfactory receptor pseudogene whose function emerged in humans: a case study in the evolution of structure-function in GPCRs. J Struct Funct Genomics 9:29–40

    Article  PubMed  CAS  Google Scholar 

  48. Lai PC, Singer MS, Crasto CJ (2005) Structural activation pathways from dynamic olfactory receptor-odorant interactions. Chem Senses 30:781–792

    Article  PubMed  CAS  Google Scholar 

  49. Lai PC, Crasto CJ (2012) Beyond modeling: all-atom olfactory receptor model simulations. Front Genet 3:61

    Article  PubMed  Google Scholar 

  50. Vaidehi N, Floriano WB, Trabanino R, Hall SE, Freddolino P, Choi EJ, Zamanakos G, Goddard WA 3rd (2002) Prediction of structure and function of G protein-coupled receptors. Proc Natl Acad Sci USA 99:12622–12627

    Article  PubMed  CAS  Google Scholar 

  51. Hall SE, Floriano WB, Vaidehi N, Goddard WA 3rd (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

    Article  PubMed  CAS  Google Scholar 

  52. Floriano WB, Vaidehi N, Goddard WA 3rd (2004) Making sense of olfaction through predictions of the 3-D structure and function of olfactory receptors. Chem Senses 29:269–290

    Article  PubMed  CAS  Google Scholar 

  53. Hummel P, Vaidehi N, Floriano WB, Hall SE, Goddard WA 3rd (2005) Test of the Binding Threshold Hypothesis for olfactory receptors: explanation of the differential binding of ketones to the mouse and human orthologs of olfactory receptor 912-93. Protein Sci 14:703–710

    Article  PubMed  CAS  Google Scholar 

  54. Palczewski K, Kumasaka T, Hori T, Behnke CA, Motoshima H, Fox BA, Le Trong I, Teller DC, Okada T, Stenkamp RE, Yamamoto M, Miyano M (2000) Crystal structure of rhodopsin: a G protein-coupled receptor. Science 289:739–745

    Article  PubMed  CAS  Google Scholar 

  55. Okada T, Sugihara M, Bondar AN, Elstner M, Entel P, Buss V (2004) The retinal conformation and its environment in rhodopsin in light of a new 2.2 A crystal structure. J Mol Biol 342:571–583

    Article  PubMed  CAS  Google Scholar 

  56. Hanson MA, Roth CB, Jo E, Griffith MT, Scott FL, Reinhart G, Desale H, Clemons B, Cahalan SM, Schuerer SC, Sanna MG, Han GW, Kuhn P, Rosen H, Stevens RC (2012) Crystal structure of a lipid G protein-coupled receptor. Science 335:851–855

    Article  PubMed  CAS  Google Scholar 

  57. Shimamura T, Shiroishi M, Weyand S, Tsujimoto H, Winter G, Katritch V, Abagyan R, Cherezov V, Liu W, Han GW, Kobayashi T, Stevens RC, Iwata S (2011) Structure of the human histamine H1 receptor complex with doxepin. Nature 475:65–70

    Article  PubMed  CAS  Google Scholar 

  58. Wu B, Chien EY, Mol CD, Fenalti G, Liu W, Katritch V, Abagyan R, Brooun A, Wells P, Bi FC, Hamel DJ, Kuhn P, Handel TM, Cherezov V, Stevens RC (2010) Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists. Science 330:1066–1071

    Article  PubMed  CAS  Google Scholar 

  59. Rasmussen SG, Choi HJ, Rosenbaum DM, Kobilka TS, Thian FS, Edwards PC, Burghammer M, Ratnala VR, Sanishvili R, Fischetti RF, Schertler GF, Weis WI, Kobilka BK (2007) Crystal structure of the human beta2 adrenergic G-protein-coupled receptor. Nature 450:383–387

    Article  PubMed  CAS  Google Scholar 

  60. Kshirsagar NA, Takle MR, Nadkarni PM, Satoskar RS (1986) Effect of standard breakfast & lunch on sulphadimidine bioavailability. Indian J Med Res 83:618–622

    PubMed  CAS  Google Scholar 

  61. Nadkarni PM, Marenco L, Chen R, Skoufos E, Shepherd G, Miller P (1999) Organization of heterogeneous scientific data using the EAV/CR representation. J Am Med Inform Assoc 6:478–493

    Article  PubMed  CAS  Google Scholar 

  62. Marenco L, Tosches N, Crasto C, Shepherd G, Miller PL, Nadkarni PM (2003) Achieving evolvable Web-database bioscience applications using the EAV/CR framework: recent advances. J Am Med Inform Assoc 10:444–453

    Article  PubMed  Google Scholar 

  63. Nadkarni P (2012) Metadata-driven software systems in biomedicine: designing systems that can adapt to changing knowledge (Health Informatics). Springer, London, New York

    Google Scholar 

  64. Litwin W, Abdellatif A (1986) Multidatabase interoperability. Computer (IEEE Comput. Soc.) 19:10–18

    Article  Google Scholar 

  65. Litwin W, Mark L, Roussopoulos N (1990) interoperability of multiple autonomous databases. ACM Comput Surv 22:267–293

    Article  Google Scholar 

  66. Noy NF, Fergerson RW, Musen MA (2000) The knowledge model of protégé-2000: combining interoperability and flexibility. In: Dieng R, Corby O (eds) Knowledge engineering and knowledge management methods, models, and tools. Springer, Heidelberg, pp 17–32

    Chapter  Google Scholar 

  67. NCBI (2012) Entrez programming utilities help. NCBI, Bethesda, MD

    Google Scholar 

Download references

Acknowledgments

This work is generously supported in part by grant R21DC011068, R01DC009977, and R01DA021253 from the National Institutes of Health.

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Marenco, L.N. et al. (2013). Databases in SenseLab for the Genomics, Proteomics, and Function of Olfactory Receptors. In: Crasto, C. (eds) Olfactory Receptors. Methods in Molecular Biology, vol 1003. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-377-0_1

Download citation

  • DOI: https://doi.org/10.1007/978-1-62703-377-0_1

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-376-3

  • Online ISBN: 978-1-62703-377-0

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics