Selective modification of rice (Oryza sativa) gene expression by rice stripe virus infection

Journal of General Virology

Volumn 91, Issue 1, 2010, Pages 294-305

  Satoh, Kouji ^a,b   Kondoh, Hiroaki ^a   Sasaya, Takahide ^b   Shimizu, Takumi ^b   Choi, Il Ryong ^c   Omura, Toshihiro ^b   Kikuchi, Shoshi ^a  

^a NATIONAL INSTITUTE OF AGROBIOLOGICAL SCIENCES   (Japan)

^b NATIONAL AGRICULTURAL RESEARCH CENTER   (Japan)

^c INTERNATIONAL RICE RESEARCH INSTITUTE   (Philippines)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHLOROPLAST; CHLOROSIS; DOWN REGULATION; ENERGY YIELD; GENE EXPRESSION; GENE SILENCING; GENE TARGETING; GENETIC TRANSCRIPTION; HORMONE SYNTHESIS; NECROSIS; NONHUMAN; PLANT VIRUS; PRIORITY JOURNAL; PROTEIN SYNTHESIS; REGULATORY MECHANISM; RICE; RICE STRIPE VIRUS; RICE STRIPE VIRUS INFECTION; UPREGULATION; VIRUS INFECTION; WEAKNESS;

DOWN-REGULATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENES, PLANT; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; ORYZA SATIVA; PLANT DISEASES; PLANT PROTEINS; TENUIVIRUS; UP-REGULATION;

ORYZA SATIVA; RICE STRIPE VIRUS;

EID: 73149085487     PISSN: 00221317     EISSN: 14652099     Source Type: Journal    
DOI: 10.1099/vir.0.015990-0     Document Type: Article

References (72)

1. Amari, K., Díaz-Vivancos, P., Pallás, V., Sánchez-Pina, M. A. & Hernández, J. A. (2007). Oxidative stress induction by Prunus necrotic ringspot virus infection in apricot seeds. Physiol Plant 131, 302-310.
2. Bannai, H., Tamada, Y., Maruyama, O., Nakai, K. & Miyano, S. (2002). Extensive feature detection of N-terminal protein sorting signals. Bioinformatics 18, 298-305.
3. Barrett, T., Troup, D. B., Wilhite, S. E., Ledoux, P., Rudnev, D., Evangelista, C., Kim, I. F., Soboleva, A., Tomashevsky, M. & Edgar, R. (2007). NCBI GEO: mining tens of millions of expression profiles - database and tools update. Nucleic Acids Res 35, D760-D765.
4. Burn, J. E., Hurley, U. A., Birch, R. J., Arioli, T., Cork, A. & Williamson, R. E. (2002). The cellulose-deficient Arabidopsis mutant rsw3 is defective in a gene encoding a putative glucosidase II, an enzyme processing N-glycans during ER quality control. Plant J 32, 949-960.
5. Cabauatan, P. Q., Kobayashi, N., Ikeda, R. & Koganezawa, H. (1993). Oryza glaberrima: an indicator plant for rice tungro spherical virus. Int J Pest Manage 39, 273-276.
6. Chen, X. & Guo, Z. (2008). Tobacco OPBP1 enhances salt tolerance and disease resistance of transgenic rice. Int J Mol Sci 9, 2601-2613.
7. Cheng, Y. Q., Liu, Z. M., Xu, J., Zhou, T., Wang, M., Chen, Y. T., Li, H. F. & Fan, Z. F. (2008). HC-Pro protein of sugar cane mosaic virus interacts specifically with maize ferredoxin-5 in vitro and in planta. J Gen Virol 89, 2046-2054.
8. Coruzzi, G. M. & Zhou, L. (2001). Carbon and nitrogen sensing and signaling in plants: emerging 'matrix effects'. Curr Opin Plant Biol 4, 247-253.
9. Dardick, C. (2007). Comparative expression profiling of Nicotiana benthamiana leaves systemically infected with three fruit tree viruses. Mol Plant Microbe Interact 20, 1004-1017.
10. Díaz-Vivancos, P., Clemente-Moreno, M. J., Rubio, M., Olmos, E., García, J. A., Martínez-Gómez, P. & Hernández, J. A. (2008). Alteration in the chloroplastic metabolism leads to ROS accumulation in pea plants in response to plum pox virus. J Exp Bot 59, 2147-2160.
11. Emanuelsson, O., Brunak, S., von Heijne, G. & Nielsen, H. (2007). Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc 2, 953-971.
12. Espinoza, C., Medina, C., Somerville, S. & Arce-Johnson, P. (2007). Senescence-associated genes induced during compatible viral interactions with grapevine and Arabidopsis. J Exp Bot 58, 3197-3212.
13. Fafournoux, P., Bruhat, A. & Jousse, C. (2000). Amino acid regulation of gene expression. Biochem J 351, 1-12.
14. Falk, B. W. & Tsai, J. H. (1998). Biology and molecular biology of viruses in the genus Tenuivirus. Annu Rev Phytopathol 36, 139-163.
15. Fang, Y., You, J., Xie, K., Xie, W. & Xiong, L. (2008). Systematic sequence analysis and identification of tissue-specific or stress-responsive genes of NAC transcription factor family in rice. Mol Genet Genomics 280, 547-563.
16. Finn, R. D., Tate, J., Mistry, J., Coggill, P. C., Sammut, S. J., Hotz, H. R., Ceric, G., Forslund, K., Eddy, S. R. & other authors (2008). The Pfam protein families database. Nucleic Acids Res 36, D281-D288.
17. Gendler, K., Paulsen, T. & Napoli, C. (2008). ChromDB: the chromatin database. Nucleic Acids Res 36, D298-D302.
18. Golem, S. & Culver, J. N. (2003). Tobacco mosaic virus induced alterations in the gene expression profile of Arabidopsis thaliana. Mol Plant Microbe Interact 16, 681-688.
19. Gutterson, N. & Reuber, T. L. (2004). Regulation of disease resistance pathways by AP2/ERF transcription factors. Curr Opin Plant Biol 7, 465-471.
20. Hedden, P. & Phillips, A. L. (2000). Gibberellin metabolism: new insights revealed by the genes. Trends Plant Sci 5, 523-530.
21. Ishiga, Y., Uppalapati, S. R., Ishiga, T., Elavarthi, S., Martin, B. & Bender, C. L. (2009). The phytotoxin coronatine induces light-dependent reactive oxygen species in tomato seedlings. New Phytol 181, 147-160.
22. Jiménez, I., López, L., Alamillo, J. M., Valli, A. & García, J. A. (2006). Identification of a plum pox virus CI-interacting protein from chloroplast that has a negative effect in virus infection. Mol Plant Microbe Interact 19, 350-358.
23. Kandoth, P. K., Ranf, S., Pancholi, S. S., Jayanty, S., Walla, M. D., Miller, W., Howe, G. A., Lincoln, D. E. & Stratmann, J. W. (2007). Tomato MAPKs LeMPK1, LeMPK2, and LeMPK3 function in the systemin-mediated defense response against herbivorous insects. Proc Natl Acad Sci U S A 104, 12205-12210.
24. Kanehisa, M., Araki, M., Goto, S., Hattori, M., Hirakawa, M., Itoh, M., Katayama, T., Kawashima, S., Okuda, S. & other authors (2008). KEGG for linking genomes to life and the environment. Nucleic Acids Res 36, D480-D484.
25. Kitanaga, Y., Jian, C., Hasegawa, M., Yazaki, J., Kishimoto, N., Kikuchi, S., Nakamura, H., Ichikawa, H., Asami, T. & other authors (2006). Sequential regulation of gibberellin, brassinosteroid, and jasmonic acid biosynthesis occurs in rice coleoptiles to control the transcript levels of anti-microbial thionin genes. Biosci Biotechnol Biochem 70, 2410-2419.
26. Lee, J. & Rudd, J. J. (2002). Calcium-dependent protein kinases: versatile plant signalling components necessary for pathogen defence. Trends Plant Sci 7, 97-98.
27. Lehto, K., Tikkanen, M., Hiriart, J. B., Paakkarinen, V. & Aro, E. M. (2003). Depletion of the photosystem II core complex in mature tobacco leaves infected by the flavum strain of tobacco mosaic virus. Mol Plant Microbe Interact 16, 1135-1144.
28. Levy, A., Dafny-Yelin, M. & Tzfira, T. (2008). Attacking the defenders: plant viruses fight back. Trends Microbiol 16, 194-197.
29. Li, H., Zhou, S. Y., Zhao, W. S., Su, S. C. & Peng, Y. L. (2009). A novel wall-associated receptor-like protein kinase gene, OsWAK1, plays important roles in rice BLAST disease resistance. Plant Mol Biol 69, 337-346.
30. Liang, D., Qu, Z., Ma, X. & Hull, R. (2005). Detection and localization of rice stripe virus gene products in vivo. Virus Genes 31, 211-221.
31. Liang, C., Jaiswal, P., Hebbard, C., Avraham, S., Buckler, E. S., Casstevens, T., Hurwitz, B., McCouch, S., Ni, J. & other authors (2008). Gramene: a growing plant comparative genomics resource. Nucleic Acids Res 36, D947-D953.
32. Loake, G. & Grant, M. (2007). Salicylic acid in plant defence - the players and protagonists. Curr Opin Plant Biol 10, 466-472.
33. Love, A. J., Laval, V., Geri, C., Laird, J., Tomos, A. D., Hooks, M. A. & Milner, J. J. (2007). Components of Arabidopsis defense- and ethylene-signaling pathways regulate susceptibility to cauliflower mosaic virus by restricting long-distance movement. Mol Plant Microbe Interact 20, 659-670.
34. Lu, L., Du, Z., Qin, M., Wang, P., Lan, H., Niu, X., Jia, D., Xie, L., Lin, Q. & other authors (2009). Pc4, a putative movement protein of rice stripe virus, interacts with a type I DnaJ protein and a small Hsp of rice. Virus Genes 38, 320-327.
35. Marathe, R., Guan, Z., Anandalakshmi, R., Zhao, H. & Dinesh-Kumar, S. P. (2004). Study of Arabidopsis thaliana resistome in response to cucumber mosaic virus infection using whole genome microarray. Plant Mol Biol 55, 501-520.
36. Mitsuhara, I., Iwai, T., Seo, S., Yanagawa, Y., Kawahigasi, H., Hirose, S., Ohkawa, Y. & Ohashi, Y. (2008). Characteristic expression of twelve rice PR1 family genes in response to pathogen infection, wounding, and defense-related signal compounds (121/180). Mol Genet Genomics 279, 415-427.
37. Nakashima, K., Tran, L. S., Van Nguyen, D., Fujita, M., Maruyama, K., Todaka, D., Ito, Y., Hayashi, N., Shinozaki, K. & Yamaguchi- Shinozaki, K. (2007). Functional analysis of a NAC-type transcription factor OsNAC6 involved in abiotic and biotic stress-responsive gene expression in rice. Plant J 51, 617-630.
38. Ou, S. H. (1972). Virus diseases. In Rice Diseases, pp. 14-22. Surrey, UK: Commonwealth Mycological Institute.
39. Ouyang, S., Zhu, W., Hamilton, J., Lin, H., Campbell, M., Childs, K., Thibaud-Nissen, F., Malek, R. L., Lee, Y. & other authors (2007). The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Res 35, D883-D887.
40. Radwan, D. E., Lu, G., Fayez, K. A. & Mahmoud, S. Y. (2008). Protective action of salicylic acid against bean yellow mosaic virus infection in Vicia faba leaves. J Plant Physiol 165, 845-857.
41. Raychaudhuri, S., Fontanes, V., Barat, B. & Dasgupta, A. (2009). Activation of ribosomal RNA transcription by hepatitis C virus involves upstream binding factor phosphorylation via induction of cyclin D1. Cancer Res 69, 2057-2064.
42. Riano-Pachon, D. M., Ruzicic, S., Dreyer, I. & Mueller-Roeber, B. (2007). PlnTFDB: an integrative plant transcription factor database. BMC Bioinformatics 8, 42.
43. Rice Annotation Project (2008). The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Res 36, D1028-D1033.
44. Rice Full-length cDNA Consortium (2003). Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science 301, 376-379.
45. Ryu, C. M., Murphy, J. F., Mysore, K. S. & Kloepper, J. W. (2004). Plant growth-promoting rhizobacteria systemically protect Arabidopsis thaliana against cucumber mosaic virus by a salicylic acid and NPR1-independent and jasmonic acid-dependent signaling pathway. Plant J 39, 381-392.
46. Ryu, H. S., Han, M., Lee, S. K., Cho, J. I., Ryoo, N., Heu, S., Lee, Y. H., Bhoo, S. H., Wang, G. L. & other authors (2006). A comprehensive expression analysis of the WRKY gene superfamily in rice plants during defense response. Plant Cell Rep 25, 836-847.
47. Saeed, A. I., Sharov, V., White, J., Li, J., Liang, W., Bhagabati, N., Braisted, J., Klapa, M., Currier, T. & other authors (2003). TM4: a free, open-source system for microarray data management and analysis. Biotechniques 34, 374-378.
48. Satoh, K., Doi, K., Nagata, T., Kishimoto, N., Suzuki, K., Otomo, Y., Kawai, J., Nakamura, M., Hirozane-Kishikawa, T. & other authors (2007). Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray. PLoS One 2, e1235.
49. Senthil, G., Liu, H., Puram, V. G., Clark, A., Stromberg, A. & Goodin, M. M. (2005). Specific and common changes in Nicotiana benthamiana gene expression in response to infection by enveloped viruses. J Gen Virol 86, 2615-2625.
50. Shamir, R., Maron-Katz, A., Tanay, A., Linhart, C., Steinfeld, I., Sharan, R., Shiloh, Y. & Elkon, R. (2005). EXPANDER - an integrative program suite for microarray data analysis. BMC Bioinformatics 6, 232.
51. Shimizu, T., Toriyama, S., Takahashi, M., Akutsu, K. & Yoneyama, K. (1996). Non-viral sequences at the 5′ termini of mRNAs derived from virus-sense and virus-complementary sequences of the ambisense RNA segments of rice stripe tenuivirus. J Gen Virol 77, 541-546.
52. Shimizu, T., Satoh, K., Kikuchi, S. & Omura, T. (2007). The repression of cell wall- and plastid-related genes and the induction of defense-related genes in rice plants infected with rice dwarf virus. Mol Plant Microbe Interact 20, 247-254.
53. Shimono, M., Sugano, S., Nakayama, A., Jiang, C. J., Ono, K., Toki, S. & Takatsuji, H. (2007). Rice WRKY45 plays a crucial role in benzothiadiazole-inducible BLAST resistance. Plant Cell 19, 2064-2076.
54. Shinkai, A. (1977). Rice waika, a new virus disease, and problems related to its occurrence and control. Jpn Agric Res Q 11, 151-155 (in Japanese).
55. Silverstein, K. A., Moskal, W. A., Jr, Wu, H. C., Underwood, B. A., Graham, M. A., Town, C. D. & VandenBosch, K. A. (2007). Small cysteine-rich peptides resembling antimicrobial peptides have been under-predicted in plants. Plant J 51, 262-280.
56. Somerville, C. (2006). Cellulose synthesis in higher plants. Annu Rev Cell Dev Biol 22, 53-78.
57. Syam Prakash, S. R. & Jayabaskaran, C. (2006). Expression and localization of calcium-dependent protein kinase isoforms in chickpea. J Plant Physiol 163, 1135-1149.
58. Takahashi, Y., Omura, T., Shohara, K. & Tsuchizaki, T. (1991). Comparison of four serological methods for practical detection of ten viruses of rice in plants and insects. Plant Dis 75, 458-461.
59. Tameling, W. I. & Baulcombe, D. C. (2007). Physical association of the NB-LRR resistance protein Rx with a Ran GTPase-activating protein is required for extreme resistance to Potato virus X. Plant Cell 19, 1682-1694.
60. Todeschini, A. L., Morillon, A., Springer, M. & Lesage, P. (2005). Severe adenine starvation activates Ty1 transcription and retrotransposition in Saccharomyces cerevisiae. Mol Cell Biol 25, 7459-7472.
61. Uzarowska, A., Dionisio, G., Sarholz, B., Piepho, H. P., Xu, M., Ingvardsen, C. R., Wenzel, G. & Lübberstedt, T. (2009). Validation of candidate genes putatively associated with resistance to SCMV and MDMV in maize (Zea mays L.) by expression profiling. BMC Plant Biol 9, 15.
62. van Loon, L. C., Rep, M. & Pieterse, C. M. (2006). Significance of inducible defense-related proteins in infected plants. Annu Rev Phytopathol 44, 135-162.
63. Wasternack, C. (2007). Jasmonates: an update on biosynthesis, signal transduction and action in plant stress response, growth and development. Ann Bot (Lond) 100, 681-697.
64. Whitham, S. A., Quan, S., Chang, H. S., Cooper, B., Estes, B., Zhu, T., Wang, X. & Hou, Y. M. (2003). Diverse RNA viruses elicit the expression of common sets of genes in susceptible Arabidopsis thaliana plants. Plant J 33, 271-283.
65. Wise, R. P., Moscou, M. J., Bogdanove, A. J. & Whitham, S. A. (2007). Transcript profiling in host-pathogen interactions. Annu Rev Phytopathol 45, 329-369.
66. Xiong, R., Wu, J., Zhou, Y. & Zhou, X. (2008). Identification of a movement protein of the tenuivirus rice stripe virus. J Virol 82, 12304-12311.
67. Xiong, R., Wu, J., Zhou, Y. & Zhou, X. (2009). Characterization and subcellular localization of an RNA silencing suppressor encoded by rice stripe tenuivirus. Virology 387, 29-40.
68. Yang, C., Guo, R., Jie, F., Nettleton, D., Peng, J., Carr, T., Yeakley, J. M., Fan, J. B. & Whitham, S. A. (2007). Spatial analysis of Arabidopsis thaliana gene expression in response to turnip mosaic virus infection. Mol Plant Microbe Interact 20, 358-370.
69. Yu, F., Fu, A., Aluru, M., Park, S., Xu, Y., Liu, H., Liu, X., Foudree, A., Nambogga, M. & Rodermel, S. (2007). Variegation mutants and mechanisms of chloroplast biogenesis. Plant Cell Environ 30, 350-365.
70. Zhang, F., Kirouac, M., Zhu, N., Hinnebusch, A. G. & Rolfes, R. J. (1997). Evidence that complex formation by Bas1p and Bas2p (Pho2p) unmasks the activation function of Bas1p in an adenine-repressible step of ADE gene transcription. Mol Cell Biol 17, 3272-3283.
71. Zhang, C., Liu, Y., Sun, X., Qian, W., Zhang, D. & Qiu, B. (2008a). Characterization of a specific interaction between IP-L, a tobacco protein localized in the thylakoid membranes, and tomato mosaic virus coat protein. Biochem Biophys Res Commun 374, 253-257.
72. Zhang, X., Wang, X. & Zhou, G. (2008b). A one-step real time RTPCR assay for quantifying rice stripe virus in rice and in the small brown planthopper (Laodelphax striatellus Fallen). J Virol Methods 151, 181-187.