Crystal structure of PXY-TDIF complex reveals a conserved recognition mechanism among CLE peptide-receptor pairs

Abstract

Plants can achieve amazing lifespans because of their continuous and repetitive formation of new organs by stem cells present within meristems. The balance between proliferation and differentiation of meristem cells is largely regulated by the CLAVATA3/ENDOSPERM SURROUNDING REGION (CLE) peptide hormones. One of the well-characterized CLE peptides, CLE41/TDIF (tracheary elements differentiation inhibitory factor), functions to suppress tracheary element differentiation and promote procambial cell proliferation, playing important roles in vascular development and wood formation. The recognition mechanisms of TDIF or other CLE peptides by their respective receptors, however, remain largely elusive. Here we report the crystal structure of TDIF in complex with its receptor PXY, a leucine-rich repeat receptor kinase (LRR-RK). Our structure reveals that TDIF mainly adopts an “Ω”-like conformation binding to the inner surface of the LRR domain of PXY. Interaction between TDIF and PXY is predominately mediated by the relatively conserved amino acids of TDIF. Structure-based sequence alignment showed that the TDIF-interacting motifs are also conserved among other known CLE receptors. Our data provide a structural template for understanding the recognition mechanism of CLE peptides by their receptors, offering an opportunity for the identification of receptors of other uncharacterized CLE peptides.

Signature motif-guided identification of receptors for peptide hormones essential for root meristem growth

“…Given the conserved C-termini of AtPep1, TDIF and RGF1, and the conserved RxR motif of AtPEPR1 and RGFRs, RGFRs might also use SERK members as co-receptors. This hypothesis is consistent with the observation that SERK members play critical but brassinosteroid-independent roles in root meristem activities [28]. Gel-filtration results showed that RGF1 induced the interaction between RGFR1 LRR or RGFR2 LRR and SERK1/2/BAK1 LRR ( Figure 5A, 5B and Supplementary information, Figure S12), further strengthening our conclusion that RGFRs 1 and 2 function as receptors of RGF1.…”

The Structural Basis of Ligand Perception and Signal Activation by Receptor Kinases

“…RPK2 contains two island domains that map to the N-terminal and central portions of its LRR domain, but their function is unknown (63,106,114). By contrast, most of the characterized peptide ligand LRR-RKs, such as HAESA, TDR/PXY, FLS2, and PEPR, do not contain island-domain structures (89,100,120,122,144). This suggests that plants may have evolved island-domain-containing LRR ectodomains to facilitate the specific binding of relatively small ligands.…”

“…In this case, however, the N-terminal capping domain of SERK1 binds on top of the IDA binding groove in HAESA, forming a lid structure that covers the three C-terminal amino acids in IDA (Figure 8a,b). These amino acids are conserved among the different IDLs and are also found in other plant peptide hormones, suggesting that these peptides also require co-receptor kinases for receptor activation (100,115,122,144) (Figure 7e). In the case of HAESA, the contribution of the SERK1 ectodomain to IDA binding has been quantitatively assessed: In the absence of the co-receptor, HAESA binds IDA with micromolar affinity, whereas SERK1 shows no detectable binding to the peptide hormone.…”

“…The same mode of binding is used by the LRRRKs PEPR1 and RGFR3, which bind AtPep1 and RGF1 peptides, respectively, with a C-terminal asparagine (115,122) (Figure 7a,d,e). Notable differences between IDA and TDIF binding are (a) that the central hydroxyproline in TDIF does not engage in polar interactions with TDR/PXY, instead binding to a rather hydrophobic pocket that provides no hydrogen-bonding partners, and (b) that TDIF features a flexible glycine residue preceding the central hydroxyproline, which induces a more pronounced kink in the peptide (144) (Figure 7b,c). The corresponding residue in IDA is an alanine (100) (Figure 7c These alignments reveal conserved sequence fingerprints (shown in orange) that are involved in the recognition of the C-terminal asparagine residue that is conserved in many plant peptide hormones.…”

“…One simple way to sort LRR-RKs is by size, because the number of individual LRRs in the ectodomains of different LRR-RKs varies greatly. All ligandbinding LRR-RKs characterized thus far (HAESA, TDR/PXY, FLS2, BRI1, and PSKR) have large LRR ectodomains consisting of 21-29 LRRs (49,100,104,114,120,122,129,144) (Figure 5d). By contrast, crystal structures of the LRR-RKs Arabidopsis thaliana SOMATIC EMBRYOGE-NESIS RECEPTOR KINASE 1 (AtSERK1), AtSERK3 [also termed Arabidopsis thaliana BRI1-ASSOCIATED RECEPTOR KINASE (AtBAK1)], and OsSERK2 confirmed the presence of small ectodomains composed of five LRRs, as predicted from their sequence.…”