The floral homeotic protein SEPALLATA3 recognizes target DNA sequences by shape readout involving a conserved arginine residue in the MADS‐domain. (4th June 2018)

• Record Type: Journal Article
• Authors: Käppel, Sandra; Melzer, Rainer; Rümpler, Florian; Gafert, Christian; Theißen, Günter
• Is Part Of: Plant journal. Volume 95:Number 2(2018)
• Page Start: 341
• Page End: 357
• Publication Date: 2018-06-04
• Subjects: Arabidopsis thaliana -- base readout -- CArG‐box -- flower development -- MADS‐box -- minor groove width -- pioneer transcription factor -- shape readout; Plant molecular biology -- Periodicals; Plant cells and tissues -- Periodicals; Botany -- Periodicals; 580
• DOI: 10.1111/tpj.13954
• Languages: English
• ISSNs: 0960-7412

Abstract

Summary: SEPALLATA3 of Arabidopsis thaliana is a MADS‐domain transcription factor (TF) and a key regulator of flower development. MADS‐domain proteins bind to sequences termed 'CArG‐boxes' [consensus 5′‐CC(A/T)6 GG‐3′]. Because only a fraction of the CArG‐boxes in the Arabidopsis genome are bound by SEPALLATA3, more elaborate principles have to be discovered to better understand which features turn CArG‐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 SEPALLATA3. We determined in vitro binding affinities of SEPALLATA3 to DNA probes that all contain the CArG‐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 SEPALLATA3. Analysis of mutant SEPALLATA3 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 TFs of this type, heavily depends on shape readout mechanisms. Significance Statement: Recent evidence indicates that some transcription factors can recognize the structure of the target DNA via a 'shape readout' mechanism. Here, we provide quantitative biophysical data on the interaction of the MADS‐domain transcription factor SEPALLATA3 with DNA and show that the binding affinity of SEPALLATA3 correlates well with certain DNA shape features. We show that shape readout is important for target gene recognition of SEPALLATA3 and potentially other MADS‐domain transcription factors.