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.
Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10-12, 08028 Barcelona, Spain; Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Baldiri Reixac 10-12, 08028 Barcelona, Spain.
D Roeland
DR
Boer
Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, the Netherlands.
Alejandra
A
Freire-Rios
Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, the Netherlands.
Willy A M
WA
van den Berg
Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, the Netherlands.
Terrens
T
Saaki
Astbury Centre for Structural Molecular Biology (IWM) and Centre for Plant Sciences (SK), Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
Iain W
IW
Manfield
Astbury Centre for Structural Molecular Biology (IWM) and Centre for Plant Sciences (SK), Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
Stefan
S
Kepinski
Genomics Unit and Department of Plant Molecular Genetics, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, 28049 Madrid, Spain.
Irene
I
López-Vidrieo
Genomics Unit and Department of Plant Molecular Genetics, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, 28049 Madrid, Spain.
Jose Manuel
JM
Franco-Zorrilla
Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, the Netherlands.
Sacco C
SC
de Vries
Genomics Unit and Department of Plant Molecular Genetics, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, 28049 Madrid, Spain.
Roberto
R
Solano
Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, the Netherlands. Electronic address: dolf.weijers@wur.nl.
Dolf
D
Weijers
Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10-12, 08028 Barcelona, Spain; Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Baldiri Reixac 10-12, 08028 Barcelona, Spain. Electronic address: miquel.coll@irbbarcelona.org.
Miquel
M
Coll
D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000737:chemistry* / Q000378:metabolism*; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism*; D019281:Dimerization; D007210:Indoleacetic Acids / Q000378:metabolism*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D014157:Transcription Factors / Q000737:chemistry* / Q000378:metabolism*
C503841:ARF1 protein, Arabidopsis; D029681:Arabidopsis Proteins; D004268:DNA-Binding Proteins; D007210:Indoleacetic Acids; C111371:MONOPTEROS protein, Arabidopsis; D014157:Transcription Factors; D004247:DNA