Characterization of autophagosome formation site by a hierarchical analysis of mammalian Atg proteins

By Eisuke Itakura, N. Mizushima. Autophagy, 2010

836 citations recorded by the source corpus.

Autophagy is an intracellular degradation process, through which cytosolic materials are delivered to the lysosome. Despite recent identification of many autophagy-related genes, how autophagosomes are generated remains unclear. Here, we examined the hierarchical relationships among mammalian Atg proteins. Under starvation conditions, ULK1, Atg14, WIPI-1, LC3 and Atg16L1 target to the same compartment, whereas DFCP1 localizes adjacently to these Atg proteins. In terms of puncta formation, the protein complex including ULK1 and FIP200 is the most upstream unit and is required for puncta formation of the Atg14-containing PI3-kinase complex. Puncta formation of both DFCP1 and WIPI-1 requires FIP200 and Atg14. The Atg12-Atg5-Atg16L1 complex and LC3 are downstream units among these factors. The punctate structures containing upstream Atg proteins such as ULK1 and Atg14 tightly associate with the ER, where the ER protein Vacuole membrane protein 1 (VMP1) also transiently localizes. These structures are formed even when cells are treated with wortmannin to suppress autophagosome formation. These hierarchical analyses suggest that ULK1, Atg14 and VMP1 localize to the ER-associated autophagosome formation sites in a PI3-kinase activity-independent manner.

Subfields: Epidemiology, Parasitology, Physiology

View Paper: https://www.semanticscholar.org/paper/00174c68d4bd0e1ed5b60b7e5956c59c02bbc687

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Citations in the corpus

Autophagy Failure in Alzheimer's Disease – Locating the Primary Defect (2011, background): “…cup-shaped omegasome, and sequesters a region of cytoplasm to form a double-membrane-limited autophagosome (Axe et al., 2008; Geng et al., 2010; Hailey et al., 2010; Hayashi-Nishino et al., 2009; Itakura and Mizushima, 2010; Ravikumar et al., 2010; Tian et al., 2010; Xie and Klionsky, 2007).”
Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition) (2012, neutral): “VMP1 is an essential autophagy gene that is conserved from Dictyostelium to mammals,(322,633) and the VMP1 protein regulates early steps of the autophagic pathway.(561) VMP1 is poorly expressed in mammalian cells under nutrient-normal conditions, but is”
Autophagy: Renovation of Cells and Tissues (2011, background): “The core Atg proteins are highly conserved in other eukaryotes, including mammals, and they act in a similar hierarchical manner in yeast and mammals (Itakura and Mizushima, 2010; Suzuki et al., 2007).”
Autophagy in immunity and inflammation (2011, background): “Although VMP1 interacts with beclin 1 and is present at the autophagosome formation site at an early stage, it seems to function at a late stage in autophagy 13 ”
Mechanisms of Selective Autophagy (2016, neutral): “ATG9A system, PI3Kc1, the WIPIs, the ATG12–ATG5-ATG16L complex and finally the ATG8-family proteins [100-102].”
WIPI2 Links LC3 Conjugation with PI3P, Autophagosome Formation, and Pathogen Clearance by Recruiting Atg12–5-16L1 (2014, background): “, 2013), recruitment of Atg12–5-16L1 depends on PtdIns(3)P formation (Itakura and Mizushima, 2010).”
Molecular mechanisms and physiological functions of mitophagy (2021, neutral): “Several autophagy-related proteins are recruited to the autophagosome formation site in a hierarchical order (Itakura & Mizushima, 2010).”
Guidelines for the use and interpretation of assays for monitoring autophagy (2012, background): “VMP1 is an essential autophagy gene that is conserved from Dictyostelium to mammals,(232,462) and the VMP1 protein regulates early steps of the autophagic pathway.(420) VMP1 is poorly expressed in mammalian cells under nutrient-normal conditions, but is highly upregulated in cells undergoing autopha”
Monitoring and Measuring Autophagy (2017, background): “The most upstream autophagy factors are the ULK1 complex, consisting of ULK1, ATG13, FIP200, and ATG101, and ATG9A on vesicles [18].”
Mitochondria-lysosome contacts regulate mitochondrial fission via Rab7 GTP hydrolysis (2018, neutral): “…10,33 , EGFP-LC3 was a gift from Karla Kirkegaard (Addgene #11546) 34 , pMXs-puro GFP-DFCP1 was a gift from Noboru Mizushima (Addgene #38269) 35 , pAc-GFPC1-Sec61beta was a gift from Tom Rapoport (Addgene #15108), pCMV3-SMAC-HA-eGFP was a gift from Richard Kahn (Addgene #67489), mVenus C1…”
mTOR inhibits autophagy by controlling ULK1 ubiquitylation, self-association and function through AMBRA1 and TRAF6 (2013, methodology): “(d) HEK293 cells were co-transfected with vectors encoding AMBRA1 together with ULK1–Myc FL (full length) or its deletion mutants encoding the kinase and the proline-rich domains (1829–1,051), and the ULK1 carboxy-terminal domain (11-828).”
The regulation of autophagy – unanswered questions (2011, background): “Thus, it is possible that, in contrast to yeast, mammalian cells have multiple PAS equivalents (Itakura and Mizushima, 2010).”
ULK1 induces autophagy by phosphorylating Beclin-1 and activating Vps34 lipid kinase (2013, methodology): “Active GST-ULK1 (1-649) and GST-ULK2 (1-478) from insect cells was purchased from CQuential Solutions (Moraga, CA).”
Role of AMPK-mTOR-Ulk1/2 in the Regulation of Autophagy: Cross Talk, Shortcuts, and Feedbacks (2011, background): “Furthermore, while ulk1 / MEFs displayed normal LC3 lipidation in response to glucose starvation (60), these cells did not respond with autophagy induction to rapamycin treatment (47).”
An Overview of Autophagy: Morphology, Mechanism, and Regulation (2014, background): “In yeast, Atg9 may cycle between the PAS and peripheral sites (122).”