Protein & Cell

, Volume 2, Issue 1, pp 55–63

A structural view of the conserved domain of rice stress-responsive NAC1

Research Article


The importance of NAC (named as NAM, ATAF1, 2, and CUC2) proteins in plant development, transcription regulation and regulatory pathways involving protein-protein interactions has been increasingly recognized. We report here the high resolution crystal structure of SNAC1 (stress-responsive NAC) NAC domain at 2.5 Å. Although the structure of the SNAC1 NAC domain shares a structural similarity with the reported structure of the ANAC NAC1 domain, some key features, especially relating to two loop regions which potentially take the responsibility for DNA-binding, distinguish the SNAC1 NAC domain from other reported NAC structures. Moreover, the dimerization of the SNAC1 NAC domain is demonstrated by both soluble and crystalline conditions, suggesting this dimeric state should be conserved in this type of NAC family. Additionally, we discuss the possible NAC-DNA binding model according to the structure and reported biological evidences.


stress-responsive NAC 1 NAC family DNA binding rice crystal structure 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Adams, P.D., Grosse-Kunstleve, R.W., Hung, L.W., Ioerger, T.R., McCoy, A.J., Moriarty, N.W., Read, R.J., Sacchettini, J.C., Sauter, N.K., and Terwilliger, T.C. (2002). PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr D Biol Crystallogr 58, 1948–1954.CrossRefPubMedGoogle Scholar
  2. Aida, M., Ishida, T., Fukaki, H., Fujisawa, H., and Tasaka, M. (1997). Genes involved in organ separation in Arabidopsis: an analysis of the cup-shaped cotyledon mutant. Plant Cell 9, 841–857.PubMedCentralCrossRefPubMedGoogle Scholar
  3. Collaborative Computational Project, Number 4. (1994). The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 50, 760–763.CrossRefGoogle Scholar
  4. Collinge, M., and Boller, T. (2001). Differential induction of two potato genes, Stprx2 and StNAC, in response to infection by Phytophthora infestans and to wounding. Plant Mol Biol 46, 521–529.CrossRefPubMedGoogle Scholar
  5. DeLano, W.L. (2002). The PyMOL Molecular Graphics System. San Carlos, CA, USA: DeLano Scientific. Scholar
  6. Delessert, C., Kazan, K., Wilson, I.W., Van Der Straeten, D., Manners, J., Dennis, E.S., and Dolferus, R. (2005). The transcription factor ATAF2 represses the expression of pathogenesis-related genes in Arabidopsis. Plant J 43, 745–757.CrossRefPubMedGoogle Scholar
  7. Demura, T., and Fukuda, H. (2007). Transcriptional regulation in wood formation. Trends Plant Sci 12, 64–70.CrossRefPubMedGoogle Scholar
  8. Du, J., and Groover, A. (2010). Transcriptional regulation of secondary growth and wood formation. J Integr Plant Biol 52, 17–27.CrossRefPubMedGoogle Scholar
  9. Duval, M., Hsieh, T.F., Kim, S.Y., and Thomas, T.L. (2002). Molecular characterization of AtNAM: a member of the Arabidopsis NAC domain superfamily. Plant Mol Biol 50, 237–248.CrossRefPubMedGoogle Scholar
  10. Emsley, P., and Cowtan, K. (2004). Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60, 2126–2132.CrossRefPubMedGoogle Scholar
  11. Ernst, H.A., Olsen, A.N., Larsen, S., and Lo Leggio, L. (2004). Structure of the conserved domain of ANAC, a member of the NAC family of transcription factors. EMBO Rep 5, 297–303.PubMedCentralCrossRefPubMedGoogle Scholar
  12. Fang, Y., You, J., Xie, K., Xie, W., and 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.CrossRefPubMedGoogle Scholar
  13. Hegedus, D., Yu, M., Baldwin, D., Gruber, M., Sharpe, A., Parkin, I., Whitwill, S., and Lydiate, D. (2003). Molecular characterization of Brassica napus NAC domain transcriptional activators induced in response to biotic and abiotic stress. Plant Mol Biol 53, 383–397.CrossRefPubMedGoogle Scholar
  14. Hu, H., Dai, M., Yao, J., Xiao, B., Li, X., Zhang, Q., and Xiong, L. (2006). Overexpressing a NAM, ATAF, and CUC (NAC) transcription factor enhances drought resistance and salt tolerance in rice. Proc Natl Acad Sci U S A 103, 12987–12992.PubMedCentralCrossRefPubMedGoogle Scholar
  15. Hu, R., Qi, G., Kong, Y., Kong, D., Gao, Q., and Zhou, G. (2010). Comprehensive analysis of NAC domain transcription factor gene family in Populus trichocarpa. BMC Plant Biol 10, 145–167.PubMedCentralCrossRefPubMedGoogle Scholar
  16. Jensen, M.K., Hagedorn, P.H., de Torres-Zabala, M., Grant, M.R., Rung, J.H., Collinge, D.B., and Lyngkjaer, M.F. (2008). Transcriptional regulation by an NAC (NAM-ATAF1,2-CUC2) transcription factor attenuates ABA signalling for efficient basal defence towards Blumeria graminis f. sp. hordei in Arabidopsis. Plant J 56, 867–880.CrossRefPubMedGoogle Scholar
  17. Jensen, M.K., Rung, J.H., Gregersen, P.L., Gjetting, T., Fuglsang, A. T., Hansen, M., Joehnk, N., Lyngkjaer, M.F., and Collinge, D.B. (2007). The HvNAC6 transcription factor: a positive regulator of penetration resistance in barley and Arabidopsis. Plant Mol Biol 65, 137–150.CrossRefPubMedGoogle Scholar
  18. Kim, S.G., Kim, S.Y., and Park, C.M. (2007). A membrane-associated NAC transcription factor regulates salt-responsive flowering via FLOWERING LOCUS T in Arabidopsis. 0032-0935 226, 64–654.Google Scholar
  19. Kim, Y.S., Kim, S.G., Park, J.E., Park, H.Y., Lim, M.H., Chua, N.H., and Park, C.M. (2006). A membrane-bound NAC transcription factor regulates cell division in Arabidopsis. Plant Cell 18, 3132–3144.PubMedCentralCrossRefPubMedGoogle Scholar
  20. Ko, J.H., Yang, S.H., Park, A.H., Lerouxel, O., and Han, K.H. (2007). ANAC012, a member of the plant-specific NAC transcription factor family, negatively regulates xylary fiber development in Arabidopsis thaliana. Plant J 50, 1035–1048.CrossRefPubMedGoogle Scholar
  21. Krissinel, E., and Henrick, K. (2004). Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr D Biol Crystallogr 60, 2256–2268.CrossRefPubMedGoogle Scholar
  22. Kubo, M., Udagawa, M., Nishikubo, N., Horiguchi, G., Yamaguchi, M., Ito, J., Mimura, T., Fukuda, H., and Demura, T. (2005). Transcription switches for protoxylem and metaxylem vessel formation. Genes Dev 19, 1855–1860.PubMedCentralCrossRefPubMedGoogle Scholar
  23. Laskowski, R., MacArthur, M., Moss, D., and Thornton, J. (1993). PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst 26, 283–291.CrossRefGoogle Scholar
  24. Lu, P.-L., Chen, N.-Z., An, R., Su, Z., Qi, B.-S., Ren, F., Chen, J., and Wang, X.-C. (2007). A novel drought-inducible gene, ATAF1, encodes a NAC family protein that negatively regulates the expression of stress-responsive genes in <i>Arabidopsis</i>. 0167-4412 63, 289–305.Google Scholar
  25. Matthews, B.W. (1968). Solvent content of protein crystals. J Mol Biol 33, 491–497.CrossRefPubMedGoogle Scholar
  26. McCarthy, R.L., Zhong, R., and Ye, Z.H. (2009). MYB83 is a direct target of SND1 and acts redundantly with MYB46 in the regulation of secondary cell wall biosynthesis in Arabidopsis. Plant Cell Physiol 50, 1950–1964.CrossRefPubMedGoogle Scholar
  27. McCoy, A.J., Grosse-Kunstleve, R.W., Adams, P.D., Winn, M.D., Storoni, L.C., and Read, R.J. (2007). Phaser crystallographic software. J Appl Crystallogr 40, 658–674.PubMedCentralCrossRefPubMedGoogle Scholar
  28. Mitsuda, N., Iwase, A., Yamamoto, H., Yoshida, M., Seki, M., Shinozaki, K., and Ohme-Takagi, M. (2007). NAC transcription factors, NST1 and NST3, are key regulators of the formation of secondary walls in woody tissues of Arabidopsis. Plant Cell 19, 270–280.PubMedCentralCrossRefPubMedGoogle Scholar
  29. Müller, C.W. (2001). Transcription factors: global and detailed views. Curr Opin Struct Biol 11, 26–32.CrossRefPubMedGoogle Scholar
  30. Nakashima, K., Tran, L.S., Van Nguyen, D., Fujita, M., Maruyama, K., Todaka, D., Ito, Y., Hayashi, N., Shinozaki, K., and 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.CrossRefPubMedGoogle Scholar
  31. Ohnishi, T., Sugahara, S., Yamada, T., Kikuchi, K., Yoshiba, Y., Hirano, H.Y., and Tsutsumi, N. (2005). OsNAC6, a member of the NAC gene family, is induced by various stresses in rice. Genes Genet Syst 80, 135–139.CrossRefPubMedGoogle Scholar
  32. Olsen, A.N., Ernst, H.A., Leggio, L.L., and Skriver, K. (2005). DNA-binding specificity and molecular functions of NAC transcription factors. 0168-9452 169, 785–797.Google Scholar
  33. Ooka, H., Satoh, K., Doi, K., Nagata, T., Otomo, Y., Murakami, K., Matsubara, K., Osato, N., Kawai, J., Carninci, P., et al. (2003). Comprehensive analysis of NAC family genes in Oryza sativa and Arabidopsis thaliana. DNA Res 10, 239–247.CrossRefPubMedGoogle Scholar
  34. Otwinowski, Z., and Minor, W. (1997). Processing of X-ray diffraction data collected in oscillation mode. In: Macromolecular Crystallography, part A. C.W. Carter Jr., and R.M. Sweet, eds. San Diego, CA: Academic Press. 307–326.CrossRefGoogle Scholar
  35. Riechmann, J.L., Heard, J., Martin, G., Reuber, L., Jiang, C., Keddie, J., Adam, L., Pineda, O., Ratcliffe, O.J., Samaha, R.R., et al. (2000). Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science 290, 2105–2110.CrossRefPubMedGoogle Scholar
  36. Sablowski, R.W.M., and Meyerowitz, E.M. (1998). A homolog of NO APICAL MERISTEM is an immediate target of the floral homeotic genes APETALA3/PISTILLATA. Cell 92, 93–103.CrossRefPubMedGoogle Scholar
  37. Souer, E., van Houwelingen, A., Kloos, D., Mol, J., and Koes, R. (1996). The no apical meristem gene of Petunia is required for pattern formation in embryos and flowers and is expressed at meristem and primordia boundaries. Cell 85, 159–170.CrossRefPubMedGoogle Scholar
  38. Sperotto, R.A., Ricachenevsky, F.K., Duarte, G.L., Boff, T., Lopes, K. L., Sperb, E.R., Grusak, M.A., and Fett, J.P. (2009). Identification of up-regulated genes in flag leaves during rice grain filling and characterization of OsNAC5, a new ABA-dependent transcription factor. 0032-0935 230, 985–1002.Google Scholar
  39. Takasaki, H., Maruyama, K., Kidokoro, S., Ito, Y., Fujita, Y., Shinozaki, K., Yamaguchi-Shinozaki, K., and Nakashima, K. (2010). The abiotic stress-responsive NAC-type transcription factor OsNAC5 regulates stress-inducible genes and stress tolerance in rice. Mol Genet Genomics 284, 173–183.CrossRefPubMedGoogle Scholar
  40. Tran, L.S., Nakashima, K., Sakuma, Y., Simpson, S.D., Fujita, Y., Maruyama, K., Fujita, M., Seki, M., Shinozaki, K., and Yamaguchi-Shinozaki, K. (2004). 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 16, 2481–2498.PubMedCentralCrossRefPubMedGoogle Scholar
  41. Uauy, C., Distelfeld, A., Fahima, T., Blechl, A., and Dubcovsky, J. (2006). A NAC Gene regulating senescence improves grain protein, zinc, and iron content in wheat. Science 314, 1298–1301.CrossRefPubMedGoogle Scholar
  42. Wang, X.e., Basnayake, B.M.V.S., Zhang, H., Li, G., Li, W., Virk, N., Mengiste, T., and Song, F. (2009). The Arabidopsis ATAF1, a NAC Transcription Factor, Is a Negative Regulator of Defense Responses Against Necrotrophic Fungal and Bacterial Pathogens. Molecular Plant-Microbe Interactions 22, 1227–1238.CrossRefPubMedGoogle Scholar
  43. Weir, I., Lu, J., Cook, H., Causier, B., Schwarz-Sommer, Z., and Davies, B. (2004). CUPULIFORMIS establishes lateral organ boundaries in Antirrhinum. 0950-1991 131, 915–922.Google Scholar
  44. Wu, Y., Deng, Z., Lai, J., Zhang, Y., Yang, C., Yin, B., Zhao, Q., Zhang, L., Li, Y., Yang, C., et al. (2009). Dual function of Arabidopsis ATAF1 in abiotic and biotic stress responses. Cell Res 19, 1279–1290.CrossRefPubMedGoogle Scholar
  45. Xie, Q., Frugis, G., Colgan, D., and Chua, N.H. (2000). Arabidopsis NAC1 transduces auxin signal downstream of TIR1 to promote lateral root development. Genes Dev 14, 3024–3036.PubMedCentralCrossRefPubMedGoogle Scholar
  46. Xiong, Y., Liu, T., Tian, C., Sun, S., Li, J., and Chen, M. (2005). Transcription factors in rice: a genome-wide comparative analysis between monocots and eudicots. Plant Mol Biol 59, 191–203.CrossRefPubMedGoogle Scholar
  47. Yamasaki, K., Kigawa, T., Inoue, M., Tateno, M., Yamasaki, T., Yabuki, T., Aoki, M., Seki, E., Matsuda, T., Tomo, Y., et al. (2005). Solution structure of an Arabidopsis WRKY DNA binding domain. Plant Cell 17, 944–956.PubMedCentralCrossRefPubMedGoogle Scholar
  48. Zhong, R., Demura, T., and Ye, Z.H. (2006). SND1, a NAC domain transcription factor, is a key regulator of secondary wall synthesis in fibers of Arabidopsis. Plant Cell 18, 3158–3170.PubMedCentralCrossRefPubMedGoogle Scholar
  49. Zhong, R., Richardson, E.A., and Ye, Z.H. (2007a). The MYB46 transcription factor is a direct target of SND1 and regulates secondary wall biosynthesis in Arabidopsis. Plant Cell 19, 2776–2792.PubMedCentralCrossRefPubMedGoogle Scholar
  50. Zhong, R., Richardson, E.A., and Ye, Z.H. (2007b). Two NAC domain transcription factors, SND1 and NST1, function redundantly in regulation of secondary wall synthesis in fibers of Arabidopsis. Planta 225, 1603–1611.CrossRefPubMedGoogle Scholar

Copyright information

© Higher Education Press and Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  1. 1.National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
  2. 2.Structural Biology LaboratoryTsinghua UniversityBeijingChina
  3. 3.College of Life Sciences and Tianjin State Laboratory of Protein ScienceNankai UniversityTianjinChina

Personalised recommendations