TNIP1 inhibits selective autophagy via bipartite interaction with LC3/GABARAP and TAX1BP1

Mitophagy is a form of selective autophagy that disposes of superfluous and potentially damage-inducing organelles in a tightly controlled manner. While the machinery involved in mitophagy induction is well known, the regulation of the components is less clear. Here, we demonstrate that TNIP1 knockout in HeLa cells accelerates mitophagy rates and that ectopic TNIP1 negatively regulates the rate of mitophagy. These functions of TNIP1 depend on an evolutionarily conserved LIR motif as well as an AHD3 domain, which are required for binding to the LC3/GABARAP family of proteins and the autophagy receptor TAX1BP1, respectively. We further show that phosphorylation appears to regulate its association with the ULK1 complex member FIP200, allowing TNIP1 to compete with autophagy receptors, which provides a molecular rationale for its inhibitory function during mitophagy. Taken together, our findings describe TNIP1 as a negative regulator of mitophagy that acts at the early steps of autophagosome biogenesis. [Display omitted] •TNIP1 possesses an LIR motif•TNIP1 endogenously inhibits mitophagy•TNIP1 interacts with TAX1BP1 and FIP200•Phosphorylation by TBK1 regulates TNIP1’s function Le Guerroué et al. show that TNIP1 acts as an inhibitor of mitophagy by binding with TAX1BP1 and FIP200 in a competitive manner. While binding to TAX1BP1 is essential for its inhibitory role, they further demonstrate that phosphorylation regulates binding to FIP200, providing a molecular rationale for TNIP1’s function.