1
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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.
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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.
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2
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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.
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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.
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3
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Arines FM, Wielenga A, Henn D, Burata OE, Garcia FN, Stockbridge RB, Li M. Lysosomal membrane transporter purification and reconstitution for functional studies. Mol Biol Cell 2024; 35:ar28. [PMID: 38117592 PMCID: PMC10916862 DOI: 10.1091/mbc.e23-06-0259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 11/20/2023] [Accepted: 12/13/2023] [Indexed: 12/22/2023] Open
Abstract
Lysosomes achieve their function through numerous transporters that import or export nutrients across their membrane. However, technical challenges in membrane protein overexpression, purification, and reconstitution hinder our understanding of lysosome transporter function. Here, we developed a platform to overexpress and purify the putative lysine transporter Ypq1 using a constitutive overexpression system in protease- and ubiquitination-deficient yeast vacuoles. Using this method, we purified and reconstituted Ypq1 into proteoliposomes and showed lysine transport function, supporting its role as a basic amino acid transporter on the vacuole membrane. We also found that the absence of lysine destabilizes purified Ypq1 and causes it to aggregate, consistent with its propensity to be downregulated in vivo upon lysine starvation. Our approach may be useful for the biochemical characterization of many transporters and membrane proteins to understand organellar transport and regulation.
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Affiliation(s)
- Felichi Mae Arines
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Aleksander Wielenga
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Danielle Henn
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Olive E. Burata
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Francisco Narro Garcia
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Randy B. Stockbridge
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Ming Li
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
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4
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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.
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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
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5
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Sakamaki JI, Mizushima N. Ubiquitination of non-protein substrates. Trends Cell Biol 2023; 33:991-1003. [PMID: 37120410 DOI: 10.1016/j.tcb.2023.03.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 05/01/2023]
Abstract
The covalent attachment of ubiquitin is a common regulatory mechanism in various proteins. Although it has long been thought that the substrates of ubiquitination are limited to proteins, recent studies have changed this view: ubiquitin can be conjugated to lipids, sugars, and nucleotides. Ubiquitin is linked to these substrates by the action of different classes of ubiquitin ligases that have distinct catalytic mechanisms. Ubiquitination of non-protein substrates likely serves as a signal for the recruitment of other proteins to bring about specific effects. These discoveries have expanded the concept of ubiquitination and have advanced our insight into the biology and chemistry of this well-established modification process. In this review we describe the molecular mechanisms and roles of non-protein ubiquitination and discuss the current limitations.
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Affiliation(s)
- Jun-Ichi Sakamaki
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan.
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6
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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.
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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
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7
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Arines FM, Wielenga A, Burata OE, Garcia FN, Stockbridge RB, Li M. Lysosome transporter purification and reconstitution identifies Ypq1 pH-gated lysine transport and regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.31.535002. [PMID: 37034749 PMCID: PMC10081341 DOI: 10.1101/2023.03.31.535002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
Lysosomes achieve their function through numerous transporters that import or export nutrients across their membrane. However, technical challenges in membrane protein overexpression, purification, and reconstitution hinder our understanding of lysosome transporter function. Here, we developed a platform to overexpress and purify the putative lysine transporter Ypq1 using a constitutive overexpression system in protease- and ubiquitination-deficient yeast vacuoles. Using this method, we purified and reconstituted Ypq1 into proteoliposomes and showed lysine transport function, supporting its role as a basic amino acid transporter on the vacuole membrane. We also found that the absence of lysine destabilizes purified Ypq1 and causes it to aggregate, consistent with its propensity to be downregulated in vivo upon lysine starvation. Our approach may be useful for the biochemical characterization of many transporters and membrane proteins to understand organellar transport and regulation.
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Affiliation(s)
- Felichi Mae Arines
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Aleksander Wielenga
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Olive E. Burata
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Francisco Narro Garcia
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Randy B. Stockbridge
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ming Li
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
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8
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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: 129] [Impact Index Per Article: 129.0] [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.
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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.
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9
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Fatty Acyl Coenzyme A Synthetase Fat1p Regulates Vacuolar Structure and Stationary-Phase Lipophagy in Saccharomyces cerevisiae. Microbiol Spectr 2023; 11:e0462522. [PMID: 36598223 PMCID: PMC9927365 DOI: 10.1128/spectrum.04625-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
During yeast stationary phase, a single spherical vacuole (lysosome) is created by the fusion of several small ones. Moreover, the vacuolar membrane is reconstructed into two distinct microdomains. Little is known, however, about how cells maintain vacuolar shape or regulate their microdomains. Here, we show that Fat1p, a fatty acyl coenzyme A (acyl-CoA) synthetase and fatty acid transporter, and not the synthetases Faa1p and Faa4p, is essential for vacuolar shape preservation, the development of vacuolar microdomains, and cell survival in stationary phase of the yeast Saccharomyces cerevisiae. Furthermore, Fat1p negatively regulates general autophagy in both log- and stationary-phase cells. In contrast, Fat1p promotes lipophagy, as the absence of FAT1 limits the entry of lipid droplets into the vacuole and reduces the degradation of liquid droplet (LD) surface proteins. Notably, supplementing with unsaturated fatty acids or overexpressing the desaturase Ole1p can reverse all aberrant phenotypes caused by FAT1 deficiency. We propose that Fat1p regulates stationary phase vacuolar morphology, microdomain differentiation, general autophagy, and lipophagy by controlling the degree of fatty acid saturation in membrane lipids. IMPORTANCE The ability to sense environmental changes and adjust the levels of cellular metabolism is critical for cell viability. Autophagy is a recycling process that makes the most of already-existing energy resources, and the vacuole/lysosome is the ultimate autophagic processing site in cells. Lipophagy is an autophagic process to select degrading lipid droplets. In yeast cells in stationary phase, vacuoles fuse and remodel their membranes to create a single spherical vacuole with two distinct membrane microdomains, which are required for yeast lipophagy. In this study, we discovered that Fat1p was capable of rapidly responding to changes in nutritional status and preserving cell survival by regulating membrane lipid saturation to maintain proper vacuolar morphology and the level of lipophagy in the yeast S. cerevisiae. Our findings shed light on how cells maintain vacuolar structure and promote the differentiation of vacuole surface microdomains for stationary-phase lipophagy.
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10
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Shi G, Chiramel AI, Li T, Lai KK, Kenney AD, Zani A, Eddy AC, Majdoul S, Zhang L, Dempsey T, Beare PA, Kar S, Yewdell JW, Best SM, Yount JS, Compton AA. Rapalogs downmodulate intrinsic immunity and promote cell entry of SARS-CoV-2. J Clin Invest 2022; 132:e160766. [PMID: 36264642 PMCID: PMC9753997 DOI: 10.1172/jci160766] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 10/18/2022] [Indexed: 12/24/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in immunocompromised individuals is associated with prolonged virus shedding and evolution of viral variants. Rapamycin and its analogs (rapalogs, including everolimus, temsirolimus, and ridaforolimus) are FDA approved as mTOR inhibitors for the treatment of human diseases, including cancer and autoimmunity. Rapalog use is commonly associated with an increased susceptibility to infection, which has been traditionally explained by impaired adaptive immunity. Here, we show that exposure to rapalogs increased susceptibility to SARS-CoV-2 infection in tissue culture and in immunologically naive rodents by antagonizing the cell-intrinsic immune response. We identified 1 rapalog (ridaforolimus) that was less potent in this regard and demonstrated that rapalogs promote spike-mediated entry into cells, by triggering the degradation of the antiviral proteins IFITM2 and IFITM3 via an endolysosomal remodeling program called microautophagy. Rapalogs that increased virus entry inhibited mTOR-mediated phosphorylation of the transcription factor TFEB, which facilitated its nuclear translocation and triggered microautophagy. In rodent models of infection, injection of rapamycin prior to and after virus exposure resulted in elevated SARS-CoV-2 replication and exacerbated viral disease, while ridaforolimus had milder effects. Overall, our findings indicate that preexisting use of certain rapalogs may elevate host susceptibility to SARS-CoV-2 infection and disease by activating lysosome-mediated suppression of intrinsic immunity.
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Affiliation(s)
- Guoli Shi
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute (NCI), NIH, Frederick, Maryland, USA
| | - Abhilash I. Chiramel
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Hamilton, Montana, USA
| | - Tiansheng Li
- Laboratory of Viral Diseases, NIAID, NIH, Bethesda, Maryland, USA
| | - Kin Kui Lai
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute (NCI), NIH, Frederick, Maryland, USA
| | - Adam D. Kenney
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
| | - Ashley Zani
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
| | - Adrian C. Eddy
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
| | - Saliha Majdoul
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute (NCI), NIH, Frederick, Maryland, USA
| | - Lizhi Zhang
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
| | - Tirhas Dempsey
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute (NCI), NIH, Frederick, Maryland, USA
| | - Paul A. Beare
- Laboratory of Bacteriology, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, Montana, USA
| | | | | | - Sonja M. Best
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Hamilton, Montana, USA
| | - Jacob S. Yount
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
| | - Alex A. Compton
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute (NCI), NIH, Frederick, Maryland, USA
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Golden CK, Kazmirchuk TDD, McNally EK, El eissawi M, Gokbayrak ZD, Richard JD, Brett CL. A two-tiered system for selective receptor and transporter protein degradation. PLoS Genet 2022; 18:e1010446. [PMID: 36215320 PMCID: PMC9584418 DOI: 10.1371/journal.pgen.1010446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 10/20/2022] [Accepted: 09/26/2022] [Indexed: 11/06/2022] Open
Abstract
Diverse physiology relies on receptor and transporter protein down–regulation and degradation mediated by ESCRTs. Loss–of–function mutations in human ESCRT genes linked to cancers and neurological disorders are thought to block this process. However, when homologous mutations are introduced into model organisms, cells thrive and degradation persists, suggesting other mechanisms compensate. To better understand this secondary process, we studied degradation of transporter (Mup1) or receptor (Ste3) proteins when ESCRT genes (VPS27, VPS36) are deleted in Saccharomyces cerevisiae using live-cell imaging and organelle biochemistry. We find that endocytosis remains intact, but internalized proteins aberrantly accumulate on vacuolar lysosome membranes within cells. Here they are sorted for degradation by the intralumenal fragment (ILF) pathway, constitutively or when triggered by substrates, misfolding or TOR activation in vivo and in vitro. Thus, the ILF pathway functions as fail–safe layer of defense when ESCRTs disregard their clients, representing a two–tiered system that ensures degradation of surface polytopic proteins. Receptor, transporter and channel proteins on the plasma membranes (or surface) of all cells mediate extensive physiology. This requires precise control of their numbers, and damaged copies must be removed to prevent cytotoxicity. Their downregulation and degradation is mediated by lysosomes after endocytosis and entry into the multi–vesicular body (MVB) pathway which depends on ESCRTs (Endosomal Sorting Complexes Required for Transport). Loss–of–function mutations in ESCRT genes are linked to cancers and neurological disease, but cells survive and some proteins continue to be degraded. Herein, we use baker’s yeast (Saccharomyces cerevisiae) as model to better understand how surface proteins are degraded in cells missing ESCRT genes. Using fluorescence microscopy matched with biochemical and genetic approaches, we find that the methionine transporter Mup1 and G-protein coupled receptor Ste3 continue to be degraded when two ESCRT genes are deleted. They are endocytosed but rerouted to membranes of vacuolar lysosomes after stimuli are applied to trigger their downregulation. Here they are sorted into intralumenal fragments and degraded by acid hydrolases within vacuolar lysosomes upon homotypic membrane fusion. We propose that this intralumenal fragment (ILF) pathway functions as a secondary mechanism to degrade surface proteins with the canonical MVB pathway is disrupted.
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Affiliation(s)
| | | | - Erin Kate McNally
- Department of Biology, Concordia University, Montreal, Quebec, Canada
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12
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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.
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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.
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13
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Shi G, Chiramel AI, Li T, Lai KK, Kenney AD, Zani A, Eddy A, Majdoul S, Zhang L, Dempsey T, Beare PA, Kar S, Yewdell JW, Best SM, Yount JS, Compton AA. Rapalogs downmodulate intrinsic immunity and promote cell entry of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2021.04.15.440067. [PMID: 33880473 PMCID: PMC8057238 DOI: 10.1101/2021.04.15.440067] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
SARS-CoV-2 infection in immunocompromised individuals is associated with prolonged virus shedding and evolution of viral variants. Rapamycin and its analogs (rapalogs, including everolimus, temsirolimus, and ridaforolimus) are FDA-approved as mTOR inhibitors for the treatment of human diseases, including cancer and autoimmunity. Rapalog use is commonly associated with increased susceptibility to infection, which has been traditionally explained by impaired adaptive immunity. Here, we show that exposure to rapalogs increases susceptibility to SARS-CoV-2 infection in tissue culture and in immunologically naive rodents by antagonizing the cell-intrinsic immune response. By identifying one rapalog (ridaforolimus) that is less potent in this regard, we demonstrate that rapalogs promote Spike-mediated entry into cells by triggering the degradation of antiviral proteins IFITM2 and IFITM3 via an endolysosomal remodeling program called microautophagy. Rapalogs that increase virus entry inhibit the mTOR-mediated phosphorylation of the transcription factor TFEB, which facilitates its nuclear translocation and triggers microautophagy. In rodent models of infection, injection of rapamycin prior to and after virus exposure resulted in elevated SARS-CoV-2 replication and exacerbated viral disease, while ridaforolimus had milder effects. Overall, our findings indicate that preexisting use of certain rapalogs may elevate host susceptibility to SARS-CoV-2 infection and disease by activating lysosome-mediated suppression of intrinsic immunity.
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Affiliation(s)
- Guoli Shi
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Abhilash I. Chiramel
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, Hamilton, MT, USA
| | - Tiansheng Li
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Kin Kui Lai
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Adam D. Kenney
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
| | - Ashley Zani
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
| | - Adrian Eddy
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
| | - Saliha Majdoul
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Lizhi Zhang
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
| | - Tirhas Dempsey
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Paul A. Beare
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, Hamilton, MT, USA
| | | | - Jonathan W. Yewdell
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Sonja M. Best
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, Hamilton, MT, USA
| | - Jacob S. Yount
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
| | - Alex A. Compton
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
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14
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Sakamaki JI, Ode KL, Kurikawa Y, Ueda HR, Yamamoto H, Mizushima N. Ubiquitination of phosphatidylethanolamine in organellar membranes. Mol Cell 2022; 82:3677-3692.e11. [PMID: 36044902 DOI: 10.1016/j.molcel.2022.08.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 06/27/2022] [Accepted: 08/04/2022] [Indexed: 12/30/2022]
Abstract
The covalent conjugation of ubiquitin family proteins is a widespread post-translational protein modification. In the ubiquitin family, the ATG8 subfamily is exceptional because it is conjugated mainly to phospholipids. However, it remains unknown whether other ubiquitin family proteins are also conjugated to phospholipids. Here, we report that ubiquitin is conjugated to phospholipids, mainly phosphatidylethanolamine (PE), in yeast and mammalian cells. Ubiquitinated PE (Ub-PE) accumulates at endosomes and the vacuole (or lysosomes), and its level increases during starvation. Ub-PE is also found in baculoviruses. In yeast, PE ubiquitination is catalyzed by the canonical ubiquitin system enzymes Uba1 (E1), Ubc4/5 (E2), and Tul1 (E3) and is reversed by Doa4. Liposomes containing Ub-PE recruit the ESCRT components Vps27-Hse1 and Vps23 in vitro. Ubiquitin-like NEDD8 and ISG15 are also conjugated to phospholipids. These findings suggest that the conjugation to membrane phospholipids is not specific to ATG8 but is a general feature of the ubiquitin family.
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Affiliation(s)
- Jun-Ichi Sakamaki
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Koji L Ode
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yoshitaka Kurikawa
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Hiroki R Ueda
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan; Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Osaka 565-0871, Japan
| | - Hayashi Yamamoto
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan.
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15
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Schnebert S, Goguet M, Vélez EJ, Depincé A, Beaumatin F, Herpin A, Seiliez I. Diving into the Evolutionary History of HSC70-Linked Selective Autophagy Pathways: Endosomal Microautophagy and Chaperone-Mediated Autophagy. Cells 2022; 11:cells11121945. [PMID: 35741074 PMCID: PMC9221867 DOI: 10.3390/cells11121945] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 06/14/2022] [Accepted: 06/15/2022] [Indexed: 12/17/2022] Open
Abstract
Autophagy is a pleiotropic and evolutionarily conserved process in eukaryotes that encompasses different types of mechanisms by which cells deliver cytoplasmic constituents to the lysosome for degradation. Interestingly, in mammals, two different and specialized autophagic pathways, (i) the chaperone-mediated autophagy (CMA) and (ii) the endosomal microautophagy (eMI), both rely on the use of the same cytosolic chaperone HSPA8 (also known as HSC70) for targeting specific substrates to the lysosome. However, this is not true for all organisms, and differences exist between species with respect to the coexistence of these two autophagic routes. In this paper, we present an in-depth analysis of the evolutionary history of the main components of CMA and eMI and discuss how the observed discrepancies between species may contribute to improving our knowledge of these two functions and their interplays.
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Affiliation(s)
- Simon Schnebert
- E2S UPPA, INRAE, NUMEA, Université de Pau et des Pays de l’Adour, 64310 Saint-Pée-sur-Nivelle, France; (S.S.); (M.G.); (E.J.V.); (F.B.)
| | - Maxime Goguet
- E2S UPPA, INRAE, NUMEA, Université de Pau et des Pays de l’Adour, 64310 Saint-Pée-sur-Nivelle, France; (S.S.); (M.G.); (E.J.V.); (F.B.)
| | - Emilio J. Vélez
- E2S UPPA, INRAE, NUMEA, Université de Pau et des Pays de l’Adour, 64310 Saint-Pée-sur-Nivelle, France; (S.S.); (M.G.); (E.J.V.); (F.B.)
| | - Alexandra Depincé
- UR1037 Laboratory of Fish Physiology and Genomics, Campus de Beaulieu, INRAE, F-35042 Rennes, France;
| | - Florian Beaumatin
- E2S UPPA, INRAE, NUMEA, Université de Pau et des Pays de l’Adour, 64310 Saint-Pée-sur-Nivelle, France; (S.S.); (M.G.); (E.J.V.); (F.B.)
| | - Amaury Herpin
- UR1037 Laboratory of Fish Physiology and Genomics, Campus de Beaulieu, INRAE, F-35042 Rennes, France;
- Correspondence: (A.H.); (I.S.)
| | - Iban Seiliez
- E2S UPPA, INRAE, NUMEA, Université de Pau et des Pays de l’Adour, 64310 Saint-Pée-sur-Nivelle, France; (S.S.); (M.G.); (E.J.V.); (F.B.)
- Correspondence: (A.H.); (I.S.)
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16
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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
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17
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Yeast cell death pathway requiring AP-3 vesicle trafficking leads to vacuole/lysosome membrane permeabilization. Cell Rep 2022; 39:110647. [PMID: 35417721 PMCID: PMC9074372 DOI: 10.1016/j.celrep.2022.110647] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 02/17/2022] [Accepted: 03/16/2022] [Indexed: 12/24/2022] Open
Abstract
Unicellular eukaryotes have been suggested as undergoing self-inflicted destruction. However, molecular details are sparse compared with the mechanisms of programmed/regulated cell death known for human cells and animal models. Here, we report a molecular cell death pathway in Saccharomyces cerevisiae leading to vacuole/lysosome membrane permeabilization. Following a transient cell death stimulus, yeast cells die slowly over several hours, consistent with an ongoing molecular dying process. A genome-wide screen for death-promoting factors identified all subunits of the AP-3 complex, a vesicle trafficking adapter known to transport and install newly synthesized proteins on the vacuole/lysosome membrane. To promote cell death, AP-3 requires its Arf1-GTPase-dependent vesicle trafficking function and the kinase Yck3, which is selectively transported to the vacuole membrane by AP-3. Video microscopy revealed a sequence of events where vacuole permeability precedes the loss of plasma membrane integrity. AP-3-dependent death appears to be conserved in the human pathogenic yeast Cryptococcus neoformans. Details about how mammalian cells die have yielded effective cancer therapies. Similarly, details about fungal cell death may explain failed responses to anti-fungal agents and inform next-generation anti-fungal strategies. Stolp et al. describe a potential mechanism of yeast cell death subversion, by inhibiting AP-3 vesicle trafficking to block vacuole/lysosome permeability.
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18
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Schwabl S, Teis D. Protein quality control at the Golgi. Curr Opin Cell Biol 2022; 75:102074. [PMID: 35364487 DOI: 10.1016/j.ceb.2022.02.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/14/2022] [Accepted: 02/17/2022] [Indexed: 11/28/2022]
Abstract
The majority of the proteome in eukaryotic cells is targeted to organelles. To maintain protein homeostasis (proteostasis), distinct protein quality control (PQC) machineries operate on organelles, where they detect misfolded proteins, orphaned and mis-localized proteins and selectively target these proteins into different ubiquitin-dependent or -independent degradation pathways. Thereby, PQC prevents proteotoxic effects that would disrupt organelle integrity and cause cellular damage that leads to diseases. Here, we will discuss emerging mechanisms for PQC machineries at the Golgi apparatus, the central station for the sorting and the modification of proteins that traffic to the endo-lysosomal system, or along the secretory pathway to the PM and to the extracellular space. We will focus on Golgi PQC pathways that (1) retrieve misfolded and orphaned proteins from the Golgi back to the endoplasmic reticulum, (2) extract these proteins from Golgi membranes for proteasomal degradation, (3) or selectively target these proteins to lysosomes for degradation.
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Affiliation(s)
- Sinead Schwabl
- Institute for Cell Biology, Biocenter, Medical University of Innsbruck, Austria
| | - David Teis
- Institute for Cell Biology, Biocenter, Medical University of Innsbruck, Austria.
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19
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Laidlaw KME, Paine KM, Bisinski DD, Calder G, Hogg K, Ahmed S, James S, O’Toole PJ, MacDonald C. Endosomal cargo recycling mediated by Gpa1 and phosphatidylinositol 3-kinase is inhibited by glucose starvation. Mol Biol Cell 2022; 33:ar31. [PMID: 35080991 PMCID: PMC9250360 DOI: 10.1091/mbc.e21-04-0163] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 01/19/2022] [Accepted: 01/21/2022] [Indexed: 01/29/2023] Open
Abstract
Cell surface protein trafficking is regulated in response to nutrient availability, with multiple pathways directing surface membrane proteins to the lysosome for degradation in response to suboptimal extracellular nutrients. Internalized protein and lipid cargoes recycle back to the surface efficiently in glucose-replete conditions, but this trafficking is attenuated following glucose starvation. We find that cells with either reduced or hyperactive phosphatidylinositol 3-kinase (PI3K) activity are defective for endosome to surface recycling. Furthermore, we find that the yeast Gα subunit Gpa1, an endosomal PI3K effector, is required for surface recycling of cargoes. Following glucose starvation, mRNA and protein levels of a distinct Gα subunit Gpa2 are elevated following nuclear translocation of Mig1, which inhibits recycling of various cargoes. As Gpa1 and Gpa2 interact at the surface where Gpa2 concentrates during glucose starvation, we propose that this disrupts PI3K activity required for recycling, potentially diverting Gpa1 to the surface and interfering with its endosomal role in recycling. In support of this model, glucose starvation and overexpression of Gpa2 alter PI3K endosomal phosphoinositide production. Glucose deprivation therefore triggers a survival mechanism to increase retention of surface cargoes in endosomes and promote their lysosomal degradation.
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Affiliation(s)
| | | | | | - Grant Calder
- Bioscience Technology Facility, Department of Biology, University of York, YO10 5DD York, UK
| | - Karen Hogg
- Bioscience Technology Facility, Department of Biology, University of York, YO10 5DD York, UK
| | - Sophia Ahmed
- Bioscience Technology Facility, Department of Biology, University of York, YO10 5DD York, UK
| | - Sally James
- Bioscience Technology Facility, Department of Biology, University of York, YO10 5DD York, UK
| | - Peter J. O’Toole
- Bioscience Technology Facility, Department of Biology, University of York, YO10 5DD York, UK
| | - Chris MacDonald
- York Biomedical Research Institute and Department of Biology and
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20
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Wróbel M, Cendrowski J, Szymańska E, Grębowicz-Maciukiewicz M, Budick-Harmelin N, Macias M, Szybińska A, Mazur M, Kolmus K, Goryca K, Dąbrowska M, Paziewska A, Mikula M, Miączyńska M. ESCRT-I fuels lysosomal degradation to restrict TFEB/TFE3 signaling via the Rag-mTORC1 pathway. Life Sci Alliance 2022; 5:5/7/e202101239. [PMID: 35354596 PMCID: PMC8967991 DOI: 10.26508/lsa.202101239] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 12/13/2022] Open
Abstract
ESCRT-I deficiency impairs lysosome membrane turnover and induces homeostatic responses to lysosomal nutrient starvation including activation of MiT-TFE signaling caused by inhibition of the substrate-specific mTORC1 pathway. Within the endolysosomal pathway in mammalian cells, ESCRT complexes facilitate degradation of proteins residing in endosomal membranes. Here, we show that mammalian ESCRT-I restricts the size of lysosomes and promotes degradation of proteins from lysosomal membranes, including MCOLN1, a Ca2+ channel protein. The altered lysosome morphology upon ESCRT-I depletion coincided with elevated expression of genes annotated to biogenesis of lysosomes due to prolonged activation of TFEB/TFE3 transcription factors. Lack of ESCRT-I also induced transcription of cholesterol biosynthesis genes, in response to inefficient delivery of cholesterol from endolysosomal compartments. Among factors that could possibly activate TFEB/TFE3 signaling upon ESCRT-I deficiency, we excluded lysosomal cholesterol accumulation and Ca2+-mediated dephosphorylation of TFEB/TFE3. However, we discovered that this activation occurs due to the inhibition of Rag GTPase–dependent mTORC1 pathway that specifically reduced phosphorylation of TFEB at S122. Constitutive activation of the Rag GTPase complex in cells lacking ESCRT-I restored S122 phosphorylation and prevented TFEB/TFE3 activation. Our results indicate that ESCRT-I deficiency evokes a homeostatic response to counteract lysosomal nutrient starvation, that is, improper supply of nutrients derived from lysosomal degradation.
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Affiliation(s)
- Marta Wróbel
- Laboratory of Cell Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Jarosław Cendrowski
- Laboratory of Cell Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Ewelina Szymańska
- Laboratory of Cell Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | | | - Noga Budick-Harmelin
- Laboratory of Cell Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Matylda Macias
- Microscopy and Cytometry Facility, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Aleksandra Szybińska
- Microscopy and Cytometry Facility, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Michał Mazur
- Laboratory of Cell Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Krzysztof Kolmus
- Laboratory of Cell Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Krzysztof Goryca
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Michalina Dąbrowska
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Agnieszka Paziewska
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Michał Mikula
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Marta Miączyńska
- Laboratory of Cell Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
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21
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Banjade S, Zhu L, Jorgensen JR, Suzuki SW, Emr SD. Recruitment and organization of ESCRT-0 and ubiquitinated cargo via condensation. SCIENCE ADVANCES 2022; 8:eabm5149. [PMID: 35363519 PMCID: PMC10938570 DOI: 10.1126/sciadv.abm5149] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 02/09/2022] [Indexed: 06/14/2023]
Abstract
The general mechanisms by which ESCRTs (Endosomal Sorting Complexes Required for Transport) are specifically recruited to various membranes, and how ESCRT subunits are spatially organized remain central questions in cell biology. At the endosome and lysosomes, ubiquitination of membrane proteins triggers ESCRT-mediated substrate recognition and degradation. Using the yeast lysosome/vacuole, we define the principles by which substrate engagement by ESCRTs occurs at this organelle. We find that multivalent interactions between ESCRT-0 and polyubiquitin are critical for substrate recognition at yeast vacuoles, with a lower-valency requirement for cargo engagement at endosomes. Direct recruitment of ESCRT-0 induces dynamic foci on the vacuole membrane and forms fluid condensates in vitro with polyubiquitin. We propose that self-assembly of early ESCRTs induces condensation, an initial step in ESCRT assembly/nucleation at membranes. This property can be tuned specifically at various organelles by modulating the number of binding interactions.
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Affiliation(s)
- Sudeep Banjade
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Lu Zhu
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Jeffrey R. Jorgensen
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Sho W. Suzuki
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Scott D. Emr
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
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22
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Lemus L, Goder V. Membrane trafficking: ESCRTs act here, there, and everywhere. Curr Biol 2022; 32:R292-R294. [PMID: 35349820 DOI: 10.1016/j.cub.2022.02.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Endosomal sorting complex required for transport (ESCRT) proteins can promote extreme membrane deformations, including scission and sealing. New work uncovers a link between these proteins and the early secretory pathway that is functionally important for programmed autophagy during Drosophila development.
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Affiliation(s)
- Leticia Lemus
- Department of Genetics, University of Seville, Av. Reina Mercedes 6, 41012 Seville, Spain.
| | - Veit Goder
- Department of Genetics, University of Seville, Av. Reina Mercedes 6, 41012 Seville, Spain.
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23
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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.
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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
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24
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Zoncu R, Perera RM. Built to last: lysosome remodeling and repair in health and disease. Trends Cell Biol 2022; 32:597-610. [DOI: 10.1016/j.tcb.2021.12.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/29/2021] [Accepted: 12/30/2021] [Indexed: 12/21/2022]
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25
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Degradation of nuclear components via different autophagy pathways. Trends Cell Biol 2022; 32:574-584. [DOI: 10.1016/j.tcb.2021.12.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/21/2021] [Accepted: 12/23/2021] [Indexed: 12/21/2022]
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26
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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.
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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.
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Li S, Cerri M, Strazzer P, Li Y, Spelt C, Bliek M, Vandenbussche M, Martínez-Calvó E, Lai B, Reale L, Koes R, Quattrocchio FM. An ancient RAB5 governs the formation of additional vacuoles and cell shape in petunia petals. Cell Rep 2021; 36:109749. [PMID: 34592147 DOI: 10.1016/j.celrep.2021.109749] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 06/11/2021] [Accepted: 09/02/2021] [Indexed: 10/20/2022] Open
Abstract
Homologous ("canonical") RAB5 proteins regulate endosomal trafficking to lysosomes in animals and to the central vacuole in plants. Epidermal petal cells contain small vacuoles (vacuolinos) that serve as intermediate stations for proteins on their way to the central vacuole. Here, we show that transcription factors required for vacuolino formation in petunia induce expression of RAB5a. RAB5a defines a previously unrecognized clade of canonical RAB5s that is evolutionarily and functionally distinct from ARA7-type RAB5s, which act in trafficking to the vacuole. Loss of RAB5a reduces cell height and abolishes vacuolino formation, which cannot be rescued by the ARA7 homologs, whereas constitutive RAB5a (over)expression alters the conical cell shape and promotes homotypic vacuolino fusion, resulting in oversized vacuolinos. These findings provide a rare example of how gene duplication and neofunctionalization increased the complexity of membrane trafficking during evolution and suggest a mechanism by which cells may form multiple vacuoles with distinct content and function.
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Affiliation(s)
- Shuangjiang Li
- Plant Development and (Epi)Genetics, Swammerdam Institute for Life Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands
| | - Martina Cerri
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy
| | - Pamela Strazzer
- Plant Development and (Epi)Genetics, Swammerdam Institute for Life Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands
| | - Yanbang Li
- Plant Development and (Epi)Genetics, Swammerdam Institute for Life Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands
| | - Cornelis Spelt
- Plant Development and (Epi)Genetics, Swammerdam Institute for Life Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands
| | - Mattijs Bliek
- Plant Development and (Epi)Genetics, Swammerdam Institute for Life Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands
| | - Michiel Vandenbussche
- Laboratoire Reproduction et Développement des Plantes (RDP), ENS de Lyon/CNRS/INRA/UCBL, 46 Allée d'Italie, 69364 Lyon, France
| | - Enric Martínez-Calvó
- Plant Development and (Epi)Genetics, Swammerdam Institute for Life Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands
| | - Biao Lai
- Plant Development and (Epi)Genetics, Swammerdam Institute for Life Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands
| | - Lara Reale
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy
| | - Ronald Koes
- Plant Development and (Epi)Genetics, Swammerdam Institute for Life Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands.
| | - Francesca M Quattrocchio
- Plant Development and (Epi)Genetics, Swammerdam Institute for Life Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands
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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.
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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:
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29
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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.
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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.
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30
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He CW, Cui XF, Ma SJ, Xu Q, Ran YP, Chen WZ, Mu JX, Li H, Zhu J, Gong Q, Xie Z. Membrane recruitment of Atg8 by Hfl1 facilitates turnover of vacuolar membrane proteins in yeast cells approaching stationary phase. BMC Biol 2021; 19:117. [PMID: 34088313 PMCID: PMC8176713 DOI: 10.1186/s12915-021-01048-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 05/07/2021] [Indexed: 12/03/2022] Open
Abstract
Background The vacuole/lysosome is the final destination of autophagic pathways, but can also itself be degraded in whole or in part by selective macroautophagic or microautophagic processes. Diverse molecular mechanisms are involved in these processes, the characterization of which has lagged behind those of ATG-dependent macroautophagy and ESCRT-dependent endosomal multivesicular body pathways. Results Here we show that as yeast cells gradually exhaust available nutrients and approach stationary phase, multiple vacuolar integral membrane proteins with unrelated functions are degraded in the vacuolar lumen. This degradation depends on the ESCRT machinery, but does not strictly require ubiquitination of cargos or trafficking of cargos out of the vacuole. It is also temporally and mechanistically distinct from NPC-dependent microlipophagy. The turnover is facilitated by Atg8, an exception among autophagy proteins, and an Atg8-interacting vacuolar membrane protein, Hfl1. Lack of Atg8 or Hfl1 led to the accumulation of enlarged lumenal membrane structures in the vacuole. We further show that a key function of Hfl1 is the membrane recruitment of Atg8. In the presence of Hfl1, lipidation of Atg8 is not required for efficient cargo turnover. The need for Hfl1 can be partially bypassed by blocking Atg8 delipidation. Conclusions Our data reveal a vacuolar membrane protein degradation process with a unique dependence on vacuole-associated Atg8 downstream of ESCRTs, and we identify a specific role of Hfl1, a protein conserved from yeast to plants and animals, in membrane targeting of Atg8. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01048-7.
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Affiliation(s)
- Cheng-Wen He
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xue-Fei Cui
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shao-Jie Ma
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.,Present address: Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Qin Xu
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yan-Peng Ran
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wei-Zhi Chen
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jun-Xi Mu
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hui Li
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jing Zhu
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qingqiu Gong
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhiping Xie
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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31
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Investigating the Antifungal Mechanism of Action of Polygodial by Phenotypic Screening in Saccharomyces cerevisiae. Int J Mol Sci 2021; 22:ijms22115756. [PMID: 34071169 PMCID: PMC8198865 DOI: 10.3390/ijms22115756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/19/2021] [Accepted: 05/25/2021] [Indexed: 11/17/2022] Open
Abstract
Polygodial is a "hot" peppery-tasting sesquiterpenoid that was first described for its anti-feedant activity against African armyworms. Using the haploid deletion mutant library of Saccharomyces cerevisiae, a genome-wide mutant screen was performed to shed more light on polygodial's antifungal mechanism of action. We identified 66 deletion strains that were hypersensitive and 47 that were highly resistant to polygodial treatment. Among the hypersensitive strains, an enrichment was found for genes required for vacuolar acidification, amino acid biosynthesis, nucleosome mobilization, the transcription mediator complex, autophagy and vesicular trafficking, while the resistant strains were enriched for genes encoding cytoskeleton-binding proteins, ribosomal proteins, mitochondrial matrix proteins, components of the heme activator protein (HAP) complex, and known regulators of the target of rapamycin complex 1 (TORC1) signaling. WE confirm that polygodial triggers a dose-dependent vacuolar alkalinization and that it increases Ca2+ influx and inhibits glucose-induced Ca2+ signaling. Moreover, we provide evidence suggesting that TORC1 signaling and its protective agent ubiquitin play a central role in polygodial resistance, suggesting that they can be targeted by polygodial either directly or via altered Ca2+ homeostasis.
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32
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Yang X, Reist L, Chomchai DA, Chen L, Arines FM, Li M. ESCRT, not intralumenal fragments, sorts ubiquitinated vacuole membrane proteins for degradation. THE JOURNAL OF CELL BIOLOGY 2021; 220:212199. [PMID: 34047770 PMCID: PMC8167898 DOI: 10.1083/jcb.202012104] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 04/19/2021] [Accepted: 05/13/2021] [Indexed: 01/05/2023]
Abstract
The lysosome (or vacuole in fungi and plants) is an essential organelle for nutrient sensing and cellular homeostasis. In response to environmental stresses such as starvation, the yeast vacuole can adjust its membrane composition by selectively internalizing membrane proteins into the lumen for degradation. Regarding the selective internalization mechanism, two competing models have been proposed. One model suggests that the ESCRT machinery is responsible for the sorting. In contrast, the ESCRT-independent intralumenal fragment (ILF) pathway proposes that the fragment generated by homotypic vacuole fusion is responsible for the sorting. Here, we applied a microfluidics-based imaging method to capture the complete degradation process in vivo. Combining live-cell imaging with a synchronized ubiquitination system, we demonstrated that ILF cargoes are not degraded through intralumenal fragments. Instead, ESCRTs function on the vacuole membrane to sort them into the lumen for degradation. We further discussed challenges in reconstituting vacuole membrane protein degradation.
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Affiliation(s)
- Xi Yang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Lucas Reist
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Dominic A Chomchai
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Liang Chen
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Felichi Mae Arines
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Ming Li
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
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33
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Arines FM, Hamlin AJ, Yang X, Liu YYJ, Li M. A selective transmembrane recognition mechanism by a membrane-anchored ubiquitin ligase adaptor. J Cell Biol 2021; 220:211632. [PMID: 33351099 PMCID: PMC7759299 DOI: 10.1083/jcb.202001116] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 09/10/2020] [Accepted: 10/30/2020] [Indexed: 12/30/2022] Open
Abstract
While it is well-known that E3 ubiquitin ligases can selectively ubiquitinate membrane proteins in response to specific environmental cues, the underlying mechanisms for the selectivity are poorly understood. In particular, the role of transmembrane regions, if any, in target recognition remains an open question. Here, we describe how Ssh4, a yeast E3 ligase adaptor, recognizes the PQ-loop lysine transporter Ypq1 only after lysine starvation. We show evidence of an interaction between two transmembrane helices of Ypq1 (TM5 and TM7) and the single transmembrane helix of Ssh4. This interaction is regulated by the conserved PQ motif. Strikingly, recent structural studies of the PQ-loop family have suggested that TM5 and TM7 undergo major conformational changes during substrate transport, implying that transport-associated conformational changes may determine the selectivity. These findings thus provide critical information concerning the regulatory mechanism through which transmembrane domains can be specifically recognized in response to changing environmental conditions.
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Affiliation(s)
- Felichi Mae Arines
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Aaron Jeremy Hamlin
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Xi Yang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Yun-Yu Jennifer Liu
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Ming Li
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
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34
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Doroodian P, Hua Z. The Ubiquitin Switch in Plant Stress Response. PLANTS (BASEL, SWITZERLAND) 2021; 10:246. [PMID: 33514032 PMCID: PMC7911189 DOI: 10.3390/plants10020246] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 01/19/2021] [Accepted: 01/22/2021] [Indexed: 12/20/2022]
Abstract
Ubiquitin is a 76 amino acid polypeptide common to all eukaryotic organisms. It functions as a post-translationally modifying mark covalently linked to a large cohort of yet poorly defined protein substrates. The resulting ubiquitylated proteins can rapidly change their activities, cellular localization, or turnover through the 26S proteasome if they are no longer needed or are abnormal. Such a selective modification is essential to many signal transduction pathways particularly in those related to stress responses by rapidly enhancing or quenching output. Hence, this modification system, the so-called ubiquitin-26S proteasome system (UPS), has caught the attention in the plant research community over the last two decades for its roles in plant abiotic and biotic stress responses. Through direct or indirect mediation of plant hormones, the UPS selectively degrades key components in stress signaling to either negatively or positively regulate plant response to a given stimulus. As a result, a tightly regulated signaling network has become of much interest over the years. The ever-increasing changes of the global climate require both the development of new crops to cope with rapid changing environment and new knowledge to survey the dynamics of ecosystem. This review examines how the ubiquitin can switch and tune plant stress response and poses potential avenues to further explore this system.
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Affiliation(s)
- Paymon Doroodian
- Department of Environment and Plant Biology, Ohio University, Athens, OH 45701, USA;
- Molecular and Cellular Biology Program, Ohio University, Athens, OH 45701, USA
| | - Zhihua Hua
- Department of Environment and Plant Biology, Ohio University, Athens, OH 45701, USA;
- Molecular and Cellular Biology Program, Ohio University, Athens, OH 45701, USA
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35
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Chen H, Miller PW, Johnson DL, Laribee RN. The Ccr4-Not complex regulates TORC1 signaling and mitochondrial metabolism by promoting vacuole V-ATPase activity. PLoS Genet 2020; 16:e1009046. [PMID: 33064727 PMCID: PMC7592917 DOI: 10.1371/journal.pgen.1009046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 10/28/2020] [Accepted: 08/12/2020] [Indexed: 01/30/2023] Open
Abstract
The Ccr4-Not complex functions as an effector of multiple signaling pathways that control gene transcription and mRNA turnover. Consequently, Ccr4-Not contributes to a diverse array of processes, which includes a significant role in cell metabolism. Yet a mechanistic understanding of how it contributes to metabolism is lacking. Herein, we provide evidence that Ccr4-Not activates nutrient signaling through the essential target of rapamycin complex 1 (TORC1) pathway. Ccr4-Not disruption reduces global TORC1 signaling, and it also upregulates expression of the cell wall integrity (CWI) pathway terminal kinase Mpk1. Although CWI signaling represses TORC1 signaling, we find that Ccr4-Not loss inhibits TORC1 independently of CWI activation. Instead, we demonstrate that Ccr4-Not promotes the function of the vacuole V-ATPase, which interacts with the Gtr1 GTPase-containing EGO complex to stimulate TORC1 in response to nutrient sufficiency. Bypassing the V-ATPase requirement in TORC1 activation using a constitutively active Gtr1 mutant fully restores TORC1 signaling in Ccr4-Not deficient cells. Transcriptome analysis and functional studies revealed that loss of the Ccr4 subunit activates the TORC1 repressed retrograde signaling pathway to upregulate mitochondrial activity. Blocking this mitochondrial upregulation in Ccr4-Not deficient cells further represses TORC1 signaling, and it causes synergistic deficiencies in mitochondrial-dependent metabolism. These data support a model whereby Ccr4-Not loss impairs V-ATPase dependent TORC1 activation that forces cells to enhance mitochondrial metabolism to sustain a minimal level of TORC1 signaling necessary for cell growth and proliferation. Therefore, Ccr4-Not plays an integral role in nutrient signaling and cell metabolism by promoting V-ATPase dependent TORC1 activation.
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Affiliation(s)
- Hongfeng Chen
- 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
| | - P. Winston Miller
- 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
| | - 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
| | - 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
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36
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Lee C, Lamech L, Johns E, Overholtzer M. Selective Lysosome Membrane Turnover Is Induced by Nutrient Starvation. Dev Cell 2020; 55:289-297.e4. [PMID: 32916093 DOI: 10.1016/j.devcel.2020.08.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 07/02/2020] [Accepted: 08/17/2020] [Indexed: 12/20/2022]
Abstract
Lysosome function is essential for cellular homeostasis, but quality-control mechanisms that maintain healthy lysosomes remain poorly characterized. Here, we developed a method to measure lysosome turnover and use this to identify a selective mechanism of membrane degradation that involves lipidation of the autophagy protein LC3 onto lysosomal membranes and the formation of intraluminal vesicles through microautophagy. This mechanism is induced in response to metabolic stress resulting from glucose starvation or by treatment with pharmacological agents that induce osmotic stress on lysosomes. Cells lacking ATG5, an essential component of the LC3 lipidation machinery, show reduced ability to regulate lysosome size and degradative capacity in response to activation of this mechanism. These findings identify a selective mechanism of lysosome membrane turnover that is induced by stress and uncover a function for LC3 lipidation in regulating lysosome size and activity through microautophagy.
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Affiliation(s)
- Chan Lee
- Cell Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA; BCMB Allied Program, Weill Cornell Medical College, New York, NY 10065, USA
| | - Lilian Lamech
- Cell Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Eleanor Johns
- Cell Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA; Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Michael Overholtzer
- Cell Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA; BCMB Allied Program, Weill Cornell Medical College, New York, NY 10065, USA; Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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37
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Schuck S. Microautophagy - distinct molecular mechanisms handle cargoes of many sizes. J Cell Sci 2020; 133:133/17/jcs246322. [PMID: 32907930 DOI: 10.1242/jcs.246322] [Citation(s) in RCA: 195] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Autophagy is fundamental for cell and organismal health. Two types of autophagy are conserved in eukaryotes: macroautophagy and microautophagy. During macroautophagy, autophagosomes deliver cytoplasmic constituents to endosomes or lysosomes, whereas during microautophagy lytic organelles take up cytoplasm directly. While macroautophagy has been investigated extensively, microautophagy has received much less attention. Nonetheless, it has become clear that microautophagy has a broad range of functions in biosynthetic transport, metabolic adaptation, organelle remodeling and quality control. This Review discusses the selective and non-selective microautophagic processes known in yeast, plants and animals. Based on the molecular mechanisms for the uptake of microautophagic cargo into lytic organelles, I propose to distinguish between fission-type microautophagy, which depends on ESCRT proteins, and fusion-type microautophagy, which requires the core autophagy machinery and SNARE proteins. Many questions remain to be explored, but the functional versatility and mechanistic diversity of microautophagy are beginning to emerge.
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Affiliation(s)
- Sebastian Schuck
- Center for Molecular Biology of Heidelberg University (ZMBH), Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
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38
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Ljubicic S, Cottet-Dumoulin D, Bosco D. Loss of cell-cell and cell-substrate contacts in single pancreatic β-cells divert insulin release to intracellular vesicular compartments. Biol Cell 2020; 112:427-438. [PMID: 32857433 DOI: 10.1111/boc.202000043] [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: 04/05/2020] [Revised: 07/31/2020] [Accepted: 08/19/2020] [Indexed: 11/28/2022]
Abstract
BACKGROUND INFORMATION Cell-cell or cell-substrate interactions are lost when cells are dissociated in culture, or during pathophysiological breakdowns, therefore impairing their structure and polarity, and affecting their function. We show that single rat β-cells, cultured under non-adhesive conditions, form intracytoplasmic vacuoles increasing in number and size over time. We characterized these structures and their implication in β-cell function. RESULTS Ultrastructurally, the vacuoles resemble vesicular apical compartments and are delimited by a membrane, containing microvilli and expressing markers of the plasma membrane, including glucose transporter 2 and actin. When insulin secretion is stimulated, insulin accumulates in the lumen of the vacuoles. By contrast, when the cells are incubated under low calcium levels, the hormone is undetectable in vesicular compartments. Insulin release studies from single cells revealed that vacuole-containing cells release less insulin as compared to control cells. When added to the medium, a non-permeant fluid phase marker becomes trapped within vacuoles. Inhibition of vesicular trafficking and exocytosis as well as dynamin-dependent endocytosis changed the percentage of vacuole-containing cells, suggesting that both endocytic and exocytic track contribute to their formation. CONCLUSIONS These results suggest that loss of cell-cell and cell-substrate contacts in isolated β-cells affect normal vesicular trafficking and redirects insulin secretion to intracellular vesicular compartments. SIGNIFICANCE Our study reveals for the first time that single β-cells develop vacuolar compartments when cultured in suspension and redirect their insulin secretion to these vacuoles. This may underlie a compensatory process for cultured cells who lost their interactions with adhesive substrates or neighbouring cells.
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Affiliation(s)
- Sanda Ljubicic
- Cell Isolation and Transplantation Center, Department of Surgery, Geneva, University Hospitals and University of Geneva, Geneva, Switzerland.,Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Diabetes Center of the Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - David Cottet-Dumoulin
- Cell Isolation and Transplantation Center, Department of Surgery, Geneva, University Hospitals and University of Geneva, Geneva, Switzerland.,Diabetes Center of the Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Domenico Bosco
- Cell Isolation and Transplantation Center, Department of Surgery, Geneva, University Hospitals and University of Geneva, Geneva, Switzerland.,Diabetes Center of the Faculty of Medicine, University of Geneva, Geneva, Switzerland
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39
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Ivashov V, Zimmer J, Schwabl S, Kahlhofer J, Weys S, Gstir R, Jakschitz T, Kremser L, Bonn GK, Lindner H, Huber LA, Leon S, Schmidt O, Teis D. Complementary α-arrestin-ubiquitin ligase complexes control nutrient transporter endocytosis in response to amino acids. eLife 2020; 9:e58246. [PMID: 32744498 PMCID: PMC7449699 DOI: 10.7554/elife.58246] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/01/2020] [Indexed: 12/12/2022] Open
Abstract
How cells adjust nutrient transport across their membranes is incompletely understood. Previously, we have shown that S. cerevisiae broadly re-configures the nutrient transporters at the plasma membrane in response to amino acid availability, through endocytosis of sugar- and amino acid transporters (AATs) (Müller et al., 2015). A genome-wide screen now revealed that the selective endocytosis of four AATs during starvation required the α-arrestin family protein Art2/Ecm21, an adaptor for the ubiquitin ligase Rsp5, and its induction through the general amino acid control pathway. Art2 uses a basic patch to recognize C-terminal acidic sorting motifs in AATs and thereby instructs Rsp5 to ubiquitinate proximal lysine residues. When amino acids are in excess, Rsp5 instead uses TORC1-activated Art1 to detect N-terminal acidic sorting motifs within the same AATs, which initiates exclusive substrate-induced endocytosis. Thus, amino acid excess or starvation activate complementary α-arrestin-Rsp5-complexes to control selective endocytosis and adapt nutrient acquisition.
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Affiliation(s)
- Vasyl Ivashov
- Institute for Cell Biology, Medical University of InnsbruckInnsbruckAustria
| | - Johannes Zimmer
- Institute for Cell Biology, Medical University of InnsbruckInnsbruckAustria
| | - Sinead Schwabl
- Institute for Cell Biology, Medical University of InnsbruckInnsbruckAustria
| | - Jennifer Kahlhofer
- Institute for Cell Biology, Medical University of InnsbruckInnsbruckAustria
| | - Sabine Weys
- Institute for Cell Biology, Medical University of InnsbruckInnsbruckAustria
| | - Ronald Gstir
- ADSI – Austrian Drug Screening Institute GmbHInnsbruckAustria
| | | | - Leopold Kremser
- Division of Clinical Biochemistry, ProteinMicroAnalysis Facility, Medical University of InnsbruckInnsbruckAustria
| | - Günther K Bonn
- ADSI – Austrian Drug Screening Institute GmbHInnsbruckAustria
| | - Herbert Lindner
- Division of Clinical Biochemistry, ProteinMicroAnalysis Facility, Medical University of InnsbruckInnsbruckAustria
| | - Lukas A Huber
- Institute for Cell Biology, Medical University of InnsbruckInnsbruckAustria
- ADSI – Austrian Drug Screening Institute GmbHInnsbruckAustria
| | - Sebastien Leon
- Université de Paris, CNRS, Institut Jacques MonodParisFrance
| | - Oliver Schmidt
- Institute for Cell Biology, Medical University of InnsbruckInnsbruckAustria
| | - David Teis
- Institute for Cell Biology, Medical University of InnsbruckInnsbruckAustria
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TM7SF1, an important autophagy regulatory protein in mouse podocytes. Biochem Biophys Res Commun 2020; 528:213-219. [PMID: 32482387 DOI: 10.1016/j.bbrc.2020.05.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/30/2020] [Accepted: 05/01/2020] [Indexed: 12/19/2022]
Abstract
The autophagy, which can be regulated by lysosomal membrane proteins, plays a critical role in maintaining normal podocyte function. TM7SF1 is a novel lysosomal membrane protein, but its effect on autophagy is still unknown. This study aimed to identify the role of TM7SF1 in mouse podocyte (MPC5) autophagy. Interestingly, we detected an increase in LC3BII and SQSTM1/P62 in MPC5 through inhibiting TM7SF1, and which can be completely corrected after blocking the autolysosome degradation with chloroquine (CQ). Moreover, inhibition of TM7SF1 expression did not increase the mRNA level of SQSTM1/P62. Theses results suggested that inhibition of TM7SF1 led to impaired degradation of autophagy products, which manifest as an abnormal accumulation of LC3BII and SQSTM1/P62. Further studies showed that the downregulation of TM7SF1 resulted in a significant decrease in the number of acid lysosomes, which directly led to decreases in the number and function of autolysosomes. In conclusion, TM7SF1 is therefore essential for autolysosomes degradation pathway at the end of autophagy flow, and for the maintenance of podocyte function.
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