Phylogenetics in the bioinformatics culture of understanding

Comparative and Functional Genomics

Volumn 5, Issue 2, 2004, Pages 128-146

  Allaby, Robin G ^a   Woodwark, Mathew ^a  

^a ASTRAZENECA   (United Kingdom)

Author keywords

Amidohydrolase; Atrazine; Evolutionary tinkering; Phylogenetics; Toll

Indexed keywords

AMIDASE; ATRAZINE; MEMBRANE PROTEIN; TOLL LIKE RECEPTOR; TOLL LIKE RECEPTOR 1; 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 9;

AUTOANALYSIS; BIOINFORMATICS; COMPUTER PROGRAM; CONVERGENT EVOLUTION; DROSOPHILA; GENE SEQUENCE; GENETIC ALGORITHM; HIGH THROUGHPUT SCREENING; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; ORTHOLOGY; PHYLOGENY; PRIORITY JOURNAL; PROTEIN DOMAIN; REVIEW; SEQUENCE HOMOLOGY; SIGNAL NOISE RATIO;

EID: 2942525490     PISSN: 15316912     EISSN: None     Source Type: Journal    
DOI: 10.1002/cfg.381     Document Type: Review

References (73)

1. Agarwal A, Eastman QM, Schatz DG. 1998. Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system. Nature 394: 744.
2. Alexopoulou L, Holt AC, Medzhitov R, Flavell RA. 2001. Recognition of double-stranded RNA and activation of NF-κB by Toll-like receptor 3. Nature 413: 732-738.
3. Allaby RG, Brown TA. 2001. Network analysis provides insights into evolution of 5S rDNA arrays in Triticum and Aegilops. Genetics 157: 1331-1341.
4. Anderson KV, Jurgens G, Nusslein-Volhard C. 1985. Establishment of the dorsal-ventral 1 polarity in the Drosophila embryo: genetic studies on the role of the Toll gene product. Cell 42: 779-789.
5. Balavoine G, Adoutte A. 1998. One or three Cambrian radiations? Science 280: 397.
6. Bockaert J, Pin JP. 1999. Molecular tinkering of G protein-coupled receptors: an evolutionary success. EMBO J 18: 1723-1729.
7. Bonnert TP, Garka KE, Parnet P, et al. 1997. The cloning and characterisation of human MyD88: a member of an IL-1 receptor related family. FEBS Lett 402: 81-84.
8. Boundy-Mills KL, de Souza ML, Mandelbaum RT, Wackett LP, Sadowsky MJ. 1997. The atzB gene of Pseudomonas sp. Strain ADP encodes the second enzyme of a novel atrazine degradation pathway. Appl Environ Microb 63: 916-923.
9. 8 barrels: implications for the evolution of metabolic pathways. J Mol Biol 303: 627-640.
10. Dehal P, Satou Y, Campbell RK, et al. 2002. The draft genome of Cona intestinalis: insights into chordate and vertebrate origins. Science 298: 2157-2167.
11. de Souza M, Sadowsky MJ, Wackett LP. 1996. Atrazine chlorohydrolase from Pseudomonas sp. ADP: gene sequence, enzyme purification, and protein characterisation. J Bacteriol 178: 4894-4900.
12. Eaton RW, Karns JS. 1991. Cloning and analysis of s-triazine catabolic genes from Pseudomonas sp. strain NRRLB-12227. J Bacteriol 173: 1215-1222.
13. Felsenstein J. 1989. PHYLIP - Phylogeny Inference Package (version 3.2). Cladistics 5: 164-166.
14. Gay NJ, Keith FJ. 1991. Drosophila Toll and IL-1 receptor. Nature 351: 355-356.
15. Goodrich JA, Lykins BW, Clark RG. 1991. Drinking water from agriculturally contaminated ground water. J Environ Qual 20: 707-717.
16. Greenfeder SA, Nunes P, Kwee L, et al. 1995. Molecular cloning and characterisation of a second subunit of the interleukin receptor complex. J Biol Chem 270: 13 757-13 765.
17. Hayashi F, Smith KD, Ozinsky A, et al. 2001. The innate immune response to bacterial flagellin is mediated by Toll-like receptor 5. Nature 410: 1099-1103.
18. Hemmi H, Kaisho T, Takeuchi O, et al. 2002. Small antiviral compounds activate immune cells via the TLR7 MyD88-dependent signalling pathway. Nature Immanol 3: 196-200.
19. Hemmi H, Takeuchi O, Kawai T, et al. 2000. A Toll-like receptor recognizes bacterial DNA. Nature 408: 740-745.
20. Hoffmann JA, Kafatos FC, Janeway CA Jr, Ezekowitz RAB. 1999. Phylogenetic perspectives in innate immunity. Science 284: 1313-1318.
21. Holm L, Sander C. 1997. An evolutionary treasure: unification of a broad set of amidohydrolases related to urease. Proteins Struct Funct Genet 28: 72-82.
22. Horng T, Barton GM, Flavell RA, Medzhitov R. 2002. The adaptor molecule TIRAP provides signalling specificity for Toll-like receptors. Nature 420: 329-333.
23. Horng T, Medzhitov R. 2001. Drosophila MyD88 is an adaptor in the Toll signalling pathway. Proc Natl Acad Sci USA 98: 12 654-12 658.
24. Howard AD, McAllister G, Feighner SD, et al. 2001. Orphan G-protein-coupled receptors and natural ligand discovery. Trends Pharm Sci 22: 132-140.
25. Hughes AL. 1998. Protein phylogenies provide evidence of a radical discontinuity between arthropod and vertebrate immune systems. Immunogenetics 47: 283-296.
26. Hughes AL, Yeager M. 1999. Coevolution of the mammalian chemokines and their receptors. Immunogenetics 49: 115-124.
27. Huson DH. 1998. SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics 14: 68-73.
28. Jacob F. 1977. Evolution and tinkering. Science 196: 1161-1166.
29. Jukes TH, Cantor CR. 1969. Evolution of protein molecules. In Mammalian Protein Metabolism, Munro HN (ed.). Academic Press: New York; 21-132.
30. Kim G-J, Kim H-S. 1998. Identification of the structural similarity in the functionally related amidohydrolases acting on the cyclic amide ring. Biochem J 330: 295-302.
31. Li W-H, Gu Z, Wang H, Nekrutenko A. 2001. Evolutionary analyses of the human genome. Nature 409: 847-849.
32. Luo C, Zheng L. 1999. Independent evolution of Toll and related genes in insects and mammals. Immunogenetics 51: 92-98.
33. Maddison DR, Maddison WP. 2002a. MacClade 4.05 Analysis of Phylogeny and Character Evolution. Sinauer Associates: Sunderland, MA.
34. Maddison WP, Maddison DR. 2002b. Mesquite: a modular system for evolutionary analysis. Version 0.992. http://mesquiteproject.org.
35. Marcotte EM, Pellegrini M, Ng H-L, et al. 1999. Detecting protein function and protein-protein interactions from genome sequences. Science 285: 751-753.
36. McGuire G, Wright F. 1998. TOPAL: recombination detection in DNA and protein sequences. Bioinformatics 14: 219-220.
37. Medzhitov R, Preston-Hurlburt P, Janeway CA. 1997. A human homologue of the Drosophila Toll protein signals activation of adaptive immunity. Nature 388: 394-397.
38. Mulbry WW. 1994. Purification and characterisation of an inducible s-triazine hydrolase from Rhodococcus corallinus NRRL B15444R. Appl Environ Microb 60: 613-618.
39. Murphy PM, Baggiolini M, Charo IF, et al. 2000. International Union of Pharmacology. XXII. Nomenclature for chemokine receptors. Pharmacol Rev 52: 145-176.
40. Muzio M, Ni J, Feng P, Dixit VM. 1997. IRAK (Pelle) family member IRAK-2 and myD88 as proximal mediators of IL-1 signalling. Science 278: 1612-1615.
41. Muzio M, Polentarutti N, Bosiso D, Prahladan MKP, Mantovani A. 2000. Toll-like receptors: a growing family of immune receptors that are differentially expressed and regulated by different leukocytes. J Leuk Biol 67: 450-456.
42. Nagy I, Compernolle F, Ghys K, Vanderleyden J, de Mot R. 1995. A single P-450 system is involved in degradation of the herbicides EPTC (S-ethyl dipropylthiocarbamate) and atrazine by Rhodococcus sp. strain NI86/21. Appl. Environ Microb 61: 2056-2060.
43. Nurminsky DI, Nurminskaya MV, de Aguiar D, Hartl D. 1998. Selective sweep of a newly evolved sperm-specific gene in Drosophila. Nature 396: 572-575.
44. Ooi JY, Yagi Y, Hu X, Ip YT. 2002. The Drosophila Toll-9 activates a constitutive antimicrobial defense. EMBO Rep 3: 82-87.
45. Oshiumi H, Matsumoto M, Funami K, et al. 2003. TICAM-1, an adaptor molecule that participates in Toll-like receptor 3-mediated interferon-β induction. Nature Immunol 4: 161-167.
46. Page RDM. 1995. Parallel phylogenies: reconstructing the history of host-parasite assemblages. Cladistics 10: 155-173.
47. Page RDM. 1998. GeneTree: comparing gene and species. phylogenies using reconciled trees. Bioinformatics 14: 819-820.
48. Patthy L. 1999. Genome evolution and the evolution of exon-shuffling - a review. Gene 238: 103-114.
49. Posada D, Crandall KA. 2001. Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proc Natl Acad Sci USA 98: 13 757-13 762.
50. Piutti S, Semon E, Landry D, et al. 2003. Isolation and characterization of Nocardioides sp. SP12, an atrazine-degrading bacterial strain possessing the gene trzN from bulk and maize rhizosphere soil. FEMS Microb Lett 221: 111-117.
51. Robertson DL, Sharp PM, McCutchen FE, Hahn BH. 1995. Recombination in HIV-1. Nature 374: 124-126.
52. Sadowsky MJ, Tong Z, de Souza M, Wackett LP. 1998. AtzC is a new member of the amidohydrolase protein superfamily and is homologous to other atrazine-metabolizing enzymes. J Bacteriol 180: 152-158.
53. Seffernick JL, Chapir N, Schoeb M, et al. 2002. Enzymatic degradation of chlorodiamono-S-triazine. Appl Environ Microb 68: 4672-4675.
54. Seffernick JL, de Souza ML, Sadowsky MJ, Wackett LM. 2001. Melamine deaminase and atrazine chlorohydrolase: 98% identical but functionally different. J Bacteriol 183: 2405-2410.
55. Shields DC. 2000. Gene conversion among chemokine receptors. Gene 246: 239-245.
56. Shao ZQ, Behki R. 1995. Cloning of the genes for degradation of the herbicides EPTC (S-ethyl dipropylthiocarbamate) and atrazine from Rhodococcus sp. strain TEI. Appl Environ Microb 61: 2061-2065.
57. Shao ZQ, Seffens W, Mulbry W, Behki RM. 1995. Cloning and expression of the S-triazine hydrolase gene (trzA) from Rhodococcus corallinus and development of the Rhodococcus recombinant strains capable of dealkylating and dechlorinating the herbicide atrazine. J Bacteriol 177: 5748-5755.
58. Shimizu N, Gojobori T. 2000. How can human and simian immunodeficiency viruses utilise chemokine receptors as their coreceptors? Gene 259: 199-205.
59. Storm CEV, Sonnhammer ELL. 2001. NIFAS: visual analysis of domain evolution in proteins. Bioinformatics 17: 343-348.
60. Takeuchi O, Hoshino K, Kawai T, et al. 1999. Different roles of TLR2 and TLR4 in recognition of Gram-negative and Gram-positive bacterial cell wall components. Immunity 11: 443-451.
61. Takeuchi O, Kawai T, Mühlradt PF, et al. 2001. Discrimination of bacterial lipoproteins by Toll-like receptor 6. Int Immunol 13: 933-940.
62. Tauszig-Delamasure S, Bilak H, Capovilla M, Hoffmann JA, Imler JL. 2002. Drosophila MyD88 is required for the response to fungal and Gram-positive bacterial infections. Nature Immunol 3: 91-97.
63. Tauszig S, Jouanguy E, Hoffmann JA, Imler JL. 2000. Toll-related receptors and the control of antimicrobial peptide expression in Drosophila. Proc Natl Acad Sci USA 97: 10 520-10 525.
64. Topp E, Mulbry WM, Zhu H, Nour SM, Cuppels D. 2000. Characterisation of S-triazine herbicide metabolism by a Nocardioides sp. isolated from agricultural soils. Appl Environ Microb 66: 3134-3141.
65. Whitham S, Dinesh-Kumar SP, Choi D, et al. 1994. The product of the tobacco mosaic virus resistance gene N: similarity to toll and the interleukin-1 receptor. Cell 78: 1101-1115.
66. 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.
67. Xu Y, Tao X, Shen B, et al. 2000. Structural basis for signal transduction by the Toll/interleukin-1 receptor domains. Nature 408: 111-115.
68. Yamamoto M, Sato S, Hemmi H, et al. 2002. Essential role for TIRAP in activation of the signalling cascade shared by TLR2 and TLR4. Nature 420: 324-329.
69. Yang R-B, Mark M, Gray A, et al. 1998. Toll-like receptor-2 mediates lipopolysaccharide-induced cellular signalling. Nature 395: 284-288.
70. Yuan G, Bin JC, McKay DJ, Snyder FF. 1999. Cloning and characterisation of human guanine deaminase. J Biol Chem 274: 8157-8180.
71. Zischler H, Geisert H, von Haesseler A, Pääbo S. 1995. A nuclear 'fossil' of the mitochondrial D-loop and the origin of modern humans. Nature 378: 489-492.
72. Zuany-Amorim C, Hastewell J, Walker C. 2002. Toll-like receptors as potential therapeutic targets for multiple diseases. Nature Rev 1: 797-807.
73. Zullo S, Sieu LL, Slightom JL, Hadler HI, Eisenstadt JM. 1991. Mitochondrial D-loop sequences are integrated in the rat nuclear genome. J Mol Biol 221: 1223-1235.