AlphaFold2-multimer guided high-accuracy prediction of typical and atypical ATG8-binding motifs
Author(s)
Type
Journal Article
Abstract
Macroautophagy/autophagy is an intracellular degradation process central to cellular homeostasis and defense against pathogens in eukaryotic cells. Regulation of autophagy relies on hierarchical binding of autophagy cargo receptors and adaptors to ATG8/LC3 protein family members. Interactions with ATG8/LC3 are typically facilitated by a conserved, short linear sequence, referred to as the ATG8/LC3 interacting motif/region (AIM/LIR), present in autophagy adaptors and receptors as well as pathogen virulence factors targeting host autophagy machinery. Since the canonical AIM/LIR sequence can be found in many proteins, identifying functional AIM/LIR motifs has proven challenging. Here, we show that protein modelling using Alphafold-Multimer (AF2-multimer) identifies both canonical and atypical AIM/LIR motifs with a high level of accuracy. AF2-multimer can be modified to detect additional functional AIM/LIR motifs by using protein sequences with mutations in primary AIM/LIR residues. By combining protein modelling data from AF2-multimer with phylogenetic analysis of protein sequences and protein-protein interaction assays, we demonstrate that AF2-multimer predicts the physiologically relevant AIM motif in the ATG8-interacting protein 2 (ATI-2) as well as the previously uncharacterized noncanonical AIM motif in ATG3 from potato (Solanum tuberosum). AF2-multimer also identified the AIM/LIR motifs in pathogen-encoded virulence factors that target ATG8 members in their plant and human hosts, revealing that cross-kingdom ATG8-LIR/AIM associations can also be predicted by AF2-multimer. We conclude that the AF2-guided discovery of autophagy adaptors/receptors will substantially accelerate our understanding of the molecular basis of autophagy in all biological kingdoms.
Date Issued
2023-02-08
Date Acceptance
2022-12-15
Citation
PLoS Biology, 2023, 21 (2), pp.1-19
ISSN
1544-9173
Publisher
Public Library of Science (PLoS)
Start Page
1
End Page
19
Journal / Book Title
PLoS Biology
Volume
21
Issue
2
Copyright Statement
Copyright: © 2023 Ibrahim et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
License URL
Identifier
https://www.ncbi.nlm.nih.gov/pubmed/36753519
PII: PBIOLOGY-D-22-02166
Subjects
Amino Acid Motifs
Autophagy
Autophagy-Related Protein 8 Family
Carrier Proteins
Furylfuramide
Humans
Microtubule-Associated Proteins
Phylogeny
Protein Binding
Publication Status
Published
Coverage Spatial
United States
Article Number
e3001962
Date Publish Online
2023-02-08