TBK1-mediated phosphorylation of WIPI2 links bacteria recognition to autophagosome formation in xenophagy.

Xenophagy, a selective autophagy pathway, is a critical innate immune defense mechanism that targets pathogens for lysosomal degradation. However, the molecular mechanisms enabling autophagosomes to specifically recognize and engulf bacteria remain incompletely understood. Here, we identify WIPI2, a core component that drives autophagosome biogenesis, as a novel phosphorylation substrate of TBK1 during Salmonella Typhimurium infection. We demonstrate that TBK1 phosphorylates WIPI2 at Ser96, which enhances its interaction with ATG16L1 and its binding to PtdIns3P. Crucially, the recruitment of WIPI2 to intracellular bacteria is dependent on its interaction with ATG16L1, which is localized to the Salmonella-containing vacuole. Furthermore, TBK1-mediated phosphorylation of WIPI2 is required for efficient bacterial clearance. Collectively, our findings reveal a molecular mechanism whereby TBK1-mediated phosphorylation of WIPI2 directs localized phagophore expansion around invading bacteria, thereby bridging bacterial recognition with autophagosome assembly.