Figure 3

Alignment of predicted MtCBF2-3;5-14 sequences. Hypothetical protein sequences are used for MtCBF12-13. These were obtained after eliminating truncating mutations from the corresponding coding sequences. For MtCBF6 and MtCBF8, proteins encoded by both transcript variants are shown. MtCBF11 protein sequence, likely resulting from a chimeric gene, is separated from others. Conserved amino acid residues are in white. They are shaded in black when shared by all sequences or in grey if a single exception exists. Conserved amino acid residues in the C-terminal regions of MtCBF5;6.2;7;8.2 resulting from intron-containing transcripts are in black and grey-shaded. The AP2/ERF domain is underlined and conserved amino acid residues therein are in red. Open squares show conserved valine and glutamic acid residues at the 14th and 19th position of the AP2/ERF domain similarly to other CBF/DREB1 sequences; V14 is critical for determining the DNA binding specificity of CBF/DREB1 proteins [48]. Solid squares indicate the conserved WLG motif in the middle of the AP2/ERF domain which is a common feature with almost all A. thaliana, G. max and Oryza sativa L. genes carrying a single AP2/ERF domain [48, 49]. Solid and open triangles show conserved amino acid residues involved in the interaction of the AP2/ERF domain with target DNA sequences and the sugar phosphate backbone, respectively [50]. The A(A/V)xxA(A/V)xxF [46] and LWSY motifs [47] are underlined with crosses and the CBF/DREB1 signature sequences bracketing the AP2/ERF domain [8] with asterisks. Open circles indicate arginine and phenylalanine residues in the PKK/RPAGRxKFxETRHP signature sequence reported to be critical for DNA binding [44]. The C-terminal clusters of hydrophobic residues [45] that may contribute positively (full lines) or negatively (broken lines) to the trans-activating properties of MtCBF2-3;5-10;12-14 are double-underlined. For MtCBF11, the second (partial) AP2/ERF domain is boxed; the LWSY motif and additional DSAWR and A(A/V)xxA(A/V)xxF motifs are dotted-underlined.