Four divergent Arabidopsis ethylene-responsive element-binding factor domains bind to a target DNA motif with a universal CG step core recognition and different flanking bases preference.

The Arabidopsis ethylene-responsive element-binding factor (AtERF) family of transcription factors has approximately 120 members, all of which possess a highly conserved ERF domain. AtERF1, AtERF4, AtEBP and CBF1 are members from different phylogenetic subgroups within the family. Electrophoretic mobility shift assay analyses revealed that the ERF domains of these four proteins were capable of binding specifically to either GCC or dehydration-responsive element (DRE) motifs. In vitro and in vivo binding assays of the four AtERFs with the DRE motif showed that the recognition of the CG step was indispensable in all four of the specific binding reactions, implying that there may be a universal binding characteristic of various ERF domains binding to a given consensus (e.g. the DRE motif). In addition, the core DNA-binding motifs preferred by the four AtERFs were identified, and all of these motifs contained a conserved CG step core. Thus, conserved recognition of the CG step may be the foundation of the formation of the stable complex by the ERF domain with the DRE motif, which is probably determined by the highly conserved residues presented in the DNA contact surface among the whole AtERF family members. The different preferences at flanking bases of individual ERF domains, which appear to be attributed to the subfamily- or subgroup-specific residues, may be essential discrimination of the target binding motif from various similar sequences by divergent AtERF domains.