Network organization of the human autophagy system
Open accessAbstract
Autophagy, the process by which proteins and organelles are sequestered in autophagosomal vesicles and delivered to the lysosome/vacuole for degradation, provides a primary route for turnover of stable and defective cellular proteins. Defects in this system are linked with numerous human diseases. Although conserved protein kinase, lipid kinase and ubiquitin-like protein conjugation subnetworks controlling autophagosome formation and cargo recruitment have been defined, our understanding of the global organization of this system is limited. Here we report a proteomic analysis of the autophagy interaction network in human cells under conditions of ongoing (basal) autophagy, revealing a network of 751 interactions among 409 candidate interacting proteins with extensive connectivity among subnetworks. Many new autophagy interaction network components have roles in vesicle trafficking, protein or lipid phosphorylation and protein ubiquitination, and affect autophagosome number or flux when depleted by RNA interference. The six ATG8 orthologues in humans (MAP1LC3/GABARAP proteins) interact with a cohort of 67 proteins, with extensive binding partner overlap between family members, and frequent involvement of a conserved surface on ATG8 proteins known to interact with LC3-interacting regions in partner proteins. These studies provide a global view of the mammalian autophagy interaction landscape and a resource for mechanistic analysis of this critical protein homeostasis pathway.
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Proteomics techniques such as yeast two-hybrid screens or pulldown analyses can be used to identify interacting pathways contributing to disease.
“Moreover, proteomics techniques such as yeast two-hybrid screens or “pulldown analyses” can be used to identify interacting pathways contributing to disease [27].”
From Multi-omics approaches to disease (2017) · cites this paper as [27]
In the case of proteins, edges can be based on physical interactions, such as those identified from yeast two-hybrid analyses or pulldowns.
“In the case of proteins, edges can be based on physical interactions, such as those identified from global yeast two-hybrid analyses or a series of “pulldowns” [27].”
From Multi-omics approaches to disease (2017) · cites this paper as [27]
Frame-shift mutations in exon 8 and exon 16 of TECPR2 (c.1319delT, c.3416delT) terminate in a premature stop codon, and an initial link between this gene and defects in autophagy was reported.
“Frame‐shift mutations in exon 8 and exon 16 of TECPR2 (c.1319delT, c.3416delT) terminate in a premature stop codon (Oz‐Levi et al, 2012; Heimer et al, 2016), and an initial link between this gene to defects in autophagy was reported (Behrends et al, 2010; Oz‐Levi et al, 2012).”
From Autophagy in major human diseases (2021) · cites this paper as Behrends et al, 2010
TECPR2 is a multi-domain protein comprised of three WD repeats at the N terminus, the mostly unstructured middle region and six TECPR2 repeats terminating with an LC3-interacting region (LIR) motif at its C terminus.
“TECPR2 is a multi‐domain protein comprised of three WD repeats at the N terminus, the mostly unstructured middle region and six TECPR2 repeats terminating with an LC3‐interacting region (LIR) motif at its C terminus (Behrends et al, 2010; Stadel et al, 2015).”
From Autophagy in major human diseases (2021) · cites this paper as Behrends et al, 2010
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- Authors
- Behrends, C., Sowa, M. E., Gygi, S. P., & Harper, J. W.
- Affiliations
- Harvard University (US)
- Corresponding author
- Harper, J. Wade
- Venue
- Nature
- Published
- 2010-06-20
- Volume
- 466
- Issue
- 7302
- Pages
- 68-76
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC2901998
- OpenAlex
- W2045373134
- Cited by
- 1,554
- References
- 38
- Citations by year
- 2026: 33 · 2025: 54 · 2024: 76 · 2023: 58 · 2022: 89 · 2021: 94 · 2020: 91 · 2019: 98 · 2018: 81 · 2017: 101 · 2016: 123 · 2015: 128 · 2014: 106 · 2013: 136 · 2012: 152
- FWCI
- 97.98
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- Glenn Foundation for Medical Research
- Takeda Oncology
- National Institute on Aging (R01AG011085)
- National Institute of General Medical Sciences (R01GM095567, R01GM054137, R01GM070565)
- Topics
- Health Sciences › Medicine › Epidemiology › Autophagy in Disease and Therapy
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Ubiquitin and proteasome pathways
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Cellular transport and secretion
- Keywords
- autophagy, protein-protein interaction network, LC3, GABARAP, LC3-interacting region, autophagosome formation, cargo recruitment, vesicle trafficking, protein phosphorylation, lipid phosphorylation, ubiquitination, proteostasis, lysosomal degradation
- MeSH terms
- Autophagy-Related Protein 8 Family, Autophagy, Homeostasis, Humans, Microfilament Proteins, Phagosomes, Phosphorylation, Protein Binding, Reproducibility of Results, Protein Interaction Mapping, RNA Interference, Proteomics, Adaptor Proteins, Signal Transducing, Ubiquitination
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