Characterisation of four major histocompatibility complex class II genes of the koala (Phascolarctos cinereus)

Immunogenetics

Volumn 65, Issue 1, 2013, Pages 37-46

  Lau, Quintin ^a   Jobbins, Sarah E ^a   Belov, Katherine ^a   Higgins, Damien P ^a  

^a UNIVERSITY OF SYDNEY   (Australia)

Author keywords

Diversity; Koala; Marsupial; MHC class II; Phascolarctos cinereus

Indexed keywords

ARGININE; CD4 ANTIGEN; HISTIDINE; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 2;

ALPHA CHAIN; AMINO ACID SUBSTITUTION; ANTIGEN BINDING; ANTIGEN PRESENTATION; ARTICLE; BETA CHAIN; CONTROLLED STUDY; DISEASE PREDISPOSITION; DNA POLYMORPHISM; EXON; GENE FREQUENCY; GENE IDENTIFICATION; GENE LOCUS; GENE SEQUENCE; GENE STRUCTURE; GENETIC VARIABILITY; GENOTYPE; GLYCOSYLATION; HETEROZYGOTE; HOMOZYGOTE; KOALA; MAJOR HISTOCOMPATIBILITY COMPLEX; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN MOTIF;

AMINO ACID SEQUENCE; ANIMALS; CHLAMYDOPHILA INFECTIONS; DNA PRIMERS; GENE AMPLIFICATION; GENES, MHC CLASS II; GENETIC VARIATION; GENOTYPE; HISTOCOMPATIBILITY ANTIGENS CLASS II; MOLECULAR SEQUENCE DATA; PHASCOLARCTIDAE; PHYLOGENY; SEQUENCE ALIGNMENT; T-LYMPHOCYTES, HELPER-INDUCER;

METATHERIA; PHASCOLARCTIDAE; PHASCOLARCTOS CINEREUS;

EID: 84872324629     PISSN: 00937711     EISSN: 14321211     Source Type: Journal    
DOI: 10.1007/s00251-012-0658-5     Document Type: Article

References (49)

1. Balakrishnan K, Adams LE (1995) The role of the lymphocyte in an immune response. Immunol Investig 24(1-2):233-244. doi: 10.3109/08820139509062775
2. Belov K, Lam MK-P, Colgan DJ (2004) Marsupial MHC class II β genes are not orthologous to the eutherian β gene families. J Hered 95(4):338-345. doi: 10.1093/jhered/esh049
3. Belov K, Deakin JE, Papenfuss AT, Baker ML, Melman SD, Siddle HV, Gouin N, Goode DL, Sargeant TJ, Robinson MD, Wakefield MJ, Mahony S, Cross JG, Benos PV, Samollow PB, Speed TP, Graves JA, Miller RD (2006) Reconstructing an ancestral mammalian immune supercomplex from a marsupial major histocompatibility complex. PLoS Biol 4(3):e46. doi: 10.1371/journal.pbio. 0040046
4. Brown JH, Jardetzky TS, Gorga JC, Stern LJ, Urban RG, Strominger JL, Wiley DC (1993) Three-dimensional structure of the human class II histocompatibility antigen HLA-DR1. Nature 364(6432):33-39. doi: 10.1038/364033a0
5. Browning TL (2009) Inbreeding, the MHC and infectious disease susceptibility in the tammar wallaby, Macropus eugenii. Macquarie University, Sydney
6. Browning TL, Belov K, Miller RD, Eldridge MDB (2004) Molecular cloning and characterization of the polymorphic MHC class II DBB from the tammar wallaby (Macropus eugenii). Immunogenetics 55:791-795. doi: 10.1007/s00251-004-0644-7
7. Canfield PJ, Hemsley S, Connolly J (1996) Histological and immunohistological study of the developing and involuting superficial cervical thymus in the koala (Phascolarctos cinereus). J Anat 189:159-169
8. Cheng Y, Siddle HV, Beck S, Eldridge MD, Belov K (2009) High levels of genetic variation at MHC class II DBB loci in the tammar wallaby (Macropus eugenii). Immunogenetics 61(2):111-118. doi: 10.1007/s00251-008-0347-6
9. Dique DS, Thompson J, Preece HJ, Penfold GC, De Villiers DL, Leslie RS (2003) Koala mortality on roads in south-east Queensland: the koala speed-zone trial. Wildl Res 30(4):419-426. doi: 10.1071/WR02029
10. Griffith JE, Dhand NK, Krockenberger MB, Higgins DP (2013) A retrospective study of admission trends of koalas to a rehabilitation facility over thirty years. J Wildl Dis 49(1):doi: 10.7589/2012-05-135
11. Higgins DP, Hemsley S, Canfield PJ (2005) Association of uterine and salpingeal fibrosis with chlamydial hsp60 and hsp10 antigen-specific antibodies in Chlamydia-infected koalas. Clin Diagn Lab Immunol 12(5):632-639. doi: 10.1128/CDLI.12.5.632-639.2005
12. Holland OJ, Cowan PE, Gleeson DM, Chamley LW (2008) Novel alleles in classical major histocompatibility complex class II loci of the brushtail possum (Trichosurus vulpecula). Immunogenetics 60(8):449-460. doi: 10.1007/s00251-008-0300-8
13. Houlden BA, England PR, Taylor AC, Greville WD, Sherwin WB (1996) Low genetic variability of the koala Phascolarctos cinereus in south-eastern Australia following a severe population bottleneck. Mol Ecol 5(2):269-281
14. Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17(8):754-755
15. Hughes AL, Friedman R (2008) Codon-based tests of positive selection, branch lengths, and the evolution of mammalian immune system genes. Immunogenetics 60(9):495-506. doi: 10.1007/s00251-008-0304-4
16. Jackson M, White N, Giffard P, Timms P (1999) Epizootiology of Chlamydia infections in two free-range koala populations. Vet Microbiol 65(4):255-264. doi: S0378113598003022
17. Jobbins SE, Sanderson CE, Griffith JE, Krockenberger MB, Belov K, Higgins DP (2012) Diversity of MHC class II DAB1 in the koala (Phascolarctos cinereus). Aust J Zool 60(1):1-9. doi: 10.1071/ZO12013
18. Kalish RS (1995) Antigen processing: the gateway to the immune response. J Am Acad Dermatol 32(4):640-652
19. Keane T, Creevey C, Pentony M, Naughton T, Mclnerney J (2006) Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol Biol 6(1):29. doi: 10.1186/1471-2148-6-29
20. Kennedy LJ, Ryvar R, Gaskell RM, Addie DD, Willoughby K, Carter SD, Thomson W, Ollier WE, Radford AD (2002) Sequence analysis of MHC DRB alleles in domestic cats from the United Kingdom. Immunogenetics 54(5):348-352. doi: 10.1007/s00251-002-0465-5
21. Klein J, Bontrop RE, Dawkins RL, Erlich HA, Gyllensten UB, Heise ER, Jones PP, Parham P, Wakeland EK, Watkins DI (1990) Nomenclature for the major histocompatibility complexes of different species: a proposal. Immunogenetics 31(4):217-219
22. Lam MK, Belov K, Harrison GA, Cooper DW (2001) Cloning of the MHC class II DRB cDNA from the brushtail possum (Trichosurus vulpecula). Immunol Lett 76(1):31-36. doi: S0165-2478(00)00314-X
23. Lau Q, Canfield PJ, Higgins DP (2012) Expression and in vitro upregulation of MHCII in koala lymphocytes. Vet Immunol Immunopathol 147(1-2):35-43. doi: 10.1016/j.vetimm.2012.04.010
24. Lee A, Martin R (1988) The koala a natural history. New South Wales University Press, Kensington
25. Lillie M, Woodward RE, Sanderson CE, Eldridge MDB, Belov K (2012) Diversity at the major histocompatibility complex class II in the platypus, Ornithorhynchus anatinus. J Hered 103(4):467-478. doi: 10.1093/jhered/ess012
26. Lunney D, Gresser S, O'Neill L, Matthews A, Rhodes JR (2007) The impact of fire and dogs on koalas at Port Stephens, New South Wales, using population viability analysis. Pac Conserv Biol 13(3):189-201
27. Marsh J, Kollipara A, Timms P, Polkinghorne A (2011) Novel molecular markers of Chlamydia pecorum genetic diversity in the koala (Phascolarctos cinereus). BMC Microbiol 11(1):77. doi: 10.1186/1471-2180-11-77
28. Mazerolles F, Durandy A, Piatier-Tonneau D, Charron D, Montagnier L, Auffray C, Fischer A (1988) Immunosuppressive properties of synthetic peptides derived from CD4 and HLA-DR antigens. Cell 55(3):497-504
29. Melzer A, Carrick F, Menkhorst P, Lunney D, John BS (2000) Overview, critical assessment, and conservation implications of koala distribution and abundance. Conserv Biol 14(3):619-628. doi: 10.1046/j.1523-1739.2000.99383.x
30. Meyer-Lucht Y, Otten C, Puttker T, Sommer S (2008) Selection, diversity and evolutionary patterns of the MHC class II DAB in free-ranging Neotropical marsupials. BMC Genet 9:39. doi: 10.1186/1471-2156-9-39
31. Meyer-Lucht Y, Otten C, Püttker T, Pardini R, Metzger J, Sommer S (2010) Variety matters: adaptive genetic diversity and parasite load in two mouse opossums from the Brazilian Atlantic forest. Conserv Genet 11(5):2001-2013. doi: 10.1007/s10592-010-0093-9
32. Miller HC, Andrews-Cookson M, Daugherty CH (2007) Two patterns of variation among MHC class I loci in Tuatara (Sphenodon punctatus). J Hered 98(7):666-677. doi: 10.1093/jhered/esm095
33. Mitchell P (1990) Social behaviour and communication of koalas. In: Lee AK, Handasyde KA, Sanson GD (eds) Biology of the koala. Surrey Beatty, Chipping Norton, (Australia), pp 151-170
34. Morrison RP, Feilzer K, Tumas DB (1995) Gene knockout mice establish a primary protective role for major histocompatibility complex class II-restricted responses in Chlamydia trachomatis genital tract infection. Infect Immun 63(12):4661-4668
35. O'Brien SJ, Evermann JF (1988) Interactive influence of infectious disease and genetic diversity in natural populations. Trends Ecol Evol 3(10):254-259
36. O'HUigin C, Sultmann H, Tichy H, Murray BW (1998) Isolation of MHC class II DMA and DMB cDNA sequences in a marsupial: the gray short-tailed opossum (Monodelphis domestica). J Mol Evol 47(5):578-585
37. Obendorf DL, Handasyde KA (1990) Pathology of chlamydial infection in the reproductive tract of the female koala. In: Lee AJ, Handasyde KA, Sanson GD (eds) Biology of the koala. Surrey and Beatty and Sons, Sydney, pp 255-259
38. Ohta T (1998) On the pattern of polymorphisms at major histocompatibility complex loci. J Mol Evol 46(6):633-638
39. Orita M, Iwahana H, Kanazawa H, Hayashi K, Sekiya T (1989) Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms. Proc Natl Acad Sci U S A 86(8):2766-2770
40. Rambaut A (2009) FigTree 1.3.1 edn
41. Schneider S, Vincek V, Tichy H, Figueroa F, Klein J (1991) MHC class II genes of a marsupial, the red-necked wallaby (Macropus rufogriseus): identification of new gene families. Mol Biol Evol 8(6):753-766
42. Siddle HV, Sanderson C, Belov K (2007) Characterization of major histocompatibility complex class I and class II genes from the Tasmanian devil (Sarcophilus harrisii). Immunogenetics 59:753-760. doi: 10.1007/s00251-007-0238- 2
43. Siddle HV, Deakin JE, Coggill P, Whilming L, Harrow J, Kaufman J, Beck S, Belov K (2011) The tammar wallaby major histocompatibility complex shows evidence of past genomic instability. BMC Genomics 12:421. doi: 10.1186/1471-2164-12-421
44. Slade RW, Mayer WE (1995) The expressed class II alpha-chain genes of the marsupial major histocompatibility complex belong to eutherian mammal gene families. Mol Biol Evol 12(3):441-450
45. Sommer S (2005) The importance of immune gene variability (MHC) in evolutionary ecology and conservation. Front Zool 2(16):doi: 10.1186/1742-9994-2-16
46. Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22(21):2688-2690. doi: 10.1093/bioinformatics/btl446
47. Stephens RS (2003) The cellular paradigm of chlamydial pathogenesis. Trends Microbiol 11(1):44-51. doi: 10.1016/S0966-842X(02)00011-2
48. 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(10):2731-2739. doi: 10.1093/molbev/msr121
49. Zhang J, Nielsen R, Yang Z (2005) Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol 22(12):2472-2479. doi: 10.1093/molbev/msi237