Diversity in nucleotide binding site-leucine-rich repeat genes in cereals

Genome Research

Volumn 12, Issue 12, 2002, Pages 1871-1884

  Bai, Jianfa ^a   Pennill, Lourdes A ^a   Ning, Jianchang ^a   Lee, Se Weon ^a   Ramalingam, Jegadeesan ^a   Webb, Craig A ^a   Zhao, Bingyu ^a   Sun, Qing ^a   Nelson, James C ^a   Leach, Jan E ^a   Hulbert, Scot H ^a  

^a KANSAS STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

INTERLEUKIN 1 RECEPTOR; LEUCINE; NUCLEOTIDE;

AMINO TERMINAL SEQUENCE; ARABIDOPSIS; CEREAL; CONTROLLED STUDY; CROSS HYBRIDIZATION; DATA BASE; GENE STRUCTURE; GENETIC RESISTANCE; GENETIC VARIABILITY; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE BINDING SITE; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT DISEASE; PLANT GENETICS; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; REVIEW; RICE; UNINDEXED SEQUENCE;

NON-PROGRAMMATIC;

AMINO ACID SEQUENCE; BINDING SITES; CEREALS; CONSENSUS SEQUENCE; DNA PROBES; GENE DOSAGE; GENES, PLANT; INTRONS; LEUCINE; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; NUCLEOTIDES; OPEN READING FRAMES; ORYZA SATIVA; PHYLOGENY; PLANT DISEASES; PROTEIN STRUCTURE, TERTIARY; PROTEINS; REPETITIVE SEQUENCES, AMINO ACID; SEQUENCE HOMOLOGY, NUCLEIC ACID; VARIATION (GENETICS);

ARABIDOPSIS; DICOTYLEDONEAE; EMBRYOPHYTA; MAMMALIA; POACEAE;

EID: 0036916368     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.454902     Document Type: Review

References (47)

1. Aarts, N., Metz, M., Holub, E., Staskawicz, B.J., Daniels, M.J., and Parker, J.E. 1998. Different requirements for EDS1 and NDR1 by disease resistance genes define at least two R gene-mediated signaling pathways in Arabidopsis. Proc. Natl. Acad. Sci. 95: 10306-10311.
2. Austin, M.J., Muskett, P., Kahn, K., Feys, B.J., Jones, J. D., and Parker, J.E. 2002. Regulatory role of SGT1 in early R gene-mediated plant defenses. Science 295: 2077-2080.
3. Azevedo, C., Sadanandom, A., Kitagawa, K., Freialdenhoven, A., Shirasu, K., and Schulze-Lefert, P. 2002. The RAR1 interactor SGT1, an essential component of R gene-triggered disease resistance. Science 295: 2073-2076.
4. Bailey, T.L., Baker, M.E., Elkan, C.P., and Grundy, W.N. 1999. MEME, MAST, and Meta-MEME: New tools for motif discovery in protein sequences. In Pattern discovery in biomolecular data: Tools, techniques, and applications. (eds. J. Wang, B. Shapiro, and D. Shashas), pp. 30-54. Oxford University Press, Oxford, UK.
5. Bateman, A., Birney, E., Cerruti, L., Durbin, R., Etwiller, L., Eddy, S.R., Griffiths-Jones, S., Howe, K.L., Marshall, M., and Sonnhammer, E.L.L. 2002. The Pfam protein families database. Nucleic Acids Res. 30: 276-280.
6. Bent, A.F. 1996. Plant disease resistance genes: Function meets structure. Plant Cell 8: 1757-1771.
7. Berger, B., Wilson, D.B., Wolf, E.T.T., Milla, M., and Kim, P.S. 1995. Predicting coiled coils by use of pairwise residue correlations. Proc. Natl. Acad. Sci. 92: 8259-8263.
8. Bryan, G.T., Wu, K.-S., Farrall, L., Jia, Y., Hershey, H.P., McAdams, S.A., Donaldson, G.K., Tarchini, R., and Valent, B. 2000. A single amino acid difference distinguishes resistant and susceptible alleles of the rice blast resistance gene Pi-ta. Plant Cell 12: 2033-2046.
9. Burge, C. and Karlin, S. 1997. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268: 78-94.
10. 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.
11. Collins, N.C., Webb, C.A., Seah, S., Ellis, J.G., Hulbert, S.H., and Pryor, A. 1998. The isolation and mapping of disease resistance gene analogs in maize. Mol. Plant Microbe Interact 11: 968-978.
12. Deslandes, L., Olivier, J., Theulieres, F., Hirsch, J., Feng, D.X., Bittner-Eddy, P.D., Beynon, J., and Marco, Y. 2002. Resistance to Ralstonia solanacearum in Arabidopsis thaliana is conferred by the recessive RRS1-R gene, a member of a novel family of resistance genes. Proc. Natl. Acad. Sci. 99: 2404-2409.
13. Dodds, P.N., Lawrence, G.J., and Ellis, J.G. 2001. Six amino acid changes confined to the LRR B-strand/B-turn motif determine the difference between the P and Ps rust resistance specificities in flax. Plant Cell 13: 163-178.
14. Ellis, J., Dodds, P., and Pryor, T. 2000. The generation of plant disease resistance gene specificities. Trends Plant Sci. 5: 373-379.
15. Ellis, J.G., Lawrence, G.J., Luck, J.E., and Dodds, P.N. 1999. Identification of regions in alleles of the flax rust resistance gene L that determine differences in gene-for-gene specificity. Plant Cell 11: 495-506.
16. Glazebrook, J. 2001. Genes controlling expression of defense responses in Arabidopsis-2001 status. Current Opinion in Plant Biology 4: 301-308.
17. Goff, S.A., Ricke, D., Lan, T.H., Presting, G., Wang, R., Dunn, M., Glazebrook, J., Sessions, A., Oeller, P., Varma, H., et al. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica) Science 296: 92-100.
18. Halterman, D.A., Zhou, F., Wei, F., Wise, R., and Schulze-Lefert, P. 2002. The MLA6 coiled-coil, NBS-LRR protein confers AvrMla6-dependent resistance specificity to Blumeria graminis F. sp. hordei in barley and wheat. Plant J. 25: 335-348.
19. Hammond-Kosack, K.E. and Jones, J.D.G. 1997. Plant disease resistance genes. Annual Review of Plant Physiology and Plant Molecular Biology 48: 575-607.
20. Henikoff, S., Henikoff, J.G, Alford, W.J, and Pietrokovski, S. 1995. Automated construction and graphical presentation of protein blocks from unaligned sequences. Gene 163: GC17-GC26.
21. Hulbert, S.H., Webb, C.A., Smith, S.M., and Sun Q. 2001. Resistance gene complexes: Evolution and utilization. Annu. Rev. Phytopathol. 39: 285-312.
22. Jeanmougin, F., Thompson, J.D., Gouy, M., Higgins, D.G., and Gibson, T.J. 1998. Multiple sequence alignment with Clustal X. Trends Biochem. Sci. 23: 403-405.
23. Leister D., Kurth, J., Laurie, D.A., Yano, M., Sasaki, T., Devos, K., Graner, A., and Schulze-Lefert, P. 1998. Rapid reorganization of resistance gene homologues in cereal genomes. Proc. Natl. Acad. Sci. 95: 370-375.
24. Letunic, I., Goodstadt, L., Dickens, N.J., Doerks, T., Schultz, J., Mott, R., Ciccarelli, F., Copley, R.R., Ponting, C.P., and Bork, P. 2002. Recent improvements to the SMART domain-based sequence annotation resource. Nucleic Acids Res. 30: 242-244.
25. Luck, J.E., Lawrence, G.L., Dodds, P.N., Shepherd, K.W., and Ellis, J.G. 2000. Regions outside of the leucine-rich repeats of flax rust resistance proteins play a role in specificity determination. Plant Cell 12: 1367-1377.
26. Lupas, A., Van Dyke, M., and Stock, J. 1991. Predicting coiled coils from protein sequences. Science 252: 1162-1164.
27. McDowell, J.M., Dhandaydham, M., Long, T.A., Aarts, M.G., Goff, S., Holub, E.B., and Dangl, J.L. 1998. Intragenic recombination and diversifying selection contribute to the evolution of downy mildew resistance at the RPP8 locus of Arabidopsis. Plant Cell 10: 1861-1874.
28. Meyers, B.C., Shen, K.A., Rohani, P., Gaut, B.S., and Michelmore, R.W. 1998. Receptor-like genes in the major resistance locus of lettuce are subject to divergent selection. Plant Cell 11: 1833-1846.
29. Meyers, B.C., Dickerman, A.W., Michelmore, R.W., Pecherer, R.M., 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.
30. Meyers, B.C., Morgante, M., and Michelmore, R.W. 2002. 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 J. 32: 77-92.
31. Michelmore, R.W. and Meyers, B.C. 1998. Clusters of resistance genes in plants evolve by divergent selection and a birth-and-death process. Genome Res. 8: 1113-1130.
32. Nicholas, K.B., Nicholas Jr., H.B., and Deerfield II, D.W. 1997. GeneDoc: Analysis and Visualization of Genetic Variation. EMBNEW NEWS 4: 14.
33. Page, R.D.M. 1996. TREEVIEW: An application to display phylogenetic trees on personal computers. Comput. Appl. Biosci. 12: 357-358.
34. Pan, Q., Liu, Y.-S., Budai-Hadrian, O., Sela, M., Carmel-Goren, L., Zamir, D., and Fluhr, R. 2000a. Comparative genetics of nucleotide binding site-leucine rich repeat resistance gene homologues in the genomes of two dicotyledons: Tomato and Arabidopsis. Genetics 155: 309-322.
35. Pan, Q., Wendel, J., and Fluhr, R. 2000b. Divergent evolution of plant NBS-LRR resistance gene homologues in dicot and cereal genomes. J. Mol. Evol. 50: 203-213.
36. Parniske, M., Hammond-Kosack, K.E., Golstein, C., Thomas, C.M., Jones, D.A., Harrison, K., Wulff, B.B.H., and Jones, J.D.G. 1997. Novel disease resistance specificities result from sequence exchange between tandemly repeated genes at the Cf-4/9 locus of tomato. Cell 91: 821-832.
37. Perrièe, G. and Gouy, M. 1996. WWW-Query: An on-line retrieval system for biological sequence banks. Biochimie 78: 364-369.
38. Solovyev V.V. 2001. Statistical approaches in Eukaryotic gene prediction. In Handbook of statistical genetics (eds. D. Balding, et al.), pp. 83-127. John Wiley & Sons, Ltd., New York, NY.
39. Sun, Q., Collins, N.C., Ayliffe, M., Smith, S.M., Drake, J., Pryor, A., and Hulbert, S.H. 2001. Recombination between paralogues at the rp1 rust resistance locus in maize. Genetics 158: 423-438.
40. Swofford, D.L. 2002. PAUP. Phylogenetic Analysis Using Parsimony. Version 4. Sinauer Associates, Sunderland, Massachusetts.
41. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., and Higgins, D.G. 1997. The ClustalX windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24: 4876-4882.
42. Wang, Z.X., Yano, M., Yamanouchi, U., Iwamoto, M., Monna, L., Hayasaka, H., Katayose, Y., and Sasaki, T. 1999. The Pib gene for rice blast resistance belongs to the nucleotide binding and leucine-rich repeat class of plant disease resistance genes. Plant J. 19: 55-64.
43. Webb, C.A., Richter, T.E., Collins, N.C., Nicolas, M., Trick, H.N., Pryor, T., and Hulbert, S.H. 2002. Genetic and molecular characterization of the maize rp3 rust resistance locus. Genetics 162: 381-394.
44. Yoshimura, S., Yamanouchi, U., Katayose, Y., Toki, S., Wang, Z.-X., Kono, I., Yano, M., Iwata, N., and Sasaki, T. 1998. Expression of Xa1, a bacterial blight-resistance gene in rice, is induced by bacterial inoculation. Proc. Natl. Acad. Sci. 95: 1663-1668.
45. Young, N.D. 2000. The genetic architecture of resistance. Curr. Opin. Plant Biol. 3: 285-290.
46. Yu, J., Hu, S., Wang, J., Wong, K.-S.-G., Li, S., Liu, B., Deng, Y., Dai, L., Zhou, Y., Zhang, X., et al. 2002. A draft sequence of the rice genome (Oryza sativa ssp. indica). Science 296: 79-92.
47. Zhou, F., Kurth, J., Wei, F., Elliott, C., Vale, G., Yahiaoui, N., Keller, B., Somerville, S., Wise, R., and Schulze-Lefert, P. 2000. Cell-autonomous expression of barley Mla1 confers race-specific resistance to the powdery mildew fungus via a Rar1 independent signaling pathway. Plant Cell 13: 337-350.