MYB.Ph3 transcription factor from Petunia hybrida induces similar DNA-bending/distortions on its two types of binding site

MYB.Ph3 from Petunia is a member of the MYB transcription factor family that recognizes two types of binding site, resembling direct and inverted repeats of the motif GTTA, respectively, and flanked on their 5' side by an A-rich sequence. In this study, it is shown that MYB.Ph3 induces similar conformational changes in both of its DNA-binding sites. Circular permutation assays indicate that the center of the distortions induced by MYB.Ph3 maps near the center of either MYB.Ph3-binding site. The degree of the distortion induced by MYB.Ph3 appears to be greatly affected by regions of the protein other than the DNA-binding domain, and differs from the distortion caused by animal c-MYB. Phasing analysis reveals that part of the distortion induced by MYB.Ph3 is DNA bending, oriented towards the minor groove, as is the case of its animal counterpart, c-MYB. DNA-binding by both MYB.Ph3 and animal c-MYB is more efficient in the presence of Ba2+, a divalent cation known to promote/stabilize DNA bending, than in the presence of other cations which do not favor this distortion, such as Na+ and Mg2+. In addition, both MYB proteins show higher affinity to selectively nicked DNA, which has increased DNA flexibility, strongly suggesting that DNA binding by these MYB proteins and DNA structural properties are mutually influenced.