Phylogeny of Toll-Like Receptor Signaling: Adapting the Innate Response

PLoS ONE

Volumn 8, Issue 1, 2013, Pages

  Roach, Jeffrey M ^a   Racioppi, Luigi ^b,c   Jones, Corbin D ^d   Masci, Anna Maria ^b  

^a UNIVERSITY OF NORTH CAROLINA   (United States)

^b DUKE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF NAPLES FEDERICO II   (Italy)

^d UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MYELOID DIFFERENTIATION FACTOR 88; TOLL LIKE RECEPTOR;

ARTICLE; GENE DUPLICATION; INNATE IMMUNITY; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; PROTEIN DOMAIN; SIGNAL TRANSDUCTION;

ADAPTATION, PHYSIOLOGICAL; CARRIER PROTEINS; EVOLUTION, MOLECULAR; GENE DUPLICATION; IMMUNITY, INNATE; MYELOID DIFFERENTIATION FACTOR 88; PHYLOGENY; RECEPTORS, INTERLEUKIN-1; SIGNAL TRANSDUCTION; TOLL-LIKE RECEPTOR 4; TOLL-LIKE RECEPTORS;

BACTERIA (MICROORGANISMS); INVERTEBRATA; PROTOZOA; VERTEBRATA;

EID: 84872251629     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0054156     Document Type: Article

References (56)

1. Masci AM, Arighi CN, Diehl AD, Lieberman AE, Mungall C, et al. (2009) An improved ontological representation of dendritic cells as a paradigm for all cell types. BMC bioinformatics 10: 70.
2. Janeway CA Jr, Medzhitov R, (2002) Innate immune recognition. Annual review of immunology 20: 197-216.
3. Takeda K, Kaisho T, Akira S, (2003) Toll-like receptors. Annual review of immunology 21: 335-376.
4. Galgani M, Busiello I, Censini S, Zappacosta S, Racioppi L, et al. (2004) Helicobacter pylori induces apoptosis of human monocytes but not monocyte-derived dendritic cells: role of the cag pathogenicity island. Infection and immunity 72: 4480-4485.
5. Galgani M, De Rosa V, De Simone S, Leonardi A, D'Oro U, et al. (2004) Cyclic AMP modulates the functional plasticity of immature dendritic cells by inhibiting Src-like kinases through protein kinase A-mediated signaling. The Journal of biological chemistry 279: 32507-32514.
6. Napolitani G, Bortoletto N, Racioppi L, Lanzavecchia A, D'Oro U, (2003) Activation of src-family tyrosine kinases by LPS regulates cytokine production in dendritic cells by controlling AP-1 formation. European journal of immunology 33: 2832-2841.
7. Illario M, Giardino-Torchia ML, Sankar U, Ribar TJ, Galgani M, et al. (2008) Calmodulin-dependent kinase IV links Toll-like receptor 4 signaling with survival pathway of activated dendritic cells. Blood 111: 723-731.
8. Racioppi L, Means AR (2012) Calcium/Calmodulin-Dependent Protein Kinase Kinase 2: Roles in Signaling and Pathophysiology. The Journal of biological chemistry.
9. Racioppi L, Noeldner PK, Lin F, Arvai S, Means AR, (2012) Calcium/calmodulin-dependent protein kinase kinase 2 regulates macrophage-mediated inflammatory responses. The Journal of biological chemistry 287: 11579-11591.
10. Racioppi L, Means AR, (2008) Calcium/calmodulin-dependent kinase IV in immune and inflammatory responses: novel routes for an ancient traveller. Trends in immunology 29: 600-607.
11. Anderson KV, Schneider DS, Morisato D, Jin Y, Ferguson EL, (1992) Extracellular morphogens in Drosophila embryonic dorsal-ventral patterning. Cold Spring Harb Symp Quant Biol 57: 409-417.
12. Lemaitre B, Nicolas E, Michaut L, Reichhart JM, Hoffmann JA, (1996) The dorsoventral regulatory gene cassette spatzle/Toll/cactus controls the potent antifungal response in Drosophila adults. Cell 86: 973-983.
13. Williams MJ, Rodriguez A, Kimbrell DA, Eldon ED, (1997) The 18-wheeler mutation reveals complex antibacterial gene regulation in Drosophila host defense. EMBO J 16: 6120-6130.
14. Nurnberger T, Brunner F, (2002) Innate immunity in plants and animals: emerging parallels between the recognition of general elicitors and pathogen-associated molecular patterns. Curr Opin Plant Biol 5: 318-324.
15. Dangl JL, Jones JD, (2001) Plant pathogens and integrated defence responses to infection. Nature 411: 826-833.
16. Friedman R, Hughes AL, (2002) Molecular evolution of the NF-kappaB signaling system. Immunogenetics 53: 964-974.
17. Zhou H, Gu J, Lamont SJ, Gu X, (2007) Evolutionary analysis for functional divergence of the toll-like receptor gene family and altered functional constraints. J Mol Evol 65: 119-123.
18. Luo C, Zheng L, (2000) Independent evolution of Toll and related genes in insects and mammals. Immunogenetics 51: 92-98.
19. Temperley ND, Berlin S, Paton IR, Griffin DK, Burt DW, (2008) Evolution of the chicken Toll-like receptor gene family: a story of gene gain and gene loss. BMC genomics 9: 62.
20. Hughes AL, Piontkivska H, (2008) Functional diversification of the toll-like receptor gene family. Immunogenetics 60: 249-256.
21. Roach JC, Glusman G, Rowen L, Kaur A, Purcell MK, et al. (2005) The evolution of vertebrate Toll-like receptors. Proc Natl Acad Sci U S A 102: 9577-9582.
22. Kanzok SM, Hoa NT, Bonizzoni M, Luna C, Huang Y, et al. (2004) Origin of Toll-like receptor-mediated innate immunity. J Mol Evol 58: 442-448.
23. Koonin EV, Wolf YI, Karev GP, (2002) The structure of the protein universe and genome evolution. Nature 420: 218-223.
24. Muller A, MacCallum RM, Sternberg MJ, (2002) Structural characterization of the human proteome. Genome Res 12: 1625-1641.
25. Dokholyan NV, Shakhnovich B, Shakhnovich EI, (2002) Expanding protein universe and its origin from the biological Big Bang. Proc Natl Acad Sci U S A 99: 14132-14136.
26. Brenner SE, Hubbard T, Murzin A, Chothia C, (1995) Gene duplications in H. influenzae. Nature 378: 140.
27. Teichmann SA, Park J, Chothia C, (1998) Structural assignments to the Mycoplasma genitalium proteins show extensive gene duplications and domain rearrangements. Proc Natl Acad Sci U S A 95: 14658-14663.
28. Pham Y, Li L, Kim A, Erdogan O, Weinreb V, et al. (2007) A minimal TrpRS catalytic domain supports sense/antisense ancestry of class I and II aminoacyl-tRNA synthetases. Mol Cell 25: 851-862.
29. O'Neill LA, Bowie AG, (2007) The family of five: TIR-domain-containing adaptors in Toll-like receptor signalling. Nat Rev Immunol 7: 353-364.
30. Takeda K, Akira S, (2004) TLR signaling pathways. Semin Immunol 16: 3-9.
31. Gay NJ, Gangloff M, (2007) Structure and function of Toll receptors and their ligands. Annu Rev Biochem 76: 141-165.
32. Bell JK, Botos I, Hall PR, Askins J, Shiloach J, et al. (2005) The molecular structure of the Toll-like receptor 3 ligand-binding domain. Proc Natl Acad Sci U S A 102: 10976-10980.
33. O'Neill LA, (2006) How Toll-like receptors signal: what we know and what we don't know. Curr Opin Immunol 18: 3-9.
34. Dunne A, O'Neill LA, (2005) Adaptor usage and Toll-like receptor signaling specificity. FEBS Lett 579: 3330-3335.
35. Kang JY, Lee JO, (2011) Structural biology of the Toll-like receptor family. Annu Rev Biochem 80: 917-941.
36. Matsushima N, Tanaka T, Enkhbayar P, Mikami T, Taga M, et al. (2007) Comparative sequence analysis of leucine-rich repeats (LRRs) within vertebrate toll-like receptors. BMC genomics 8: 124.
37. Uematsu S, Akira S (2008) Toll-Like receptors (TLRs) and their ligands. Handb Exp Pharmacol: 1-20.
38. Werling D, Jann OC, Offord V, Glass EJ, Coffey TJ, (2009) Variation matters: TLR structure and species-specific pathogen recognition. Trends Immunol 30: 124-130.
39. Wu B, Xin B, Jin M, Wei T, Bai Z, (2011) Comparative and phylogenetic analyses of three TIR domain-containing adaptors in metazoans: implications for evolution of TLR signaling pathways. Dev Comp Immunol 35: 764-773.
40. Towb P, Sun H, Wasserman SA, (2009) Tube Is an IRAK-4 homolog in a Toll pathway adapted for development and immunity. J Innate Immun 1: 309-321.
41. Tanji T, Ip YT, (2005) Regulators of the Toll and Imd pathways in the Drosophila innate immune response. Trends Immunol 26: 193-198.
42. Wang L, Ligoxygakis P, (2006) Pathogen recognition and signalling in the Drosophila innate immune response. Immunobiology 211: 251-261.
43. Meylan E, Burns K, Hofmann K, Blancheteau V, Martinon F, et al. (2004) RIP1 is an essential mediator of Toll-like receptor 3-induced NF-kappa B activation. Nat Immunol 5: 503-507.
44. Zhang Q, Zmasek CM, Cai X, Godzik A, (2011) TIR domain-containing adaptor SARM is a late addition to the ongoing microbe-host dialog. Dev Comp Immunol 35: 461-468.
45. Fornarino S, Laval G, Barreiro LB, Manry J, Vasseur E, et al. (2011) Evolution of the TIR domain-containing adaptors in humans: swinging between constraint and adaptation. Mol Biol Evol 28: 3087-3097.
46. Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, et al. (2007) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 35: D5-12.
47. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948.
48. SIPPL MJ, (1999) Biological sequence analysis. Probabilistic models of proteins and nucleic acids, edited by R. Durbin, S. Eddy, A. Krogh, and G. Mitchinson. 1998. Cambridge: Cambridge University Press. 356 pp. £55.00 ($80.00) (hardcover); £19.95 ($34.95) (paper). PRS 8: 695-695.
49. Pruitt KD, Tatusova T, Maglott DR, (2007) NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 35: D61-65.
50. Satake H, Sasaki N, (2010) Comparative overview of toll-like receptors in lower animals. Zoolog Sci 27: 154-161.
51. Kasamatsu J, Oshiumi H, Matsumoto M, Kasahara M, Seya T, (2010) Phylogenetic and expression analysis of lamprey toll-like receptors. Dev Comp Immunol 34: 855-865.
52. Zhang Q, Zmasek CM, Godzik A, (2010) Domain architecture evolution of pattern-recognition receptors. Immunogenetics 62: 263-272.
53. Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, et al. (2008) The Pfam protein families database. Nucleic Acids Res 36: D281-288.
54. Felsenstein J, (1989) Mathematics vs. Evolution: Mathematical Evolutionary Theory. Science 246: 941-942.
55. Desper R, Gascuel O, (2002) Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle. J Comput Biol 9: 687-705.
56. Conow C, Fielder D, Ovadia Y, Libeskind-Hadas R, (2010) Jane: a new tool for the cophylogeny reconstruction problem. Algorithms Mol Biol 5: 16.