Exploring the evolutionary conservation of SCR–SHR and RBR–SCR interactions across Viridiplantae

In Arabidopsis thaliana, one of the most important gene families involved in plant development is the one encoding the GRAS transcription factors. In this family, SHORT-ROOT (SHR) and SCARECROW (SCR) play key roles in asymmetric cell division and the maintenance of the root stem cell niche, while SCR is additionally regulated by RETINOBLASTOMA-RELATED (RBR) through the LxCxE motif. GRAS proteins can be traced back to Zygnematophyceae algae, indicating an early origin of this protein family; therefore, we sought to determine whether protein–protein interactions could have originated in this clade, including the SCR–SHR interaction, as well as the potential interaction between RBR and a GRAS protein carrying an LxCxE motif, and to assess how conserved are these interactions across land plants. We addressed this question by identifying all GRAS proteins in Zygnematophyceae and analyzing their domains, revealing that not all GRAS proteins contain the full set of characteristic GRAS elements and that only a few sequences harbor pseudo–LxCxE motifs. Through in silico prediction of protein–protein interactions between SCR–SHR and RBR–SCR_LxCxE across the Viridiplantae lineage, and by comparing the three-dimensional interactions of heterodimers from different species, our results suggest that both SCR–SHR and RBR–SCR_LxCxE interactions likely originated in Zygnematophyceae and were subsequently refined in land plants through amino acid changes that enhance protein–protein binding, leading to increasingly similar interactions along land plants.