TIR-X and TIR-NBS proteins: Two new families related to disease resistance TIR-NBS-LRR proteins encoded in Arabidopsis and other plant genomes

Plant Journal

Volumn 32, Issue 1, 2002, Pages 77-92

  Meyers, Blake C ^a,c   Morgante, Michele ^b   Michelmore, Richard W ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b DUPONT COMPANY   (United States)

^c UNIVERSITY OF DELAWARE   (United States)

Author keywords

Adapter protein; Arabidopsis; Disease resistance; Gene cluster; LRR; NBS; Signal transduction; TIR

Indexed keywords

DEGRADATION; DISEASES; GENES; PROTEINS;

GENE ENCODING;

PLANTS (BOTANY);

AMINO ACID SEQUENCE; ARABIDOPSIS; ARABIDOPSIS PROTEINS; CONSERVED SEQUENCE; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENOME, PLANT; GTP-BINDING PROTEINS; IMMUNITY, NATURAL; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; PHYLOGENY; PINUS; PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID;

ARABIDOPSIS; CONIFEROPHYTA; EMBRYOPHYTA; MAMMALIA;

EID: 0036793439     PISSN: 09607412     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1365-313X.2002.01404.x     Document Type: Article

References (51)

1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. J. Mol Biol. 215, 403-410.
2. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
3. Arabidopsis Genome Initiative. (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796-815.
4. Aravind, L., Dixit, V.M. and Koonin, E.V. (1999) The domains of death: evolution of the apoptosis machinery. Trends Biochem. Sci. 24, 47-53.
5. Aravind, L., Dixit, V.M. and Koonin, E.V. (2001) Apoptotic molecular machinery: vastly increased complexity in vertebrates revealed by genome comparisons. Science 291, 1279-1284.
6. Ayliffe, M.A., Frost, D.V., Finnegan, E.J., Lawrence, G.J., Anderson, P.A. and Ellis, J.G. (1999) Analysis of alternative transcripts of the flax L6 rust resistance gene. Plant J. 17, 287-292.
7. Bai, J., Pennill, A., Ning, J., Lee, S.W., Ramalingam, J., Webb, C.R., Zhao, B., Sun, Q., Nelson, J.C., Leach, J.E. and Hulbert, S.H. (2002) Diversity in nucleotide binding site-leucine-rich repeat genes in cereals. Genome Res, (in press).
8. Bailey, T.L. and Elkan, C. (1995) The value of prior knowledge in discovering motifs with MEME. Proc. Int. Conf Intell Syst Mol Biol. 3, 21-29.
9. van der Biezen, E.A. and Jones, J.D. (1998) The NB-ARC domain: a novel signalling motif shared by plant resistance gene products and regulators of cell death in animals. Curr. Biol. 8, R226-R227.
10. Brenner, S., Johnson, M., Bridgham, J., Golda, G., Lloyd, D.H., Johnson, D., Luo, S., McCurdy, J.C., Foy, M., Ewan, M., Roth, R., George, D., Eletr, S., Albrecht, G., Vermass, E., Williams, S.R., Moon, K., Burcham, T., Palias, M., DuBridge, R.B., Kirchner, J., Fearon, K., Mao, J. and Corcoran, K. (2000a) Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat. Biotechnol. 18, 630-634.
11. Brenner, S., Williams, S.R., Vermaas, E.H., Storck, T., Moon, K., McCollum, C., Mao, J.I., Luo, S., Kirchner, J.J., Eletr, S., DuBridge, R.B., Burcham, T. and Albrecht, G. (2000b) In vitro cloning of complex mixtures of DNA on microbeads: physical separation of differentially expressed cDNAs. Proc. Natl Acad. Sci. USA 97, 1665-1670.
12. Cannon, S.B., Zhu, H., Baumgarten, A.M., Spangler, R., May, G., Cook, D.R. and Young, N.D. (2002) Diversity, distribution, and ancient taxonomic relationships within the TIR and non-TIR NBS-LRR resistance gene subfamilies. J. Mol. Evol. 54, 548-562.
13. Dangl, J.L. and Jones, J.D. (2001) Plant pathogens and integrated defence responses to infection. Nature 411, 826-833.
14. Dinesh-Kumar, S.P. and Baker, B.J. (2000) Alternatively spliced resistance gene transcripts: their possible role in tobacco mosaic virus resistance. Proc. Natl Acad. Sci. USA 97, 1908-1913.
15. Du, X., Poltorak, A., Wei, Y. and Beutler, B. (2000) Three novel mammalian toll-like receptors: gene structure, expression, and evolution. Eur Cytokine Netw 11, 362-371.
16. Fitzgerald, K.A., Palsson-McDermott, E.M., Bowie, A.G., Jefferies, C.A., Mansell, A.S., Brady, G., Brint, E., Dunne, A., Gray, P., Harte, M.T., McMurray, D., Smith, D.E., Sims, J.E., Bird, T.A. and O'Neill, L.A. (2001) Mal (MyD88-adapter-like) is required for Toll-like receptor-4 signal transduction. Nature 413, 78-83.
17. Fluhr, R. (2001) Sentinels of disease. Plant resistance genes. Plant Physiol, 127, 1367-1374.
18. Franklin-Tong, N.E. (2002) Receptor-ligand interaction demonstrated in Brassica self-incompatibility. Trends Genet. 18, 113-115.
19. Gassmann, W., Hinsch, M.E. and Staskawicz, B.J. (1999) The Arabidopsis RPS4 bacterial-resistance gene is a member of the TIR-NBS-LRR family of disease-resistance genes. Plant J. 20, 265-277.
20. Glazebrook, J. (2001) Genes controlling expression of defense responses in Arabidopsis-2001 status. Curr. Opin. Plant Biol. 4, 301-308.
21. Gowda, B.S., Riopel, J.L. and Timko, M.P. (1999) NRSA-1: a resistance gene homolog expressed in roots of non-host plants following parasitism by Striga asiatica (witchweed). Plant J. 20, 217-230.
22. Gribskov, M., McLachlan, A.D. and Eisenberg, D. (1987) Profile analysis: detection of distantly related proteins. Plant. Natl. Acad. Sci. USA 84, 4355-4358.
23. Heath, M.C. (2000) Hypersensitive response-related death. Plant Mol. Biol. 44, 321-334.
24. Horng, T. and Medzhitov, R. (2001) Drosophila MyD88 is an adapter in the Toll signaling pathway. Proc. Natl Acad. Sci. USA 98, 12654-12658.
25. Hu, Y., Ding, L., Spencer, D.M. and Nunez, G. (1998) WD-40 repeat region regulates Apaf-1 self association and procaspase-9 activation. J. Biol. Chem. 273, 33489-33494.
26. Kaisho, T. and Akira, S. (2001) Dendritic-cell function in Toll-like receptor- and MyD88-knockout mice. Trends Immunol. 22, 78-83.
27. Kopp, E.B. and Medzhitov, R. (1999) The Toll-receptor family and control of innate immunity. Curr. Opin. Immunol. 11, 13-18.
28. Kruglyak, S. and Tang, H. (2000) Regulation of adjacent yeast genes. Trends Genet. 16, 109-111.
29. Lawrence, G.J., Finnegan, E.J., Ayliffe, M.A. and Ellis, J.G. (1995) The L6 gene for flax rust resistance is related to the Arabidopsis bacterial resistance gene RPS2 and the tobacco viral resistance gene N. Plant Cell 7, 1195-1206.
30. Marcotte, E.M., Pellegrini, M., Ng, H.L., Rice, D.W., Yeates, T.O. and Eisenberg, D. (1999) Detecting protein function and protein-protein interactions from genome sequences. Science 285, 751-753.
31. Medzhitov, R., Preston-Hurlburt, P., Kopp, E., Stadlen, A., Chen, C., Ghosh, S. and Janeway, C.A., Jr (1998) MyD88 is an adaptor protein in the hToll/IL-1 receptor family signaling pathways. Mol. Cell. 2, 253-258.
32. Meyers, B.C., Dickerman, A.W., Michelmore, R.W., Sivaramakrishnan, S., Sobral, B.W. and Young, N.D. (1999) Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamily. Plant J. 20, 317-332.
33. Noel, L., Moores, T.L., van Der Biezen, E.A., Parniske, M., Daniels, M.J., Parker, J.E. and Jones, J.D. (1999) Pronounced intraspecific haplotype divergence at the RPP5 complex disease resistance locus of Arabidopsis. Plant Cell 11, 2099-2112.
34. Pan, Q., Wendel, J. and Fluhr, R. (2000) Divergent evolution of plant NBS-LRR resistance gene homologues in dicot and cereal genomes. J. Mol. Evol. 50, 203-213.
35. Parker, J.E., Coleman, M.J., Szabo, V., Frost, L.N., Schmidt, R., van der Biezen, E.A., Moores, T., Dean, C., Daniels, M.J. and Jones, J.D. (1997) The Arabidopsis downy mildew resistance gene RPP5 shares similarity to the Toll and interleukin-1 receptors with N and L6. Plant Cell 9, 879-894.
36. Pearson, W.R. and Lipman, D.J. (1988) Improved tools for biological sequence comparison. Proc. Natl Acad. Sci. USA 85, 2444-2448.
37. Poltorak, A., Ricciardi-Castagnoli, P., Citterio, S. and Beutler, B. (2000) Physical contact between lipopolysaccharide and Toll-like receptor 4 revealed by genetic complementation. Proc. Natl Acad. Sci. USA 97, 2163-2167.
38. Richly, E., Kurth, J. and Leister, D. (2002) Mode of amplification and reorganization of resistance genes during recent Arabidopsis thaliana evolution. Mol Biol. Evol. 19, 76-84.
39. Salmeron, J.M., Oldroyd, G.E., Rommens, C.M., Scofield, S.R., Kim, H.S., Lavelle, D.T., Dahlbeck, D. and Staskawicz, B.J. (1996) Tomato Prf is a member of the leucine-rich repeat class of plant disease resistance genes and lies embedded within the Pto kinase gene cluster. Cell 86, 123-133.
40. Savard, L., Li, P., Strauss, S.H., Chase, M.W., Michaud, M. and Bousquet, J. (1994) Chloroplast and nuclear gene sequences indicate late Pennsylvanian time for the last common ancestor of extant seed plants. Proc. Natl Acad. Sci. USA 91, 5163-5167.
41. Sawant, S.V., Kiran, K., Singh, P.K. and Tuli, R. (2001) Sequence architecture downstream of the initiator codon enhances gene expression and protein stability in plants. Plant Physiol. 126, 1630-1636.
42. Schopfer, C.R., Nasrallah, M.E. and Nasrallah, J.B. (1999) The male determinant of self-incompatibility in Brassica. Science 286, 1697-1700.
43. Schultz, J., Milpetz, F., Bork, P. and Ponting, C.P. (1998) SMART, a simple modular architecture research tool: identification of signaling domains. Proc. Natl Acad. Sci. USA 95, 5857-5864.
44. Seoighe, C., Federspiel, N., Jones, T., Hansen, N., Bivolarovic, V., Surzycki, R., Tamse, R., Komp, C., Huizar, L., Davis, R.W., Scherer, S., Tait, E., Shaw, D.J., Harris, D., Murphy, L., Oliver, K., Taylor, K., Rajandream, M.A., Barrell, B.G. and Wolfe, K.H. (2000) Prevalence of small inversions in yeast gene order evolution. Proc. Natl Acad. Sci. USA 97, 14433-14437.
45. Slack, J.L., Schooley, K., Bonnert, T.P., Mitcham, J.L., Qwarnstrom, E.E., Sims, J.E. and Dower, S.K. (2000) Identification of two major sites in the type I interleukin-1 receptor cytoplasmic region responsible for coupling to pro-inflammatory signaling pathways. J. Biol. Chem. 275, 4670-4678.
46. Srinivasula, S.M., Ahmad, M., Fernandes-Alnemri, T. and Alnemri, E.S. (1998) Autoactivation of procaspase-9 by Apaf-1-mediated oligomerization. Mol. Cell 1, 949-957.
47. Swofford, D. (2000) PAUP*. Phytogenetic Analysis Using Parsimony. Sunderland, MA: Sinauer.
48. Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLU STAL 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.
49. Whitham, S., Dinesh-Kumar, S.P., Choi, D., Hehl, R., Corr, C. and Baker, B. (1994) The product of the tobacco mosaic virus resistance gene N: similarity to Toll and the interleukin-1 receptor. Cell 78, 1101-1115.
50. Xiao, S., Ellwood, S., Calis, O., Patrick, E., Li, T., Coleman, M. and Turner, J.G. (2001) Broad-spectrum mildew resistance in Arabidopsis thaliana mediated by RPW8. Science 291, 118-120.
51. Xu, Y., Tao, X., Shen, B., Horng, T., Medzhitov, R., Manley, J.L. and Tong, L. (2000) Structural basis for signal transduction by the Toll/interleukin-1 receptor domains. Nature 408, 111-115.