Tissue specific co-factors promote FD binding to an unusual binding site

The bZIP transcription factor FD plays a pivotal role in the correct timing of floral transition in Arabidopsis thaliana and many other species. We have recently shown that FD binds the canonical G-box motif (CACGTG), both when mis-expressed in phloem companion cells and in its normal expression domain at the shoot apical meristem (SAM)1. In addition, we found that FD binds another DNA-binding site specifically at the SAM. This atypical DNA-binding site of 16 nucleotides consists of two highly conserved palindromic sequences separated by a 6 nucleotide linker sequence. Screening public plant DNA-binding site databases did not reveal homology with any known motifs. For this reason, at the moment, we refer to this atypical binding site of FD as “new-box”. Our goal is to find co-factors expressed at the SAM that promote the binding of FD to the new box. We found that the two highly conserved palindromic sequences of the new-box share partial similarity with the binding sites of some candidate genes. FD ChIP and ChIPseq in wild type and mutant plants for putative FD-interactors show that FD binds to the new box specifically at the SAM in a co-factor dependent manner. We further validated the interaction of FD with these candidate proteins by both in vitro and in vivo assays. In order to gain biological insights from the possible interaction of FD with these genes, we selected 22 FD-target genes containing the new-box in their promoter and phenotyped the corresponding mutant lines. Three of these mutants display interesting pleiotropic phenotypes and we are currently characterizing these lines in detail. If these interactions are confirmed, our research would add another layer of complexity to the regulation of floral transition and flower develompent as well as shed some light on the evolution of transcription factor binding sites.