Structure of the SHR–SCR heterodimer bound to the BIRD/IDD transcriptional factor JKD

Abstract

The plant-specific GAI-RGA-and-SCR (GRAS) family proteins play critical roles in plant development and signaling. Two GRAS proteins, SHORT-ROOT (SHR) and SCARECROW (SCR), cooperatively direct asymmetric cell division and the patterning of root cell types by transcriptional control in conjunction with BIRD/INDETERMINATE DOMAIN (IDD) transcription factors, although precise details of these specific interactions and actions remain unknown. Here, we present the crystal structures of the SHR-SCR binary and JKD/IDD10-SHR-SCR ternary complexes. Each GRAS domain comprises one α/β core subdomain with an α-helical cap that mediates hetero-dimerization by forming an intermolecular helix bundle. The α/β core subdomain of SHR forms the BIRD-binding groove, which specifically recognizes the zinc fingers of JKD. We identified a conserved SHR-binding motif (SHBM) in 13 BIRD/IDD transcription factors. Our results establish a structural basis for GRAS-GRAS and GRAS-BIRD interactions and provide valuable clues towards our understanding of these regulators involved in plant-specific signaling networks.

Structural basis of the specific interactions of GRAS family proteins

“…). However, GRAS domains lack the SAM‐binding motifs, which are conserved in SAM‐MT members and no binding was observed for SAM, S ‐adenosyl homocysteine, or the product monomethyl‐L‐lysine in our binding assays using isothermal titration calorimetry (ITC) , suggesting that the GRAS domains lack methyltransferase activity.…”

“…More definitive evidence showing oligomerization of GRAS proteins has been obtained using hydrodynamic analyses such as analytical ultracentrifugation (AUC) with purified protein samples (Fig. ) . The analyses using AUC clarified the stable monodispersed states of Arabidopsis GRAS proteins in solution with estimated molecular masses showing that SCL5 exists as a monomer, while SCL3 exists as a homodimer, and SHR‐SCR exist as a 1 : 1 heterodimer.…”

“…The reported crystal structures of the SHR‐SCR heterodimer and the SCL7 homodimer were determined at 2.0 and 1.8 Å resolution, respectively . These structures revealed a common subdomain organization of the GRAS domain comprising an α‐helical cap and α/β core subdomains (Fig.…”

Uncovering Gene Regulatory Networks Controlling Plant Cell Differentiation

“…Yeast-2-hybrid experiments have shown that SHR and SCR can bind to JACKDAW, as well as to its closest homologs BALD IBIS, and MAGPIE [18,20]. Moreover, a recent manuscript describes the crystal structure of the SHR-SCR-JKD and SHR-SCR-MGP complexes [21]. These results indicate that SHR-SCR cannot bind to DNA alone, but require formation of a complex with an IDD TF.…”

The beauty of the small

“…For example, Hirano et al 1 have investigated the interactions that lie at the heart of root patterning by determining the structure of a heterodimer of SCARECROW (SCR) and SHORT-ROOT (SHR), both on its own and when bound to the transcription factor JACKDAW (JKD). These specific interactions are important for determining cell fates in the developing root, but SCR and SHR are also representatives of a large family of transcriptional regulators known as GRAS proteins due to their homologous GRAS domains.…”