TBK1 phosphorylates HDAC3 to promote NDP52 deacetylation and accelerate intracellular bacterial clearance.

Xenophagy is a selective autophagy process crucial for eliminating intracellular pathogens, yet its regulatory mechanisms remain poorly defined. In this study, acetylome profiling identifies dynamic acetylation of the xenophagy receptor NDP52 at K202, and its deacetylation enhances during Salmonella Typhimurium infection. Acetyltransferase CREBBP/KAT3A and deacetylase HDAC3 reciprocally regulate NDP52 K202 acetylation. Deacetylated NDP52 binds more strongly to ATG8 family proteins (MAP1LC3A/B and GABARAPL2), promotes autophagosome-lysosome fusion and pathogen degradation. Innate immune kinase TBK1 phosphorylates HDAC3 at S424, stabilizes it by inhibiting ubiquitination-dependent degradation, and this regulatory cascade links innate immunity to xenophagy. Liver-specific overexpression of deacetylation-mimetic NDP52K202R in mice reduces hepatic Salmonella Typhimurium burden, attenuates liver necrosis, and suppresses proinflammatory cytokines. This study uncovers a post-translational modification paradigm in xenophagy, where NDP52 acetylation dynamics fine-tune receptor function in antibacterial responses, highlighting the HDAC3-NDP52 axis as a potential therapeutic target for infectious diseases.