Dimorphisms of the proteasome subunit beta type 8 gene (PSMB8) of ectothermic tetrapods originated in multiple independent evolutionary events

Immunogenetics

Volumn 65, Issue 11, 2013, Pages 811-821

  Huang, Ching Huei ^a   Tanaka, Yuta ^a   Fujito, Naoko T ^a   Nonaka, Masaru ^a  

^a UNIVERSITY OF TOKYO   (Japan)

Author keywords

Balancing selection; Dimorphism; Immunoproteasome; PSMB8; Tetrapods

Indexed keywords

COMPLEMENTARY DNA; GENOMIC DNA; IMMUNOPROTEASOME; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 1; PROTEASOME; RNA; UNCLASSIFIED DRUG;

ALLELE; AMPHIBIA; ARTICLE; DNA SEQUENCE; ENZYME SUBUNIT; EVOLUTION; FISH; GENE; GENE FREQUENCY; HUMAN; MAJOR HISTOCOMPATIBILITY COMPLEX; MAXIMUM LIKELIHOOD METHOD; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PHYLOGENY; PRIORITY JOURNAL; PROTEASOME SUBUNIT BETA TYPE 8 GENE; REPTILE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; TETRAPOD; VERTEBRATE; XENOPUS;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; BIOLOGICAL EVOLUTION; GENE FREQUENCY; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMORPHISM, GENETIC; PROTEASOME ENDOPEPTIDASE COMPLEX; SEQUENCE HOMOLOGY, AMINO ACID; SEQUENCE HOMOLOGY, NUCLEIC ACID; TEMPERATURE; VERTEBRATES;

ACTINOPTERYGII; AMPHIBIA; ANIMALIA; GEKKONIDAE; REPTILIA; SALAMANDRIDAE; TETRAPODA; VERTEBRATA;

EID: 84886782594     PISSN: 00937711     EISSN: 14321211     Source Type: Journal    
DOI: 10.1007/s00251-013-0729-2     Document Type: Article

References (27)

1. Agarwal AK, Xing C, DeMartino GN, Mizrachi D, Hernandez MD, Sousa AB, Martinez de Villarreal L, dos Santos HG, Garg A (2010) PSMB8 encoding the β5i proteasome subunit is mutated in joint contractures, muscle atrophy, microcytic anemia, and panniculitis-induced lipodystrophy syndrome. Am J Hum Genet 87:866-872
2. Akiyama K, Yokota K, Kagawa S, Shimbara N, Tamura T, Akioka H, Nothwang HG, Noda C, Tanaka K, Ichihara A (1994) cDNA cloning and interferon gamma down-regulation of proteasomal subunits X and Y. Science 265:1231-1234
3. Arima K, Kinoshita A, Mishima H et al (2011) Proteasome assembly defect due to a proteasome subunit beta type 8 (PSMB8) mutation causes the autoinflammatory disorder, Nakajo-Nishimura syndrome. Proc Natl Acad Sci U S A 108:14914-14919
4. Dalloul RA, Long JA, Zimin AV et al (2010) Multiplatform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol 8:e1000475
5. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792-1797
6. Fehling HJ, Swat W, Laplace C, Kühn R, Rajewsky K, Müller U, von Boehmer H (1994) MHC class I expression in mice lacking the proteasome subunit LMP-7. Science 265:1234-1237
7. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791
8. Früh K, Gossen M, Wang K, Bujard H, Peterson PA, Yang Y (1994) Displacement of housekeeping proteasome subunits by MHC encoded LMPs: a newly discovered mechanism for modulating the multicatalytic proteinase complex. EMBO J 13:3236-3244
9. Fujito NT, Nonaka M (2012) Highly divergent dimorphic alleles of the proteasome subunit beta type-8 (PSMB8) gene of the bichir Polypterus senegalus: implication for evolution of the PSMB8 gene of jawed vertebrates. Immunogenetics 64:447-453
10. Groll M, Ditzel L, Lowe J, Stock D, Bochtler M, Bartunik HD, Huber R (1997) Structure of 20S proteasome from yeast at 2.4 A resolution. Nature 386:463-471
11. Hillier LW, Miller W, Birney E et al (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432:695-716
12. Kasahara M (1997) New insights into the genomic organization and origin of the major histocompatibility complex: role of chromosomal (genome) duplication in the emergence of the adaptive immune system. Hereditas 127:59-65
13. 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
14. Kitamura A, Maekawa Y, Uehara H et al (2011) A mutation in the immunoproteasome subunit PSMB8 causes autoinflammation and lipodystrophy in humans. J Clin Invest 121:4150-4160
15. Miura F, Tsukamoto K, Mehta RB, Naruse K, Magtoon W, Nonaka M (2010) Transspecies dimorphic allelic lineages of the proteasome subunit beta-type 8 gene (PSMB8) in the teleost genus Oryzias. Proc Natl Acad Sci U S A 107:21599-21604
16. Nei M, Kumar S (2000) Molecular evolution and phylogenetics. Oxford University Press, Oxford
17. 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
18. 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
19. Ohta Y, Powis SJ, Lohr RL, Nonaka M, Du Pasquier L, Flajnik MF (2003) Two highly divergent ancient allelic lineages of the transporter associated with antigen processing (TAP) gene in Xenopus: further evidence for co-evolution among MHC class I region genes. Eur J Immunol 33:3017-3027
20. Saitou N, Nei M (1987) The neighbor-joining method - a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
21. Shen XX, Liang D, Wen JZ, Zhang P (2011) Multiple genome alignments facilitate development of NPCL markers: a case study of tetrapod phylogeny focusing on the position of turtles. Mol Biol Evol 28:3237-3252
22. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731-2739
23. 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
24. Tsukamoto K, Hayashi S, Matsuo MY, Nonaka MI, Kondo M, Shima A, Asakawa S, Shimizu N, Nonaka M (2005) Unprecedented intraspecific diversity of the MHC class I region of a teleost medaka, Oryzias latipes. Immunogenetics 57:420-431
25. Tsukamoto K, Miura F, Fujito NT, Yoshizaki G, Nonaka M (2012) Long-lived dichotomous lineages of the proteasome subunit beta type 8 (PSMB8) gene surviving more than 500 million years as alleles or paralogs. Mol Biol Evol 29:3071-3079
26. Unno M, Mizushima T, Morimoto Y, Tomisugi Y, Tanaka K, Yasuoka N, Tsukihara T (2002) The structure of the mammalian 20S proteasome at 2.75 A resolution. Structure 10:609-618
27. Warren WC, Clayton DF, Ellegren H et al (2010) The genome of a songbird. Nature 464:757-762