Plant Molecular Biology

, Volume 74, Issue 6, pp 549–562 | Cite as

Role of OsNPR1 in rice defense program as revealed by genome-wide expression analysis

  • Shoji Sugano
  • Chang-Jie Jiang
  • Shin-Ichi Miyazawa
  • Chisato Masumoto
  • Katsumi Yazawa
  • Nagao Hayashi
  • Masaki Shimono
  • Akira Nakayama
  • Mitsue Miyao
  • Hiroshi Takatsuji


NPR1 is a central regulator of salicylic-acid (SA)-mediated defense signaling in Arabidopsis. Here, we report the characterization of OsNPR1, an Oryzae sativa (rice) ortholog of NPR1, focusing on its role in blast disease resistance and identification of OsNPR1-regulated genes. Blast resistance tests using OsNPR1 knockdown and overexpressing rice lines demonstrated the essential role of OsNPR1 in benzothiadiazole (BTH)-induced blast resistance. Genome-wide transcript profiling using OsNPR1-knockdown lines revealed that 358 genes out of 1,228 BTH-upregulated genes and 724 genes out of 1,069 BTH-downregulated genes were OsNPR1-dependent with respect to BTH responsiveness, thereby indicating that OsNPR1 plays a more vital role in gene downregulation. The OsNPR1-dependently downregulated genes included many of those involved in photosynthesis and in chloroplast translation and transcription. Reduction of photosynthetic activity after BTH treatment and its negation by OsNPR1 knockdown were indeed reflected in the changes in Fv/Fm values in leaves. These results imply the role of OsNPR1 in the reallocation of energy and resources during defense responses. We also examined the OsNPR1-dependence of SA-mediated suppression of ABA-induced genes.


Benzothiadiazole Blast resistance OsNPR1 NPR1 Photosynthesis Abscisic acid 



This work was supported by grants from the Ministry of Agriculture, Forestry, and Fisheries of Japan (Green Technology Project, IP-4006, and Genomics for Agricultural Innovation, PMI-0008). We are grateful for the excellent technical support provided by Ms. M. Ishikawa and Ms. T. Yasuhara. We thank Prof. K. Shimamoto for providing the RNAi vector pANDA; Dr. S. Toki and Ms. K. Ono, for technical advice; and Mr. T. Numa, for advice on microarray data analysis. We also thank the Rice Genome Resource Center at NIAS for the use of the rice microarray analysis system, as well as Dr. Y. Nagamura and Ms. R. Motoyama for their technical support.

Supplementary material

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Supplementary material 1 (XLS 392 kb)
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Supplementary material 2 (XLS 408 kb)
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Supplementary material 3 (PDF 303 kb)
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Supplementary material 4 (PDF 681 kb)
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Supplementary material 5 (DOCX 12 kb)


  1. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Royal Statistical Soc B57:289–300Google Scholar
  2. Blanco F, Salinas P, Cecchini N, Jordana X, Van Hummelen P, Alvarez M, Holuigue L (2009) Early genomic responses to salicylic acid in Arabidopsis. Plant Mol Biol 70:79–102PubMedCrossRefGoogle Scholar
  3. Cao H, Bowling SA, Gordon AS, Dong X (1994) Characterization of an Arabidopsis mutant that is nonresponsive to inducers of systemic acquired resistance. Plant Cell 6:1583–1592PubMedCrossRefGoogle Scholar
  4. Chern MS, Fitzgerald HA, Yadav RC, Canlas PE, Dong X, Ronald PC (2001) Evidence for a disease-resistance pathway in rice similar to the NPR1-mediated signaling pathway in Arabidopsis. Plant J 27:101–113PubMedCrossRefGoogle Scholar
  5. Chern M, Fitzgerald HA, Canlas PE, Navarre DA, Ronald PC (2005) Overexpression of a rice NPR1 homolog leads to constitutive activation of defense response and hypersensitivity to light. Mol Plant-Microbe Interact 18:511–520PubMedCrossRefGoogle Scholar
  6. Conrath U, Pieterse CM, Mauch-Mani B (2002) Priming in plant-pathogen interactions. Trends Plant Sci 7:210–216PubMedCrossRefGoogle Scholar
  7. Delaney TP, Friedrich L, Ryals JA (1995) Arabidopsis signal transduction mutant defective in chemically and biologically induced disease resistance. Proc Natl Acad Sci USA 92:6602–6606PubMedCrossRefGoogle Scholar
  8. Despres C, Chubak C, Rochon A, Clark R, Bethune T, Desveaux D, Fobert PR (2003) The Arabidopsis NPR1 disease resistance protein is a novel cofactor that confers redox regulation of DNA binding activity to the basic domain/leucine zipper transcription factor TGA1. Plant Cell 15:2181–2191PubMedCrossRefGoogle Scholar
  9. Fan W, Dong X (2002) In vivo interaction between NPR1 and transcription factor TGA2 leads to salicylic acid-mediated gene activation in Arabidopsis. Plant Cell 14:1377–1389PubMedCrossRefGoogle Scholar
  10. Fitzgerald HA, Chern MS, Navarre R, Ronald PC (2004) Overexpression of (At)NPR1 in rice leads to a BTH- and environment-induced lesion-mimic/cell death phenotype. Mol Plant-Microbe Interact 17:140–151PubMedCrossRefGoogle Scholar
  11. Gene-Ontology-Consortium (2006) The Gene Ontology (GO) project in 2006. Nucleic Acids Res 34:D322–D326CrossRefGoogle Scholar
  12. Gorlach J, Volrath S, Knauf-Beiter G, Hengy G, Beckhove U, Kogel KH, Oostendorp M, Staub T, Ward E, Kessmann H, Ryals J (1996) Benzothiadiazole, a novel class of inducers of systemic acquired resistance, activates gene expression and disease resistance in wheat. Plant Cell 8:629–643PubMedCrossRefGoogle Scholar
  13. Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel S, Fisk DG, Hirschman JE, Hong EL, Nash RS, Sethuraman A, Theesfeld CL, Botstein D, Dolinski K, Feierbach B, Berardini T, Mundodi S, Rhee SY, Apweiler R, Barrell D, Camon E, Dimmer E, Lee V, Chisholm R, Gaudet P, Kibbe W, Kishore R, Schwarz EM, Sternberg P, Gwinn M, Hannick L, Wortman J, Berriman M, Wood V, De la Cruz N, Tonellato P, Jaiswal P, Seigfried T, White R (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 32:D258–D261PubMedCrossRefGoogle Scholar
  14. Heidel AJ, Dong X (2006) Fitness benefits of systemic acquired resistance during Hyaloperonospora parasitica infection in Arabidopsis thaliana. Genetics 173:1621–1628PubMedCrossRefGoogle Scholar
  15. Heidel AJ, Clarke JD, Antonovics J, Dong X (2004) Fitness costs of mutations affecting the systemic acquired resistance pathway in Arabidopsis thaliana. Genetics 168:2197–2206PubMedCrossRefGoogle Scholar
  16. Ishizaki Y, Tsunoyama Y, Hatano K, Ando K, Kato K, Shinmyo A, Kobori M, Takeba G, Nakahira Y, Shiina T (2005) A nuclear-encoded sigma factor, Arabidopsis SIG6, recognizes sigma-70 type chloroplast promoters and regulates early chloroplast development in cotyledons. Plant J 42:133–144PubMedCrossRefGoogle Scholar
  17. Jiang CJ, Shimono M, Sugano S, Kojima M, Yazawa K, Yoshida R, Inoue H, Hayashi N, Sakakibara H, Takatsuji H (2010) Abscisic acid interacts antagonistically with salicylic acid signaling pathway in rice-Magnaporthe grisea interaction. Mol Plant-Microbe Interact 23:791–798PubMedCrossRefGoogle Scholar
  18. Johnson C, Boden E, Arias J (2003) Salicylic acid and NPR1 induce the recruitment of trans-activating TGA factors to a defense gene promoter in Arabidopsis. Plant Cell 15:1846–1858PubMedCrossRefGoogle Scholar
  19. Kanamaru K, Nagashima A, Fujiwara M, Shimada H, Shirano Y, Nakabayashi K, Shibata D, Tanaka K, Takahashi H (2001) An Arabidopsis sigma factor (SIG2)-dependent expression of plastid-encoded tRNAs in chloroplasts. Plant Cell Physiol 42:1034–1043PubMedCrossRefGoogle Scholar
  20. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res 32:D277–D280PubMedCrossRefGoogle Scholar
  21. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res 36:D480–D484PubMedCrossRefGoogle Scholar
  22. Kasai K, Kawagishi-Kobayashi M, Teraishi M, Ito Y, Ochi K, Wakasa K, Tozawa Y (2004) Differential expression of three plastidial sigma factors, OsSIG1, OsSIG2A, and OsSIG2B, during leaf development in rice. Biosci Biotechnol Biochem 68:973–977PubMedCrossRefGoogle Scholar
  23. Kinkema M, Fan W, Dong X (2000) Nuclear localization of NPR1 is required for activation of PR gene expression. Plant Cell 12:2339–2350PubMedCrossRefGoogle Scholar
  24. Lawton KA, Friedrich L, Hunt M, Weymann K, Delaney T, Kessmann H, Staub T, Ryals J (1996) Benzothiadiazole induces disease resistance in Arabidopsis by activation of the systemic acquired resistance signal transduction pathway. Plant J 10:71–82PubMedCrossRefGoogle Scholar
  25. Lerdau M (1992) Future discounts and resource-allocation in plants. Funct Ecology 6:371–375CrossRefGoogle Scholar
  26. Miki D, Shimamoto K (2004) Simple RNAi vectors for stable and transient suppression of gene function in rice. Plant Cell Physiol 45:490–495PubMedCrossRefGoogle Scholar
  27. Miki D, Itoh R, Shimamoto K (2005) RNA silencing of single and multiple members in a gene family of rice. Plant Physiol 138:1903–1913PubMedCrossRefGoogle Scholar
  28. Mou Z, Fan W, Dong X (2003) Inducers of plant systemic acquired resistance regulate NPR1 function through redox changes. Cell 113:935–944PubMedCrossRefGoogle Scholar
  29. Nettleton D (2006) A discussion of statistical methods for design and analysis of microarray experiments for plant scientists. Plant Cell 18:2112–2121PubMedCrossRefGoogle Scholar
  30. Qi M, Yang Y (2002) Quantification of Magnaporthe grisea during infection of rice plants using real-time polymerase chain reaction and northern blot/phosphoimaging analyses. Phytopathology 92:870–876PubMedCrossRefGoogle Scholar
  31. Quilis J, Penas G, Messeguer J, Brugidou C, San Segundo B (2008) The Arabidopsis AtNPR1 inversely modulates defense responses against fungal, bacterial, or viral pathogens while conferring hypersensitivity to abiotic stresses in transgenic rice. Mol Plant-Microbe Interact 21:1215–1231PubMedCrossRefGoogle Scholar
  32. Ryals JA, Neuenschwander UH, Willits MG, Molina A, Steiner HY, Hunt MD (1996) Systemic acquired resistance. Plant Cell 8:1809–1819PubMedCrossRefGoogle Scholar
  33. Schloles J (1992) Photosynthesis: cellular and tissue aspects in diseased leaves. In: Ayres P (ed) Pests and pathogens. Bios Scientific Publishers, Oxford, pp 85–106Google Scholar
  34. Shah J, Tsui F, Klessig DF (1997) Characterization of a salicylic acid-insensitive mutant (sai1) of Arabidopsis thaliana, identified in a selective screen utilizing the SA-inducible expression of the tms2 gene. Mol Plant-Microbe Interact 10:69–78PubMedCrossRefGoogle Scholar
  35. 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 20:247–254PubMedCrossRefGoogle Scholar
  36. Shimono M, Sugano S, Nakayama A, Jiang CJ, Ono K, Toki S, Takatsuji H (2007) Rice WRKY45 plays a crucial role in benzothiadiazole-inducible blast resistance. Plant Cell 19:2064–2076PubMedCrossRefGoogle Scholar
  37. Shobbar ZS, Oane R, Gamuyao R, De Palma J, Malboobi MA, Karimzadeh G, Javaran MJ, Bennett J (2008) Abscisic acid regulates gene expression in cortical fiber cells and silica cells of rice shoots. New Phytol 178:68–79PubMedCrossRefGoogle Scholar
  38. Silverman P, Seskar M, Kanter D, Schweizer P, Metraux JP, Raskin I (1995) Salicylic acid in rice: biosynthesis, conjugation, and possible role. Plant Physiol 108:633–639PubMedGoogle Scholar
  39. Somssich IE, Hahlbrock K (1998) Pathogen defence in plants—a paradigm of biological complexity. Trends Plant Sci 3:86–90CrossRefGoogle Scholar
  40. Spoel SH, Mou Z, Tada Y, Spivey NW, Genschik P, Dong X (2009) Proteasome-mediated turnover of the transcription coactivator NPR1 plays dual roles in regulating plant immunity. Cell 137:860–872PubMedCrossRefGoogle Scholar
  41. Toki S, Hara N, Ono K, Onodera H, Tagiri A, Oka S, Tanaka H (2006) Early infection of scutellum tissue with Agrobacterium allows high speed transformation of rice. Plant J 47:969–976PubMedCrossRefGoogle Scholar
  42. van Hulten M, Pelser M, van Loon LC, Pieterse CM, Ton J (2006) Costs and benefits of priming for defense in Arabidopsis. Proc Natl Acad Sci USA 103:5602–5607PubMedCrossRefGoogle Scholar
  43. Wang D, Amornsiripanitch N, Dong X (2006) A genomic approach to identify regulatory nodes in the transcriptional network of systemic acquired resistance in plants. PLoS Pathog 2:e123PubMedCrossRefGoogle Scholar
  44. Wang D, Pajerowska-Mukhtar K, Culler AH, Dong X (2007) Salicylic acid inhibits pathogen growth in plants through repression of the auxin signaling pathway. Curr Biol 17:1784–1790PubMedCrossRefGoogle Scholar
  45. Yang Y, Qi M, Mei C (2004) Endogenous salicylic acid protects rice plants from oxidative damage caused by aging as well as biotic and abiotic stress. Plant J 40:909–919PubMedCrossRefGoogle Scholar
  46. Yasuda M, Ishikawa A, Jikumaru Y, Seki M, Umezawa T, Asami T, Maruyama-Nakashita A, Kudo T, Shinozaki K, Yoshida S, Nakashita H (2008) Antagonistic interaction between systemic acquired resistance and the abscisic acid-mediated abiotic stress response in Arabidopsis. Plant Cell 20:1678–1692PubMedCrossRefGoogle Scholar
  47. Yuan Y, Zhong S, Li Q, Zhu Z, Lou Y, Wang L, Wang J, Wang M, Li Q, Yang D, He Z (2007) Functional analysis of rice NPR1-like genes reveals that OsNPR1/NH1 is the rice orthologue conferring disease resistance with enhanced herbivore susceptibility. Plant Biotechnol J 5:313–324PubMedCrossRefGoogle Scholar
  48. Zhang Y, Fan W, Kinkema M, Li X, Dong X (1999) Interaction of NPR1 with basic leucine zipper protein transcription factors that bind sequences required for salicylic acid induction of the PR-1 gene. Proc Natl Acad Sci USA 96:6523–6528PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Shoji Sugano
    • 1
  • Chang-Jie Jiang
    • 1
  • Shin-Ichi Miyazawa
    • 2
  • Chisato Masumoto
    • 2
  • Katsumi Yazawa
    • 1
  • Nagao Hayashi
    • 1
  • Masaki Shimono
    • 1
    • 3
  • Akira Nakayama
    • 1
    • 4
  • Mitsue Miyao
    • 2
  • Hiroshi Takatsuji
    • 1
  1. 1.Plant Disease Resistance Research Unit, Division of Plant SciencesNational Institute of Agrobiological SciencesTsukubaJapan
  2. 2.Photobiology and Photosynthesis Research Unit, Division of Plant SciencesNational Institute of Agrobiological SciencesTsukubaJapan
  3. 3.Department of Plant PathologyMichigan State UniversityEast LansingUSA
  4. 4.Maebashi Institute of TechnologyMaebashiJapan

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