Structure of the unique tetrameric STENOFOLIA homeodomain bound with target promoter DNA.

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

doi:10.1107/s205979832100632x

Abstract

Homeobox transcription factors are key regulators of morphogenesis and development in both animals and plants. In plants, the WUSCHEL-related homeobox (WOX) family of transcription factors function as central organizers of several developmental programs ranging from embryo patterning to meristematic stem-cell maintenance through transcriptional activation and repression mechanisms. The Medicago truncatula STENOFOLIA (STF) gene is a master regulator of leaf-blade lateral development. Here, the crystal structure of the homeodomain (HD) of STF (STF-HD) in complex with its promoter DNA is reported at 2.1 Å resolution. STF-HD binds DNA as a tetramer, enclosing nearly the entire bound DNA surface. The STF-HD tetramer is partially stabilized by docking of the C-terminal tail of one protomer onto a conserved hydrophobic surface on the head of another protomer in a head-to-tail manner. STF-HD specifically binds TGA motifs, although the promoter sequence also contains TAAT motifs. Helix α3 not only serves a canonical role as a base reader in the major groove, but also provides DNA binding in the minor groove through basic residues located at its C-terminus. The structural and functional data in planta reported here provide new insights into the DNA-binding mechanisms of plant-specific HDs from the WOX family of transcription factors.

Highlights

Homeodomain (HD)-containing transcription factors are some of the most important regulators of morphology and differentiation in fungi, animals and plants (Garcia-Fernandez, 2005; Miksiunas et al, 2020; Burglin & Affolter, 2016)
WUS clade members, including WUS and WOX1–WOX7, share a conserved WUS box at the C-terminus that is specific to the WUS clade (Haecker et al, 2004; Ikeda et al, 2009; Lin, Niu, McHale et al, 2013) and a conserved HD that is typical of the whole WUCHEL-related homeobox (WOX) family (Costanzo et al, 2014)
After screening a number of synthetic DNA oligonucleotides, we found that STF-HD readily crystallized when in complex with a 22 bp target promoter DNA

Summary

Introduction

Homeodomain (HD)-containing transcription factors are some of the most important regulators of morphology and differentiation in fungi, animals and plants (Garcia-Fernandez, 2005; Miksiunas et al, 2020; Burglin & Affolter, 2016). WUS clade WOX members have a promiscuous ability to substitute for each others’ function if driven by specific promoters, as demonstrated by the complementation of the lam mutant in leaf development (Lin, Niu, McHale et al, 2013) and of the wus mutant in SAM maintenance (Dolzblasz et al, 2016), suggesting a conserved mechanism of DNA recognition and transcriptional repression. While the HD contacts DNA, the WUS box is essential for the recruitment of the TOPLESS (TPL) family of transcriptional co-repressors (Busch et al, 2010; Zhang et al, 2014) Both the WUS box and HD are essential for the roles of STF in leaf development and of WUS in shoot meristem maintenance

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Results

Conclusion