1
|
Amari C, Carletti M, Yan S, Michaud M, Salvaing J. Lipid droplets degradation mechanisms from microalgae to mammals, a comparative overview. Biochimie 2024:S0300-9084(24)00216-5. [PMID: 39299537 DOI: 10.1016/j.biochi.2024.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 08/15/2024] [Accepted: 09/16/2024] [Indexed: 09/22/2024]
Abstract
Lipid droplets (LDs) are organelles composed of a hydrophobic core (mostly triacylglycerols and steryl esters) delineated by a lipid monolayer and found throughout the tree of life. LDs were seen for a long time as simple energy storage organelles but recent works highlighted their versatile roles in several fundamental cellular processes, particularly during stress response. LDs biogenesis occurs in the ER and their number and size can be dynamically regulated depending on their function, e.g. during development or stress. Understanding their biogenesis and degradation mechanisms is thus essential to better apprehend their roles. LDs degradation can occur in the cytosol by lipolysis or after their internalization into lytic compartments (e.g. vacuoles or lysosomes) using diverse mechanisms that depend on the considered organism, tissue, developmental stage or environmental condition. In this review, we summarize our current knowledge on the different LDs degradation pathways in several main phyla of model organisms, unicellular or pluricellular, photosynthetic or not (budding yeast, mammals, land plants and microalgae). We highlight the conservation of the main degradation pathways throughout evolution, but also the differences between organisms, or inside an organism between different organs. Finally, we discuss how this comparison can help to shed light on relationships between LDs degradation pathways and LDs functions.
Collapse
Affiliation(s)
- Chems Amari
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Centre National de la Recherche Scientifique, Commissariat à l'Energie Atomique et Aux Energies Alternatives, IRIG, CEA-Grenoble, 17 Rue des Martyrs, 38000, Grenoble, France; Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, Paris, France
| | - Marta Carletti
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Centre National de la Recherche Scientifique, Commissariat à l'Energie Atomique et Aux Energies Alternatives, IRIG, CEA-Grenoble, 17 Rue des Martyrs, 38000, Grenoble, France
| | - Siqi Yan
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Centre National de la Recherche Scientifique, Commissariat à l'Energie Atomique et Aux Energies Alternatives, IRIG, CEA-Grenoble, 17 Rue des Martyrs, 38000, Grenoble, France
| | - Morgane Michaud
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Centre National de la Recherche Scientifique, Commissariat à l'Energie Atomique et Aux Energies Alternatives, IRIG, CEA-Grenoble, 17 Rue des Martyrs, 38000, Grenoble, France
| | - Juliette Salvaing
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Centre National de la Recherche Scientifique, Commissariat à l'Energie Atomique et Aux Energies Alternatives, IRIG, CEA-Grenoble, 17 Rue des Martyrs, 38000, Grenoble, France.
| |
Collapse
|
2
|
Manik MIN, Tasnin MN, Takuma T, Ushimaru T. The yeast VAPs Scs2 and Scs22 are required for NVJ integrity and micronucleophagy. Biochem Biophys Res Commun 2024; 734:150628. [PMID: 39232457 DOI: 10.1016/j.bbrc.2024.150628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2024] [Revised: 08/23/2024] [Accepted: 08/29/2024] [Indexed: 09/06/2024]
Abstract
Microautophagy degrades cargos in the vacuole by direct engulfment of the vacuolar membrane. Micronucleophagy selectively degrades a portion of the nucleus in budding yeast. The vacuole contacts the nucleus via the nucleus-vacuole junction (NVJ), and in micronucleophagy a portion of the nucleus containing nucleolar proteins is made to protrude into the vacuole at the NVJ, followed by abscission and degradation. Microautophagy and micronucleophagy are induced by inactivation of target of rapamycin complex 1 (TORC1) protein kinase after nutrient starvation. Here, we show that the VAMP-associated proteins (VAPs) Scs2 and its paralog Scs22 are required for NVJ integrity and micronucleophagic degradation of nucleolar proteins. On the other hand, nucleolar dynamics prerequisite for micronucleophagy were not impaired in VAP mutant cells. Finally, yeast VAPs were critical for viability during prolonged nutrient starvation. This study sheds light on the emerging role of VAP in adaptation in responses to nutrient starvation.
Collapse
Affiliation(s)
- Md Imran Nur Manik
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, 422-8021, Japan
| | - Most Naoshia Tasnin
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, 422-8021, Japan
| | - Tsuneyuki Takuma
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, 422-8021, Japan
| | - Takashi Ushimaru
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, 422-8021, Japan; Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, 422-8021, Japan; Research Institute of Green Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, 422-8021, Japan.
| |
Collapse
|
3
|
Johnson DL, Kumar R, Kakhniashvili D, Pfeffer LM, Laribee RN. Ccr4-not ubiquitin ligase signaling regulates ribosomal protein homeostasis and inhibits 40S ribosomal autophagy. J Biol Chem 2024; 300:107582. [PMID: 39025453 PMCID: PMC11357857 DOI: 10.1016/j.jbc.2024.107582] [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: 12/18/2023] [Revised: 06/27/2024] [Accepted: 07/10/2024] [Indexed: 07/20/2024] Open
Abstract
The Ccr4-Not complex contains the poorly understood Not4 ubiquitin ligase that functions in transcription, mRNA decay, translation, proteostasis, and endolysosomal nutrient signaling. To gain further insight into the in vivo functions of the ligase, we performed quantitative proteomics in Saccharomyces cerevisiae using yeast cells lacking Not4, or cells overexpressing wild-type Not4 or an inactive Not4 mutant. Herein, we provide evidence that balanced Not4 activity maintains ribosomal protein (RP) homeostasis independent of changes to RP mRNA or known Not4 ribosomal substrates. Intriguingly, we also find that Not4 loss activates 40S ribosomal autophagy independently of canonical Atg7-dependent macroautophagy, indicating that microautophagy is responsible. We previously demonstrated that Ccr4-Not stimulates the target of rapamycin complex 1 (TORC1) signaling, which activates RP expression and inhibits autophagy, by maintaining vacuole V-ATPase H+ pump activity. Importantly, combining Not4 deficient cells with a mutant that blocks vacuole H+ export fully restores RP expression and increases 40S RP autophagy efficiency. In contrast, restoring TORC1 activity alone fails to rescue either process, indicating that Not4 loss disrupts additional endolysosomal functions that regulate RP expression and 40S autophagy. Analysis of the Not4-regulated proteome reveals increases in endolysosomal and autophagy-related factors that functionally interact with Not4 to control RP expression and affect 40S autophagy. Collectively, our data indicate that balanced Ccr4-Not ubiquitin ligase signaling maintains RP homeostasis and inhibits 40S autophagy via the ligase's emerging role as an endolysosomal regulator.
Collapse
Affiliation(s)
- Daniel L Johnson
- Molecular Bioinformatics Core and the University of Tennessee Health Science Center Office of Research, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Ravinder Kumar
- Department of Pathology and Laboratory Medicine, College of Medicine and the Center for Cancer Research, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - David Kakhniashvili
- Proteomics and Metabolomics Core and the University of Tennessee Health Science Center Office of Research, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Lawrence M Pfeffer
- Department of Pathology and Laboratory Medicine, College of Medicine and the Center for Cancer Research, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - R Nicholas Laribee
- Department of Pathology and Laboratory Medicine, College of Medicine and the Center for Cancer Research, University of Tennessee Health Science Center, Memphis, Tennessee, USA.
| |
Collapse
|
4
|
Wang H, Li X, Zhang Q, Fu C, Jiang W, Xue J, Liu S, Meng Q, Ai L, Zhi X, Deng S, Liang W. Autophagy in Disease Onset and Progression. Aging Dis 2024; 15:1646-1671. [PMID: 37962467 PMCID: PMC11272186 DOI: 10.14336/ad.2023.0815] [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: 05/03/2023] [Accepted: 08/15/2023] [Indexed: 11/15/2023] Open
Abstract
Autophagy is a biological phenomenon whereby components of cells can self-degrade using autophagosomes. During this process, cells can clear dysfunctional organelles or unwanted elements. Autophagy can recycle unnecessary biomolecules into new components or sometimes, even destroy the cells themselves. This cellular process was first observed in 1962 by Keith R. Porter et al. Since then, autophagy has been studied for over 60 years, and much has been learned on the topic. Nevertheless, the process is still not fully understood. It has been proven, for example, that autophagy can be a positive force for maintaining good health by removing older or damaged cells. By contrast, autophagy is also involved in the onset and progression of various conditions caused by pathogenic infections. These diseases generally involve several important organs in the human body, including the liver, kidney, heart, and central nervous system. The regulation of the defects of autophagy defects may potentially be used to treat some diseases. This review comprehensively discusses recent research frontiers and topics of interest regarding autophagy-related diseases.
Collapse
Affiliation(s)
- Hao Wang
- Shenzhen Baoan Women's and Children's Hospital, Jinan University, Shenzhen, Guangdong, China.
| | - Xiushen Li
- Department of Obstetrics and Gynecology, Shenzhen University General Hospital, Shenzhen, Guangdong, China.
| | - Qi Zhang
- Department of Obstetrics and Gynecology, Shenzhen University General Hospital, Shenzhen, Guangdong, China.
| | - Chengtao Fu
- School of Medicine, Huzhou University, Zhejiang, China.
| | - Wenjie Jiang
- Department of Artificial Intelligence and Data Science, Hebei University of Technology, Tianjin, China.
| | - Jun Xue
- Department of General Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei, China.
| | - Shan Liu
- Bioimaging Core of Shenzhen Bay Laboratory Shenzhen, China.
| | - Qingxue Meng
- Technology Department, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei, China.
| | - Lisha Ai
- Department of Teaching and Research, Shenzhen University General Hospital, Shenzhen, Guangdong, China.
| | - Xuejun Zhi
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei, China.
| | - Shoulong Deng
- National Health Commission of China (NHC) Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China.
| | - Weizheng Liang
- Central Laboratory, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei, China.
| |
Collapse
|
5
|
Prashar A, Bussi C, Fearns A, Capurro MI, Gao X, Sesaki H, Gutierrez MG, Jones NL. Lysosomes drive the piecemeal removal of mitochondrial inner membrane. Nature 2024; 632:1110-1117. [PMID: 39169179 PMCID: PMC7616637 DOI: 10.1038/s41586-024-07835-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 07/16/2024] [Indexed: 08/23/2024]
Abstract
Mitochondrial membranes define distinct structural and functional compartments. Cristae of the inner mitochondrial membrane (IMM) function as independent bioenergetic units that undergo rapid and transient remodelling, but the significance of this compartmentalized organization is unknown1. Using super-resolution microscopy, here we show that cytosolic IMM vesicles, devoid of outer mitochondrial membrane or mitochondrial matrix, are formed during resting state. These vesicles derived from the IMM (VDIMs) are formed by IMM herniation through pores formed by voltage-dependent anion channel 1 in the outer mitochondrial membrane. Live-cell imaging showed that lysosomes in proximity to mitochondria engulfed the herniating IMM and, aided by the endosomal sorting complex required for transport machinery, led to the formation of VDIMs in a microautophagy-like process, sparing the remainder of the organelle. VDIM formation was enhanced in mitochondria undergoing oxidative stress, suggesting their potential role in maintenance of mitochondrial function. Furthermore, the formation of VDIMs required calcium release by the reactive oxygen species-activated, lysosomal calcium channel, transient receptor potential mucolipin 1, showing an interorganelle communication pathway for maintenance of mitochondrial homeostasis. Thus, IMM compartmentalization could allow for the selective removal of damaged IMM sections via VDIMs, which should protect mitochondria from localized injury. Our findings show a new pathway of intramitochondrial quality control.
Collapse
Affiliation(s)
- Akriti Prashar
- Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- NHLBI, NIH, Bethesda, MD, USA
| | - Claudio Bussi
- Host-Pathogen Interactions in Tuberculosis Laboratory, The Francis Crick Institute, London, UK
- School of Biological Sciences, Nanyang Technical University, Singapore, Singapore
| | - Antony Fearns
- Host-Pathogen Interactions in Tuberculosis Laboratory, The Francis Crick Institute, London, UK
| | - Mariana I Capurro
- Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Xiaodong Gao
- Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Hiromi Sesaki
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Maximiliano G Gutierrez
- Host-Pathogen Interactions in Tuberculosis Laboratory, The Francis Crick Institute, London, UK
| | - Nicola L Jones
- Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada.
- Division of Gastroenterology, Hepatology and Nutrition, The Hospital for Sick Children, Toronto, Ontario, Canada.
- Departments of Paediatrics and Physiology, University of Toronto, Toronto, Ontario, Canada.
| |
Collapse
|
6
|
Zhang J, Pan X, Ji W, Zhou J. Autophagy mediated targeting degradation, a promising strategy in drug development. Bioorg Chem 2024; 149:107466. [PMID: 38843684 DOI: 10.1016/j.bioorg.2024.107466] [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: 03/18/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 06/17/2024]
Abstract
Targeted protein degradation (TPD) technologies have become promising therapeutic approaches through degrading disease-causing proteins via the protein degradation system. Autophagy is a fundamental biological process with a high relationship to protein degradation, which belongs to one of two main protein degradation pathways, the autophagy-lysosomal system. Recently, various autophagy-based TPD techniques ATTECs, AUTACs, and AUTOTACs, etc, have also been gradually developed, and they have achieved efficient degradation potency for the targeted protein, expanding the potential of degradation for large-size proteins or protein aggregates. Herein, we introduce the machinery of autophagy and its relation to protein degradation, and multiple methods for using autophagy to specifically degrade target proteins.
Collapse
Affiliation(s)
- Jiantao Zhang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, 688 Yingbin Road, Jinhua 321004, PR China
| | - Xiangyi Pan
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, 688 Yingbin Road, Jinhua 321004, PR China
| | - Wenshu Ji
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, 688 Yingbin Road, Jinhua 321004, PR China
| | - Jinming Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, 688 Yingbin Road, Jinhua 321004, PR China.
| |
Collapse
|
7
|
Kuchitsu Y, Taguchi T. Lysosomal microautophagy: an emerging dimension in mammalian autophagy. Trends Cell Biol 2024; 34:606-616. [PMID: 38104013 DOI: 10.1016/j.tcb.2023.11.005] [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: 08/23/2023] [Revised: 11/08/2023] [Accepted: 11/13/2023] [Indexed: 12/19/2023]
Abstract
Autophagy is a self-catabolic process through which cellular components are delivered to lysosomes for degradation. There are three types of autophagy, i.e., macroautophagy, chaperone-mediated autophagy (CMA), and microautophagy. In macroautophagy, a portion of the cytoplasm is wrapped by the autophagosome, which then fuses with lysosomes and delivers the engulfed cytoplasm for degradation. In CMA, the translocation of cytosolic substrates to the lysosomal lumen is directly across the limiting membrane of lysosomes. In microautophagy, lytic organelles, including endosomes or lysosomes, take up a portion of the cytoplasm directly. Although macroautophagy has been investigated extensively, microautophagy has received much less attention. Nonetheless, it has become evident that microautophagy plays a variety of cellular roles from yeast to mammals. Here we review the very recent updates of microautophagy. In particular, we focus on the feature of the degradative substrates and the molecular machinery that mediates microautophagy.
Collapse
Affiliation(s)
- Yoshihiko Kuchitsu
- Laboratory of Organelle Pathophysiology, Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan.
| | - Tomohiko Taguchi
- Laboratory of Organelle Pathophysiology, Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan.
| |
Collapse
|
8
|
Bai X, Xiong J, Li L, Yu C, Sun C. Suppression of hypoxia-induced CAV1 autophagic degradation enhances nanoalbumin-paclitaxel transcytosis and improves therapeutic activity in pancreatic cancer. Eur J Pharmacol 2024; 969:176431. [PMID: 38395374 DOI: 10.1016/j.ejphar.2024.176431] [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: 10/29/2023] [Revised: 02/13/2024] [Accepted: 02/15/2024] [Indexed: 02/25/2024]
Abstract
Nanoalbumin-paclitaxel (nab-paclitaxel) is a standard chemotherapy for pancreatic cancer but has shown limited efficacy. However, the mechanism through which circulating nab-paclitaxel passes through the tumour vascular endothelium has not been determined. In our study, a new nonradioactive and highly sensitive method for analysing nab-paclitaxel transcytosis was established. Based on these methods, we found that hypoxia significantly enhanced the autophagic degradation of CAV1 and therefore attenuated caveolae-mediated nab-paclitaxel transcytosis across endothelial cells (ECs). In a proof-of-concept experiment, higher levels of CAV1, accompanied by lower levels of LC3B, were observed in the vascular endothelium of pancreatic cancer tissues collected from patients who showed a good response to nab-paclitaxel compared with those from patients who showed a poor response to nab-paclitaxel. Furthermore, both in vivo and in vitro studies confirmed that suppressing the autophagic degradation of CAV1 via EC-specific ATG5 knockdown or hydroxychloroquine sulfate (HCQ) treatment significantly enhanced nab-paclitaxel translocation across the endothelial barrier into pancreatic cancer cells and amplified the inhibitory effect of nab-paclitaxel on pancreatic tumour growth. The stimulation of CAV1 expression by EC-specific overexpression of exogenous CAV1 or administration of gemcitabine hydrochloride (GE) had the same effect. These results demonstrated that suppressing CAV1 autophagic degradation is a novel translatable strategy for enhancing nab-paclitaxel chemotherapeutic activity in the treatment of pancreatic cancer.
Collapse
Affiliation(s)
- Xiangli Bai
- School of Basic Medicine, Guizhou Medical University, 5500025, Guiyang, Guizhou, China; Department of Hepatic-Biliary-Pancreatic Surgery, The Affiliated Hospital of Guizhou Medical University, 550004, Guiyang, Guizhou, China; Department of Laboratory Medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430077, Wuhan, Hubei, China
| | - Jia Xiong
- Department of Cardiovascular Surgery, Jinan University 2nd Clinical Medicine College People's Hospital of Shenzhen, 518020, Shenzhen, Guangdong, China
| | - Lin Li
- School of Basic Medicine, Guizhou Medical University, 5500025, Guiyang, Guizhou, China; Department of Hepatic-Biliary-Pancreatic Surgery, The Affiliated Hospital of Guizhou Medical University, 550004, Guiyang, Guizhou, China
| | - Chao Yu
- Department of Hepatic-Biliary-Pancreatic Surgery, The Affiliated Hospital of Guizhou Medical University, 550004, Guiyang, Guizhou, China
| | - Chengyi Sun
- School of Basic Medicine, Guizhou Medical University, 5500025, Guiyang, Guizhou, China; Department of Hepatic-Biliary-Pancreatic Surgery, The Affiliated Hospital of Guizhou Medical University, 550004, Guiyang, Guizhou, China.
| |
Collapse
|
9
|
Martins TS, Correia M, Pinheiro D, Lemos C, Mendes MV, Pereira C, Costa V. Sit4 Genetically Interacts with Vps27 to Regulate Mitochondrial Function and Lifespan in Saccharomyces cerevisiae. Cells 2024; 13:655. [PMID: 38667270 PMCID: PMC11049076 DOI: 10.3390/cells13080655] [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: 01/06/2024] [Revised: 03/27/2024] [Accepted: 04/06/2024] [Indexed: 04/28/2024] Open
Abstract
The Sit4 protein phosphatase plays a key role in orchestrating various cellular processes essential for maintaining cell viability during aging. We have previously shown that SIT4 deletion promotes vacuolar acidification, mitochondrial derepression, and oxidative stress resistance, increasing yeast chronological lifespan. In this study, we performed a proteomic analysis of isolated vacuoles and yeast genetic interaction analysis to unravel how Sit4 influences vacuolar and mitochondrial function. By employing high-resolution mass spectrometry, we show that sit4Δ vacuolar membranes were enriched in Vps27 and Hse1, two proteins that are part of the endosomal sorting complex required for transport-0. In addition, SIT4 exhibited a negative genetic interaction with VPS27, as sit4∆vps27∆ double mutants had a shortened lifespan compared to sit4∆ and vps27∆ single mutants. Our results also show that Vps27 did not increase sit4∆ lifespan by improving protein trafficking or vacuolar sorting pathways. However, Vps27 was critical for iron homeostasis and mitochondrial function in sit4∆ cells, as sit4∆vps27∆ double mutants exhibited high iron levels and impaired mitochondrial respiration. These findings show, for the first time, cross-talk between Sit4 and Vps27, providing new insights into the mechanisms governing chronological lifespan.
Collapse
Affiliation(s)
- Telma S. Martins
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (T.S.M.); (M.C.); (D.P.); (C.L.); (M.V.M.)
- IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Miguel Correia
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (T.S.M.); (M.C.); (D.P.); (C.L.); (M.V.M.)
- IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
| | - Denise Pinheiro
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (T.S.M.); (M.C.); (D.P.); (C.L.); (M.V.M.)
- IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
| | - Carolina Lemos
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (T.S.M.); (M.C.); (D.P.); (C.L.); (M.V.M.)
- IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Marta Vaz Mendes
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (T.S.M.); (M.C.); (D.P.); (C.L.); (M.V.M.)
- IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
| | - Clara Pereira
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (T.S.M.); (M.C.); (D.P.); (C.L.); (M.V.M.)
- IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
| | - Vítor Costa
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (T.S.M.); (M.C.); (D.P.); (C.L.); (M.V.M.)
- IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| |
Collapse
|
10
|
Álvarez-Guerra I, Block E, Broeskamp F, Gabrijelčič S, Infant T, de Ory A, Habernig L, Andréasson C, Levine TP, Höög JL, Büttner S. LDO proteins and Vac8 form a vacuole-lipid droplet contact site to enable starvation-induced lipophagy in yeast. Dev Cell 2024; 59:759-775.e5. [PMID: 38354739 DOI: 10.1016/j.devcel.2024.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 11/15/2023] [Accepted: 01/18/2024] [Indexed: 02/16/2024]
Abstract
Lipid droplets (LDs) are fat storage organelles critical for energy and lipid metabolism. Upon nutrient exhaustion, cells consume LDs via gradual lipolysis or via lipophagy, the en bloc uptake of LDs into the vacuole. Here, we show that LDs dock to the vacuolar membrane via a contact site that is required for lipophagy in yeast. The LD-localized LDO proteins carry an intrinsically disordered region that directly binds vacuolar Vac8 to form vCLIP, the vacuolar-LD contact site. Nutrient limitation drives vCLIP formation, and its inactivation blocks lipophagy, resulting in impaired caloric restriction-induced longevity. We establish a functional link between lipophagy and microautophagy of the nucleus, both requiring Vac8 to form respective contact sites upon metabolic stress. In sum, we identify the tethering machinery of vCLIP and find that Vac8 provides a platform for multiple and competing contact sites associated with autophagy.
Collapse
Affiliation(s)
- Irene Álvarez-Guerra
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Emma Block
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Filomena Broeskamp
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Sonja Gabrijelčič
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Terence Infant
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Ana de Ory
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Lukas Habernig
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Claes Andréasson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Tim P Levine
- UCL Institute of Ophthalmology, Bath Street, London EC1V 9EL, UK
| | - Johanna L Höög
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Sabrina Büttner
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden.
| |
Collapse
|
11
|
Feng Y, Chen Y, Wu X, Chen J, Zhou Q, Liu B, Zhang L, Yi C. Interplay of energy metabolism and autophagy. Autophagy 2024; 20:4-14. [PMID: 37594406 PMCID: PMC10761056 DOI: 10.1080/15548627.2023.2247300] [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: 07/01/2022] [Revised: 07/27/2023] [Accepted: 07/31/2023] [Indexed: 08/19/2023] Open
Abstract
Macroautophagy/autophagy, is widely recognized for its crucial role in enabling cell survival and maintaining cellular energy homeostasis during starvation or energy stress. Its regulation is intricately linked to cellular energy status. In this review, covering yeast, mammals, and plants, we aim to provide a comprehensive overview of the understanding of the roles and mechanisms of carbon- or glucose-deprivation related autophagy, showing how cells effectively respond to such challenges for survival. Further investigation is needed to determine the specific degraded substrates by autophagy during glucose or energy deprivation and the diverse roles and mechanisms during varying durations of energy starvation.Abbreviations: ADP: adenosine diphosphate; AMP: adenosine monophosphate; AMPK: AMP-activated protein kinase; ATG: autophagy related; ATP: adenosine triphosphate; ER: endoplasmic reticulum; ESCRT: endosomal sorting complex required for transport; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GD: glucose deprivation; GFP: green fluorescent protein; GTPases: guanosine triphosphatases; HK2: hexokinase 2; K phaffii: Komagataella phaffii; LD: lipid droplet; MAP1LC3/LC3: microtubule-associated protein1 light chain 3; MAPK: mitogen-activated protein kinase; Mec1: mitosis entry checkpoint 1; MTOR: mechanistic target of rapamycin kinase; NAD (+): nicotinamide adenine dinucleotide; OGD: oxygen and glucose deprivation; PAS: phagophore assembly site; PCD: programmed cell death; PtdIns3K: class III phosphatidylinositol 3-kinase; PtdIns3P: phosphatidylinositol-3-phosphate; ROS: reactive oxygen species; S. cerevisiae: Saccharomyces cerevisiae; SIRT1: sirtuin 1; Snf1: sucrose non-fermenting 1; STK11/LKB1: serine/threonine kinase 11; TFEB: transcription factor EB; TORC1: target of rapamycin complex 1; ULK1: unc-51 like kinase 1; Vps27: vacuolar protein sorting 27; Vps4: vacuolar protein sorting 4.
Collapse
Affiliation(s)
- Yuyao Feng
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, School of Life Sciences, Huzhou University, Huzhou, China
- Department of Biochemistry, and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, China
| | - Ying Chen
- Department of Biochemistry, and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoyong Wu
- Department of Biochemistry, and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Junye Chen
- Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, China
| | - Qingyan Zhou
- Department of Biochemistry, and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Bao Liu
- Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, China
| | - Liqin Zhang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, School of Life Sciences, Huzhou University, Huzhou, China
| | - Cong Yi
- Department of Biochemistry, and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| |
Collapse
|
12
|
Sakai Y, Oku M. ATG and ESCRT control multiple modes of microautophagy. FEBS Lett 2024; 598:48-58. [PMID: 37857501 DOI: 10.1002/1873-3468.14760] [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: 07/20/2023] [Revised: 08/30/2023] [Accepted: 09/01/2023] [Indexed: 10/21/2023]
Abstract
The discovery of microautophagy, the direct engulfment of cytoplasmic material by the lysosome, dates back to 1966 in a morphological study of mammalian cells by Christian de Duve. Since then, studies on microautophagy have shifted toward the elucidation of the physiological significance of the process. However, in contrast to macroautophagy, studies on the molecular mechanisms of microautophagy have been limited. Only recent studies revealed that ATG proteins involved in macroautophagy are also operative in several types of microautophagy and that ESCRT proteins, responsible for the multivesicular body pathway, play a central role in most microautophagy processes. In this review, we summarize our current knowledge on the function of ATG and ESCRT proteins in microautophagy.
Collapse
Affiliation(s)
- Yasuyoshi Sakai
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Japan
| | - Masahide Oku
- Department of Bioscience and Biotechnology, Faculty of Bioenvironmental Sciences, Kyoto University of Advanced Science, Kameoka, Japan
| |
Collapse
|
13
|
Kagohashi Y, Sasaki M, May AI, Kawamata T, Ohsumi Y. The mechanism of Atg15-mediated membrane disruption in autophagy. J Cell Biol 2023; 222:e202306120. [PMID: 37917025 PMCID: PMC10622257 DOI: 10.1083/jcb.202306120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/25/2023] [Accepted: 10/03/2023] [Indexed: 11/03/2023] Open
Abstract
Autophagy is a lysosomal/vacuolar delivery system that degrades cytoplasmic material. During autophagy, autophagosomes deliver cellular components to the vacuole, resulting in the release of a cargo-containing autophagic body (AB) into the vacuole. AB membranes must be disrupted for degradation of cargo to occur. The lipase Atg15 and vacuolar proteases Pep4 and Prb1 are known to be necessary for this disruption and cargo degradation, but the mechanistic underpinnings remain unclear. In this study, we establish a system to detect lipase activity in the vacuole and show that Atg15 is the sole vacuolar phospholipase. Pep4 and Prb1 are required for the activation of Atg15 lipase function, which occurs following delivery of Atg15 to the vacuole by the MVB pathway. In vitro experiments reveal that Atg15 is a phospholipase B of broad substrate specificity that is likely implicated in the disruption of a range of membranes. Further, we use isolated ABs to demonstrate that Atg15 alone is able to disrupt AB membranes.
Collapse
Affiliation(s)
- Yoko Kagohashi
- Research Center for Cell Biology, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
- POLA Chemical Industries, Inc., Yokohama, Japan
| | - Michiko Sasaki
- Research Center for Cell Biology, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Alexander I. May
- Research Center for Cell Biology, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Tomoko Kawamata
- Research Center for Cell Biology, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Yoshinori Ohsumi
- Research Center for Cell Biology, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| |
Collapse
|
14
|
Kimura Y, Tsuji T, Shimizu Y, Watanabe Y, Kimura M, Fujimoto T, Higuchi M. Physicochemical properties of the vacuolar membrane and cellular factors determine formation of vacuolar invaginations. Sci Rep 2023; 13:16187. [PMID: 37759072 PMCID: PMC10533490 DOI: 10.1038/s41598-023-43232-5] [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: 02/26/2023] [Accepted: 09/21/2023] [Indexed: 09/29/2023] Open
Abstract
Vacuoles change their morphology in response to stress. In yeast exposed to chronically high temperatures, vacuolar membranes get deformed and invaginations are formed. We show that phase-separation of vacuolar membrane occurred after heat stress leading to the formation of the invagination. In addition, Hfl1, a vacuolar membrane-localized Atg8-binding protein, was found to suppress the excess vacuolar invaginations after heat stress. At that time, Hfl1 formed foci at the neck of the invaginations in wild-type cells, whereas it was efficiently degraded in the vacuole in the atg8Δ mutant. Genetic analysis showed that the endosomal sorting complex required for transport machinery was necessary to form the invaginations irrespective of Atg8 or Hfl1. In contrast, a combined mutation with the vacuole BAR domain protein Ivy1 led to vacuoles in hfl1Δivy1Δ and atg8Δivy1Δ mutants having constitutively invaginated structures; moreover, these mutants showed stress-sensitive phenotypes. Our findings suggest that vacuolar invaginations result from the combination of changes in the physiochemical properties of the vacuolar membrane and other cellular factors.
Collapse
Affiliation(s)
- Yoko Kimura
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, 422-8529, Japan.
- Department of Agriculture, Shizuoka University, Shizuoka, 422-8529, Japan.
| | - Takuma Tsuji
- Laboratory of Molecular Cell Biology, Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yosuke Shimizu
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, 422-8529, Japan
| | - Yuki Watanabe
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, 422-8529, Japan
| | - Masafumi Kimura
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, 422-8529, Japan
| | - Toyoshi Fujimoto
- Laboratory of Molecular Cell Biology, Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Miyuki Higuchi
- Department of Agriculture, Shizuoka University, Shizuoka, 422-8529, Japan
| |
Collapse
|
15
|
Mutvei AP, Nagiec MJ, Blenis J. Balancing lysosome abundance in health and disease. Nat Cell Biol 2023; 25:1254-1264. [PMID: 37580388 DOI: 10.1038/s41556-023-01197-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 06/28/2023] [Indexed: 08/16/2023]
Abstract
Lysosomes are catabolic organelles that govern numerous cellular processes, including macromolecule degradation, nutrient signalling and ion homeostasis. Aberrant changes in lysosome abundance are implicated in human diseases. Here we outline the mechanisms of lysosome biogenesis and turnover, and discuss how changes in the lysosome pool impact physiological and pathophysiological processes.
Collapse
Affiliation(s)
- Anders P Mutvei
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, Huddinge, Sweden.
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
| | - Michal J Nagiec
- Meyer Cancer Center and Department of Pharmacology, Weill Cornell Medical College, New York, NY, USA
| | - John Blenis
- Meyer Cancer Center and Department of Pharmacology, Weill Cornell Medical College, New York, NY, USA.
| |
Collapse
|
16
|
Yang H, Tan JX. Lysosomal quality control: molecular mechanisms and therapeutic implications. Trends Cell Biol 2023; 33:749-764. [PMID: 36717330 PMCID: PMC10374877 DOI: 10.1016/j.tcb.2023.01.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/08/2023] [Accepted: 01/10/2023] [Indexed: 01/29/2023]
Abstract
Lysosomes are essential catabolic organelles with an acidic lumen and dozens of hydrolytic enzymes. The detrimental consequences of lysosomal leakage have been well known since lysosomes were discovered during the 1950s. However, detailed knowledge of lysosomal quality control mechanisms has only emerged relatively recently. It is now clear that lysosomal leakage triggers multiple lysosomal quality control pathways that replace, remove, or directly repair damaged lysosomes. Here, we review how lysosomal damage is sensed and resolved in mammalian cells, with a focus on the molecular mechanisms underlying different lysosomal quality control pathways. We also discuss the clinical implications and therapeutic potential of these pathways.
Collapse
Affiliation(s)
- Haoxiang Yang
- Aging Institute, University of Pittsburgh School of Medicine/University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA
| | - Jay Xiaojun Tan
- Aging Institute, University of Pittsburgh School of Medicine/University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA; Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA.
| |
Collapse
|
17
|
Johnson DL, Kumar R, Kakhniashvili D, Pfeffer LM, Laribee RN. Ccr4-Not ubiquitin ligase signaling regulates ribosomal protein homeostasis and inhibits 40S ribosomal autophagy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.28.555095. [PMID: 37693548 PMCID: PMC10491097 DOI: 10.1101/2023.08.28.555095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
The Ccr4-Not complex containing the Not4 ubiquitin ligase regulates gene transcription and mRNA decay, yet it also has poorly defined roles in translation, proteostasis, and endolysosomal-dependent nutrient signaling. To define how Ccr4-Not mediated ubiquitin signaling regulates these additional processes, we performed quantitative proteomics in the yeast Saccharomyces cerevisiae lacking the Not4 ubiquitin ligase, and also in cells overexpressing either wild-type or functionally inactive ligase. Herein, we provide evidence that both increased and decreased Ccr4-Not ubiquitin signaling disrupts ribosomal protein (RP) homeostasis independently of reduced RP mRNA changes or reductions in known Not4 ribosomal substrates. Surprisingly, we also find that both Not4-mediated ubiquitin signaling, and the Ccr4 subunit, actively inhibit 40S ribosomal autophagy. This 40S autophagy is independent of canonical Atg7-dependent macroautophagy, thus indicating microautophagy activation is responsible. Furthermore, the Not4 ligase genetically interacts with endolysosomal pathway effectors to control both RP expression and 40S autophagy efficiency. Overall, we demonstrate that balanced Ccr4-Not ligase activity maintains RP homeostasis, and that Ccr4-Not ubiquitin signaling interacts with the endolysosomal pathway to both regulate RP expression and inhibit 40S ribosomal autophagy.
Collapse
Affiliation(s)
- Daniel L. Johnson
- Molecular Bioinformatics Core and the University of Tennessee Health Science Center Office of Research, University of Tennessee Health Science Center, Memphis, TN, United States of America
| | - Ravinder Kumar
- Department of Pathology and Laboratory Medicine, College of Medicine and the Center for Cancer Research, University of Tennessee Health Science Center, Memphis, TN, United States of America
| | - David Kakhniashvili
- Proteomics and Metabolomics Core and the University of Tennessee Health Science Center Office of Research, University of Tennessee Health Science Center, Memphis, TN, United States of America
| | - Lawrence M. Pfeffer
- Department of Pathology and Laboratory Medicine, College of Medicine and the Center for Cancer Research, University of Tennessee Health Science Center, Memphis, TN, United States of America
| | - R. Nicholas Laribee
- Department of Pathology and Laboratory Medicine, College of Medicine and the Center for Cancer Research, University of Tennessee Health Science Center, Memphis, TN, United States of America
| |
Collapse
|
18
|
Lan ZQ, Ge ZY, Lv SK, Zhao B, Li CX. The regulatory role of lipophagy in central nervous system diseases. Cell Death Discov 2023; 9:229. [PMID: 37414782 DOI: 10.1038/s41420-023-01504-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/04/2023] [Accepted: 06/19/2023] [Indexed: 07/08/2023] Open
Abstract
Lipid droplets (LDs) are the organelles for storing neutral lipids, which are broken down when energy is insufficient. It has been suggested that excessive accumulation of LDs can affect cellular function, which is important to coordinate homeostasis of lipids in vivo. Lysosomes play an important role in the degradation of lipids, and the process of selective autophagy of LDs through lysosomes is known as lipophagy. Dysregulation of lipid metabolism has recently been associated with a variety of central nervous system (CNS) diseases, but the specific regulatory mechanisms of lipophagy in these diseases remain to be elucidated. This review summarizes various forms of lipophagy and discusses the role that lipophagy plays in the development of CNS diseases in order to reveal the related mechanisms and potential therapeutic targets for these diseases.
Collapse
Affiliation(s)
- Zhuo-Qing Lan
- Department of General practice medicine, the Fourth Affiliated Hospital, School of Medicine, Zhejiang University, Yiwu, P.R. China
| | - Zi-Yi Ge
- Department of Anesthesiology, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, P.R. China
| | - Shu-Kai Lv
- Department of General practice medicine, the Fourth Affiliated Hospital, School of Medicine, Zhejiang University, Yiwu, P.R. China
| | - Bing Zhao
- Department of Anesthesiology, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, P.R. China.
| | - Cai-Xia Li
- Department of General practice medicine, the Fourth Affiliated Hospital, School of Medicine, Zhejiang University, Yiwu, P.R. China.
- Department of Anesthesiology, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, P.R. China.
| |
Collapse
|
19
|
Wang L, Klionsky DJ, Shen HM. The emerging mechanisms and functions of microautophagy. Nat Rev Mol Cell Biol 2023; 24:186-203. [PMID: 36097284 DOI: 10.1038/s41580-022-00529-z] [Citation(s) in RCA: 130] [Impact Index Per Article: 130.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/02/2022] [Indexed: 02/08/2023]
Abstract
'Autophagy' refers to an evolutionarily conserved process through which cellular contents, such as damaged organelles and protein aggregates, are delivered to lysosomes for degradation. Different forms of autophagy have been described on the basis of the nature of the cargoes and the means used to deliver them to lysosomes. At present, the prevailing categories of autophagy in mammalian cells are macroautophagy, microautophagy and chaperone-mediated autophagy. The molecular mechanisms and biological functions of macroautophagy and chaperone-mediated autophagy have been extensively studied, but microautophagy has received much less attention. In recent years, there has been a growth in research on microautophagy, first in yeast and then in mammalian cells. Here we review this form of autophagy, focusing on selective forms of microautophagy. We also discuss the upstream regulatory mechanisms, the crosstalk between macroautophagy and microautophagy, and the functional implications of microautophagy in diseases such as cancer and neurodegenerative disorders in humans. Future research into microautophagy will provide opportunities to develop novel interventional strategies for autophagy- and lysosome-related diseases.
Collapse
Affiliation(s)
- Liming Wang
- School of Biomedical Sciences, Hunan University, Changsha, China
| | - Daniel J Klionsky
- Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
| | - Han-Ming Shen
- Faculty of Health Sciences, Ministry of Education Frontiers Science Center for Precision Oncology, University of Macau, Macau, China. .,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
| |
Collapse
|
20
|
Huang S, Liu Z, Cao W, Li H, Zhang W, Cui Y, Hu S, Luo M, Zhu Y, Zhao Q, Xie L, Gao C, Xiao S, Jiang L. The plant ESCRT component FREE1 regulates peroxisome-mediated turnover of lipid droplets in germinating Arabidopsis seedlings. THE PLANT CELL 2022; 34:4255-4273. [PMID: 35775937 PMCID: PMC9614499 DOI: 10.1093/plcell/koac195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 06/20/2022] [Indexed: 05/28/2023]
Abstract
Lipid droplets (LDs) stored during seed development are mobilized and provide essential energy and lipids to support seedling growth upon germination. Triacylglycerols (TAGs) are the main neutral lipids stored in LDs. The lipase SUGAR DEPENDENT 1 (SDP1), which hydrolyzes TAGs in Arabidopsis thaliana, is localized on peroxisomes and traffics to the LD surface through peroxisomal extension, but the underlying mechanism remains elusive. Here, we report a previously unknown function of a plant-unique endosomal sorting complex required for transport (ESCRT) component FYVE DOMAIN PROTEIN REQUIRED FOR ENDOSOMAL SORTING 1 (FREE1) in regulating peroxisome/SDP1-mediated LD turnover in Arabidopsis. We showed that LD degradation was impaired in germinating free1 mutant; moreover, the tubulation of SDP1- or PEROXIN 11e (PEX11e)-marked peroxisomes and the migration of SDP1-positive peroxisomes to the LD surface were altered in the free1 mutant. Electron tomography analysis showed that peroxisomes failed to form tubules to engulf LDs in free1, unlike in the wild-type. FREE1 interacted directly with both PEX11e and SDP1, suggesting that these interactions may regulate peroxisomal extension and trafficking of the lipase SDP1 to LDs. Taken together, our results demonstrate a pivotal role for FREE1 in LD degradation in germinating seedlings via regulating peroxisomal tubulation and SDP1 targeting.
Collapse
Affiliation(s)
- Shuxian Huang
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, China
| | - Zhiqi Liu
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, China
| | - Wenhan Cao
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, China
| | - Hongbo Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University (SCNU), Guangzhou, 510631, China
| | - Wenxin Zhang
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, China
| | - Yong Cui
- School of Life Sciences, State Key Laboratory of Cellular Stress Biology, Xiamen University, Xiamen, 361102, China
| | - Shuai Hu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Mengqian Luo
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, China
| | - Ying Zhu
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, China
| | - Qiong Zhao
- School of Life Sciences, East China Normal University, Shanghai, 200062, China
| | - Lijuan Xie
- College of Plant Protection, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Caiji Gao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University (SCNU), Guangzhou, 510631, China
| | - Shi Xiao
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China
| | | |
Collapse
|
21
|
Yang Y, Wang M, Zhang YY, Zhao SZ, Gu S. The endosomal sorting complex required for transport repairs the membrane to delay cell death. Front Oncol 2022; 12:1007446. [PMID: 36330465 PMCID: PMC9622947 DOI: 10.3389/fonc.2022.1007446] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 09/20/2022] [Indexed: 08/15/2023] Open
Abstract
The endosomal sorting complex required for transport (ESCRT) machinery plays a key role in the repair of damaged plasma membranes with puncta form and removes pores from the plasma membrane in regulated cell death, apoptosis, necroptosis, pyroptosis, ferroptosis, and autophagy. ESCRT-I overexpression and ESCRT-III-associated charged multivesicular body protein (CHMP) 4B participate in apoptosis, and the ESCRT-1 protein TSG 101 maintains low levels of ALIX and ALG-2 and prevents predisposition to apoptosis. The ESCRT-III components CHMP2A and CHMP4B are recruited to broken membrane bubble sites with the requirement of extracellular Ca2+, remove membrane vesicles from cells, and delay the time required for active MLKL to mediate necroptosis, thus preserving cell survival. CHMP4B disturbed pyroptosis by recruiting around the plasma membrane neck to remove the GSDMD pores and preserve plasma membrane integrity depending on Ca2+ influx. The accumulation of the ESCRT-III subunits CHMP5 and CHMP6 in the plasma membrane is increased by the classical ferroptosis activators erastin-1 and ras-selective lethal small molecule 3 (RSL3) upon cytosolic calcium influx and repairs the ferroptotic plasma membrane. ESCRT-III- and VPS4-induced macroautophagy, ESCRT-0-initiated microautophagy. ESCRT-I, ESCRT-II, ESCRT-III, ALIX, and VPS4A are recruited to damaged lysosomes and precede lysophagy, indicating that ESCRT is a potential target to overcome drug resistance during tumor therapy.
Collapse
Affiliation(s)
- Ye Yang
- Obstetrics and Gynecology Department, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Min Wang
- General Surgery Department, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ying-Ying Zhang
- Respiratory and Critical Care Medicine Department, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shu-Zhi Zhao
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People’s Hospital), Shanghai Jiao Tong University School of Medicine, Shanghai, China
- National Clinical Research Center for Eye Diseases, Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, Shanghai, China
| | - Song Gu
- Trauma Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| |
Collapse
|
22
|
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: 6] [Impact Index Per Article: 3.0] [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.
Collapse
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
| |
Collapse
|
23
|
Zhang W, Yang X, Li Y, Yu L, Zhang B, Zhang J, Cho WJ, Venkatarangan V, Chen L, Burugula BB, Bui S, Wang Y, Duan C, Kitzman JO, Li M. GCAF(TMEM251) regulates lysosome biogenesis by activating the mannose-6-phosphate pathway. Nat Commun 2022; 13:5351. [PMID: 36096887 PMCID: PMC9468337 DOI: 10.1038/s41467-022-33025-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/29/2022] [Indexed: 11/09/2022] Open
Abstract
The mannose-6-phosphate (M6P) biosynthetic pathway for lysosome biogenesis has been studied for decades and is considered a well-understood topic. However, whether this pathway is regulated remains an open question. In a genome-wide CRISPR/Cas9 knockout screen, we discover TMEM251 as the first regulator of the M6P modification. Deleting TMEM251 causes mistargeting of most lysosomal enzymes due to their loss of M6P modification and accumulation of numerous undigested materials. We further demonstrate that TMEM251 localizes to the Golgi and is required for the cleavage and activity of GNPT, the enzyme that catalyzes M6P modification. In zebrafish, TMEM251 deletion leads to severe developmental defects including heart edema and skeletal dysplasia, which phenocopies Mucolipidosis Type II. Our discovery provides a mechanism for the newly discovered human disease caused by TMEM251 mutations. We name TMEM251 as GNPTAB cleavage and activity factor (GCAF) and its related disease as Mucolipidosis Type V.
Collapse
Affiliation(s)
- Weichao Zhang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Xi Yang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Yingxiang Li
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Linchen Yu
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Bokai Zhang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jianchao Zhang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Woo Jung Cho
- BRCF Microscopy Core, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Varsha Venkatarangan
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Liang Chen
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Bala Bharathi Burugula
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Sarah Bui
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Yanzhuang Wang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Cunming Duan
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jacob O Kitzman
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Ming Li
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA.
| |
Collapse
|
24
|
Carinci M, Palumbo L, Pellielo G, Agyapong ED, Morciano G, Patergnani S, Giorgi C, Pinton P, Rimessi A. The Multifaceted Roles of Autophagy in Infectious, Obstructive, and Malignant Airway Diseases. Biomedicines 2022; 10:biomedicines10081944. [PMID: 36009490 PMCID: PMC9405571 DOI: 10.3390/biomedicines10081944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022] Open
Abstract
Autophagy is a highly conserved dynamic process by which cells deliver their contents to lysosomes for degradation, thus ensuring cell homeostasis. In response to environmental stress, the induction of autophagy is crucial for cell survival. The dysregulation of this degradative process has been implicated in a wide range of pathologies, including lung diseases, representing a relevant potential target with significant clinical outcomes. During lung disease progression and infections, autophagy may exert both protective and harmful effects on cells. In this review, we will explore the implications of autophagy and its selective forms in several lung infections, such as SARS-CoV-2, Respiratory Syncytial Virus (RSV) and Mycobacterium tuberculosis (Mtb) infections, and different lung diseases such as Cystic Fibrosis (CF), Chronic Obstructive Pulmonary Disease (COPD), and Malignant Mesothelioma (MM).
Collapse
Affiliation(s)
- Marianna Carinci
- Laboratory for Technologies of Advanced Therapies, Section of Experimental Medicine, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Laura Palumbo
- Laboratory for Technologies of Advanced Therapies, Section of Experimental Medicine, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Giulia Pellielo
- Laboratory for Technologies of Advanced Therapies, Section of Experimental Medicine, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Esther Densu Agyapong
- Laboratory for Technologies of Advanced Therapies, Section of Experimental Medicine, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Giampaolo Morciano
- Laboratory for Technologies of Advanced Therapies, Section of Experimental Medicine, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Simone Patergnani
- Laboratory for Technologies of Advanced Therapies, Section of Experimental Medicine, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Carlotta Giorgi
- Laboratory for Technologies of Advanced Therapies, Section of Experimental Medicine, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Paolo Pinton
- Laboratory for Technologies of Advanced Therapies, Section of Experimental Medicine, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
- Center of Research for Innovative Therapies in Cystic Fibrosis, University of Ferrara, Via Fossato di Mortara, 70, 44121 Ferrara, Italy
| | - Alessandro Rimessi
- Laboratory for Technologies of Advanced Therapies, Section of Experimental Medicine, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
- Center of Research for Innovative Therapies in Cystic Fibrosis, University of Ferrara, Via Fossato di Mortara, 70, 44121 Ferrara, Italy
- Correspondence:
| |
Collapse
|
25
|
Cell Autophagy in NASH and NASH-Related Hepatocellular Carcinoma. Int J Mol Sci 2022; 23:ijms23147734. [PMID: 35887082 PMCID: PMC9322157 DOI: 10.3390/ijms23147734] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/10/2022] [Accepted: 07/11/2022] [Indexed: 12/21/2022] Open
Abstract
Autophagy, a cellular self-digestion process, involves the degradation of targeted cell components such as damaged organelles, unfolded proteins, and intracellular pathogens by lysosomes. It is a major quality control system of the cell and plays an important role in cell differentiation, survival, development, and homeostasis. Alterations in the cell autophagic machinery have been implicated in several disease conditions, including neurodegeneration, autoimmunity, cancer, infection, inflammatory diseases, and aging. In non-alcoholic fatty liver disease, including its inflammatory form, non-alcoholic steatohepatitis (NASH), a decrease in cell autophagic activity, has been implicated in the initial development and progression of steatosis to NASH and hepatocellular carcinoma (HCC). We present an overview of autophagy as it occurs in mammalian cells with an insight into the emerging understanding of the role of autophagy in NASH and NASH-related HCC.
Collapse
|
26
|
Fairman G, Ouimet M. Lipophagy pathways in yeast are controlled by their distinct modes of induction. Yeast 2022; 39:429-439. [PMID: 35652813 DOI: 10.1002/yea.3705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/18/2022] [Accepted: 04/04/2022] [Indexed: 11/06/2022] Open
Abstract
Lipid droplet (LD) autophagy (lipophagy) is a recently discovered selective form of autophagy and is a pathway for LD catabolism. This ubiquitous process has been an ongoing area of research within the budding yeast, Saccharomyces cerevisiae. Yeast lipophagy phenotypically resembles microautophagy, although it has a distinct set of genetic requirements depending on the mode of induction. This review highlights the similarities and differences between different forms of yeast lipophagy and offers perspectives on how our knowledge of lipophagy in yeast may guide our understanding of this process within mammalian cells to ultimately inform future applications of lipophagy.
Collapse
Affiliation(s)
- Garrett Fairman
- University of Ottawa Heart Institute, Ottawa, Ontario, Canada.,Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Mireille Ouimet
- University of Ottawa Heart Institute, Ottawa, Ontario, Canada.,Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| |
Collapse
|
27
|
Arines FM, Li M. An optimized protocol to analyze membrane protein degradation in yeast using quantitative western blot and flow cytometry. STAR Protoc 2022; 3:101274. [PMID: 35403002 PMCID: PMC8987394 DOI: 10.1016/j.xpro.2022.101274] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/30/2022] Open
Abstract
Membrane proteins (MPs) are essential in many cellular functions. To maintain proteostasis, MPs are downregulated via ubiquitination and degradation. Here, we describe an optimized protocol to analyze MP degradation using quantitative western blot and flow cytometry-based approaches. We use the degradation of Ypq1, a vacuole membrane lysine transporter, to demonstrate the protocol, which can be adapted for other organelle MPs and thus provide useful tools to study MP regulation in yeast and other model organisms. For complete details on the use and execution of this protocol, please refer to Arines et al. (2021) and Yang et al. (2020). Two complementary protocols for quantifying membrane protein degradation in yeast Measures the decrease of full-length protein by quantitative western blot Quantifies the quenching of GFP fluorescence by flow cytometry Adaptable to other fluorescent protein tags and mammalian cells
Collapse
|
28
|
Xu C, Fan J. Links between autophagy and lipid droplet dynamics. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2848-2858. [PMID: 35560198 DOI: 10.1093/jxb/erac003] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/06/2022] [Indexed: 06/15/2023]
Abstract
Autophagy is a catabolic process in which cytoplasmic components are delivered to vacuoles or lysosomes for degradation and nutrient recycling. Autophagy-mediated degradation of membrane lipids provides a source of fatty acids for the synthesis of energy-rich, storage lipid esters such as triacylglycerol (TAG). In eukaryotes, storage lipids are packaged into dynamic subcellular organelles, lipid droplets. In times of energy scarcity, lipid droplets can be degraded via autophagy in a process termed lipophagy to release fatty acids for energy production via fatty acid β-oxidation. On the other hand, emerging evidence suggests that lipid droplets are required for the efficient execution of autophagic processes. Here, we review recent advances in our understanding of metabolic interactions between autophagy and TAG storage, and discuss mechanisms of lipophagy. Free fatty acids are cytotoxic due to their detergent-like properties and their incorporation into lipid intermediates that are toxic at high levels. Thus, we also discuss how cells manage lipotoxic stresses during autophagy-mediated mobilization of fatty acids from lipid droplets and organellar membranes for energy generation.
Collapse
Affiliation(s)
- Changcheng Xu
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Jilian Fan
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| |
Collapse
|
29
|
Takuma T, Ushimaru T. Vacuolar fragmentation promotes fluxes of microautophagy and micronucleophagy but not of macroautophagy. Biochem Biophys Res Commun 2022; 614:161-168. [PMID: 35597153 DOI: 10.1016/j.bbrc.2022.05.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 05/07/2022] [Indexed: 11/17/2022]
Abstract
Vacuoles and lysosomes are organelles involved in the degradation of cytoplasmic proteins and organelles. Vacuolar morphology is dynamically regulated by fission and fusion in budding yeast. Vacuolar fusion is elicited in nutrient-depleted conditions and mediated by inactivation of target of rapamycin complex 1 (TORC1) protein kinase. However, it is unknown whether and how vacuolar morphology affects macroautophagy and microautophagy, which are induced by nutrient starvation and TORC1 inactivation. Here, we developed a system to control vacuolar fission in budding yeast. Vacuolar fragmentation promoted microautophagy but not macroautophagy. Vacuolar fragmentation caused multiple nucleus-vacuole junctions. Multiple vacuoles caused by vacuolar fragmentation also improved micronucleophagy (microautophagic degradation of a portion of the nucleus). However, vacuolar morphology did not impact nucleolar remodeling, condensation of the rDNA (rRNA gene) region, or separation of ribosomal DNA from nucleolar proteins, which is evoked by TORC1 inactivation. Thus, this study provides insights into the impacts of vacuolar/lysosomal morphology on macroautophagy and microautophagy.
Collapse
Affiliation(s)
- Tsuneyuki Takuma
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, 422-8021, Japan
| | - Takashi Ushimaru
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, 422-8021, Japan; Research Institute of Green Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, 422-8021, Japan.
| |
Collapse
|
30
|
Duarte PV, Hardenberg R, Mari M, Walter S, Reggiori F, Fröhlich F, Montoro AG, Ungermann C. The yeast LYST homolog Bph1 is a Rab5 effector and prevents Atg8 lipidation at endosomes. J Cell Sci 2022; 135:274866. [PMID: 35343566 DOI: 10.1242/jcs.259421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 03/18/2022] [Indexed: 01/18/2023] Open
Abstract
Lysosomes mediate degradation of macromolecules to their precursors for their cellular recycling. Additionally, lysosome-related organelles mediate cell type-specific functions. The Chédiak-Higashi syndrome is an autosomal, recessive disease, in which loss of the protein LYST causes defects in lysosomes and lysosome-related organelles. The molecular function of LYST, however, is largely unknown. Here, we dissected the function of the yeast LYST homolog, Bph1. We show that Bph1 is an endosomal protein, and an effector of the minor Rab5 isoform Ypt52. Strikingly, the bph1▵ mutant has lipidated Atg8 on their endosomes, which is sorted via late endosomes into the vacuole lumen under non-autophagy inducing conditions. In agreement, proteomics of bph1▵ vacuoles reveal an accumulation of Atg8, reduced flux via selective autophagy, and defective endocytosis. Additionally, bph1▵ cells have reduced autophagic flux under starvation conditions. Our observations suggest that Bph1 is a novel Rab5 effector that maintains endosomal functioning. When lost, Atg8 is lipidated at endosomes even during normal growth and ends up in the vacuole lumen. Thus, our results contribute to the understanding of the role of LYST-related proteins and associated diseases.
Collapse
Affiliation(s)
- Prado Vargas Duarte
- Osnabrück University, Department of Biology/Chemistry, Biochemistry section, Barbarastrasse 13, 49076 Osnabrück, Germany
| | - Ralph Hardenberg
- 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
| | - Stefan Walter
- Osnabrück University, Center of Cellular Nanoanalytic Osnabrück (CellNanOs), Barbarastrasse 11, 49076 Osnabrück, Germany
| | - Fulvio Reggiori
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Florian Fröhlich
- Osnabrück University, Center of Cellular Nanoanalytic Osnabrück (CellNanOs), Barbarastrasse 11, 49076 Osnabrück, Germany.,Osnabrück University, Department of Biology/Chemistry, Molecular Membrane Biology section, Barbarastrasse 13, 49076 Osnabrück, Germany
| | - Ayelén González Montoro
- Osnabrück University, Center of Cellular Nanoanalytic Osnabrück (CellNanOs), Barbarastrasse 11, 49076 Osnabrück, Germany.,Osnabrück University, Department of Biology/Chemistry, Cellular Communication Laboratory, Barbarastrasse 13, 49076 Osnabrück, Germany
| | - Christian Ungermann
- Osnabrück University, Department of Biology/Chemistry, Biochemistry section, Barbarastrasse 13, 49076 Osnabrück, Germany.,Osnabrück University, Center of Cellular Nanoanalytic Osnabrück (CellNanOs), Barbarastrasse 11, 49076 Osnabrück, Germany
| |
Collapse
|
31
|
Abstract
Lipophagy is a central cellular process for providing the cell with a readily utilized, high energy source of neutral lipids. Since its discovery over a decade ago, we are just starting to understand the molecular components that drive lipophagy, how it is activated in response to nutrient availability, and its potential as a therapeutic target in disease. In this Cell Science at a Glance article and the accompanying poster, we first provide a brief overview of the different structural and enzymatic proteins that comprise the lipid droplet (LD) proteome and reside within the limiting phospholipid monolayer of this complex organelle. We then highlight key players in the catabolic breakdown of LDs during the functionally linked lipolysis and lipophagy processes. Finally, we discuss what is currently known about macro- and micro-lipophagy based on findings in yeast, mammalian and other model systems, and how impairment of these important functions can lead to disease states.
Collapse
Affiliation(s)
- Micah B. Schott
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, 985870 Nebraska Medical Center, Omaha, NE 68198, USA
| | - Cody N. Rozeveld
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, 985870 Nebraska Medical Center, Omaha, NE 68198, USA
| | - Shaun G. Weller
- Department of Biochemistry and Molecular Biology and the Center for Digestive Diseases, Mayo Clinic, 200 1st St SW, Rochester, MN 55905, USA
| | - Mark A. McNiven
- Department of Biochemistry and Molecular Biology and the Center for Digestive Diseases, Mayo Clinic, 200 1st St SW, Rochester, MN 55905, USA
| |
Collapse
|
32
|
Liao PC, Yang EJ, Borgman T, Boldogh IR, Sing CN, Swayne TC, Pon LA. Touch and Go: Membrane Contact Sites Between Lipid Droplets and Other Organelles. Front Cell Dev Biol 2022; 10:852021. [PMID: 35281095 PMCID: PMC8908909 DOI: 10.3389/fcell.2022.852021] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 02/03/2022] [Indexed: 12/26/2022] Open
Abstract
Lipid droplets (LDs) have emerged not just as storage sites for lipids but as central regulators of metabolism and organelle quality control. These critical functions are achieved, in part, at membrane contact sites (MCS) between LDs and other organelles. MCS are sites of transfer of cellular constituents to or from LDs for energy mobilization in response to nutrient limitations, as well as LD biogenesis, expansion and autophagy. Here, we describe recent findings on the mechanisms underlying the formation and function of MCS between LDs and mitochondria, ER and lysosomes/vacuoles and the role of the cytoskeleton in promoting LD MCS through its function in LD movement and distribution in response to environmental cues.
Collapse
Affiliation(s)
- Pin-Chao Liao
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, United States
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, Taiwan
| | - Emily J. Yang
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, United States
| | - Taylor Borgman
- Institute of Human Nutrition, Columbia University Irving Medical Center, New York, NY, United States
| | - Istvan R. Boldogh
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, United States
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, United States
| | - Cierra N. Sing
- Institute of Human Nutrition, Columbia University Irving Medical Center, New York, NY, United States
| | - Theresa C. Swayne
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, United States
| | - Liza A. Pon
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, United States
- Institute of Human Nutrition, Columbia University Irving Medical Center, New York, NY, United States
- *Correspondence: Liza A. Pon,
| |
Collapse
|
33
|
Reggiori F, Molinari M. ER-phagy: mechanisms, regulation and diseases connected to the lysosomal clearance of the endoplasmic reticulum. Physiol Rev 2022; 102:1393-1448. [PMID: 35188422 PMCID: PMC9126229 DOI: 10.1152/physrev.00038.2021] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
ER-phagy (reticulo-phagy) defines the degradation of portions of the endoplasmic reticulum (ER) within lysosomes or vacuoles. It is part of the self-digestion (i.e., auto-phagic) programs recycling cytoplasmic material and organelles, which rapidly mobilize metabolites in cells confronted with nutrient shortage. Moreover, selective clearance of ER subdomains participates to the control of ER size and activity during ER stress, the re-establishment of ER homeostasis after ER stress resolution and the removal of ER parts, in which aberrant and potentially cytotoxic material has been segregated. ER-phagy relies on the individual and/or concerted activation of the ER-phagy receptors, ER peripheral or integral membrane proteins that share the presence of LC3/Atg8-binding motifs in their cytosolic domains. ER-phagy involves the physical separation of portions of the ER from the bulk ER network, and their delivery to the endolysosomal/vacuolar catabolic district. This last step is accomplished by a variety of mechanisms including macro-ER-phagy (in which ER fragments are sequestered by double-membrane autophagosomes that eventually fuse with lysosomes/vacuoles), micro-ER-phagy (in which ER fragments are directly engulfed by endosomes/lysosomes/vacuoles), or direct fusion of ER-derived vesicles with lysosomes/vacuoles. ER-phagy is dysfunctional in specific human diseases and its regulators are subverted by pathogens, highlighting its crucial role for cell and organism life.
Collapse
Affiliation(s)
- Fulvio Reggiori
- Department of Biomedical Sciences of Cells & Systems, grid.4830.fUniversity of Groningen, Netherlands
| | - Maurizio Molinari
- Protein Folding and Quality Control, grid.7722.0Institute for Research in Biomedicine, Bellinzona, Switzerland
| |
Collapse
|
34
|
Li J, Hochstrasser M. Selective microautophagy of proteasomes is initiated by ESCRT-0 and is promoted by proteasome ubiquitylation. J Cell Sci 2022; 135:274460. [PMID: 35099016 PMCID: PMC8919337 DOI: 10.1242/jcs.259393] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 01/20/2022] [Indexed: 01/18/2023] Open
Abstract
The proteasome is central to proteolysis by the ubiquitin-proteasome system under normal growth conditions but is itself degraded through macroautophagy under nutrient stress. A recently described AMP-activated protein kinase (AMPK)-regulated endosomal sorting complex required for transport (ESCRT)-dependent microautophagy pathway also regulates proteasome trafficking and degradation in low-glucose conditions in yeast. Aberrant proteasomes are more prone to microautophagy, suggesting the ESCRT system fine-tunes proteasome quality control under low-glucose stress. Here, we uncover additional features of the selective microautophagy of proteasomes in budding yeast. Genetic or pharmacological induction of aberrant proteasomes is associated with increased mono- or oligo-ubiquitylation of proteasome components, which appears to be recognized by ESCRT-0. AMPK controls this pathway in part by regulating the trafficking of ESCRT-0 to the vacuole surface, which also leads to degradation of the Vps27 subunit of ESCRT-0. The Rsp5 ubiquitin ligase contributes to proteasome subunit ubiquitylation, and multiple ubiquitin-binding elements in Vps27 are involved in their recognition. We propose that ESCRT-0 at the vacuole surface recognizes ubiquitylated proteasomes and initiates their microautophagic elimination during glucose depletion. This article has an associated First Person interview with the first author of the paper.
Collapse
Affiliation(s)
- Jianhui Li
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA,Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA,Author for correspondence ()
| |
Collapse
|
35
|
Ding X, Zhang X, Paez-Valencia J, McLoughlin F, Reyes FC, Morohashi K, Grotewold E, Vierstra RD, Otegui MS. Microautophagy Mediates Vacuolar Delivery of Storage Proteins in Maize Aleurone Cells. FRONTIERS IN PLANT SCIENCE 2022; 13:833612. [PMID: 35251104 PMCID: PMC8894768 DOI: 10.3389/fpls.2022.833612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
The molecular machinery orchestrating microautophagy, whereby eukaryotic cells sequester autophagic cargo by direct invagination of the vacuolar/lysosomal membrane, is still largely unknown, especially in plants. Here, we demonstrate microautophagy of storage proteins in the maize aleurone cells of the endosperm and analyzed proteins with potential regulatory roles in this process. Within the cereal endosperm, starchy endosperm cells accumulate storage proteins (mostly prolamins) and starch whereas the peripheral aleurone cells store oils, storage proteins, and specialized metabolites. Although both cell types synthesize prolamins, they employ different pathways for their subcellular trafficking. Starchy endosperm cells accumulate prolamins in protein bodies within the endoplasmic reticulum (ER), whereas aleurone cells deliver prolamins to vacuoles via an autophagic mechanism, which we show is by direct association of ER prolamin bodies with the tonoplast followed by engulfment via microautophagy. To identify candidate proteins regulating this process, we performed RNA-seq transcriptomic comparisons of aleurone and starchy endosperm tissues during seed development and proteomic analysis on tonoplast-enriched fractions of aleurone cells. From these datasets, we identified 10 candidate proteins with potential roles in membrane modification and/or microautophagy, including phospholipase-Dα5 and a possible EUL-like lectin. We found that both proteins increased the frequency of tonoplast invaginations when overexpressed in Arabidopsis leaf protoplasts and are highly enriched at the tonoplast surface surrounding ER protein bodies in maize aleurone cells, thus supporting their potential connections to microautophagy. Collectively, this candidate list now provides useful tools to study microautophagy in plants.
Collapse
Affiliation(s)
- Xinxin Ding
- Department of Botany, University of Wisconsin-Madison, Madison, WI, United States
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI, United States
| | - Xiaoguo Zhang
- Department of Botany, University of Wisconsin-Madison, Madison, WI, United States
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI, United States
| | - Julio Paez-Valencia
- Department of Botany, University of Wisconsin-Madison, Madison, WI, United States
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI, United States
| | - Fionn McLoughlin
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
| | - Francisca C. Reyes
- Department of Botany, University of Wisconsin-Madison, Madison, WI, United States
| | - Kengo Morohashi
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Richard D. Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
| | - Marisa S. Otegui
- Department of Botany, University of Wisconsin-Madison, Madison, WI, United States
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI, United States
| |
Collapse
|
36
|
Peselj C, Ebrahimi M, Broeskamp F, Prokisch S, Habernig L, Alvarez-Guerra I, Kohler V, Vögtle FN, Büttner S. Sterol Metabolism Differentially Contributes to Maintenance and Exit of Quiescence. Front Cell Dev Biol 2022; 10:788472. [PMID: 35237594 PMCID: PMC8882848 DOI: 10.3389/fcell.2022.788472] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 01/20/2022] [Indexed: 01/01/2023] Open
Abstract
Nutrient starvation initiates cell cycle exit and entry into quiescence, a reversible, non-proliferative state characterized by stress tolerance, longevity and large-scale remodeling of subcellular structures. Depending on the nature of the depleted nutrient, yeast cells are assumed to enter heterogeneous quiescent states with unique but mostly unexplored characteristics. Here, we show that storage and consumption of neutral lipids in lipid droplets (LDs) differentially impacts the regulation of quiescence driven by glucose or phosphate starvation. Upon prolonged glucose exhaustion, LDs were degraded in the vacuole via Atg1-dependent lipophagy. In contrast, yeast cells entering quiescence due to phosphate exhaustion massively over-accumulated LDs that clustered at the vacuolar surface but were not engulfed via lipophagy. Excessive LD biogenesis required contact formation between the endoplasmic reticulum and the vacuole at nucleus-vacuole junctions and was accompanied by a shift of the cellular lipid profile from membrane towards storage lipids, driven by a transcriptional upregulation of enzymes generating neutral lipids, in particular sterol esters. Importantly, sterol ester biogenesis was critical for long-term survival of phosphate-exhausted cells and supported rapid quiescence exit upon nutrient replenishment, but was dispensable for survival and regrowth of glucose-exhausted cells. Instead, these cells relied on de novo synthesis of sterols and fatty acids for quiescence exit and regrowth. Phosphate-exhausted cells efficiently mobilized storage lipids to support several rounds of cell division even in presence of inhibitors of fatty acid and sterol biosynthesis. In sum, our results show that neutral lipid biosynthesis and mobilization to support quiescence maintenance and exit is tailored to the respective nutrient scarcity.
Collapse
Affiliation(s)
- Carlotta Peselj
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Mahsa Ebrahimi
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Filomena Broeskamp
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Simon Prokisch
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Lukas Habernig
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Irene Alvarez-Guerra
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Verena Kohler
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - F.-Nora Vögtle
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
- Network Aging Research, Heidelberg University, Heidelberg, Germany
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Sabrina Büttner
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| |
Collapse
|
37
|
Goyal S, Segarra VA, N, Stecher AM, Truman AW, Reitzel AM, Chi RJ. Vps501, a novel vacuolar SNX-BAR protein cooperates with the SEA complex to regulate TORC1 signaling. Traffic 2022; 23. [PMID: 35098628 PMCID: PMC9305297 DOI: 10.1111/tra.12833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/05/2022] [Accepted: 01/10/2022] [Indexed: 12/01/2022]
Abstract
The sorting nexins (SNX), constitute a diverse family of molecules that play varied roles in membrane trafficking, cell signaling, membrane remodeling, organelle motility and autophagy. In particular, the SNX-BAR proteins, a SNX subfamily characterized by a C-terminal dimeric Bin/Amphiphysin/Rvs (BAR) lipid curvature domain and a conserved Phox-homology domain, are of great interest. In budding yeast, many SNX-BARs proteins have well-characterized endo-vacuolar trafficking roles. Phylogenetic analyses allowed us to identify an additional SNX-BAR protein, Vps501, with a novel endo-vacuolar role. We report that Vps501 uniquely localizes to the vacuolar membrane and has physical and genetic interactions with the SEA complex to regulate TORC1 inactivation. We found cells displayed a severe deficiency in starvation-induced/nonselective autophagy only when SEA complex subunits are ablated in combination with Vps501, indicating a cooperative role with the SEA complex during TORC1 signaling during autophagy induction. Additionally, we found the SEACIT complex becomes destabilized in vps501Δsea1Δ cells, which resulted in aberrant endosomal TORC1 activity and subsequent Atg13 hyperphosphorylation. We have also discovered that the vacuolar localization of Vps501 is dependent upon a direct interaction with Sea1 and a unique lipid binding specificity that is also required for its function. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Shreya Goyal
- Department of Biological SciencesUniversity of North CarolinaCharlotteNorth CarolinaUSA
| | | | - Nitika
- Department of Biological SciencesUniversity of North CarolinaCharlotteNorth CarolinaUSA
| | - Aaron M. Stecher
- Department of Biological SciencesUniversity of North CarolinaCharlotteNorth CarolinaUSA
| | - Andrew W. Truman
- Department of Biological SciencesUniversity of North CarolinaCharlotteNorth CarolinaUSA
| | - Adam M. Reitzel
- Department of Biological SciencesUniversity of North CarolinaCharlotteNorth CarolinaUSA
| | - Richard J. Chi
- Department of Biological SciencesUniversity of North CarolinaCharlotteNorth CarolinaUSA
| |
Collapse
|
38
|
Degradation of nuclear components via different autophagy pathways. Trends Cell Biol 2022; 32:574-584. [DOI: 10.1016/j.tcb.2021.12.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/21/2021] [Accepted: 12/23/2021] [Indexed: 12/21/2022]
|
39
|
Liao PC, Garcia EJ, Tan G, Tsang CA, Pon LA. Roles for L o microdomains and ESCRT in ER stress-induced lipid droplet microautophagy in budding yeast. Mol Biol Cell 2021; 32:br12. [PMID: 34668753 PMCID: PMC8694086 DOI: 10.1091/mbc.e21-04-0179] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Microlipophagy (µLP), degradation of lipid droplets (LDs) by microautophagy, occurs by autophagosome-independent direct uptake of LDs at lysosomes/vacuoles in response to nutrient limitations and ER stressors in Saccharomyces cerevisiae. In nutrient-limited yeast, liquid-ordered (Lo) microdomains, sterol-rich raftlike regions in vacuolar membranes, are sites of membrane invagination during LD uptake. The endosome sorting complex required for transport (ESCRT) is required for sterol transport during Lo formation under these conditions. However, ESCRT has been implicated in mediating membrane invagination during µLP induced by ER stressors or the diauxic shift from glycolysis- to respiration-driven growth. Here we report that ER stress induced by lipid imbalance and other stressors induces Lo microdomain formation. This process is ESCRT independent and dependent on Niemann-Pick type C sterol transfer proteins. Inhibition of ESCRT or Lo microdomain formation partially inhibits lipid imbalance-induced µLP, while inhibition of both blocks this µLP. Finally, although the ER stressors dithiothreitol or tunicamycin induce Lo microdomains, µLP in response to these stressors is ESCRT dependent and Lo microdomain independent. Our findings reveal that Lo microdomain formation is a yeast stress response, and stress-induced Lo microdomain formation occurs by stressor-specific mechanisms. Moreover, ESCRT and Lo microdomains play functionally distinct roles in LD uptake during stress-induced µLP.
Collapse
Affiliation(s)
- Pin-Chao Liao
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032
| | - Enrique J Garcia
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032
| | - Gary Tan
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032
| | - Catherine A Tsang
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032
| | - Liza A Pon
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032
| |
Collapse
|
40
|
Over Fifty Years of Life, Death, and Cannibalism: A Historical Recollection of Apoptosis and Autophagy. Int J Mol Sci 2021; 22:ijms222212466. [PMID: 34830349 PMCID: PMC8618802 DOI: 10.3390/ijms222212466] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 01/18/2023] Open
Abstract
Research in biomedical sciences has changed dramatically over the past fifty years. There is no doubt that the discovery of apoptosis and autophagy as two highly synchronized and regulated mechanisms in cellular homeostasis are among the most important discoveries in these decades. Along with the advancement in molecular biology, identifying the genetic players in apoptosis and autophagy has shed light on our understanding of their function in physiological and pathological conditions. In this review, we first describe the history of key discoveries in apoptosis with a molecular insight and continue with apoptosis pathways and their regulation. We touch upon the role of apoptosis in human health and its malfunction in several diseases. We discuss the path to the morphological and molecular discovery of autophagy. Moreover, we dive deep into the precise regulation of autophagy and recent findings from basic research to clinical applications of autophagy modulation in human health and illnesses and the available therapies for many diseases caused by impaired autophagy. We conclude with the exciting crosstalk between apoptosis and autophagy, from the early discoveries to recent findings.
Collapse
|
41
|
Tasnin MN, Ito K, Katsuta H, Takuma T, Sharmin T, Ushimaru T. The PI3 Kinase Complex II-PI3P-Vps27 Axis on Vacuolar Membranes is Critical for Microautophagy Induction and Nutrient Stress Adaptation. J Mol Biol 2021; 434:167360. [PMID: 34798133 DOI: 10.1016/j.jmb.2021.167360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 12/27/2022]
Abstract
Phosphatidylinositol 3-phosphate (PI3P), a scaffold of membrane-associated proteins required for diverse cellular events, is produced by Vps34-containing phosphatidylinositol 3-kinase (PI3K). PI3K complex I (PI3KCI)-generated PI3P is required for macroautophagy, whereas PI3K complex II (PI3KCII)-generated PI3P is required for endosomal sorting complex required for transport (ESCRT)-mediated multi-vesicular body (MVB) formation in late endosomes. ESCRT also promotes vacuolar membrane remodeling in microautophagy after nutrient starvation and inactivation of target of rapamycin complex 1 (TORC1) protein kinase in budding yeast. Whereas PI3KCI and macroautophagy are critical for the nutrient starvation response, the physiological roles of PI3KCII and microautophagy during starvation are largely unknown. Here, we showed that PI3KCII-produced PI3P on vacuolar membranes is required for microautophagy induction and survival in nutrient-stressed conditions. PI3KCII is required for Vps27 (an ESCRT-0 component) recruitment and ESCRT-0 complex formation on vacuolar surfaces after TORC1 inactivation. Forced recruitment of Vps27 onto vacuolar membranes rescued the defect in microautophagy induction in PI3KCII-deficient cells, indicating that a critical role of PI3P on microautophagy induction is Vps27 recruitment onto vacuolar surfaces. Finally, vacuolar membrane-associated Vps27 was able to recover survival during nutrient starvation in cells lacking PI3KCII or Vps27. This study revealed that the PI3KCII-PI3P-Vps27 axis on vacuolar membranes is critical for ESCRT-mediated microautophagy induction and nutrient stress adaptation.
Collapse
Affiliation(s)
- Most Naoshia Tasnin
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Kisara Ito
- Department of Bioscience, Faculty of Science, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Haruko Katsuta
- Course of Biological Science, Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Tsuneyuki Takuma
- Course of Biological Science, Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Tasnuva Sharmin
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Takashi Ushimaru
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan; Department of Bioscience, Faculty of Science, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan; Course of Biological Science, Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan.
| |
Collapse
|
42
|
Isono E. ESCRT Is a Great Sealer: Non-Endosomal Function of the ESCRT Machinery in Membrane Repair and Autophagy. PLANT & CELL PHYSIOLOGY 2021; 62:766-774. [PMID: 33768242 DOI: 10.1093/pcp/pcab045] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/18/2021] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
Components of the endosomal sorting complex required for transport (ESCRTs) were first identified in a genetic screen in budding yeast as factors interfering with vacuolar protein sorting. In the last three decades, intensive studies have revealed the subunit composition of ESCRT-0, ESCRT-I, ESCRT-II, ESCRT-III, their structure, the assembling mechanisms and their molecular and physiological functions. In plants, ESCRTs are essential for development, growth and stress responses. ESCRTs are best known for their function in endosomal trafficking, during which they are required for sorting ubiquitylated membrane proteins into intraluminal vesicles (ILVs) of multivesicular endosomes (MVEs). The formation of ILVs requires the function of ESCRT-III, which has been shown to mediate the membrane scission. Although the function of plant ESCRTs has been predominantly discussed in the context of endosomal trafficking, recent studies in other model organisms revealed a versatile role of ESCRTs in diverse cellular events with broad physiological implications. The non-endosomal functions of ESCRTs include cytokinesis, viral budding, autophagy, nuclear envelope reformation and membrane repair, although many of these have not yet been studied in plants. In this review, recent findings on non-endosomal ESCRT functions in plant, yeast and animals are highlighted and discussed.
Collapse
Affiliation(s)
- Erika Isono
- Department of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz 78464, Germany
| |
Collapse
|
43
|
Molecular mechanisms of mammalian autophagy. Biochem J 2021; 478:3395-3421. [PMID: 34554214 DOI: 10.1042/bcj20210314] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/19/2021] [Accepted: 07/28/2021] [Indexed: 02/06/2023]
Abstract
The ubiquitin-proteasome pathway (UPP) and autophagy play integral roles in cellular homeostasis. As part of their normal life cycle, most proteins undergo ubiquitination for some form of redistribution, localization and/or functional modulation. However, ubiquitination is also important to the UPP and several autophagic processes. The UPP is initiated after specific lysine residues of short-lived, damaged or misfolded proteins are conjugated to ubiquitin, which targets these proteins to proteasomes. Autophagy is the endosomal/lysosomal-dependent degradation of organelles, invading microbes, zymogen granules and macromolecules such as protein, carbohydrates and lipids. Autophagy can be broadly separated into three distinct subtypes termed microautophagy, chaperone-mediated autophagy and macroautophagy. Although autophagy was once thought of as non-selective bulk degradation, advancements in the field have led to the discovery of several selective forms of autophagy. Here, we focus on the mechanisms of primary and selective mammalian autophagy pathways and highlight the current knowledge gaps in these molecular pathways.
Collapse
|
44
|
Abstract
Lipid droplets (LDs) are endoplasmic reticulum-derived organelles that consist of a core of neutral lipids encircled by a phospholipid monolayer decorated with proteins. As hubs of cellular lipid and energy metabolism, LDs are inherently involved in the etiology of prevalent metabolic diseases such as obesity and nonalcoholic fatty liver disease. The functions of LDs are regulated by a unique set of associated proteins, the LD proteome, which includes integral membrane and peripheral proteins. These proteins control key activities of LDs such as triacylglycerol synthesis and breakdown, nutrient sensing and signal integration, and interactions with other organelles. Here we review the mechanisms that regulate the composition of the LD proteome, such as pathways that mediate selective and bulk LD protein degradation and potential connections between LDs and cellular protein quality control.
Collapse
Affiliation(s)
- Melissa A Roberts
- Department of Molecular and Cell Biology and Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California 94720, USA;
| | - James A Olzmann
- Department of Molecular and Cell Biology and Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California 94720, USA; .,Chan Zuckerberg Biohub, San Francisco, California 94158, USA
| |
Collapse
|
45
|
Abstract
Lysosomes (vacuoles in yeast) are master regulators of metabolism and protein turnover, but how they degrade their own resident proteins is unclear. Recently, multiple models have been proposed explaining yeast vacuole protein sorting, but the role of the ESCRT pathway was unclear. In this JCB issue, work from Yang et al. (https://doi.org/10.1083/jcb.202012104) highlights how the ESCRT pathway localizes to the vacuole surface to execute protein sorting of its resident proteins.
Collapse
Affiliation(s)
- W Mike Henne
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX
| |
Collapse
|
46
|
Rahman MA, Kumar R, Sanchez E, Nazarko TY. Lipid Droplets and Their Autophagic Turnover via the Raft-Like Vacuolar Microdomains. Int J Mol Sci 2021; 22:8144. [PMID: 34360917 PMCID: PMC8348048 DOI: 10.3390/ijms22158144] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 01/01/2023] Open
Abstract
Although once perceived as inert structures that merely serve for lipid storage, lipid droplets (LDs) have proven to be the dynamic organelles that hold many cellular functions. The LDs' basic structure of a hydrophobic core consisting of neutral lipids and enclosed in a phospholipid monolayer allows for quick lipid accessibility for intracellular energy and membrane production. Whereas formed at the peripheral and perinuclear endoplasmic reticulum, LDs are degraded either in the cytosol by lipolysis or in the vacuoles/lysosomes by autophagy. Autophagy is a regulated breakdown of dysfunctional, damaged, or surplus cellular components. The selective autophagy of LDs is called lipophagy. Here, we review LDs and their degradation by lipophagy in yeast, which proceeds via the micrometer-scale raft-like lipid domains in the vacuolar membrane. These vacuolar microdomains form during nutrient deprivation and facilitate internalization of LDs via the vacuolar membrane invagination and scission. The resultant intra-vacuolar autophagic bodies with LDs inside are broken down by vacuolar lipases and proteases. This type of lipophagy is called microlipophagy as it resembles microautophagy, the type of autophagy when substrates are sequestered right at the surface of a lytic compartment. Yeast microlipophagy via the raft-like vacuolar microdomains is a great model system to study the role of lipid domains in microautophagic pathways.
Collapse
Affiliation(s)
- Muhammad Arifur Rahman
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA; (M.A.R.); (E.S.)
| | - Ravinder Kumar
- Department of Obstetrics, Gynecology and Reproductive Science, University of California, San Francisco, CA 94143, USA;
| | - Enrique Sanchez
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA; (M.A.R.); (E.S.)
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Taras Y. Nazarko
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA; (M.A.R.); (E.S.)
| |
Collapse
|
47
|
Zhang W, Yang X, Chen L, Liu YY, Venkatarangan V, Reist L, Hanson P, Xu H, Wang Y, Li M. A conserved ubiquitin- and ESCRT-dependent pathway internalizes human lysosomal membrane proteins for degradation. PLoS Biol 2021; 19:e3001361. [PMID: 34297722 PMCID: PMC8337054 DOI: 10.1371/journal.pbio.3001361] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 08/04/2021] [Accepted: 07/09/2021] [Indexed: 12/15/2022] Open
Abstract
The lysosome is an essential organelle to recycle cellular materials and maintain nutrient homeostasis, but the mechanism to down-regulate its membrane proteins is poorly understood. In this study, we performed a cycloheximide (CHX) chase assay to measure the half-lives of approximately 30 human lysosomal membrane proteins (LMPs) and identified RNF152 and LAPTM4A as short-lived membrane proteins. The degradation of both proteins is ubiquitin dependent. RNF152 is a transmembrane E3 ligase that ubiquitinates itself, whereas LAPTM4A uses its carboxyl-terminal PY motifs to recruit NEDD4-1 for ubiquitination. After ubiquitination, they are internalized into the lysosome lumen by the endosomal sorting complexes required for transport (ESCRT) machinery for degradation. Strikingly, when ectopically expressed in budding yeast, human RNF152 is still degraded by the vacuole (yeast lysosome) in an ESCRT-dependent manner. Thus, our study uncovered a conserved mechanism to down-regulate lysosome membrane proteins.
Collapse
Affiliation(s)
- Weichao Zhang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Xi Yang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Liang Chen
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Yun-Yu Liu
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Varsha Venkatarangan
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Lucas Reist
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Phyllis Hanson
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Haoxing Xu
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Yanzhuang Wang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Ming Li
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
| |
Collapse
|
48
|
Lemus L, Matić Z, Gal L, Fadel A, Schuldiner M, Goder V. Post-ER degradation of misfolded GPI-anchored proteins is linked with microautophagy. Curr Biol 2021; 31:4025-4037.e5. [PMID: 34314677 DOI: 10.1016/j.cub.2021.06.078] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/07/2021] [Accepted: 06/25/2021] [Indexed: 01/08/2023]
Abstract
Glycosylphosphatidylinositol-anchored proteins (GPI-APs) are membrane-conjugated cell-surface proteins with diverse structural, developmental, and signaling functions and clinical relevance. Typically, after biosynthesis and attachment to the preassembled GPI anchor, GPI-APs rapidly leave the endoplasmic reticulum (ER) and rely on post-ER quality control. Terminally misfolded GPI-APs end up inside the vacuole/lysosome for degradation, but their trafficking itinerary to this organelle and the processes linked to their uptake by the vacuole/lysosome remain uncharacterized. In a yeast mutant that is lacking Pep4, a key vacuolar protease, several misfolded model GPI-APs accumulated in the vacuolar membrane. In the same mutant, macroautophagy and the multi-vesicular body (MVB) pathway were intact, hinting at a hitherto-unknown trafficking pathway for the degradation of misfolded GPI-APs. To unravel it, we used a genome-wide screen coupled to high-throughput fluorescence microscopy and followed the fate of the misfolded GPI-AP: Gas1∗. We found that components of the early secretory and endocytic pathways are involved in its targeting to the vacuole and that vacuolar transporter chaperones (VTCs), with roles in microautophagy, negatively affect the vacuolar uptake of Gas1∗. In support, we demonstrate that Gas1∗ internalizes from vacuolar membranes into membrane-bound intravacuolar vesicles prior to degradation. Our data link post-ER degradation with microautophagy.
Collapse
Affiliation(s)
- Leticia Lemus
- Department of Genetics, University of Seville, Ave Reina Mercedes, 6, 41012 Seville, Spain.
| | - Zrinka Matić
- Department of Genetics, University of Seville, Ave Reina Mercedes, 6, 41012 Seville, Spain
| | - Lihi Gal
- Department of Molecular Genetics, Meyer Bldg. Room 122, Weizmann Institute of Sciences, 76100 Rehovot, Israel
| | - Amir Fadel
- Department of Molecular Genetics, Meyer Bldg. Room 122, Weizmann Institute of Sciences, 76100 Rehovot, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, Meyer Bldg. Room 122, Weizmann Institute of Sciences, 76100 Rehovot, Israel
| | - Veit Goder
- Department of Genetics, University of Seville, Ave Reina Mercedes, 6, 41012 Seville, Spain.
| |
Collapse
|
49
|
Lemke MD, Fisher KE, Kozlowska MA, Tano DW, Woodson JD. The core autophagy machinery is not required for chloroplast singlet oxygen-mediated cell death in the Arabidopsis thaliana plastid ferrochelatase two mutant. BMC PLANT BIOLOGY 2021; 21:342. [PMID: 34281507 PMCID: PMC8290626 DOI: 10.1186/s12870-021-03119-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 06/22/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Chloroplasts respond to stress and changes in the environment by producing reactive oxygen species (ROS) that have specific signaling abilities. The ROS singlet oxygen (1O2) is unique in that it can signal to initiate cellular degradation including the selective degradation of damaged chloroplasts. This chloroplast quality control pathway can be monitored in the Arabidopsis thaliana mutant plastid ferrochelatase two (fc2) that conditionally accumulates chloroplast 1O2 under diurnal light cycling conditions leading to rapid chloroplast degradation and eventual cell death. The cellular machinery involved in such degradation, however, remains unknown. Recently, it was demonstrated that whole damaged chloroplasts can be transported to the central vacuole via a process requiring autophagosomes and core components of the autophagy machinery. The relationship between this process, referred to as chlorophagy, and the degradation of 1O2-stressed chloroplasts and cells has remained unexplored. RESULTS To further understand 1O2-induced cellular degradation and determine what role autophagy may play, the expression of autophagy-related genes was monitored in 1O2-stressed fc2 seedlings and found to be induced. Although autophagosomes were present in fc2 cells, they did not associate with chloroplasts during 1O2 stress. Mutations affecting the core autophagy machinery (atg5, atg7, and atg10) were unable to suppress 1O2-induced cell death or chloroplast protrusion into the central vacuole, suggesting autophagosome formation is dispensable for such 1O2-mediated cellular degradation. However, both atg5 and atg7 led to specific defects in chloroplast ultrastructure and photosynthetic efficiencies, suggesting core autophagy machinery is involved in protecting chloroplasts from photo-oxidative damage. Finally, genes predicted to be involved in microautophagy were shown to be induced in stressed fc2 seedlings, indicating a possible role for an alternate form of autophagy in the dismantling of 1O2-damaged chloroplasts. CONCLUSIONS Our results support the hypothesis that 1O2-dependent cell death is independent from autophagosome formation, canonical autophagy, and chlorophagy. Furthermore, autophagosome-independent microautophagy may be involved in degrading 1O2-damaged chloroplasts. At the same time, canonical autophagy may still play a role in protecting chloroplasts from 1O2-induced photo-oxidative stress. Together, this suggests chloroplast function and degradation is a complex process utilizing multiple autophagy and degradation machineries, possibly depending on the type of stress or damage incurred.
Collapse
Affiliation(s)
- Matthew D. Lemke
- The School of Plant Sciences, University of Arizona, Tucson, AZ 85721-0036 USA
| | - Karen E. Fisher
- The School of Plant Sciences, University of Arizona, Tucson, AZ 85721-0036 USA
| | - Marta A. Kozlowska
- The School of Plant Sciences, University of Arizona, Tucson, AZ 85721-0036 USA
| | - David W. Tano
- The School of Plant Sciences, University of Arizona, Tucson, AZ 85721-0036 USA
| | - Jesse D. Woodson
- The School of Plant Sciences, University of Arizona, Tucson, AZ 85721-0036 USA
| |
Collapse
|
50
|
Wu Z, Xu H, Liu J, Zhou F, Liang Y. The ESCRT-III complex contributes to macromitophagy in yeast. Traffic 2021; 22:258-273. [PMID: 34089296 DOI: 10.1111/tra.12805] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 05/29/2021] [Accepted: 05/31/2021] [Indexed: 12/19/2022]
Abstract
Mitochondria play important roles in energy generation and homeostasis maintenance in eukaryotic cells. The damaged or superfluous mitochondria can be nonselectively or selectively removed through the autophagy/lysosome pathway, which was referred as mitophagy. According to the molecular machinery for degrading mitochondria, the selectively removed mitochondria can occur through macromitophagy or micromitophagy. In this study, we show that the endosomal sorting complex required for transport III (ESCRT-III) in budding yeast regulates macromitophagy induced by nitrogen starvation, but not by the post-logarithmic phase growth in lactate medium by monitoring a mitochondrial marker, Om45. Firstly, loss of ESCRT-III subunit Snf7 or Vps4-Vta1 complex subunit Vps4, two representative subunits of the ESCRT complex, suppresses the delivery and degradation of Om45-GFP to vacuoles. Secondly, we show that the mitochondrial marker Om45 and mitophagy receptor Atg32 accumulate on autophagosomes marked with Atg8 (mitophagosomes, MPs) in ESCRT mutants. Moreover, the protease-protection assay indicates that Snf7 and Vps4 are involved in MP closure. Finally, Snf7 interacts with Atg11, which was detected by two ways, glutathione-S-transferase (GST) pulldown and bimolecular fluorescence complementation (BiFC) assay, and this BiFC interaction happens on mitochondrial reticulum. Therefore, we proposed that the ESCRT-III machinery mediates nitrogen starvation-induced macromitophagy by the interaction between Snf7 and Atg11 so that Snf7 is recruited to Atg32-marked MPs by the known Atg11-Atg32 interaction to seal them. These results reveal that the ESCRT-III complex plays a new role in yeast on macromitophagy.
Collapse
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
| |
Collapse
|