Molecular evolution of the vertebrate TLR1 gene family - A complex history of gene duplication, gene conversion, positive selection and co-evolution

BMC Evolutionary Biology

Volumn 11, Issue 1, 2011, Pages

  Huang, Yinhua ^a   Temperley, Nicholas D ^b   Ren, Liming ^c   Smith, Jacqueline ^a   Li, Ning ^c   Burt, David W ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b UNIVERSITY OF EDINBURGH   (United Kingdom)

^c CHINA AGRICULTURAL UNIVERSITY   (China)

Author keywords

Co evolution; Gene Conversion; Gene Duplication; Positive Selection; TLR1 gene family

Indexed keywords

AMINO ACID; COEVOLUTION; EVOLUTIONARY BIOLOGY; GENE EXPRESSION; GENETIC ANALYSIS; HOST-PATHOGEN INTERACTION; MOLECULAR ANALYSIS; NATURAL SELECTION; PHYLOGENETICS; PROTEIN; VERTEBRATE;

AMPHIBIA; AVES; MAMMALIA; MELEAGRIS GALLOPAVO; VERTEBRATA;

TOLL LIKE RECEPTOR 1; TOLL LIKE RECEPTOR 10; TOLL LIKE RECEPTOR 2; TOLL LIKE RECEPTOR 6;

ANIMAL; ARTICLE; BIRD; DUCK; GENE CONVERSION; GENE DUPLICATION; GENETICS; HUMAN; MAMMAL; MOLECULAR EVOLUTION; PHYLOGENY; TURKEY (REPUBLIC);

ANIMALS; BIRDS; DUCKS; EVOLUTION, MOLECULAR; GENE CONVERSION; GENE DUPLICATION; HUMANS; MAMMALS; PHYLOGENY; TOLL-LIKE RECEPTOR 1; TOLL-LIKE RECEPTOR 10; TOLL-LIKE RECEPTOR 2; TOLL-LIKE RECEPTOR 6; TURKEY;

EID: 79957444584     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-11-149     Document Type: Article

References (58)

1. The evolution of vertebrate Toll-like receptors. JC Roach G Glusman L Rowen A Kaur MK Purcell KD Smith LE Hood A Aderem, Proc Natl Acad Sci USA 2005 102 27 9577 9582 10.1073/pnas.0502272102 15976025 (Pubitemid 40981723)
2. Evolution of the chicken Toll-like receptor gene family: a story of gene gain and gene loss. ND Temperley S Berlin IR Paton DK Griffin DW Burt, BMC Genomics 2008 9 62 10.1186/1471-2164-9-62 18241342
3. Comparative sequence analysis of leucine-rich repeats (LRRs) within vertebrate toll-like receptors. N Matsushima T Tanaka P Enkhbayar T Mikami M Taga K Yamada Y Kuroki, BMC Genomics 2007 8 124 10.1186/1471-2164-8-124 17517123
4. The origin of new genes: glimpses from the young and old. M Long E Betran K Thornton W Wang, Nat Rev Genet 2003 4 11 865 875 14634634 (Pubitemid 37345613)
5. Evolution after gene duplication: models, mechanisms, sequences, systems, and organisms. C Roth S Rastogi L Arvestad K Dittmar S Light D Ekman DA Liberles, J Exp Zool B Mol Dev Evol 2007 308 1 58 73 16838295 (Pubitemid 46302791)
6. Invasion and maintenance of a gene duplication. AG Clark, Proc Natl Acad Sci USA 1994 91 8 2950 2954 10.1073/pnas.91.8.2950 8159686 (Pubitemid 24130152)
7. The probability of duplicate gene preservation by subfunctionalization. M Lynch A Force, Genetics 2000 154 1 459 473 10629003 (Pubitemid 30045935)
8. Population-genetic models of the fates of duplicate genes. B Walsh, Genetica 2003 118 2-3 279 294 12868616 (Pubitemid 36821056)
9. The evolutionary history of the CD209 (DC-SIGN) family in humans and non-human primates. M Ortiz H Kaessmann K Zhang A Bashirova M Carrington L Quintana-Murci A Telenti, Genes Immun 2008 9 6 483 492 10.1038/gene.2008.40 18528403
10. Patterns of positive selection in six Mammalian genomes. C Kosiol T Vinar RR da Fonseca MJ Hubisz CD Bustamante R Nielsen A Siepel, PLoS Genet 2008 4 8 1000144 10.1371/journal.pgen.1000144 18670650
11. Natural selection in the TLR-related genes in the course of primate evolution. T Nakajima H Ohtani Y Satta Y Uno H Akari T Ishida A Kimura, Immunogenetics 2008 60 12 727 735 10.1007/s00251-008-0332-0 18810425
12. Evolutionary dynamics of human Toll-like receptors and their different contributions to host defense. LB Barreiro M Ben-Ali H Quach G Laval E Patin JK Pickrell C Bouchier M Tichit O Neyrolles B Gicquel JR Kidd KK Kidd A Alcais J Ragimbeau S Pellegrini L Abel JL Casanova L Quintana-Murci, PLoS Genet 2009 5 7 1000562 10.1371/journal.pgen.1000562 19609346
13. Adaptation and constraint at Toll-like receptors in primates. G Wlasiuk MW Nachman, Mol Biol Evol 2010 27 9 2172 2186 10.1093/molbev/msq104 20410160
14. The differential evolutionary dynamics of avian cytokine and TLR gene classes. T Downing AT Lloyd C O'Farrelly DG Bradley, J Immunol 2010 184 12 6993 7000 10.4049/jimmunol.0903092 20483729
15. Identification and sequence analysis of chicken Toll-like receptors. A Yilmaz S Shen DL Adelson S Xavier JJ Zhu, Immunogenetics 2005 56 10 743 753 10.1007/s00251-004-0740-8 15578175 (Pubitemid 40174969)
16. Crystal structure of the TLR1-TLR2 heterodimer induced by binding of a tri-acylated lipopeptide. MS Jin SE Kim JY Heo ME Lee HM Kim SG Paik H Lee JO Lee, Cell 2007 130 6 1071 1082 10.1016/j.cell.2007.09.008 17889651 (Pubitemid 47410281)
17. Recognition of lipopeptide patterns by Toll-like receptor 2-Toll-like receptor 6 heterodimer. JY Kang X Nan MS Jin SJ Youn YH Ryu S Mah SH Han H Lee SG Paik JO Lee, Immunity 2009 31 6 873 884 10.1016/j.immuni.2009.09.018 19931471
18. Human TLRs 10 and 1 share common mechanisms of innate immune sensing but not signaling. Y Guan DR Ranoa S Jiang SK Mutha X Li J Baudry RI Tapping, J Immunol 2010 184 9 5094 5103 10.4049/jimmunol.0901888 20348427
19. The central leucine-rich repeat region of chicken TLR16 dictates unique ligand specificity and species-specific interaction with TLR2. AM Keestra MR de Zoete RA van Aubel JP van Putten, J Immunol 2007 178 11 7110 7119 17513760 (Pubitemid 46847437)
20. Combinational recognition of bacterial lipoproteins and peptidoglycan by chicken Toll-like receptor 2 subfamily. M Higuchi A Matsuo M Shingai K Shida A Ishii K Funami Y Suzuki H Oshiumi M Matsumoto T Seya, Dev Comp Immunol 2008 32 2 147 155 10.1016/j.dci.2007.05.003 17614130 (Pubitemid 350160923)
21. Gene conversion limits divergence of mammalian TLR1 and TLR6. EK Kruithof N Satta JW Liu S Dunoyer-Geindre RJ Fish, BMC Evol Biol 2007 7 148 10.1186/1471-2148-7-148 17727694
22. The avian Toll-Like receptor pathway - subtle differences amidst general conformity. P Cormican AT Lloyd T Downing SJ Connell D Bradley C O'Farrelly, Dev Comp Immunol 2009 33 9 967 973 10.1016/j.dci.2009.04.001 19539094
23. Avian toll-like receptors. R Brownlie B Allan, Cell Tissue Res 2011 343 1 121 30 10.1007/s00441-010-1026-0 20809414
24. Construction and characterization of a duck bacterial artificial chromosome library. X Yuan M Zhang W Ruan C Song L Ren Y Guo X Hu N Li, Anim Genet 2006 37 6 599 600 10.1111/j.1365-2052.2006.01526.x 17121612 (Pubitemid 44789669)
25. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. B Ewing L Hillier MC Wendl P Green, Genome Res 1998 8 3 175 185 9521921 (Pubitemid 28177229)
26. Base-calling of automated sequencer traces using phred. II. Error probabilities. B Ewing P Green, Genome Res 1998 8 3 186 194 9521922 (Pubitemid 28177230)
27. Consed: a graphical tool for sequence finishing. D Gordon C Abajian P Green, Genome Res 1998 8 3 195 202 9521923 (Pubitemid 28177231)
28. Automated finishing with autofinish. D Gordon C Desmarais P Green, Genome Res 2001 11 4 614 625 10.1101/gr.171401 11282977 (Pubitemid 32331559)
29. Picture: dynamic alignment and visualization tool for analyzing conservation profiles. I Ovcharenko GG Loots RC Hardison W Miller L Stubbs, Genome Res 2004 14 3 472 477 10.1101/gr.2129504 14993211 (Pubitemid 38380402)
30. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. SF Altschul TL Madden AA Schaffer J Zhang Z Zhang W Miller DJ Lipman, Nucleic Acids Res 1997 25 17 3389 3402 10.1093/nar/25.17.3389 9254694 (Pubitemid 27359211)
31. Clustal W and Clustal X version 2.0. Bioinformatics. MA Larkin G Blackshields NP Brown R Chenna PA McGettigan H McWilliam F Valentin IM Wallace A Wilm R Lopez JD Thompson TJ Gibson DG Higgins, 2007 23 21 2947 2948
32. Jalview Version 2 - a multiple sequence alignment editor and analysis workbench. AM Waterhouse JB Procter DM Martin M Clamp GJ Barton, Bioinformatics 2009 25 9 1189 1191 10.1093/bioinformatics/btp033 19151095
33. Statistical tests for detecting gene conversion. S Sawyer, Mol Biol Evol 1989 6 5 526 538 2677599 (Pubitemid 19210235)
34. Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. KS Lole RC Bollinger RS Paranjape D Gadkari SS Kulkarni NG Novak R Ingersoll HW Sheppard SC Ray, J Virol 1999 73 1 152 160 9847317 (Pubitemid 28565356)
35. Data incongruence and the problem of avian louse phylogeny. VS Smith RDM Page KP Johnson, Zool Scr 2004 33 239 259 10.1111/j.0300-3256.2004.00149.x (Pubitemid 38601034)
36. Likelihood-mapping: a simple method to visualize phylogenetic content of a sequence alignment. K Strimmer A von Haeseler, Proc Natl Acad Sci USA 1997 94 13 6815 6819 10.1073/pnas.94.13.6815 9192648 (Pubitemid 27281947)
37. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. S Guindon O Gascuel, Syst Biol 2003 52 5 696 704 10.1080/10635150390235520 14530136 (Pubitemid 37365050)
38. PAML 4: phylogenetic analysis by maximum likelihood. Z Yang, Mol Biol Evol 2007 24 8 1586 1591 10.1093/molbev/msm088 17483113 (Pubitemid 47236688)
39. DAMBE: software package for data analysis in molecular biology and evolution. X Xia Z Xie, J Hered 2001 92 4 371 373 10.1093/jhered/92.4.371 11535656 (Pubitemid 32848767)
40. Phylogenetic methods come of age: testing hypotheses in an evolutionary context. JP Huelsenbeck B Rannala, Science 1997 276 5310 227 232 10.1126/science.276.5310.227 9092465 (Pubitemid 27172674)
41. A novel method for detecting intramolecular coevolution: adding a further dimension to selective constraints analyses. MA Fares SA Travers, Genetics 2006 173 1 9 23 10.1534/genetics.105.053249 16547113 (Pubitemid 43800180)
42. CAPS: coevolution analysis using protein sequences. MA Fares D McNally, Bioinformatics 2006 22 22 2821 2822 10.1093/bioinformatics/btl493 17005535 (Pubitemid 44742405)
43. Amino acid substitution matrices from protein blocks. S Henikoff JG Henikoff, Proc Natl Acad Sci USA 1992 89 22 10915 10919 10.1073/pnas.89.22.10915 1438297
44. Cytoscape: a software environment for integrated models of biomolecular interaction networks. P Shannon A Markiel O Ozier NS Baliga JT Wang D Ramage N Amin B Schwikowski T Ideker, Genome Res 2003 13 11 2498 2504 10.1101/gr.1239303 14597658 (Pubitemid 37428274)
45. CPHmodels 2.0: X3M a computor Program to Extract 3D Models. O Lund M Nielsen C Lundegaard P Worning, CASP5 conference 2002 102
46. Statistical methods for detecting molecular adaptation. Z Yang JP Bielawski, Trends Ecol Evol 2000 15 12 496 503 10.1016/S0169-5347(00)01994-7 11114436
47. Innate immune recognition. CA Janeway Jr R Medzhitov, Annu Rev Immunol 2002 20 197 216 10.1146/annurev.immunol.20.083001.084359 11861602 (Pubitemid 34293424)
48. Innate immune sensing and its roots: the story of endotoxin. B Beutler ET Rietschel, Nat Rev Immunol 2003 3 2 169 176 10.1038/nri1004 12563300 (Pubitemid 37328694)
49. Recognition and signaling by toll-like receptors. AP West AA Koblansky S Ghosh, Annu Rev Cell Dev Biol 2006 22 409 437 10.1146/annurev.cellbio.21.122303. 115827 16822173
50. Toll-like receptor signalling. S Akira K Takeda, Nat Rev Immunol 2004 4 7 499 511 10.1038/nri1391 15229469 (Pubitemid 38931765)
51. Crystal structure of the TLR4-MD-2 complex with bound endotoxin antagonist Eritoran. HM Kim BS Park JI Kim SE Kim J Lee SC Oh P Enkhbayar N Matsushima H Lee OJ Yoo JO Lee, Cell 2007 130 5 906 917 10.1016/j.cell.2007.08. 002 17803912 (Pubitemid 47332573)
52. Induction of a novel chicken Toll-like receptor following Salmonella enterica serovar Typhimurium infection. R Higgs P Cormican S Cahalane B Allan AT Lloyd K Meade T James DJ Lynn LA Babiuk C O'Farrelly, Infect Immun 2006 74 3 1692 1698 10.1128/IAI.74.3.1692-1698.2006 16495540 (Pubitemid 43346802)
53. Expression patterns of chicken Toll-like receptor mRNA in tissues, immune cell subsets and cell lines. M Iqbal VJ Philbin AL Smith, Vet Immunol Immunopathol 2005 104 1-2 117 127 10.1016/j.vetimm.2004.11.003 15661337 (Pubitemid 40127447)
54. Molecular cloning and functional characterization of chicken toll-like receptors. A single chicken toll covers multiple molecular patterns. A Fukui N Inoue M Matsumoto M Nomura K Yamada Y Matsuda K Toyoshima T Seya, J Biol Chem 2001 276 50 47143 47149 10.1074/jbc.M103902200 11590137
55. Positive selection on the human genome. EJ Vallender BT Lahn, Hum Mol Genet 2004 13 Spec No 2 245 254 15358731
56. Positive selection of primate TRIM5alpha identifies a critical species-specific retroviral restriction domain. SL Sawyer LI Wu M Emerman HS Malik, Proc Natl Acad Sci USA 2005 102 8 2832 2837 10.1073/pnas.0409853102 15689398 (Pubitemid 40299877)
57. Domain exchange between human toll-like receptors 1 and 6 reveals a region required for lipopeptide discrimination. KO Omueti JM Beyer CM Johnson EA Lyle RI Tapping, J Biol Chem 2005 280 44 36616 36625 10.1074/jbc.M504320200 16129684 (Pubitemid 41587738)
58. Genetic analysis of Toll/Interleukin-1 Receptor (TIR) domain sequences from rhesus macaque Toll-like receptors (TLRs) 1-10 reveals high homology to human TLR/TIR sequences. SK Sanghavi R Shankarappa TA Reinhart, Immunogenetics 2004 56 9 667 674 10.1007/s00251-004-0734-6 15578265 (Pubitemid 40100800)