Rapid expansion of killer cell immunoglobulin-like receptor genes in primates and their coevolution with MHC Class I genes

Gene

Volumn 347, Issue 2 SPEC. ISS., 2005, Pages 149-159

  Hao, Li ^a   Nei, Masatoshi ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

Adaptive evolution; Ancestral sequence; KIR; MHC; Positive selection

Indexed keywords

IMMUNOGLOBULIN RECEPTOR; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 1;

AMINO ACID SEQUENCE; ANIMAL CELL; ANTIGEN BINDING; ANTIGEN SPECIFICITY; ARTICLE; BINDING SITE; CELL TRANSFORMATION; COEVOLUTION; CONTROLLED STUDY; GENE ACTIVITY; GENE DUPLICATION; GENE FUNCTION; GENE IDENTIFICATION; GENE SEQUENCE; GENE STRUCTURE; GENETIC VARIABILITY; HUMAN; HUMAN CELL; IMMUNE RESPONSE; IMMUNOGENETICS; IMMUNOGENICITY; KILLER CELL; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; MONKEY; MULTIGENE FAMILY; NATURAL KILLER CELL; NATURAL KILLER CELL MEDIATED CYTOTOXICITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIMATE; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; RECEPTOR GENE; SEQUENCE ANALYSIS; STRUCTURAL HOMOLOGY; VIRUS INFECTION;

EID: 15544386937     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2004.12.012     Document Type: Article

References (35)

1. E.J. Adams, and P. Parham Species-specific evolution of MHC class I genes in the higher primates Immunol. Rev. 183 2001 41 64
2. J.C. Boyington, and P.D. Sun A structural perspective on MHC class I recognition by killer cell immunoglobulin-like receptors Mol. Immunol. 38 2001 1007 1021
3. G. Glazko, and M. Nei Estimation of divergence times for major lineages of primate species Mol. Biol. Evol. 20 2003 424 434
4. L.A. Guethlein, L.R. Flodin, E.J. Adams, and P. Parham NK cell receptors of the orangutan (Pongo pygmaeus): a pivotal species for tracking the coevolution of killer cell Ig-like receptors with MHC-C J. Immunol. 169 2002 220 229
5. J.E. Gumperz Conserved and variable residues within the Bw4 motif of HLA-B make separable contributions to recognition by the NKB1 killer cell-inhibitory receptor J. Immunol. 158 1997 5237 5241
6. L. Hao, and M. Nei Genomic organization and evolutionary analysis of Ly49 genes encoding the rodent natural killer cell receptors: rapid evolution by repeated gene duplication Immunogenetics 56 2004 343 354
7. K.L. Hershberger, R. Shyam, A. Miura, and N.L. Letvin Diversity of the killer cell Ig-like receptors of rhesus monkeys J. Immunol. 166 2001 4380 4390
8. S.E. Hoelsbrekken Cutting edge: molecular cloning of a killer cell Ig-like receptor in the mouse and rat J. Immunol. 170 2003 2259 2263
9. K.C. Hsu, S. Chida, D.E. Geraghty, and B. Dupont The killer cell immunoglobulin-like receptor (KIR) genomic region: gene-order, haplotypes and allelic polymorphism Immunol. Rev. 190 2002 40 52
10. A.L. Hughes Evolution of the human killer cell inhibitory receptor family Mol. Phylogenet. Evol. 25 2002 330 340
11. M.E. Johnson Positive selection of a gene family during the emergence of humans and African apes Nature 413 2001 514 519
12. S.I. Khakoo Rapid evolution of NK cell receptor systems demonstrated by comparison of chimpanzees and humans Immunity 12 2000 687 698
13. S. Kumar, K. Tamura, I. Jakobsen, and M. Nei MEGA2: molecular evolutionary genetics analysis software Bioinformatics 17 2001 1244 1245
14. W.-H. Li, and L.A. Sadler Low nucleotide diversity in man Genetics 129 1991 513 613
15. S.G. Marsh Killer-cell immunoglobulin-like receptor (KIR) nomenclature report, 2002 Tissue Antigens 62 2003 79 86
16. A.M. Martin Comparative genomic analysis, diversity and evolution of two KIR haplotypes A and B Gene 335 2004 121 131
17. K.L. McQueen, B.T. Wilhelm, K.D. Harden, and D.L. Mager Evolution of NK receptors: a single Ly49 and multiple KIR genes in the cow Eur. J. Immunol. 32 2002 810 817
18. M. Nei Molecular evolutionary genetics 1987 Columbia University Press New York
19. M. Nei, and S. Kumar Molecular evolution and phylogenetics 2000 Oxford University Press Oxford, New York
20. M. Nei, X. Gu, and T. Sitnikova Evolution by the birth-and-death process in multigene families of the vertebrate system Proc. Natl. Acad. Sci. U. S. A. 94 1997 7799 7806
21. P. Parham Events in the adaptation of natural killer cell receptors to MHC class I polymorphisms Res. Immunol. 3 1997 190 194
22. H. Piontkivska, and M. Nei Birth-and-death evolution in primate MHC class I genes: divergence time estimates Mol. Biol. Evol. 20 2003 601 609
23. R. Rajalingam, P. Parham, and L. Abi-Rached Domain shuffling has been the main mechanism forming new hominoid killer cell Ig-like receptors J. Immunol. 172 2004 356 369
24. N. Saitou, and M. Nei The neighbour-joining method: a new method for constructing phylogenetic trees Mol. Biol. Evol. 4 1987 406 425
25. A.K. Storset, I.O. Slettedal, J.L. Williams, A. Law, and E. Dissen Natural killer cell receptors in cattle: a bovine killer cell immunoglobulin-like receptor multigene family contains members with divergent signaling motifs Eur. J. Immunol. 33 2003 980 990
26. D.L. Swofford PAUP. Phylogenetic analysis using parsimony 1998 Sinauer Associates Sunderland, Massachusetts
27. K. Takahashi, A.P. Rooney, and M. Nei Origins and divergence times of mammalian class II MHC gene clusters J. Hered. 91 2000 198 204
28. N. Takezaki, A. Rzhetsky, and M. Nei Phylogenetic test of the molecular clock and linearized trees Mol. Biol. Evol. 12 1995 823 833
29. J.D. Thompson, T.J. Gibson, F. Plewniak, F. Jeanmougin, and D.G. Higgins The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Nucleic Acids Res. 24 1997 4876 4882
30. M. Toneva Genomic diversity of natural killer cell receptor genes in three populations Tissue Antigens 57 2001 358 362
31. J. Trowsdale, R. Barten, A. Haude, C.A. Stewart, S. Beck, and M.J. Wilson The genomic context of natural killer receptor extended gene families Immunol. Rev. 181 2001 20 38
32. C. Vilches, M.J. Pando, and P. Parham Genes encoding human killer-cell Ig-like receptors with D1 and D2 extracellular domains all contain untranslated pseudoexons encoding a third Ig-like domain Immunogenetics 51 2000 639 646
33. B.T. Wilhelm, L. Gagnier, and D.L. Mager Sequence analysis of the Ly49 cluster in C57BL/6 mice: a rapidly evolving multigene family in the immune system Genomics 80 2002 646 661
34. C.C. Winter, and E.O. Long A single amino acid in the p58 killer cell inhibitory receptor controls the ability of natural killer cells to discriminate between the two groups of HLA-C allotypes J. Immunol. 158 1997 4026 4028
35. J. Zhang, and M. Nei Accuracies of ancestral amino acid sequences inferred by the parsimony, likelihood, and distance methods J. Mol. Evol. 44 Suppl. 1 1997 S139 S146