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Takeda E, Isoda T, Hosokawa S, Oikawa Y, Hotta-Ren S, May AI, Ohsumi Y. Receptor-mediated cargo hitchhiking on bulk autophagy. EMBO J 2024; 43:3116-3140. [PMID: 38755257 PMCID: PMC11294605 DOI: 10.1038/s44318-024-00091-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 02/24/2024] [Accepted: 02/28/2024] [Indexed: 05/18/2024] Open
Abstract
While the molecular mechanism of autophagy is well studied, the cargoes delivered by autophagy remain incompletely characterized. To examine the selectivity of autophagy cargo, we conducted proteomics on isolated yeast autophagic bodies, which are intermediate structures in the autophagy process. We identify a protein, Hab1, that is highly preferentially delivered to vacuoles. The N-terminal 42 amino acid region of Hab1 contains an amphipathic helix and an Atg8-family interacting motif, both of which are necessary and sufficient for the preferential delivery of Hab1 by autophagy. We find that fusion of this region with a cytosolic protein results in preferential delivery of this protein to the vacuole. Furthermore, attachment of this region to an organelle allows for autophagic delivery in a manner independent of canonical autophagy receptor or scaffold proteins. We propose a novel mode of selective autophagy in which a receptor, in this case Hab1, binds directly to forming isolation membranes during bulk autophagy.
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Affiliation(s)
- Eigo Takeda
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan.
| | - Takahiro Isoda
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
- School and Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
- Frontier Research Center, POLA Chemical Industries Inc., Yokohama, Japan
| | - Sachiko Hosokawa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Yu Oikawa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Shukun Hotta-Ren
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Alexander I May
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Yoshinori Ohsumi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan.
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2
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Isoda T, Takeda E, Hosokawa S, Hotta-Ren S, Ohsumi Y. Atg45 is an autophagy receptor for glycogen, a non-preferred cargo of bulk autophagy in yeast. iScience 2024; 27:109810. [PMID: 38832010 PMCID: PMC11145338 DOI: 10.1016/j.isci.2024.109810] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/03/2023] [Accepted: 04/22/2024] [Indexed: 06/05/2024] Open
Abstract
The mechanisms governing autophagy of proteins and organelles have been well studied, but how other cytoplasmic components such as RNA and polysaccharides are degraded remains largely unknown. In this study, we examine autophagy of glycogen, a storage form of glucose. We find that cells accumulate glycogen in the cytoplasm during nitrogen starvation and that this carbohydrate is rarely observed within autophagosomes and autophagic bodies. However, sequestration of glycogen by autophagy is observed following prolonged nitrogen starvation. We identify a yet-uncharacterized open reading frame, Yil024c (herein Atg45), as encoding a cytosolic receptor protein that mediates autophagy of glycogen (glycophagy). Furthermore, we show that, during sporulation, Atg45 is highly expressed and is associated with an increase in glycophagy. Our results suggest that cells regulate glycophagic activity by controlling the expression level of Atg45.
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Affiliation(s)
- Takahiro Isoda
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
- School and Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8503, Japan
- Frontier Research Center, POLA Chemical Industries, Inc, Yokohama 244-0812, Japan
| | - Eigo Takeda
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Sachiko Hosokawa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Shukun Hotta-Ren
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Yoshinori Ohsumi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
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3
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Shatz O, Fraiberg M, Isola D, Das S, Gogoi O, Polyansky A, Shimoni E, Dadosh T, Dezorella N, Wolf SG, Elazar Z. Rim aperture of yeast autophagic membranes balances cargo inclusion with vesicle maturation. Dev Cell 2024; 59:911-923.e4. [PMID: 38447569 DOI: 10.1016/j.devcel.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 11/28/2023] [Accepted: 02/06/2024] [Indexed: 03/08/2024]
Abstract
Autophagy eliminates cytoplasmic material by engulfment in membranous vesicles targeted for lysosome degradation. Nonselective autophagy coordinates sequestration of bulk cargo with the growth of the isolation membrane (IM) in a yet-unknown manner. Here, we show that in the budding yeast Saccharomyces cerevisiae, IMs expand while maintaining a rim sufficiently wide for sequestration of large cargo but tight enough to mature in due time. An obligate complex of Atg24/Snx4 with Atg20 or Snx41 assembles locally at the rim in a spatially extended manner that specifically depends on autophagic PI(3)P. This assembly stabilizes the open rim to promote autophagic sequestration of large cargo in correlation with vesicle expansion. Moreover, constriction of the rim by the PI(3)P-dependent Atg2-Atg18 complex and clearance of PI(3)P by Ymr1 antagonize rim opening to promote autophagic maturation and consumption of small cargo. Tight regulation of membrane rim aperture by PI(3)P thus couples the mechanism and physiology of nonselective autophagy.
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Affiliation(s)
- Oren Shatz
- Departments of Biomolecular Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Milana Fraiberg
- Departments of Biomolecular Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Damilola Isola
- Departments of Biomolecular Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Shubhankar Das
- Departments of Biomolecular Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Olee Gogoi
- Departments of Biomolecular Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Alexandra Polyansky
- Departments of Biomolecular Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Eyal Shimoni
- Chemical Research Support, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Tali Dadosh
- Chemical Research Support, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Nili Dezorella
- Chemical Research Support, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Sharon G Wolf
- Chemical Research Support, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Zvulun Elazar
- Departments of Biomolecular Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel.
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4
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Wijewantha NV, Kumar R, Nazarko TY. Glycogen Granules Are Degraded by Non-Selective Autophagy in Nitrogen-Starved Komagataella phaffii. Cells 2024; 13:467. [PMID: 38534311 DOI: 10.3390/cells13060467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 03/03/2024] [Accepted: 03/06/2024] [Indexed: 03/28/2024] Open
Abstract
Autophagy was initially recognized as a bulk degradation process that randomly sequesters and degrades cytoplasmic material in lysosomes (vacuoles in yeast). In recent years, various types of selective autophagy have been discovered. Glycophagy, the selective autophagy of glycogen granules, is one of them. While autophagy of glycogen is an important contributor to Pompe disease, which is characterized by the lysosomal accumulation of glycogen, its selectivity is still a matter of debate. Here, we developed the Komagataella phaffii yeast as a simple model of glycogen autophagy under nitrogen starvation conditions to address the question of its selectivity. For this, we turned the self-glucosylating initiator of glycogen synthesis, Glg1, which is covalently bound to glycogen, into the Glg1-GFP autophagic reporter. Our results revealed that vacuolar delivery of Glg1-GFP and its processing to free GFP were strictly dependent on autophagic machinery and vacuolar proteolysis. Notably, this process was independent of Atg11, the scaffold protein common for many selective autophagy pathways. Importantly, the non-mutated Glg1-GFP (which synthesizes and marks glycogen) and mutated Glg1Y212F-GFP (which does not synthesize glycogen and is degraded by non-selective autophagy as cytosolic Pgk1-GFP) were equally well delivered to the vacuole and had similar levels of released GFP. Therefore, we concluded that glycogen autophagy is a non-selective process in K. phaffii yeast under nitrogen starvation conditions.
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Affiliation(s)
| | - Ravinder Kumar
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Taras Y Nazarko
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
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5
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Gross AS, Ghillebert R, Schuetter M, Reinartz E, Rowland A, Bishop BC, Stumpe M, Dengjel J, Graef M. A metabolite sensor subunit of the Atg1/ULK complex regulates selective autophagy. Nat Cell Biol 2024; 26:366-377. [PMID: 38316984 PMCID: PMC10940145 DOI: 10.1038/s41556-024-01348-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 01/03/2024] [Indexed: 02/07/2024]
Abstract
Cells convert complex metabolic information into stress-adapted autophagy responses. Canonically, multilayered protein kinase networks converge on the conserved Atg1/ULK kinase complex (AKC) to induce non-selective and selective forms of autophagy in response to metabolic changes. Here we show that, upon phosphate starvation, the metabolite sensor Pho81 interacts with the adaptor subunit Atg11 at the AKC via an Atg11/FIP200 interaction motif to modulate pexophagy by virtue of its conserved phospho-metabolite sensing SPX domain. Notably, core AKC components Atg13 and Atg17 are dispensable for phosphate starvation-induced autophagy revealing significant compositional and functional plasticity of the AKC. Our data indicate that, instead of functioning as a selective autophagy receptor, Pho81 compensates for partially inactive Atg13 by promoting Atg11 phosphorylation by Atg1 critical for pexophagy during phosphate starvation. Our work shows Atg11/FIP200 adaptor subunits bind not only selective autophagy receptors but also modulator subunits that convey metabolic information directly to the AKC for autophagy regulation.
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Affiliation(s)
- A S Gross
- Max Planck Research Group of Autophagy and Cellular Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany
- Gregor Mendel Institute of Molecular Plant Biology, Vienna Biocenter, Vienna, Austria
| | - R Ghillebert
- Max Planck Research Group of Autophagy and Cellular Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - M Schuetter
- Max Planck Research Metabolomics Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - E Reinartz
- Max Planck Research Group of Autophagy and Cellular Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - A Rowland
- Max Planck Research Group of Autophagy and Cellular Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - B C Bishop
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - M Stumpe
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - J Dengjel
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - M Graef
- Max Planck Research Group of Autophagy and Cellular Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany.
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
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6
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Kang Y, Lin W, Nagy PD. Subversion of selective autophagy for the biogenesis of tombusvirus replication organelles inhibits autophagy. PLoS Pathog 2024; 20:e1012085. [PMID: 38484009 DOI: 10.1371/journal.ppat.1012085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 03/26/2024] [Accepted: 02/29/2024] [Indexed: 03/27/2024] Open
Abstract
Elaborate viral replication organelles (VROs) are formed to support positive-strand RNA virus replication in infected cells. VRO formation requires subversion of intracellular membranes by viral replication proteins. Here, we showed that the key ATG8f autophagy protein and NBR1 selective autophagy receptor were co-opted by Tomato bushy stunt virus (TBSV) and the closely-related carnation Italian ringspot virus. Knockdown of ATG8f or NBR1 in plants led to reduced tombusvirus replication, suggesting pro-viral function for selective autophagy. BiFC and proximity-labeling experiments showed that the TBSV p33 replication protein interacted with ATG8f and NBR1 to recruit them to VROs. In addition, we observed that several core autophagy proteins, such as ATG1a, ATG4, ATG5, ATG101 and the plant-specific SH3P2 autophagy adaptor proteins were also re-localized to TBSV VROs, suggesting that TBSV hijacks the autophagy machinery in plant cells. We demonstrated that subversion of autophagy components facilitated the recruitment of VPS34 PI3 kinase and enrichment of phospholipids, such as phosphatidylethanolamine and PI3P phosphoinositide in the VRO membranes. Hijacking of autophagy components into TBSV VROs led to inhibition of autophagic flux. We also found that a fraction of the subverted ATG8f and NBR1 was sequestered in biomolecular condensates associated with VROs. We propose that the VRO-associated condensates trap those autophagy proteins, taking them away from the autophagy pathway. Overall, tombusviruses hijack selective autophagy to provide phospholipid-rich membranes for replication and to regulate the antiviral autophagic flux.
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Affiliation(s)
- Yuanrong Kang
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, United States of America
| | - Wenwu Lin
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, United States of America
| | - Peter D Nagy
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, United States of America
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7
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Mota MN, Matos M, Bahri N, Sá-Correia I. Shared and more specific genetic determinants and pathways underlying yeast tolerance to acetic, butyric, and octanoic acids. Microb Cell Fact 2024; 23:71. [PMID: 38419072 PMCID: PMC10903034 DOI: 10.1186/s12934-024-02309-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 01/17/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND The improvement of yeast tolerance to acetic, butyric, and octanoic acids is an important step for the implementation of economically and technologically sustainable bioprocesses for the bioconversion of renewable biomass resources and wastes. To guide genome engineering of promising yeast cell factories toward highly robust superior strains, it is instrumental to identify molecular targets and understand the mechanisms underlying tolerance to those monocarboxylic fatty acids. A chemogenomic analysis was performed, complemented with physiological studies, to unveil genetic tolerance determinants in the model yeast and cell factory Saccharomyces cerevisiae exposed to equivalent moderate inhibitory concentrations of acetic, butyric, or octanoic acids. RESULTS Results indicate the existence of multiple shared genetic determinants and pathways underlying tolerance to these short- and medium-chain fatty acids, such as vacuolar acidification, intracellular trafficking, autophagy, and protein synthesis. The number of tolerance genes identified increased with the linear chain length and the datasets for butyric and octanoic acids include the highest number of genes in common suggesting the existence of more similar toxicity and tolerance mechanisms. Results of this analysis, at the systems level, point to a more marked deleterious effect of an equivalent inhibitory concentration of the more lipophilic octanoic acid, followed by butyric acid, on the cell envelope and on cellular membranes function and lipid remodeling. The importance of mitochondrial genome maintenance and functional mitochondria to obtain ATP for energy-dependent detoxification processes also emerged from this chemogenomic analysis, especially for octanoic acid. CONCLUSIONS This study provides new biological knowledge of interest to gain further mechanistic insights into toxicity and tolerance to linear-chain monocarboxylic acids of increasing liposolubility and reports the first lists of tolerance genes, at the genome scale, for butyric and octanoic acids. These genes and biological functions are potential targets for synthetic biology approaches applied to promising yeast cell factories, toward more robust superior strains, a highly desirable phenotype to increase the economic viability of bioprocesses based on mixtures of volatiles/medium-chain fatty acids derived from low-cost biodegradable substrates or lignocellulose hydrolysates.
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Affiliation(s)
- Marta N Mota
- iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001, Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001, Lisbon, Portugal
- i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001, Lisbon, Portugal
| | - Madalena Matos
- iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001, Lisbon, Portugal
- i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001, Lisbon, Portugal
| | - Nada Bahri
- iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001, Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001, Lisbon, Portugal
- i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001, Lisbon, Portugal
| | - Isabel Sá-Correia
- iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001, Lisbon, Portugal.
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001, Lisbon, Portugal.
- i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001, Lisbon, Portugal.
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Hanley SE, Willis SD, Doyle SJ, Strich R, Cooper KF. Ksp1 is an autophagic receptor protein for the Snx4-assisted autophagy of Ssn2/Med13. Autophagy 2024; 20:397-415. [PMID: 37733395 PMCID: PMC10813586 DOI: 10.1080/15548627.2023.2259708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 09/11/2023] [Indexed: 09/22/2023] Open
Abstract
Ksp1 is a casein II-like kinase whose activity prevents aberrant macroautophagy/autophagy induction in nutrient-rich conditions in yeast. Here, we describe a kinase-independent role of Ksp1 as a novel autophagic receptor protein for Ssn2/Med13, a known cargo of Snx4-assisted autophagy of transcription factors. In this pathway, a subset of conserved transcriptional regulators, Ssn2/Med13, Rim15, and Msn2, are selectively targeted for vacuolar proteolysis following nitrogen starvation, assisted by the sorting nexin heterodimer Snx4-Atg20. Here we show that phagophores also engulf Ksp1 alongside its cargo for vacuolar proteolysis. Ksp1 directly associates with Atg8 following nitrogen starvation at the interface of an Atg8-family interacting motif (AIM)/LC3-interacting region (LIR) in Ksp1 and the LIR/AIM docking site (LDS) in Atg8. Mutating the LDS site prevents the autophagic degradation of Ksp1. However, deletion of the C terminal canonical AIM still permitted Ssn2/Med13 proteolysis, suggesting that additional non-canonical AIMs may mediate the Ksp1-Atg8 interaction. Ksp1 is recruited to the perivacuolar phagophore assembly site by Atg29, a member of the trimeric scaffold complex. This interaction is independent of Atg8 and Snx4, suggesting that Ksp1 is recruited early to phagophores, with Snx4 delivering Ssn2/Med13 thereafter. Finally, normal cell survival following prolonged nitrogen starvation requires Ksp1. Together, these studies define a kinase-independent role for Ksp1 as an autophagic receptor protein mediating Ssn2/Med13 degradation. They also suggest that phagophores built by the trimeric scaffold complex are capable of receptor-mediated autophagy. These results demonstrate the dual functionality of Ksp1, whose kinase activity prevents autophagy while it plays a scaffolding role supporting autophagic degradation.Abbreviations: 3-AT: 3-aminotriazole; 17C: Atg17-Atg31-Atg29 trimeric scaffold complex; AIM: Atg8-family interacting motif; ATG: autophagy related; CKM: CDK8 kinase module; Cvt: cytoplasm-to-vacuole targeting; IDR: intrinsically disordered region; LIR: LC3-interacting region; LDS: LIR/AIM docking site; MoRF: molecular recognition feature; NPC: nuclear pore complex; PAS: phagophore assembly site; PKA: protein kinase A; RBP: RNA-binding protein; UPS: ubiquitin-proteasome system. SAA-TF: Snx4-assisted autophagy of transcription factors; Y2H: yeast two-hybrid.
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Affiliation(s)
- Sara E. Hanley
- Department of Molecular Biology, Rowan-Virtua School of Translational Biomedical Engineering & Sciences, Rowan University, Stratford, NJ, USA
| | - Stephen D. Willis
- Department of Molecular Biology, Rowan-Virtua School of Translational Biomedical Engineering & Sciences, Rowan University, Stratford, NJ, USA
| | - Steven J. Doyle
- Department of Molecular Biology, Rowan-Virtua School of Translational Biomedical Engineering & Sciences, Rowan University, Stratford, NJ, USA
- School of Osteopathic Medicine, Rowan University, Stratford, NJ, USA
| | - Randy Strich
- Department of Molecular Biology, Rowan-Virtua School of Translational Biomedical Engineering & Sciences, Rowan University, Stratford, NJ, USA
| | - Katrina F. Cooper
- Department of Molecular Biology, Rowan-Virtua School of Translational Biomedical Engineering & Sciences, Rowan University, Stratford, NJ, USA
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Qian W, Lu J, Gao C, Liu Q, Yao W, Wang T, Wang X, Wang Z. Isobavachalcone exhibits antifungal and antibiofilm effects against C. albicans by disrupting cell wall/membrane integrity and inducing apoptosis and autophagy. Front Cell Infect Microbiol 2024; 14:1336773. [PMID: 38322671 PMCID: PMC10845358 DOI: 10.3389/fcimb.2024.1336773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 01/03/2024] [Indexed: 02/08/2024] Open
Abstract
Isobavachalcone (IBC) is a natural flavonoid with multiple pharmacological properties. This study aimed to evaluate the efficacy of IBC against planktonic growth and biofilms of Candida albicans (C. albicans) and the mechanisms underlying its antifungal action. The cell membrane integrity, cell metabolic viability, and cell morphology of C. albicans treated with IBC were evaluated using CLSM and FESEM analyses. Crystal violet staining, CLSM, and FESEM were used to assess the inhibition of biofilm formation, as well as dispersal and killing effects of IBC on mature biofilms. RNA-seq combined with apoptosis and autophagy assays was used to examine the mechanisms underlying the antifungal action of IBC. IBC exhibited excellent antifungal activity with 8 μg/mL of MIC for C. albicans. IBC disrupted the cell membrane integrity, and inhibited biofilm formation. IBC dispersed mature biofilms and damaged biofilm cells of C. albicans at 32 μg/mL. Moreover, IBC induced apoptosis and autophagy-associated cell death of C. albicans. The RNA-seq analysis revealed upregulation or downregulation of key genes involved in cell wall synthesis (Wsc1 and Fks1), ergosterol biosynthesis (Erg3, and Erg11), apoptisis (Hsp90 and Aif1), as well as autophagy pathways (Atg8, Atg13, and Atg17), and so forth, in response to IBC, as evidenced by the experiment-based phenotypic analysis. These results suggest that IBC inhibits C. albicans growth by disrupting the cell wall/membrane, caused by the altered expression of genes associated with β-1,3-glucan and ergosterol biosynthesis. IBC induces apoptosis and autophagy-associated cell death by upregulating the expression of Hsp90, and altering autophagy-related genes involved in the formation of the Atg1 complex and the pre-autophagosomal structure. Together, our findings provide important insights into the potential multifunctional mechanism of action of IBC.
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Affiliation(s)
- Weidong Qian
- School of Biological and Pharmaceutical Engineering, Shaanxi University of Science and Technology, Xi’an, China
| | - Jiaxing Lu
- School of Biological and Pharmaceutical Engineering, Shaanxi University of Science and Technology, Xi’an, China
| | - Chang Gao
- School of Biological and Pharmaceutical Engineering, Shaanxi University of Science and Technology, Xi’an, China
| | - Qiming Liu
- School of Biological and Pharmaceutical Engineering, Shaanxi University of Science and Technology, Xi’an, China
| | - Wendi Yao
- Department of Urology, Henan Provincial People’s Hospital, Zhengzhou University People’s Hospital, Zhengzhou, China
| | - Ting Wang
- School of Biological and Pharmaceutical Engineering, Shaanxi University of Science and Technology, Xi’an, China
| | - Xiaobin Wang
- Department of Urology, Southern University of Science and Technology Hospital, Shenzhen, China
| | - Zhifeng Wang
- Department of Urology, Henan Provincial People’s Hospital, Zhengzhou University People’s Hospital, Zhengzhou, China
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10
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Cadena-Ramos AI, De-la-Peña C. Picky eaters: selective autophagy in plant cells. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:364-384. [PMID: 37864806 DOI: 10.1111/tpj.16508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/21/2023] [Accepted: 10/10/2023] [Indexed: 10/23/2023]
Abstract
Autophagy, a fundamental cellular process, plays a vital role in maintaining cellular homeostasis by degrading damaged or unnecessary components. While selective autophagy has been extensively studied in animal cells, its significance in plant cells has only recently gained attention. In this review, we delve into the intriguing realm selective autophagy in plants, with specific focus on its involvement in nutrient recycling, organelle turnover, and stress response. Moreover, recent studies have unveiled the interesting interplay between selective autophagy and epigenetic mechanisms in plants, elucidating the significance of epigenetic regulation in modulating autophagy-related gene expression and finely tuning the selective autophagy process in plants. By synthesizing existing knowledge, this review highlights the emerging field of selective autophagy in plant cells, emphasizing its pivotal role in maintaining nutrient homeostasis, facilitating cellular adaptation, and shedding light on the epigenetic regulation that governs these processes. Our comprehensive study provides the way for a deeper understanding of the dynamic control of cellular responses to nutrient availability and stress conditions, opening new avenues for future research in this field of autophagy in plant physiology.
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Affiliation(s)
- Alexis I Cadena-Ramos
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34 Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico
| | - Clelia De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34 Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico
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11
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Zhang R, Feng W, Qian S, Wang F. Autophagy-mediated surveillance of Rim4-mRNA interaction safeguards programmed meiotic translation. Cell Rep 2023; 42:113051. [PMID: 37659076 PMCID: PMC10591816 DOI: 10.1016/j.celrep.2023.113051] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 07/13/2023] [Accepted: 08/15/2023] [Indexed: 09/04/2023] Open
Abstract
In yeast meiosis, autophagy is active and essential. Here, we investigate the fate of Rim4, a meiosis-specific RNA-binding protein (RBP), and its associated transcripts during meiotic autophagy. We demonstrate that Rim4 employs a nuclear localization signal (NLS) to enter the nucleus, where it loads its mRNA substrates before nuclear export. Upon reaching the cytoplasm, active autophagy selectively spares the Rim4-mRNA complex. During meiotic divisions, autophagy preferentially degrades Rim4 in an Atg11-dependent manner, coinciding with the release of Rim4-bound mRNAs for translation. Intriguingly, these released mRNAs also become vulnerable to autophagy. In vitro, purified Rim4 and its RRM-motif-containing variants activate Atg1 kinase in meiotic cell lysates and in immunoprecipitated (IP) Atg1 complexes. This suggests that the conserved RNA recognition motifs (RRMs) of Rim4 are involved in stimulating Atg1 and thereby facilitating selective autophagy. Taken together, our findings indicate that autophagy surveils Rim4-mRNA interaction to ensure stage-specific translation during meiosis.
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Affiliation(s)
- Rudian Zhang
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Wenzhi Feng
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Suhong Qian
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Fei Wang
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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12
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Kotani T, Sakai Y, Kirisako H, Kakuta C, Kakuta S, Ohsumi Y, Nakatogawa H. A mechanism that ensures non-selective cytoplasm degradation by autophagy. Nat Commun 2023; 14:5815. [PMID: 37726301 PMCID: PMC10509180 DOI: 10.1038/s41467-023-41525-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 09/07/2023] [Indexed: 09/21/2023] Open
Abstract
In autophagy, a membrane cisterna called the isolation membrane expands, bends, becomes spherical, and closes to sequester cytoplasmic constituents into the resulting double-membrane vesicle autophagosome for lysosomal/vacuolar degradation. Here, we discover a mechanism that allows the isolation membrane to expand with a large opening to ensure non-selective cytoplasm sequestration within the autophagosome. A sorting nexin complex that localizes to the opening edge of the isolation membrane plays a critical role in this process. Without the complex, the isolation membrane expands with a small opening that prevents the entry of particles larger than about 25 nm, including ribosomes and proteasomes, although autophagosomes of nearly normal size eventually form. This study sheds light on membrane morphogenesis during autophagosome formation and selectivity in autophagic degradation.
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Affiliation(s)
- Tetsuya Kotani
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Yuji Sakai
- Department of Biosystems Science, Institute for Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Hiromi Kirisako
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Chika Kakuta
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Soichiro Kakuta
- Laboratory of Morphology and Image Analysis, Biomedical Research Core Facilities, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Yoshinori Ohsumi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Hitoshi Nakatogawa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8501, Japan.
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan.
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13
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Hitomi K, Kotani T, Noda NN, Kimura Y, Nakatogawa H. The Atg1 complex, Atg9, and Vac8 recruit PI3K complex I to the pre-autophagosomal structure. J Cell Biol 2023; 222:e202210017. [PMID: 37436710 PMCID: PMC10337603 DOI: 10.1083/jcb.202210017] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 03/31/2023] [Accepted: 05/18/2023] [Indexed: 07/13/2023] Open
Abstract
In macroautophagy, cellular components are sequestered within autophagosomes and transported to lysosomes/vacuoles for degradation. Although phosphatidylinositol 3-kinase complex I (PI3KCI) plays a pivotal role in the regulation of autophagosome biogenesis, little is known about how this complex localizes to the pre-autophagosomal structure (PAS). In Saccharomyces cerevisiae, PI3KCI is composed of PI3K Vps34 and conserved subunits Vps15, Vps30, Atg14, and Atg38. In this study, we discover that PI3KCI interacts with the vacuolar membrane anchor Vac8, the PAS scaffold Atg1 complex, and the pre-autophagosomal vesicle component Atg9 via the Atg14 C-terminal region, the Atg38 C-terminal region, and the Vps30 BARA domain, respectively. While the Atg14-Vac8 interaction is constitutive, the Atg38-Atg1 complex interaction and the Vps30-Atg9 interaction are enhanced upon macroautophagy induction depending on Atg1 kinase activity. These interactions cooperate to target PI3KCI to the PAS. These findings provide a molecular basis for PAS targeting of PI3KCI during autophagosome biogenesis.
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Affiliation(s)
- Kanae Hitomi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Tetsuya Kotani
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Nobuo N. Noda
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Yayoi Kimura
- Advanced Medical Research Center, Yokohama City University, Yokohama, Japan
| | - Hitoshi Nakatogawa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
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14
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Shen ZF, Li L, Zhu XM, Liu XH, Klionsky DJ, Lin FC. Current opinions on mitophagy in fungi. Autophagy 2023; 19:747-757. [PMID: 35793406 PMCID: PMC9980689 DOI: 10.1080/15548627.2022.2098452] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 11/02/2022] Open
Abstract
Mitophagy, as one of the most important cellular processes to ensure quality control of mitochondria, aims at transporting damaged, aging, dysfunctional or excess mitochondria to vacuoles (plants and fungi) or lysosomes (mammals) for degradation and recycling. The normal functioning of mitophagy is critical for cellular homeostasis from yeasts to humans. Although the role of mitophagy has been well studied in mammalian cells and in certain model organisms, especially the budding yeast Saccharomyces cerevisiae, our understanding of its significance in other fungi, particularly in pathogenic filamentous fungi, is still at the preliminary stage. Recent studies have shown that mitophagy plays a vital role in spore production, vegetative growth and virulence of pathogenic fungi, which are very different from its roles in mammal and yeast. In this review, we summarize the functions of mitophagy for mitochondrial quality and quantity control, fungal growth and pathogenesis that have been reported in the field of molecular biology over the past two decades. These findings may help researchers and readers to better understand the multiple functions of mitophagy and provide new perspectives for the study of mitophagy in fungal pathogenesis.Abbreviations: AIM/LIR: Atg8-family interacting motif/LC3-interacting region; BAR: Bin-Amphiphysin-Rvs; BNIP3: BCL2 interacting protein 3; CK2: casein kinase 2; Cvt: cytoplasm-to-vacuole targeting; ER: endoplasmic reticulum; IMM: inner mitochondrial membrane; mETC: mitochondrial electron transport chain; OMM: outer mitochondrial membrane; OPTN: optineurin; PAS: phagophore assembly site; PD: Parkinson disease; PE: phosphatidylethanolamine; PHB2: prohibitin 2; PX: Phox homology; ROS, reactive oxygen species; TM: transmembrane.
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Affiliation(s)
- Zi-Fang Shen
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Lin Li
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Xue-Ming Zhu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Xiao-Hong Liu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Daniel J. Klionsky
- Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Fu-Cheng Lin
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
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15
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Picchianti L, Sánchez de Medina Hernández V, Zhan N, Irwin NA, Groh R, Stephani M, Hornegger H, Beveridge R, Sawa-Makarska J, Lendl T, Grujic N, Naumann C, Martens S, Richards TA, Clausen T, Ramundo S, Karagöz GE, Dagdas Y. Shuffled ATG8 interacting motifs form an ancestral bridge between UFMylation and autophagy. EMBO J 2023; 42:e112053. [PMID: 36762703 PMCID: PMC10183829 DOI: 10.15252/embj.2022112053] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 01/12/2023] [Accepted: 01/18/2023] [Indexed: 02/11/2023] Open
Abstract
UFMylation involves the covalent modification of substrate proteins with UFM1 (Ubiquitin-fold modifier 1) and is important for maintaining ER homeostasis. Stalled translation triggers the UFMylation of ER-bound ribosomes and activates C53-mediated autophagy to clear toxic polypeptides. C53 contains noncanonical shuffled ATG8-interacting motifs (sAIMs) that are essential for ATG8 interaction and autophagy initiation. However, the mechanistic basis of sAIM-mediated ATG8 interaction remains unknown. Here, we show that C53 and sAIMs are conserved across eukaryotes but secondarily lost in fungi and various algal lineages. Biochemical assays showed that the unicellular alga Chlamydomonas reinhardtii has a functional UFMylation pathway, refuting the assumption that UFMylation is linked to multicellularity. Comparative structural analyses revealed that both UFM1 and ATG8 bind sAIMs in C53, but in a distinct way. Conversion of sAIMs into canonical AIMs impaired binding of C53 to UFM1, while strengthening ATG8 binding. Increased ATG8 binding led to the autoactivation of the C53 pathway and sensitization of Arabidopsis thaliana to ER stress. Altogether, our findings reveal an ancestral role of sAIMs in UFMylation-dependent fine-tuning of C53-mediated autophagy activation.
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Affiliation(s)
- Lorenzo Picchianti
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.,Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Víctor Sánchez de Medina Hernández
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.,Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Ni Zhan
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Nicholas At Irwin
- Department of Zoology, University of Oxford, Oxford, UK.,Merton College, University of Oxford, Oxford, UK
| | - Roan Groh
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.,Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Madlen Stephani
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.,Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Harald Hornegger
- Max Perutz Labs, Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Rebecca Beveridge
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, UK
| | - Justyna Sawa-Makarska
- Max Perutz Labs, Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Thomas Lendl
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Nenad Grujic
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Christin Naumann
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | - Sascha Martens
- Max Perutz Labs, Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | | | - Tim Clausen
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Silvia Ramundo
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - G Elif Karagöz
- Max Perutz Labs, Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Yasin Dagdas
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
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16
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Zhao J, Bui MT, Ma J, Künzl F, Picchianti L, De La Concepcion JC, Chen Y, Petsangouraki S, Mohseni A, García-Leon M, Gomez MS, Giannini C, Gwennogan D, Kobylinska R, Clavel M, Schellmann S, Jaillais Y, Friml J, Kang BH, Dagdas Y. Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole. J Cell Biol 2022; 221:213556. [PMID: 36260289 PMCID: PMC9584626 DOI: 10.1083/jcb.202203139] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 08/12/2022] [Accepted: 09/14/2022] [Indexed: 12/13/2022] Open
Abstract
Autophagosomes are double-membraned vesicles that traffic harmful or unwanted cellular macromolecules to the vacuole for recycling. Although autophagosome biogenesis has been extensively studied, autophagosome maturation, i.e., delivery and fusion with the vacuole, remains largely unknown in plants. Here, we have identified an autophagy adaptor, CFS1, that directly interacts with the autophagosome marker ATG8 and localizes on both membranes of the autophagosome. Autophagosomes form normally in Arabidopsis thaliana cfs1 mutants, but their delivery to the vacuole is disrupted. CFS1's function is evolutionarily conserved in plants, as it also localizes to the autophagosomes and plays a role in autophagic flux in the liverwort Marchantia polymorpha. CFS1 regulates autophagic flux by bridging autophagosomes with the multivesicular body-localized ESCRT-I component VPS23A, leading to the formation of amphisomes. Similar to CFS1-ATG8 interaction, disrupting the CFS1-VPS23A interaction blocks autophagic flux and renders plants sensitive to nitrogen starvation. Altogether, our results reveal a conserved vacuolar sorting hub that regulates autophagic flux in plants.
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Affiliation(s)
- Jierui Zhao
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria,Vienna BioCenter PhD Program, Doctoral School of the University at Vienna and Medical University of Vienna, Vienna, Austria
| | - Mai Thu Bui
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Juncai Ma
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Fabian Künzl
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Lorenzo Picchianti
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria,Vienna BioCenter PhD Program, Doctoral School of the University at Vienna and Medical University of Vienna, Vienna, Austria
| | | | - Yixuan Chen
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Sofia Petsangouraki
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Azadeh Mohseni
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Marta García-Leon
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Marta Salas Gomez
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Caterina Giannini
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Dubois Gwennogan
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, École normale supérieure de Lyon, Centre national de la recherche scientifique (CNRS), Institut National de la Recherche Agronomique (INRAE), Lyon, France
| | - Roksolana Kobylinska
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Marion Clavel
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Swen Schellmann
- Botanik III, Biocenter, University of Cologne, Cologne, Germany
| | - Yvon Jaillais
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, École normale supérieure de Lyon, Centre national de la recherche scientifique (CNRS), Institut National de la Recherche Agronomique (INRAE), Lyon, France
| | - Jiri Friml
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Byung-Ho Kang
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China,Correspondence to Byung-Ho Kang:
| | - Yasin Dagdas
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria,Yasin Dagdas:
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17
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Jing Y, Kobayashi M, Vu HT, Kasahara A, Chen X, Pham LT, Kurayoshi K, Tadokoro Y, Ueno M, Todo T, Nakada M, Hirao A. Therapeutic advantage of targeting lysosomal membrane integrity supported by lysophagy in malignant glioma. Cancer Sci 2022; 113:2716-2726. [PMID: 35657693 PMCID: PMC9357661 DOI: 10.1111/cas.15451] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/26/2022] [Accepted: 05/31/2022] [Indexed: 12/01/2022] Open
Abstract
Lysosomes function as the digestive system of a cell and are involved in macromolecular recycling, vesicle trafficking, metabolic reprogramming, and progrowth signaling. Although quality control of lysosome biogenesis is thought to be a potential target for cancer therapy, practical strategies have not been established. Here, we show that lysosomal membrane integrity supported by lysophagy, a selective autophagy for damaged lysosomes, is a promising therapeutic target for glioblastoma (GBM). In this study, we found that ifenprodil, an FDA‐approved drug with neuromodulatory activities, efficiently inhibited spheroid formation of patient‐derived GBM cells in a combination with autophagy inhibition. Ifenprodil increased intracellular Ca2+ level, resulting in mitochondrial reactive oxygen species–mediated cytotoxicity. The ifenprodil‐induced Ca2+ elevation was due to Ca2+ release from lysosomes, but not endoplasmic reticulum, associated with galectin‐3 punctation as an indicator of lysosomal membrane damage. As the Ca2+ release was enhanced by ATG5 deficiency, autophagy protected against lysosomal membrane damage. By comparative analysis of 765 FDA‐approved compounds, we identified another clinically available drug for central nervous system (CNS) diseases, amoxapine, in addition to ifenprodil. Both compounds promoted degradation of lysosomal membrane proteins, indicating a critical role of lysophagy in quality control of lysosomal membrane integrity. Importantly, a synergistic inhibitory effect of ifenprodil and chloroquine, a clinically available autophagy inhibitor, on spheroid formation was remarkable in GBM cells, but not in nontransformed neural progenitor cells. Finally, chloroquine dramatically enhanced effects of the compounds inducing lysosomal membrane damage in a patient‐derived xenograft model. These data demonstrate a therapeutic advantage of targeting lysosomal membrane integrity in GBM.
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Affiliation(s)
- Yongwei Jing
- Division of Molecular Genetics Cancer Research Institute Kanazawa University, Kakuma‐machi, Kanazawa 920‐1192 Japan
| | - Masahiko Kobayashi
- Division of Molecular Genetics Cancer Research Institute Kanazawa University, Kakuma‐machi, Kanazawa 920‐1192 Japan
| | - Ha Thi Vu
- Division of Molecular Genetics Cancer Research Institute Kanazawa University, Kakuma‐machi, Kanazawa 920‐1192 Japan
- Present address: Department of Molecular Biology and Genetics Hanoi Medical University No1‐Ton That Tung street‐Dong Da district, Ha Noi Vietnam
| | - Atsuko Kasahara
- Institute for Frontier Science Initiative Kanazawa University, Kakuma‐machi, Kanazawa, 920‐1192 Japan
- WPI Nano Life Science Institute (WPI‐Nano LSI) Kanazawa University, Kakuma‐machi, Kanazawa 920‐1192 Japan
| | - Xi Chen
- Division of Molecular Genetics Cancer Research Institute Kanazawa University, Kakuma‐machi, Kanazawa 920‐1192 Japan
| | - Loc Thi Pham
- Division of Molecular Genetics Cancer Research Institute Kanazawa University, Kakuma‐machi, Kanazawa 920‐1192 Japan
| | - Kenta Kurayoshi
- Division of Molecular Genetics Cancer Research Institute Kanazawa University, Kakuma‐machi, Kanazawa 920‐1192 Japan
| | - Yuko Tadokoro
- Division of Molecular Genetics Cancer Research Institute Kanazawa University, Kakuma‐machi, Kanazawa 920‐1192 Japan
- WPI Nano Life Science Institute (WPI‐Nano LSI) Kanazawa University, Kakuma‐machi, Kanazawa 920‐1192 Japan
| | - Masaya Ueno
- Division of Molecular Genetics Cancer Research Institute Kanazawa University, Kakuma‐machi, Kanazawa 920‐1192 Japan
- WPI Nano Life Science Institute (WPI‐Nano LSI) Kanazawa University, Kakuma‐machi, Kanazawa 920‐1192 Japan
| | - Tomoki Todo
- Division of Innovative Cancer Therapy, Institute of Medical Science The University of Tokyo Tokyo Japan
| | - Mitsutoshi Nakada
- Department of Neurosurgery, Graduate School of Medical Science Kanazawa University Kanazawa Ishikawa Japan
| | - Atsushi Hirao
- Division of Molecular Genetics Cancer Research Institute Kanazawa University, Kakuma‐machi, Kanazawa 920‐1192 Japan
- WPI Nano Life Science Institute (WPI‐Nano LSI) Kanazawa University, Kakuma‐machi, Kanazawa 920‐1192 Japan
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18
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Kang Y, Lin W, Liu Y, Nagy PD. Key tethering function of Atg11 autophagy scaffold protein in formation of virus-induced membrane contact sites during tombusvirus replication. Virology 2022; 572:1-16. [DOI: 10.1016/j.virol.2022.04.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/15/2022] [Accepted: 04/25/2022] [Indexed: 01/04/2023]
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19
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Molecular regulation of autophagosome formation. Biochem Soc Trans 2022; 50:55-69. [PMID: 35076688 PMCID: PMC9022990 DOI: 10.1042/bst20210819] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/21/2021] [Accepted: 01/04/2022] [Indexed: 12/11/2022]
Abstract
Macroautophagy, hereafter autophagy, is a degradative process conserved among eukaryotes, which is essential to maintain cellular homeostasis. Defects in autophagy lead to numerous human diseases, including various types of cancer and neurodegenerative disorders. The hallmark of autophagy is the de novo formation of autophagosomes, which are double-membrane vesicles that sequester and deliver cytoplasmic materials to lysosomes/vacuoles for degradation. The mechanism of autophagosome biogenesis entered a molecular era with the identification of autophagy-related (ATG) proteins. Although there are many unanswered questions and aspects that have raised some controversies, enormous advances have been done in our understanding of the process of autophagy in recent years. In this review, we describe the current knowledge about the molecular regulation of autophagosome formation, with a particular focus on budding yeast and mammalian cells.
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20
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Mochida K, Otani T, Katsumata Y, Kirisako H, Kakuta C, Kotani T, Nakatogawa H. Atg39 links and deforms the outer and inner nuclear membranes in selective autophagy of the nucleus. J Cell Biol 2022; 221:212974. [PMID: 35061008 PMCID: PMC8789198 DOI: 10.1083/jcb.202103178] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 11/12/2021] [Accepted: 12/10/2021] [Indexed: 01/07/2023] Open
Abstract
In selective autophagy of the nucleus (hereafter nucleophagy), nucleus-derived double-membrane vesicles (NDVs) are formed, sequestered within autophagosomes, and delivered to lysosomes or vacuoles for degradation. In Saccharomyces cerevisiae, the nuclear envelope (NE) protein Atg39 acts as a nucleophagy receptor, which interacts with Atg8 to target NDVs to the forming autophagosomal membranes. In this study, we revealed that Atg39 is anchored to the outer nuclear membrane via its transmembrane domain and also associated with the inner nuclear membrane via membrane-binding amphipathic helices (APHs) in its perinuclear space region, thereby linking these membranes. We also revealed that autophagosome formation-coupled Atg39 crowding causes the NE to protrude toward the cytoplasm, and the tips of the protrusions are pinched off to generate NDVs. The APHs of Atg39 are crucial for Atg39 crowding in the NE and subsequent NE protrusion. These findings suggest that the nucleophagy receptor Atg39 plays pivotal roles in NE deformation during the generation of NDVs to be degraded by nucleophagy.
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Affiliation(s)
- Keisuke Mochida
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Toshifumi Otani
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Yuto Katsumata
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Hiromi Kirisako
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Chika Kakuta
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Tetsuya Kotani
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Hitoshi Nakatogawa
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
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21
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Zheng Q, Duan L, Zhang Y, Li J, Zhang S, Wang H. A dynamically evolving war between autophagy and pathogenic microorganisms. J Zhejiang Univ Sci B 2022; 23:19-41. [PMID: 35029086 PMCID: PMC8758936 DOI: 10.1631/jzus.b2100285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Autophagy is an intracellular degradation process that maintains cellular homeostasis. It is essential for protecting organisms from environmental stress. Autophagy can help the host to eliminate invading pathogens, including bacteria, viruses, fungi, and parasites. However, pathogens have evolved multiple strategies to interfere with autophagic signaling pathways or inhibit the fusion of autophagosomes with lysosomes to form autolysosomes. Moreover, host cell matrix degradation by different types of autophagy can be used for the proliferation and reproduction of pathogens. Thus, determining the roles and mechanisms of autophagy during pathogen infections will promote understanding of the mechanisms of pathogen‒host interactions and provide new strategies for the treatment of infectious diseases.
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Affiliation(s)
- Qianqian Zheng
- Henan Key Laboratory of Immunology and Targeted Drugs, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang 453003, China.,Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang 453003, China
| | - Liangwei Duan
- Henan Key Laboratory of Immunology and Targeted Drugs, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang 453003, China.,Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang 453003, China
| | - Yang Zhang
- Henan Key Laboratory of Immunology and Targeted Drugs, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang 453003, China.,Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang 453003, China
| | - Jiaoyang Li
- Henan Key Laboratory of Immunology and Targeted Drugs, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang 453003, China.,Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang 453003, China
| | - Shiyu Zhang
- Henan Key Laboratory of Immunology and Targeted Drugs, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang 453003, China.,Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang 453003, China
| | - Hui Wang
- Henan Key Laboratory of Immunology and Targeted Drugs, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang 453003, China. .,Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang 453003, China.
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22
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Degradation of nuclear components via different autophagy pathways. Trends Cell Biol 2022; 32:574-584. [DOI: 10.1016/j.tcb.2021.12.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/21/2021] [Accepted: 12/23/2021] [Indexed: 12/21/2022]
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23
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Hernandez SJ, Fote G, Reyes-Ortiz AM, Steffan JS, Thompson LM. Cooperation of cell adhesion and autophagy in the brain: Functional roles in development and neurodegenerative disease. Matrix Biol Plus 2021; 12:100089. [PMID: 34786551 PMCID: PMC8579148 DOI: 10.1016/j.mbplus.2021.100089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/11/2021] [Accepted: 10/18/2021] [Indexed: 12/19/2022] Open
Abstract
Cellular adhesive connections directed by the extracellular matrix (ECM) and maintenance of cellular homeostasis by autophagy are seemingly disparate functions that are molecularly intertwined, each regulating the other. This is an emerging field in the brain where the interplay between adhesion and autophagy functions at the intersection of neuroprotection and neurodegeneration. The ECM and adhesion proteins regulate autophagic responses to direct protein clearance and guide regenerative programs that go awry in brain disorders. Concomitantly, autophagic flux acts to regulate adhesion dynamics to mediate neurite outgrowth and synaptic plasticity with functional disruption contributed by neurodegenerative disease. This review highlights the cooperative exchange between cellular adhesion and autophagy in the brain during health and disease. As the mechanistic alliance between adhesion and autophagy has been leveraged therapeutically for metastatic disease, understanding overlapping molecular functions that direct the interplay between adhesion and autophagy might uncover therapeutic strategies to correct or compensate for neurodegeneration.
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Affiliation(s)
- Sarah J. Hernandez
- Neurobiology and Behavior, University of California Irvine, Irvine, CA 92697, USA
- Sue and Bill Gross Stem Cell Research Center, University of California Irvine, Irvine, CA 92697, USA
| | - Gianna Fote
- Department of Biological Chemistry, University of California Irvine, Irvine, CA 92697, USA
| | - Andrea M. Reyes-Ortiz
- Sue and Bill Gross Stem Cell Research Center, University of California Irvine, Irvine, CA 92697, USA
- Department of Biological Chemistry, University of California Irvine, Irvine, CA 92697, USA
| | - Joan S. Steffan
- Psychaitry and Human Behavior, University of California Irvine, Irvine, CA 92697, USA
- Institute of Memory Impairments and Neurological Disorders, University of California Irvine, Irvine, CA 92617, USA
| | - Leslie M. Thompson
- Neurobiology and Behavior, University of California Irvine, Irvine, CA 92697, USA
- Sue and Bill Gross Stem Cell Research Center, University of California Irvine, Irvine, CA 92697, USA
- Department of Biological Chemistry, University of California Irvine, Irvine, CA 92697, USA
- Psychaitry and Human Behavior, University of California Irvine, Irvine, CA 92697, USA
- Institute of Memory Impairments and Neurological Disorders, University of California Irvine, Irvine, CA 92617, USA
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24
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Ebrahimi M, Habernig L, Broeskamp F, Aufschnaiter A, Diessl J, Atienza I, Matz S, Ruiz FA, Büttner S. Phosphate Restriction Promotes Longevity via Activation of Autophagy and the Multivesicular Body Pathway. Cells 2021; 10:3161. [PMID: 34831384 PMCID: PMC8620443 DOI: 10.3390/cells10113161] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 11/05/2021] [Accepted: 11/08/2021] [Indexed: 01/05/2023] Open
Abstract
Nutrient limitation results in an activation of autophagy in organisms ranging from yeast, nematodes and flies to mammals. Several evolutionary conserved nutrient-sensing kinases are critical for efficient adaptation of yeast cells to glucose, nitrogen or phosphate depletion, subsequent cell-cycle exit and the regulation of autophagy. Here, we demonstrate that phosphate restriction results in a prominent extension of yeast lifespan that requires the coordinated activity of autophagy and the multivesicular body pathway, enabling efficient turnover of cytoplasmic and plasma membrane cargo. While the multivesicular body pathway was essential during the early days of aging, autophagy contributed to long-term survival at later days. The cyclin-dependent kinase Pho85 was critical for phosphate restriction-induced autophagy and full lifespan extension. In contrast, when cell-cycle exit was triggered by exhaustion of glucose instead of phosphate, Pho85 and its cyclin, Pho80, functioned as negative regulators of autophagy and lifespan. The storage of phosphate in form of polyphosphate was completely dispensable to in sustaining viability under phosphate restriction. Collectively, our results identify the multifunctional, nutrient-sensing kinase Pho85 as critical modulator of longevity that differentially coordinates the autophagic response to distinct kinds of starvation.
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Affiliation(s)
- Mahsa Ebrahimi
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden; (M.E.); (L.H.); (F.B.); (J.D.); (S.M.)
| | - Lukas Habernig
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden; (M.E.); (L.H.); (F.B.); (J.D.); (S.M.)
| | - Filomena Broeskamp
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden; (M.E.); (L.H.); (F.B.); (J.D.); (S.M.)
| | - Andreas Aufschnaiter
- Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden;
| | - Jutta Diessl
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden; (M.E.); (L.H.); (F.B.); (J.D.); (S.M.)
| | - Isabel Atienza
- Instituto de Investigación e Innovación Biomédica de Cádiz (INIBICA), University of Cadiz, 11001 Cadiz, Spain; (I.A.); (F.A.R.)
| | - Steffen Matz
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden; (M.E.); (L.H.); (F.B.); (J.D.); (S.M.)
| | - Felix A. Ruiz
- Instituto de Investigación e Innovación Biomédica de Cádiz (INIBICA), University of Cadiz, 11001 Cadiz, Spain; (I.A.); (F.A.R.)
| | - Sabrina Büttner
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden; (M.E.); (L.H.); (F.B.); (J.D.); (S.M.)
- Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria
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25
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Hanley SE, Willis SD, Cooper KF. Snx4-assisted vacuolar targeting of transcription factors defines a new autophagy pathway for controlling ATG expression. Autophagy 2021; 17:3547-3565. [PMID: 33678121 PMCID: PMC8632336 DOI: 10.1080/15548627.2021.1877934] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 01/14/2021] [Indexed: 12/18/2022] Open
Abstract
Autophagy, in part, is controlled by the repression and activation of autophagy-related (ATG) genes. Here, we describe a new selective autophagy pathway that targets functional transcriptional regulators to control their activity. This pathway is activated in response to nitrogen starvation and recycles transcriptional activators (Msn2 and Rim15) and a repressor (Ssn2/Med13) of ATG expression. Further analysis of Ssn2/Med13 vacuolar proteolysis revealed that this pathway utilizes the core autophagic machinery. However, it is independent of known nucleophagy mechanisms, receptor proteins, and the scaffold protein Atg11. Instead, Ssn2/Med13 exits the nucleus through the nuclear pore complex (NPC) and associates with the cytoplasmic nucleoporin Gle1, a member of the RNA remodeling complex. Dbp5 and Nup159, that act in concert with Gle1, are also required for Ssn2/Med13 clearance. Ssn2/Med13 is retrieved from the nuclear periphery and degraded by Atg17-initiated phagophores anchored to the vacuole. Efficient transfer to phagophores depends on the sorting nexin heterodimer Snx4/Atg24-Atg20, which binds to Atg17, and relocates to the perinucleus following nitrogen starvation. To conclude, this pathway defines a previously undescribed autophagy mechanism that targets select transcriptional regulators for rapid vacuolar proteolysis, utilizing the RNA remodeling complex, the sorting nexin heterodimer Snx4-Atg20, Atg17, and the core autophagic machinery. It is physiologically relevant as this Snx4-assisted vacuolar targeting pathway permits cells to fine-tune the autophagic response by controlling the turnover of both positive and negative regulators of ATG transcription.Abbreviations: AIM: Atg8 interacting motif; ATG: autophagy-related; CKM: CDK8 kinase module; IDR: intrinsically disordered region; IP6: phosphoinositide inositol hexaphosphate; NPC: nuclear pore complex; PAS: phagophore assembly site; UPS: ubiquitin-proteasomal system.
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Affiliation(s)
- Sara E. Hanley
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University, Stratford, NJ, USA
| | - Stephen D. Willis
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University, Stratford, NJ, USA
| | - Katrina F. Cooper
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University, Stratford, NJ, USA
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26
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Montella-Manuel S, Pujol-Carrion N, de la Torre-Ruiz MA. The Cell Wall Integrity Receptor Mtl1 Contributes to Articulate Autophagic Responses When Glucose Availability Is Compromised. J Fungi (Basel) 2021; 7:jof7110903. [PMID: 34829194 PMCID: PMC8623553 DOI: 10.3390/jof7110903] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/21/2021] [Accepted: 10/23/2021] [Indexed: 01/02/2023] Open
Abstract
Mtl1protein is a cell wall receptor belonging to the CWI pathway. Mtl1 function is related to glucose and oxidative stress signaling. In this report, we show data demonstrating that Mtl1 plays a critical role in the detection of a descent in glucose concentration, in order to activate bulk autophagy machinery as a response to nutrient deprivation and to maintain cell survival in starvation conditions. Autophagy is a tightly regulated mechanism involving several signaling pathways. The data here show that in Saccharomyces cerevisiae, Mtl1 signals glucose availability to either Ras2 or Sch9 proteins converging in Atg1 phosphorylation and autophagy induction. TORC1 complex function is not involved in autophagy induction during the diauxic shift when glucose is limited. In this context, the GCN2 gene is required to regulate autophagy activation upon amino acid starvation independent of the TORC1 complex. Mtl1 function is also involved in signaling the autophagic degradation of mitochondria during the stationary phase through both Ras2 and Sch9, in a manner dependent on either Atg33 and Atg11 proteins and independent of the Atg32 protein, the mitophagy receptor. All of the above suggest a pivotal signaling role for Mtl1 in maintaining correct cell homeostasis function in periods of glucose scarcity in budding yeast.
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27
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Escobar-Niño A, Morano Bermejo IM, Carrasco Reinado R, Fernandez-Acero FJ. Deciphering the Dynamics of Signaling Cascades and Virulence Factors of B. cinerea during Tomato Cell Wall Degradation. Microorganisms 2021; 9:microorganisms9091837. [PMID: 34576732 PMCID: PMC8466851 DOI: 10.3390/microorganisms9091837] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/11/2021] [Accepted: 08/24/2021] [Indexed: 11/30/2022] Open
Abstract
The ascomycete Botrytis cinerea is one of the most relevant plant pathogenic fungi, affecting fruits, flowers, and greenhouse-grown crops. The infection strategy used by the fungus comprises a magnificent set of tools to penetrate and overcome plant defenses. In this context, the plant-pathogen communication through membrane receptors and signal transduction cascades is essential to trigger specific routes and the final success of the infection. In previous reports, proteomics approaches to B. cinerea signal transduction cascades changes in response to different carbon source and plant-based elicitors have been performed. Analyzing the secretome, membranome, phosphoproteome, and the phosphomembranome. Moreover, phenotypic changes in fungal biology was analyzed, specifically toxin production. To obtain the whole picture of the process and reveal the network from a system biology approach, this proteomic information has been merged with the phenotypic characterization, to be analyzed using several bioinformatics algorithms (GO, STRING, MCODE) in order to unravel key points in the signal transduction regulation crucial to overcome plant defenses, as well as new virulence/pathogenicity factors that could be used as therapeutic targets in the control of the gray mold rot disease. A total of 1721 and 663 exclusive or overexpressed proteins were identified under glucose (GLU) and deproteinized tomato cell walls (TCW), summarizing all of the protein identifications under phenotypic characterized stages. Under GO analysis, there are more biological process and molecular functions described in GLU, highlighting the increase in signaling related categories. These results agree with the high number of total identified proteins in GLU, probably indicating a more varied and active metabolism of the fungus. When analyzing only GO annotations related with signal transduction, it was revealed that there were proteins related to TOR signaling, the phosphorelay signal transduction system, and inositol lipid-mediated signaling, only under GLU conditions. On the contrary, calcium-mediated signaling GO annotation is only present between the proteins identified under TCW conditions. To establish a potential relationship between expressed proteins, cluster analyses showed 41 and 14 clusters under GLU and TCW conditions, confirming an increase in biological activity in GLU, where we identified a larger number of clusters related to transcription, translation, and cell division, between others. From these analyses, clusters related to signal transduction and clusters related to mycotoxin production were found, which correlated with the phenotypic characterization. The identification of the proteins encompassed in each condition and signal transduction cascade would provide the research community with new information about the B. cinerea infection process and potential candidates of pathogenicity/virulence factors, overcoming plant defenses, and new therapeutic targets.
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28
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Huang YJ, Klionsky DJ. Yeast mitophagy: Unanswered questions. Biochim Biophys Acta Gen Subj 2021; 1865:129932. [PMID: 34022298 PMCID: PMC8205991 DOI: 10.1016/j.bbagen.2021.129932] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/13/2021] [Accepted: 05/17/2021] [Indexed: 01/18/2023]
Abstract
Superfluous and damaged mitochondria need to be efficiently repaired or removed. Mitophagy is a selective type of autophagy that can engulf a portion of mitochondria within a double-membrane structure, called a mitophagosome, and deliver it to the vacuole for degradation. Mitophagy has significant physiological functions from yeast to human, and recent advances in yeast mitophagy shed light on the molecular mechanisms of mitophagy, especially the regulation of mitophagy induction. This review summarizes our current knowledge about yeast mitophagy and considers several unsolved questions, with a particular focus on Saccharomyces cerevisiae.
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Affiliation(s)
- Yuxiang J Huang
- Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Daniel J Klionsky
- Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
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29
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Wu Z, Xu H, Liu J, Zhou F, Liang Y. The ESCRT-III complex contributes to macromitophagy in yeast. Traffic 2021; 22:258-273. [PMID: 34089296 DOI: 10.1111/tra.12805] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 05/29/2021] [Accepted: 05/31/2021] [Indexed: 12/19/2022]
Abstract
Mitochondria play important roles in energy generation and homeostasis maintenance in eukaryotic cells. The damaged or superfluous mitochondria can be nonselectively or selectively removed through the autophagy/lysosome pathway, which was referred as mitophagy. According to the molecular machinery for degrading mitochondria, the selectively removed mitochondria can occur through macromitophagy or micromitophagy. In this study, we show that the endosomal sorting complex required for transport III (ESCRT-III) in budding yeast regulates macromitophagy induced by nitrogen starvation, but not by the post-logarithmic phase growth in lactate medium by monitoring a mitochondrial marker, Om45. Firstly, loss of ESCRT-III subunit Snf7 or Vps4-Vta1 complex subunit Vps4, two representative subunits of the ESCRT complex, suppresses the delivery and degradation of Om45-GFP to vacuoles. Secondly, we show that the mitochondrial marker Om45 and mitophagy receptor Atg32 accumulate on autophagosomes marked with Atg8 (mitophagosomes, MPs) in ESCRT mutants. Moreover, the protease-protection assay indicates that Snf7 and Vps4 are involved in MP closure. Finally, Snf7 interacts with Atg11, which was detected by two ways, glutathione-S-transferase (GST) pulldown and bimolecular fluorescence complementation (BiFC) assay, and this BiFC interaction happens on mitochondrial reticulum. Therefore, we proposed that the ESCRT-III machinery mediates nitrogen starvation-induced macromitophagy by the interaction between Snf7 and Atg11 so that Snf7 is recruited to Atg32-marked MPs by the known Atg11-Atg32 interaction to seal them. These results reveal that the ESCRT-III complex plays a new role in yeast on macromitophagy.
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Affiliation(s)
- Zulin Wu
- College of Life Sciences, Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, China
| | - Haiqian Xu
- College of Life Sciences, Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, China
| | - Junze Liu
- College of Life Sciences, Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, China
| | - Fan Zhou
- College of Life Sciences, Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, China
| | - Yongheng Liang
- College of Life Sciences, Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, China
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30
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Autophagy in Plant Abiotic Stress Management. Int J Mol Sci 2021; 22:ijms22084075. [PMID: 33920817 PMCID: PMC8071135 DOI: 10.3390/ijms22084075] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/03/2021] [Accepted: 04/05/2021] [Indexed: 12/11/2022] Open
Abstract
Plants can be considered an open system. Throughout their life cycle, plants need to exchange material, energy and information with the outside world. To improve their survival and complete their life cycle, plants have developed sophisticated mechanisms to maintain cellular homeostasis during development and in response to environmental changes. Autophagy is an evolutionarily conserved self-degradative process that occurs ubiquitously in all eukaryotic cells and plays many physiological roles in maintaining cellular homeostasis. In recent years, an increasing number of studies have shown that autophagy can be induced not only by starvation but also as a cellular response to various abiotic stresses, including oxidative, salt, drought, cold and heat stresses. This review focuses mainly on the role of autophagy in plant abiotic stress management.
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31
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Tomioka Y, Kotani T, Kirisako H, Oikawa Y, Kimura Y, Hirano H, Ohsumi Y, Nakatogawa H. TORC1 inactivation stimulates autophagy of nucleoporin and nuclear pore complexes. J Cell Biol 2021; 219:151819. [PMID: 32453403 PMCID: PMC7337488 DOI: 10.1083/jcb.201910063] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 03/05/2020] [Accepted: 04/20/2020] [Indexed: 02/08/2023] Open
Abstract
The mechanisms underlying turnover of the nuclear pore complex (NPC) and the component nucleoporins (Nups) are still poorly understood. In this study, we found that the budding yeast Saccharomyces cerevisiae triggers NPC degradation by autophagy upon the inactivation of Tor kinase complex 1. This degradation largely depends on the selective autophagy-specific factor Atg11 and the autophagy receptor-binding ability of Atg8, suggesting that the NPC is degraded via receptor-dependent selective autophagy. Immunoelectron microscopy revealed that NPCs embedded in nuclear envelope-derived double-membrane vesicles are sequestered within autophagosomes. At least two pathways are involved in NPC degradation: Atg39-dependent nucleophagy (selective autophagy of the nucleus) and a pathway involving an unknown receptor. In addition, we found the interaction between Nup159 and Atg8 via the Atg8-family interacting motif is important for degradation of this nucleoporin not assembled into the NPC. Thus, this study provides the first evidence for autophagic degradation of the NPC and Nups, which we term "NPC-phagy" and "nucleoporinophagy."
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Affiliation(s)
- Yui Tomioka
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Tetsuya Kotani
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Hiromi Kirisako
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Yu Oikawa
- Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Yayoi Kimura
- Advanced Medical Research Center, Yokohama City University, Yokohama, Japan
| | - Hisashi Hirano
- Advanced Medical Research Center, Yokohama City University, Yokohama, Japan
| | - Yoshinori Ohsumi
- Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Hitoshi Nakatogawa
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
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32
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Huang YJ, Klionsky DJ. Did evolution choose Atg11 as the scaffolding platform beyond selective autophagy? Autophagy 2021; 17:835-836. [PMID: 33404291 DOI: 10.1080/15548627.2021.1872176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
It has been well established that Atg11 plays a critical role in selective macroautophagy/autophagy, but not in nonselective autophagy in the budding yeast Saccharomyces cerevisiae. However, its mammalian ortholog RB1CC1/FIP200 is indispensable for both types of autophagy, and the molecular mechanism behind its function is a mystery. Recently, Pan et al. showed that in the fission yeast Schizosaccharomyces pombe, Atg11 could also promote nonselective autophagy via activation of Atg1 kinase. These results prompt an interesting idea that Atg11 might have gained an additional ability to mediate nonselective autophagy through evolution.
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Affiliation(s)
- Yuxiang J Huang
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA.,Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Daniel J Klionsky
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA.,Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
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33
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Meguro S, Zhuang X, Kirisako H, Nakatogawa H. Pex3 confines pexophagy receptor activity of Atg36 to peroxisomes by regulating Hrr25-mediated phosphorylation and proteasomal degradation. J Biol Chem 2020; 295:16292-16298. [PMID: 32958557 DOI: 10.1074/jbc.ra120.013565] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 08/09/2020] [Indexed: 01/10/2023] Open
Abstract
In macroautophagy (hereafter autophagy), cytoplasmic molecules and organelles are randomly or selectively sequestered within double-membrane vesicles called autophagosomes and delivered to lysosomes or vacuoles for degradation. In selective autophagy, the specificity of degradation targets is determined by autophagy receptors. In the budding yeast Saccharomyces cerevisiae, autophagy receptors interact with specific targets and Atg11, resulting in the recruitment of a protein complex that initiates autophagosome formation. Previous studies have revealed that autophagy receptors are regulated by posttranslational modifications. In selective autophagy of peroxisomes (pexophagy), the receptor Atg36 localizes to peroxisomes by binding to the peroxisomal membrane protein Pex3. We previously reported that Atg36 is phosphorylated by Hrr25 (casein kinase 1δ), increasing the Atg36-Atg11 interaction and thereby stimulating pexophagy initiation. However, the regulatory mechanisms underlying Atg36 phosphorylation are unknown. Here, we show that Atg36 phosphorylation is abolished in cells lacking Pex3 or expressing a Pex3 mutant defective in the interaction with Atg36, suggesting that the interaction with Pex3 is essential for the Hrr25-mediated phosphorylation of Atg36. Using recombinant proteins, we further demonstrated that Pex3 directly promotes Atg36 phosphorylation by Hrr25. A co-immunoprecipitation analysis revealed that the interaction of Atg36 with Hrr25 depends on Pex3. These results suggest that Pex3 increases the Atg36-Hrr25 interaction and thereby stimulates Atg36 phosphorylation on the peroxisomal membrane. In addition, we found that Pex3 binding protects Atg36 from proteasomal degradation. Thus, Pex3 confines Atg36 activity to the peroxisome by enhancing its phosphorylation and stability on this organelle.
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Affiliation(s)
- Sota Meguro
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Xizhen Zhuang
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Hiromi Kirisako
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Hitoshi Nakatogawa
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.
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34
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Navarro-Espíndola R, Suaste-Olmos F, Peraza-Reyes L. Dynamic Regulation of Peroxisomes and Mitochondria during Fungal Development. J Fungi (Basel) 2020; 6:E302. [PMID: 33233491 PMCID: PMC7711908 DOI: 10.3390/jof6040302] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/22/2020] [Accepted: 10/23/2020] [Indexed: 12/11/2022] Open
Abstract
Peroxisomes and mitochondria are organelles that perform major functions in the cell and whose activity is very closely associated. In fungi, the function of these organelles is critical for many developmental processes. Recent studies have disclosed that, additionally, fungal development comprises a dynamic regulation of the activity of these organelles, which involves a developmental regulation of organelle assembly, as well as a dynamic modulation of the abundance, distribution, and morphology of these organelles. Furthermore, for many of these processes, the dynamics of peroxisomes and mitochondria are governed by common factors. Notably, intense research has revealed that the process that drives the division of mitochondria and peroxisomes contributes to several developmental processes-including the formation of asexual spores, the differentiation of infective structures by pathogenic fungi, and sexual development-and that these processes rely on selective removal of these organelles via autophagy. Furthermore, evidence has been obtained suggesting a coordinated regulation of organelle assembly and dynamics during development and supporting the existence of regulatory systems controlling fungal development in response to mitochondrial activity. Gathered information underscores an important role for mitochondrial and peroxisome dynamics in fungal development and suggests that this process involves the concerted activity of these organelles.
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Affiliation(s)
| | | | - Leonardo Peraza-Reyes
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (R.N.-E.); (F.S.-O.)
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35
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Pan ZQ, Shao GC, Liu XM, Chen Q, Dong MQ, Du LL. Atg1 kinase in fission yeast is activated by Atg11-mediated dimerization and cis-autophosphorylation. eLife 2020; 9:58073. [PMID: 32909946 PMCID: PMC7511232 DOI: 10.7554/elife.58073] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 09/10/2020] [Indexed: 12/28/2022] Open
Abstract
Autophagy is a proteolytic pathway that is conserved from yeasts to mammals. Atg1 kinase is essential for autophagy, but how its activity is controlled remains insufficiently understood. Here, we show that, in the fission yeast Schizosaccharomyces pombe, Atg1 kinase activity requires Atg11, the ortholog of mammalian FIP200/RB1CC1, but does not require Atg13, Atg17, or Atg101. Remarkably, a 62 amino acid region of Atg11 is sufficient for the autophagy function of Atg11 and for supporting the Atg1 kinase activity. This region harbors an Atg1-binding domain and a homodimerization domain. Dimerizing Atg1 is the main role of Atg11, as it can be bypassed by artificially dimerizing Atg1. In an Atg1 dimer, only one Atg1 molecule needs to be catalytically active, suggesting that Atg1 activation can be achieved through cis-autophosphorylation. We propose that mediating Atg1 oligomerization and activation may be a conserved function of Atg11/FIP200 family proteins and cis-autophosphorylation may be a general mechanism of Atg1 activation.
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Affiliation(s)
- Zhao-Qian Pan
- College of Life Sciences, Beijing Normal University, Beijing, China.,National Institute of Biological Sciences, Beijing, China
| | - Guang-Can Shao
- National Institute of Biological Sciences, Beijing, China
| | - Xiao-Man Liu
- National Institute of Biological Sciences, Beijing, China
| | - Quan Chen
- National Institute of Biological Sciences, Beijing, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
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Margolis HK, Katzenell S, Leary KA, Ragusa MJ. The Third Coiled Coil Domain of Atg11 Is Required for Shaping Mitophagy Initiation Sites. J Mol Biol 2020; 432:5752-5764. [PMID: 32896530 DOI: 10.1016/j.jmb.2020.08.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 11/26/2022]
Abstract
Selective autophagy is the capture of specific cytosolic contents in double-membrane vesicles that subsequently fuse with the vacuole or lysosome, thereby delivering cargo for degradation. Selective autophagy receptors (SARs) mark the cargo for degradation and, in yeast, recruit Atg11, the scaffolding protein for selective autophagy initiation. The mitochondrial protein Atg32 is the yeast SAR that mediates mitophagy, the selective autophagic capture of mitochondria. Atg11-Atg32 interactions concentrate Atg32 into puncta that are thought to represent sites of mitophagy initiation. However, it is unclear how Atg11 concentrates Atg32 to generate mitophagy initiation sites. We show here that the coiled coil 3 (CC3) domain of Atg11 is required for concentrating Atg32 into puncta. We determined the structure of the majority of the CC3, demonstrating that the CC3 forms a parallel homodimer whose dimer interface is formed by a small number of hydrophobic residues. We further show that the CC3 interface is not required for Atg11 dimerization but is required for shaping Atg32 into functional mitophagy initiation sites and for delivery of mitochondria to the vacuole. Our findings suggest that Atg11 self-interactions help concentrate SARs as a necessary precondition for cargo capture.
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Affiliation(s)
| | - Sarah Katzenell
- Department of Chemistry, Dartmouth College, Hanover, NH 03755, USA
| | - Kelsie A Leary
- Department of Chemistry, Dartmouth College, Hanover, NH 03755, USA
| | - Michael J Ragusa
- Department of Chemistry, Dartmouth College, Hanover, NH 03755, USA; Department of Biochemistry and Cell Biology, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA.
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37
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The Roles of Ubiquitin in Mediating Autophagy. Cells 2020; 9:cells9092025. [PMID: 32887506 PMCID: PMC7564124 DOI: 10.3390/cells9092025] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/25/2020] [Accepted: 08/28/2020] [Indexed: 12/20/2022] Open
Abstract
Ubiquitination, the post-translational modification essential for various intracellular processes, is implicated in multiple aspects of autophagy, the major lysosome/vacuole-dependent degradation pathway. The autophagy machinery adopted the structural architecture of ubiquitin and employs two ubiquitin-like protein conjugation systems for autophagosome biogenesis. Ubiquitin chains that are attached as labels to protein aggregates or subcellular organelles confer selectivity, allowing autophagy receptors to simultaneously bind ubiquitinated cargos and autophagy-specific ubiquitin-like modifiers (Atg8-family proteins). Moreover, there is tremendous crosstalk between autophagy and the ubiquitin-proteasome system. Ubiquitination of autophagy-related proteins or regulatory components plays significant roles in the precise control of the autophagy pathway. In this review, we summarize and discuss the molecular mechanisms and functions of ubiquitin and ubiquitination, in the process and regulation of autophagy.
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Antón Z, Betin VMS, Simonetti B, Traer CJ, Attar N, Cullen PJ, Lane JD. A heterodimeric SNX4--SNX7 SNX-BAR autophagy complex coordinates ATG9A trafficking for efficient autophagosome assembly. J Cell Sci 2020; 133:jcs246306. [PMID: 32513819 PMCID: PMC7375690 DOI: 10.1242/jcs.246306] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 06/02/2020] [Indexed: 11/24/2022] Open
Abstract
The sorting nexins (SNXs) are a family of peripheral membrane proteins that direct protein trafficking decisions within the endocytic network. Emerging evidence in yeast and mammalian cells implicates a subgroup of SNXs in selective and non-selective forms of autophagy. Using siRNA and CRISPR-Cas9, we demonstrate that the SNX-BAR protein SNX4 is needed for efficient LC3 (also known as MAP1LC3) lipidation and autophagosome assembly in mammalian cells. SNX-BARs exist as homo- and hetero-dimers, and we show that SNX4 forms functional heterodimers with either SNX7 or SNX30 that associate with tubulovesicular endocytic membranes. Detailed image-based analysis during the early stages of autophagosome assembly reveals that SNX4-SNX7 is an autophagy-specific SNX-BAR heterodimer, required for efficient recruitment and/or retention of core autophagy regulators at the nascent isolation membrane. SNX4 partially colocalises with juxtanuclear ATG9A-positive membranes, with our data linking the autophagy defect upon SNX4 disruption to the mis-trafficking and/or retention of ATG9A in the Golgi region. Taken together, our findings show that the SNX4-SNX7 heterodimer coordinates ATG9A trafficking within the endocytic network to establish productive autophagosome assembly sites, thus extending knowledge of SNXs as positive regulators of autophagy.
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Affiliation(s)
- Zuriñe Antón
- Cell Biology Laboratories, School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Virginie M S Betin
- Cell Biology Laboratories, School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Boris Simonetti
- Henry Wellcome Integrated Signalling Laboratories, School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Colin J Traer
- Henry Wellcome Integrated Signalling Laboratories, School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Naomi Attar
- Henry Wellcome Integrated Signalling Laboratories, School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Peter J Cullen
- Henry Wellcome Integrated Signalling Laboratories, School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Jon D Lane
- Cell Biology Laboratories, School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
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Nakatogawa H. Mechanisms governing autophagosome biogenesis. Nat Rev Mol Cell Biol 2020; 21:439-458. [PMID: 32372019 DOI: 10.1038/s41580-020-0241-0] [Citation(s) in RCA: 435] [Impact Index Per Article: 108.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2020] [Indexed: 12/20/2022]
Abstract
Autophagosomes are double-membrane vesicles newly formed during autophagy to engulf a wide range of intracellular material and transport this autophagic cargo to lysosomes (or vacuoles in yeasts and plants) for subsequent degradation. Autophagosome biogenesis responds to a plethora of signals and involves unique and dynamic membrane processes. Autophagy is an important cellular mechanism allowing the cell to meet various demands, and its disruption compromises homeostasis and leads to various diseases, including metabolic disorders, neurodegeneration and cancer. Thus, not surprisingly, the elucidation of the molecular mechanisms governing autophagosome biogenesis has attracted considerable interest. Key molecules and organelles involved in autophagosome biogenesis, including autophagy-related (ATG) proteins and the endoplasmic reticulum, have been discovered, and their roles and relationships have been investigated intensely. However, several fundamental questions, such as what supplies membranes/lipids to build the autophagosome and how the membrane nucleates, expands, bends into a spherical shape and finally closes, have proven difficult to address. Nonetheless, owing to recent studies with new approaches and technologies, we have begun to unveil the mechanisms underlying these processes on a molecular level. We now know that autophagosome biogenesis is a highly complex process, in which multiple proteins and lipids from various membrane sources, supported by the formation of membrane contact sites, cooperate with biophysical phenomena, including membrane shaping and liquid-liquid phase separation, to ensure seamless segregation of the autophagic cargo. Together, these studies pave the way to obtaining a holistic view of autophagosome biogenesis.
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Affiliation(s)
- Hitoshi Nakatogawa
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.
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40
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Affiliation(s)
- Sascha Martens
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, 1030 Vienna, Austria.
| | - Christian Behrends
- Munich Cluster for Systems Neurology, Ludwig-Maximilians-Universität München, Feodor-Lynen Strasse 17, 81377 München, Germany.
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NAKATOGAWA H. Autophagic degradation of the endoplasmic reticulum. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2020; 96:1-9. [PMID: 31932525 PMCID: PMC6974406 DOI: 10.2183/pjab.96.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 10/11/2019] [Indexed: 06/10/2023]
Abstract
Autophagy is an intracellular degradation system that is present in most eukaryotes. In the process of autophagy, double membrane vesicles called autophagosomes sequester a wide variety of cellular constituents and deliver them to lytic organelles: lysosomes in mammals and vacuoles in yeast and plants. Although autophagy used to be considered a non-selective process in its target sequestration into autophagosomes, recent studies have revealed that autophagosomes can also selectively sequester certain proteins and organelles that have become unnecessary or harmful for the cell. We recently discovered that the endoplasmic reticulum (ER) is degraded by autophagy in a selective manner in the budding yeast Saccharomyces cerevisiae, and identified "receptor proteins" that play pivotal roles in this "ER-phagy" pathway. Moreover, several ER-phagy receptors in mammalian cells have also been reported. This report provides an overview of our current knowledge on ER-phagy and discuss their mechanisms, physiological roles, and possible links to human diseases.
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Affiliation(s)
- Hitoshi NAKATOGAWA
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan
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