DNA binding by the Arabidopsis CBF1 transcription factor requires the PKKP/RAGRxKFxETRHP signature sequence

The CBF/DREB1 transcriptional activators are key regulators of plant freezing tolerance. They are members of the AP2/ERF multi-gene family, which in Arabidopsis comprises about 145 members. Common to these proteins is the AP2/ERF DNA-binding domain, a 60-amino-acid fold composed of a three-stranded β-sheet followed by a C-terminal α-helix. A feature that distinguishes the CBF proteins from the other AP2/ERF proteins is the presence of “signature sequences,” PKKP/RAGRxKFxETRHP (abbreviated PKKPAGR) and DSAWR, which are located immediately upstream and downstream, respectively, of the AP2/ERF DNA-binding domain. The signature sequences are highly conserved in CBF proteins from diverse plant species suggesting that they have an important functional role. Here we show that the PKKPAGR sequence of AtCBF1 is essential for its transcriptional activity. Deletion of the sequence or mutations within it greatly impaired the ability of CBF1 to induce expression of its target genes. This impairment was not due to the mutations eliminating CBF1 localization to the nucleus or preventing protein accumulation. Rather, we show that this loss of function was due to the mutations greatly impairing the ability of the CBF1 protein to bind to its DNA recognition sequence, the CRT/DRE element. These results establish that the ability of the CBF proteins to bind to the CRT/DRE element requires amino acids that extend beyond the AP2/ERF DNA-binding domain and raise the possibility that the PKKPAGR sequence contributes to determining the DNA-binding specificity of the CBF proteins.