Transspecies dimorphic allelic lineages of the proteasome subunit β-type 8 gene (PSMB8) in the teleost genus Oryzias

Proceedings of the National Academy of Sciences of the United States of America

Volumn 107, Issue 50, 2010, Pages 21599-21604

  Miura, Fumi ^a   Tsukamoto, Kentaro ^a,b,d   Mehta, Ratnesh Bhai ^a   Naruse, Kiyoshi ^b   Magtoon, Wichian ^c   Nonaka, Masaru ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b NATIONAL INSTITUTE FOR BASIC BIOLOGY   (Japan)

^c SRINAKHARINWIROT UNIVERSITY   (Thailand)

^d FUJITA HEALTH UNIVERSITY   (Japan)

Author keywords

Antigen processing; Long term balancing selection; Transspecies polymorphism

Indexed keywords

MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 1; PROTEASOME SUBUNIT BETA TYPE 8; PROTEIN; UNCLASSIFIED DRUG;

ALLELE; AMINO ACID ANALYSIS; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; EVOLUTION; EXON; GENE SEQUENCE; INTRON; NONHUMAN; NUCLEOTIDE SEQUENCE; ORYZIAS; PRIORITY JOURNAL; SPECIES DIFFERENTIATION; TELEOST; VERTEBRATE;

ALLELES; AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; EVOLUTION, MOLECULAR; HISTOCOMPATIBILITY ANTIGENS CLASS I; MAJOR HISTOCOMPATIBILITY COMPLEX; MOLECULAR SEQUENCE DATA; ORYZIAS; PHYLOGENY; POLYMORPHISM, GENETIC; PROTEASOME ENDOPEPTIDASE COMPLEX; PROTEIN SUBUNITS;

GNATHOSTOMATA (VERTEBRATE); ORYZIAS; ORYZIAS LATIPES; ORYZIINAE; TELEOSTEI;

EID: 78650733024     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1012881107     Document Type: Article

References (40)

1. Klein J, Sato A, Nikolaidis N (2007) MHC, TSP, and the origin of species: From immunogenetics to evolutionary genetics. Annu Rev Genet 41:281-304.
2. Hedrick PW (2006) Genetic polymorphism in heterogeneous environments: The age of genomics. Annu Rev Ecol Evol Syst 37:67-93.
3. Figueroa F, Günther E, Klein J (1988) MHC polymorphism pre-dating speciation. Nature 335:265-267.
4. LawlorDA, Ward FE, Ennis PD, Jackson AP, ParhamP (1988) HLA-A and B polymorphisms predate the divergence of humans and chimpanzees. Nature 335:268-271.
5. Hughes AL, Nei M (1988) Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature 335:167-170.
6. Satta Y, Mayer WE, Klein J (1996) HLA-DRB intron 1 sequences: Implications for the evolution of HLA-DRB genes and haplotypes. Hum Immunol 51:1-12. (Pubitemid 26365651)
7. Esteves PJ, et al. (2005) The evolution of the immunoglobulin heavy chain variable region (IgVH) in Leporids: An unusual case of transspecies polymorphism. Immunogenetics 57: 874-882.
8. Su C, Nei M (1999) Fifty-million-year-old polymorphism at an immunoglobulin variable region gene locus in the rabbit evolutionary lineage. Proc Natl Acad Sci USA 96: 9710-9715.
9. Ferguson W, Dvora S, Gallo J, Orth A, Boissinot S (2008) Long-term balancing selection at the West Nile Virus resistance gene, Oas1b, maintains transspecific polymorphisms in the house mouse. Mol Biol Evol 25:1609-1618.
10. Newman RM, et al. (2006) Balancing selection and the evolution of functional polymorphism in Old World monkey TRIM5alpha. Proc Natl Acad Sci USA 103: 19134-19139.
11. Wheat CW, Haag CR, Marden JH, Hanski I, Frilander MJ (2010) Nucleotide polymorphism at a gene (Pgi) under balancing selection in a butterfly metapopulation. Mol Biol Evol 27:267-281.
12. Groll M, et al. (1997) Structure of 20S proteasome from yeast at 2.4 A resolution. Nature 386:463-471.
13. Unno M, et al. (2002) The structure of the mammalian 20S proteasome at 2.75 A resolution. Structure 10:609-618.
14. Tanaka K, Kasahara M (1998) The MHC class I ligand-generating system: Roles of immunoproteasomes and the interferon-gamma-inducible proteasome activator PA28. Immunol Rev 163:161-176.
15. Akiyama K, et al. (1994) cDNA cloning and interferon gamma down-regulation of proteasomal subunits X and Y. Science 265:1231-1234.
16. Früh K, et al. (1994) Displacement of housekeeping proteasome subunits by MHCencoded LMPs: A newly discovered mechanism for modulating the multicatalytic proteinase complex. EMBO J 13:3236-3244.
17. Fehling HJ, et al. (1994) MHC class I expression in mice lacking the proteasome subunit LMP-7. Science 265:1234-1237.
18. Takehana Y, Naruse K, SakaizumiM(2005) Molecular phylogeny of the medaka fishes genus Oryzias (Beloniformes: Adrianichthyidae) based on nuclear and mitochondrial DNA sequences. Mol Phylogenet Evol 36:417-428.
19. Setiamarga DH, et al. (2009) Divergence time of the two regional medaka populations in Japan as a new time scale for comparative genomics of vertebrates. Biol Lett 5:812-816.
20. Matsuo MY, Asakawa S, Shimizu N, Kimura H, Nonaka M (2002) Nucleotide sequence of the MHC class I genomic region of a teleost, the medaka (Oryzias latipes). Immunogenetics 53:930-940.
21. Tsukamoto K, et al. (2005) Unprecedented intraspecific diversity of the MHC class I region of a teleost medaka, Oryzias latipes. Immunogenetics 57:420-431.
22. Kasahara M, et al. (2007) The medaka draft genome and insights into vertebrate genome evolution. Nature 447:714-719.
23. Nonaka MI, Nonaka M (2010) Evolutionary analysis of two classical MHC class I loci of the medaka fish, Oryzias latipes: Haplotype-specific genomic diversity, locus-specific polymorphisms, and interlocus homogenization. Immunogenetics 62:319-332.
24. Tsukamoto K, et al. (2009) Dichotomous haplotypic lineages of the immunoproteasome subunit genes, PSMB8 and PSMB10, in the MHC class I region of a teleost medaka, Oryzias latipes. Mol Biol Evol 26:769-781.
25. Iwamatsu T, Kobayashi H, Yamashita M, Shibata Y, Yusa A (2003) Experimental hybridization among Oryzias species. II. Karyogamy and abnormality of chromosome separation in the cleavage of interspecific hybrids between Oryzias latipes and O. javanicus. Zoolog Sci 20:1381-1387.
26. Iwamatsu T, Uwa H, Inden A, Hirata K (1984) Experiments on interspecific hybridization between Oryzias latipes and Oryzias celebensis. Zoolog Sci 1:653-663.
27. Hamaguchi S, Sakaizumi M (1992) Sexually differentiated mechanisms of sterility in interspecific hybrids between Oryzias latipes and O. curvinotus. J Exp Zool 263: 323-329.
28. Guntoro A (1999) The formation of the Makassar Strait and the separation between SE Kalimantan and SW Sulawesi. J Asian Earth Sci 17:79-98.
29. Namikawa C, et al. (1995) Isolation of Xenopus LMP-7 homologues. Striking allelic diversity and linkage to MHC. J Immunol 155:1964-1971.
30. Kandil E, et al. (1996) Isolation of low molecular mass polypeptide complementary DNA clones from primitive vertebrates. Implications for the origin of MHC class Irestricted antigen presentation. J Immunol 156:4245-4253.
31. Ohta Y, McKinney EC, Criscitiello MF, Flajnik MF (2002) Proteasome, transporter associated with antigen processing, and class I genes in the nurse shark Ginglymostoma cirratum: Evidence for a stable class I region and MHC haplotype lineages. J Immunol 168:771-781.
32. Mehta RB, Nonaka MI, Nonaka M (2009) Comparative genomic analysis of the major histocompatibility complex class I region in the teleost genus Oryzias. Immunogenetics 61:385-399.
33. Saitou N, Nei M (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425.
34. Novacek MJ (1992) Mammalian phylogeny: Shaking the tree. Nature 356:121-125.
35. Yamanoue Y, Miya M, Inoue JG, Matsuura K, Nishida M (2006) The mitochondrial genome of spotted green pufferfish Tetraodon nigroviridis (Teleostei: Tetraodontiformes) and divergence time estimation among model organisms in fishes. Genes Genet Syst 81: 29-39.
36. Nonaka M, Yamada-Namikawa C, Flajnik MF, Du Pasquier L (2000) Trans-species polymorphism of the major histocompatibility complex-encoded proteasome subunit LMP7 in an amphibian genus, Xenopus. Immunogenetics 51:186-192.
37. Larkin MA, et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948.
38. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16: 111-120.
39. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596-1599.
40. Schwartz S, et al. (2000) PipMaker-a web server for aligning two genomic DNA sequences. Genome Res 10:577-586.