Structural Basis of Salicylic Acid Perception by Arabidopsis NPR Proteins

Salicylic acid (SA) is a plant hormone critical for pathogen resistance(1–3). The NPR proteins have been identified as SA receptors(4–10), although how they perceive SA and coordinate hormonal signalling remains elusive. Here we report the mapping of the SA-binding core (SBC) of Arabidopsis thaliana NPR4 and its ligand-bound crystal structure at 2.3 Å resolution. The NPR4 SBC domain, refolded with SA, adopts a unique α-helical fold, which completely buries SA in its hydrophobic core. The lack of ligand entry pathway suggests that SA binding involves a major conformational remodelling of NPR4-SBC, which is validated by HDX-MS analysis of the full-length protein and SA-induced disruption of NPR1-NPR4 interactions. We show that, despite sharing nearly identical hormone-binding residues, NPR1 displays a minimal SA-binding activity compared to NPR4. We further identify two SBC surface residues, whose mutations can alter NPR4’s SA-binding ability and interaction with NPR1. Moreover, we demonstrate that expressing a SA-hypersensitive NPR4 variant could enhance SA-mediated basal immunity without compromising effector-triggered immunity because of its intact ability to re-associate with NPR1 at high SA levels. By unveiling the structural mechanisms of SA perception, our work paves the way for future investigation on the specific roles of the NPR proteins in SA signalling and their potential for engineering plant immunity.