ATG8 Family Proteins Act as Scaffolds for Assembly of the ULK Complex

Abstract

Background:The ULK complex regulates autophagy, but how it interacts with the basal autophagy apparatus is unknown. Results: ULK1, -2, ATG13, and FIP200 bind to ATG8 family proteins via LIR (LC3 interacting region) motifs. Conclusion: ATG8 family proteins act as scaffolds anchoring the ULK complex on autophagosomes. Significance: We define sequence requirements for the LIR motifs and suggest how the ULK complex interacts with autophagosomes.

Analysis of the native conformation of the LIR/AIM motif in the Atg8/LC3/GABARAP-binding proteins

“…In most cases, these flexible regions undergo disorderto-order transition into a b sheet, which is induced by interaction with Atg8/LC3/ GABARAP. To further verify this finding, we tested the sequences of other Atg8/LC3/GABARAP-binding proteins 3,9 that were not crystalized in a complex with their ubiquitin-like partner, but for which the amino acid sequences are available in the UniProt database (http://www.uniprot.org/uniprot). The outcome was again the same, the LIR/AIM motif of Atg1, Atg3, Atg30, ATG4B, TBC1D5, BNIP3, FUNDC1, TP53INP1, STBD1, or RB1CC1/FIP200 overlaps with an IDPR detected by a high PONDR-FIT score (Fig.…”

FLCN, a novel autophagy component, interacts with GABARAP and is regulated by ULK1 phosphorylation

“…36 We observed a weak interaction between V5-tagged ULK1 and untagged FLCN (Fig. 4A), which suggests that FLCN might influence autophagy at the level of ULK1.…”

“…36,43 ULK1, along with its binding partners, ATG13 and RB1CC1, contain LC3-interacting region (LIR) motifs which preferentially bind to the GABARAP subfamily of Atg8 ortholog proteins. 36,43 As FLCN appears to have a preference for binding GABARAP over MAP1LC3B, it is likely that FLCN modulates autophagy through GABARAP-dependent processes. Additionally, FNIP2 has a potential LIR motif (Fig.…”

PEBP1, a RAF kinase inhibitory protein, negatively regulates starvation-induced autophagy by direct interaction with LC3

“…For example, ULK1, which is functionally equivalent to Atg1 in yeast, have canonical LIR motifs and form a large complex with ATG13 and RB1CC1/FIP200, regulating the initial step of autophagosome biogenesis and late events of autophagy. [46][47][48] Other core members of the autophagy machinery, Atg3, Atg32 in yeast or ATG4B, ATG7, and ATG13 in mammals, undergo LIR-dependent interactions with LC3 that potentially contribute to autophagy regulation. 17,21,22,[49][50][51] Moreover, some vesicle trafficking proteins, such as the RAB7-interacting protein FYCO1 or the GAP TBC1D5, interact with LC3 and play critical roles in intracellular trafficking of autophagosomes in a LIR-dependent manner.…”