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Yang Y, Pan Z, Sun J, Welch J, Klionsky DJ. Autophagy and machine learning: Unanswered questions. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167263. [PMID: 38801963 DOI: 10.1016/j.bbadis.2024.167263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/27/2024] [Accepted: 05/21/2024] [Indexed: 05/29/2024]
Abstract
Autophagy is a critical conserved cellular process in maintaining cellular homeostasis by clearing and recycling damaged organelles and intracellular components in lysosomes and vacuoles. Autophagy plays a vital role in cell survival, bioenergetic homeostasis, organism development, and cell death regulation. Malfunctions in autophagy are associated with various human diseases and health disorders, such as cancers and neurodegenerative diseases. Significant effort has been devoted to autophagy-related research in the context of genes, proteins, diagnosis, etc. In recent years, there has been a surge of studies utilizing state of the art machine learning (ML) tools to analyze and understand the roles of autophagy in various biological processes. We taxonomize ML techniques that are applicable in an autophagy context, comprehensively review existing efforts being taken in this direction, and outline principles to consider in a biomedical context. In recognition of recent groundbreaking advances in the deep-learning community, we discuss new opportunities in interdisciplinary collaborations and seek to engage autophagy and computer science researchers to promote autophagy research with joint efforts.
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Affiliation(s)
- Ying Yang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA; Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Zhaoying Pan
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jianhui Sun
- Department of Computer Science, University of Virginia, Charlottesville, VA 22903, USA
| | - Joshua Welch
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Daniel J Klionsky
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA; Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA.
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Shi Y, Suzuki K. Quantitative analysis of the spatial distance between autophagy-related membrane structures and the endoplasmic reticulum in Saccharomyces cerevisiae. Autophagy 2024:1-8. [PMID: 38478967 DOI: 10.1080/15548627.2024.2330033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 03/08/2024] [Indexed: 03/25/2024] Open
Abstract
Macroautophagy/autophagy is the process by which cells degrade their cytoplasmic proteins or organelles in vacuoles to maintain cellular homeostasis under severe environmental conditions. In the yeast Saccharomyces cerevisiae, autophagy-related (Atg) proteins essential for autophagosome formation accumulate near the vacuole to form the dot-shaped phagophore assembly site/pre-autophagosomal structure (PAS). The PAS then generates the phagophore/isolation membrane (PG), which expands to become a closed double-membrane autophagosome. Hereinafter, we refer to the PAS, PG, and autophagosome as autophagy-related structures (ARSs). During autophagosome formation, Atg2 is responsible for tethering the ARS to the endoplasmic reticulum (ER) via ER exit sites (ERESs), and for transferring phospholipids from the ER to ARSs. Therefore, ARS and the ER are spatially close in the presence of Atg2 but are separated in its absence. Because the contact of an ARS with the ER must be established at the earliest stage of autophagosome formation, it is important to know whether the ARS is tethered to the ER. In this study, we developed a rapid and objective method to estimate tethering of the ARS to the ER by measuring the distance between the ARS and ERES under fluorescence microscopy, and found that tethering of the ARS to the ER was lost without Atg1. This method might be useful to predict the tethering activity of Atg2.Abbreviation: ARS, autophagy-related structure; Dautas, automated measurement of the distance between autophagy-related structures and ER exit sites analysis system; ERES, endoplasmic reticulum exit site; PAS, phagophore assembly site/pre-autophagosomal structure; PCR, polymerase chain reaction; PG, phagophore/isolation membrane; prApe1, precursor of vacuolar aminopeptidase I; Qautas, quantitative autophagy-related structure analysis system; SD/CA; synthetic dextrose plus casamino acid medium; WT, wild-type.
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Affiliation(s)
- Yang Shi
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba, Japan
| | - Kuninori Suzuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba, Japan
- Life Science Data Research Center, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
- Collaborative Research Institute for Innovative Microbiology, the University of Tokyo, Bunkyo-ku, Tokyo, Japan
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Hirata E, Shirai K, Kawaoka T, Sato K, Kodama F, Suzuki K. Atg15 in Saccharomyces cerevisiae consists of two functionally distinct domains. Mol Biol Cell 2021; 32:645-663. [PMID: 33625870 PMCID: PMC8108511 DOI: 10.1091/mbc.e20-07-0500] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Autophagy is a cellular degradation system widely conserved among eukaryotes. During autophagy, cytoplasmic materials fated for degradation are compartmentalized in double membrane-bound organelles called autophagosomes. After fusing with the vacuole, their inner membrane-bound structures are released into the vacuolar lumen to become autophagic bodies and eventually degraded by vacuolar hydrolases. Atg15 is a lipase that is essential for disintegration of autophagic body membranes and has a transmembrane domain at the N-terminus and a lipase domain at the C-terminus. However, the roles of the two domains in vivo are not well understood. In this study, we found that the N-terminal domain alone can travel to the vacuole via the multivesicular body pathway, and that targeting of the C-terminal lipase domain to the vacuole is required for degradation of autophagic bodies. Moreover, we found that the C-terminal domain could disintegrate autophagic bodies when it was transported to the vacuole via the Pho8 pathway instead of the multivesicular body pathway. Finally, we identified H435 as one of the residues composing the putative catalytic triad and W466 as an important residue for degradation of autophagic bodies. This study may provide a clue to how the C-terminal lipase domain recognizes autophagic bodies to degrade them.
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Affiliation(s)
- Eri Hirata
- Department of Integrated Biosciences, University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Kyo Shirai
- Department of Integrated Biosciences, University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Tatsuya Kawaoka
- Department of Integrated Biosciences, University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Kosuke Sato
- Department of Integrated Biosciences, University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Fumito Kodama
- Department of Integrated Biosciences, University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Kuninori Suzuki
- Department of Integrated Biosciences, University of Tokyo, Kashiwa, Chiba 277-8562, Japan.,Life Science Data Research Center, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8562, Japan.,Collaborative Research Institute for Innovative Microbiology, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
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Yamasaki A, Alam JM, Noshiro D, Hirata E, Fujioka Y, Suzuki K, Ohsumi Y, Noda NN. Liquidity Is a Critical Determinant for Selective Autophagy of Protein Condensates. Mol Cell 2020; 77:1163-1175.e9. [PMID: 31995729 DOI: 10.1016/j.molcel.2019.12.026] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 11/22/2019] [Accepted: 12/20/2019] [Indexed: 12/12/2022]
Abstract
Clearance of biomolecular condensates by selective autophagy is thought to play a crucial role in cellular homeostasis. However, the mechanism underlying selective autophagy of condensates and whether liquidity determines a condensate's susceptibility to degradation by autophagy remain unknown. Here, we show that the selective autophagic cargo aminopeptidase I (Ape1) undergoes phase separation to form semi-liquid droplets. The Ape1-specific receptor protein Atg19 localizes to the surface of Ape1 droplets both in vitro and in vivo, with the "floatability" of Atg19 preventing its penetration into droplets. In vitro reconstitution experiments reveal that Atg19 and lipidated Atg8 are necessary and sufficient for selective sequestration of Ape1 droplets by membranes. This sequestration is impaired by mutational solidification of Ape1 droplets or diminished ability of Atg19 to float. Taken together, we propose that cargo liquidity and the presence of sufficient amounts of autophagic receptor on cargo are crucial for selective autophagy of biomolecular condensates.
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Affiliation(s)
- Akinori Yamasaki
- Institute of Microbial Chemistry (BIKAKEN), Tokyo 141-0021, Japan; Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Jahangir Md Alam
- Institute of Microbial Chemistry (BIKAKEN), Tokyo 141-0021, Japan
| | - Daisuke Noshiro
- Institute of Microbial Chemistry (BIKAKEN), Tokyo 141-0021, Japan
| | - Eri Hirata
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277-8562, Japan
| | - Yuko Fujioka
- Institute of Microbial Chemistry (BIKAKEN), Tokyo 141-0021, Japan
| | - Kuninori Suzuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277-8562, Japan; Life Science Data Research Center, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277-8562, Japan; Collaborative Research Institute for Innovative Microbiology, University of Tokyo, Tokyo 113-8657, Japan
| | - Yoshinori Ohsumi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Nobuo N Noda
- Institute of Microbial Chemistry (BIKAKEN), Tokyo 141-0021, Japan.
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Atg2 mediates direct lipid transfer between membranes for autophagosome formation. Nat Struct Mol Biol 2019; 26:281-288. [PMID: 30911189 DOI: 10.1038/s41594-019-0203-4] [Citation(s) in RCA: 266] [Impact Index Per Article: 53.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 02/15/2019] [Indexed: 12/30/2022]
Abstract
A key event in autophagy is autophagosome formation, whereby the newly synthesized isolation membrane (IM) expands to form a complete autophagosome using endomembrane-derived lipids. Atg2 physically links the edge of the expanding IM with the endoplasmic reticulum (ER), a role that is essential for autophagosome formation. However, the molecular function of Atg2 during ER-IM contact remains unclear, as does the mechanism of lipid delivery to the IM. Here we show that the conserved amino-terminal region of Schizosaccharomyces pombe Atg2 includes a lipid-transfer-protein-like hydrophobic cavity that accommodates phospholipid acyl chains. Atg2 bridges highly curved liposomes, thereby facilitating efficient phospholipid transfer in vitro, a function that is inhibited by mutations that impair autophagosome formation in vivo. These results suggest that Atg2 acts as a lipid-transfer protein that supplies phospholipids for autophagosome formation.
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