All roads lead to the lysosome: exploring the degradation of TNIP1 by selective autophagy

Abstract

Selective autophagy is important for maintaining cellular homeostasis. Generally, autophagy is considered cytoprotective and anti-inflammatory, acting to limit infection and accumulation of deleterious material. Key to this function is the ability to select cargo to be degraded, and here, selective autophagy receptors play a central role. In this thesis, we show that the anti-inflammatory and pro-survival adaptor TNIP1 is a selective autophagy substrate. Moreover, we identify two LIR motifs in TNIP1, of which LIR2 is primarily responsible for binding to ATG8 proteins. While TNIP1 is constitutively degraded by autophagy in resting cells, inflammatory signaling via TLR3 resulted in increased degradation of TNIP1. Activation of the kinase TBK1 was demonstrated to directly phosphorylate LIR2 in TNIP1, leading to enhanced ATG8 interaction and increased TNIP1 degradation by ATG7-dependent macroautophagy. The degradation of TNIP1 correlated with the increased activation of downstream inflammatory signaling. This suggests that the reduction of TNIP1 protein levels by autophagy upon inflammatory stimuli occurs to allow the mounting of a robust inflammatory response.

Many studies of TNIP1 function have been done using mouse models. We found that human LIR1 is impaired by the presence of a proline, making LIR2 the main functional LIR in human TNIP1. In mice, however, LIR1 can augment binding to LC3A in conjunction with LIR2. Nonetheless, we discover that the constitutive turnover of human and mouse TNIP1 occurs independently of LIRs, contrary to the inflammation-induced degradation by macroautophagy. We show that a part of TNIP1 that binds to TAX1BP1 and NBR1 is required for lysosomal degradation. Our study of the constitutive turnover of TNIP1 highlights the existence of alternative routes to the lysosome beyond canonical macroautophagy.

Finally, we provide an overview of the ancestral selective autophagy receptor NBR1. Here, we explore the evolution of NBR1 and selective autophagy, and discuss the role of NBR1 in different forms of selective autophagy.