Structural Basis for DNA Binding Specificity by the Auxin-Dependent ARF Transcription Factors

Auxin regulates numerous plant developmental processes by controlling gene expression via a family of functionally distinct DNA-binding auxin response factors (ARFs), yet the mechanistic basis for generating specificity in auxin response is unknown. Here, we address this question by solving high-resolution crystal structures of the pivotal Arabidopsis developmental regulator ARF5/MONOPTEROS (MP), its divergent paralog ARF1, and a complex of ARF1 and a generic auxin response DNA element (AuxRE). We show that ARF DNA-binding domains also homodimerize to generate cooperative DNA binding, which is critical for in vivo ARF5/MP function. Strikingly, DNA-contacting residues are conserved between ARFs, and we discover that monomers have the same intrinsic specificity. ARF1 and ARF5 homodimers, however, differ in spacing tolerated between binding sites. Our data identify the DNA-binding domain as an ARF dimerization domain, suggest that ARF dimers bind complex sites as molecular calipers with ARF-specific spacing preference, and provide an atomic-scale mechanistic model for specificity in auxin response.

[1]  G. Jürgens,et al.  Auxin triggers transient local signaling for cell specification in Arabidopsis embryogenesis. , 2006, Developmental cell.

[2]  M. Berger,et al.  Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors , 2009, Nature Protocols.

[3]  J. Kim,et al.  Protein-protein interactions among the Aux/IAA proteins. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[4]  Kazuo Shinozaki,et al.  Solution Structure of the B3 DNA Binding Domain of the Arabidopsis Cold-Responsive Transcription Factor RAV1w⃞ , 2004, The Plant Cell Online.

[5]  D. Weijers,et al.  A Versatile Set of Ligation-Independent Cloning Vectors for Functional Studies in Plants1[C][W][OA] , 2011, Plant Physiology.

[6]  G. Murshudov,et al.  Refinement of macromolecular structures by the maximum-likelihood method. , 1997, Acta crystallographica. Section D, Biological crystallography.

[7]  K Henrick,et al.  Electronic Reprint Biological Crystallography Secondary-structure Matching (ssm), a New Tool for Fast Protein Structure Alignment in Three Dimensions Biological Crystallography Secondary-structure Matching (ssm), a New Tool for Fast Protein Structure Alignment in Three Dimensions , 2022 .

[8]  Thomas R. Schneider,et al.  HKL2MAP: a graphical user interface for macromolecular phasing with SHELX programs , 2004 .

[9]  K. Peterson,et al.  The plant B3 superfamily. , 2008, Trends in plant science.

[10]  Owen Johnson,et al.  iMOSFLM: a new graphical interface for diffraction-image processing with MOSFLM , 2011, Acta crystallographica. Section D, Biological crystallography.

[11]  G. Hagen,et al.  ARF1, a transcription factor that binds to auxin response elements. , 1997, Science.

[12]  Ana I. Caño-Delgado,et al.  Heterodimerization and Endocytosis of Arabidopsis Brassinosteroid Receptors BRI1 and AtSERK3 (BAK1) , 2004, The Plant Cell Online.

[13]  Shujing Liu,et al.  Characterization of MADS-domain transcription factor complexes in Arabidopsis flower development , 2012, Proceedings of the National Academy of Sciences.

[14]  D. Wagner,et al.  A molecular framework for auxin-mediated initiation of flower primordia. , 2013, Developmental cell.

[15]  B. Volkman,et al.  Structure of the B3 domain from Arabidopsis thaliana protein At1g16640 , 2005, Protein science : a publication of the Protein Society.

[16]  Joon Kim,et al.  Determinants of half-site spacing preferences that distinguish AP-1 and ATF/CREB bZIP domains , 1995, Nucleic Acids Res..

[17]  G. Hagen,et al.  Dimerization and DNA binding of auxin response factors. , 1999, The Plant journal : for cell and molecular biology.

[18]  G. Hagen,et al.  Auxin Response Factors , 2001, Journal of Plant Growth Regulation.

[19]  J. Friml,et al.  The march of the PINs: developmental plasticity by dynamic polar targeting in plant cells , 2010, The EMBO journal.

[20]  Steffen Vanneste,et al.  Auxin: A Trigger for Change in Plant Development , 2009, Cell.

[21]  G. Hagen,et al.  The Roles of Auxin Response Factor Domains in Auxin-Responsive Transcription Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.008417. , 2003, The Plant Cell Online.

[22]  S. Khorasanizadeh,et al.  Nuclear-receptor interactions on DNA-response elements. , 2001, Trends in biochemical sciences.

[23]  Rodrigo Lopez,et al.  Clustal W and Clustal X version 2.0 , 2007, Bioinform..

[24]  C. Hardtke,et al.  The Arabidopsis gene MONOPTEROS encodes a transcription factor mediating embryo axis formation and vascular development , 1998, The EMBO journal.

[25]  P. Emsley,et al.  Features and development of Coot , 2010, Acta crystallographica. Section D, Biological crystallography.

[26]  M. Estelle,et al.  Mechanism of auxin-regulated gene expression in plants. , 2009, Annual review of genetics.

[27]  M. Schmid,et al.  MONOPTEROS controls embryonic root initiation by regulating a mobile transcription factor , 2010, Nature.

[28]  Thorsten Hamann,et al.  Developmental specificity of auxin response by pairs of ARF and Aux/IAA transcriptional regulators , 2005, The EMBO journal.

[29]  K. Umesono,et al.  Direct repeats as selective response elements for the thyroid hormone, retinoic acid, and vitamin D3 receptors , 1991, Cell.

[30]  J. Long,et al.  TOPLESS Mediates Auxin-Dependent Transcriptional Repression During Arabidopsis Embryogenesis , 2008, Science.

[31]  D. Weijers,et al.  Auxin enters the matrix--assembly of response machineries for specific outputs. , 2009, Current opinion in plant biology.

[32]  J. Franco-Zorrilla,et al.  Improved protein-binding microarrays for the identification of DNA-binding specificities of transcription factors. , 2011, The Plant journal : for cell and molecular biology.

[33]  D. Svergun,et al.  CRYSOL : a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates , 1995 .

[34]  Christophe Godin,et al.  The auxin signalling network translates dynamic input into robust patterning at the shoot apex , 2011, Molecular systems biology.

[35]  P. Chambon,et al.  Dimerization interfaces formed between the DNA binding domains determine the cooperative binding of RXR/RAR and RXR/TR heterodimers to DR5 and DR4 elements. , 1994, The EMBO journal.

[36]  Hans Meinhardt,et al.  Auxin triggers a genetic switch , 2011, Nature Cell Biology.

[37]  W. Delano.  The PyMOL Molecular Graphics System , 2002 .

[38]  Jan Willem Borst,et al.  Different auxin response machineries control distinct cell fates in the early plant embryo. , 2012, Developmental cell.

[39]  Gerhard K. H. Przemeck,et al.  Studies on the role of the Arabidopsis gene MONOPTEROS in vascular development and plant cell axialization , 2004, Planta.

[40]  Randy J. Read,et al.  Overview of the CCP4 suite and current developments , 2011, Acta crystallographica. Section D, Biological crystallography.

[41]  Wenzislava Ckurshumova,et al.  Deletion of MP/ARF5 domains III and IV reveals a requirement for Aux/IAA regulation in Arabidopsis leaf vascular patterning. , 2012, The New phytologist.

[42]  Carl O. Pabo,et al.  Crystal structure of MyoD bHLH domain-DNA complex: Perspectives on DNA recognition and implications for transcriptional activation , 1994, Cell.

[43]  C. Scutt,et al.  Evolution of the ARF gene family in land plants: old domains, new tricks. , 2013, Molecular biology and evolution.

[44]  Liisa Holm,et al.  Dali server: conservation mapping in 3D , 2010, Nucleic Acids Res..

[45]  G. Jürgens,et al.  The role of the monopteros gene in organising the basal body region of the Arabidopsis embryo , 1993 .

[46]  G. Hagen,et al.  Composite structure of auxin response elements. , 1995, The Plant cell.

[47]  Daniel E. Newburger,et al.  Variation in Homeodomain DNA Binding Revealed by High-Resolution Analysis of Sequence Preferences , 2008, Cell.

[48]  Karin Ljung,et al.  Auxin metabolism and homeostasis during plant development , 2013, Development.

[49]  J. Reed,et al.  AUXIN RESPONSE FACTOR1 and AUXIN RESPONSE FACTOR2 regulate senescence and floral organ abscission in Arabidopsis thaliana , 2005, Development.

[50]  C. Bian,et al.  Crystal structures of the Tudor domains of human PHF20 reveal novel structural variations on the Royal Family of proteins , 2012, FEBS letters.

[51]  G. Stormo,et al.  Analysis of Homeodomain Specificities Allows the Family-wide Prediction of Preferred Recognition Sites , 2008, Cell.

[52]  D. Weijers,et al.  A cellular expression map of the Arabidopsis AUXIN RESPONSE FACTOR gene family. , 2011, The Plant journal : for cell and molecular biology.

[53]  M. Siegal,et al.  Robustness: mechanisms and consequences. , 2009, Trends in genetics : TIG.

[54]  K. Umesono,et al.  The nuclear receptor superfamily: The second decade , 1995, Cell.

[55]  Yi Zhang,et al.  Recognition of Histone H3 Lysine-4 Methylation by the Double Tudor Domain of JMJD2A , 2006, Science.

[56]  George M. Sheldrick,et al.  Macromolecular phasing with SHELXE , 2002 .

[57]  Patrice Gouet,et al.  ESPript: analysis of multiple sequence alignments in PostScript , 1999, Bioinform..

[58]  Joseph R. Ecker,et al.  Auxin response factors ARF6 and ARF8 promote jasmonic acid production and flower maturation , 2005, Development.

[59]  K. Thimann,et al.  Identity of the Growth-Promoting and Root-Forming Substances ofPlants , 1935, Nature.

[60]  Dmitri I. Svergun,et al.  PRIMUS: a Windows PC-based system for small-angle scattering data analysis , 2003 .

[61]  P. Evans,et al.  Scaling and assessment of data quality. , 2006, Acta crystallographica. Section D, Biological crystallography.