Structure, function and networks of transcription factors involved in abiotic stress responses

International Journal of Molecular Sciences

Volumn 14, Issue 3, 2013, Pages 5842-5878

  Lindemose, Søren ^a   O'Shea, Charlotte ^a   Jensen, Michael Krogh ^a   Skriver, Karen ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

Abiotic stress; Gene regulatory network; Genetic engineering of crops; Interactome; Protein intrinsic disorder; Transcription factor

Indexed keywords

ABSCISIC ACID; PHYTOHORMONE; PROTEASOME; TRANSCRIPTION FACTOR; UBIQUITIN; UBIQUITIN PROTEIN LIGASE E3;

ABIOTIC STRESS; BIOTIC STRESS; DROUGHT; GENE REGULATORY NETWORK; GENE TARGETING; HIGH TEMPERATURE; NONHUMAN; OSMOLARITY; PLANT STRESS; PLANT YIELD LOSS; PROTEIN DEGRADATION; PROTEIN EXPRESSION; PROTEIN FAMILY; PROTEIN FUNCTION; PROTEIN STRUCTURE; PROTEIN TERTIARY STRUCTURE; REVIEW; SALINITY; SIGNAL TRANSDUCTION; SUMOYLATION;

EID: 84875516131     PISSN: 16616596     EISSN: 14220067     Source Type: Journal    
DOI: 10.3390/ijms14035842     Document Type: Review

References (198)

1. Matsui, A.; Ishida, J.; Morosawa, T.; Mochizuki, Y.; Kaminuma, E.; Endo, T.A.; Okamoto, M.; Nambara, E.; Nakajima, M.; Kawashima, M.; et al. Arabidopsis transcriptome analysis under drought, cold, high-salinity and ABA treatment conditions using a tiling array. Plant Cell Physiol. 2008, 49, 1135-1149.
2. Cutler, S.R.; Rodriguez, P.L.; Finkelstein, R.R.; Abrams, S.R. Abscisic acid: Emergence of a core signaling network. Annu. Rev. Plant Biol. 2010, 61, 651-679.
3. Finkelstein, R.R.; Gampala, S.S.; Rock, C.D. Abscisic acid signaling in seeds and seedlings. Plant Cell. 2002, 14, S15-S45.
4. Udvardi, M.K.; Kakar, K.; Wandrey, M.; Montanari, O.; Murray, J.; Andriankaja, A.; Zhang, J.Y.; Benedito, V.; Hofer, J.M.; Chueng, F.; et al. Legume transcription factors: Global regulators of plant development and response to the environment. Plant Physiol. 2007, 144, 538-549.
5. Kilian, J.; Peschke, F.; Berendzen, K.W.; Harter, K.; Wanke, D. Prerequisites, performance and profits of transcriptional profiling the abiotic stress response. Biochim. Biophys. Acta 2012, 1819, 166-175.
6. Golldack, D.; Lüking, I.; Yang, O. Plant tolerance to draught and salinity: Stress regulating transcription factors and their functional significance in the cellular transcriptional network. Plant Cell Rep. 2011, 30, 1389-1391.
7. Chen, L.; Song, Y.; Li, S.; Zhang, L.; Zou, C.; Yu, D. The role of WRKY transcription factors in plant abiotic stresses. Biochim. Biophys. Acta 2012, 1819, 120-128.
8. Ciftci-Yilmaz, S.; Mittler, R. The zinc finger network of plants. Cell Mol. Life Sci. 2008, 65, 1150-1160.
9. Dubos, C.; Stracke, R.; Grotewold, E.; Weisshaar, B.; Martin, C.; Lepiniec, L. MYB transcription factors in Arabidopsis. Trends Plant Sci. 2010, 15, 573-581.
10. Fujita, Y.; Fujita, M.; Shinozaki, K.; Yamaguchi-Shinozaki, K. ABA-mediated transcriptional regulation in response to osmotic stress in plants. J. Plant Res. 2011, 124, 509-525.
11. Mizoi, J.; Shinozaki, K.; Yamaguchi-Shinozaki, K. AP2/ERF family transcription factors in plant abiotic stress responses. Biochim. Biophys. Acta 2012, 1819, 86-96.
12. Nakashima, K.; Takasaki, H.; Mizoi, J.; Shinozaki, K.; Yamaguchi-Shinozaki, K. NAC transcription factors in plant abiotic stress responses. Biochim. Biophys. Acta 2012, 1819, 97-103.
13. Puranik, S.; Sahu, P.P.; Srivastava, P.S.; Prasad, M. NAC proteins: Regulation and role in stress tolerance. Trends Plant Sci. 2012, 17, 369-381.
14. Rushton, D.L.; Tripathi, P.; Rabara, R.C.; Lin, J.; Ringler, P.; Boken, A.K.; Langum, T.J.; Smidt, L.; Boomsma, D.D.; Emme, N.J.; et al. WRKY transcription factors: Key components in abscisic acid signalling. Plant Biotechnol. J. 2012, 10, 2-11.
15. Umezawa, T.; Nakashima, K.; Miyakawa, T.; Kuromori, T.; Tanokura, M.; Shinozaki, K.; Yamaguchi-Shinozaki, K. Molecular basis of the core regulatory network in ABA responses: Sensing, signaling and transport. Plant Cell Physiol. 2010, 51, 1821-1839.
16. Gene Ontology search tool. Available online: http://www.arabidopsis.org/tools/bulk/go/index.jsp (accessed on 27 February 2013).
17. Jakoby, M.; Weisshaar, B.; Droge-Laser, W.; Vicente-Carbajosa, J.; Tiedemann, J.; Kroj, T.; Parcy, F. bZIP transcription factors in Arabidopsis. Trends Plant Sci. 2002, 7, 106-111.
18. Kang, J.Y.; Choi, H.I.; Im, M.Y.; Kim, S.Y. Arabidopsis basic leucine zipper proteins that mediate stress-responsive abscisic acid signaling. Plant Cell. 2002, 14, 343-357.
19. Fujita, Y.; Fujita, M.; Satoh, R.; Maruyama, K.; Parvez, M.M.; Seki, M.; Hiratsu, K.; Ohme-Takagi, M.; Shinozaki, K.; Yamaguchi-Shinozaki, K. AREB1 is a transcription activator of novel ABRE-dependent ABA signaling that enhances drought stress tolerance in Arabidopsis. Plant Cell. 2005, 17, 3470-3488.
20. Uno, Y.; Furihata, T.; Abe, H.; Yoshida, R.; Shinozaki, K.; Yamaguchi-Shinozaki, K. Arabidopsis basic leucine zipper transcription factors involved in an abscisic acid-dependent signal transduction pathway under drought and high-salinity conditions. Proc. Natl. Acad. Sci. USA 2000, 97, 11632-11637.
21. Yoshida, T.; Fujita, Y.; Sayama, H.; Kidokoro, S.; Maruyama, K.; Mizoi, J.; Shinozaki, K.; Yamaguchi-Shinozaki, K. AREB1, AREB2, and ABF3 are master transcription factors that cooperatively regulate ABRE-dependent ABA signaling involved in drought stress tolerance and require ABA for full activation. Plant J. 2010, 61, 672-685.
22. Kim, J.S.; Mizoi, J.; Yoshida, T.; Fujita, Y.; Nakajima, J.; Ohori, T.; Todaka, D.; Nakashima, K.; Hirayama, T.; Shinozaki, K.; et al. An ABRE promoter sequence is involved in osmotic stress-responsive expression of the DREB2A gene, which encodes a transcription factor regulating drought-inducible genes in Arabidopsis. Plant Cell Physiol. 2011, 52, 2136-2146.
23. Miura, K.; Lee, J.; Jin, J.B.; Yoo, C.Y.; Miura, T.; Hasegawa, P.M. Sumoylation of ABI5 by the Arabidopsis SUMO E3 ligase SIZ1 negatively regulates abscisic acid signaling. Proc. Natl. Acad. Sci. USA 2009, 106, 5418-5423.
24. Finkelstein, R.R. Maternal Effects Govern Variable Dominance of Two Abscisic Acid Response Mutations in Arabidopsis thaliana. Plant Physiol. 1994, 105, 1203-1208.
25. Nakashima, K.; Fujita, Y.; Katsura, K.; Maruyama, K.; Narusaka, Y.; Seki, M.; Shinozaki, K.; Yamaguchi-Shinozaki, K. Transcriptional regulation of. Plant Mol Biol. 2006, 60, 51-68.
26. Kim, S.Y.; Ma, J.; Perret, P.; Li, Z.; Thomas, T.L. Arabidopsis ABI5 subfamily members have distinct DNA-binding and transcriptional activities. Plant Physiol. 2002, 130, 688-697.
27. Finkelstein, R.; Gampala, S.S.; Lynch, T.J.; Thomas, T.L.; Rock, C.D. Redundant and distinct functions of the ABA response loci ABA-INSENSITIVE(ABI)5 and ABRE-BINDING FACTOR (ABF)3. Plant Mol. Biol. 2005, 59, 253-267.
28. Bensmihen, S.; Rippa, S.; Lambert, G.; Jublot, D.; Pautot, V.; Granier, F.; Giraudat, J.; Parcy, F. The homologous ABI5 and EEL transcription factors function antagonistically to fine-tune gene expression during late embryogenesis. Plant Cell. 2002, 14, 1391-1403.
29. Lopez-Molina, L.; Mongrand, S.; McLachlin, D.T.; Chait, B.T.; Chua, N.H. ABI5 acts downstream of ABI3 to execute an ABA-dependent growth arrest during germination. Plant J. 2002, 32, 317-328.
30. Liu, J.X.; Srivastava, R.; Che, P.; Howell, S.H. Salt stress responses in Arabidopsis utilize a signal transduction pathway related to endoplasmic reticulum stress signaling. Plant J. 2007, 51, 897-909.
31. Yang, O.; Popova, O.V.; Suthoff, U.; Luking, I.; Dietz, K.J.; Golldack, D. The Arabidopsis basic leucine zipper transcription factor AtbZIP24 regulates complex transcriptional networks involved in abiotic stress resistance. Gene 2009, 436, 45-55.
32. Amir, H.M.; Lee, Y.; Cho, J.I.; Ahn, C.H.; Lee, S.K.; Jeon, J.S.; Kang, H.; Lee, C.H.; An, G.; Park, P.B. The bZIP transcription factor OsABF1 is an ABA responsive element binding factor that enhances abiotic stress signaling in rice. Plant Mol. Biol. 2010, 72, 557-566.
33. Hsieh, T.H.; Li, C.W.; Su, R.C.; Cheng, C.P.; Tsai, Y.C.; Chan, M.T. A tomato bZIP transcription factor, SlAREB, is involved in water deficit and salt stress response. Planta 2010, 231, 1459-1473.
34. Xiang, Y.; Tang, N.; Du, H.; Ye, H.; Xiong, L. Characterization of OsbZIP23 as a key player of the basic leucine zipper transcription factor family for conferring abscisic acid sensitivity and salinity and drought tolerance in rice. Plant Physiol. 2008, 148, 1938-1952.
35. Tang, N.; Zhang, H.; Li, X.; Xiao, J.; Xiong, L. Constitutive activation of transcription factor OsbZIP46 improves drought tolerance in rice. Plant Physiol. 2012, 158, 1755-1768.
36. Gao, S.Q.; Chen, M.; Xu, Z.S.; Zhao, C.P.; Li, L.; Xu, H.J.; Tang, Y.M.; Zhao, X.; Ma, Y.Z. The soybean GmbZIP1 transcription factor enhances multiple abiotic stress tolerances in transgenic plants. Plant Mol. Biol. 2011, 75, 537-553.
37. Liu, Q.; Kasuga, M.; Sakuma, Y.; Abe, H.; Miura, S.; Yamaguchi-Shinozaki, K.; Shinozaki, K. Two transcription factors, DREB1 and DREB2, with an EREBP/AP2 DNA binding domain separate two cellular signal transduction pathways in drought-and low-temperature-responsive gene expression, respectively, in Arabidopsis. Plant Cell. 1998, 10, 1391-1406.
38. Stockinger, E.J.; Gilmour, S.J.; Thomashow, M.F. Arabidopsis thaliana CBF1 encodes an AP2 domain-containing transcriptional activator that binds to the C-repeat/DRE, a cis-acting DNA regulatory element that stimulates transcription in response to low temperature and water deficit. Proc. Natl. Acad. Sci. USA 1997, 94, 1035-1040.
39. Novillo, F.; Medina, J.; Salinas, J. Arabidopsis CBF1 and CBF3 have a different function than CBF2 in cold acclimation and define different gene classes in the CBF regulon. Proc. Natl. Acad. Sci. USA 2007, 104, 21002-21007.
40. Haake, V.; Cook, D.; Riechmann, J.L.; Pineda, O.; Thomashow, M.F.; Zhang, J.Z. Transcription factor CBF4 is a regulator of drought adaptation in Arabidopsis. Plant Physiol. 2002, 130, 639-648.
41. Magome, H.; Yamaguchi, S.; Hanada, A.; Kamiya, Y.; Oda, K. The DDF1 transcriptional activator upregulates expression of a gibberellin-deactivating gene, GA2ox7, under high-salinity stress in Arabidopsis. Plant J. 2008, 56, 613-626.
42. Nakashima, K.; Shinwari, Z.K.; Sakuma, Y.; Seki, M.; Miura, S.; Shinozaki, K.; Yamaguchi-Shinozaki, K. Organization and expression of two Arabidopsis DREB2 genes encoding DRE-binding proteins involved in dehydration-and high-salinity-responsive gene expression. Plant Mol. Biol. 2000, 42, 657-665.
43. Sakuma, Y.; Maruyama, K.; Osakabe, Y.; Qin, F.; Seki, M.; Shinozaki, K.; Yamaguchi-Shinozaki, K. Functional analysis of an Arabidopsis transcription factor, DREB2A, involved in drought-responsive gene expression. Plant Cell. 2006, 18, 1292-1309.
44. Sakuma, Y.; Maruyama, K.; Qin, F.; Osakabe, Y.; Shinozaki, K.; Yamaguchi-Shinozaki, K. Dual function of an Arabidopsis transcription factor DREB2A in water-stress-responsive and heat-stress-responsive gene expression. Proc. Natl. Acad. Sci USA 2006, 103, 18822-18827.
45. Schramm, F.; Larkindale, J.; Kiehlmann, E.; Ganguli, A.; Englich, G.; Vierling, E.; von Koskull-Doring, P. A cascade of transcription factor DREB2A and heat stress transcription factor HsfA3 regulates the heat stress response of Arabidopsis. Plant J. 2008, 53, 264-274.
46. Chen, H.; Hwang, J.E.; Lim, C.J.; Kim, D.Y.; Lee, S.Y.; Lim, C.O. Arabidopsis DREB2C functions as a transcriptional activator of HsfA3 during the heat stress response. Biochem. Biophys. Res. Commun. 2010, 401, 238-244.
47. Lee, S.J.; Kang, J.Y.; Park, H.J.; Kim, M.D.; Bae, M.S.; Choi, H.I.; Kim, S.Y. DREB2C interacts with ABF2, a bZIP protein regulating abscisic acid-responsive gene expression, and its overexpression affects abscisic acid sensitivity. Plant Physiol. 2010, 153, 716-727.
48. Reeves, W.M.; Lynch, T.J.; Mobin, R.; Finkelstein, R.R. Direct targets of the transcription factors ABA-Insensitive(ABI)4 and ABI5 reveal synergistic action by ABI4 and several bZIP ABA response factors. Plant Mol. Biol. 2011, 75, 347-363.
49. Dong, C.J.; Liu, J.Y. The Arabidopsis EAR-motif-containing protein RAP2.1 functions as an active transcriptional repressor to keep stress responses under tight control. BMC Plant Biol. 2010, 10, 47.
50. Krishnaswamy, S.; Verma, S.; Rahman, M.H.; Kav, N.N. Functional characterization of four APETALA2-family genes (RAP2.6, RAP2.6L, DREB19 and DREB26) in Arabidopsis. Plant Mol. Biol. 2011, 75, 107-127.
51. Pandey, G.K.; Grant, J.J.; Cheong, Y.H.; Kim, B.G.; Li, L.; Luan, S. ABR1, an APETALA2-domain transcription factor that functions as a repressor of ABA response in Arabidopsis. Plant Physiol. 2005, 139, 1185-1193.
52. Song, C.P.; Agarwal, M.; Ohta, M.; Guo, Y.; Halfter, U.; Wang, P.; Zhu, J.K. Role of an Arabidopsis AP2/EREBP-type transcriptional repressor in abscisic acid and drought stress responses. Plant Cell. 2005, 17, 2384-2396.
53. Yang, S.; Vanderbeld, B.; Wan, J.; Huang, Y. Narrowing down the targets: Towards successful genetic engineering of drought-tolerant crops. Mol. Plant. 2010, 3, 469-490.
54. Xiao, B.Z.; Chen, X.; Xiang, C.B.; Tang, N.; Zhang, Q.F.; Xiong, L.Z. Evaluation of seven function-known candidate genes for their effects on improving drought resistance of transgenic rice under field conditions. Mol. Plant. 2009, 2, 73-83.
55. Karaba, A.; Dixit, S.; Greco, R.; Aharoni, A.; Trijatmiko, K.R.; Marsch-Martinez, N.; Krishnan, A.; Nataraja, K.N.; Udayakumar, M.; Pereira, A. Improvement of water use efficiency in rice by expression of HARDY, an Arabidopsis drought and salt tolerance gene. Proc. Natl. Acad. Sci. USA 2007, 104, 15270-15275.
56. Cui, M.; Zhang, W.; Zhang, Q.; Xu, Z.; Zhu, Z.; Duan, F.; Wu, R. Induced over-expression of the transcription factor OsDREB2A improves drought tolerance in rice. Plant Physiol. Biochem. 2011, 49, 1384-1391.
57. Jensen, M.K.; Kjaersgaard, T.; Nielsen, M.M.; Galberg, P.; Petersen, K.; O'Shea, C.; Skriver, K. The Arabidopsis thaliana NAC transcription factor family: Structure-function relationships and determinants of ANAC019 stress signalling. Biochem. J. 2010, 426, 183-196.
58. Nuruzzaman, M.; Manimekalai, R.; Sharoni, A.M.; Satoh, K.; Kondoh, H.; Ooka, H.; Kikuchi, S. Genome-wide analysis of NAC transcription factor family in rice. Gene 2010, 465, 30-44.
59. Olsen, A.N.; Ernst, H.A.; Leggio, L.L.; Skriver, K. NAC transcription factors: Structurally distinct, functionally diverse. Trends Plant Sci. 2005, 10, 79-87.
60. Tran, L.S.; Nakashima, K.; Sakuma, Y.; Simpson, S.D.; Fujita, Y.; Maruyama, K.; Fujita, M.; Seki, M.; Shinozaki, K.; Yamaguchi-Shinozaki, K. Isolation and functional analysis of Arabidopsis stress-inducible NAC transcription factors that bind to a drought-responsive cis-element in the early responsive to dehydration stress 1 promoter. Plant Cell. 2004, 16, 2481-2498.
61. Tran, L.S.; Nakashima, K.; Sakuma, Y.; Osakabe, Y.; Qin, F.; Simpson, S.D.; Maruyama, K.; Fujita, Y.; Shinozaki, K.; Yamaguchi-Shinozaki, K. Co-expression of the stress-inducible zinc finger homeodomain ZFHD1 and NAC transcription factors enhances expression of the ERD1 gene in Arabidopsis. Plant J. 2007, 49, 46-63.
62. Fujita, M.; Fujita, Y.; Maruyama, K.; Seki, M.; Hiratsu, K.; Ohme-Takagi, M.; Tran, L.S.; Yamaguchi-Shinozaki, K.; Shinozaki, K. A dehydration-induced NAC protein, RD26, is involved in a novel ABA-dependent stress-signaling pathway. Plant J. 2004, 39, 863-876.
63. Lu, P.L.; Chen, N.Z.; An, R.; Su, Z.; Qi, B.S.; Ren, F.; Chen, J.; Wang, X.C. A novel drought-inducible gene, ATAF1, encodes a NAC family protein that negatively regulates the expression of stress-responsive genes in Arabidopsis. Plant Mol. Biol. 2007, 63, 289-305.
64. Wu, Y.; Deng, Z.; Lai, J.; Zhang, Y.; Yang, C.; Yin, B.; Zhao, Q.; Zhang, L.; Li, Y.; Yang, C.; et al. Dual function of Arabidopsis ATAF1 in abiotic and biotic stress responses. Cell Res. 2009, 19, 1279-1290.
65. Bu, Q.; Jiang, H.; Li, C.B.; Zhai, Q.; Zhang, J.; Wu, X.; Sun, J.; Xie, Q.; Li, C. Role of the Arabidopsis thaliana NAC transcription factors ANAC019 and ANAC055 in regulating jasmonic acid-signaled defense responses. Cell Res. 2008, 18, 756-767.
66. Jiang, H.; Li, H.; Bu, Q.; Li, C. The RHA2a-interacting proteins ANAC019 and ANAC055 may play a dual role in regulating ABA response and jasmonate response. Plant Signal. Behav. 2009, 4, 464-466.
67. He, X.J.; Mu, R.L.; Cao, W.H.; Zhang, Z.G.; Zhang, J.S.; Chen, S.Y. AtNAC2, a transcription factor downstream of ethylene and auxin signaling pathways, is involved in salt stress response and lateral root development. Plant J. 2005, 44, 903-916.
68. Balazadeh, S.; Siddiqui, H.; Allu, A.D.; Matallana-Ramirez, L.P.; Caldana, C.; Mehrnia, M.; Zanor, M.I.; Kohler, B.; Mueller-Roeber, B. A gene regulatory network controlled by the NAC transcription factor ANAC092/AtNAC2/ORE1 during salt-promoted senescence. Plant J. 2010, 62, 250-264.
69. Yang, S.D.; Seo, P.J.; Yoon, H.K.; Park, C.M. The Arabidopsis NAC transcription factor VNI2 integrates abscisic acid signals into leaf senescence via the COR/RD genes. Plant Cell. 2011, 23, 2155-2168.
70. Yamaguchi, M.; Ohtani, M.; Mitsuda, N.; Kubo, M.; Ohme-Takagi, M.; Fukuda, H.; Demura, T. VND-INTERACTING2, a NAC domain transcription factor, negatively regulates xylem vessel formation in Arabidopsis. Plant Cell. 2010, 22, 1249-1263.
71. Seo, P.J.; Kim, M.J.; Park, J.Y.; Kim, S.Y.; Jeon, J.; Lee, Y.H.; Kim, J.; Park, C.M. Cold activation of a plasma membrane-tethered NAC transcription factor induces a pathogen resistance response in Arabidopsis. Plant J. 2010, 61, 661-671.
72. Seo, P.J.; Park, C.M. A membrane-bound NAC transcription factor as an integrator of biotic and abiotic stress signals. Plant Signal. Behav. 2010, 5, 481-483.
73. Kim, S.G.; Lee, A.K.; Yoon, H.K.; Park, C.M. A membrane-bound NAC transcription factor NTL8 regulates gibberellic acid-mediated salt signaling in Arabidopsis seed germination. Plant J. 2008, 55, 77-88.
74. Yoon, H.K.; Kim, S.G.; Kim, S.Y.; Park, C.M. Regulation of leaf senescence by NTL9-mediated osmotic stress signaling in Arabidopsis. Mol. Cells 2008, 25, 438-445.
75. Lee, S.; Seo, P.J.; Lee, H.J.; Park, C.M. A NAC transcription factor NTL4 promotes reactive oxygen species production during drought-induced leaf senescence in Arabidopsis. Plant J. 2012, 70, 831-844.
76. Hu, H.; Dai, M.; Yao, J.; Xiao, B.; Li, X.; Zhang, Q.; Xiong, L. Overexpressing a NAM, ATAF, and CUC (NAC) transcription factor enhances drought resistance and salt tolerance in rice. Proc. Natl. Acad. Sci. USA 2006, 103, 12987-12992.
77. Hu, H.; You, J.; Fang, Y.; Zhu, X.; Qi, Z.; Xiong, L. Characterization of transcription factor gene SNAC2 conferring cold and salt tolerance in rice. Plant Mol. Biol. 2008, 67, 169-181.
78. Nakashima, K.; Tran, L.S.; Van, N.D.; Fujita, M.; Maruyama, K.; Todaka, D.; Ito, Y.; Hayashi, N.; Shinozaki, K.; Yamaguchi-Shinozaki, K. Functional analysis of a NAC-type transcription factor OsNAC6 involved in abiotic and biotic stress-responsive gene expression in rice. Plant J. 2007, 51, 617-630.
79. Takasaki, H.; Maruyama, K.; Kidokoro, S.; Ito, Y.; Fujita, Y.; Shinozaki, K.; Yamaguchi-Shinozaki, K.; Nakashima, K. The abiotic stress-responsive NAC-type transcription factor OsNAC5 regulates stress-inducible genes and stress tolerance in rice. Mol. Genet. Genomics 2010, 284, 173-183.
80. Jeong, J.S.; Kim, Y.S.; Baek, K.H.; Jung, H.; Ha, S.H.; Do, C.Y.; Kim, M.; Reuzeau, C.; Kim, J.K. Root-specific expression of OsNAC10 improves drought tolerance and grain yield in rice under field drought conditions. Plant Physiol. 2010, 153, 185-197.
81. Zheng, X.; Chen, B.; Lu, G.; Han, B. Overexpression of a NAC transcription factor enhances rice drought and salt tolerance. Biochem. Biophys. Res. Commun. 2009, 379, 985-989.
82. Xue, G.P.; Way, H.M.; Richardson, T.; Drenth, J.; Joyce, P.A.; McIntyre, C.L. Overexpression of TaNAC69 leads to enhanced transcript levels of stress up-regulated genes and dehydration tolerance in bread wheat. Mol. Plant. 2011, 4, 697-712.
83. Hao, Y.J.; Wei, W.; Song, Q.X.; Chen, H.W.; Zhang, Y.Q.; Wang, F.; Zou, H.F.; Lei, G.; Tian, A.G.; Zhang, W.K.; et al. Soybean NAC transcription factors promote abiotic stress tolerance and lateral root formation in transgenic plants. Plant J. 2011, 68, 302-313.
84. Eulgem, T.; Rushton, P.J.; Robatzek, S.; Somssich, I.E. The WRKY superfamily of plant transcription factors. Trends Plant Sci. 2000, 5, 199-206.
85. Jiang, Y.; Deyholos, M.K. Functional characterization of Arabidopsis NaCl-inducible WRKY25 and WRKY33 transcription factors in abiotic stresses. Plant Mol. Biol. 2009, 69, 91-105.
86. Li, S.; Fu, Q.; Chen, L.; Huang, W.; Yu, D. Arabidopsis thaliana WRKY25, WRKY26, and WRKY33 coordinate induction of plant thermotolerance. Planta 2011, 233, 1237-1252.
87. Andreasson, E.; Jenkins, T.; Brodersen, P.; Thorgrimsen, S.; Petersen, N.H.; Zhu, S.; Qiu, J.L.; Micheelsen, P.; Rocher, A.; Petersen, M.; et al. The MAP kinase substrate MKS1 is a regulator of plant defense responses. EMBO J. 2005, 24, 2579-2589.
88. Li, S.; Zhou, X.; Chen, L.; Huang, W.; Yu, D. Functional characterization of Arabidopsis thaliana WRKY39 in heat stress. Mol. Cells 2010, 29, 475-483.
89. Zou, C.; Jiang, W.; Yu, D. Male gametophyte-specific WRKY34 transcription factor mediates cold sensitivity of mature pollen in Arabidopsis. J. Exp. Bot. 2010, 61, 3901-3914.
90. Jiang, Y.; Liang, G.; Yu, D. Activated Expression of WRKY57 Confers Drought Tolerance in Arabidopsis. Mol. Plant. 2012, 5, 1375-1388.
91. Ren, X.; Chen, Z.; Liu, Y.; Zhang, H.; Zhang, M.; Liu, Q.; Hong, X.; Zhu, J.K.; Gong, Z. ABO3, a WRKY transcription factor, mediates plant responses to abscisic acid and drought tolerance in Arabidopsis. Plant J. 2010, 63, 417-429.
92. Chen, H.; Lai, Z.; Shi, J.; Xiao, Y.; Chen, Z.; Xu, X. Roles of arabidopsis WRKY18, WRKY40 and WRKY60 transcription factors in plant responses to abscisic acid and abiotic stress. BMC Plant Biol. 2010, 10, 281.
93. Shang, Y.; Yan, L.; Liu, Z.Q.; Cao, Z.; Mei, C.; Xin, Q.; Wu, F.Q.; Wang, X.F.; Du, S.Y.; Jiang, T.; et al. The Mg-chelatase H subunit of Arabidopsis antagonizes a group of WRKY transcription repressors to relieve ABA-responsive genes of inhibition. Plant Cell. 2010, 22, 1909-1935.
94. Liu, Z.Q.; Yan, L.; Wu, Z.; Mei, C.; Lu, K.; Yu, Y.T.; Liang, S.; Zhang, X.F.; Wang, X.F.; Zhang, D.P. Cooperation of three WRKY-domain transcription factors WRKY18, WRKY40, and WRKY60 in repressing two ABA-responsive genes ABI4 and ABI5 in Arabidopsis. J. Exp. Bot. 2012, 63, 6371-6392.
95. Jiang, W.; Yu, D. Arabidopsis WRKY2 transcription factor mediates seed germination and postgermination arrest of development by abscisic acid. BMC Plant Biol. 2009, 9, 96.
96. Wu, X.; Shiroto, Y.; Kishitani, S.; Ito, Y.; Toriyama, K. Enhanced heat and drought tolerance in transgenic rice seedlings overexpressing OsWRKY11 under the control of HSP101 promoter. Plant Cell Rep. 2009, 28, 21-30.
97. Tao, Z.; Kou, Y.; Liu, H.; Li, X.; Xiao, J.; Wang, S. OsWRKY45 alleles play different roles in abscisic acid signalling and salt stress tolerance but similar roles in drought and cold tolerance in rice. J. Exp. Bot. 2011, 62, 4863-4874.
98. Zhou, Q.Y.; Tian, A.G.; Zou, H.F.; Xie, Z.M.; Lei, G.; Huang, J.; Wang, C.M.; Wang, H.W.; Zhang, J.S.; Chen, S.Y. Soybean WRKY-type transcription factor genes, GmWRKY13, GmWRKY21, and GmWRKY54, confer differential tolerance to abiotic stresses in transgenic Arabidopsis plants. Plant Biotechnol. J. 2008, 6, 486-503.
99. Englbrecht, C.C.; Schoof, H.; Bohm, S. Conservation, diversification and expansion of C2H2 zinc finger proteins in the Arabidopsis thaliana genome. BMC Genomics 2004, 5, 39.
100. Ciftci-Yilmaz, S.; Morsy, M.R.; Song, L.; Coutu, A.; Krizek, B.A.; Lewis, M.W.; Warren, D.; Cushman, J.; Connolly, E.L.; Mittler, R. The EAR-motif of the Cys2/His2-type zinc finger protein Zat7 plays a key role in the defense response of Arabidopsis to salinity stress. J. Biol. Chem. 2007, 282, 9260-9268.
101. Lee, H.; Guo, Y.; Ohta, M.; Xiong, L.; Stevenson, B.; Zhu, J.K. LOS2, a genetic locus required for cold-responsive gene transcription encodes a bi-functional enolase. EMBO J. 2002, 21, 2692-2702.
102. Mittler, R.; Kim, Y.; Song, L.; Coutu, J.; Coutu, A.; Ciftci-Yilmaz, S.; Lee, H.; Stevenson, B.; Zhu, J.K. Gain-and loss-of-function mutations in Zat10 enhance the tolerance of plants to abiotic stress. FEBS Lett. 2006, 580, 6537-6542.
103. Vogel, J.T.; Zarka, D.G.; Van Buskirk, H.A.; Fowler, S.G.; Thomashow, M.F. Roles of the CBF2 and ZAT12 transcription factors in configuring the low temperature transcriptome of Arabidopsis. Plant J. 2005, 41, 195-211.
104. Kodaira, K.S.; Qin, F.; Tran, L.S.; Maruyama, K.; Kidokoro, S.; Fujita, Y.; Shinozaki, K.; Yamaguchi-Shinozaki, K. Arabidopsis Cys2/His2 zinc-finger proteins AZF1 and AZF2 negatively regulate abscisic acid-repressive and auxin-inducible genes under abiotic stress conditions. Plant Physiol. 2011, 157, 742-756.
105. Jiang, C.J.; Aono, M.; Tamaoki, M.; Maeda, S.; Sugano, S.; Mori, M.; Takatsuji, H. SAZ, a new SUPERMAN-like protein, negatively regulates a subset of ABA-responsive genes in Arabidopsis. Mol. Genet. Genomics 2008, 279, 183-192.
106. Huang, X.Y.; Chao, D.Y.; Gao, J.P.; Zhu, M.Z.; Shi, M.; Lin, H.X. A previously unknown zinc finger protein, DST, regulates drought and salt tolerance in rice via stomatal aperture control. Genes Dev. 2009, 23, 1805-1817.
107. Xu, D.Q.; Huang, J.; Guo, S.Q.; Yang, X.; Bao, Y.M.; Tang, H.J.; Zhang, H.S. Overexpression of a TFIIIA-type zinc finger protein gene ZFP252 enhances drought and salt tolerance in rice (Oryza sativa L.). FEBS Lett. 2008, 582, 1037-1043.
108. Huang, J.; Sun, S.; Xu, D.; Lan, H.; Sun, H.; Wang, Z.; Bao, Y.; Wang, J.; Tang, H.; Zhang, H. A TFIIIA-type zinc finger protein confers multiple abiotic stress tolerances in transgenic rice (Oryza sativa L.). Plant Mol. Biol. 2012, 80, 337-350.
109. Cominelli, E.; Galbiati, M.; Vavasseur, A.; Conti, L.; Sala, T.; Vuylsteke, M.; Leonhardt, N.; Dellaporta, S.L.; Tonelli, C. A guard-cell-specific MYB transcription factor regulates stomatal movements and plant drought tolerance. Curr. Biol. 2005, 15, 1196-1200.
110. Jung, C.; Seo, J.S.; Han, S.W.; Koo, Y.J.; Kim, C.H.; Song, S.I.; Nahm, B.H.; Choi, Y.D.; Cheong, J.J. Overexpression of AtMYB44 enhances stomatal closure to confer abiotic stress tolerance in transgenic Arabidopsis. Plant Physiol. 2008, 146, 623-635.
111. Jung, C.; Shim, J.S.; Seo, J.S.; Lee, H.Y.; Kim, C.H.; Choi, Y.D.; Cheong, J.J. Non-specific phytohormonal induction of AtMYB44 and suppression of jasmonate-responsive gene activation in Arabidopsis thaliana. Mol. Cells. 2010, 29, 71-86.
112. Seo, P.J.; Xiang, F.; Qiao, M.; Park, J.Y.; Lee, Y.N.; Kim, S.G.; Lee, Y.H.; Park, W.J.; Park, C.M. The MYB96 transcription factor mediates abscisic acid signaling during drought stress response in Arabidopsis. Plant Physiol. 2009, 151, 275-289.
113. Abe, H.; Urao, T.; Ito, T.; Seki, M.; Shinozaki, K.; Yamaguchi-Shinozaki, K. Arabidopsis AtMYC2 (bHLH) and AtMYB2 (MYB) function as transcriptional activators in abscisic acid signaling. Plant Cell. 2003, 15, 63-78.
114. Abe, H.; Yamaguchi-Shinozaki, K.; Urao, T.; Iwasaki, T.; Hosokawa, D.; Shinozaki, K. Role of arabidopsis MYC and MYB homologs in drought-and abscisic acid-regulated gene expression. Plant Cell. 1997, 9, 1859-1868.
115. Agarwal, M.; Hao, Y.; Kapoor, A.; Dong, C.H.; Fujii, H.; Zheng, X.; Zhu, J.K. A R2R3 type MYB transcription factor is involved in the cold regulation of CBF genes and in acquired freezing tolerance. J. Biol. Chem. 2006, 281, 37636-37645.
116. Ding, Z.; Li, S.; An, X.; Liu, X.; Qin, H.; Wang, D. Transgenic expression of MYB15 confers enhanced sensitivity to abscisic acid and improved drought tolerance in Arabidopsis thaliana. J. Genet. Genomics 2009, 36, 17-29.
117. Yang, A.; Dai, X.; Zhang, W.H. A R2R3-type MYB gene, OsMYB2, is involved in salt, cold, and dehydration tolerance in rice. J. Exp. Bot. 2012, 63, 2541-2556.
118. Ma, Q.; Dai, X.; Xu, Y.; Guo, J.; Liu, Y.; Chen, N.; Xiao, J.; Zhang, D.; Xu, Z.; Zhang, X.; et al. Enhanced tolerance to chilling stress in OsMYB3R-2 transgenic rice is mediated by alteration in cell cycle and ectopic expression of stress genes. Plant Physiol. 2009, 150, 244-256.
119. Zhang, Z.; Liu, X.; Wang, X.; Zhou, M.; Zhou, X.; Ye, X.; Wei, X. An R2R3 MYB transcription factor in wheat, TaPIMP1, mediates host resistance to Bipolaris sorokiniana and drought stresses through regulation of defense-and stress-related genes. New Phytol. 2012, 196, 1155-1170.
120. Bailey, P.C.; Martin, C.; Toledo-Ortiz, G.; Quail, P.H.; Huq, E.; Heim, M.A.; Jakoby, M.; Werber, M.; Weisshaar, B. Update on the basic helix-loop-helix transcription factor gene family in Arabidopsis thaliana. Plant Cell. 2003, 15, 2497-2502.
121. Kazan, K.; Manners, J.M. MYC2: The Master in Action. Mol. Plant. 2012, doi:10.1093/mp/sss128.
122. Li, H.; Sun, J.; Xu, Y.; Jiang, H.; Wu, X.; Li, C. The bHLH-type transcription factor AtAIB positively regulates ABA response in Arabidopsis. Plant Mol. Biol. 2007, 65, 655-665.
123. Jiang, Y.; Yang, B.; Deyholos, M.K. Functional characterization of the Arabidopsis bHLH92 transcription factor in abiotic stress. Mol. Genet. Genomics 2009, 282, 503-516.
124. Chinnusamy, V.; Ohta, M.; Kanrar, S.; Lee, B.H.; Hong, X.; Agarwal, M.; Zhu, J.K. ICE1: A regulator of cold-induced transcriptome and freezing tolerance in Arabidopsis. Genes Dev. 2003, 17, 1043-1054.
125. Zhu, Y.; Yang, H.; Mang, H.G.; Hua, J. Induction of BAP1 by a moderate decrease in temperature is mediated by ICE1 in Arabidopsis. Plant Physiol. 2011, 155, 580-588.
126. Kim, J.S.; Mizoi, J.; Kidokoro, S.; Maruyama, K.; Nakajima, J.; Nakashima, K.; Mitsuda, N.; Takiguchi, Y.; Ohme-Takagi, M.; Kondou, Y.; et al. Arabidopsis growth-regulating factor7 functions as a transcriptional repressor of abscisic acid-and osmotic stress-responsive genes, including DREB2A. Plant Cell. 2012, 24, 3393-3405.
127. Yoshida, T.; Ohama, N.; Nakajima, J.; Kidokoro, S.; Mizoi, J.; Nakashima, K.; Maruyama, K.; Kim, J.M.; Seki, M.; Todaka, D.; et al. Arabidopsis HsfA1 transcription factors function as the main positive regulators in heat shock-responsive gene expression. Mol. Genet. Genomics. 2011, 286, 321-332.
128. Park, J.; Lee, N.; Kim, W.; Lim, S.; Choi, G. ABI3 and PIL5 collaboratively activate the expression of SOMNUS by directly binding to its promoter in imbibed Arabidopsis seeds. Plant Cell. 2011, 23, 1404-1415.
129. Yamaguchi-Shinozaki, K.; Shinozaki, K. Organization of cis-acting regulatory elements in osmotic-and cold-stress-responsive promoters. Trends Plant Sci. 2005, 10, 88-94.
130. Tompa, P.; Kovacs, D. Intrinsically disordered chaperones in plants and animals. Biochem. Cell Biol. 2010, 88, 167-174.
131. Luscombe, N.M.; Thornton, J.M. Protein-DNA interactions: Amino acid conservation and the effects of mutations on binding specificity. J. Mol. Biol. 2002, 320, 991-1009.
132. Dyson, H.J.; Wright, P.E. Intrinsically unstructured proteins and their functions. Nat Rev Mol. Cell Biol. 2005, 6, 197-208.
133. Kjaersgaard, T.; Jensen, M.K.; Christiansen, M.W.; Gregersen, P.; Kragelund, B.B.; Skriver, K. Senescence-associated barley NAC (NAM, ATAF1,2, CUC) transcription factor interacts with radical-induced cell death 1 through a disordered regulatory domain. J. Biol. Chem. 2011, 286, 35418-35429.
134. Kragelund, B.B.; Jensen, M.K.; Skriver, K. Order by disorder in plant signaling. Trends Plant Sci. 2012, 17, 625-632.
135. Xue, B.; Dunbrack, R.L.; Williams, R.W.; Dunker, A.K.; Uversky, V.N. PONDR-FIT: A meta-predictor of intrinsically disordered amino acids. Biochim. Biophys. Acta 2010, 1804, 996-1010.
136. Schumacher, M.A.; Goodman, R.H.; Brennan, R.G. The structure of a CREB bZIP. somatostatin CRE complex reveals the basis for selective dimerization and divalent cation-enhanced DNA binding. J. Biol. Chem. 2000, 275, 35242-35247.
137. Skriver, K.; Olsen, F.L.; Rogers, J.C.; Mundy, J. cis-acting DNA elements responsive to gibberellin and its antagonist abscisic acid. Proc. Natl. Acad. Sci. USA 1991, 88, 7266-7270.
138. Nakamura, S.; Lynch, T.J.; Finkelstein, R.R. Physical interactions between ABA response loci of Arabidopsis. Plant J. 2001, 26, 627-635.
139. Yamasaki, K.; Kigawa, T.; Seki, M.; Shinozaki, K.; Yokoyama, S. DNA-binding domains of plant-specific transcription factors: Structure, function, and evolution. Trends Plant Sci. 2012, doi:10.1016/j.tplants.2012.09.001.
140. Allen, M.D.; Yamasaki, K.; Ohme-Takagi, M.; Tateno, M.; Suzuki, M. A novel mode of DNA recognition by a beta-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA. EMBO J. 1998, 17, 5484-5496.
141. Canella, D.; Gilmour, S.J.; Kuhn, L.A.; Thomashow, M.F. DNA binding by the Arabidopsis CBF1 transcription factor requires the PKKP/RAGRxKFxETRHP signature sequence. Biochim. Biophys. Acta 2010, 1799, 454-462.
142. Nole-Wilson, S.; Krizek, B.A. DNA binding properties of the Arabidopsis floral development protein AINTEGUMENTA. Nucleic Acids Res. 2000, 28, 4076-4082.
143. Kagaya, Y.; Ohmiya, K.; Hattori, T. RAV1, a novel DNA-binding protein, binds to bipartite recognition sequence through two distinct DNA-binding domains uniquely found in higher plants. Nucleic Acids Res. 1999, 27, 470-478.
144. Blomberg, J.; Aguilar, X.; Brannstrom, K.; Rautio, L.; Olofsson, A.; Wittung-Stafshede, P.; Bjorklund, S. Interactions between DNA, transcriptional regulator Dreb2a and the Med25 mediator subunit from Arabidopsis thaliana involve conformational changes. Nucleic Acids Res. 2012, 40, 5938-5950.
145. Ernst, H.A.; Olsen, A.N.; Larsen, S.; Lo, L.L. Structure of the conserved domain of ANAC, a member of the NAC family of transcription factors. EMBO Rep. 2004, 5, 297-303.
146. Chen, Q.; Wang, Q.; Xiong, L.; Lou, Z. A structural view of the conserved domain of rice stress-responsive NAC1. Protein Cell. 2011, 2, 55-63.
147. Olsen, A.N.; Ernst, H.A.; Leggio, L.L.; Skriver, K. DNA-binding specificity and molecular finctions of NAC transcription factros. Plant Sci. 2005, 169, 785-797.
148. Welner, D.H.; Lindemose, S.; Grossmann, J.G.; Mollegaard, N.E.; Olsen, A.N.; Helgstrand, C.; Skriver, K.; Lo, L.L. DNA binding by the plant-specific NAC transcription factors in crystal and solution: A firm link to WRKY and GCM transcription factors. Biochem J. 2012, 444, 395-404.
149. Cohen, S.X.; Moulin, M.; Hashemolhosseini, S.; Kilian, K.; Wegner, M.; Muller, C.W. Structure of the GCM domain-DNA complex: A DNA-binding domain with a novel fold and mode of target site recognition. EMBO J. 2003, 22, 1835-1845.
150. Yamasaki, K.; Kigawa, T.; Watanabe, S.; Inoue, M.; Yamasaki, T.; Seki, M.; Shinozaki, K.; Yokoyama, S. Structural basis for sequence-specific DNA recognition by an Arabidopsis WRKY transcription factor. J. Biol. Chem. 2012, 287, 7683-7691.
151. Duan, M.R.; Nan, J.; Liang, Y.H.; Mao, P.; Lu, L.; Li, L.; Wei, C.; Lai, L.; Li, Y.; Su, X.D. DNA binding mechanism revealed by high resolution crystal structure of Arabidopsis thaliana WRKY1 protein. Nucleic Acids Res. 2007, 35, 1145-1154.
152. Yamasaki, K.; Kigawa, T.; Inoue, M.; Tateno, M.; Yamasaki, T.; Yabuki, T.; Aoki, M.; Seki, E.; Matsuda, T.; Tomo, Y.; et al. Solution structure of an Arabidopsis WRKY DNA binding domain. Plant Cell. 2005, 17, 944-956.
153. Rushton, P.J.; Somssich, I.E.; Ringler, P.; Shen, Q.J. WRKY transcription factors. Trends Plant Sci. 2010, 15, 247-258.
154. Maeo, K.; Hayashi, S.; Kojima-Suzuki, H.; Morikami, A.; Nakamura, K. Role of conserved residues of the WRKY domain in the DNA-binding of tobacco WRKY family proteins. Biosci. Biotechnol. Biochem. 2001, 65, 2428-2436.
155. Pavletich, N.P.; Pabo, C.O. Zinc finger-DNA recognition: Crystal structure of a Zif268-DNA complex at 2.1 A. Science 1991, 252, 809-817.
156. Kubo, K.; Sakamoto, A.; Kobayashi, A.; Rybka, Z.; Kanno, Y.; Nakagawa, H.; Takatsuji, H. Cys2/His2 zinc-finger protein family of petunia: Evolution and general mechanism of target-sequence recognition. Nucleic Acids Res. 1998, 26, 608-615.
157. Ogata, K.; Kanei-Ishii, C.; Sasaki, M.; Hatanaka, H.; Nagadoi, A.; Enari, M.; Nakamura, H.; Nishimura, Y.; Ishii, S.; Sarai, A. The cavity in the hydrophobic core of Myb DNA-binding domain is reserved for DNA recognition and trans-activation. Nat. Struct. Biol. 1996, 3, 178-187.
158. Romero, I.; Fuertes, A.; Benito, M.J.; Malpica, J.M.; Leyva, A.; Paz-Ares, J. More than 80R2R3-MYB regulatory genes in the genome of Arabidopsis thaliana. Plant J. 1998, 14, 273-284.
159. Hanaoka, S.; Nagadoi, A.; Nishimura, Y. Comparison between TRF2 and TRF1 of their telomeric DNA-bound structures and DNA-binding activities. Protein Sci. 2005, 14, 119-130.
160. Toledo-Ortiz, G.; Huq, E.; Quail, P.H. The Arabidopsis basic/helix-loop-helix transcription factor family. Plant Cell. 2003, 15, 1749-1770.
161. Ma, P.C.; Rould, M.A.; Weintraub, H.; Pabo, C.O. Crystal structure of MyoD bHLH domain-DNA complex: Perspectives on DNA recognition and implications for transcriptional activation. Cell 1994, 77, 451-459.
162. Fuxreiter, M.; Simon, I.; Bondos, S. Dynamic protein-DNA recognition: Beyond what can be seen. Trends Biochem. Sci. 2001, 36, 415-423.
163. Guo, X.; Bulyk, M.L.; Hartemink, A.J. Intrinsic disorder within and flanking the DNA-binding domains of human transcription factors. Pac. Symp. Biocomput. 2012, 104-115.
164. Fuxreiter, M.; Tompa, P.; Simon, I. Local structural disorder imparts plasticity on linear motifs. Bioinformatics 2007, 23, 950-956.
165. Han, J.D.; Bertin, N.; Hao, T.; Goldberg, D.S.; Berriz, G.F.; Zhang, L.V.; Dupuy, D.; Walhout, A.J.; Cusick, M.E.; Roth, F.P.; et al. Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 2004, 430, 88-93.
166. Han, S.K.; Sang, Y.; Rodrigues, A.; Wu, M.F.; Rodriguez, P.L.; Wagner, D. The SWI2/SNF2 Chromatin Remodeling ATPase BRAHMA Represses Abscisic Acid Responses in the Absence of the Stress Stimulus in Arabidopsis. Plant Cell. 2012, 24, 4892-4906.
167. Li, B.; Qin, Y.; Duan, H.; Yin, W.; Xia, X. Genome-wide characterization of new and drought stress responsive microRNAs in Populus euphratica. J. Exp. Bot. 2011, 62, 3765-3779.
168. Vainonen, J.P.; Jaspers, P.; Wrzaczek, M.; Lamminmaki, A.; Reddy, R.A.; Vaahtera, L.; Brosche, M.; Kangasjarvi, J. RCD1-DREB2A interaction in leaf senescence and stress responses in Arabidopsis thaliana. Biochem. J. 2012, 442, 573-581.
169. Kao, H.L.; Gunsalus, K.C. Browsing multidimensional molecular networks with the generic network browser (N-Browse). Curr. Protoc. Bioinform. 2008, doi:10.1002/0471250953.bi0911s23.
170. Fujii, H.; Verslues, P.E.; Zhu, J.K. Identification of two protein kinases required for abscisic acid regulation of seed germination, root growth, and gene expression in Arabidopsis. Plant Cell. 2007, 19, 485-494.
171. Nakashima, K.; Fujita, Y.; Kanamori, N.; Katagiri, T.; Umezawa, T.; Kidokoro, S.; Maruyama, K.; Yoshida, T.; Ishiyama, K.; Kobayashi, M.; et al. Three Arabidopsis SnRK2 protein kinases, SRK2D/SnRK2.2, SRK2E/SnRK2.6/OST1 and SRK2I/SnRK2.3, involved in ABA signaling are essential for the control of seed development and dormancy. Plant Cell Physiol. 2009, 50, 1345-1363.
172. Garcia, M.E.; Lynch, T.; Peeters, J.; Snowden, C.; Finkelstein, R. A small plant-specific protein family of ABI five binding proteins (AFPs) regulates stress response in germinating Arabidopsis seeds and seedlings. Plant Mol. Biol. 2008, 67, 643-658.
173. Lopez-Molina, L.; Mongrand, S.; Kinoshita, N.; Chua, N.H. AFP is a novel negative regulator of ABA signaling that promotes ABI5 protein degradation. Genes Dev. 2003, 17, 410-418.
174. Liu, H.; Stone, S.L.; Abscisic acid increases Arabidopsis ABI5 transcription factor levels by promoting KEG E3 ligase self-ubiquitination and proteasomal degradation. Plant Cell. 2010, 22, 2630-2641.
175. Stone, S.L.; Williams, L.A.; Farmer, L.M.; Vierstra, R.D.; Callis, J. KEEP ON GOING, a RING E3 ligase essential for Arabidopsis growth and development, is involved in abscisic acid signaling. Plant Cell. 2006, 18, 3415-3428.
176. Smalle, J.; Kurepa, J.; Yang, P.; Emborg, T.J.; Babiychuk, E.; Kushnir, S.; Vierstra, R.D. The pleiotropic role of the 26S proteasome subunit RPN10 in Arabidopsis growth and development supports a substrate-specific function in abscisic acid signaling. Plant Cell. 2003, 15, 965-980.
177. Miura, K.; Hasegawa, P.M. Sumoylation and abscisic acid signaling. Plant Signal. Behav. 2009, 4, 1176-1178.
178. Chen, R.; Jiang, H.; Li, L.; Zhai, Q.; Qi, L.; Zhou, W.; Liu, X.; Li, H.; Zheng, W.; Sun, J.; et al. The Arabidopsis mediator subunit MED25 differentially regulates jasmonate and abscisic acid signaling through interacting with the MYC2 and ABI5 transcription factors. Plant Cell. 2012, 24, 2898-2916.
179. Qin, F.; Sakuma, Y.; Tran, L.S.; Maruyama, K.; Kidokoro, S.; Fujita, Y.; Fujita, M.; Umezawa, T.; Sawano, Y.; Miyazono, K.; et al. Arabidopsis DREB2A-interacting proteins function as RING E3 ligases and negatively regulate plant drought stress-responsive gene expression. Plant Cell. 2008, 20, 1693-1707.
180. Jaspers, P.; Blomster, T.; Brosche, M.; Salojarvi, J.; Ahlfors, R.; Vainonen, J.P.; Reddy, R.A.; Immink, R.; Angenent, G.; Turck, F.; et al. Unequally redundant RCD1 and SRO1 mediate stress and developmental responses and interact with transcription factors. Plant J. 2009, 60, 268-279.
181. Greve, K.; La Cour, T.; Jensen, M.K.; Poulsen, F.M.; Skriver, K. Interactions between plant RING-H2 and plant-specific NAC (NAM/ATAF1/2/CUC2) proteins: RING-H2 molecular specificity and cellular localization. Biochem J. 2003, 371, 97-108.
182. Xie, Q.; Guo, H.S.; Dallman, G.; Fang, S.; Weissman, A.M.; Chua, N.H. SINAT5 promotes ubiquitin-related degradation of NAC1 to attenuate auxin signals. Nature 2002, 419, 167-170.
183. Bu, Q.; Li, H.; Zhao, Q.; Jiang, H.; Zhai, Q.; Zhang, J.; Wu, X.; Sun, J.; Xie, Q.; Wang, D.; et al. The Arabidopsis RING finger E3 ligase RHA2a is a novel positive regulator of abscisic acid signaling during seed germination and early seedling development. Plant Physiol. 2009, 150, 463-481.
184. Bang, W.Y.; Kim, S.W.; Jeong, I.S.; Koiwa, H.; Bahk, J.D. The C-terminal region (640-967) of Arabidopsis CPL1 interacts with the abiotic stress-and ABA-responsive transcription factors. Biochem. Biophys. Res. Commun. 2008, 372, 907-912.
185. Xu, X.; Chen, C.; Fan, B.; Chen, Z. Physical and functional interactions between pathogen-induced Arabidopsis WRKY18, WRKY40, and WRKY60 transcription factors. Plant Cell. 2006, 18, 1310-1326.
186. Davletova, S.; Rizhsky, L.; Liang, H.; Shengqiang, Z.; Oliver, D.J.; Coutu, J.; Shulaev, V.; Schlauch, K.; Mittler, R. Cytosolic ascorbate peroxidase 1 is a central component of the reactive oxygen gene network of Arabidopsis. Plant Cell. 2005, 17, 268-281.
187. Pnueli, L.; Liang, H.; Rozenberg, M.; Mittler, R. Growth suppression, altered stomatal responses, and augmented induction of heat shock proteins in cytosolic ascorbate peroxidase (Apx1)-deficient Arabidopsis plants. Plant J. 2003, 34, 187-203.
188. Li, J.; Brader, G.; Palva, E.T. The WRKY70 transcription factor: A node of convergence for jasmonate-mediated and salicylate-mediated signals in plant defense. Plant Cell. 2004, 16, 319-331.
189. Dong, C.H.; Agarwal, M.; Zhang, Y.; Xie, Q.; Zhu, J.K. The negative regulator of plant cold responses, HOS1, is a RING E3 ligase that mediates the ubiquitination and degradation of ICE1. Proc. Natl. Acad. Sci. USA 2006, 103, 8281-8286.
190. Miura, K.; Ohta, M.; Nakazawa, M.; Ono, M.; Hasegawa, P.M. ICE1 Ser403 is necessary for protein stabilization and regulation of cold signaling and tolerance. Plant J. 2011, 67, 269-279.
191. Miura, K.; Hasegawa, P.M. Regulation of cold signaling by sumoylation of ICE1. Plant Signal. Behav. 2008, 3, 52-53.
192. Miura, K.; Jin, J.B.; Lee, J.; Yoo, C.Y.; Stirm, V.; Miura, T.; Ashworth, E.N.; Bressan, R.A.; Yun, D.J.; Hasegawa, P.M. SIZ1-mediated sumoylation of ICE1 controls CBF3/DREB1A expression and freezing tolerance in Arabidopsis. Plant Cell. 2007, 19, 1403-1414.
193. Chen, C.C.; Liang, C.S.; Kao, A.L.; Yang, C.C. HHP1, a novel signalling component in the cross-talk between the cold and osmotic signalling pathways in Arabidopsis. J. Exp. Bot. 2010, 61, 3305-3320.
194. Kanaoka, M.M.; Pillitteri, L.J.; Fujii, H.; Yoshida, Y.; Bogenschutz, N.L.; Takabayashi, J.; Zhu, J.K.; Torii, K.U. SCREAM/ICE1 and SCREAM2 specify three cell-state transitional steps leading to arabidopsis stomatal differentiation. Plant Cell. 2008, 20, 1775-1785.
195. Sadanandom, A.; Bailey, M.; Ewan, R.; Lee, J.; Nelis, S. The ubiquitin-proteasome system: Central modifier of plant signalling. New Phytol. 2012, 196, 13-28.
196. Castro, P.H.; Tavares, R.M.; Bejarano, E.R.; Azevedo, H. SUMO, a heavyweight player in plant abiotic stress responses. Cell. Mol. Life. Sci. 2012, 69, 3269-3283.
197. Dunker, A.K.; Cortese, M.S.; Romero, P.; Iakoucheva, L.M.; Uversky, V.N. Flexible nets. The roles of intrinsic disorder in protein interaction networks. FEBS J. 2005, 272, 5129-5148.
198. Oldfield, C.J.; Meng, J.; Yang, J.Y.; Yang, M.Q.; Uversky, V.N.; Dunker, A.K. Flexible nets: Disorder and induced fit in the associations of p53 and 14-3-3 with their partners. BMC Genomics 2008, 9, doi:10.1186/1471-2164-9-S1-S1.