Allaby, Robin G. and Woodwark, Mathew. (2007) Phylogenomic analysis reveals extensive phylogenetic mosaicism in the Human GPCR Superfamily. Evolutionary Bioinformatics, Vol.3 . pp. 357-370. ISSN 1176-9343

Preview

PDF WRAP_Allaby_Phylogenomic_analysis.pdf - Requires a PDF viewer such as GSview, Xpdf or Adobe Acrobat Reader Download (1113Kb)

Abstract

A novel high throughput phylogenomic analysis (HTP) was applied to the rhodopsin G-protein coupled receptor (GPCR) family. Instances of phylogenetic mosaicism between receptors were found to be frequent, often as instances of correlated mosaicism and repeated mosaicism. A null data set was constructed with the same phylogenetic topology as the rhodopsin GPCRs. Comparison of the two data sets revealed that mosaicism was found in GPCRs in a higher frequency than would be expected by homoplasy or the effects of topology alone. Various evolutionary models of differential conservation, recombination and homoplasy are explored which could result in the patterns observed in this analysis. We find that the results are most consistent with frequent recombination events. A complex evolutionary history is illustrated in which it is likely frequent recombination has endowed GPCRs with new functions. The pattern of mosaicism is shown to be informative for functional prediction for orphan receptors. HTP analysis is complementary to conventional phylogenomic analyses revealing mosaicism that would not otherwise have been detectable through conventional phylogenetics.

Item Type:	Journal Article
Subjects:	Q Science > QH Natural history > QH426 Genetics
Divisions:	Faculty of Science > Life Sciences (2010- ) > Warwick HRI (2004-2010)
Library of Congress Subject Headings (LCSH):	Human beings -- Phylogeny, G proteins, Mosaicism, Evolutionary genetics, Human genetics
Journal or Publication Title:	Evolutionary Bioinformatics
Publisher:	Libertas Academica Ltd.
ISSN:	1176-9343
Date:	26 September 2007
Volume:	Vol.3
Page Range:	pp. 357-370
Status:	Peer Reviewed
Access rights to Published version:	Open Access
References:	Allaby, R.G. and Woodwark, M. 2004. Phylogenetics in the bioinformatics culture of understanding. Comp. Funct. Genom., 5:128–46. 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. Bockaert, J. and Pin, J.P.P. 1999. Molecular tinkering of G protein-coupled receptors: an evolutionary success. EMBO. J., 18:1723–29. Choi, S.S. and Lahn, B.T. 2003. The Evolution of MRG, a neuron-specifi c gene family implicated in nociception. Genome Res., 13 2252–59. Dong, X., Han, S-K., Zylka, M.J., Simon, M.I. and Anderson, D.J. 2001. A diverse family of GPCRs Expressed in specifi c subsets of nociceptive sensory neurons. Cell, 106:619–32. Eisan, J.A. and Fraser, C.M. 2003. Phylogenomics: Intersection of evolution and genomics. Science, 300:1706–7. Eisan, J.A. 1998. Phylogenomics: Improving functional predictions for uncharacterised genes by evolutionary analysis. Genome Res., 8:163–7. Felsenstein, J. 1989. PHYLIP—Phylogeny Inference Package (version 3.2). Cladistics, 5:164–6. Flower, D.R. 1999. Modelling G-protein-coupled receptors for drug design. Biochim. Biophys. Acta., 1422:207–34. 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. 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. 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. 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. 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. 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. Li, W-H., Gu, Z., Wang, H. and Nekrutenko, A. 2001. Evolutionary analysis of the human genome. Nature, 409:847–9. 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. Identifi cation of relaxin-3/INSL7 as an endogenous ligand for the orphan G-protein coupled receptor GPCR135. J. Biol. Chem., 278:50754–64. Maddison, W.P., Maddison, D.R. 2003. Mesquite: a modular system for evolutionary analysis. Version 1.0. http://mesquiteproject.org. 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. Patthy, L. 1999. Genome evolution and the evolution of exon shuffling—a review. Gene, 238:103–14. Shields, D.C. 2000. Gene conversion among chemokine receptors. Gene, 246:239–45. 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. Sjölander, K. 2004. Phylogenomic inference of protein molecular function: advances and challenges. Bioinformatics, 20:170–9. 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 signifi cant protein sequence homology. Comput. Appl. Biosc., 12, 327–45. 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. Thompson JD, Higgins DG and Gibson TJ. 1994. CLUSTALW: improving the sensitivity of progressive sequence alignment through sequence weighting, position specifi c gap-penalties and weight matrix choice. Nucleic. Acids Res., 22:4673-4680.
URI:	http://wrap.warwick.ac.uk/id/eprint/716

Request changes to a record

Actions (login required)

View Item