Positive selection signatures in the TLR7 family

Genes and Genomics

Volumn 32, Issue 2, 2010, Pages 143-150

  Park, Seung Gu ^a   Park, Donghyun ^b   Jung, Yu Jin ^a   Chung, Eunkyung ^c   Choi, Sun Shim ^a  

^a Kangwon National University   (South Korea)

^b UNIVERSITY OF CHICAGO   (United States)

^c Hallym University   (South Korea)

Author keywords

ECD Ectodomain; LRR Leucine rich receptor; LRT Likelihood ratio test; MRCA Most recent common ancestor; PAMP Pathogen associated molecular pattern; TIR Toll IL 1 receptor; TLR Toll like receptor

Indexed keywords

BACTERIA (MICROORGANISMS);

EID: 77956641690     PISSN: 19769571     EISSN: 20929293     Source Type: Journal    
DOI: 10.1007/s13258-009-0837-4     Document Type: Article

References (59)

1. Baccala R, Hoebe K, Kono DH, Beutler B and Theofilopoulos AN (2007) TLR-dependent and TLR-independent pathways of type I interferon induction in systemic autoimmunity. Nat. Med. 13: 543-551.
2. Barton GM (2007) Viral recognition by Toll-like receptors. Semin ImmunoL. 19: 33-40.
3. Bell JK, Mullen GE, Leifer CA, Mazzoni A, Davies DR and Segal DM (2003) Leucine-rich repeats and pathogen recognition in Toll-like receptors. Trends ImmunoL. 24: 528-533.
4. Bilak H, Tauszig-Delamasure S and Imler JL (2003) Toll and Toll-like receptors in Drosophila. Biochem. Soc. Trans. 31: 648-651.
5. Brodsky I and Medzhitov R (2007) Two modes of ligand recognition by TLRs. Cell 130: 979-981.
6. Choi SS and Lahn BT (2003) Adaptive evolution of MRG, a neuron-specific gene family implicated in nociception. Genome Res. 13: 2252-2259.
7. Dorus S, Evans PD, Wyckoff GJ, Choi SS and Lahn BT (2004) Rate of molecular evolution of the seminal protein gene SEMG2 correlates with levels of female promiscuity. Nat. Genet. 36: 1326-1329 BMC Genomics 8: 124.
8. Medvedev AE, Sabroe I, Hasday JD and Vogel SN (2006) Tolerance to microbial TLR ligands: molecular mechanisms and relevance to disease. J. Endotoxin Res. 12: 133-150.
9. Medzhitov R (2001) Toll-like receptors and innate immunity. Nat. Rev. ImmunoL. 1: 135-145.
10. Medzhitov R and Janeway C, Jr. (2000a) Innate immune recognition: mechanisms and pathways. ImmunoL. Rev. 173: 89-97.
11. Medzhitov R and Janeway C, Jr. (2000b) The Toll receptor family and microbial recognition. Trends MicrobioL. 8: 452-456.
12. Murphy WJ, Eizirik E, O'Brien SJ, Madsen O, Scally M, Douady CJ, Teeling E, Ryder OA, Stanhope MJ, de Jong WW, et al. (2001) Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294: 2348-2351. (Pubitemid 33140557)
13. Nei M and Gojobori T (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. MoL. BioL. EvoL. 3: 418-426.
14. Roach JC, Glusman G, Rowen L, Kaur A, Purcell MK, Smith KD, Hood LE and Aderem A (2005) The evolution of vertebrate Toll-like receptors. Proc. NatL. Acad. Sci. USA 102: 9577-9582.
15. Sanghavi SK, Shankarappa R and Reinhart TA (2004) 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. Immunogenetics 56: 667-674.
16. Springer MS, Murphy WJ, Eizirik E and O'Brien SJ (2003) Placental mammal diversification and the Cretaceous-Tertiary boundary. Proc. NatL. Acad. Sci. USA 100: 1056-1061.
17. Thompson JD, Higgins DG and Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
18. Towb P, Galindo RL and Wasserman SA (1998) Recruitment of Tube and Pelle to signaling sites at the surface of the Drosophila embryo. Development 125: 2443-2450.
19. Yang Z (1998) Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. MoL. BioL. EvoL. 15: 568-573.
20. Yang Z (2007) PAML 4: phylogenetic analysis by maximum likelihood. MoL. BioL. EvoL. 24: 1586-1591.
21. Yang Z and Nielsen R (2000) Estimating synonymous and non-synonymous substitution rates under realistic evolutionary models. MoL. BioL. EvoL. 17: 32-43.
22. Yang Z, Wong WS and Nielsen R (2005) Bayes empirical bayes inference of amino acid sites under positive selection. MoL. BioL. EvoL. 22: 1107-1118.
23. Zelus D, Robinson-Rechavi M, Delacre M, Auriault C and Laudet V (2000) Fast evolution of interleukin-2 in mammals and positive selection in ruminants. J. MoL. EvoL. 51: 234-244.
24. Zhang J, Nielsen R and Yang Z (2005) Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular leveL. MoL. BioL. EvoL. 22: 2472-2479.
25. Gangloff M and Gay NJ (2008) Baseless assumptions: activation of TLR9 by DNA. Immunity. 28: 293-294.
26. Gay NJ and Gangloff M (2007) Structure and function of Toll receptors and their ligands. Annu. Rev. Biochem. 76: 141-165.
27. Gay NJ, Gangloff M and Weber AN (2006) Toll-like receptors as molecular switches. Nat. Rev. ImmunoL. 6: 693-698.
28. Gilbert SL, Dobyns WB and Lahn BT (2005) Genetic links between brain development and brain evolution. Nat. Rev. Genet. 6: 581-590.
29. Gorden KK, Qiu X, Battiste JJ, Wightman PP, Vasilakos JP and Alkan SS (2006) Oligodeoxynucleotides differentially modulate activation of TLR7 and TLR8 by imidazoquinolines. J. ImmunoL. 177: 8164-8170.
30. Haas T, Metzger J, Schmitz F, Heit A, Muller T, Latz E and Wagner H (2008) The DNA sugar backbone 2' deoxyribose determines Toll-like receptor 9 activation. Immunity 28: 315-323.
31. Hughes AL (1997) Rapid evolution of immunoglobulin superfamily C2 domains expressed in immune system cells. MoL. BioL. EvoL. 14: 1-5.
32. Iwasaki A and Medzhitov R (2004) Toll-like receptor control of the adaptive immune responses. Nat. ImmunoL. 5: 987-995.
33. Krieg AM (2002) A role for Toll in autoimmunity. Nat. ImmunoL. 3: 423-424.
34. Krieg AM and Vollmer J (2007) Toll-like receptors 7, 8, and 9: linking innate immunity to autoimmunity. ImmunoL. Rev. 220: 251-269.
35. Krug A, Towarowski A, BrITSch S, Rothenfusser S, Hornung V, Bals R, Giese T, Engelmann H, Endres S, Krieg AM, et al. (2001) Toll-like receptor expression reveals CpG DNA as a unique mi-crobial stimulus for plasmacytoid dendritic cells which synergizes with CD40 ligand to induce high amounts of IL-12. Eur. J. ImmunoL. 31: 3026-3037. (Pubitemid 32994554)
36. Kumagai Y, Takeuchi O and Akira S (2008) TLR9 as a key receptor for the recognition of DNA. Adv. Drug Deliv. Rev. 60: 795-804.
37. Kumar S and Hedges SB (1998) A molecular timescale for vertebrate evolution. Nature 392: 917-920.
38. Leadbetter EA, Rifkin IR, Hohlbaum AM, Beaudette BC, Shlomchik MJ and Marshak-Rothstein A (2002) Chromatin-IgG complexes activate B cells by dual engagement of IgM and Toll-like receptors. Nature 416: 603-607.
39. Leulier F and Lemaitre B (2008) Toll-like receptors-taking an evolutionary approach. Nat. Rev. Genet. 9: 165-178.
40. Li WH, Wu CI and Luo CC (1985) A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. MoL. BioL. EvoL. 2: 150-174.
41. Martinelli C and Reichhart JM (2005) Evolution and integration of innate immune systems from fruit flies to man: lessons and questions. J. Endotoxin Res. 11: 243-248.
42. Matsushima N, Tanaka T, Enkhbayar P, Mikami T, Taga M, Yamada K and Kuroki Y (2007) Comparative sequence analysis of leu-cine-rich repeats (LRRs) within vertebrate Toll-like receptors. BMC Genomics 8: 124.
43. Medvedev AE, Sabroe I, Hasday JD and Vogel SN (2006) Tolerance to microbial TLR ligands: molecular mechanisms and relevance to disease. J. Endotoxin Res. 12: 133-150.
44. Medzhitov R (2001) Toll-like receptors and innate immunity. Nat. Rev. ImmunoL. 1: 135-145.
45. Medzhitov R and Janeway C, Jr. (2000a) Innate immune recognition: mechanisms and pathways. ImmunoL. Rev. 173: 89-97.
46. Medzhitov R and Janeway C, Jr. (2000b) The Toll receptor family and microbial recognition. Trends MicrobioL. 8: 452-456.
47. Murphy WJ, Eizirik E, O'Brien SJ, Madsen O, Scally M, Douady CJ, Teeling E, Ryder OA, Stanhope MJ, de Jong WW, et al. (2001) Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294: 2348-2351. (Pubitemid 33140557)
48. Nei M and Gojobori T (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. MoL. BioL. EvoL. 3: 418-426.
49. Roach JC, Glusman G, Rowen L, Kaur A, Purcell MK, Smith KD, Hood LE and Aderem A (2005) The evolution of vertebrate Toll-like receptors. Proc. NatL. Acad. Sci. USA 102: 9577-9582.
50. Sanghavi SK, Shankarappa R and Reinhart TA (2004) 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. Immunogenetics 56: 667-674.
51. Springer MS, Murphy WJ, Eizirik E and O'Brien SJ (2003) Placental mammal diversification and the Cretaceous-Tertiary boundary. Proc. NatL. Acad. Sci. USA 100: 1056-1061.
52. Thompson JD, Higgins DG and Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
53. Towb P, Galindo RL and Wasserman SA (1998) Recruitment of Tube and Pelle to signaling sites at the surface of the Drosophila embryo. Development 125: 2443-2450.
54. Yang Z (1998) Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. MoL. BioL. EvoL. 15: 568-573.
55. Yang Z (2007) PAML 4: phylogenetic analysis by maximum likelihood. MoL. BioL. EvoL. 24: 1586-1591.
56. Yang Z and Nielsen R (2000) Estimating synonymous and non-synonymous substitution rates under realistic evolutionary models. MoL. BioL. EvoL. 17: 32-43.
57. Yang Z, Wong WS and Nielsen R (2005) Bayes empirical bayes in-ference of amino acid sites under positive selection. MoL. BioL. EvoL. 22: 1107-1118.
58. Zelus D, Robinson-Rechavi M, Delacre M, Auriault C and Laudet V (2000) Fast evolution of interleukin-2 in mammals and positive selection in ruminants. J. MoL. EvoL. 51: 234-244.
59. Zhang J, Nielsen R and Yang Z (2005) Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular leveL. MoL. BioL. EvoL. 22: 2472-2479.