Nonsynonymous substitution rate heterogeneity in the peptide-binding region among different HLA-DRB1 lineages in humans

G3: Genes, Genomes, Genetics

Volumn 4, Issue 7, 2014, Pages 1217-1226

  Yasukochi, Yoshiki ^a   Satta, Yoko ^b  

^a UNIVERSITY OF TSUKUBA   (Japan)

^b GRADUATE UNIVERSITY FOR ADVANCED STUDIES   (Japan)

Author keywords

Allelic lineage; Balancing selection; Complex genetics; Complex immunity; Genetics of immunity; HLA; Infection; Innate immunity; Pathogen; Peptide binding region; Resistance; Tolerance

Indexed keywords

HLA A ANTIGEN; HLA B ANTIGEN; HLA C ANTIGEN; HLA DPB1 ANTIGEN; HLA DQB1 ANTIGEN; HLA DRB1 ANTIGEN; HLA DRB3 ANTIGEN; HLA DRB4 ANTIGEN; HLA DRB5 ANTIGEN;

ALLELE; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; BALANCING SELECTION; COMPUTER SIMULATION; GENE LOCATION; GENE SEQUENCE; GENETIC HETEROGENEITY; GENETIC VARIABILITY; HLA SYSTEM; HUMAN; MACACA FASCICULARIS; MAJOR HISTOCOMPATIBILITY COMPLEX; MOLECULAR CLOCK; MONOPHYLY; NONHUMAN; NONSYNONYMOUS SUBSTITUTION; NUCLEOTIDE SEQUENCE; PAN TROGLODYTES; PEPTIDE BINDING REGION; PHYLOGENETIC TREE; PROTEIN STRUCTURE; RHESUS MONKEY; SEQUENCE ALIGNMENT;

EID: 84904540031     PISSN: None     EISSN: 21601836     Source Type: Journal    
DOI: 10.1534/g3.114.011726     Document Type: Article

References (44)

1. Andersson, G., 1998 Evolution of the human HLA-DR region. Front. Biosci. 3: d739-d745.
2. Brown, J. H., T. S. Jardetzky, J. C. Gorga, L. J. Stern, R. G. Urban et al., 1993 Three-dimensional structure of the human class II histocompatibility antigen HLA-DR1. Nature 364: 33-39.
3. Carrington, M., G. W. Nelson, M. P. Martin, T. Kissner, D. Vlahov et al., 1999 HLA and HIV-1: heterozygote advantage and B*35-Cw*04 disadvantage. Science 283: 1748-1752.
4. Demotz, S., C. Barbey, G. Corradin, A. Amoroso, and A. Lanzavecchia, 1993 The set of naturally processed peptides displayed by DR molecules is tuned by polymorphism of residue 86. Eur. J. Immunol. 23: 425-432.
5. Doherty, P. C., and R. M. Zinkernagel, 1975 Enhanced immunological surveillance in mice heterozygous at the H-2 gene complex. Nature 256: 50-52.
6. Felsenstein, J., 2009 PHYLIP (Phylogeny Inference Package) ver.3.69. Distributed by the author, Department of Genome Sciences, University of Washington, Seattle, USA.
7. Gongora, R., F. Figueroa, and J. Klein, 1997 Complex origin of the HLADR10 haplotype. J. Immunol. 159: 6044-6051.
8. Gonzalez-Galarza, F. F., S. Christmas, D. Middleton, and A. R. Jones, 2011 Allele frequency net: a database and online repository for immune gene frequencies in worldwide populations. Nucleic Acids Res. 39: D913-D919.
9. Gregersen, P. K., M. Shen, Q. L. Song, P. Merryman, S. Degar et al., 1986 Molecular diversity of HLA-DR4 haplotypes. Proc. Natl. Acad. Sci. USA 83: 2642-2646.
10. Hasegawa, M., H. Kishino, and T. Yano, 1985 Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22: 160-174.
11. Hertz, T., D. Nolan, I. James, M. John, S. Gaudieri et al., 2011 Mapping the landscape of host-pathogen coevolution: HLA class I binding and its relationship with evolutionary conservation in human and viral proteins. J. Virol. 85: 1310-1321.
12. Hill, A. V. S., 1991 HLA associations with malaria in Africa: some implications for MHC evolution, pp. 403-419 in Molecular evolution of the major histocompatibility complex, edited by J. Klein, and D. Klein. Springer, Berlin, Heidelberg.
13. Hughes, A. L., and M. Nei, 1988 Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature 335: 167-170.
14. Hughes, A. L., and M. Nei, 1989 Nucleotide substitution at major histocompatibility complex class II loci: evidence for overdominant selection. Proc. Natl. Acad. Sci. USA 86: 958-962.
15. Hughes, A. L., and M. Yeager, 1998 Natural selection at major histocompatibility complex loci of vertebrates. Annu. Rev. Genet. 32: 415-435.
16. Jones, D., W. Taylor, and J. Thornton, 1992 The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8: 275-282.
17. Klein, J., A. Sato, and N. Nikolaidis, 2007 MHC, TSP, and the origin of species: from immunogenetics to evolutionary genetics. Annu. Rev. Genet. 41: 281-304.
18. Kusaba, M., T. Nishio, Y. Satta, K. Hinata, and D. Ockendon, 1997 Striking sequence similarity in inter- and intra-specific comparisons of class I SLG alleles from Brassica oleracea and Brassica campestris: implications for the evolution and recognition mechanism. Proc. Natl. Acad. Sci. USA 94: 7673-7678.
19. Musolf, K., Y. Meyer-Lucht, and S. Sommer, 2004 Evolution of MHC-DRB class II polymorphism in the genus Apodemus and a comparison of DRB sequences within the family Muridae (Mammalia: Rodentia). Immunogenetics 56: 420-426.
20. Nowak, M., K. Tarczy-Hornoch, and J. Austyn, 1992 The optimal number of major histocompatibility complex molecules in an individual. Proc. Natl. Acad. Sci. USA 89: 10896-10899.
21. Oliver, M. K., S. Telfer, and S. B. Piertney, 2009 Major histocompatibility complex (MHC) heterozygote superiority to natural multi-parasite infections in the water vole (Arvicola terrestris). Proc. Biol. Sci. 276: 1119-1128.
22. Ong, B., N. Willcox, P. Wordsworth, D. Beeson, A. Vincent et al., 1991 Critical role for the Val/Gly86 HLA-DRb dimorphism in autoantigen presentation to human T cells. Proc. Natl. Acad. Sci. USA 88: 7343-7347.
23. Penn, D. J., K. Damjanovich, and W. K. Potts, 2002 MHC heterozygosity confers a selective advantage against multiple-strain infections. Proc. Natl. Acad. Sci. USA 99: 11260-11264.
24. Reche, P. A., and E. L. Reinherz, 2003 Sequence variability analysis of human class I and class II MHC molecules: Functional and structural correlates of amino acid polymorphisms. J. Mol. Biol. 331: 623-641.
25. Robinson, J., M. J. Waller, P. Stoehr, and S. G. E. Marsh, 2005 IPD-the Immuno Polymorphism Database. Nucleic Acids Res. 33: D523-D526.
26. Robinson, J., K. Mistry, H. McWilliam, R. Lopez, P. Parham et al., 2011 The IMGT/HLA database. Nucleic Acids Res. 39: D1171-D1176.
27. Saitou, N., and M. Nei, 1987 The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.
28. Satta, Y., 1992 Balancing selection at HLA loci, pp. 111-131 in The Proceedings of the 17th Taniguchi Symposium, edited by N. Takahata. Japan Science Society Press, Tokyo.
29. Satta, Y., C. O'hUigin, N. Takahata, and J. Klein., 1994 Intensity of natural selection at the major histocompatibility complex loci. Proc. Natl. Acad. Sci. USA 91: 7184-7188.
30. Sawyer, S., 1989 Statistical tests for detecting gene conversion. Mol. Biol. Evol. 6: 526-538.
31. Slade, R. W., and H. I. McCallum, 1992 Overdominant vs. frequencydependent selection at MHC loci. Genetics 132: 861-862.
32. Sommer, S., 2005 The importance of immune gene variability (MHC) in evolutionary ecology and conservation. Front. Zool. 2: 16.
33. Spurgin, L. G., and D. S. Richardson, 2010 How pathogens drive genetic diversity: MHC, mechanisms and misunderstandings. Proc. Biol. Sci. 277: 979-988.
34. Stern, L. J., J. H. Brown, T. S. Jardetzky, J. C. Gorga, R. G. Urban et al., 1994 Crystal structure of the human class II MHC protein HLA-DR1 complexed with an influenza virus peptide. Nature 368: 215-221.
35. Takahata, N., 1990 A simple genealogical structure of strongly balanced allelic lines and trans-species evolution of polymorphism. Proc. Natl. Acad. Sci. USA 87: 2419-2423.
36. Takahata, N., and M. Nei, 1990 Allelic genealogy under overdominant and frequency-dependent selection and polymorphism of major histocompatibility complex loci. Genetics 124: 967-978.
37. Takahata, N., and F. Tajima, 1991 Sampling Errors in Phylogeny. 8: 494-502.
38. Takahata, N., Y. Satta, and J. Klein, 1992 Polymorphism and balancing selection at major histocompatibility complex loci. Genetics 130: 925-938.
39. Tamura, K., D. Peterson, N. Peterson, G. Stecher, M. Nei et al., 2011 MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28: 2731-2739.
40. Thursz, M. R., H. C. Thomas, B. M. Greenwood, and A. V. Hill, 1997 Heterozygote advantage for HLA class-II type in hepatitis B virus infection. Nat. Genet. 17: 11-12.
41. Verreck, F. A., A. van de Poel, J. W. Drijfhout, R. Amons, J. E. Coligan et al., 1996 Natural peptides isolated from Gly86/Val86-containing variants of HLA-DR1, -DR11, -DR13, and -DR52. Immunogenetics 43: 392-397.
42. Vidović, D., and P. Matzinger, 1988 Unresponsiveness to a foreign antigen can be caused by self-tolerance. Nature 336: 222-225.
43. Vita, R., L. Zarebski, J. A. Greenbaum, H. Emami, I. Hoof et al., 2010 The immune epitope database 2.0. Nucleic Acids Res. 38: D854-D862.
44. Woelfing, B., A. Traulsen, M. Milinski, and T. Boehm, 2009 Does intraindividual major histocompatibility complex diversity keep a golden mean? Philos. Trans. R. Soc. Lond. B Biol. Sci. 364: 117-128.