Journal:Acta Cryst D:S205979832100632X

Structure of the unique tetrameric STENOFOLIA homeodomain bound with promoter DNA

Prabhat Kumar Pathak, Fei Zhang, Shuxia Peng, Lifang Niu, Juhi Chaturvedi, Justin Yoshida Elliott, Yan Xiang, Million Tadege, Junpeng Deng ^[1]

Molecular Tour
Homeodomain (HD) containing transcription factors are one of the most important regulators of morphology and differentiation in fungi, animals and plants. Among different types of HD containing transcriptional regulators, the WUCHEL-RELATED HOMEOBOX (WOX) family is unique to plants and instructs plant growth and development. The Medicago truncatula STENOFOLIA (STF) is a master regulator of leaf blade lateral development. Here, we report the crystal structure of the HD of STF in complex with its promoter DNA at 2.1 Å resolution. (HDA in green, HDB in yellow) bound on a 22-bps DNA (color in magenta and alice blue for each strand respectively) in the ASU. , enclosing nearly entire bound DNA surface. Depicted are four STF-HDs (HDA' in blue and HDB' in wheat) bound on the DNA. HDA/HDA' and HDB/HDB' are crystallographic symmetry mates, respectively. A second DNA molecule in crystal packing is shown (DNAsym, colored in light pink and teal) forming a pseudo-continuous helix. is shown in sacefill representaion. The bound dsDNA is shown as cartoons. Notice nearly the entire DNA surface is clamped by the protein. Although the target promoter DNA sequence contains a mixture of 'TGA' and 'TAAT' motifs, STF-HD specifically binds 'TGA'.

Major groove DNA base recognitions:

• (in cyan).
• (im green).
• (in hot pink).
• (in yellow).

When compared to DNA recognition by other HDs, the 'base reader' helix alpha 3 in STF-HD not only specifies DNA sequence in the major groove of DNA, but also interacts with DNA from the minor groove providing important interactions:

Our structure based mutagenesis and functional studies in planta support the structural observations. The findings from this study provide new insights into the DNA binding mechanisms of plant specific HDs from WOX family or transcription factors.

References

1. ↑ Pathak PK, Zhang F, Peng S, Niu L, Chaturvedi J, Elliott J, Xiang Y, Tadege M, Deng J. Structure of the unique tetrameric STENOFOLIA homeodomain bound with target promoter DNA. Acta Crystallogr D Struct Biol. 2021 Aug 1;77(Pt 8):1050-1063. doi:, 10.1107/S205979832100632X. Epub 2021 Jul 29. PMID:34342278 doi:http://dx.doi.org/10.1107/S205979832100632X