Towards establishment of a rice stress response interactome

PLoS Genetics

Volumn 7, Issue 4, 2011, Pages

  Seo, Young Su ^a   Chern, Mawsheng ^a,b   Bartley, Laura E ^a,b   Han, Muho ^c   Jung, Ki Hong ^a,b,c   Lee, Insuk ^d   Walia, Harkamal ^a   Richter, Todd ^a   Xu, Xia ^a   Cao, Peijian ^a   Bai, Wei ^a   Ramanan, Rajeshwari ^a,e   Amonpant, Fawn ^a   Arul, Loganathan ^a   Canlas, Patrick E ^a   Ruan, Randy ^a   Park, Chang Jin ^a   Chen, Xuewei ^a   Hwang, Sohyun ^d   Jeon, Jong Seong ^c   Ronald, Pamela C ^a,b,c   more..

^a UNIVERSITY OF CALIFORNIA   (United States)

^b JOINT BIOENERGY INSTITUTE   (United States)

^c Kyung Hee University   (South Korea)

^d Yonsei University   (South Korea)

^e CENTRE FOR CELLULAR AND MOLECULAR BIOLOGY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

DIHYDRODIPICOLINATE REDUCTASE; MITOGEN ACTIVATED PROTEIN KINASE; NH1 PROTEIN; PROTEIN KINASE; PROTEIN TYROSINE KINASE; SUB1 PROTEIN; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR AP 2; UNCLASSIFIED DRUG; VEGETABLE PROTEIN; XA21 PROTEIN;

ABIOTIC STRESS; AGRONOMIC TRAIT; ARTICLE; BIOTIC STRESS; CROP PRODUCTION; HARVEST; MOLECULAR MECHANICS; NONHUMAN; PHENOTYPE; PLANT STRESS; PREDICTION; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; RICE; SIGNAL TRANSDUCTION; TWO HYBRID SYSTEM; ADAPTATION; GENE EXPRESSION PROFILING; GENETICS; HOST PATHOGEN INTERACTION; IMMUNOLOGY; INNATE IMMUNITY; METABOLISM; MICROBIOLOGY; MOLECULAR CLONING; PATHOGENICITY; PHYSIOLOGICAL STRESS; PLANT DISEASE; PROTEIN ANALYSIS; XANTHOMONAS;

ORYZA SATIVA; POACEAE;

ADAPTATION, PHYSIOLOGICAL; CLONING, MOLECULAR; GENE EXPRESSION PROFILING; HOST-PATHOGEN INTERACTIONS; IMMUNITY, INNATE; ORYZA SATIVA; PHENOTYPE; PLANT DISEASES; PLANT PROTEINS; PROTEIN INTERACTION MAPPING; STRESS, PHYSIOLOGICAL; TRANSCRIPTION FACTORS; TWO-HYBRID SYSTEM TECHNIQUES; XANTHOMONAS;

EID: 79955605835     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1002020     Document Type: Article

References (58)

1. Dhlamini Z, Spillane C, Moss JP, Ruane J, Urquia N, et al. (2005) Status of Research and Application of Crop Biotechnologies in Developing Countries. Rome, Italy Food and Agriculture Oganization of the United Nations Natural Resources Management and Environment Department.
2. Fujita M, Fujita Y, Noutoshi Y, Takahashi F, Narusaka Y, et al. (2006) Crosstalk between abiotic and biotic stress responses: a current view from the points of convergence in the stress signaling networks. Curr Opin Plant Biol 9: 436-442.
3. Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, et al. (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature 437: 1173-1178.
4. Song WY, Wang GL, Chen LL, Kim HS, Pi LY, et al. (1995) A receptor kinase-like protein encoded by the rice disease resistance gene, Xa21. Science 270: 1804-1806.
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: 511-520.
6. Durrant WE, Dong X, (2004) Systemic acquired resistance. Annu Rev Phytopathol 42: 185-209.
7. Xu K, Xu X, Fukao T, Canlas P, Maghirang-Rodriguez R, et al. (2006) Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice. Nature 442: 705-708.
8. Lee SW, Han SW, Sririyanum M, Park CJ, Seo YS, et al. (2009) A type I-secreted, sulfated peptide triggers XA21-mediated innate immunity. Science 326: 850-853.
9. Ronald PC, Beutler B, (2010) Plant and animal host sensors of conserved microbial signatures. Science In Press.
10. Shimono M, Sugano S, Nakayama A, Jiang CJ, Ono K, et al. (2007) Rice WRKY45 plays a crucial role in benzothiadiazole-inducible blast resistance. Plant Cell 19: 2064-2076.
11. Bracha-Drori K, Shichrur K, Katz A, Oliva M, Angelovici R, et al. (2004) Detection of protein-protein interactions in plants using bimolecular fluorescence complementation. Plant J 40: 419-427.
12. Grefen C, Lalonde S, Obrdlik P, (2007) Split-ubiquitin system for identifying protein-protein interactions in membrane and full-length proteins. Curr Protoc Neurosci Chapter 5 (Unit 5): 27.
13. Park CJ, Peng Y, Chen X, Dardick C, Ruan D, et al. (2008) Rice XB15, a protein phosphatase 2C, negatively regulates cell death and XA21-mediated innate immunity. PLoS Biol 6: e231 doi:10.1371/journal.pbio.0060231.
14. Ding X, Richter T, Chen M, Fujii H, Seo YS, et al. (2009) A rice kinase-protein interaction map. Plant Physiol 149: 1478-1492.
15. Nakashima A, Chen L, Thao NP, Fujiwara M, Wong HL, et al. (2008) RACK1 functions in rice innate immunity by interacting with the Rac1 immune complex. Plant Cell 20: 2265-2279.
16. Thao NP, Chen L, Nakashima A, Hara S, Umemura K, et al. (2007) RAR1 and HSP90 form a complex with Rac/Rop GTPase and function in innate-immune responses in rice. Plant Cell 19: 4035-4045.
17. Wong HL, Pinontoan R, Hayashi K, Tabata R, Yaeno T, et al. (2007) Regulation of rice NADPH oxidase by binding of Rac GTPase to its N-terminal extension. Plant Cell 19: 4022-4034.
18. Cheong YH, Moon BC, Kim JK, Kim CY, Kim MC, et al. (2003) BWMK1, a rice mitogen-activated protein kinase, locates in the nucleus and mediates pathogenesis-related gene expression by activation of a transcription factor. Plant Physiol 132: 1961-1972.
19. Zhu S, Tytgat J, (2004) Evolutionary epitopes of Hsp90 and p23: implications for their interaction. FASEB J 18: 940-947.
20. Shirasu K, (2009) The HSP90-SGT1 chaperone complex for NLR immune sensors. Annu Rev Plant Biol 60: 139-164.
21. Chern M, Canlas PE, Fitzgerald HA, Ronald PC, (2005) Rice NRR, a negative regulator of disease resistance, interacts with Arabidopsis NPR1 and rice NH1. Plant J 43: 623-635.
22. Storey JD, Tibshirani R, (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci U S A 100: 9440-9445.
23. Jeong H, Mason SP, Barabasi AL, Oltvai ZN, (2001) Lethality and centrality in protein networks. Nature 411: 41-42.
24. Gandhi TK, Zhong J, Mathivanan S, Karthick L, Chandrika KN, et al. (2006) Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nat Genet 38: 285-293.
25. Park CJ, Han SW, Chen X, Ronald PC, (2010) Elucidation of XA21-mediated innate immunity. Cell Microbiol 12: 1017-1025.
26. de Folter S, Immink RG, Kieffer M, Parenicova L, Henz SR, et al. (2005) Comprehensive interaction map of the Arabidopsis MADS Box transcription factors. Plant Cell 17: 1424-1433.
27. Wang YS, Pi LY, Chen X, Chakrabarty PK, Jiang J, et al. (2006) Rice XA21 binding protein 3 is a ubiquitin ligase required for full Xa21-mediated disease resistance. Plant Cell 18: 3635-3646.
28. Peng Y, Bartley LE, Chen X, Dardick C, Chern M, et al. (2008) OsWRKY62 is a negative regulator of basal and Xa21-mediated defense against Xanthomonas oryzae pv. oryzae in rice. Mol Plant 1: 446-458.
29. Chen X, Chern M, Canlas PE, Ruan D, Jiang C, et al. (2010) An ATPase promotes autophosphorylation of the pattern recognition receptor XA21 and inhibits XA21-mediated immunity. Proc Natl Acad Sci U S A 107: 8029-8034.
30. He X, Zhang J, (2006) Why do hubs tend to be essential in protein networks? PLoS Genet 2: e88 doi:10.1371/journal.pgen.0020088.
31. Luscombe NM, Babu MM, Yu H, Snyder M, Teichmann SA, et al. (2004) Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431: 308-312.
32. Jung KH, Seo YS, Walia H, Cao P, Fukao T, et al. (2010) The submergence tolerance regulator Sub1A mediates stress-responsive expression of AP2/ERF transcription factors. Plant Physiol 152: 1674-1692.
33. Sana TR, Fischer S, Wohlgemuth G, Katrekar A, Jung KH, et al. (2010) Metabolomic and transcriptomic analysis of the rice response to the bacterial blight pathogen Xanthomonas oryzae pv. oryzae. Metabolomics 6: 451-465.
34. Kadota Y, Shirasu K, Guerois R, (2010) NLR sensors meet at the SGT1-HSP90 crossroad. Trends Biochem Sci 35: 199-207.
35. Shang Y, Li X, Cui H, He P, Thilmony R, et al. (2006) RAR1, a central player in plant immunity, is targeted by Pseudomonas syringae effector AvrB. Proc Natl Acad Sci U S A 103: 19200-19205.
36. Chen L, Hamada S, Fujiwara M, Zhu T, Thao NP, et al. (2010) The Hop/Sti1-Hsp90 chaperone complex facilitates the maturation and transport of a PAMP receptor in rice innate immunity. Cell Host Microbe 7: 185-196.
37. Brutus A, Sicilia F, Macone A, Cervone F, De Lorenzo G, (2010) A domain swap approach reveals a role of the plant wall-associated kinase 1 (WAK1) as a receptor of oligogalacturonides. Proc Natl Acad Sci U S A 107: 9452-9457.
38. Chinchilla D, Zipfel C, Robatzek S, Kemmerling B, Nurnberger T, et al. (2007) A flagellin-induced complex of the receptor FLS2 and BAK1 initiates plant defence. Nature 448: 497-500.
39. Xiong L, Yang Y, (2003) Disease resistance and abiotic stress tolerance in rice are inversely modulated by an abscisic acid-inducible mitogen-activated protein kinase. Plant Cell 15: 745-759.
40. Asai T, Tena G, Plotnikova J, Willmann MR, Chiu WL, et al. (2002) MAP kinase signalling cascade in Arabidopsis innate immunity. Nature 415: 977-983.
41. Ren D, Liu Y, Yang KY, Han L, Mao G, et al. (2008) A fungal-responsive MAPK cascade regulates phytoalexin biosynthesis in Arabidopsis. Proc Natl Acad Sci U S A 105: 5638-5643.
42. Shen QH, Saijo Y, Mauch S, Biskup C, Bieri S, et al. (2007) Nuclear activity of MLA immune receptors links isolate-specific and basal disease-resistance responses. Science 315: 1098-1103.
43. Peng Y, Bartley LE, Canlas PE, Ronald PC, (2010) OsWRKY IIa Transcription Factors Modulate Rice Innate Immunity. Rice 3: 36-42.
44. Saiga S, Furumizu C, Yokoyama R, Kurata T, Sato S, et al. (2008) The Arabidopsis OBERON1 and OBERON2 genes encode plant homeodomain finger proteins and are required for apical meristem maintenance. Development 135: 1751-1759.
45. Korfhage U, Trezzini GF, Meier I, Hahlbrock K, Somssich IE, (1994) Plant homeodomain protein involved in transcriptional regulation of a pathogen defense-related gene. Plant Cell 6: 695-708.
46. Century KS, Lagman RA, Adkisson M, Morlan J, Tobias R, et al. (1999) Short communication: developmental control of Xa21-mediated disease resistance in rice. Plant J 20: 231-236.
47. Park CJ, Lee SW, Chern M, Sharma R, Canlas PE, et al. (2010) Ectopic expression of rice Xa21 overcomes developmentally controlled resistance to Xanthomonas oryzae pv. oryzae. Plant Sci 179: 466-471.
48. Halford NG, Hey SJ, (2009) Snf1-related protein kinases (SnRKs) act within an intricate network that links metabolic and stress signalling in plants. Biochem J 419: 247-259.
49. Jossier M, Bouly JP, Meimoun P, Arjmand A, Lessard P, et al. (2009) SnRK1 (SNF1-related kinase 1) has a central role in sugar and ABA signalling in Arabidopsis thaliana. Plant J 59: 316-328.
50. Asselbergh B, De Vleesschauwer D, Hofte M, (2008) Global switches and fine-tuning-ABA modulates plant pathogen defense. Mol Plant Microbe Interact 21: 709-719.
51. Lee I, Lehner B, Crombie C, Wong W, Fraser AG, et al. (2008) A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans. Nat Genet 40: 181-188.
52. Collavin L, Lunardi A, Del Sal G, (2010) p53-family proteins and their regulators: hubs and spokes in tumor suppression. Cell Death Differ 17: 901-911.
53. Hazbun TR, Fields S, (2001) Networking proteins in yeast. Proc Natl Acad Sci U S A 98: 4277-4278.
54. Wang PI, Marcotte EM, (2010) It's the machine that matters: predicting gene function and phenotype from protein networks. J Proteomics 73: 2277-2289.
55. Orchard S, Aranda B, Hermjakob H, (2010) The publication and database deposition of molecular interaction data. Curr Protoc Protein Sci Chapter 25.
56. Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, et al. (2009) NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Res 37: D885-890.
57. Parkinson H, Kapushesky M, Kolesnikov N, Rustici G, Shojatalab M, et al. (2009) ArrayExpress update-from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Res 37: D868-872.
58. Jung KH, Dardick C, Bartley LE, Cao P, Phetsom J, et al. (2008) Refinement of light-responsive transcript lists using rice oligonucleotide arrays: evaluation of gene-redundancy. PLoS ONE 3: e3337 doi:10.1371/journal.pone.0003337.