TBK1 puts the brakes on IRGQ-mediated autophagy

Selective autophagy requires cargo receptors that not only recognize substrates but also coordinate their engagement with the autophagy machinery. Our findings identify IRGQ as a signaling-sensitive organizer of autophagy initiation rather than a passive cargo adaptor. IRGQ contains two distinct LC3-interacting region motifs: one with unusual selectivity for GABARAPL2 and another that supports broader interaction with LC3-family proteins. Proteomics, co-immunoprecipitation and imaging place the IRGQ-GABARAPL2 complex at the interface between hATG8 proteins and core autophagy-initiation components, including ATG3, ATG7, ULK1 and ATG13. Consistently, IRGQ expression promotes hATG8 lipidation and correlates with increased LC3B puncta, supporting a model in which IRGQ nucleates a local initiation hub that couples cargo recognition to autophagosome formation. Unexpectedly, this hub is negatively regulated by TBK1. TBK1-dependent phosphorylation of GABARAPL2 at serine 10 does not broadly disrupt canonical LDS-mediated interactions, but selectively destabilizes the IRGQ-GABARAPL2 complex and weakens association with autophagy-initiation factors. This phosphorylation is induced during selective-autophagy-associated conditions, including mitophagy, xenophagy and IFNγ treatment, but not during starvation-induced bulk autophagy. Functionally, GABARAPL2 S10 phosphorylation leaves LC3 and p62 bulk-autophagy readouts largely intact while reducing GABARAPL2 flux and impairing lysosomal delivery of HLA, an IRGQ cargo. Thus, TBK1 acts as a context-dependent negative regulator of a receptor-specific autophagy axis, revealing that kinase signaling can tune selective autophagy by controlling the stability and lifetime of receptor-centered initiation hubs.