TBK1 phosphorylation activates LIR-dependent degradation of the inflammation repressor TNIP1

Abstract

Limitation of excessive inflammation due to selective degradation of pro-inflammatory proteins is one of the cytoprotective functions attributed to autophagy. In the current study, we highlight that selective autophagy also plays a vital role in promoting the establishment of a robust inflammatory response. Under inflammatory conditions, here TLR3-activation by poly(I:C) treatment, the inflammation repressor TNIP1 (TNFAIP3 interacting protein 1) is phosphorylated by Tank-binding kinase 1 (TBK1) activating an LIR motif that leads to the selective autophagy-dependent degradation of TNIP1, supporting the expression of pro-inflammatory genes and proteins. This selective autophagy efficiently reduces TNIP1 protein levels early (0–4 h) upon poly(I:C) treatment to allow efficient initiation of the inflammatory response. At 6 h, TNIP1 levels are restored due to increased transcription avoiding sustained inflammation. Thus, similarly as in cancer, autophagy may play a dual role in controlling inflammation depending on the exact state and timing of the inflammatory response.

Targeted proteomics addresses selectivity and complexity of protein degradation by autophagy

“…To cover bulk and selective autophagy subtypes by targeted proteomics, we screened the respective literature for relevant proteins (1, 4, 7, 16). In addition, we included selected, autophagy-relevant proteins from ongoing research projects in our groups (17), which led to a list of 41 proteins-of-interest (POIs) ( supplemental Table S1 ). MS-compatible peptides of POIs for targeted proteomics are commonly generated by proteolytic digestion using the endoprotease trypsin.…”

Repressive Control of Keratinocyte Cytoplasmic Inflammatory Signaling

“…More recently, TNIP1's interaction with a number of autophagy-related proteins has sparked interest in not only its degradation by autophagy but also, a potential role as a selective-autophagy receptor itself [189,190]. Autophagy is now understood to be another potential control on inflammation through its selective degradation of pathway components as well as pathogens and damaged organelles [191].…”

“…The relationship between both processes is certainly more intricate, as repressors of inflammation can also be degraded [192]. TNIP1 directly interacts with LC3, an important autophagy protein, and localizes to autophagosomes with this interaction being enhanced by TBK1 phosphorylation on amino acid S83 [190]. It has been likened to the well-known autophagy receptor p62/SQSTM1 which itself has been shown to negatively regulate keratinocyte TLR2/6 and TLR4 inflammatory pathways in a TRAF6-and MyD88-dependent manner [193].…”

“…The capacity of TNIP1 to repress inflammation is derived from a complex interplay of events and factors regulating its ultimate protein levels. These include its relatively low level of basal expression in many different cells, reduced protein levels in some inflammatory disease states, and availability of partner proteins [23,159,177,178,190,201]. While TNIP1 gene expression is positively regulated by inflammation-associated NF-κB activation, initial response to inflammatory signals includes TNIP1 protein degradation [190,202,203].…”

“…These include its relatively low level of basal expression in many different cells, reduced protein levels in some inflammatory disease states, and availability of partner proteins [23,159,177,178,190,201]. While TNIP1 gene expression is positively regulated by inflammation-associated NF-κB activation, initial response to inflammatory signals includes TNIP1 protein degradation [190,202,203]. TNIP1 breakdown may be stimuli-and cell-type-dependent based on data to-date and includes proteasome-and autophagy-dependent routes [190,[202][203][204].…”