A functionally required unfoldome from the plant kingdom: intrinsically disordered N-terminal domains of GRAS proteins are involved in molecular recognition during plant development

Abstract

The intrinsic disorder is highly abundant in eukaryotic genomes. In the animal kingdom, numerous intrinsically disordered proteins (IDPs) have been characterized, especially in cell signalling and transcription regulation. An intrinsically disordered region often folds in different structures allowing an IDP to recognize and bind different partners at various binding interfaces. In contrast, there have only been a few reports of IDPs from the plant kingdom. Plant-specific GRAS proteins play critical and diverse roles in plant development and signalling and often act as integrators of signals from multiple plant growth regulatory inputs. Using computational and bioinformatics tools, we demonstrate here that the GRAS proteins are intrinsically disordered, thus forming the first functionally required unfoldome in the plant kingdom. Furthermore, the N-terminal domains of GRAS proteins are predicted to contain numerous Molecular Recognition Features (MoRFs), short interaction-prone segments that are located within extended disorder regions and are able to recognize their interacting partners and to undergo disorder-to-order transitions upon binding to these specific partners. Overlapping with the relatively conserved motifs in the N-terminal domains of GRAS proteins, these predicted MoRFs represent the potential protein-protein binding sites and may be involved in molecular recognition during plant development. This study enables us to propose a conceptual framework that guides future experimental approaches to understand structure-function relationships of the entire GRAS family.

Two GRAS Proteins, SCARECROW-LIKE21 and PHYTOCHROME A SIGNAL TRANSDUCTION1, Function Cooperatively in Phytochrome A Signal Transduction

“…It is possible that the divergence of the N terminus of the GRAS proteins during evolution increased the functional capacity of the protein family, including the mediation of gibberellin and phyA signals. Sun et al (2011) predicted that molecular recognition features within GRAS protein N termini can adopt different tertiary structures facilitating the recruitment of additional protein partners. This could suggest that the N-terminal domain determines the specificity for a distinct pathway, whereas the C-terminal so-called "GRAS domain" carries out an as yet unknown function.…”

Subclassifying Disordered Proteins by the Ch-CDF Plot Method

“…Together these observations suggest that the quadrant (Q3) is likely to contain proteins containing relatively balanced contributions of structured and disordered regions. For this reason here we have named the proteins in this quadrant mixed rather than collapsed disorder, a description that may have appeared in previous publications [16][17][18]. These observations don't rule out the possibility that some of the proteins in (Q3) or even in (Q4) might be native molten globules.…”

“…Interestingly, the plant developmental proteins called GRAS straddled the structure and mixed quadrant (Q2, Q3). The N-domains of these proteins localized to the mixed and disordered quadrants (Q4, Q3), while almost all of the C-domains of these proteins localized to the structured quadrant (Q2) [18].…”

“…The CH-CDF plot has also been used to classify the transcription factors associated with the induction of pluripotent stem cells [17] and a collection of plant-specific developmental proteins as well as their distinctive domains [18]. In all three cases, the distributions of the various proteins and domains among the four outcomes provide overviews of similarities and differences between the different sets of proteins [16][17][18]. According to these prior studies, the CH-CDF plot appears to be useful for identifying overall structure-disorder trends for collections of proteins.…”

Homology-based analysis of the GRAS gene family in tobacco

“…The N-terminal region of GRAS proteins is variable, whereas the C-terminal sequence is highly conserved, and contains five motifs; leucine heptad repeat I (LHRI), VHIID, leucine heptad repeat II (LHRII), PFYRE, and SAW (Pysh et al, 1999;Bolle, 2004). It is noted that the conserved domains in the C-terminus are related to transcriptional regulation; however, the N-terminus targets the downstream proteins and determines the specificity of function (Sun et al, 2011). The GRAS protein family can be divided into eight subfamilies that have been named either after their members or after a common motif: DELLA, HAM, LISCL, PAT, LS, SCR, SHR, and SCL3 subfamilies (Tian et al, 2004).…”