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Chen T, Jia Y, Tang Y, Chen J, Xu H, Qi G. Cotton leaf curl Multan virus activates autophagy in the whitefly AsiaII7, weakening its vectorial capacity for transmission. PEST MANAGEMENT SCIENCE 2025; 81:3039-3047. [PMID: 39871813 DOI: 10.1002/ps.8674] [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: 06/13/2024] [Revised: 01/01/2025] [Accepted: 01/08/2025] [Indexed: 01/29/2025]
Abstract
BACKGROUND Autophagy plays an important role against pathogen infections in both insects and plants. Insect vectors employ autophagy as an intrinsic antiviral defense mechanism against viral infections, whereas viruses can exploit autophagy to enhance their transmission via insect vectors. The Cotton leaf curl Multan virus (CLCuMuV) is transmitted by the AsiaII7 cryptic species of Bemisia tabaci, however, the role of autophagy is involved in regulating the transmission of this virus remains unclear. RESULT In this study, it was observed that CLCuMuV infection induced autophagy in AsiaII7 whitefly, as evidenced by an elevated in the level of ATG8-II and the upregulation of Atg3, Atg8, Atg9 and Atg12. Both the administration of the autophagy inhibitor bafilomycin A1 and the silencing of Atg9 expression increased the viral load and enhanced CLCuMuV transmission. Conversely, the activation of autophagy via rapamycin feeding significantly reduced the amount of CLCuMuV and inhibited the efficiency of virus transmission. CONCLUSION CLCuMuV infection can activate the autophagy pathway in whiteflies. The activation of autophagy leads to the subsequent degradation of the virus and suppresses CLCuMuV transmission efficiency, whereas suppression of autophagy promotes virus transmission. Our research provides insight into the potential role of autophagy in antiviral defense mechanisms. © 2025 Society of Chemical Industry.
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Affiliation(s)
- Ting Chen
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences Guangzhou, Guangzhou, China
| | - Yanbo Jia
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences Guangzhou, Guangzhou, China
- Department of Life Sciences, Heibei University, Baoding, China
| | - Yafei Tang
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences Guangzhou, Guangzhou, China
| | - Jie Chen
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences Guangzhou, Guangzhou, China
| | - Haiyun Xu
- Department of Life Sciences, Heibei University, Baoding, China
| | - Guojun Qi
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences Guangzhou, Guangzhou, China
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2
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Wang J, Fu S, Zhou Y. Research progress on the autophagy gene ATG6 in planta. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2025; 359:112577. [PMID: 40412441 DOI: 10.1016/j.plantsci.2025.112577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2025] [Revised: 05/19/2025] [Accepted: 05/21/2025] [Indexed: 05/27/2025]
Abstract
Autophagy is a highly conserved intracellular degradation pathway in eukaryotes. Double-membrane autophagosomes engulf damaged organelles, misfolded proteins and pathogenic microorganisms and transport them to vacuoles (in yeast and plants) or lysosomes (in animals) for degradation to maintain cellular homeostasis. As a core regulatory component of class III PI3K-I and PI3K-II complexes, ATG6 is not only involved in autophagosome formation and vesicle trafficking, but also plays an important role in plant growth, development and stress responses. This paper reviews recent progress on the structural features, molecular functions and regulatory mechanisms of plant ATG6 in response to biotic and abiotic stresses, and discusses its potential application value in future stress-resistant plant breeding.
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Affiliation(s)
- Jiajun Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University/National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Chongqing 400712, China
| | - Shimin Fu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University/National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Chongqing 400712, China
| | - Yan Zhou
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University/National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Chongqing 400712, China.
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3
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Fesenko M, Moore DJ, Ewbank P, Courthold E, Royle SJ. ATG9A vesicles are a subtype of intracellular nanovesicle. J Cell Sci 2025; 138:jcs263852. [PMID: 40067248 PMCID: PMC12045599 DOI: 10.1242/jcs.263852] [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: 01/15/2025] [Accepted: 02/27/2025] [Indexed: 04/10/2025] Open
Abstract
Cells are filled with thousands of vesicles, which mediate protein transport and ensure homeostasis of the endomembrane system. Distinguishing these vesicles functionally and molecularly represents a major challenge. Intracellular nanovesicles (INVs) are a large class of transport vesicles that likely comprise multiple subtypes. Here, we define the INV proteome and find that it is molecularly heterogeneous and enriched for transmembrane cargo molecules, including integrins, transporters and ATG9A, a lipid scramblase associated with autophagy. ATG9A is known to reside in 'ATG9A vesicles' - small vesicles that contribute to autophagosome formation. Here, using in-cell vesicle capture assays, we found that ATG9A, as well as other ATG9A vesicle cargoes, are in INVs. Quantitative analysis showed that virtually all ATG9A vesicles are INVs, but that only ∼20% of INVs are ATG9A vesicles, suggesting that ATG9A vesicles are in fact a subtype of INV, which we term ATG9A-flavor INVs. Finally, we show that perturbing ATG9A-flavor INVs impairs the autophagy response induced by starvation.
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Affiliation(s)
- Mary Fesenko
- Centre for Mechanochemical Cell Biology and Warwick Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Daniel J. Moore
- Centre for Mechanochemical Cell Biology and Warwick Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Peyton Ewbank
- Centre for Mechanochemical Cell Biology and Warwick Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Elizabeth Courthold
- Centre for Mechanochemical Cell Biology and Warwick Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Stephen J. Royle
- Centre for Mechanochemical Cell Biology and Warwick Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
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4
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Braun MM, Sheehan BK, Shapiro SL, Ding Y, Rubinstein CD, Lehman BP, Puglielli L. Ca +2 and Nε-lysine acetylation regulate the CALR-ATG9A interaction in the lumen of the endoplasmic reticulum. Sci Rep 2024; 14:25532. [PMID: 39462136 PMCID: PMC11513142 DOI: 10.1038/s41598-024-76854-4] [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: 08/22/2024] [Accepted: 10/17/2024] [Indexed: 10/28/2024] Open
Abstract
The acetylation of autophagy protein 9 A (ATG9A) in the lumen of the endoplasmic reticulum (ER) by ATase1 and ATase2 regulates the induction of reticulophagy. Analysis of the ER-specific ATG9A interactome identified calreticulin (CALR), an ER luminal Ca+2-binding chaperone, as key for ATG9A activity. Specifically, if acetylated, ATG9A is sequestered by CALR and prevented from engaging FAM134B and SEC62. Under this condition, ATG9A is unable to activate the autophagy core machinery. In contrast, when non-acetylated, ATG9A is released by CALR and able to engage FAM134B and SEC62. In this study, we report that Ca+2 dynamics across the ER membrane regulate the ATG9A-CALR interaction as well as the ability of ATG9A to trigger reticulophagy. We show that the Ca+2-binding sites situated on the C-domain of CALR are essential for the ATG9A-CALR interaction. Finally, we show that K359 and K363 on ATG9A can influence the ATG9A-CALR interaction. Collectively, our results disclose a previously unidentified aspect of the complex mechanisms that regulate ATG9A activity. They also offer a possible area of intersection between Ca+2 metabolism, acetyl-CoA metabolism, and ER proteostasis.
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Affiliation(s)
- Megan M Braun
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Waisman Center, University of Wisconsin-Madison, 1500 Highland Ave, Madison, WI, 53705, USA
- Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Brendan K Sheehan
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Waisman Center, University of Wisconsin-Madison, 1500 Highland Ave, Madison, WI, 53705, USA
- Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Samantha L Shapiro
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Waisman Center, University of Wisconsin-Madison, 1500 Highland Ave, Madison, WI, 53705, USA
| | - Yun Ding
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Lilly Oncology, San Diego, CA, 92121, USA
| | - C Dustin Rubinstein
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Brent P Lehman
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Luigi Puglielli
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA.
- Waisman Center, University of Wisconsin-Madison, 1500 Highland Ave, Madison, WI, 53705, USA.
- Geriatric Research Education Clinical Center, Veterans Affairs Medical Center, Madison, WI, 53705, USA.
- Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA.
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5
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Holzer E, Martens S, Tulli S. The Role of ATG9 Vesicles in Autophagosome Biogenesis. J Mol Biol 2024; 436:168489. [PMID: 38342428 DOI: 10.1016/j.jmb.2024.168489] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/02/2024] [Accepted: 02/07/2024] [Indexed: 02/13/2024]
Abstract
Autophagy mediates the degradation and recycling of cellular material in the lysosomal system. Dysfunctional autophagy is associated with a plethora of diseases including uncontrolled infections, cancer and neurodegeneration. In macroautophagy (hereafter autophagy) this material is encapsulated in double membrane vesicles, the autophagosomes, which form upon induction of autophagy. The precursors to autophagosomes, referred to as phagophores, first appear as small flattened membrane cisternae, which gradually enclose the cargo material as they grow. The assembly of phagophores during autophagy initiation has been a major subject of investigation over the past decades. A special focus has been ATG9, the only conserved transmembrane protein among the core machinery. The majority of ATG9 localizes to small Golgi-derived vesicles. Here we review the recent advances and breakthroughs regarding our understanding of how ATG9 and the vesicles it resides in serve to assemble the autophagy machinery and to establish membrane contact sites for autophagosome biogenesis. We also highlight open questions in the field that need to be addressed in the years to come.
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Affiliation(s)
- Elisabeth Holzer
- Max Perutz Labs, Vienna BioCenter Campus (VBC), Vienna, Austria; University of Vienna, Max Perutz Labs, Department of Biochemistry and Cell Biology, Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Campus-Vienna-Biocenter 1, Vienna, Austria.
| | - Sascha Martens
- Max Perutz Labs, Vienna BioCenter Campus (VBC), Vienna, Austria; University of Vienna, Max Perutz Labs, Department of Biochemistry and Cell Biology, Vienna, Austria.
| | - Susanna Tulli
- Max Perutz Labs, Vienna BioCenter Campus (VBC), Vienna, Austria; University of Vienna, Max Perutz Labs, Department of Biochemistry and Cell Biology, Vienna, Austria.
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6
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Liu M, Duan Y, Dong J, Zhang K, Jin X, Gao M, Jia H, Chen J, Liu M, Wei M, Zhong X. Early signs of neurodegenerative diseases: Possible mechanisms and targets for Golgi stress. Biomed Pharmacother 2024; 175:116646. [PMID: 38692058 DOI: 10.1016/j.biopha.2024.116646] [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: 02/28/2024] [Revised: 04/17/2024] [Accepted: 04/24/2024] [Indexed: 05/03/2024] Open
Abstract
The Golgi apparatus plays a crucial role in mediating the modification, transport, and sorting of intracellular proteins and lipids. The morphological changes occurring in the Golgi apparatus are exceptionally important for maintaining its function. When exposed to external pressure or environmental stimulation, the Golgi apparatus undergoes adaptive changes in both structure and function, which are known as Golgi stress. Although certain signal pathway responses or post-translational modifications have been observed following Golgi stress, further research is needed to comprehensively summarize and understand the related mechanisms. Currently, there is evidence linking Golgi stress to neurodegenerative diseases; however, the role of Golgi stress in the progression of neurodegenerative diseases such as Alzheimer's disease remains largely unexplored. This review focuses on the structural and functional alterations of the Golgi apparatus during stress, elucidating potential mechanisms underlying the involvement of Golgi stress in regulating immunity, autophagy, and metabolic processes. Additionally, it highlights the pivotal role of Golgi stress as an early signaling event implicated in the pathogenesis and progression of neurodegenerative diseases. Furthermore, this study summarizes prospective targets that can be therapeutically exploited to mitigate neurodegenerative diseases by targeting Golgi stress. These findings provide a theoretical foundation for identifying novel breakthroughs in preventing and treating neurodegenerative diseases.
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Affiliation(s)
- Mengyu Liu
- School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, China
| | - Ying Duan
- Liaoning Maternal and Child Health Hospital, Shayang, Liaoning 110005, China
| | - Jianru Dong
- School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, China
| | - Kaisong Zhang
- School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, China
| | - Xin Jin
- School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, China
| | - Menglin Gao
- School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, China
| | - Huachao Jia
- School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, China
| | - Ju Chen
- School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, China
| | - Mingyan Liu
- School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, China.
| | - Minjie Wei
- School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, China; Liaoning Medical Diagnosis and Treatment Center, Shenyang, Liaoning 110167, China.
| | - Xin Zhong
- School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, China.
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7
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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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8
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Ijabi J, Ijabi R, Roozehdar P, Kaminsky ZA, Moradi-Sardareh H, Tehranian N, Ahmed N. Tumor Targeting via siRNA-COG3 to Suppress Tumor Progression in Mice and Inhibit Cancer Metastasis and Angiogenesis in Ovarian Cancer Cell Lines. Microrna 2024; 13:140-154. [PMID: 38243930 DOI: 10.2174/0122115366275856240101083442] [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: 08/05/2023] [Revised: 12/03/2023] [Accepted: 12/15/2023] [Indexed: 01/22/2024]
Abstract
BACKGROUND The COG complex is implicated in the tethering of retrograde intra-Golgi vesicles, which involves vesicular tethering and SNAREs. SNARE complexes mediate the invasion and metastasis of cancer cells through MMPs which activate growth factors for ECM fragments by binding to integrin receptors. Increasing MMPs is in line with YKL40 since YKL40 is linked to promoting angiogenesis through VEGF and can increase ovarian cancer (OC) resistance to chemotropic and cell migration. OBJECTIVE The aim of this study is an assessment of siRNA-COG3 on proliferation, invasion, and apoptosis of OC cells. In addition, siRNA-COG3 may prevent the growth of OC cancer in mice with tumors. METHODS Primary OC cell lines will be treated with siRNA-COG3 to assay YKL40 and identified angiogenesis by Tube-like structure formation in HOMECs. The Golgi morphology was analyzed using Immunofluorescence microscopy. Furthermore, the effects of siRNA-COG3 on the proliferation and apoptosis of cells were evaluated using MTT and TUNEL assays. Clones of the HOSEpiC OC cell line were subcutaneously implanted in FVB/N mice. Mice were treated after two weeks of injection of cells using siRNA-COG3. Tumor development suppression was detected by D-luciferin. RT-PCR and western blotting analyses were applied to determine COG3, MT1- MMP, SNAP23, and YKL40 expression to investigate the effects of COG3 gene knockdown. RESULTS siRNA-COG3 exhibited a substantial effect in suppressing tumor growth in mice. It dramatically reduced OC cell proliferation and triggered apoptosis (all p < 0.01). Inhibition of COG3, YKL-40, and MT1-MPP led to suppression of angiogenesis and reduction of microvessel density through SNAP23 in OC cells. CONCLUSION Overall, by knockdown of the COG3 gene, MT1-MMP and YKL40 were dropped, leading to suppressed angiogenesis along with decreasing migration and proliferation. SiRNACOG3 may be an ideal agent to consider for clinical trial assessment therapy for OC, especially when an antiangiogenic SNAR-pathway targeting drug.
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Affiliation(s)
- Janat Ijabi
- Department of Hematology, School of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
- Department of Hematology, Faculty of Medicine and Health Sciences, University Sains Malaysia, Kubang Kerian, 15200 Kota Bharu, Kelantan, Malaysia
| | - Roghayeh Ijabi
- Faculty of Reproductive Health, Golestan University of Medical Sciences, Gorgan, Iran
- Department of Pharmacology, Faculty of Medicine and Health Sciences, University Putra Malaysia, 43400 Serdang, Selangor Darul Ehsan, Malaysia
| | - Parisa Roozehdar
- Department of Medical Veterinary, Azad University, Garmsar Branch, Garmsar, Iran
| | - Zachary A Kaminsky
- Faculty of Medicine, Department of Cellular and Molecular Medicine, Royal's Institute of Mental Health Research, University of Ottawa, Ottawa, Canada
| | - Hemen Moradi-Sardareh
- Department of Basic Sciences, Asadabad School of Medical Sciences, Hamedan University of Medical Sciences, Hamedan, Iran
| | - Najmeh Tehranian
- Department of Midwifery & Reproductive Health, Faculty of Medical Sciences, Tarbiat Modares University, Jalal Ale Ahmad Highway, Tehran, Iran
| | - Naveed Ahmed
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, 16150, Malaysia
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9
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Li XH, Yu CWH, Gomez-Navarro N, Stancheva V, Zhu H, Murthy A, Wozny M, Malhotra K, Johnson CM, Blackledge M, Santhanam B, Liu W, Huang J, Freund SMV, Miller EA, Babu MM. Dynamic conformational changes of a tardigrade group-3 late embryogenesis abundant protein modulate membrane biophysical properties. PNAS NEXUS 2024; 3:pgae006. [PMID: 38269070 PMCID: PMC10808001 DOI: 10.1093/pnasnexus/pgae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 12/26/2023] [Indexed: 01/26/2024]
Abstract
A number of intrinsically disordered proteins (IDPs) encoded in stress-tolerant organisms, such as tardigrade, can confer fitness advantage and abiotic stress tolerance when heterologously expressed. Tardigrade-specific disordered proteins including the cytosolic-abundant heat-soluble proteins are proposed to confer stress tolerance through vitrification or gelation, whereas evolutionarily conserved IDPs in tardigrades may contribute to stress tolerance through other biophysical mechanisms. In this study, we characterized the mechanism of action of an evolutionarily conserved, tardigrade IDP, HeLEA1, which belongs to the group-3 late embryogenesis abundant (LEA) protein family. HeLEA1 homologs are found across different kingdoms of life. HeLEA1 is intrinsically disordered in solution but shows a propensity for helical structure across its entire sequence. HeLEA1 interacts with negatively charged membranes via dynamic disorder-to-helical transition, mainly driven by electrostatic interactions. Membrane interaction of HeLEA1 is shown to ameliorate excess surface tension and lipid packing defects. HeLEA1 localizes to the mitochondrial matrix when expressed in yeast and interacts with model membranes mimicking inner mitochondrial membrane. Yeast expressing HeLEA1 shows enhanced tolerance to hyperosmotic stress under nonfermentative growth and increased mitochondrial membrane potential. Evolutionary analysis suggests that although HeLEA1 homologs have diverged their sequences to localize to different subcellular organelles, all homologs maintain a weak hydrophobic moment that is characteristic of weak and reversible membrane interaction. We suggest that such dynamic and weak protein-membrane interaction buffering alterations in lipid packing could be a conserved strategy for regulating membrane properties and represent a general biophysical solution for stress tolerance across the domains of life.
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Affiliation(s)
- Xiao-Han Li
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Conny W H Yu
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | | | - Hongni Zhu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Andal Murthy
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Michael Wozny
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Ketan Malhotra
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | - Martin Blackledge
- Université Grenoble Alpes, CNRS, Commissariat à l’Energie Atomique et aux Energies Alternatives, Institut de Biologie Structurale, 38000 Grenoble, France
| | - Balaji Santhanam
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
- Department of Structural Biology, Center of Excellence for Data-Driven Discovery, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Wei Liu
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Jinqing Huang
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | | | | | - M Madan Babu
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
- Department of Structural Biology, Center of Excellence for Data-Driven Discovery, St Jude Children's Research Hospital, Memphis, TN 38105, USA
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10
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Komarla A, Dufresne S, Towers CG. Recent Advances in the Role of Autophagy in Endocrine-Dependent Tumors. Endocr Rev 2023; 44:629-646. [PMID: 36631217 PMCID: PMC10335171 DOI: 10.1210/endrev/bnad001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 10/31/2022] [Accepted: 01/10/2023] [Indexed: 01/13/2023]
Abstract
Autophagy plays a complex role in several cancer types, including endocrine-dependent cancers, by fueling cellular metabolism and clearing damaged substrates. This conserved recycling process has a dual function across tumor types where it can be tumor suppressive at early stages but tumor promotional in established disease. This review highlights the controversial roles of autophagy in endocrine-dependent tumors regarding cancer initiation, tumorigenesis, metastasis, and treatment response. We summarize clinical trial results thus far and highlight the need for additional mechanistic, preclinical, and clinical studies in endocrine-dependent tumors, particularly in breast cancer and prostate cancer.
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Affiliation(s)
- Anvita Komarla
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
- The Cell and Molecular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Suzanne Dufresne
- The Cell and Molecular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Christina G Towers
- The Cell and Molecular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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11
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Arlt H, Raman B, Filali-Mouncef Y, Hu Y, Leytens A, Hardenberg R, Guimarães R, Kriegenburg F, Mari M, Smaczynska-de Rooij II, Ayscough KR, Dengjel J, Ungermann C, Reggiori F. The dynamin Vps1 mediates Atg9 transport to the sites of autophagosome formation. J Biol Chem 2023; 299:104712. [PMID: 37060997 DOI: 10.1016/j.jbc.2023.104712] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/14/2023] [Accepted: 04/06/2023] [Indexed: 04/17/2023] Open
Abstract
Autophagy is a key process in eukaryotes to maintain cellular homeostasis by delivering cellular components to lysosomes/vacuoles for degradation and reuse of the resulting metabolites. Membrane rearrangements and trafficking events are mediated by the core machinery of autophagy-related (Atg) proteins, which carry out a variety of functions. How Atg9, a lipid scramblase and the only conserved transmembrane protein within this core Atg machinery, is trafficked during autophagy remained largely unclear. Here, we addressed this question in yeast Saccharomyces cerevisiae and found that retromer complex and dynamin Vps1 mutants alter Atg9 subcellular distribution and severely impair the autophagic flux by affecting two separate autophagy steps. We provide evidence that Vps1 interacts with Atg9 at Atg9 reservoirs. In the absence of Vps1, Atg9 fails to reach the sites of autophagosome formation, and this results in an autophagy defect. The function of Vps1 in autophagy requires its GTPase activity. Moreover, Vps1 point mutants associated with human diseases such as microcytic anemia and Charcot-Marie-Tooth are unable to sustain autophagy and affect Atg9 trafficking. Together, our data provide novel insights on the role of dynamins in Atg9 trafficking and suggest that a defect in this autophagy step could contribute to severe human pathologies.
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Affiliation(s)
- Henning Arlt
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; University of Osnabrück, Department of Biology/Chemistry, Biochemistry section, Barbarastrasse 13, 49076 Osnabrück, Germany
| | - Babu Raman
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Yasmina Filali-Mouncef
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Yan Hu
- Department of Biomedicine, Aarhus University, Ole Worms Allé 4, 8000 Aarhus C, Denmark
| | - Alexandre Leytens
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Ralph Hardenberg
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Rodrigo Guimarães
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Franziska Kriegenburg
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Muriel Mari
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Department of Biomedicine, Aarhus University, Ole Worms Allé 4, 8000 Aarhus C, Denmark
| | | | - Kathryn R Ayscough
- Department of Biomedical Sciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Jörn Dengjel
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Christian Ungermann
- University of Osnabrück, Department of Biology/Chemistry, Biochemistry section, Barbarastrasse 13, 49076 Osnabrück, Germany
| | - Fulvio Reggiori
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Department of Biomedicine, Aarhus University, Ole Worms Allé 4, 8000 Aarhus C, Denmark; Aarhus Institute of Advanced Studies (AIAS), Aarhus University, Høegh-Guldbergs Gade 6B, 8000 Aarhus C, Denmark.
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12
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Pitcairn C, Murata N, Zalon AJ, Stojkovska I, Mazzulli JR. Impaired Autophagic-Lysosomal Fusion in Parkinson's Patient Midbrain Neurons Occurs through Loss of ykt6 and Is Rescued by Farnesyltransferase Inhibition. J Neurosci 2023; 43:2615-2629. [PMID: 36788031 PMCID: PMC10082462 DOI: 10.1523/jneurosci.0610-22.2023] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 01/19/2023] [Accepted: 01/26/2023] [Indexed: 02/16/2023] Open
Abstract
Macroautophagy is a catabolic process that coordinates with lysosomes to degrade aggregation-prone proteins and damaged organelles. Loss of macroautophagy preferentially affects neuron viability and is associated with age-related neurodegeneration. We previously found that α-synuclein (α-syn) inhibits lysosomal function by blocking ykt6, a farnesyl-regulated soluble NSF attachment protein receptor (SNARE) protein that is essential for hydrolase trafficking in midbrain neurons. Using Parkinson's disease (PD) patient iPSC-derived midbrain cultures, we find that chronic, endogenous accumulation of α-syn directly inhibits autophagosome-lysosome fusion by impairing ykt6-SNAP-29 complexes. In wild-type (WT) cultures, ykt6 depletion caused a near-complete block of autophagic flux, highlighting its critical role for autophagy in human iPSC-derived neurons. In PD, macroautophagy impairment was associated with increased farnesyltransferase (FTase) activity, and FTase inhibitors restored macroautophagic flux through promoting active forms of ykt6 in human cultures, and male and female mice. Our findings indicate that ykt6 mediates cellular clearance by coordinating autophagic-lysosomal fusion and hydrolase trafficking, and that macroautophagy impairment in PD can be rescued by FTase inhibitors.SIGNIFICANCE STATEMENT The pathogenic mechanisms that lead to the death of neurons in Parkinson's disease (PD) and Dementia with Lewy bodies (LBD) are currently unknown. Furthermore, disease modifying treatments for these diseases do not exist. Our study indicates that a cellular clearance pathway termed autophagy is impaired in patient-derived culture models of PD and in vivo We identified a novel druggable target, a soluble NSF attachment protein receptor (SNARE) protein called ykt6, that rescues autophagy in vitro and in vivo upon blocking its farnesylation. Our work suggests that farnesyltransferase (FTase) inhibitors may be useful therapies for PD and DLB through enhancing autophagic-lysosomal clearance of aggregated proteins.
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Affiliation(s)
- Caleb Pitcairn
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
| | - Naomi Murata
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
| | - Annie J Zalon
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
| | - Iva Stojkovska
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
| | - Joseph R Mazzulli
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
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13
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Marquardt L, Taylor M, Kramer F, Schmitt K, Braus GH, Valerius O, Thumm M. Vacuole fragmentation depends on a novel Atg18-containing retromer-complex. Autophagy 2023; 19:278-295. [PMID: 35574911 PMCID: PMC9809942 DOI: 10.1080/15548627.2022.2072656] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The yeast PROPPIN Atg18 folds as a β-propeller with two binding sites for phosphatidylinositol-3-phosphate (PtdIns3P) and PtdIns(3,5)P2 at its circumference. Membrane insertion of an amphipathic loop of Atg18 leads to membrane tubulation and fission. Atg18 has known functions at the PAS during macroautophagy, but the functional relevance of its endosomal and vacuolar pool is not well understood. Here we show in a proximity-dependent labeling approach and by co-immunoprecipitations that Atg18 interacts with Vps35, a central component of the retromer complex. The binding of Atg18 to Vps35 is competitive with the sorting nexin dimer Vps5 and Vps17. This suggests that Atg18 within the retromer can substitute for both the phosphoinositide binding and the membrane bending capabilities of these sorting nexins. Indeed, we found that Atg18-retromer is required for PtdIns(3,5)P2-dependent vacuolar fragmentation during hyperosmotic stress. The Atg18-retromer is further involved in the normal sorting of the integral membrane protein Atg9. However, PtdIns3P-dependent macroautophagy and the selective cytoplasm-to-vacuole targeting (Cvt) pathway are only partially affected by the Atg18-retromer. We expect that this is due to the plasticity of the different sorting pathways within the endovacuolar system.Abbreviations: BAR: bin/amphiphysin/Rvs; FOA: 5-fluoroorotic acid; PAS: phagophore assembly site; PROPPIN: beta-propeller that binds phosphoinositides; PtdIns3P: phosphatidylinositol-3-phosphate; PX: phox homology.
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Affiliation(s)
- Lisa Marquardt
- Institute of Cellular Biochemistry, University Medicine, Goettingen, Germany
| | - Matthew Taylor
- Institute of Cellular Biochemistry, University Medicine, Goettingen, Germany
| | - Florian Kramer
- Institute of Cellular Biochemistry, University Medicine, Goettingen, Germany
| | - Kerstin Schmitt
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Georg-August-University, Goettingen, Germany
| | - Gerhard H. Braus
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Georg-August-University, Goettingen, Germany
| | - Oliver Valerius
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Georg-August-University, Goettingen, Germany
| | - Michael Thumm
- Institute of Cellular Biochemistry, University Medicine, Goettingen, Germany,CONTACT Michael Thumm ; Institute of Cellular Biochemistry, University Medicine, Humboldtallee 23, D-37073Goettingen, Germany
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14
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Zhou L, Xue X, Yang K, Feng Z, Liu M, Pastor-Pareja JC. Convergence of secretory, endosomal, and autophagic routes in trans-Golgi-associated lysosomes. J Cell Biol 2022; 222:213547. [PMID: 36239631 PMCID: PMC9577102 DOI: 10.1083/jcb.202203045] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 08/17/2022] [Accepted: 09/23/2022] [Indexed: 12/15/2022] Open
Abstract
At the trans-Golgi, complex traffic connections exist to the endolysosomal system additional to the main Golgi-to-plasma membrane secretory route. Here, we investigated three hits in a Drosophila screen displaying secretory cargo accumulation in autophagic vesicles: ESCRT-III component Vps20, SNARE-binding Rop, and lysosomal pump subunit VhaPPA1-1. We found that Vps20, Rop, and lysosomal markers localize near the trans-Golgi. Furthermore, we document that the vicinity of the trans-Golgi is the main cellular location for lysosomes and that early, late, and recycling endosomes associate as well with a trans-Golgi-associated degradative compartment where basal microautophagy of secretory cargo and other materials occurs. Disruption of this compartment causes cargo accumulation in our hits, including Munc18 homolog Rop, required with Syx1 and Syx4 for Rab11-mediated endosomal recycling. Finally, besides basal microautophagy, we show that the trans-Golgi-associated degradative compartment contributes to the growth of autophagic vesicles in developmental and starvation-induced macroautophagy. Our results argue that the fly trans-Golgi is the gravitational center of the whole endomembrane system.
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Affiliation(s)
- Lingjian Zhou
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Xutong Xue
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Ke Yang
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Zhi Feng
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Min Liu
- School of Life Sciences, Tsinghua University, Beijing, China
| | - José C. Pastor-Pareja
- School of Life Sciences, Tsinghua University, Beijing, China,Tsinghua-Peking Center for Life Sciences, Beijing, China,Institute of Neurosciences, Consejo Superior de Investigaciones Científicas–Universidad Miguel Hernández, San Juan de Alicante, Spain
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15
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Kriegenburg F, Huiting W, van Buuren-Broek F, Zwilling E, Hardenberg R, Mari M, Kraft C, Reggiori F. The lipid flippase Drs2 regulates anterograde transport of Atg9 during autophagy. AUTOPHAGY REPORTS 2022; 1:345-367. [PMID: 38106996 PMCID: PMC7615381 DOI: 10.1080/27694127.2022.2104781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Macroautophagy/autophagy is a conserved catabolic pathway during which cellular material is sequestered within newly formed double-membrane vesicles called autophagosomes and delivered to the lytic compartment of eukaryotic cells for degradation. Autophagosome biogenesis depends on the core autophagy-related (Atg) machinery, and involves a massive supply and remodelling of membranes. To gain insight into the lipid remodelling mechanisms during autophagy, we have systematically investigated whether lipid flippases are required for this pathway in the yeast Saccharomyces cerevisiae. We found that the flippase Drs2, which transfers phosphatidylserine and phosphatidylethanolamine from the lumenal to the cytosolic leaflet of the limiting membrane at the trans-Golgi network, is required for normal progression of autophagy. We also show that Drs2 is important for the trafficking of the core Atg protein Atg9. Atg9 is a transmembrane protein important for autophagosome biogenesis and its anterograde transport from its post-Golgi reservoirs to the site of autophagosome formation is severely impaired in the absence of Drs2. Thus, our results identify a novel autophagy player and highlight that membrane asymmetry regulates early autophagy steps.
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Affiliation(s)
- Franziska Kriegenburg
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University medical Centre Groningen, 9713AV Groningen, The Netherlands
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104, Freiburg, Germany
| | - Wouter Huiting
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University medical Centre Groningen, 9713AV Groningen, The Netherlands
| | - Fleur van Buuren-Broek
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University medical Centre Groningen, 9713AV Groningen, The Netherlands
| | - Emma Zwilling
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University medical Centre Groningen, 9713AV Groningen, The Netherlands
- Department of Biomedicine, Aarhus University, Ole Worms Allé 4, 8000 Aarhus C, Denmark
| | - Ralph Hardenberg
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University medical Centre Groningen, 9713AV Groningen, The Netherlands
| | - Muriel Mari
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University medical Centre Groningen, 9713AV Groningen, The Netherlands
- Department of Biomedicine, Aarhus University, Ole Worms Allé 4, 8000 Aarhus C, Denmark
| | - Claudine Kraft
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104, Freiburg, Germany
| | - Fulvio Reggiori
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University medical Centre Groningen, 9713AV Groningen, The Netherlands
- Department of Biomedicine, Aarhus University, Ole Worms Allé 4, 8000 Aarhus C, Denmark
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16
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Mokhtari T. Targeting autophagy and neuroinflammation pathways with plant-derived natural compounds as potential antidepressant agents. Phytother Res 2022; 36:3470-3489. [PMID: 35794794 DOI: 10.1002/ptr.7551] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 06/13/2022] [Accepted: 06/17/2022] [Indexed: 11/06/2022]
Abstract
Major depressive disorder (MDD) is a life-threatening disease that presents several characteristics. The pathogenesis of depression still remains poorly understood. Moreover, the mechanistic interactions of natural components in treating depression to target autophagy and neuroinflammation are yet to be evaluated. This study overviewed the effects of plant-derived natural components in regulating critical pathways, particularly neuroinflammation and autophagy, associated with depression. A list of natural components, including luteolin, apigenin, hyperforin, resveratrol, salvianolic acid b, isoliquiritin, nobiletin, andrographolide, and oridonin, have been investigated. All peer-reviewed journal articles were searched by Scopus, MEDLINE, PubMed, Web of Science, and Google Scholar using the appropriated keywords, including depression, neuroinflammation, autophagy, plant, natural components, etc. The neuroinflammation and autophagy dysfunction are critically associated with the pathophysiology of depression. Natural components with higher efficiency and lower complications can be used for targeting neuroinflammation and autophagy. These components with different doses showed the beneficial antidepressant properties in rodents. These can modulate autophagy markers, mainly AMPK, LC3II/LC3I ratio, Beclin-1. Moreover, they can regulate the NLRP3 inflammasome, resulting in the suppression of proinflammatory cytokines (e.g., IL-1β and IL-18). Future in vitro and in vivo studies are required to develop novel therapeutic approaches based on plant-derived active components to treat MDD.
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Affiliation(s)
- Tahmineh Mokhtari
- CAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing, China.,Department of Psychology, University of Chinese Academy of Sciences, Beijing, China
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17
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Chen Y, Wu Z, Dong L, You X, Ji Y, Liang Y. Yeast phospholipase D, Spo14, is not required for macroautophagy. Yeast 2022; 39:401-411. [PMID: 35711110 DOI: 10.1002/yea.3803] [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: 07/13/2021] [Revised: 05/09/2022] [Accepted: 06/14/2022] [Indexed: 12/25/2022] Open
Abstract
Autophagy-related gene (Atg) proteins are key players in autophagy. Some proteins that function in vesicle trafficking and lipid metabolism are also involved in autophagy. The SPO14 in yeast, which encodes phospholipase D (PLD), is involved in membrane trafficking and plays a vital role in sporulation during meiosis. Crosstalk has been identified between autophagy and sporulation. Although the PLD is required for macroautophagy in mammals, its role in yeast macroautophagy remains unclear. We observed that Spo14 is not required for macroautophagy in yeast and that it is dispensable for Atg8 lipidation, which plays an important role in phagophore extension. Our results also revealed that green fluorescent protein (GFP)-Atg8 degradation is not completely blocked in atg1Δ/atg1Δ cells under sporulation condition. Therefore, Spo14 is not required for macroautophagy in yeast.
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Affiliation(s)
- Yun Chen
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Zulin Wu
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Lin Dong
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xia You
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yanling Ji
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yongheng Liang
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
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18
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Yang S, Park D, Manning L, Hill SE, Cao M, Xuan Z, Gonzalez I, Dong Y, Clark B, Shao L, Okeke I, Almoril-Porras A, Bai J, De Camilli P, Colón-Ramos DA. Presynaptic autophagy is coupled to the synaptic vesicle cycle via ATG-9. Neuron 2022; 110:824-840.e10. [PMID: 35065714 PMCID: PMC9017068 DOI: 10.1016/j.neuron.2021.12.031] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 10/20/2021] [Accepted: 12/20/2021] [Indexed: 01/01/2023]
Abstract
Autophagy is a cellular degradation pathway essential for neuronal health and function. Autophagosome biogenesis occurs at synapses, is locally regulated, and increases in response to neuronal activity. The mechanisms that couple autophagosome biogenesis to synaptic activity remain unknown. In this study, we determine that trafficking of ATG-9, the only transmembrane protein in the core autophagy pathway, links the synaptic vesicle cycle with autophagy. ATG-9-positive vesicles in C. elegans are generated from the trans-Golgi network via AP-3-dependent budding and delivered to presynaptic sites. At presynaptic sites, ATG-9 undergoes exo-endocytosis in an activity-dependent manner. Mutations that disrupt endocytosis, including a lesion in synaptojanin 1 associated with Parkinson's disease, result in abnormal ATG-9 accumulation at clathrin-rich synaptic foci and defects in activity-induced presynaptic autophagy. Our findings uncover regulated key steps of ATG-9 trafficking at presynaptic sites and provide evidence that ATG-9 exo-endocytosis couples autophagosome biogenesis at presynaptic sites with the activity-dependent synaptic vesicle cycle.
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Affiliation(s)
- Sisi Yang
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Departments of Neuroscience and of Cell Biology, Yale University School of Medicine, 260 Whitney Avenue, YSB C167, New Haven, CT 06511, USA
| | - Daehun Park
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Departments of Neuroscience and of Cell Biology, Yale University School of Medicine, 260 Whitney Avenue, YSB C167, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Laura Manning
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Departments of Neuroscience and of Cell Biology, Yale University School of Medicine, 260 Whitney Avenue, YSB C167, New Haven, CT 06511, USA
| | - Sarah E Hill
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Departments of Neuroscience and of Cell Biology, Yale University School of Medicine, 260 Whitney Avenue, YSB C167, New Haven, CT 06511, USA
| | - Mian Cao
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Departments of Neuroscience and of Cell Biology, Yale University School of Medicine, 260 Whitney Avenue, YSB C167, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Zhao Xuan
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Departments of Neuroscience and of Cell Biology, Yale University School of Medicine, 260 Whitney Avenue, YSB C167, New Haven, CT 06511, USA
| | - Ian Gonzalez
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Departments of Neuroscience and of Cell Biology, Yale University School of Medicine, 260 Whitney Avenue, YSB C167, New Haven, CT 06511, USA
| | - Yongming Dong
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Benjamin Clark
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Departments of Neuroscience and of Cell Biology, Yale University School of Medicine, 260 Whitney Avenue, YSB C167, New Haven, CT 06511, USA
| | - Lin Shao
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Departments of Neuroscience and of Cell Biology, Yale University School of Medicine, 260 Whitney Avenue, YSB C167, New Haven, CT 06511, USA
| | - Ifechukwu Okeke
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Departments of Neuroscience and of Cell Biology, Yale University School of Medicine, 260 Whitney Avenue, YSB C167, New Haven, CT 06511, USA
| | - Agustin Almoril-Porras
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Departments of Neuroscience and of Cell Biology, Yale University School of Medicine, 260 Whitney Avenue, YSB C167, New Haven, CT 06511, USA
| | - Jihong Bai
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Pietro De Camilli
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Departments of Neuroscience and of Cell Biology, Yale University School of Medicine, 260 Whitney Avenue, YSB C167, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510, USA; Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT 06510, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Daniel A Colón-Ramos
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Departments of Neuroscience and of Cell Biology, Yale University School of Medicine, 260 Whitney Avenue, YSB C167, New Haven, CT 06511, USA; Instituto de Neurobiología José del Castillo, Recinto de Ciencias Médicas, Universidad de Puerto Rico, 201 Boulevard del Valle, San Juan, PR 00901, USA; Wu Tsai Institute, Yale University, New Haven, CT 06510, USA.
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19
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Wang R, Miao G, Shen JL, Fortier TM, Baehrecke EH. ESCRT dysfunction compromises endoplasmic reticulum maturation and autophagosome biogenesis in Drosophila. Curr Biol 2022; 32:1262-1274.e4. [PMID: 35134326 PMCID: PMC8969116 DOI: 10.1016/j.cub.2022.01.040] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/09/2021] [Accepted: 01/13/2022] [Indexed: 12/20/2022]
Abstract
Autophagy targets cytoplasmic materials for degradation and influences cell health. Organelle contact and trafficking systems provide membranes for autophagosome formation, but how different membrane systems are selected for use during autophagy remains unclear. Here, we report a novel function of the endosomal sorting complex required for transport (ESCRT) in the regulation of endoplasmic reticulum (ER) coat protein complex II (COPII) vesicle formation that influences autophagy. The ESCRT functions in a pathway upstream of Vps13D to influence COPII vesicle transport, ER-Golgi intermediate compartment (ERGIC) assembly, and autophagosome formation. Atg9 functions downstream of the ESCRT to facilitate ERGIC and autophagosome formation. Interestingly, cells lacking either ESCRT or Vps13D functions exhibit dilated ER structures that are similar to cranio-lenticulo-sutural dysplasia patient cells with SEC23A mutations, which encodes a component of COPII vesicles. Our data reveal a novel ESCRT-dependent pathway that influences the ERGIC and autophagosome formation.
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Affiliation(s)
- Ruoxi Wang
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Guangyan Miao
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - James L Shen
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Tina M Fortier
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Eric H Baehrecke
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
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20
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Coudevylle N, Banaś B, Baumann V, Schuschnig M, Zawadzka-Kazimierczuk A, Koźmiński W, Martens S. Mechanism of Atg9 recruitment by Atg11 in the cytoplasm-to-vacuole targeting pathway. J Biol Chem 2022; 298:101573. [PMID: 35007534 PMCID: PMC8814668 DOI: 10.1016/j.jbc.2022.101573] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 11/22/2022] Open
Abstract
Autophagy is a lysosomal degradation pathway for the removal of damaged and superfluous cytoplasmic material. This is achieved by the sequestration of this cargo material within double-membrane vesicles termed autophagosomes. Autophagosome formation is mediated by the conserved autophagy machinery. In selective autophagy, this machinery including the transmembrane protein Atg9 is recruited to specific cargo material via cargo receptors and the Atg11/FIP200 scaffold protein. The molecular details of the interaction between Atg11 and Atg9 are unclear, and it is still unknown how the recruitment of Atg9 is regulated. Here we employ NMR spectroscopy of the N-terminal disordered domain of Atg9 (Atg9-NTD) to map its interaction with Atg11 revealing that it involves two short peptides both containing a PLF motif. We show that the Atg9-NTD binds to Atg11 with an affinity of about 1 μM and that both PLF motifs contribute to the interaction. Mutation of the PLF motifs abolishes the interaction of the Atg9-NTD with Atg11, reduces the recruitment of Atg9 to the precursor aminopeptidase 1 (prApe1) cargo, and blocks prApe1 transport into the vacuole by the selective autophagy-like cytoplasm-to-vacuole (Cvt) targeting pathway while not affecting bulk autophagy. Our results provide mechanistic insights into the interaction of the Atg11 scaffold with the Atg9 transmembrane protein in selective autophagy and suggest a model where only clustered Atg11 when bound to the prApe1 cargo is able to efficiently recruit Atg9 vesicles.
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Affiliation(s)
| | - Bartłomiej Banaś
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Verena Baumann
- Max Perutz Laboratories, University of Vienna, Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | | | | | - Wiktor Koźmiński
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Sascha Martens
- Max Perutz Laboratories, University of Vienna, Vienna, Austria.
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21
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Mailler E, Guardia CM, Bai X, Jarnik M, Williamson CD, Li Y, Maio N, Golden A, Bonifacino JS. The autophagy protein ATG9A enables lipid mobilization from lipid droplets. Nat Commun 2021; 12:6750. [PMID: 34799570 PMCID: PMC8605025 DOI: 10.1038/s41467-021-26999-x] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 10/26/2021] [Indexed: 01/18/2023] Open
Abstract
The multispanning membrane protein ATG9A is a scramblase that flips phospholipids between the two membrane leaflets, thus contributing to the expansion of the phagophore membrane in the early stages of autophagy. Herein, we show that depletion of ATG9A does not only inhibit autophagy but also increases the size and/or number of lipid droplets in human cell lines and C. elegans. Moreover, ATG9A depletion blocks transfer of fatty acids from lipid droplets to mitochondria and, consequently, utilization of fatty acids in mitochondrial respiration. ATG9A localizes to vesicular-tubular clusters (VTCs) that are tightly associated with an ER subdomain enriched in another multispanning membrane scramblase, TMEM41B, and also in close proximity to phagophores, lipid droplets and mitochondria. These findings indicate that ATG9A plays a critical role in lipid mobilization from lipid droplets to autophagosomes and mitochondria, highlighting the importance of ATG9A in both autophagic and non-autophagic processes.
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Affiliation(s)
- Elodie Mailler
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Carlos M Guardia
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Xiaofei Bai
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michal Jarnik
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Chad D Williamson
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Yan Li
- Proteomics Core Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Nunziata Maio
- Metals Biology and Molecular Medicine Group, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Andy Golden
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Juan S Bonifacino
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
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22
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Ohashi Y. Activation Mechanisms of the VPS34 Complexes. Cells 2021; 10:cells10113124. [PMID: 34831348 PMCID: PMC8624279 DOI: 10.3390/cells10113124] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/09/2021] [Accepted: 11/09/2021] [Indexed: 01/18/2023] Open
Abstract
Phosphatidylinositol-3-phosphate (PtdIns(3)P) is essential for cell survival, and its intracellular synthesis is spatially and temporally regulated. It has major roles in two distinctive cellular pathways, namely, the autophagy and endocytic pathways. PtdIns(3)P is synthesized from phosphatidylinositol (PtdIns) by PIK3C3C/VPS34 in mammals or Vps34 in yeast. Pathway-specific VPS34/Vps34 activity is the consequence of the enzyme being incorporated into two mutually exclusive complexes: complex I for autophagy, composed of VPS34/Vps34-Vps15/Vps15-Beclin 1/Vps30-ATG14L/Atg14 (mammals/yeast), and complex II for endocytic pathways, in which ATG14L/Atg14 is replaced with UVRAG/Vps38 (mammals/yeast). Because of its involvement in autophagy, defects in which are closely associated with human diseases such as cancer and neurodegenerative diseases, developing highly selective drugs that target specific VPS34/Vps34 complexes is an essential goal in the autophagy field. Recent studies on the activation mechanisms of VPS34/Vps34 complexes have revealed that a variety of factors, including conformational changes, lipid physicochemical parameters, upstream regulators, and downstream effectors, greatly influence the activity of these complexes. This review summarizes and highlights each of these influences as well as clarifying key questions remaining in the field and outlining future perspectives.
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Affiliation(s)
- Yohei Ohashi
- MRC Laboratory of Molecular Biology, Protein and Nucleic Acid Chemistry Division, Francis Crick Avenue, Cambridge CB2 0QH, UK
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23
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Guardia CM, Jain A, Mattera R, Friefeld A, Li Y, Bonifacino JS. RUSC2 and WDR47 oppositely regulate kinesin-1-dependent distribution of ATG9A to the cell periphery. Mol Biol Cell 2021; 32:ar25. [PMID: 34432492 PMCID: PMC8693955 DOI: 10.1091/mbc.e21-06-0295] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/10/2021] [Accepted: 08/18/2021] [Indexed: 01/12/2023] Open
Abstract
Autophagy-related protein 9 (ATG9) is a transmembrane protein component of the autophagy machinery that cycles between the trans-Golgi network (TGN) in the perinuclear area and other compartments in the peripheral area of the cell. In mammalian cells, export of the ATG9A isoform from the TGN into ATG9A-containing vesicles is mediated by the adaptor protein 4 (AP-4) complex. However, the mechanisms responsible for the subsequent distribution of these vesicles to the cell periphery are unclear. Herein we show that the AP-4-accessory protein RUSC2 couples ATG9A-containing vesicles to the plus-end-directed microtubule motor kinesin-1 via an interaction between a disordered region of RUSC2 and the kinesin-1 light chain. This interaction is counteracted by the microtubule-associated protein WDR47. These findings uncover a mechanism for the peripheral distribution of ATG9A-containing vesicles involving the function of RUSC2 as a kinesin-1 adaptor and WDR47 as a negative regulator of this function.
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Affiliation(s)
- Carlos M. Guardia
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development
| | - Akansha Jain
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development
| | - Rafael Mattera
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development
| | - Alex Friefeld
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development
| | - Yan Li
- Proteomics Core Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892
| | - Juan S. Bonifacino
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development
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24
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Natural compounds modulate the autophagy with potential implication of stroke. Acta Pharm Sin B 2021; 11:1708-1720. [PMID: 34386317 PMCID: PMC8343111 DOI: 10.1016/j.apsb.2020.10.018] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/12/2020] [Accepted: 08/21/2020] [Indexed: 12/12/2022] Open
Abstract
Stroke is considered a leading cause of mortality and neurological disability, which puts a huge burden on individuals and the community. To date, effective therapy for stroke has been limited by its complex pathological mechanisms. Autophagy refers to an intracellular degrading process with the involvement of lysosomes. Autophagy plays a critical role in maintaining the homeostasis and survival of cells by eliminating damaged or non-essential cellular constituents. Increasing evidence support that autophagy protects neuronal cells from ischemic injury. However, under certain circumstances, autophagy activation induces cell death and aggravates ischemic brain injury. Diverse naturally derived compounds have been found to modulate autophagy and exert neuroprotection against stroke. In the present work, we have reviewed recent advances in naturally derived compounds that regulate autophagy and discussed their potential application in stroke treatment.
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Key Words
- AD, Alzheimer's disease
- ALS, amyotrophic lateral sclerosis
- AMPK, 5′-adenosine monophosphate-activated protein kinase
- ATF6, activating transcription factor 6
- ATG, autophagy related genes
- Autophagy
- BCL-2, B-cell lymphoma 2
- BNIP3L, BCL2/adenovirus
- COPII, coat protein complex II
- Cerebral ischemia
- ER, endoplasmic reticulum
- FOXO, forkhead box O
- FUNDC1, FUN14 domain containing 1
- GPCR, G-protein coupled receptor
- HD, Huntington's disease
- IPC, ischemic preconditioning
- IRE1, inositol-requiring enzyme 1
- JNK, c-Jun N-terminal kinase
- LAMP, lysosomal-associated membrane protein
- LC3, light chain 3
- LKB1, liver kinase B1
- Lysosomal activation
- Mitochondria
- Mitophagy
- Natural compounds
- Neurological disorders
- Neuroprotection
- OGD/R, oxygen and glucose deprivation-reperfusion
- PD, Parkinson's disease
- PERK, protein kinase R (PKR)-like endoplasmic reticulum kinase
- PI3K, phosphatidylinositol 3-kinase
- ROS, reactive oxygen species
- SQSTM1, sequestosome 1
- TFEB, transcription factor EB
- TIGAR, TP53-induced glycolysis and apoptosis regulator
- ULK, Unc-51- like kinase
- Uro-A, urolithin A
- eIF2a, eukaryotic translation-initiation factor 2
- mTOR, mechanistic target of rapamycin
- ΔΨm, mitochondrial membrane potential
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25
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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: 0.5] [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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26
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Jo YH, Lee JH, Patnaik BB, Keshavarz M, Lee YS, Han YS. Autophagy in Tenebrio molitor Immunity: Conserved Antimicrobial Functions in Insect Defenses. Front Immunol 2021; 12:667664. [PMID: 34135896 PMCID: PMC8202003 DOI: 10.3389/fimmu.2021.667664] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 05/13/2021] [Indexed: 12/16/2022] Open
Abstract
The yellow mealworm beetle (Tenebrio molitor) has been exploited as an experimental model to unravel the intricacies of cellular and humoral immunity against pathogenic infections. Studies on this insect model have provided valuable insights into the phenotypic plasticity of immune defenses against parasites and pathogens. It has thus been possible to characterize the hemocoelic defenses of T. molitor that rely on the recognition of non-self-components of pathogens by pattern recognition receptors (PRRs). The subsequent signaling cascade activating pathways such as the NF-κB controlled by Toll and IMD pathways lead to the synthesis of antimicrobial peptides (AMPs), onset of hemocyte-driven phagocytosis, and activation of the prophenoloxidase cascade regulating the process of melanization. Nevertheless, the activation of autophagy-mediated defenses of T. molitor against the facultative intracellular gram-positive bacterium Listeria monocytogenes provides clear evidence of the existence of a cross-talk between autophagy and the IMD pathway. Moreover, the identification of several autophagy-related genes (Atgs) in T. molitor transcriptome and expressed sequence tag (EST) databases has contributed to the understanding of the autophagy-signaling cascade triggered by L. monocytogenes challenge. Providing further evidence of the cross-talk hypothesis, TmRelish has been shown to be required not only for regulating the synthesis of AMPs through the PGRP-LE/IMD pathway activation but also for the expression of Atgs in T. molitor larvae following L. monocytogenes challenge. Notably, L. monocytogenes can stimulate the T. molitor innate immune system by producing molecules recognized by the multifunctional PRR (TmPGRP-LE), which stimulates intracellular activation of the IMD pathway and autophagy. Considering the conservation of autophagy components involved in combating intracellular pathogens, it will be interesting to extrapolate a dynamic cross-talk model of immune activation. This review summarizes the most significant findings on the regulation of autophagy in T. molitor during L. monocytogenes infection and on the role of the innate immunity machinery, including the NF-κB pathway, in the control of pathogenic load.
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Affiliation(s)
- Yong Hun Jo
- Department of Applied Biology, Institute of Environmentally-Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
| | - Jung Hee Lee
- Department of Applied Biology, Institute of Environmentally-Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
| | - Bharat Bhusan Patnaik
- P. G. Department of Biosciences and Biotechnology, Fakir Mohan University, Balasore, India
| | - Maryam Keshavarz
- Department of Evolutionary Biology, Institute for Biology-Zoology, Free University of Berlin, Berlin, Germany
| | - Yong Seok Lee
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan City, South Korea
| | - Yeon Soo Han
- Department of Applied Biology, Institute of Environmentally-Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
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27
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Sheehan BK, Orefice NS, Peng Y, Shapiro SL, Puglielli L. ATG9A regulates proteostasis through reticulophagy receptors FAM134B and SEC62 and folding chaperones CALR and HSPB1. iScience 2021; 24:102315. [PMID: 33870132 PMCID: PMC8042170 DOI: 10.1016/j.isci.2021.102315] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 02/18/2021] [Accepted: 03/12/2021] [Indexed: 12/01/2022] Open
Abstract
The acetylation of ATG9A within the endoplasmic reticulum (ER) lumen regulates the induction of reticulophagy. ER acetylation is ensured by AT-1/SLC33A1, a membrane transporter that maintains the cytosol-to-ER flux of acetyl-CoA. Defective AT-1 activity, as caused by heterozygous/homozygous mutations and gene duplication events, results in severe disease phenotypes. Here, we show that although the acetylation of ATG9A occurs in the ER lumen, the induction of reticulophagy requires ATG9A to engage FAM134B and SEC62 on the cytosolic side of the ER. To address this conundrum, we resolved the ATG9A interactome in two mouse models of AT-1 dysregulation: AT-1 sTg, a model of systemic AT-1 overexpression with hyperacetylation of ATG9A, and AT-1S113R/+, a model of AT-1 haploinsufficiency with hypoacetylation of ATG9A. We identified CALR and HSPB1 as two ATG9A partners that regulate the induction of reticulophagy as a function of ATG9A acetylation and discovered that ATG9A associates with several proteins that maintain ER proteostasis. The ATG9A-FAM134B and ATG9A-SEC62 interaction requires specific structural features Opposite Ca++-binding EF hands regulate ATG9A-FAM134B interaction HSBP1 and CALR regulate ATG9A-mediated induction of reticulophagy Many of the proteins that ensure ER proteostasis display spatial vicinity/cross talk
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Affiliation(s)
- Brendan K Sheehan
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA.,Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Nicola S Orefice
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA.,Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Yajing Peng
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA.,Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Samantha L Shapiro
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA.,Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Luigi Puglielli
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA.,Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA.,Geriatric Research Education Clinical Center, Veterans Affairs Medical Center, Madison, WI 53705, USA.,Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53705, USA
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28
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Maeda S, Yamamoto H, Kinch LN, Garza CM, Takahashi S, Otomo C, Grishin NV, Forli S, Mizushima N, Otomo T. Structure, lipid scrambling activity and role in autophagosome formation of ATG9A. Nat Struct Mol Biol 2020; 27:1194-1201. [PMID: 33106659 PMCID: PMC7718406 DOI: 10.1038/s41594-020-00520-2] [Citation(s) in RCA: 212] [Impact Index Per Article: 42.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 09/22/2020] [Indexed: 01/01/2023]
Abstract
De novo formation of the double-membrane compartment autophagosome is seeded by small vesicles carrying membrane protein autophagy-related 9 (ATG9), the function of which remains unknown. Here we find that ATG9A scrambles phospholipids of membranes in vitro. Cryo-EM structures of human ATG9A reveal a trimer with a solvated central pore, which is connected laterally to the cytosol through the cavity within each protomer. Similarities to ABC exporters suggest that ATG9A could be a transporter that uses the central pore to function. Moreover, molecular dynamics simulation suggests that the central pore opens laterally to accommodate lipid headgroups, thereby enabling lipids to flip. Mutations in the pore reduce scrambling activity and yield markedly smaller autophagosomes, indicating that lipid scrambling by ATG9A is essential for membrane expansion. We propose ATG9A acts as a membrane-embedded funnel to facilitate lipid flipping and to redistribute lipids added to the outer leaflet of ATG9 vesicles, thereby enabling growth into autophagosomes.
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Affiliation(s)
- Shintaro Maeda
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Hayashi Yamamoto
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Lisa N Kinch
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
| | - Christina M Garza
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Satoru Takahashi
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Neurosurgery, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Chinatsu Otomo
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Nick V Grishin
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
| | - Stefano Forli
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takanori Otomo
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
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29
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Abstract
Autophagy is an adaptive catabolic process functioning to promote cell survival in the event of inappropriate living conditions such as nutrient shortage and to cope with diverse cytotoxic insults. It is regarded as one of the key survival mechanisms of living organisms. Cells undergo autophagy to accomplish the lysosomal digestion of intracellular materials including damaged proteins, organelles, and foreign bodies, in a bulk, non-selective or a cargo-specific manner. Studies in the past decades have shed light on the association of autophagy pathways with various diseases and also highlighted the therapeutic value of autophagy modulation. Hence, it is crucial to develop effective approaches for monitoring intracellular autophagy dynamics, as a comprehensive account of methodology establishment is far from complete. In this review, we aim to provide an overview of the major current fluorescence-based techniques utilized for visualizing, sensing or measuring autophagic activities in cells or tissues, which are categorized firstly by targets detected and further by the types of fluorescence tools. We will mainly focus on the working mechanisms of these techniques, put emphasis on the insight into their roles in biomedical science and provide perspectives on the challenges and future opportunities in this field.
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Affiliation(s)
- Siyang Ding
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne Victoria 3086, Australia.
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30
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Deng S, Liu J, Wu X, Lu W. Golgi Apparatus: A Potential Therapeutic Target for Autophagy-Associated Neurological Diseases. Front Cell Dev Biol 2020; 8:564975. [PMID: 33015059 PMCID: PMC7509445 DOI: 10.3389/fcell.2020.564975] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 08/17/2020] [Indexed: 12/13/2022] Open
Abstract
Autophagy has dual effects in human diseases: appropriate autophagy may protect cells from stress, while excessive autophagy may cause cell death. Additionally, close interactions exist between autophagy and the Golgi. This review outlines recent advances regarding the role of the Golgi apparatus in autophagy. The signaling processes of autophagy are dependent on the normal function of the Golgi. Specifically, (i) autophagy-related protein 9 is mainly located in the Golgi and forms new autophagosomes in response to stressors; (ii) Golgi fragmentation is induced by Golgi-related proteins and accompanied with autophagy induction; and (iii) the endoplasmic reticulum-Golgi intermediate compartment and the reticular trans-Golgi network play essential roles in autophagosome formation to provide a template for lipidation of microtubule-associated protein 1A/1B-light chain 3 and induce further ubiquitination. Golgi-related proteins regulate formation of autophagosomes, and disrupted formation of autophagy can influence Golgi function. Notably, aberrant autophagy has been demonstrated to be implicated in neurological diseases. Thus, targeted therapies aimed at protecting the Golgi or regulating Golgi proteins might prevent or ameliorate autophagy-related neurological diseases. Further studies are needed to investigate the potential application of Golgi therapy in autophagy-based neurological diseases.
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Affiliation(s)
- Shuwen Deng
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Jia Liu
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Xiaomei Wu
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Wei Lu
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, China
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31
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Sawa-Makarska J, Baumann V, Coudevylle N, von Bülow S, Nogellova V, Abert C, Schuschnig M, Graef M, Hummer G, Martens S. Reconstitution of autophagosome nucleation defines Atg9 vesicles as seeds for membrane formation. Science 2020; 369:eaaz7714. [PMID: 32883836 PMCID: PMC7610778 DOI: 10.1126/science.aaz7714] [Citation(s) in RCA: 190] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 05/16/2020] [Accepted: 07/06/2020] [Indexed: 12/15/2022]
Abstract
Autophagosomes form de novo in a manner that is incompletely understood. Particularly enigmatic are autophagy-related protein 9 (Atg9)-containing vesicles that are required for autophagy machinery assembly but do not supply the bulk of the autophagosomal membrane. In this study, we reconstituted autophagosome nucleation using recombinant components from yeast. We found that Atg9 proteoliposomes first recruited the phosphatidylinositol 3-phosphate kinase complex, followed by Atg21, the Atg2-Atg18 lipid transfer complex, and the E3-like Atg12-Atg5-Atg16 complex, which promoted Atg8 lipidation. Furthermore, we found that Atg2 could transfer lipids for Atg8 lipidation. In selective autophagy, these reactions could potentially be coupled to the cargo via the Atg19-Atg11-Atg9 interactions. We thus propose that Atg9 vesicles form seeds that establish membrane contact sites to initiate lipid transfer from compartments such as the endoplasmic reticulum.
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Affiliation(s)
- Justyna Sawa-Makarska
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, 1030 Vienna, Austria.
| | - Verena Baumann
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, 1030 Vienna, Austria
| | - Nicolas Coudevylle
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, 1030 Vienna, Austria
| | - Sören von Bülow
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Veronika Nogellova
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, 1030 Vienna, Austria
| | - Christine Abert
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, 1030 Vienna, Austria
| | - Martina Schuschnig
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, 1030 Vienna, Austria
| | - Martin Graef
- Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
- Institute for Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Sascha Martens
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, 1030 Vienna, Austria.
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Ornatowski W, Lu Q, Yegambaram M, Garcia AE, Zemskov EA, Maltepe E, Fineman JR, Wang T, Black SM. Complex interplay between autophagy and oxidative stress in the development of pulmonary disease. Redox Biol 2020; 36:101679. [PMID: 32818797 PMCID: PMC7451718 DOI: 10.1016/j.redox.2020.101679] [Citation(s) in RCA: 261] [Impact Index Per Article: 52.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/20/2020] [Accepted: 08/04/2020] [Indexed: 12/16/2022] Open
Abstract
The autophagic pathway involves the encapsulation of substrates in double-membraned vesicles, which are subsequently delivered to the lysosome for enzymatic degradation and recycling of metabolic precursors. Autophagy is a major cellular defense against oxidative stress, or related conditions that cause accumulation of damaged proteins or organelles. Selective forms of autophagy can maintain organelle populations or remove aggregated proteins. Dysregulation of redox homeostasis under pathological conditions results in excessive generation of reactive oxygen species (ROS), leading to oxidative stress and the associated oxidative damage of cellular components. Accumulating evidence indicates that autophagy is necessary to maintain redox homeostasis. ROS activates autophagy, which facilitates cellular adaptation and diminishes oxidative damage by degrading and recycling intracellular damaged macromolecules and dysfunctional organelles. The cellular responses triggered by oxidative stress include the altered regulation of signaling pathways that culminate in the regulation of autophagy. Current research suggests a central role for autophagy as a mammalian oxidative stress response and its interrelationship to other stress defense systems. Altered autophagy phenotypes have been observed in lung diseases such as chronic obstructive lung disease, acute lung injury, cystic fibrosis, idiopathic pulmonary fibrosis, and pulmonary arterial hypertension, and asthma. Understanding the mechanisms by which ROS regulate autophagy will provide novel therapeutic targets for lung diseases. This review highlights our current understanding on the interplay between ROS and autophagy in the development of pulmonary disease.
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Affiliation(s)
- Wojciech Ornatowski
- Department of Medicine, The University of Arizona Health Sciences, Tucson, AZ, USA
| | - Qing Lu
- Department of Medicine, The University of Arizona Health Sciences, Tucson, AZ, USA
| | | | - Alejandro E Garcia
- Department of Medicine, The University of Arizona Health Sciences, Tucson, AZ, USA
| | - Evgeny A Zemskov
- Department of Medicine, The University of Arizona Health Sciences, Tucson, AZ, USA
| | - Emin Maltepe
- Department of Pediatrics, The University of California, San Francisco, San Francisco, CA, USA
| | - Jeffrey R Fineman
- Department of Pediatrics, The University of California, San Francisco, San Francisco, CA, USA; Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Ting Wang
- Department of Internal Medicine, The University of Arizona Health Sciences, Phoenix, AZ, USA
| | - Stephen M Black
- Department of Medicine, The University of Arizona Health Sciences, Tucson, AZ, USA.
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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: 24] [Impact Index Per Article: 4.8] [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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Haijes HA, Jaeken J, van Hasselt PM. Hypothesis: determining phenotypic specificity facilitates understanding of pathophysiology in rare genetic disorders. J Inherit Metab Dis 2020; 43:701-711. [PMID: 31804708 PMCID: PMC7383723 DOI: 10.1002/jimd.12201] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 11/28/2019] [Accepted: 12/03/2019] [Indexed: 12/17/2022]
Abstract
In the rapidly growing group of rare genetic disorders, data scarcity demands an intelligible use of available data, in order to improve understanding of underlying pathophysiology. We hypothesize, based on the principle that clinical similarities may be indicative of shared pathophysiology, that determining phenotypic specificity could provide unsuspected insights in pathophysiology of rare genetic disorders. We explored our hypothesis by studying subunit deficiencies of the conserved oligomeric Golgi (COG) complex, a subgroup of congenital disorders of glycosylation (CDG). In this systematic data assessment, all 45 reported patients with COG-CDG were included. The vocabulary of the Human Phenotype Ontology was used to annotate all phenotypic features and to assess occurrence in other genetic disorders. Gene occurrence ratios were calculated by dividing the frequency in the patient cohort over the number of associated genes, according to the Human Phenotype Ontology. Prioritisation based on phenotypic specificity was highly informative and captured phenotypic features commonly associated with glycosylation disorders. Moreover, it captured features not seen in any other glycosylation disorder, among which episodic fever, likely reflecting underappreciated other cellular functions of the COG complex. Interestingly, the COG complex was recently implicated in the autophagy pathway, as are more than half of the genes underlying disorders that present with episodic fever. This suggests that whereas many phenotypic features in these patients are caused by disrupted glycosylation, episodic fever might be caused by disrupted autophagy. Thus, we here demonstrate support for our hypothesis that determining phenotypic specificity could facilitate understanding of pathophysiology in rare genetic disorders.
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Affiliation(s)
- Hanneke A. Haijes
- Department of Biomedical Genetics, Section Metabolic DiagnosticsWilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht UniversityUtrechtThe Netherlands
- Department of Pediatrics, Subdivision Metabolic DiseasesWilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht UniversityUtrechtThe Netherlands
| | - Jaak Jaeken
- Department of PediatricsCentre for Metabolic Diseases, University Hospital GasthuisbergLeuvenBelgium
| | - Peter M. van Hasselt
- Department of Pediatrics, Subdivision Metabolic DiseasesWilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht UniversityUtrechtThe Netherlands
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Ren S, Ding C, Sun Y. Morphology Remodeling and Selective Autophagy of Intracellular Organelles during Viral Infections. Int J Mol Sci 2020; 21:ijms21103689. [PMID: 32456258 PMCID: PMC7279407 DOI: 10.3390/ijms21103689] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 05/14/2020] [Accepted: 05/21/2020] [Indexed: 12/17/2022] Open
Abstract
Viruses have evolved different strategies to hijack subcellular organelles during their life cycle to produce robust infectious progeny. Successful viral reproduction requires the precise assembly of progeny virions from viral genomes, structural proteins, and membrane components. Such spatial and temporal separation of assembly reactions depends on accurate coordination among intracellular compartmentalization in multiple organelles. Here, we overview the rearrangement and morphology remodeling of virus-triggered intracellular organelles. Focus is given to the quality control of intracellular organelles, the hijacking of the modified organelle membranes by viruses, morphology remodeling for viral replication, and degradation of intracellular organelles by virus-triggered selective autophagy. Understanding the functional reprogram and morphological remodeling in the virus-organelle interplay can provide new insights into the development of broad-spectrum antiviral strategies.
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Affiliation(s)
- Shanhui Ren
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute. Chinese Academy of Agricultural Science, Shanghai 200241, China;
| | - Chan Ding
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute. Chinese Academy of Agricultural Science, Shanghai 200241, China;
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Correspondence: (C.D.); (Y.S.); Tel.: +86-21-34293441 (C.D. & Y.S.); Fax: +86-21-54081818 (C.D. & Y.S.)
| | - Yingjie Sun
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute. Chinese Academy of Agricultural Science, Shanghai 200241, China;
- Correspondence: (C.D.); (Y.S.); Tel.: +86-21-34293441 (C.D. & Y.S.); Fax: +86-21-54081818 (C.D. & Y.S.)
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36
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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: 546] [Impact Index Per Article: 109.2] [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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37
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Lv W, Xu Z, Talbot NJ, Wang Z. The sorting nexin FgAtg20 is involved in the Cvt pathway, non-selective macroautophagy, pexophagy and pathogenesis in Fusarium graminearum. Cell Microbiol 2020; 22:e13208. [PMID: 32281734 DOI: 10.1111/cmi.13208] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 03/19/2020] [Accepted: 03/31/2020] [Indexed: 01/07/2023]
Abstract
The sorting nexin Atg20/Snx42 plays an important role in autophagy. The wheat head blight pathogen Fusarium graminearum contains an FgAtg20 protein orthologous to Saccharomyces cerevisiae Atg20/Snx42, but its function remains largely unknown. Here, we report a role for FgAtg20 in regulating morphogenesis and fungal pathogenicity. Cytological observation and Western blot analysis revealed that ΔFgAtg20 mutants are defective in vacuolar transport and proteolysis of GFP-FgAtg8, indicating that FgAtg20 is required for non-selective macroautophagy. Furthermore, we found that FgATG20 is necessary for the maturation of FgApe1, an indicator of the cytoplasm-to-vacuole targeting (Cvt) pathway. Immunoblot analysis displayed lower level of FgPex14, a peroxisomal integral membrane protein in ΔFgAtg20 mutants, suggesting that pexophagy is impaired. Furthermore, we demonstrate that FgAtg20 forms a complex with FgAtg1, FgAtg11, FgAtg17 and FgAtg24. When considered together, we conclude that FgAtg20 plays a critical role in vegetative growth, conidiation and pathogenicity of the head blight pathogen, and is involved in the Cvt pathway, non-selective macroautophagy and pexophagy.
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Affiliation(s)
- Wuyun Lv
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Zhe Xu
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | | | - Zhengyi Wang
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
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38
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Shiozaki Y, Miyazaki-Anzai S, Okamura K, Keenan AL, Masuda M, Miyazaki M. GPAT4-Generated Saturated LPAs Induce Lipotoxicity through Inhibition of Autophagy by Abnormal Formation of Omegasomes. iScience 2020; 23:101105. [PMID: 32408172 PMCID: PMC7225743 DOI: 10.1016/j.isci.2020.101105] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 12/16/2019] [Accepted: 04/22/2020] [Indexed: 12/26/2022] Open
Abstract
Excessive levels of saturated fatty acids are toxic to vascular smooth muscle cells (VSMCs). We previously reported that mice lacking VSMC-stearoyl-CoA desaturase (SCD), a major enzyme catalyzing the detoxification of saturated fatty acids, develop severe vascular calcification from the massive accumulation of lipid metabolites containing saturated fatty acids. However, the mechanism by which SCD deficiency causes vascular calcification is not completely understood. Here, we demonstrate that saturated fatty acids significantly inhibit autophagic flux in VSMCs, contributing to vascular calcification and apoptosis. Mechanistically, saturated fatty acids are accumulated as saturated lysophosphatidic acids (LPAs) (i.e. 1-stearoyl-LPA) possibly synthesized through the reaction of GPAT4 at the contact site between omegasomes and the MAM. The accumulation of saturated LPAs at the contact site causes abnormal formation of omegasomes, resulting in accumulation of autophagosomal precursor isolation membranes, leading to inhibition of autophagic flux. Thus, saturated LPAs are major metabolites mediating autophagy inhibition and vascular calcification.
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Affiliation(s)
- Yuji Shiozaki
- Division of Renal Diseases and Hypertension, University of Colorado-Denver, Aurora, CO, USA
| | - Shinobu Miyazaki-Anzai
- Division of Renal Diseases and Hypertension, University of Colorado-Denver, Aurora, CO, USA
| | - Kayo Okamura
- Division of Renal Diseases and Hypertension, University of Colorado-Denver, Aurora, CO, USA
| | - Audrey L Keenan
- Division of Renal Diseases and Hypertension, University of Colorado-Denver, Aurora, CO, USA
| | - Masashi Masuda
- Division of Renal Diseases and Hypertension, University of Colorado-Denver, Aurora, CO, USA
| | - Makoto Miyazaki
- Division of Renal Diseases and Hypertension, University of Colorado-Denver, Aurora, CO, USA.
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39
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Besemer AS, Maus J, Ax MDA, Stein A, Vo S, Freese C, Nalbach K, von Hilchen C, Pfalzgraf IF, Koziollek-Drechsler I, Silva B, Huesmann H, Boukhallouk F, Florin L, Kern A, Behl C, Clement AM. Receptor-mediated endocytosis 8 (RME-8)/DNAJC13 is a novel positive modulator of autophagy and stabilizes cellular protein homeostasis. Cell Mol Life Sci 2020; 78:645-660. [PMID: 32322926 PMCID: PMC7873018 DOI: 10.1007/s00018-020-03521-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 03/20/2020] [Accepted: 04/06/2020] [Indexed: 12/15/2022]
Abstract
The cellular protein homeostasis (proteostasis) network responds effectively to insults. In a functional screen in C. elegans, we recently identified the gene receptor-mediated endocytosis 8 (rme-8; human ortholog: DNAJC13) as a component of the proteostasis network. Accumulation of aggregation-prone proteins, such as amyloid-β 42 (Aβ), α-synuclein, or mutant Cu/Zn-superoxide dismutase (SOD1), were aggravated upon the knockdown of rme-8/DNAJC13 in C. elegans and in human cell lines, respectively. DNAJC13 is involved in endosomal protein trafficking and associated with the retromer and the WASH complex. As both complexes have been linked to autophagy, we investigated the role of DNAJC13 in this degradative pathway. In knockdown and overexpression experiments, DNAJC13 acts as a positive modulator of autophagy. In contrast, the overexpression of the Parkinson’s disease-associated mutant DNAJC13(N855S) did not enhance autophagy. Reduced DNAJC13 levels affected ATG9A localization at and its transport from the recycling endosome. As a consequence, ATG9A co-localization at LC3B-positive puncta under steady-state and autophagy-induced conditions is impaired. These data demonstrate a novel function of RME-8/DNAJC13 in cellular homeostasis by modulating ATG9A trafficking and autophagy.
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Affiliation(s)
- Anna S Besemer
- Institute of Pathobiochemistry, University Medical Center of the Johannes Gutenberg-University, Duesbergweg 6, 55128, Mainz, Germany
| | - Joanna Maus
- Institute of Pathobiochemistry, University Medical Center of the Johannes Gutenberg-University, Duesbergweg 6, 55128, Mainz, Germany
| | - Mirjam D A Ax
- Institute of Pathobiochemistry, University Medical Center of the Johannes Gutenberg-University, Duesbergweg 6, 55128, Mainz, Germany
| | - Anna Stein
- Institute of Pathobiochemistry, University Medical Center of the Johannes Gutenberg-University, Duesbergweg 6, 55128, Mainz, Germany
| | - Stella Vo
- Institute of Pathobiochemistry, University Medical Center of the Johannes Gutenberg-University, Duesbergweg 6, 55128, Mainz, Germany
| | - Christian Freese
- Institute of Pathobiochemistry, University Medical Center of the Johannes Gutenberg-University, Duesbergweg 6, 55128, Mainz, Germany
| | - Karsten Nalbach
- Institute of Pathobiochemistry, University Medical Center of the Johannes Gutenberg-University, Duesbergweg 6, 55128, Mainz, Germany
| | - Christian von Hilchen
- Institute of Pathobiochemistry, University Medical Center of the Johannes Gutenberg-University, Duesbergweg 6, 55128, Mainz, Germany
| | - Ines F Pfalzgraf
- Institute of Pathobiochemistry, University Medical Center of the Johannes Gutenberg-University, Duesbergweg 6, 55128, Mainz, Germany
| | - Ingrid Koziollek-Drechsler
- Institute of Pathobiochemistry, University Medical Center of the Johannes Gutenberg-University, Duesbergweg 6, 55128, Mainz, Germany
| | - Beate Silva
- Institute of Pathobiochemistry, University Medical Center of the Johannes Gutenberg-University, Duesbergweg 6, 55128, Mainz, Germany
| | - Heike Huesmann
- Institute of Pathobiochemistry, University Medical Center of the Johannes Gutenberg-University, Duesbergweg 6, 55128, Mainz, Germany
| | - Fatima Boukhallouk
- Institute of Medical Microbiology and Hygiene, University Medical Center of the Johannes Gutenberg-University, 55101 Mainz, Germany
| | - Luise Florin
- Institute for Virology and Research Center for Immunotherapy (FZI), University Medical Center of the Johannes Gutenberg-University, 55101 Mainz, Germany
| | - Andreas Kern
- Institute of Pathobiochemistry, University Medical Center of the Johannes Gutenberg-University, Duesbergweg 6, 55128, Mainz, Germany
| | - Christian Behl
- Institute of Pathobiochemistry, University Medical Center of the Johannes Gutenberg-University, Duesbergweg 6, 55128, Mainz, Germany.
| | - Albrecht M Clement
- Institute of Pathobiochemistry, University Medical Center of the Johannes Gutenberg-University, Duesbergweg 6, 55128, Mainz, Germany.
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40
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Lőrincz P, Juhász G. Autophagosome-Lysosome Fusion. J Mol Biol 2020; 432:2462-2482. [DOI: 10.1016/j.jmb.2019.10.028] [Citation(s) in RCA: 195] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 10/11/2019] [Accepted: 10/15/2019] [Indexed: 12/26/2022]
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Belgrad J, De Pace R, Fields RD. Autophagy in Myelinating Glia. J Neurosci 2020; 40:256-266. [PMID: 31744863 PMCID: PMC6948934 DOI: 10.1523/jneurosci.1066-19.2019] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 10/17/2019] [Accepted: 11/08/2019] [Indexed: 12/14/2022] Open
Abstract
Autophagy is the cellular process involved in transportation and degradation of membrane, proteins, pathogens, and organelles. This fundamental cellular process is vital in development, plasticity, and response to disease and injury. Compared with neurons, little information is available on autophagy in glia, but it is paramount for glia to perform their critical responses to nervous system disease and injury, including active tissue remodeling and phagocytosis. In myelinating glia, autophagy has expanded roles, particularly in phagocytosis of mature myelin and in generating the vast amounts of membrane proteins and lipids that must be transported to form new myelin. Notably, autophagy plays important roles in removing excess cytoplasm to promote myelin compaction and development of oligodendrocytes, as well as in remyelination by Schwann cells after nerve trauma. This review summarizes the cell biology of autophagy, detailing the major pathways and proteins involved, as well as the roles of autophagy in Schwann cells and oligodendrocytes in development, plasticity, and diseases in which myelin is affected. This includes traumatic brain injury, Alexander's disease, Alzheimer's disease, hypoxia, multiple sclerosis, hereditary spastic paraplegia, and others. Promising areas for future research are highlighted.
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Affiliation(s)
| | - Raffaella De Pace
- Section on Intracellular Protein Trafficking, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
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42
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Mechanisms of Autophagy in Metabolic Stress Response. J Mol Biol 2020; 432:28-52. [DOI: 10.1016/j.jmb.2019.09.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 09/06/2019] [Accepted: 09/06/2019] [Indexed: 01/17/2023]
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43
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Ma M, Burd CG. Retrograde trafficking and plasma membrane recycling pathways of the budding yeast Saccharomyces cerevisiae. Traffic 2019; 21:45-59. [PMID: 31471931 DOI: 10.1111/tra.12693] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 08/23/2019] [Accepted: 08/27/2019] [Indexed: 02/06/2023]
Abstract
The endosomal system functions as a network of protein and lipid sorting stations that receives molecules from endocytic and secretory pathways and directs them to the lysosome for degradation, or exports them from the endosome via retrograde trafficking or plasma membrane recycling pathways. Retrograde trafficking pathways describe endosome-to-Golgi transport while plasma membrane recycling pathways describe trafficking routes that return endocytosed molecules to the plasma membrane. These pathways are crucial for lysosome biogenesis, nutrient acquisition and homeostasis and for the physiological functions of many types of specialized cells. Retrograde and recycling sorting machineries of eukaryotic cells were identified chiefly through genetic screens using the budding yeast Saccharomyces cerevisiae system and discovered to be highly conserved in structures and functions. In this review, we discuss advances regarding retrograde trafficking and recycling pathways, including new discoveries that challenge existing ideas about the organization of the endosomal system, as well as how these pathways intersect with cellular homeostasis pathways.
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Affiliation(s)
- Mengxiao Ma
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut
| | - Christopher G Burd
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut
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Zientara-Rytter K, Subramani S. Mechanistic Insights into the Role of Atg11 in Selective Autophagy. J Mol Biol 2019; 432:104-122. [PMID: 31238043 DOI: 10.1016/j.jmb.2019.06.017] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/11/2019] [Accepted: 06/13/2019] [Indexed: 12/19/2022]
Abstract
Macroautophagy (referred to hereafter as autophagy) is an intracellular degradation pathway in which the formation of a double-membrane vesicle called the autophagosome is a key event in the transport of multiple cytoplasmic cargo (e.g., proteins, protein aggregates, lipid droplets or organelles) to the vacuole (lysosome in mammals) for degradation and recycling. During this process, autophagosomes are formed de novo by membrane fusion events leading to phagophore formation initiated at the phagophore assembly site. In yeast, Atg11 and Atg17 function as protein scaffolds, essential for selective and non-selective types of autophagy, respectively. While Atg17 functions in non-selective autophagy are well-defined in the literature, less attention is concentrated on recent findings regarding the roles of Atg11 in selective autophagy. Here, we summarize current knowledge about the Atg11 scaffold protein and review recent findings in the context of its role in selective autophagy initiation and autophagosome formation.
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Affiliation(s)
- Katarzyna Zientara-Rytter
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.
| | - Suresh Subramani
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
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45
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Singh S, Kumari R, Chinchwadkar S, Aher A, Matheshwaran S, Manjithaya R. Exocyst Subcomplex Functions in Autophagosome Biogenesis by Regulating Atg9 Trafficking. J Mol Biol 2019; 431:2821-2834. [PMID: 31103773 PMCID: PMC6698439 DOI: 10.1016/j.jmb.2019.04.048] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 04/24/2019] [Accepted: 04/29/2019] [Indexed: 01/16/2023]
Abstract
During autophagy, double-membrane vesicles called autophagosomes capture and degrade the intracellular cargo. The de novo formation of autophagosomes requires several vesicle transport and membrane fusion events which are not completely understood. We studied the involvement of exocyst, an octameric tethering complex, which has a primary function in tethering post-Golgi secretory vesicles to plasma membrane, in autophagy. Our findings indicate that not all subunits of exocyst are involved in selective and general autophagy. We show that in the absence of autophagy specific subunits, autophagy arrest is accompanied by accumulation of incomplete autophagosome-like structures. In these mutants, impaired Atg9 trafficking leads to decreased delivery of membrane to the site of autophagosome biogenesis thereby impeding the elongation and completion of the autophagosomes. The subunits of exocyst, which are dispensable for autophagic function, do not associate with the autophagy specific subcomplex of exocyst.
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Affiliation(s)
- Sunaina Singh
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, 560064, Karnataka, India
| | - Ruchika Kumari
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, 560064, Karnataka, India
| | - Sarika Chinchwadkar
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, 560064, Karnataka, India
| | - Amol Aher
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, 560064, Karnataka, India
| | - Saravanan Matheshwaran
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 208016, Uttar Pradesh, India
| | - Ravi Manjithaya
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, 560064, Karnataka, India.
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46
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Li W, Wu Z, Liang Y. Vrl1 relies on its VPS9-domain to play a role in autophagy in Saccharomyces cerevisiae. Cell Biol Int 2019; 43:875-889. [PMID: 31038239 DOI: 10.1002/cbin.11156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 04/28/2019] [Indexed: 11/10/2022]
Abstract
Autophagy is an intracellular degradation process involving many Atg proteins, which are recruited hierarchically to regulate this process. Rab/Ypt GTPases and their activators, guanine nucleotide exchange factors (GEFs), which are critical for regulating vesicle trafficking, are also involved in autophagy. Previously, we reported that yeast Vps21 and its GEF Vps9 are required for autophagy. Later, a third yeast VPS9-domain-containing protein, VARP-like 1 (Vrl1), which was identified as a mutant in major laboratory strains, had partially overlapping functions with Vps9 in trafficking. In this study, we showed that Vrl1 performed roles in autophagy, and its VPS9-domain was crucial for its role in autophagy. We found that localization of Vrl1 differed from the other two VPS9-domain-containing proteins, Vps9 and Muk1, and only Vrl1 changed from multipoint to diffusion after starvation. Like Vps9, Vrl1 suppressed autophagic defects caused by the VPS9 deletion. We further showed that these VPS9-domain-containing proteins, Vps9, Muk1, and Vrl1, all co-localized with Atg8 on autophagosomes in cells blocked in any late step of starvation-induced autophagy, with Vrl1 most often co-localizing with Atg8. A small portion (<25%) of these VPS9-domain-containing proteins were degraded through autophagy. However, a large portion (>60%) of Vrl1 decreased independently of autophagy. We propose that Vrl1 may regulate autophagy in a similar way as Vps9, and the level of Vrl1 partly decreases through both autophagy-dependent and -independent routes.
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Affiliation(s)
- Wenjing Li
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zulin Wu
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yongheng Liang
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
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47
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Ravenhill BJ, Boyle KB, von Muhlinen N, Ellison CJ, Masson GR, Otten EG, Foeglein A, Williams R, Randow F. The Cargo Receptor NDP52 Initiates Selective Autophagy by Recruiting the ULK Complex to Cytosol-Invading Bacteria. Mol Cell 2019; 74:320-329.e6. [PMID: 30853402 PMCID: PMC6477152 DOI: 10.1016/j.molcel.2019.01.041] [Citation(s) in RCA: 223] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 11/19/2018] [Accepted: 01/29/2019] [Indexed: 12/27/2022]
Abstract
Xenophagy, a selective autophagy pathway that protects the cytosol against bacterial invasion, relies on cargo receptors that juxtapose bacteria and phagophore membranes. Whether phagophores are recruited from a constitutive pool or are generated de novo at prospective cargo remains unknown. Phagophore formation in situ would require recruitment of the upstream autophagy machinery to prospective cargo. Here, we show that, essential for anti-bacterial autophagy, the cargo receptor NDP52 forms a trimeric complex with FIP200 and SINTBAD/NAP1, which are subunits of the autophagy-initiating ULK and the TBK1 kinase complex, respectively. FIP200 and SINTBAD/NAP1 are each recruited independently to bacteria via NDP52, as revealed by selective point mutations in their respective binding sites, but only in their combined presence does xenophagy proceed. Such recruitment of the upstream autophagy machinery by NDP52 reveals how detection of cargo-associated “eat me” signals, induction of autophagy, and juxtaposition of cargo and phagophores are integrated in higher eukaryotes. NDP52 recruits upstream autophagy machinery to damaged Salmonella-containing vacuoles NDP52 trimerizes with the ULK subunit FIP200 and the TBK1 adaptor SINTBAD NDP52-dependent recruitment of FIP200-ULK and SINTBAD-TBK1 required for xenophagy Recruitment of ULK and TBK1 complexes promotes phagophore formation in situ
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Affiliation(s)
- Benjamin J Ravenhill
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Keith B Boyle
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Natalia von Muhlinen
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Cara J Ellison
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Glenn R Masson
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Elsje G Otten
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Agnes Foeglein
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Roger Williams
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Felix Randow
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; Addenbrooke's Hospital, Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK.
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48
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Farrugia MA, Puglielli L. Nε-lysine acetylation in the endoplasmic reticulum - a novel cellular mechanism that regulates proteostasis and autophagy. J Cell Sci 2018; 131:131/22/jcs221747. [PMID: 30446507 DOI: 10.1242/jcs.221747] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Protein post-translational modifications (PTMs) take many shapes, have many effects and are necessary for cellular homeostasis. One of these PTMs, Nε-lysine acetylation, was thought to occur only in the mitochondria, cytosol and nucleus, but this paradigm was challenged in the past decade with the discovery of lysine acetylation in the lumen of the endoplasmic reticulum (ER). This process is governed by the ER acetylation machinery: the cytosol:ER-lumen acetyl-CoA transporter AT-1 (also known as SLC33A1), and the ER-resident lysine acetyltransferases ATase1 and ATase2 (also known as NAT8B and NAT8, respectively). This Review summarizes the more recent biochemical, cellular and mouse model studies that underscore the importance of the ER acetylation process in maintaining protein homeostasis and autophagy within the secretory pathway, and its impact on developmental and age-associated diseases.
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Affiliation(s)
- Mark A Farrugia
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA.,Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Luigi Puglielli
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA .,Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA.,Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53705, USA.,Geriatric Research Education Clinical Center, VA Medical Center, Madison, WI 53705, USA
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49
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Moparthi SB, Wollert T. Reconstruction of destruction – in vitro reconstitution methods in autophagy research. J Cell Sci 2018; 132:132/4/jcs223792. [DOI: 10.1242/jcs.223792] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
ABSTRACT
Autophagy is one of the most elaborative membrane remodeling systems in eukaryotic cells. Its major function is to recycle cytoplasmic material by delivering it to lysosomes for degradation. To achieve this, a membrane cisterna is formed that gradually captures cargo such as organelles or protein aggregates. The diversity of cargo requires autophagy to be highly versatile to adapt the shape of the phagophore to its substrate. Upon closure of the phagophore, a double-membrane-surrounded autophagosome is formed that eventually fuses with lysosomes. In response to environmental cues such as cytotoxicity or starvation, bulk cytoplasm can be captured and delivered to lysosomes. Autophagy thus supports cellular survival under adverse conditions. During the past decades, groundbreaking genetic and cell biological studies have identified the core machinery involved in the process. In this Review, we are focusing on in vitro reconstitution approaches to decipher the details and spatiotemporal control of autophagy, and how such studies contributed to our current understanding of the pathways in yeast and mammals. We highlight studies that revealed the function of the autophagy machinery at a molecular level with respect to its capacity to remodel membranes.
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Affiliation(s)
- Satish Babu Moparthi
- Membrane Biochemistry and Transport, Institute Pasteur, 28 rue du Dr Roux, 75015 Paris, France
| | - Thomas Wollert
- Membrane Biochemistry and Transport, Institute Pasteur, 28 rue du Dr Roux, 75015 Paris, France
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50
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Zhu X, Cai J, Zhou F, Wu Z, Li D, Li Y, Xie Z, Zhou Y, Liang Y. Genome-wide screening of budding yeast with honokiol to associate mitochondrial function with lipid metabolism. Traffic 2018; 19:867-878. [PMID: 30120820 DOI: 10.1111/tra.12611] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 08/11/2018] [Accepted: 08/13/2018] [Indexed: 12/24/2022]
Abstract
Honokiol (HNK), an important medicinal component of Magnolia officinalis, is reported to possess pharmacological activities against a variety of diseases. However, the molecular mechanisms of HNK medicinal functions are not fully clear. To systematically study the mechanisms of HNK action, we screened a yeast mutant library based on the conserved nature of its genes among eukaryotes. We identified genes associated with increased resistance or sensitivity to HNK after mutation. After functional classification of these genes, we found that most HNK-resistant strains in the largest functional category were petites with mutations in mitochondrial genes, indicating that mitochondria were related to HNK resistance. Additional analysis showed that resistance of petite mutants to HNK was associated with upregulation of the ATP-binding cassette transporter Pdr5, which pumps out HNK. We also found that several HNK-sensitive mitochondria mutants were not petites, and had larger lipid droplets (LDs). Furthermore, HNK treatment on wild-type yeast cells seemed to disrupt mitochondrial morphology, induced triacylglycerol synthesis, and generated supersized LDs surrounded by mitochondria and endoplasmic reticulum (ER). These changes are also applied to atp7Δ mutant if no carbon resource was available. These results suggested that HNK treatment partly impaired normal mitochondrial function to form larger LDs by altering lipid metabolism.
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Affiliation(s)
- Xiaolong Zhu
- College of Life Sciences, Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, China.,Central Laboratory of Yijishan Hospital, Wannan Medical College, Wuhu, China
| | - Juan Cai
- 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
| | - Zulin Wu
- College of Life Sciences, Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, China
| | - Dan Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Technology, Shanghai Jiao Tong University, Shanghai, China
| | - Youbin Li
- School of Pharmacy, Hainan Medical University, Haikou, China
| | - Zhiping Xie
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Technology, Shanghai Jiao Tong University, Shanghai, China
| | - Yiting Zhou
- Department of Biochemistry and Molecular Biology, Dr. Li Dak Sam & Yap Yio Chin Center for Stem Cell and Regenerative Medicine, School of Medicine, Zhejiang University, Hangzhou, 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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