Adaptive evolution of MRG, a neuron-specific gene family implicated in nociception

Genome Research

Volumn 13, Issue 10, 2003, Pages 2252-2259

  Choi, Sun Shim ^a   Lahn, Bruce T ^a  

^a UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; G PROTEIN COUPLED RECEPTOR; LIGAND; NUCLEOTIDE; PROTEIN MRG; UNCLASSIFIED DRUG;

AMINO ACID SUBSTITUTION; ANIMAL CELL; ARTICLE; CELL MEMBRANE; CONTROLLED STUDY; CYTOPLASM; EVOLUTIONARY ADAPTATION; EXTRACELLULAR SPACE; GENETIC CODE; GENETIC MODEL; GENETIC SELECTION; HUMAN; HUMAN CELL; LIGAND BINDING; MOUSE; MULTIGENE FAMILY; NERVE CELL; NERVE CELL STIMULATION; NERVOUS SYSTEM; NOCICEPTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN DOMAIN; SENSITIVITY ANALYSIS; STATISTICAL ANALYSIS;

ADAPTATION, PHYSIOLOGICAL; AMINO ACID SUBSTITUTION; ANIMALS; CARRIER PROTEINS; DATABASES, GENETIC; EVOLUTION, MOLECULAR; GENES; GENES, TUMOR SUPPRESSOR; HUMANS; MACACA; MICE; MULTIGENE FAMILY; NEURONS; NOCICEPTORS; ORGAN SPECIFICITY; PAIN THRESHOLD; PHYLOGENY; RATS; RECEPTORS, G-PROTEIN-COUPLED; SELECTION (GENETICS); TUMOR SUPPRESSOR PROTEINS;

ANIMALIA;

EID: 0142092547     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.1431603     Document Type: Article

References (67)

1. Bielawski, J.P. and Yang, Z. 2001. Positive and negative selection in the DAZ gene family. Mol. Biol. Evol. 18: 523-529.
2. Bockaert, J. and Pin, J.P. 1999. Molecular tinkering of G protein-coupled receptors: An evolutionary success. EMBO J. 18: 1723-1729.
3. Chen, A.C., Dworkin, S.F., Haug, J., and Gehrig, J. 1989. Human pain responsivity in a tonic pain model: Psychological determinants. Pain 37: 143-160.
4. Dagan, T., Talmor, Y., and Graur, D. 2002. Ratios of radical to conservative amino acid replacement are affected by mutational and compositional factors and may not be indicative of positive Darwinian selection. Mol. Biol. Evol. 19: 1022-1025.
5. Ding, Y.C., Chi, H.C., Grady, D.L., Morishima, A., Kidd, J.R., Kidd, K.K., Flodman, P., Spence, M.A., Schuck, S., Swanson, J.M., et al. 2002. Evidence of positive selection acting at the human dopamine receptor D4 gene locus. Proc. Natl. Acad. Sci. 99: 309-314.
6. Dong, X., Han, S., 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: 619-632.
7. Dores, R.M., McDonald, L.K., Steveson, T.C., and Sei, C.A. 1990. The molecular evolution of neuropeptides: Prospects for the '90s. Brain Behav. Evol. 36: 80-99.
8. Duret, L. and Mouchiroud, D. 2000. Determinants of substitution rates in mammalian genes: Expression pattern affects selection intensity but not mutation rate. Mol. Biol. Evol. 17: 68-74.
9. Enard, W., Przeworski, M., Fisher, S.E., Lai, C.S., Wiebe, V., Kitano, T., Monaco, A.P., and Paabo, S. 2002. Molecular evolution of FOXP2, a gene involved in speech and language. Nature 418: 869-872.
10. Force, A., Lynch, M., Pickett, F.B., Amores, A., Yan, Y.L., and Postlethwait, J. 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: 1531-1545.
11. Friedberg, F. and Jason, L.A. 2001. Chronic fatigue syndrome and fibromyalgia: Clinical assessment and treatment. J. Clin. Psychol. 57: 433-455.
12. Gilad, Y., Segre, D., Skorecki, K., Nachman, M.W., Lancet, D., and Sharon, D. 2000. Dichotomy of single-nucleotide polymorphism haplotypes in olfactory receptor genes and pseudogenes. Nat. Genet. 26: 221-224.
13. Gilad, Y., Rosenberg, S., Przeworski, M., Lancet, D., and Skorecki, K. 2002. Evidence for positive selection and population structure at the human MAO-A gene. Proc. Natl. Acad. Sci. 99: 862-867.
14. Goldman, N. and Yang, Z. 1994. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 11: 725-736.
15. Grantham, R. 1974. Amino acid difference formula to help explain molecular evolution. Science 185: 862-864.
16. Hall, R.A., Premont, R.T., Chow, C.W., Blitzer, J.T., Pitcher, J.A., Claing, A., Stoffel, R.H., Barak, L.S., Shenolikar, S., Weinman, E.J., et al. 1998. The β2-adrenergic receptor interacts with the Na+/H+-exchanger regulatory factor to control Na+/H+ exchange. Nature 392: 626-630.
17. Han, S.K., Dong, X., Hwang, J.I., Zylka, M.J., Anderson, D.J., and Simon, M.I. 2002. Orphan G protein-coupled receptors MrgA1 and MrgC11 are distinctively activated by RF-amide-related peptides through the Gα q/11 pathway. Proc. Natl. Acad. Sci. 99: 14740-14745.
18. Hastings, K.E. 1996. Strong evolutionary conservation of broadly expressed protein isoforms in the troponin I gene family and other vertebrate gene families. J. Mol. Evol. 42: 631-640.
19. Henderson, G. and McKnight, A.T. 1997. The orphan opioid receptor and its endogenous ligand-nociceptin/orphanin FQ. Trends Pharmacol. Sci. 18: 293-300.
20. Hill, R.E. and Hastie, N.D. 1987. Accelerated evolution in the reactive centre regions of serine protease inhibitors. Nature 326: 96-99.
21. Hollt, V., Haarmann, I., Grimm, C., Herz, A., Tulunay, F.C., and Loh, H.H. 1982. Proenkephalin intermediates in bovine brain and adrenal medulla: Characterization of immunoreactive peptides related to BAM-22P and peptide F. Life Sci. 31: 1883-1886.
22. Hughes, A.L. 1994. The evolution of functionally novel proteins after gene duplication. Proc. R Soc. Lond. B Biol. Sci. 256: 119-124.
23. Hughes, A.L. and Hughes, M.K. 1993. Adaptive evolution in the rat olfactory receptor gene family. J. Mol. Evol. 36: 249-254.
24. Hughes, A.L. and Nei, M. 1988. Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature 335: 167-170.
25. Hughes, A.L., Green, J.A., Garbayo, J.M., and Roberts, R.M. 2000. Adaptive diversification within a large family of recently duplicated, placentally expressed genes. Proc. Natl. Acad. Sci. 97: 3319-3323.
26. Indo, Y., Tsuruta, M., Hayashida, Y., Karim, M.A., Ohta, K., Kawano, T., Mitsubuchi, H., Tonoki, H., Awaya, Y., and Matsuda, I. 1996. Mutations in the TRKA/NGF receptor gene in patients with congenital insensitivity to pain with anhidrosis. Nat. Genet. 13: 485-488.
27. Johnson, M.E., Viggiano, L., Bailey, J.A., Abdul-Rauf, M., Goodwin, G., Rocchi, M., and Eichler, E.E. 2001. Positive selection of a gene family during the emergence of humans and African apes. Nature 413: 514-519.
28. Kavaliers, M. 1988. Evolutionary and comparative aspects of nociception. Brain Res. Bull. 21: 923-931.
29. Kondrashov, F.A., Rogozin, I.B., Wolf, Y.I., and Koonin, E.V. 2002. Selection in the evolution of gene duplications. Genome Biol. 3: research0008.1-0008.9.
30. Lembo, P.M., Grazzini, E., Groblewski, T., O'Donnell, D., Roy, M.O., Zhang, J., Hoffert, C., Cao, J., Schmidt, R., Pelletier, M., et al. 2002. Proenkephalin A gene products activate a new family of sensory neuron-specific GPCRs. Nat. Neurosci. 5: 201-209.
31. Li, W.H. 1993. Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol. 36: 96-99.
32. Li, W.H. 1997. Molecular evolution. Sinauer Associates, Sunderland, MA.
33. Li, W.H., Wu, C.-I., and Luo, C.C. 1985. A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol. Bio. Evo. 2: 150-174.
34. Liberles, D.A., Schreiber, D.R., Govindarajan, S., Chamberlin, S.G., and Benner, S.A. 2001. The adaptive evolution database (TAED). Genome Biol. 2: research0028.1-0028.6.
35. Libman, E. 1934. Observations on individual sensitiveness to pain. J. Am. Med. Assoc. 102: 335-341.
36. Lynch, M. and Conery, J.S. 2000. The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1155.
37. Lynch, M. and Force, A. 2000. The probability of duplicate gene preservation by subfunctionalization. Genetics 154: 459-473.
38. Makolowski, W. and Boguski, M.S. 1998. Evolutionary parameters of the transcribed mammalian genome: An analysis of 2,820 orthologous rodent and human sequences. Proc. Natl. Acad. Sci. 95: 9407-9412.
39. Mansour, A., Hoversten, M.T., Taylor, L.P., Watson, S.J., and Akil, H. 1995. The cloned μ, δ, and κ receptors and their endogenous ligands: Evidence for two opioid peptide recognition cores. Brain Res. 700: 89-98.
40. Messier, W. and Stewart, C.B. 1997. Episodic adaptive evolution of primate lysozymes. Nature 385: 151-154.
41. Mogil, J.S., Wilson, S.G., Bon, K., Lee, S.E., Chung, K., Raber, P., Pieper, J.O., Hain, H.S., Belknap, J.K., Hubert, L., et al. 1999. Heritability of nociception I: Responses of 11 inbred mouse strains on 12 measures of nociception. Pain 80: 67-82.
42. Mukhopadhyay, N., Almasy, L., Schroeder, M., Mulvihill, W.P., and Weeks, D.E. 1999. Mega2, a data-handling program for facilitating genetic linkage and association analyses. Am. J. Hum. Genet. 65: A436.
43. Nielsen, R. and Yang, Z. 1998. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148: 929-936.
44. Ohno, S. 1970. Evolution by gene duplication. Springer-Verlag, Berlin.
45. 2+ channel gene CACNL1A4. Cell 87: 543-552.
46. Pittius, C.W., Seizinger, B.R., Pasi, A., Mehraein, P., and Herz, A. 1984. Distribution and characterization of opioid peptides derived from proenkephalin A in human and rat central nervous system. Brain Res. 304: 127-136.
47. Posada, D. and Crandall, K.A. 1998. MODELTEST: Testing the model of DNA substitution. Bioinformatics 14: 817-818.
48. Prince, V.E. and Pickett, F.B. 2002. Splitting pairs: The diverging fates of duplicated genes. Nat. Rev. Genet. 3: 827-837.
49. Sabeti, P.C., Reich, D.E., Higgins, J.M., Levine, H.Z., Richter, D.J., Schaffner, S.F., Gabriel, S.B., Platko, J.V., Patterson, N.J., McDonald, G.J., et al. 2002. Detecting recent positive selection in the human genome from haplotype structure. Nature 419: 832-837.
50. Sharon, D., Gilad, Y., Glusman, G., Khen, M., Lancet, D., and Kalush, F. 2000. Identification and characterization of coding single-nucleotide polymorphisms within a human olfactory receptor gene cluster. Gene 260: 87-94.
51. Shyue, S.K., Hewett-Emmett, D., Sperling, H.G., Hunt, D.M., Bowmaker, J.K., Mollon, J.D., and Li, W.H. 1995. Adaptive evolution of color vision genes in higher primates. Science 269: 1265-1267.
52. Sidow, A. 1996. Gen(om)e duplications in the evolution of early vertebrates. Curr. Opin. Genet. Dev. 6: 715-722.
53. Stewart, C.B., Schilling, J.W., and Wilson, A.C. 1987. Adaptive evolution in the stomach lysozymes of foregut fermenters. Nature 330: 401-404.
54. Suzuki, Y. and Nei, M. 2002. Simulation study of the reliability and robustness of the statistical methods for detecting positive selection at single amino acid sites. Mol. Biol. Evol. 19: 1865-1869.
55. Tanaka, T. and Nei, M. 1989. Positive Darwinian selection observed at the variable-region genes of immunoglobulins. Mol. Biol. Evol. 6: 447-459.
56. Tishkoff, S.A., Varkonyi, R., Cahinhinan, N., Abbes, S., Argyropoulos, G., Destro-Bisol, G., Drousiotou, A., Dangerfield, B., Lefranc, G., Loiselet, J., et al. 2001. Haplotype diversity and linkage disequilibrium at human G6PD: Recent origin of alleles that confer malarial resistance. Science 293: 455-462.
57. Wolfe, K.H. and Li, W.H. 2003. Molecular evolution meets the genomics revolution. Nat. Genet. 33 Suppl: 255-265.
58. Wyckoff, G.J., Wang, W., and Wu, C.-I. 2000. Rapid evolution of male reproductive genes in the descent of man. Nature 403: 304-309.
59. Yang, J., Huang, J., Gu, H., Zhong, Y., and Yang, Z. 2002. Duplication and adaptive evolution of the chalcone synthase genes of Dendranthema (Asteraceae). Mol. Biol. Evol. 19: 1752-1759.
60. Yang, Z. 1997. PAML: A program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13: 555-556.
61. Yang, Z. 1998. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol. Biol. Evol. 15: 568-573.
62. Yang, Z. 2000. Maximum likelihood estimation on large phylogenies and analysis of adaptive evolution in human influenza virus A. J. Mol. Evol. 51: 423-432.
63. Yang, Z. 2001. Maximum likelihood analysis of adaptive evolution in HIV-1 gp120 env gene. Pac. Symp. Biocomput. 226-237.
64. Yokoyama, S. and Yokoyama, R. 1989. Molecular evolution of human visual pigment genes. Mol. Biol. Evol. 6: 186-197.
65. Zhang, J., Zhang, Y.P., and Rosenberg, H.F. 2002. Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey. Nat. Genet. 30: 411-415.
66. Zhu, Y. and Pintar, J.E. 1998. Expression of opioid receptors and ligands in pregnant mouse uterus and placenta. Biol. Reprod. 59: 925-932.
67. Zhu, Y., Hsu, M.S., and Pintar, J.E. 1998. Developmental expression of the μ, κ, and δ opioid receptor mRNAs in mouse. J. Neurosci. 18: 2538-2549.