Unveiling Silica Nanoparticle Targets in Rice and Mechanistic Insights into Apoplastic Remodeling

Silica nanoparticles (SiNPs) have emerged as promising agents for enhancing crop growth and stress resilience, yet their molecular targets remain unclear. Using the limited proteolysis–mass spectrometry technique, we identified 171 proteins that showed significant changes upon SiNP exposure, with marked enrichment in cysteine residues and cysteine-containing dipeptide motifs. Given that large SiNPs are mainly confined to the apoplastic space, we concentrated on their effects on extracellular protein function. Functional assays demonstrated that SiNPs modulate the activity of antifungal proteins by either enhancing or attenuating their efficacy, while markedly inhibiting the activities of superoxide dismutase OsSOD2 and Class III peroxidase OsPRX30. By monitoring changes in the reactive oxygen species (ROS) levels in vivo, we demonstrated that, by inactivating ROS-scavenging enzymes, SiNPs trigger a localized burst of ROS that primes antioxidant defenses. Collectively, our findings reveal direct targets of SiNPs, guiding novel pesticide design and crop genetic improvement in the future.