SNP marker discovery in koala TLR genes

PLoS ONE

Volumn 10, Issue 3, 2015, Pages

  Cui, Jian ^a   Frankham, Greta J ^b   Johnson, Rebecca N ^b   Polkinghorne, Adam ^c   Timms, Peter ^c   O'Meally, Denis ^a   Cheng, Yuanyuan ^a   Belov, Katherine ^a  

^a UNIVERSITY OF SYDNEY   (Australia)

^b AUSTRALIAN MUSEUM   (Australia)

^c UNIVERSITY OF THE SUNSHINE COAST   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

TOLL LIKE RECEPTOR; TOLL LIKE RECEPTOR 10; TOLL LIKE RECEPTOR 13; TOLL LIKE RECEPTOR 2; TOLL LIKE RECEPTOR 3; TOLL LIKE RECEPTOR 4; TOLL LIKE RECEPTOR 5; TOLL LIKE RECEPTOR 6; TOLL LIKE RECEPTOR 7; TOLL LIKE RECEPTOR 8; TOLL LIKE RECEPTOR 9; TRANSCRIPTOME; UNCLASSIFIED DRUG;

ANIMAL TISSUE; ARTICLE; AUSTRALIA; CONTROLLED STUDY; GENETIC VARIABILITY; INNATE IMMUNITY; KOALA; MALE; NONHUMAN; SINGLE NUCLEOTIDE POLYMORPHISM; TLR10 GENE; TLR13 GENE; TLR2 GENE; TLR3 GENE; TLR4 GENE; TLR5 GENE; TLR6 GENE; TLR7 GENE; TLR8 GENE; TLR9 GENE; ANIMAL; CLASSIFICATION; GENETICS; PHYLOGENY;

METATHERIA; PHASCOLARCTIDAE;

ANIMALS; PHASCOLARCTIDAE; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; TOLL-LIKE RECEPTOR 10;

EID: 84925874506     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0121068     Document Type: Article

References (74)

1. Melzer A, Carrick F, Menkhorst P, Lunney D, John BS. Overview, critical assessment, and conservation implications of koala distribution and abundance. Conserv Biol. 2000; 14: 619-628.
2. Lee AK, Martin RW The koala: a natural history: New South Wales University Press Kensington. 1988
3. Houlden B, England P, Taylor A, Greville W, Sherwin W. Low genetic variability of the koala Phascolarctos cinereus in south-eastern Australia following a severe population bottleneck. Mol Ecol. 1996; 5: 269-281. PMID: 8673272
4. Lee KE, Seddon JM, Corley SW, Ellis WA, Johnston SD, de Villiers DL, et al. Genetic variation and structuring in the threatened koala populations of Southeast Queensland. Conserv Genet. 2010; 11: 2091-2103.
5. Houlden BA, Costello BH, Sharkey D, Fowler EV, Melzer A, Ellis W, et al. Phylogeographic differentiation in the mitochondrial control region in the koala, Phascolarctos cinereus (Goldfuss 1817). Mol Ecol. 1999; 8: 999-1011. PMID: 10434420
6. Fowler E, Houlden B, Hoeben P, Timms P. Genetic diversity and gene flow among southeastern Queensland koalas (Phascolarctos cinereus). Mol Ecol. 2000; 9: 155-164. PMID: 10672159
7. Jobbins SE, Sanderson CE, Griffith JE, Krockenberger MB, Belov K, Higgins DP. Diversity of MHC class II DAB1 in the koala (Phascolarctos cinereus). Aust J Zool. 2012; 60: 1-9.
8. Lau Q, Jobbins SE, Belov K, Higgins DP. Characterisation of four major histocompatibility complex class II genes of the koala (Phascolarctos cinereus). Immunogenetics. 2013; 65: 37-46. doi: 10.1007/ s00251-012-0658-5 PMID: 23089959
9. Tarlinton RE, Meers J, Young PR. Retroviral invasion of the koala genome. Nature. 2006; 442: 79-81. PMID: 16823453
10. Mehta SD, Moses S, Agot K, Parker C, Ndinya-Achola JO, Maclean I, et al. Adult male circumcision does not reduce the risk of incident Neisseria gonorrhoeae, Chlamydia trachomatis, or Trichomonas vaginalis infection: results from a randomized, controlled trial in Kenya. J Infect Dis. 2009; 200: 370-378. doi: 10.1086/600074 PMID: 19545209
11. Polkinghorne A, Hanger J, Timms P. Recent advances in understanding the biology, epidemiology and control of chlamydial infections in koalas. Vet Microbiol. 2013; 165: 214-223. doi: 10.1016/j.vetmic. 2013.02.026 PMID: 23523170
12. Wan C, Loader J, Hanger J, Beagley K, Timms P, Polkinghorne A. Using quantitative polymerase chain reaction to correlate Chlamydia pecorum infectious load with ocular, urinary and reproductive tract disease in the koala (Phascolarctos cinereus). Aust Vet J. 2011; 89: 409-412. doi: 10.1111/j.1751-0813. 2011.00827.x PMID: 21933169
13. Bachmann NL, Polkinghorne A, Timms P. Chlamydia genomics: providing novel insights into chlamydial biology. Trends Microbiol. 2014.
14. Darville T, Hiltke TJ. Pathogenesis of genital tract disease due to Chlamydia trachomatis. J Infect Dis. 2010; 201: S114-S125. PMID: 20524234
15. Denner J, Young PR. Koala retroviruses: characterization and impact on the life of koalas. Retrovirology. 2013; 10: 108.101-108.107.
16. Akira S, Takeda K, Kaisho T. Toll-like receptors: critical proteins linking innate and acquired immunity. Nat Immunol. 2001; 2: 675-680. PMID: 11477402
17. McGuire K, Jones M, Werling D, Williams J, Glass E, Jann O. Radiation hybrid mapping of all 10 characterized bovine Toll-like receptors. Anim Genet. 2006; 37: 47-50. PMID: 16441295
18. Werling D, Coffey TJ. Pattern recognition receptors in companion and farm animals-The key to unlocking the door to animal disease? Vet J. 2007; 174: 240-251. PMID: 17137812
19. Roach JC, Glusman G, Rowen L, Kaur A, Purcell MK, Smith KD, et al. The evolution of vertebrate Tolllike receptors. P Natl Acad Sci USA. 2005; 102: 9577-9582. PMID: 15976025
20. Cui J, Cheng Y, Belov K. Diversity in the Toll-like receptor genes of the Tasmanian devil (Sarcophilus harrisii). Immunogenetics. 2015: 1-7.
21. Alexopoulou L, Holt AC, Medzhitov R, Flavell RA. Recognition of double-stranded RNA and activation of NF-êB by Toll-like receptor 3. Nature. 2001; 413: 732-738. PMID: 11607032
22. Heil F, Hemmi H, Hochrein H, Ampenberger F, Kirschning C, Akira S, et al. Species-specific recognition of single-stranded RNA via toll-like receptor 7 and 8. Science. 2004; 303: 1526-1529. PMID: 14976262
23. McCartney SA, Colonna M. Viral sensors: diversity in pathogen recognition. Immunol Rev. 2009; 227: 87-94. doi: 10.1111/j.1600-065X.2008.00726.x PMID: 19120478
24. Campos MA, Almeida IC, Takeuchi O, Akira S, Valente EP, Procópio DO, et al. Activation of Toll-like re-ceptor-2 by glycosylphosphatidylinositol anchors from a protozoan parasite. J Immunol. 2001; 167: 416-423. PMID: 11418678
25. Bell JK, Mullen GE, Leifer CA, Mazzoni A, Davies DR, Segal DM. Leucine-rich repeats and pathogen recognition in Toll-like receptors. Trends Immunol. 2003; 24: 528-533. PMID: 14552836
26. Poltorak A, He X, Smirnova I, Liu M-Y, Van Huffel C, Du X, et al. Defective LPS signaling in C3H/HeJ and C57BL/10ScCr mice: mutations in Tlr4 gene. Science. 1998; 282: 2085-2088. PMID: 9851930
27. Oldenburg M, Krüger A, Ferstl R, Kaufmann A, Nees G, Sigmund A, et al. TLR13 Recognizes Bacterial 23S rRNA Devoid of Erythromycin Resistance-Forming Modification. Science. 2012; 337: 1111-1115. doi: 10.1126/science.1220363 PMID: 22821982
28. Yang X, Joyee A. Role of toll-like receptors in immune responses to chlamydial infections. Curr Pharm Design. 2008; 14: 593-600. PMID: 18336303
29. Taylor BD, Darville T, Ferrell RE, Kammerer CM, Ness RB, Haggerty CL. Variants in toll-like receptor 1 and 4 genes are associated with Chlamydia trachomatis among women with pelvic inflammatory disease. J Infect Dis. 2012; 205: 603-609. doi: 10.1093/infdis/jir822 PMID: 22238472
30. Houlden BA, Greville WD, Sherwin WB. Evolution of MHC class I loci in marsupials: characterization of sequences from koala (Phascolarctos cinereus). Mol Biol Evol. 1996; 13: 1119-1127. PMID: 8865665
31. Morris K, Prentis PJ, O'Meally D, Pavasovic A, Brown AT, Timms P, et al. The koala immunological toolkit: sequence identification and comparison of key markers of the koala (Phascolarctos cinereus) immune response. Aust J Zool. 2014.
32. Mathew M, Beagley KW, Timms P, Polkinghorne A. Preliminary characterisation of tumor necrosis factor alpha and interleukin-10 responses to Chlamydia pecorum infection in the koala (Phascolarctos cinereus). Plos one. 2013; 8: e59958. doi: 10.1371/journal.pone.0059958 PMID: 23527290
33. Mathew M, Waugh C, Beagley KW, Timms P, Polkinghorne A. Interleukin 17A is an immune marker for chlamydial disease severity and pathogenesis in the koala (Phascolarctos cinereus). Dev Comp Immunol. 2014; 46: 423-429. doi: 10.1016/j.dci.2014.05.015 PMID: 24915607
34. Maher IE, Griffith JE, Lau Q, Reeves T, Higgins DP. Expression profiles of the immune genes CD4, CD8β, IFNã, IL-4, IL-6 and IL-10 in mitogen-stimulated koala lymphocytes (Phascolarctos cinereus) by qRT-PCR. PeerJ. 2014; 2: e280. doi: 10.7717/peerj.280 PMID: 24688858
35. Mathew M, Pavasovic A, Prentis PJ, Beagley KW, Timms P, Polkinghorne A. Molecular characterisation and expression analysis of Interferon gamma in response to natural Chlamydia infection in the koala, Phascolarctos cinereus. Gene. 2013; 527: 570-577. doi: 10.1016/j.gene.2013.06.019 PMID: 23792018
36. Johnson RN, Hobbs M, Eldridge MDB, King AG, Colgan DJ, Wilkins MR, et al. The Koala Genome Consortium. Tech. Rep. Aust. Mus., Online. 2014: No. 24, pp.91-92.
37. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011; 28: 2731-2739. doi: 10.1093/molbev/msr121 PMID: 21546353
38. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987; 4: 406-425. PMID: 3447015
39. Frankham GJ, Handasyde KA, Norton M, Murray A, Eldridge MD. Molecular detection of intra-population structure in a threatened potoroid, Potorous tridactylus: conservation management and sampling implications. Conserv Genet. 2014; 15: 547-560.
40. Zhang X-y, Gao Y-n. To design PCR primers with Oligo 6 and Primer Premier 5 [J]. Bioinformatiocs. 2004; 4: 003.
41. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT; 1999. pp. 95-98.
42. Medzhitov R, Janeway C Jr. The Toll receptor family and microbial recognition. Trends Microbiol. 2000; 8: 452-456. PMID: 11044679
43. Kopp EB, Medzhitov R. The Toll-receptor family and control of innate immunity. Curr Opin Immunol. 1999; 11: 13-18. PMID: 10047546
44. Purcell MK, Smith KD, Aderem A, Hood L, Winton JR, Roach JC. Conservation of Toll-like receptor signaling pathways in teleost fish. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics. 2006; 1: 77-88. PMID: 17330145
45. Meijer AH, Gabby Krens S, Medina Rodriguez IA, He S, Bitter W, Ewa Snaar-Jagalska B, et al. Expression analysis of the Toll-like receptor and TIR domain adaptor families of zebrafish. Mol Immunol. 2004; 40: 773-783. PMID: 14687934
46. Ishii A, Kawasaki M, Matsumoto M, Tochinai S, Seya T. Phylogenetic and expression analysis of amphibian Xenopus Toll-like receptors. Immunogenetics. 2007; 59: 281-293. PMID: 17265063
47. Temperley ND, Berlin S, Paton IR, Griffin DK, Burt DW. Evolution of the chicken Toll-like receptor gene family: a story of gene gain and gene loss. BMC genomics. 2008; 9: 62. doi: 10.1186/1471-2164-9-62 PMID: 18241342
48. Iqbal M, Philbin VJ, Smith AL. Expression patterns of chicken Toll-like receptor mRNA in tissues, immune cell subsets and cell lines. Vet Immunol Immunop. 2005; 104: 117-127. PMID: 15661337
49. Akira S. Mammalian Toll-like receptors. Curr Opin Immunol. 2003; 15: 5-11. PMID: 12495726
50. Kaisho T, Akira S. Toll-like receptor function and signaling. J Allergy Clin Immun. 2006; 117: 979-987. PMID: 16675322
51. Akira S, Takeda K. Toll-like receptor signalling. Nat Rev Immunol. 2004; 4: 499-511. PMID: 15229469
52. Matsushima N, Tanaka T, Enkhbayar P, Mikami T, Taga M, Yamada K, et al. Comparative sequence analysis of leucine-rich repeats (LRRs) within vertebrate toll-like receptors. BMC genomics. 2007; 8:124. PMID: 17517123
53. Bell JK, Askins J, Hall PR, Davies DR, Segal DM. The dsRNA binding site of human Toll-like receptor 3. P Natl A Sci. 2006; 103: 8792-8797. PMID: 16720699
54. Bell JK, Botos I, Hall PR, Askins J, Shiloach J, Segal DM, et al. The molecular structure of the Toll-like receptor 3 ligand-binding domain. P Natl Acad Sci USA. 2005; 102: 10976-10980. PMID: 16043704
55. Hajjar AM, Ernst RK, Tsai JH, Wilson CB, Miller SI. Human Toll-like receptor 4 recognizes host-specific LPS modifications. Nat Immunol. 2002; 3: 354-359. PMID: 11912497
56. Mizel SB, West AP, Hantgan RR. Identification of a sequence in human toll-like receptor 5 required for the binding of Gram-negative flagellin. J Biol Chem. 2003; 278: 23624-23629. PMID: 12711596
57. Huang Y, Temperley ND, Ren L, Smith J, Li N, Burt DW. Molecular evolution of the vertebrate TLR1 gene family-a complex history of gene duplication, gene conversion, positive selection and co-evolution. BMC Evol Biol. 2011; 11: 149. doi: 10.1186/1471-2148-11-149 PMID: 21619680
58. Jin MS, Kim SE, Heo JY, Lee ME, Kim HM, Paik S-G, et al. Crystal structure of the TLR1-TLR2 heterodimer induced by binding of a tri-acylated lipopeptide. Cell. 2007; 130: 1071-1082. PMID: 17889651
59. Kang JY, Nan X, Jin MS, Youn S-J, Ryu YH, Mah S, et al. Recognition of lipopeptide patterns by Tolllike receptor 2-Toll-like receptor 6 heterodimer. Immunity. 2009; 31: 873-884. doi: 10.1016/j.immuni. 2009.09.018 PMID: 19931471
60. Guan Y, Ranoa DRE, Jiang S, Mutha SK, Li X, Baudry J, et al. Human TLRs 10 and 1 share common mechanisms of innate immune sensing but not signaling. J Immunol. 2010; 184: 5094-5103. doi: 10. 4049/jimmunol.0901888 PMID: 20348427
61. Higuchi M, Matsuo A, Shingai M, Shida K, Ishii A, Funami K, et al. Combinational recognition of bacterial lipoproteins and peptidoglycan by chicken Toll-like receptor 2 subfamily. Dev Comp Immunol. 2008; 32: 147-155. PMID: 17614130
62. Smirnova I, Poltorak A, Chan E, McBride C, Beutler B. Phylogenetic variation and polymorphism at the toll-like receptor 4 locus (TLR4). Genome Biol. 2000; 1: 1-002.010. PMID: 11178226
63. Miller SI, Ernst RK, Bader MW. LPS, TLR4 and infectious disease diversity. Nat Rev Microbiol. 2005; 3: 36-46. PMID: 15608698
64. Seabury CM, Seabury PM, Decker JE, Schnabel RD, Taylor JF, Womack JE. Diversity and evolution of 11 innate immune genes in Bos taurus taurus and Bos taurus indicus cattle. P Natl A Sci. 2010; 107: 151-156.
65. Grueber CE, Wallis GP, King TM, Jamieson IG. Variation at innate immunity Toll-like receptor genes in a bottlenecked population of a New Zealand robin. Plos one. 2012; 7: e45011. PMID: 23024782
66. Barreiro LB, Ben-Ali M, Quach H, Laval G, Patin E, Pickrell JK, et al. Evolutionary dynamics of human Toll-like receptors and their different contributions to host defense. Plos Genet. 2009; 5: e1000562. doi: 10.1371/journal.pgen.1000562 PMID: 19609346
67. Palermo S, Capra E, Torremorell M, Dolzan M, Davoli R, Haley C, et al. Toll-like receptor 4 genetic diversity among pig populations. Anim Genet. 2009; 40: 289-299. doi: 10.1111/j.1365-2052.2008. 01833.x PMID: 19290993
68. Yang Z. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol Biol Evol. 1998; 15: 568-573. PMID: 9580986
69. Zhang DX, Hewitt GM. Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects. Mol Ecol. 2003; 12: 563-584. PMID: 12675814
70. Woehrle T, Du W, Goetz A, Hsu H-Y, Joos TO, Weiss M, et al. Pathogen specific cytokine release reveals an effect of TLR2 Arg753Gln during Candida sepsis in humans. Cytokine. 2008; 41: 322-329. doi: 10.1016/j.cyto.2007.12.006 PMID: 18249133
71. Hawn TR, Verbon A, Janer M, Zhao LP, Beutler B, Aderem A. Toll-like receptor 4 polymorphisms are associated with resistance to Legionnaires' disease. P Natl Acad Sci USA. 2005; 102: 2487-2489. PMID: 15699327
72. Simmons G, Young P, Hanger J, Jones K, Clarke D, McKee J, et al. Prevalence of koala retrovirus in geographically diverse populations in Australia. Aust Vet J. 2012; 90: 404-409. doi: 10.1111/j.1751-0813.2012.00964.x PMID: 23004234
73. Hobbs M, Pavasovic A, King AG, Prentis PJ, Eldridge MD, Chen Z, et al. A transcriptome resource for the koala (Phascolarctos cinereus): insights into koala retrovirus transcription and sequence diversity. BMC Genomics. 2014; 15: 786. doi: 10.1186/1471-2164-15-786 PMID: 25214207
74. Kollipara A, George C, Hanger J, Loader J, Polkinghorne A, Beagley K, et al. Vaccination of healthy and diseased koalas (Phascolarctos cinereus) with a Chlamydia pecorum multi-subunit vaccine: Evaluation of immunity and pathology. Vaccine. 2012; 30: 1875-1885. doi: 10.1016/j.vaccine.2011.12.125 PMID: 22230583