Phylogenomic analysis reveals extensive phylogenetic mosaicism in the human GPCR superfamily

Evolutionary Bioinformatics

Volumn 3, Issue , 2007, Pages 357-370

  Allaby, Robin G ^a   Woodwark, Mathew ^b  

^a UNIVERSITY OF WARWICK   (United Kingdom)

^b MEDIMMUNE LTD   (United Kingdom)

Author keywords

Evolution; GPCRs; Mosaicism; Phylogenomics

Indexed keywords

ALPHA 1B ADRENERGIC RECEPTOR; BETA 2 ADRENERGIC RECEPTOR; CHEMOKINE RECEPTOR CCR5; CHEMOKINE RECEPTOR CXCR1; CHEMOKINE RECEPTOR CXCR2; DELTA OPIATE RECEPTOR; G PROTEIN COUPLED RECEPTOR; GALANIN RECEPTOR; OREXIN 1 RECEPTOR; OREXIN 2 RECEPTOR; SOMATOSTATIN RECEPTOR 3; SOMATOSTATIN RECEPTOR 5; UROTENSIN RECEPTOR;

ARTICLE; CONTROLLED STUDY; GENE CONVERSION; GENE LOCUS; GENETIC CONSERVATION; GENETIC DISTANCE; GENETIC RECOMBINATION; HIGH THROUGHPUT PHYLOGENOMIC; HOMOPLASY; HUMAN; MOSAICISM; PARALOGY; PHYLOGENETIC DISTANCE; PHYLOGENOMICS; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY;

EID: 84928228932     PISSN: None     EISSN: 11769343     Source Type: Journal    
DOI: 10.1177/117693430700300002     Document Type: Article

References (26)

1. Allaby, R.G. and Woodwark, M. 2004. Phylogenetics in the bioinformatics culture of understanding. Comp. Funct. Genom., 5:128-46.
2. Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25:3389-402.
3. Bockaert, J. and Pin, J.P.P. 1999. Molecular tinkering of G protein-coupled receptors: an evolutionary success. EMBO. J., 18:1723-29.
4. Choi, S.S. and Lahn, B.T. 2003. The Evolution of MRG, a neuron-specific gene family implicated in nociception. Genome Res., 13 2252-59.
5. Dong, X., Han, S-K., Zylka, M.J., Simon, M.I. and Anderson, D.J. 2001. A diverse family of GPCRs Expressed in specific subsets of nociceptive sensory neurons. Cell, 106:619-32.
6. Eisan, J.A. and Fraser, C.M. 2003. Phylogenomics: Intersection of evolution and genomics. Science, 300:1706-7.
7. Eisan, J.A. 1998. Phylogenomics: Improving functional predictions for uncharacterised genes by evolutionary analysis. Genome Res., 8:163-7.
8. Felsenstein, J. 1989. PHYLIP-Phylogeny Inference Package (version 3.2). Cladistics, 5:164-6.
9. Flower, D.R. 1999. Modelling G-protein-coupled receptors for drug design. Biochim. Biophys. Acta., 1422:207-34.
10. Fredriksson, R., Lagerström, M.C., Lundin, L-G. and Schiöth, H.B. 2003. The G-protein coupled receptors in the human genome form five main families. Phylogenetic analysis, paralogon groups and fingerprints. Mol. Pharmacol., 63:1256-72.
11. Grassly, N., Adachi, J. and Rambaut, A. 1997. PSeq-Gen: an application for the Monte Carlo simulation of protein sequence evolution along phylogenetic trees. Comput. Appl. Biosci., 13:559-60.
12. Howard, A.D., McAllister, G., Feighner, S.D., Liu, Q.Y., Nargund, R.P., Van der Ploeg, L.H.T. and Patchett, A.A. 2001. Orphan G-protein-coupled receptors and natural ligand discovery. Trends Pharm. Sci., 22:132-40.
13. Hsu, S.Y., Nakabayashi, K., Nishi, S., Kumagai, J., Kudo, M., Sherwood, O.D. and Hsueh, A.J.W. 2002. Activation of orphan receptors by the hormone relaxin. Science, 295:671-4.
14. Jones, D.T., Taylor, W.R. and Thornton, J.M. 1992. The rapid generation of mutation data matrices from protein sequences. Comput. Applic. Biosci., 8:275-82.
15. Joost, P. and Methner, A. 2002. Phylogenetic analysis of 277 human Gprotein-coupled receptors as a tool for the prediction of orphan receptor ligands. Genome Biology, 3:1-16.
16. Li, W-H., Gu, Z., Wang, H. and Nekrutenko, A. 2001. Evolutionary analysis of the human genome. Nature, 409:847-9.
17. Liu, C.L., Eriste, E., Sutton, S., Chen, J.C., Roland, B., Kuei, C., Farmer, N., Jornvall, H., Sillard, R. and Lovenberg, T.W. 2003. Identification of relaxin-3/INSL7 as an endogenous ligand for the orphan G-protein coupled receptor GPCR135. J. Biol. Chem., 278:50754-64.
18. Maddison, W.P., Maddison, D.R. 2003. Mesquite: a modular system for evolutionary analysis. Version 1.0. http://mesquiteproject.org.
19. Notredame, C., Higgins, D.G. and Hering, J. 2000. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol., 302:205-17.
20. Patthy, L. 1999. Genome evolution and the evolution of exon shuffling-a review. Gene, 238:103-14.
21. Shields, D.C. 2000. Gene conversion among chemokine receptors. Gene, 246:239-45.
22. Shulman, A,I., Larson, C., Mangelsdorf, D.J. and Ranganathan, R. 2004. Structural determinants of allosteric ligand activation in RXR heterodimers. Cell, 116:417-29.
23. Sjölander, K. 2004. Phylogenomic inference of protein molecular function: advances and challenges. Bioinformatics, 20:170-9.
24. Sjölander, K., Karplus, K., Brown, M., Hughey, R., Krogh, A., Mian, I.S., Haussler, D. 1996. Dirichlet mixtures: a method of improved detection of weak but significant protein sequence homology. Comput. Appl. Biosc., 12, 327-45.
25. Tanaka, H., Yoshida, T., Miyamoto, N., Motoike, T., Kurosu, H., Shibata, K., Yamanaka, A., Williams, S.C., Richardson, J.A., Tsujino, N., Garry, M.G., Lerner, M.R., King, D.S., O'Dowd, B.F., Sakurai, T. and Yanagisawa, M. 2003. Characterisation of a family of endogenous neuropeptide ligands for the G protein-coupled receptors GPR7 and GPR8. Proc. Natl. Acad. Sci., USA 100, 6251-56.
26. Thompson JD, Higgins DG and Gibson TJ. 1994. CLUSTALW: improving the sensitivity of progressive sequence alignment through sequence weighting, position specific gap-penalties and weight matrix choice. Nucleic. Acids Res., 22:4673-4680.