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The floral homeotic protein SEPALLATA 3 recognizes target DNA sequences by shape readout involving a conserved arginine residue in the MADS ‐domain
Author(s) -
Käppel Sandra,
Melzer Rainer,
Rümpler Florian,
Gafert Christian,
Theißen Günter
Publication year - 2018
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1111/tpj.13954
Subject(s) - biology , dna , arabidopsis , mads box , mutant , transcription factor , protein–dna interaction , genetics , dna binding protein , gene
Summary SEPALLATA 3 of Arabidopsis thaliana is a MADS ‐domain transcription factor ( TF ) and a key regulator of flower development. MADS ‐domain proteins bind to sequences termed ‘ CA rG‐boxes’ [consensus 5′‐ CC (A/T) 6 GG ‐3′]. Because only a fraction of the CA rG‐boxes in the Arabidopsis genome are bound by SEPALLATA 3, more elaborate principles have to be discovered to better understand which features turn CA rG‐boxes into genuine recognition sites. Here, we investigate to what extent the shape of the DNA is involved in a ‘shape readout’ that contributes to the binding of SEPALLATA 3. We determined in vitro binding affinities of SEPALLATA 3 to DNA probes that all contain the CA rG‐box motif, but differ in their predicted DNA shape. We found that binding affinity correlates well with a narrow minor groove of the DNA . Substitution of canonical bases with non‐standard bases supports the hypothesis of minor groove shape readout by SEPALLATA 3. Analysis of mutant SEPALLATA 3 proteins further revealed that a highly conserved arginine residue, which is expected to contact the DNA minor groove, contributes significantly to the shape readout. Our studies show that the specific recognition of cis ‐regulatory elements by a plant MADS ‐domain TF , and by inference probably also of other TF s of this type, heavily depends on shape readout mechanisms.