Abstract
BRZ-INSENSITIVE-LONG HYPOCOTYL 1 (BIL1)/BRASSINAZOLE-RESISTANT 1 (BZR1) is a master transcription factor of brassinosteroid (BR) signalling. The varieties of nucleobase recognition of the NN-BRRE-core motif (NNCGTG), one of variant G-box motifs, distinguish BIL1/BZR1 from basic helix-loop-helix transcription factors, underlying the specific regulation of BR-responsive genes. Here, we show the non-canonical bHLH dimer formation of BIL1/BZR1 to optimize the interaction network with DNA and the orientation of a key residue for NN-BRRE-core motif recognition.
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Data availability
The atomic coordinates and structural factors are available from the PDB under accession code 5ZD4 for the mutant MBP-fused BIL1/BZR1-DNA complex. The other data that support the findings of this study are available from the corresponding author on request.
References
Li, J. & Chory, J. Brassinosteroid actions in plants. J. Exp. Bot. 50, 275–282 (1999).
Gudesblat, G. E. & Russinova, E. Plants grow on brassinosteroids. Curr. Opin. Plant Biolo. 14, 530–537 (2011).
Krishna, P. Brassinosteroid-mediated stress responses. J. Plant. Growth Regul. 22, 289–297 (2003).
Ye, Q. et al. Brassinosteroids control male fertility by regulating the expression of key genes involved in Arabidopsis anther and pollen development. Proc. Natl Acad. Sci. USA 107, 6100–6105 (2010).
Wang, Z. Y. et al. Nuclear-localized BZR1 mediates brassinosteroid-induced growth and feedback suppression of brassinosteroid biosynthesis. Dev. Cell. 2, 505–513 (2002).
Yin, Y. et al. BES1 accumulates in the nucleus in response to brassinosteroids to regulate gene expression and promote stem elongation. Cell 109, 181–191 (2002).
Asami, T. et al. The influence of chemical genetics on plant science: shedding light on functions and mechanism of action of brassinosteroids using biosynthesis inhibitors. J. Plant. Growth Regul. 22, 336–349 (2003).
He, J. X. et al. BZR1 is a transcriptional repressor with dual roles in brassinosteroid homeostasis and growth responses. Science 307, 1634–1638 (2005).
Yin, Y. et al. A new class of transcription factors mediates brassinosteroid-regulated gene expression in Arabidopsis. Cell 120, 249–259 (2005).
Sun, Y. et al. Integration of brassinosteroid signal transduction with the transcription network for plant growth regulation in Arabidopsis. Dev. Cell. 19, 765–777 (2010).
Yu, X. et al. A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana. Plant J. 65, 634–646 (2011).
Shimada, S. et al. Formation and dissociation of the BSS1 protein complex regulates plant development via brassinosteroid signaling. Plant Cell 27, 375–390 (2015).
Toledo-Ortiz, G., Huq, E. & Quail, P. H. The Arabidopsis basic / helix-loop-helix transcription factor family. Plant Cell 15, 1749–1770 (2003).
Jones, S. An overview of the basic helix-loop-helix proteins. Genome Biol. 5, 226 (2004).
Castillon, A., Shen, H. & Huq, E. Phytochrome interacting factors: central players in phytochrome-mediated light signaling networks. Trends Plant Sci. 12, 514–521 (2007).
Oh, E., Zhu, J. Y. & Wang, Z. Y. Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses. Nat. Cell Biol. 14, 802–809 (2012).
Lorrain, S., Allen, T., Duek, P. D., Whitelam, G. C. & Fankhauser, C. Phytochrome-mediated inhibition of shade avoidance involves degradation of growth-promoting bHLH transcription factors. Plant J. 53, 312–323 (2008).
Friedrichsen, D. M. et al. Three redundant brassinosteroid early response genes encode putative bHLH transcription factors required for normal growth. Genetics 162, 1445–1456 (2002).
Ferré-D’Amaré, A. R., Prendergast, G. C., Ziff, E. B. & Burley, S. K. Recognition by Max of its cognate DNA through a dimeric b/HLH/Z domain. Nature 363, 38–45 (1993).
Nair, S. K. & Burley, S. K. X-ray structures of Myc-Max and Mad-Max recognizing DNA: molecular bases of regulation by proto-oncogenic transcription factors. Cell 112, 193–205 (2003).
Wang, Z., Wu, Y., Li, L. & Su, X. D. Intermolecular recognition revealed by the complex structure of human CLOCK-BMAL1 basic helix-loop-helix domains with E-box DNA. Cell Res. 23, 213–224 (2013).
Smyth, D. R., Mrozkiewicz, M. K., McGrath, W. J., Listwan, P. & Kobe, B. Crystal structures of fusion proteins with large-affinity tags. Protein Sci. 12, 1313–1322 (2003).
Moon, A. F., Mueller, G. A., Zhong, X. & Pedersen, L. C. A synergistic approach to protein crystallization: combination of a fixed-arm carrier with surface entropy reduction. Protein Sci. 19, 901–913 (2010).
Lian, T., Xu, Y., Li, L. & Su, X. D. Crystal structure of tetrameric Arabidopsis MYC2 reveals the mechanism of enhanced interaction with DNA. Cell Rep. 19, 1334–1342 (2017).
Bowman, J. L. et al. Insights into land plant evolution garnered from the Marchantia polymorpha genome. Cell. 171, 287–304 (2017).
Guo, A. Y. et al. PlantTFDB: A comprehensive plant transcription factor database. Nucleic Acids Res 36, D966–D969 (2008).
Ezer, D. et al. The G-box transcriptional regulatory code in Arabidopsis. Plant Physiol. 2, 628–640 (2017).
Gordân, R. et al. Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape. Cell Rep. 3, 1093–1104 (2013).
Zhou, T. et al. Quantitative modeling of transcription factor binding specificities using DNA shape. Proc. Natl Acad. Sci. USA 112, 4654–4659 (2015).
Sievers, F. et al. Fast, scalable generation of high quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7, 539 (2011).
Gouet, P., Courcelle, E., Stuart, D. I. & Metoz, F. ESPript: analysis of multiple sequence alignments in PostScript. Bioinformatics 15, 305–308 (1999).
Kabsch, W. XDS. Acta Crystallogr. Sect. D Biol. Crystallogr. 66, 125–132 (2010).
Evans, P. R. & Murshudov, G. N. How good are my data and what is the resolution? Acta Crystallogr. Sect. D Biol. Crystallogr 69, 1204–1214 (2013).
Matthews, B. W. Solvent content of protein crystals. J. Mol. Biol. 33, 491–497 (1968).
McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007).
Cowtan, K. The Buccaneer software for automated model building. 1. Tracing protein chains. Acta Crystallogr. Sect. D. Biol. Crystallogr. 62, 1002–1011 (2006).
Winn, M. D. et al. Overview of the CCP4 suite and current developments. Acta Crystallogr. Sect. D Biol.Crystallogr. 67, 235–242 (2011).
Adams, P. D. et al. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr. Sect. D Biol. Crystallogr. 58, 1948–1954 (2002).
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. Sect. D Biol. Crystallogr. 60, 2126–2132 (2004).
Lovell, S. C. et al. Structure validation by Calpha geometry: phi, psi and Cbeta deviation. Proteins 50, 437–450 (2003).
Blanchet, C., Pasi, M., Zakrzewska, K. & Lavery, R. CURVES+ web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structures. Nucleic Acids Res. 39, W68–W73 (2011).
Acknowledgements
The synchrotron-radiation experiments were performed on beamlines AR NE3A at the Photon Factory with the approval of the High Energy Accelerator Research Organization (Proposal No. 2016G648). This work was supported by a Grant-in-Aid for Scientific Research on Innovative Areas No. 17H05835 from the Japan Society for the Promotion of Science (JSPS) (T.M.), the Platform for Drug Discovery, Informatics, and Structural Life Science from the Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT) (M.T.), the Basis for Supporting Innovative Drug Discovery and Life Science Research from the MEXT (T.M.), and the Core Research for Evolutional Science and Technology (CREST) Program of Japan Science and Technology Agency (JST) (T.A. and T.N.).
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M.T. conceived and designed the research. S.N., T.M., Y.X. and A.N. performed the biochemical experiments and collected X-ray diffraction data. S.N., T.M., Y.X., A.N. and K.H. analysed the data. S.N., T.M., T.A., T.N. and M.T. wrote the paper. M.T. edited the manuscript.
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Nosaki, S., Miyakawa, T., Xu, Y. et al. Structural basis for brassinosteroid response by BIL1/BZR1. Nature Plants 4, 771–776 (2018). https://doi.org/10.1038/s41477-018-0255-1
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DOI: https://doi.org/10.1038/s41477-018-0255-1
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