1
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Wang L, Xu Y, Fukushige T, Saidi L, Wang X, Yu C, Lee JG, Krause M, Huang L, Ye Y. Mono-UFMylation promotes misfolding-associated secretion of α-synuclein. SCIENCE ADVANCES 2024; 10:eadk2542. [PMID: 38489364 PMCID: PMC10942102 DOI: 10.1126/sciadv.adk2542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 02/12/2024] [Indexed: 03/17/2024]
Abstract
Stressed cells secret misfolded proteins lacking signaling sequence via an unconventional protein secretion (UcPS) pathway, but how misfolded proteins are targeted selectively in UcPS is unclear. Here, we report that misfolded UcPS clients are subject to modification by a ubiquitin-like protein named ubiquitin-fold modifier 1 (UFM1). Using α-synuclein (α-Syn) as a UcPS model, we show that mutating the UFMylation sites in α-Syn or genetic inhibition of the UFMylation system mitigates α-Syn secretion, whereas overexpression of UFBP1, a component of the endoplasmic reticulum-associated UFMylation ligase complex, augments α-Syn secretion in mammalian cells and in model organisms. UFM1 itself is cosecreted with α-Syn, and the serum UFM1 level correlates with that of α-Syn. Because UFM1 can be directly recognized by ubiquitin specific peptidase 19 (USP19), a previously established UcPS stimulator known to associate with several chaperoning activities, UFMylation might facilitate substrate engagement by USP19, allowing stringent and regulated selection of misfolded proteins for secretion and proteotoxic stress alleviation.
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Affiliation(s)
- Lihui Wang
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yue Xu
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tetsunari Fukushige
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Layla Saidi
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xiaorong Wang
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA 92697, USA
| | - Clinton Yu
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA 92697, USA
| | - Jin-Gu Lee
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael Krause
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lan Huang
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA 92697, USA
| | - Yihong Ye
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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2
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Fernández-López MG, Batista-García RA, Aréchiga-Carvajal ET. Alkaliphilic/Alkali-Tolerant Fungi: Molecular, Biochemical, and Biotechnological Aspects. J Fungi (Basel) 2023; 9:652. [PMID: 37367588 DOI: 10.3390/jof9060652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/08/2023] [Accepted: 05/08/2023] [Indexed: 06/28/2023] Open
Abstract
Biotechnologist interest in extremophile microorganisms has increased in recent years. Alkaliphilic and alkali-tolerant fungi that resist alkaline pH are among these. Alkaline environments, both terrestrial and aquatic, can be created by nature or by human activities. Aspergillus nidulans and Saccharomyces cerevisiae are the two eukaryotic organisms whose pH-dependent gene regulation has received the most study. In both biological models, the PacC transcription factor activates the Pal/Rim pathway through two successive proteolytic mechanisms. PacC is a repressor of acid-expressed genes and an activator of alkaline-expressed genes when it is in an active state. It appears, however, that these are not the only mechanisms associated with pH adaptations in alkali-tolerant fungi. These fungi produce enzymes that are resistant to harsh conditions, i.e., alkaline pH, and can be used in technological processes, such as in the textile, paper, detergent, food, pharmaceutical, and leather tanning industries, as well as in bioremediation of pollutants. Consequently, it is essential to understand how these fungi maintain intracellular homeostasis and the signaling pathways that activate the physiological mechanisms of alkali resistance in fungi.
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Affiliation(s)
- Maikel Gilberto Fernández-López
- Unidad de Manipulación Genética, Laboratorio de Micología y Fitopatología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 66451, Mexico
| | - Ramón Alberto Batista-García
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Mexico
| | - Elva Teresa Aréchiga-Carvajal
- Unidad de Manipulación Genética, Laboratorio de Micología y Fitopatología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 66451, Mexico
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3
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Hepowit NL, Blalock E, Lee S, Bretland KM, MacGurn JA, Dickson RC. Reduced sphingolipid biosynthesis modulates proteostasis networks to enhance longevity. Aging (Albany NY) 2023; 15:472-491. [PMID: 36640272 PMCID: PMC9925692 DOI: 10.18632/aging.204485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 12/29/2022] [Indexed: 01/15/2023]
Abstract
As the elderly population increases, chronic, age-associated diseases are challenging healthcare systems around the world. Nutrient limitation is well known to slow the aging process and improve health. Regrettably, practicing nutrient restriction to improve health is unachievable for most people. Alternatively, pharmacological strategies are being pursued including myriocin which increases lifespan in budding yeast. Myriocin impairs sphingolipid synthesis, resulting in lowered amino acid pools which promote entry into a quiescent, long-lived state. Here we present transcriptomic data during the first 6 hours of drug treatment that improves our mechanistic understanding of the cellular response to myriocin and reveals a new role for ubiquitin in longevity. Previously we found that the methionine transporter Mup1 traffics to the plasma membrane normally in myriocin-treated cells but is not active and undergoes endocytic clearance. We now show that UBI4, a gene encoding stressed-induced ubiquitin, is vital for myriocin-enhanced lifespan. Furthermore, we show that Mup1 fused to a deubiquitinase domain impairs myriocin-enhanced longevity. Broader effects of myriocin treatment on ubiquitination are indicated by our finding of a significant increase in K63-linked ubiquitin polymers following myriocin treatment. Although proteostasis is broadly accepted as a pillar of aging, our finding that ubiquitination of an amino acid transporter promotes longevity in myriocin-treated cells is novel. Addressing the role of ubiquitination/deubiquitination in longevity has the potential to reveal new strategies and targets for promoting healthy aging.
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Affiliation(s)
- Nathaniel L. Hepowit
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Eric Blalock
- Department of Pharmacology and Nutritional Science, University of Kentucky, Lexington, KY 40536, USA
| | - Sangderk Lee
- College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA
| | - Kimberly M. Bretland
- Department of Pharmacology and Nutritional Science, University of Kentucky, Lexington, KY 40536, USA
| | - Jason A. MacGurn
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Robert C. Dickson
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
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4
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Hepowit NL, Denise AS, MacGurn JA. Use of Deubiquitinase Fusion Proteins to Characterize Endocytic Trafficking in Yeast. Methods Mol Biol 2023; 2591:283-295. [PMID: 36350555 DOI: 10.1007/978-1-0716-2803-4_17] [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] [Indexed: 06/16/2023]
Abstract
Ubiquitin modification is known to regulate endocytic trafficking of many different types of cargo in eukaryotic cells, but it can be challenging to determine what role, if any, ubiquitin plays in the trafficking of a novel or uncharacterized endocytic cargo. Here, we describe a useful approach that leverages fusion to deubiquitinase (DUB) catalytic domains to explore the role ubiquitin plays in endocytic trafficking. This approach can be applied to the analysis of many different endocytic cargos in different cell types, and it can also be used to study linkage specificity in endocytic trafficking. Several different trafficking assays are described to illustrate the broad utility of this "DUB fusion" approach.
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Affiliation(s)
- Nathaniel L Hepowit
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Aeva S Denise
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Jason A MacGurn
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA.
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5
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Lecinski S, Shepherd JW, Bunting K, Dresser L, Quinn SD, MacDonald C, Leake MC. Correlating viscosity and molecular crowding with fluorescent nanobeads and molecular probes: in vitro and in vivo. Interface Focus 2022; 12:20220042. [PMID: 36330320 PMCID: PMC9560789 DOI: 10.1098/rsfs.2022.0042] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/05/2022] [Indexed: 02/02/2023] Open
Abstract
In eukaryotes, intracellular physico-chemical properties like macromolecular crowding and cytoplasmic viscoelasticity influence key processes such as metabolic activities, molecular diffusion and protein folding. However, mapping crowding and viscoelasticity in living cells remains challenging. One approach uses passive rheology in which diffusion of exogenous fluorescent particles internalized in cells is tracked and physico-chemical properties inferred from derived mean square displacement relations. Recently, the crGE2.3 Förster resonance energy transfer biosensor was developed to quantify crowding in cells, though it is unclear how this readout depends on viscoelasticity and the molecular weight of the crowder. Here, we present correlative, multi-dimensional data to explore diffusion and molecular crowding characteristics of molecular crowding agents using super-resolved fluorescence microscopy and ensemble time-resolved spectroscopy. We firstly characterize in vitro and then apply these insights to live cells of budding yeast Saccharomyces cerevisiae. It is to our knowledge the first time this has been attempted. We demonstrate that these are usable both in vitro and in the case of endogenously expressed sensors in live cells. Finally, we present a method to internalize fluorescent beads as in situ viscoelasticity markers in the cytoplasm of live yeast cells and discuss limitations of this approach including impairment of cellular function.
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Affiliation(s)
- Sarah Lecinski
- Department of Physics, University of York, York YO10 5DD, UK
| | - Jack W. Shepherd
- Department of Physics, University of York, York YO10 5DD, UK
- Department of Biology, University of York, York YO10 5DD, UK
| | - Kate Bunting
- Department of Biology, University of York, York YO10 5DD, UK
| | - Lara Dresser
- Department of Physics, University of York, York YO10 5DD, UK
| | - Steven D. Quinn
- Department of Physics, University of York, York YO10 5DD, UK
| | - Chris MacDonald
- Department of Biology, University of York, York YO10 5DD, UK
| | - Mark C. Leake
- Department of Physics, University of York, York YO10 5DD, UK
- Department of Biology, University of York, York YO10 5DD, UK
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6
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Laidlaw KME, Calder G, MacDonald C. Recycling of cell surface membrane proteins from yeast endosomes is regulated by ubiquitinated Ist1. J Cell Biol 2022; 221:213481. [PMID: 36125415 PMCID: PMC9491851 DOI: 10.1083/jcb.202109137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 07/28/2022] [Accepted: 08/23/2022] [Indexed: 11/22/2022] Open
Abstract
Upon internalization, many surface membrane proteins are recycled back to the plasma membrane. Although these endosomal trafficking pathways control surface protein activity, the precise regulatory features and division of labor between interconnected pathways are poorly defined. In yeast, we show recycling back to the surface occurs through distinct pathways. In addition to retrograde recycling pathways via the late Golgi, used by synaptobrevins and driven by cargo ubiquitination, we find nutrient transporter recycling bypasses the Golgi in a pathway driven by cargo deubiquitination. Nutrient transporters rapidly internalize to, and recycle from, endosomes marked by the ESCRT-III associated factor Ist1. This compartment serves as both “early” and “recycling” endosome. We show Ist1 is ubiquitinated and that this is required for proper endosomal recruitment and cargo recycling to the surface. Additionally, the essential ATPase Cdc48 and its adaptor Npl4 are required for recycling, potentially through regulation of ubiquitinated Ist1. This collectively suggests mechanistic features of recycling from endosomes to the plasma membrane are conserved.
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Affiliation(s)
- Kamilla M E Laidlaw
- York Biomedical Research Institute and Department of Biology, University of York, York, UK
| | - Grant Calder
- Imaging and Cytometry Laboratory, Bioscience Technology Facility, Department of Biology, University of York, York, UK
| | - Chris MacDonald
- York Biomedical Research Institute and Department of Biology, University of York, York, UK
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7
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Tseng CC, Piper RC, Katzmann DJ. Bro1 family proteins harmonize cargo sorting with vesicle formation. Bioessays 2022; 44:e2100276. [PMID: 35770783 PMCID: PMC9575758 DOI: 10.1002/bies.202100276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 05/31/2022] [Accepted: 06/08/2022] [Indexed: 11/06/2022]
Abstract
The Endosomal Sorting Complexes Required for Transport (ESCRTs) drive membrane remodeling in a variety of cellular processes that include the formation of endosomal intralumenal vesicles (ILVs) during multivesicular body (MVB) biogenesis. During MVB sorting, ESCRTs recognize ubiquitin (Ub) attached to membrane protein cargo and execute ILV formation by controlling the activities of ESCRT-III polymers regulated by the AAA-ATPase Vps4. Exactly how these events are coordinated to ensure proper cargo loading into ILVs remains unclear. Here we discuss recent work documenting the ability of Bro1, an ESCRT-associated Ub-binding protein, to coordinate ESCRT-III and Vps4-dependent ILV biogenesis with upstream events such as cargo recognition.
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Affiliation(s)
- Chun-Che Tseng
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA.,Biochemistry and Molecular Biology Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | - Robert C Piper
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - David J Katzmann
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA.,Biochemistry and Molecular Biology Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, Minnesota, USA
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8
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Lee J, Xu Y, Ye Y. Safeguarding Lysosomal Homeostasis by DNAJC5/CSPα-Mediated Unconventional Protein Secretion and Endosomal Microautophagy. Front Cell Dev Biol 2022; 10:906453. [PMID: 35620055 PMCID: PMC9127312 DOI: 10.3389/fcell.2022.906453] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 04/25/2022] [Indexed: 11/24/2022] Open
Abstract
Neuronal ceroid lipofuscinosis (NCL) is a collection of genetically inherited neurological disorders characterized by vision loss, seizure, brain death, and premature lethality. At the cellular level, a key pathologic hallmark of NCL is the build-up of autofluorescent storage materials (AFSM) in lysosomes of both neurons and non-neuronal cells. Molecular dissection of the genetic lesions underlying NCLs has shed significant insights into how disruption of lysosomal homeostasis may lead to lipofuscin accumulation and NCLs. Intriguingly, recent studies on DNAJC5/CSPα, a membrane associated HSC70 co-chaperone, have unexpectedly linked lipofuscin accumulation to two intimately coupled protein quality control processes at endolysosomes. This review discusses how deregulation of unconventional protein secretion and endosomal microautophagy (eMI) contributes to lipofuscin accumulation and neurodegeneration.
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Affiliation(s)
| | | | - Yihong Ye
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
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9
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Gao J, Nicastro R, Péli-Gulli MP, Grziwa S, Chen Z, Kurre R, Piehler J, De Virgilio C, Fröhlich F, Ungermann C. The HOPS tethering complex is required to maintain signaling endosome identity and TORC1 activity. J Biophys Biochem Cytol 2022; 221:213121. [PMID: 35404387 PMCID: PMC9011323 DOI: 10.1083/jcb.202109084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 01/27/2022] [Accepted: 02/28/2022] [Indexed: 12/04/2022] Open
Abstract
The endomembrane system of eukaryotic cells is essential for cellular homeostasis during growth and proliferation. Previous work showed that a central regulator of growth, namely the target of rapamycin complex 1 (TORC1), binds both membranes of vacuoles and signaling endosomes (SEs) that are distinct from multivesicular bodies (MVBs). Interestingly, the endosomal TORC1, which binds membranes in part via the EGO complex, critically defines vacuole integrity. Here, we demonstrate that SEs form at a branch point of the biosynthetic and endocytic pathways toward the vacuole and depend on MVB biogenesis. Importantly, function of the HOPS tethering complex is essential to maintain the identity of SEs and proper endosomal and vacuolar TORC1 activities. In HOPS mutants, the EGO complex redistributed to the Golgi, which resulted in a partial mislocalization of TORC1. Our study uncovers that SE function requires a functional HOPS complex and MVBs, suggesting a tight link between trafficking and signaling along the endolysosomal pathway.
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Affiliation(s)
- Jieqiong Gao
- Department of Biology/Chemistry, Biochemistry Section, Osnabrück University, Osnabrück, Germany
| | - Raffaele Nicastro
- Department of Biology, University of Fribourg, Chemin du Musée, Fribourg, Switzerland
| | | | - Sophie Grziwa
- Department of Biology/Chemistry, Biochemistry Section, Osnabrück University, Osnabrück, Germany
| | - Zilei Chen
- Department of Biology/Chemistry, Biochemistry Section, Osnabrück University, Osnabrück, Germany
| | - Rainer Kurre
- Center of Cellular Nanoanalytic Osnabrück (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Jacob Piehler
- Center of Cellular Nanoanalytic Osnabrück (CellNanOs), Osnabrück University, Osnabrück, Germany
- Department of Biology/Chemistry, Biophysics Section, Osnabrück University, Osnabrück, Germany
| | - Claudio De Virgilio
- Department of Biology, University of Fribourg, Chemin du Musée, Fribourg, Switzerland
| | - Florian Fröhlich
- Center of Cellular Nanoanalytic Osnabrück (CellNanOs), Osnabrück University, Osnabrück, Germany
- Department of Biology/Chemistry, Molecular Membrane Biology Section, Osnabrück University, Osnabrück, Germany
| | - Christian Ungermann
- Department of Biology/Chemistry, Biochemistry Section, Osnabrück University, Osnabrück, Germany
- Center of Cellular Nanoanalytic Osnabrück (CellNanOs), Osnabrück University, Osnabrück, Germany
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10
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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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11
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Ubiquitination of the ubiquitin-binding machinery: how early ESCRT components are controlled. Essays Biochem 2022; 66:169-177. [PMID: 35352804 PMCID: PMC9400068 DOI: 10.1042/ebc20210042] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/04/2022] [Accepted: 03/16/2022] [Indexed: 12/22/2022]
Abstract
To be able to quickly and accurately respond to the environment, cells need to tightly control the amount and localization of plasma membrane proteins. The post-translation modification by the protein modifier ubiquitin is the key signal for guiding membrane-associated cargo to the lysosome/vacuole for their degradation. The machinery responsible for such sorting contains several subunits that function as ubiquitin receptors, many of which are themselves subjected to ubiquitination. This review will focus on what is currently known about the modulation of the machinery itself by ubiquitination and how this might affect its function with a special emphasis on current findings from the plant field.
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12
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Ge Y, Wang J, Zhang H, Li J, Ye M, Jin X. Fate of hematopoietic stem cells determined by Notch1 signaling (Review). Exp Ther Med 2022; 23:170. [PMID: 35069851 PMCID: PMC8764575 DOI: 10.3892/etm.2021.11093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 11/17/2021] [Indexed: 11/05/2022] Open
Abstract
Regulation of the fate of hematopoietic stem cells (HSCs), including silencing, self-renewal or differentiation into blood line cells, is crucial to maintain the homeostasis of the human blood system and prevent leukemia. Notch1, a key receptor in the Notch signaling pathway, plays an important regulatory role in these properties of HSCs, particularly in the maintenance of the stemness of HSCs. In recent decades, the ubiquitination modification of Notch1 has been gradually revealed, and also demonstrated to affect the proliferation and differentiation of HSCs. Therefore, a detailed elucidation of Notch1 and its ubiquitination modification may help to improve understanding of the maintenance of HSC properties and the pathogenesis of leukemia. In addition, it may aid in identifying potential therapeutic targets for specific leukemias and provide potential prognostic indicators for HSC transplantation (HSCT). In the present review, the association between Notch1 and HSCs and the link between the ubiquitination modification of Notch1 and HSCs were described. In addition, the association between abnormal HSCs mediated by Notch1 or ubiquitinated Notch1and T-cell acute lymphoblastic leukemia (T-ALL) was also examined, which provides a promising direction for clinical application.
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Affiliation(s)
- Yidong Ge
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo, Zhejiang 315020, P.R. China
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Jie Wang
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo, Zhejiang 315020, P.R. China
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Hui Zhang
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo, Zhejiang 315020, P.R. China
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Jinyun Li
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo, Zhejiang 315020, P.R. China
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Meng Ye
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo, Zhejiang 315020, P.R. China
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Xiaofeng Jin
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo, Zhejiang 315020, P.R. China
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, Zhejiang 315211, P.R. China
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13
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Buysse D, West M, Leih M, Odorizzi G. Bro1 binds the Vps20 subunit of ESCRT-III and promotes ESCRT-III regulation by Doa4. Traffic 2022; 23:109-119. [PMID: 34908216 PMCID: PMC8792227 DOI: 10.1111/tra.12828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 11/19/2021] [Accepted: 12/09/2021] [Indexed: 02/03/2023]
Abstract
The budding of intralumenal vesicles (ILVs) at endosomes requires membrane scission by the ESCRT-III complex. This step is negatively regulated in yeast by Doa4, the ubiquitin hydrolase that deubiquitinates transmembrane proteins sorted as cargoes into ILVs. Doa4 acts non-enzymatically to inhibit ESCRT-III membrane scission activity by directly binding the Snf7 subunit of ESCRT-III. This interaction inhibits the remodeling/disassembly of Snf7 polymers required for the ILV membrane scission reaction. Thus, Doa4 is thought to have a structural role that delays ILV budding while it also functions enzymatically to deubiquitinate ILV cargoes. In this study, we show that Doa4 binding to Snf7 in vivo is antagonized by another ESCRT-III subunit, Vps20. Doa4 is restricted from interacting with Snf7 in yeast expressing a mutant Vps20 allele that constitutively binds Doa4. This inhibitory effect of Vps20 is suppressed by overexpression of another ESCRT-III-associated protein, Bro1. We show that Bro1 binds directly to Vps20, suggesting that Bro1 has a central role in relieving the antagonistic relationship that Vps20 has toward Doa4.
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Affiliation(s)
- Dalton Buysse
- Department of Molecular Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Matt West
- Department of Molecular Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Mitchell Leih
- Department of Molecular Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Greg Odorizzi
- Department of Molecular Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA,Author for correspondence ()
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14
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Pashkova N, Yu L, Schnicker NJ, Tseng CC, Gakhar L, Katzmann DJ, Piper RC. Interactions of ubiquitin and CHMP5 with the V domain of HD-PTP reveals role for regulation of Vps4 ATPase. Mol Biol Cell 2021; 32:ar42. [PMID: 34586919 PMCID: PMC8694081 DOI: 10.1091/mbc.e21-04-0219] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The family of Bro1 proteins coordinates the activity of the Endosomal Sorting Complexes Required for Transport (ESCRTs) to mediate a number of membrane remodeling events. These events culminate in membrane scission catalyzed by ESCRT-III, whose polymerization and disassembly is controlled by the AAA-ATPase, Vps4. Bro1-family members Alix and HD-PTP as well as yeast Bro1 have central “V” domains that noncovalently bind Ub and connect ubiquitinated proteins to ESCRT-driven functions such as the incorporation of ubiquitinated membrane proteins into intralumenal vesicles of multivesicular bodies. Recently, it was discovered that the V domain of yeast Bro1 binds the MIT domain of Vps4 to stimulate its ATPase activity. Here we determine the structural basis for how the V domain of human HD-PTP binds ubiquitin. The HD-PTP V domain also binds the MIT domain of Vps4, and ubiquitin binding to the HD-PTP V domain enhances its ability to stimulate Vps4 ATPase activity. Additionally, we found that V domains of both HD-PTP and Bro1 bind CHMP5 and Vps60, respectively, providing another potential molecular mechanism to alter Vps4 activity. These data support a model whereby contacts between ubiquitin, ESCRT-III, and Vps4 by V domains of the Bro1 family may coordinate late events in ESCRT-driven membrane remodeling events.
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Affiliation(s)
- Natalya Pashkova
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242
| | - Liping Yu
- NMR facility, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242.,Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242
| | | | - Chun-Che Tseng
- Biochemistry and Molecular Biology Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN, 55905.,Protein Crystallography Facility, University of Iowa, Iowa City, IA, 52242
| | - Lokesh Gakhar
- Protein Crystallography Facility, University of Iowa, Iowa City, IA, 52242
| | - David J Katzmann
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905
| | - Robert C Piper
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242
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15
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Tseng CC, Dean S, Davies BA, Azmi IF, Pashkova N, Payne JA, Staffenhagen J, West M, Piper RC, Odorizzi G, Katzmann DJ. Bro1 stimulates Vps4 to promote intralumenal vesicle formation during multivesicular body biogenesis. J Cell Biol 2021; 220:212434. [PMID: 34160559 PMCID: PMC8240856 DOI: 10.1083/jcb.202102070] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 05/18/2021] [Accepted: 05/23/2021] [Indexed: 01/20/2023] Open
Abstract
Endosomal sorting complexes required for transport (ESCRT-0, -I, -II, -III) execute cargo sorting and intralumenal vesicle (ILV) formation during conversion of endosomes to multivesicular bodies (MVBs). The AAA-ATPase Vps4 regulates the ESCRT-III polymer to facilitate membrane remodeling and ILV scission during MVB biogenesis. Here, we show that the conserved V domain of ESCRT-associated protein Bro1 (the yeast homologue of mammalian proteins ALIX and HD-PTP) directly stimulates Vps4. This activity is required for MVB cargo sorting. Furthermore, the Bro1 V domain alone supports Vps4/ESCRT–driven ILV formation in vivo without efficient MVB cargo sorting. These results reveal a novel activity of the V domains of Bro1 homologues in licensing ESCRT-III–dependent ILV formation and suggest a role in coordinating cargo sorting with membrane remodeling during MVB sorting. Moreover, ubiquitin binding enhances V domain stimulation of Vps4 to promote ILV formation via the Bro1–Vps4–ESCRT-III axis, uncovering a novel role for ubiquitin during MVB biogenesis in addition to facilitating cargo recognition.
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Affiliation(s)
- Chun-Che Tseng
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN.,Biochemistry and Molecular Biology Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN
| | - Shirley Dean
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN.,Biochemistry and Molecular Biology Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN
| | - Brian A Davies
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN
| | - Ishara F Azmi
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN.,Biochemistry and Molecular Biology Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN
| | - Natalya Pashkova
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Johanna A Payne
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN
| | | | - Matt West
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO
| | - Robert C Piper
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Greg Odorizzi
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO
| | - David J Katzmann
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN.,Biochemistry and Molecular Biology Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN
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16
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Beatriz M, Vilaça R, Lopes C. Exosomes: Innocent Bystanders or Critical Culprits in Neurodegenerative Diseases. Front Cell Dev Biol 2021; 9:635104. [PMID: 34055771 PMCID: PMC8155522 DOI: 10.3389/fcell.2021.635104] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 04/06/2021] [Indexed: 12/11/2022] Open
Abstract
Extracellular vesicles (EVs) are nano-sized membrane-enclosed particles released by cells that participate in intercellular communication through the transfer of biologic material. EVs include exosomes that are small vesicles that were initially associated with the disposal of cellular garbage; however, recent findings point toward a function as natural carriers of a wide variety of genetic material and proteins. Indeed, exosomes are vesicle mediators of intercellular communication and maintenance of cellular homeostasis. The role of exosomes in health and age-associated diseases is far from being understood, but recent evidence implicates exosomes as causative players in the spread of neurodegenerative diseases. Cells from the central nervous system (CNS) use exosomes as a strategy not only to eliminate membranes, toxic proteins, and RNA species but also to mediate short and long cell-to-cell communication as carriers of important messengers and signals. The accumulation of protein aggregates is a common pathological hallmark in many neurodegenerative diseases, including Alzheimer’s disease, Parkinson’s disease, Huntington’s disease, amyotrophic lateral sclerosis, and prion diseases. Protein aggregates can be removed and delivered to degradation by the endo-lysosomal pathway or can be incorporated in multivesicular bodies (MVBs) that are further released to the extracellular space as exosomes. Because exosome transport damaged cellular material, this eventually contributes to the spread of pathological misfolded proteins within the brain, thus promoting the neurodegeneration process. In this review, we focus on the role of exosomes in CNS homeostasis, their possible contribution to the development of neurodegenerative diseases, the usefulness of exosome cargo as biomarkers of disease, and the potential benefits of plasma circulating CNS-derived exosomes.
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Affiliation(s)
- Margarida Beatriz
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,IIIUC-Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | - Rita Vilaça
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,IIIUC-Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | - Carla Lopes
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,IIIUC-Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
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17
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Dutta D, Sharma V, Mutsuddi M, Mukherjee A. Regulation of Notch signaling by E3 ubiquitin ligases. FEBS J 2021; 289:937-954. [PMID: 33644958 DOI: 10.1111/febs.15792] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 02/07/2021] [Accepted: 02/25/2021] [Indexed: 12/11/2022]
Abstract
Notch signaling is an evolutionarily conserved pathway that is widely used for multiple cellular events during development. Activation of the Notch pathway occurs when the ligand from a neighboring cell binds to the Notch receptor and induces cleavage of the intracellular domain of Notch, which further translocates into the nucleus to activate its downstream genes. The involvement of the Notch pathway in diverse biological events is possible due to the complexity in its regulation. In order to maintain tight spatiotemporal regulation, the Notch receptor, as well as its ligand, undergoes a series of physical and biochemical modifications that, in turn, helps in proper maintenance and fine-tuning of the signaling outcome. Ubiquitination is the post-translational addition of a ubiquitin molecule to a substrate protein, and the process is regulated by E3 ubiquitin ligases. The present review describes the involvement of different E3 ubiquitin ligases that play an important role in the regulation and maintenance of proper Notch signaling and how perturbation in ubiquitination results in abnormal Notch signaling leading to a number of human diseases.
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Affiliation(s)
- Debdeep Dutta
- Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Vartika Sharma
- Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Mousumi Mutsuddi
- Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Ashim Mukherjee
- Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi, India
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18
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Laidlaw KME, Bisinski DD, Shashkova S, Paine KM, Veillon MA, Leake MC, MacDonald C. A glucose-starvation response governs endocytic trafficking and eisosomal retention of surface cargoes in budding yeast. J Cell Sci 2021; 134:jcs257733. [PMID: 33443082 PMCID: PMC7860119 DOI: 10.1242/jcs.257733] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 12/07/2020] [Indexed: 12/29/2022] Open
Abstract
Eukaryotic cells adapt their metabolism to the extracellular environment. Downregulation of surface cargo proteins in response to nutrient stress reduces the burden of anabolic processes whilst elevating catabolic production in the lysosome. We show that glucose starvation in yeast triggers a transcriptional response that increases internalisation from the plasma membrane. Nuclear export of the Mig1 transcriptional repressor in response to glucose starvation increases levels of the Yap1801 and Yap1802 clathrin adaptors, which is sufficient to increase cargo internalisation. Beyond this, we show that glucose starvation results in Mig1-independent transcriptional upregulation of various eisosomal factors. These factors serve to sequester a portion of nutrient transporters at existing eisosomes, through the presence of Ygr130c and biochemical and biophysical changes in Pil1, allowing cells to persist throughout the starvation period and maximise nutrient uptake upon return to replete conditions. This provides a physiological benefit for cells to rapidly recover from glucose starvation. Collectively, this remodelling of the surface protein landscape during glucose starvation calibrates metabolism to available nutrients.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Kamilla M E Laidlaw
- York Biomedical Research Institute and Department of Biology, University of York, York, UK
| | - Daniel D Bisinski
- York Biomedical Research Institute and Department of Biology, University of York, York, UK
| | - Sviatlana Shashkova
- York Biomedical Research Institute and Department of Biology, University of York, York, UK
- Department of Physics, University of York, York YO10 5DD, UK
| | - Katherine M Paine
- York Biomedical Research Institute and Department of Biology, University of York, York, UK
| | - Malaury A Veillon
- York Biomedical Research Institute and Department of Biology, University of York, York, UK
| | - Mark C Leake
- York Biomedical Research Institute and Department of Biology, University of York, York, UK
- Department of Physics, University of York, York YO10 5DD, UK
| | - Chris MacDonald
- York Biomedical Research Institute and Department of Biology, University of York, York, UK
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19
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Adaptors as the regulators of HECT ubiquitin ligases. Cell Death Differ 2021; 28:455-472. [PMID: 33402750 DOI: 10.1038/s41418-020-00707-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/04/2020] [Accepted: 11/04/2020] [Indexed: 12/15/2022] Open
Abstract
The HECT (homologous to E6AP C-terminus) ubiquitin ligases (E3s) are a small family of highly conserved enzymes involved in diverse cellular functions and pathological conditions. Characterised by a C-terminal HECT domain that accepts ubiquitin from E2 ubiquitin conjugating enzymes, these E3s regulate key signalling pathways. The activity and functional regulation of HECT E3s are controlled by several factors including post-translational modifications, inter- and intramolecular interactions and binding of co-activators and adaptor proteins. In this review, we focus on the regulation of HECT E3s by accessory proteins or adaptors and discuss various ways by which adaptors mediate their regulatory roles to affect physiological outcomes. We discuss common features that are conserved from yeast to mammals, regardless of the type of E3s as well as shed light on recent discoveries explaining some existing enigmas in the field.
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20
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Norris A, Grant BD. Endosomal microdomains: Formation and function. Curr Opin Cell Biol 2020; 65:86-95. [PMID: 32247230 PMCID: PMC7529669 DOI: 10.1016/j.ceb.2020.02.018] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/24/2020] [Accepted: 02/25/2020] [Indexed: 12/18/2022]
Abstract
It is widely recognized that after endocytosis, internalized cargo is delivered to endosomes that act as sorting stations. The limiting membrane of endosomes contain specialized subregions, or microdomains, that represent distinct functions of the endosome, including regions competing for cargo capture leading to degradation or recycling. Great progress has been made in defining the endosomal protein coats that sort cargo in these domains, including Retromer that recycles transmembrane cargo, and ESCRT (endosomal sorting complex required for transport) that degrades transmembrane cargo. In this review, we discuss recent work that is beginning to unravel how such coat complexes contribute to the creation and maintenance of endosomal microdomains. We highlight data that indicates that adjacent microdomains do not act independently but rather interact to cross-regulate. We posit that these interactions provide an agile means for the cell to adjust sorting in response to extracellular signals and intracellular metabolic cues.
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Affiliation(s)
- Anne Norris
- Rutgers University, Department of Molecular Biology and Biochemistry, Piscataway, NJ, 08854, USA
| | - Barth D Grant
- Rutgers University, Department of Molecular Biology and Biochemistry, Piscataway, NJ, 08854, USA.
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21
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Casler JC, Glick BS. A microscopy-based kinetic analysis of yeast vacuolar protein sorting. eLife 2020; 9:56844. [PMID: 32584255 PMCID: PMC7338053 DOI: 10.7554/elife.56844] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 06/23/2020] [Indexed: 12/25/2022] Open
Abstract
Saccharomyces cerevisiae is amenable to studying membrane traffic by live-cell fluorescence microscopy. We used this system to explore two aspects of cargo protein traffic through prevacuolar endosome (PVE) compartments to the vacuole. First, at what point during Golgi maturation does a biosynthetic vacuolar cargo depart from the maturing cisternae? To address this question, we modified a regulatable fluorescent secretory cargo by adding a vacuolar targeting signal. Traffic of the vacuolar cargo requires the GGA clathrin adaptors, which arrive during the early-to-late Golgi transition. Accordingly, the vacuolar cargo begins to exit the Golgi near the midpoint of maturation, significantly before exit of a secretory cargo. Second, how are cargoes delivered from PVE compartments to the vacuole? To address this question, we tracked biosynthetic and endocytic cargoes after they had accumulated in PVE compartments. The results suggest that stable PVE compartments repeatedly deliver material to the vacuole by a kiss-and-run mechanism.
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Affiliation(s)
- Jason C Casler
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, United States
| | - Benjamin S Glick
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, United States
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22
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Moulinier-Anzola J, Schwihla M, De-Araújo L, Artner C, Jörg L, Konstantinova N, Luschnig C, Korbei B. TOLs Function as Ubiquitin Receptors in the Early Steps of the ESCRT Pathway in Higher Plants. MOLECULAR PLANT 2020; 13:717-731. [PMID: 32087370 DOI: 10.1016/j.molp.2020.02.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 01/17/2020] [Accepted: 02/13/2020] [Indexed: 05/21/2023]
Abstract
Protein abundance and localization at the plasma membrane (PM) shapes plant development and mediates adaptation to changing environmental conditions. It is regulated by ubiquitination, a post-translational modification crucial for the proper sorting of endocytosed PM proteins to the vacuole for subsequent degradation. To understand the significance and the variety of roles played by this reversible modification, the function of ubiquitin receptors, which translate the ubiquitin signature into a cellular response, needs to be elucidated. In this study, we show that TOL (TOM1-like) proteins function in plants as multivalent ubiquitin receptors, governing ubiquitinated cargo delivery to the vacuole via the conserved Endosomal Sorting Complex Required for Transport (ESCRT) pathway. TOL2 and TOL6 interact with components of the ESCRT machinery and bind to K63-linked ubiquitin via two tandemly arranged conserved ubiquitin-binding domains. Mutation of these domains results not only in a loss of ubiquitin binding but also altered localization, abolishing TOL6 ubiquitin receptor activity. Function and localization of TOL6 is itself regulated by ubiquitination, whereby TOL6 ubiquitination potentially modulates degradation of PM-localized cargoes, assisting in the fine-tuning of the delicate interplay between protein recycling and downregulation. Taken together, our findings demonstrate the function and regulation of a ubiquitin receptor that mediates vacuolar degradation of PM proteins in higher plants.
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Affiliation(s)
- Jeanette Moulinier-Anzola
- Institute of Molecular Plant Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Maximilian Schwihla
- Institute of Molecular Plant Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Lucinda De-Araújo
- Institute of Molecular Plant Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Christina Artner
- Institute of Molecular Plant Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Lisa Jörg
- Institute of Molecular Plant Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Nataliia Konstantinova
- Institute of Molecular Plant Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Christian Luschnig
- Institute of Molecular Plant Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Barbara Korbei
- Institute of Molecular Plant Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria.
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23
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MacDonald C, Shields SB, Williams CA, Winistorfer S, Piper RC. A Cycle of Ubiquitination Regulates Adaptor Function of the Nedd4-Family Ubiquitin Ligase Rsp5. Curr Biol 2020; 30:465-479.e5. [PMID: 31956026 PMCID: PMC7197006 DOI: 10.1016/j.cub.2019.11.086] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 10/28/2019] [Accepted: 11/29/2019] [Indexed: 10/25/2022]
Abstract
In yeast, the main ubiquitin ligase responsible for the sorting of proteins to the lysosomal vacuole is Rsp5, a member of the Nedd4 family of ligases whose distinguishing features are a catalytic homologous to E6AP C terminus (HECT) domain and 3 central WW domains that bind PY motifs in target proteins. Many substrates do not bind Rsp5 directly and instead rely on PY-containing adaptor proteins that interact with Rsp5. Recent studies indicate that the activities of these adaptors are elevated when they undergo ubiquitination, yet the mechanism whereby ubiquitination activates the adaptors and how this process is regulated remain unclear. Here, we report on a mechanism that explains how ubiquitination stimulates adaptor function and how this process can be regulated by the Rsp5-associated deubiquitinase, Ubp2. Our overexpression experiments revealed that several adaptors compete for Rsp5 in vivo. We found that the ability of the adaptors to compete effectively was enhanced by their ubiquitination and diminished by a block of their ubiquitination. Ubiquitination-dependent adaptor activation required a ubiquitin-binding surface within the Rsp5 catalytic HECT domain. Finally, like constitutively ubiquitinated adaptors, a Ubp2 deficiency increased both the adaptor activity and the ability to compete for Rsp5. Our data support a model whereby ubiquitinated Rsp5 adaptors are more active when "locked" onto Rsp5 via its N-lobe ubiquitin-binding surface and less active when they are "unlocked" by Ubp2-mediated deubiquitination.
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Affiliation(s)
- Chris MacDonald
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA USA, 52242,Current Address: Department of Biology, University of York, York, UK YO10 5DD
| | - S. Brookhart Shields
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA USA, 52242,Current Address: Gustavus Adolphus College, 800 West College Ave. Saint Peter, MN USA, 56082
| | - Charlotte A. Williams
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA USA, 52242
| | - Stanley Winistorfer
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA USA, 52242
| | - Robert C. Piper
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA USA, 52242,Lead Contact:
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24
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Horstmann C, Kim DS, Campbell C, Kim K. Transcriptome Profile Alteration with Cadmium Selenide/Zinc Sulfide Quantum Dots in Saccharomyces cerevisiae. Biomolecules 2019; 9:biom9110653. [PMID: 31731522 PMCID: PMC6920935 DOI: 10.3390/biom9110653] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/18/2019] [Accepted: 10/21/2019] [Indexed: 02/07/2023] Open
Abstract
Quantum Dots (QDs) are becoming more prevalent in products used in our daily lives, such as TVs and laptops, due to their unique and tunable optical properties. The possibility of using QDs as fluorescent probes in applications, such as medical imaging, has been a topic of interest for some time, but their potential toxicity and long-term effects on the environment are not well understood. In the present study, we investigated the effects of yellow CdSe/ZnS-QDs on Saccharomyces cerevisiae. We utilized growth assays, RNA-seq, reactive oxygen species (ROS) detection assays, and cell wall stability experiments to investigate the potential toxic effects of CdSe/ZnS-QDs. We found CdSe/ZnS-QDs had no negative effects on cell viability; however, cell wall-compromised cells showed more sensitivity in the presence of 10 µg/mL CdSe/ZnS-QDs compared to non-treated cells. In CdSe/ZnS-treated and non-treated cells, no significant change in superoxide was detected, but according to our transcriptomic analysis, thousands of genes in CdSe/ZnS-treated cells became differentially expressed. Four significantly differentiated genes found, including FAF1, SDA1, DAN1, and TIR1, were validated by consistent results with RT-qPCR assays. Our transcriptome analysis led us to conclude that exposure of CdSe/ZnS-QDs on yeast significantly affected genes implicated in multiple cellular processes.
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Affiliation(s)
- Cullen Horstmann
- Department of Biology, Missouri State University, 901 S National, Springfield, MO 65897, USA; (C.H.); (C.C.)
| | - Daniel S Kim
- Kickapoo High School, 3710 South Jefferson Ave, Springfield, MO 65807, USA;
| | - Chelsea Campbell
- Department of Biology, Missouri State University, 901 S National, Springfield, MO 65897, USA; (C.H.); (C.C.)
| | - Kyoungtae Kim
- Department of Biology, Missouri State University, 901 S National, Springfield, MO 65897, USA; (C.H.); (C.C.)
- Correspondence: ; Tel.: +1-417-836-5440; Fax: +1-417-836-5126
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25
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Guiney EL, Zhu L, Sardana R, Emr SD, Baile MG. Methods for studying the regulation of membrane traffic by ubiquitin and the ESCRT pathway. Methods Enzymol 2019; 619:269-291. [PMID: 30910024 DOI: 10.1016/bs.mie.2018.12.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Covalent modification of proteins with ubiquitin dynamically regulates their function and fate. The ubiquitination of most plasma membrane proteins initiates endocytosis and ESCRT-mediated sorting to the lysosomal lumen for degradation. Powerful genetic approaches in the budding yeast Saccharomyces cerevisiae have been particularly instrumental in the discovery and elucidation of these molecular mechanisms, which are conserved in all eukaryotes. Here we provide two detailed protocols and tools for studying ubiquitination-dependent membrane trafficking mechanisms in yeast. The first utilizes fusions between a protein of interest and an auxotrophic marker to screen for mutants that affect ubiquitin-mediated endocytosis. The second method artificially ubiquitinates a protein of interest, allowing downstream trafficking steps to be studied independently from the regulatory signals that initiate endocytosis.
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Affiliation(s)
- Evan L Guiney
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States
| | - Lu Zhu
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States
| | - Richa Sardana
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States
| | - Scott D Emr
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States.
| | - Matthew G Baile
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States
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26
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Distribution of Proteins at the Inner Nuclear Membrane Is Regulated by the Asi1 E3 Ligase in Saccharomyces cerevisiae. Genetics 2019; 211:1269-1282. [PMID: 30709848 PMCID: PMC6456303 DOI: 10.1534/genetics.119.301911] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 01/30/2019] [Indexed: 12/11/2022] Open
Abstract
Inner nuclear membrane (INM) protein composition regulates nuclear function, affecting processes such as gene expression, chromosome organization, nuclear shape, and stability. Mechanisms that drive changes in the INM proteome are poorly understood, in part because it is difficult to definitively assay INM composition rigorously and systematically. Using a split-GFP complementation system to detect INM access, we examined the distribution of all C-terminally tagged Saccharomyces cerevisiae membrane proteins in wild-type cells and in mutants affecting protein quality control pathways, such as INM-associated degradation (INMAD), ER-associated degradation, and vacuolar proteolysis. Deletion of the E3 ligase Asi1 had the most specific effect on the INM compared to mutants in vacuolar or ER-associated degradation pathways, consistent with a role for Asi1 in the INMAD pathway. Our data suggest that Asi1 not only removes mistargeted proteins at the INM, but also controls the levels and distribution of native INM components, such as the membrane nucleoporin Pom33. Interestingly, loss of Asi1 does not affect Pom33 protein levels but instead alters Pom33 distribution in the nuclear envelope through Pom33 ubiquitination, which drives INM redistribution. Taken together, our data demonstrate that the Asi1 E3 ligase has a novel function in INM protein regulation in addition to protein turnover.
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27
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Cullen PJ, Steinberg F. To degrade or not to degrade: mechanisms and significance of endocytic recycling. Nat Rev Mol Cell Biol 2018; 19:679-696. [PMID: 30194414 DOI: 10.1038/s41580-018-0053-7] [Citation(s) in RCA: 314] [Impact Index Per Article: 52.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Newly endocytosed integral cell surface proteins are typically either directed for degradation or subjected to recycling back to the plasma membrane. The sorting of integral cell surface proteins, including signalling receptors, nutrient transporters, ion channels, adhesion molecules and polarity markers, within the endolysosomal network for recycling is increasingly recognized as an essential feature in regulating the complexities of physiology at the cell, tissue and organism levels. Historically, endocytic recycling has been regarded as a relatively passive process, where the majority of internalized integral proteins are recycled via a nonspecific sequence-independent 'bulk membrane flow' pathway. Recent work has increasingly challenged this view. The discovery of sequence-specific sorting motifs and the identification of cargo adaptors and associated coat complexes have begun to uncover the highly orchestrated nature of endosomal cargo recycling, thereby providing new insight into the function and (patho)physiology of this process.
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Affiliation(s)
- Peter J Cullen
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, Bristol, UK.
| | - Florian Steinberg
- Center for Biological Systems Analysis, Albert Ludwigs Universitaet Freiburg, Freiburg im Breisgau, Germany.
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28
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Endosomal trafficking of yeast membrane proteins. Biochem Soc Trans 2018; 46:1551-1558. [PMID: 30381337 DOI: 10.1042/bst20180258] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 09/01/2018] [Accepted: 09/14/2018] [Indexed: 01/19/2023]
Abstract
Various membrane trafficking pathways transport molecules through the endosomal system of eukaryotic cells, where trafficking decisions control the localisation and activity of a diverse repertoire of membrane protein cargoes. The budding yeast Saccharomyces cerevisiae has been used to discover and define many mechanisms that regulate conserved features of endosomal trafficking. Internalised surface membrane proteins first localise to endosomes before sorting to other compartments. Ubiquitination of endosomal membrane proteins is a signal for their degradation. Ubiquitinated cargoes are recognised by the endosomal sorting complex required for transport (ESCRT) apparatus, which mediate sorting through the multivesicular body pathway to the lysosome for degradation. Proteins that are not destined for degradation can be recycled to other intracellular compartments, such as the Golgi and the plasma membrane. In this review, we discuss recent developments elucidating the mechanisms that drive membrane protein degradation and recycling pathways in yeast.
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29
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Roles for ER:endosome membrane contact sites in ligand-stimulated intraluminal vesicle formation. Biochem Soc Trans 2018; 46:1055-1062. [PMID: 30242114 PMCID: PMC6195632 DOI: 10.1042/bst20170432] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 07/31/2018] [Accepted: 08/08/2018] [Indexed: 12/12/2022]
Abstract
Multivesicular endosomes/bodies (MVBs) sort membrane proteins between recycling and degradative pathways. Segregation of membrane proteins onto intraluminal vesicles (ILVs) of MVBs removes them from the recycling pathway and facilitates their degradation following fusion of MVBs with lysosomes. Sorting of many cargos onto ILVs depends on the ESCRT (Endosomal Sorting Complex Required for Transport) machinery, although ESCRT-independent mechanisms also exist. In mammalian cells, efficient sorting of ligand-stimulated epidermal growth factor receptors onto ILVs also depends on the tyrosine phosphatase, PTP1B, an ER-localised enzyme that interacts with endosomal targets at membrane contacts between MVBs and the ER. This review focuses on the potential roles played by ER:MVB membrane contact sites in regulating ESCRT-dependent ILV formation.
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30
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Monoubiquitination of Cancer Stem Cell Marker CD133 at Lysine 848 Regulates Its Secretion and Promotes Cell Migration. Mol Cell Biol 2018; 38:MCB.00024-18. [PMID: 29760280 DOI: 10.1128/mcb.00024-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 05/07/2018] [Indexed: 12/12/2022] Open
Abstract
CD133, a widely known marker of cancer stem cells, was recently found in extracellular vesicles. However, the mechanisms underlying CD133 translocation to the extracellular space remain largely unknown. Here we report that CD133 is monoubiquitinated. Ubiquitination occurs primarily on complex glycosylated CD133. The lysine 848 residue at the intracellular carboxyl terminus is one of the sites for CD133 ubiquitination. The K848R mutation does not affect CD133 degradation by the lysosomal pathway but significantly reduces CD133 secretion by inhibiting the interaction between CD133 and tumor susceptibility gene 101 (Tsg101). Furthermore, knockdown of the E3 ubiquitin protein ligase Nedd4 largely impairs CD133 ubiquitination and vesicle secretion. Importantly, CD133-containing vesicles are taken up by recipient cells, consequently promoting cell migration. The K848R mutation reduces cell migration induced by CD133. Taken together, our findings show that monoubiquitination contributes to CD133 vesicle secretion and promotes recipient cell migration. These findings provide a clue to the mechanisms of CD133 secretion and cancer stem cell microenvironment interactional effects.
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31
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Crespo-Yàñez X, Aguilar-Gurrieri C, Jacomin AC, Journet A, Mortier M, Taillebourg E, Soleilhac E, Weissenhorn W, Fauvarque MO. CHMP1B is a target of USP8/UBPY regulated by ubiquitin during endocytosis. PLoS Genet 2018; 14:e1007456. [PMID: 29933386 PMCID: PMC6033466 DOI: 10.1371/journal.pgen.1007456] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 07/05/2018] [Accepted: 05/30/2018] [Indexed: 11/29/2022] Open
Abstract
Integration and down-regulation of cell growth and differentiation signals rely on plasma membrane receptor endocytosis and sorting towards either recycling vesicles or degradative lysosomes via multivesicular bodies (MVB). In this process, the endosomal sorting complex-III required for transport (ESCRT-III) controls membrane deformation and scission triggering intraluminal vesicle (ILV) formation at early endosomes. Here, we show that the ESCRT-III member CHMP1B can be ubiquitinated within a flexible loop known to undergo conformational changes during polymerization. We demonstrate further that CHMP1B is deubiquitinated by the ubiquitin specific protease USP8 (syn. UBPY) and found fully devoid of ubiquitin in a ~500 kDa large complex that also contains its ESCRT-III partner IST1. Moreover, EGF stimulation induces the rapid and transient accumulation of ubiquitinated forms of CHMP1B on cell membranes. Accordingly, CHMP1B ubiquitination is necessary for CHMP1B function in both EGF receptor trafficking in human cells and wing development in Drosophila. Based on these observations, we propose that CHMP1B is dynamically regulated by ubiquitination in response to EGF and that USP8 triggers CHMP1B deubiquitination possibly favoring its subsequent assembly into a membrane-associated ESCRT-III polymer. In multicellular organisms, the interpretation and transmission of cell growth and differentiation signals strongly rely on plasma membrane receptors. Once activated by their ligands, these receptors activate downstream signaling cascades and are rapidly internalized into intracellular vesicles that fuse inside the cell to form the endosomal compartment. From there, the receptors are sorted towards either recycling vesicles or degradative lysosomes via multivesicular bodies. Receptors sorting therefore plays a crucial role in the integration and regulation of intracellular signals during development and numerous physio-pathological processes. It requires extensive membrane remodeling and scission events at the level of the endosomal compartment by so-called ESCRT proteins, including CHMP1B. In this study, we provide evidence for dynamic regulation of CHMP1B function and subcellular localization by ubiquitin linkage. We also show the contribution of the ubiquitin specific protease USP8 in this regulation, which is a known actor of intracellular trafficking and Cushing’s disease.
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Affiliation(s)
- Xènia Crespo-Yàñez
- Institut de Biosciences et Biotechnologies de Grenoble (BIG), Univ. Grenoble Alpes, INSERM U1038, CEA, Grenoble, France
| | - Carmen Aguilar-Gurrieri
- Institut de Biosciences et Biotechnologies de Grenoble (BIG), Univ. Grenoble Alpes, INSERM U1038, CEA, Grenoble, France
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CNRS, CEA, Grenoble, France
| | - Anne-Claire Jacomin
- Institut de Biosciences et Biotechnologies de Grenoble (BIG), Univ. Grenoble Alpes, INSERM U1038, CEA, Grenoble, France
| | - Agnès Journet
- Institut de Biosciences et Biotechnologies de Grenoble (BIG), Univ. Grenoble Alpes, INSERM U1038, CEA, Grenoble, France
| | - Magda Mortier
- Institut de Biosciences et Biotechnologies de Grenoble (BIG), Univ. Grenoble Alpes, INSERM U1038, CEA, Grenoble, France
| | - Emmanuel Taillebourg
- Institut de Biosciences et Biotechnologies de Grenoble (BIG), Univ. Grenoble Alpes, INSERM U1038, CEA, Grenoble, France
| | - Emmanuelle Soleilhac
- Institut de Biosciences et Biotechnologies de Grenoble (BIG), Univ. Grenoble Alpes, INSERM U1038, CEA, Grenoble, France
| | - Winfried Weissenhorn
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CNRS, CEA, Grenoble, France
| | - Marie-Odile Fauvarque
- Institut de Biosciences et Biotechnologies de Grenoble (BIG), Univ. Grenoble Alpes, INSERM U1038, CEA, Grenoble, France
- * E-mail:
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32
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Zhang J, Liu J, Norris A, Grant BD, Wang X. A novel requirement for ubiquitin-conjugating enzyme UBC-13 in retrograde recycling of MIG-14/Wntless and Wnt signaling. Mol Biol Cell 2018; 29:2098-2112. [PMID: 29927348 PMCID: PMC6232959 DOI: 10.1091/mbc.e17-11-0639] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
After endocytosis, transmembrane cargoes such as signaling receptors, channels, and transporters enter endosomes where they are sorted to different destinations. Retromer and ESCRT (endosomal sorting complex required for transport) are functionally distinct protein complexes on endosomes that direct cargo sorting into the recycling retrograde transport pathway and the degradative multivesicular endosome pathway (MVE), respectively. Cargoes destined for degradation in lysosomes are decorated with K63-linked ubiquitin chains, which serve as an efficient sorting signal for entry into the MVE pathway. Defects in K63-linked ubiquitination disrupt MVE sorting and degradation of membrane proteins. Here, we unexpectedly found that UBC-13, the E2 ubiquitin-conjugating enzyme that generates K63-linked ubiquitin chains, is essential for retrograde transport of multiple retromer-dependent cargoes including MIG-14/Wntless. Loss of ubc-13 disrupts MIG-14/Wntless trafficking from endosomes to the Golgi, causing missorting of MIG-14 to lysosomes and impairment of Wnt-dependent processes. We observed that retromer-associated SNX-1 and the ESCRT-0 subunit HGRS-1/Hrs localized to distinct regions on a common endosome in wild type but overlapped on ubc-13(lf) endosomes, indicating that UBC-13 is important for the separation of retromer and ESCRT microdomains on endosomes. Our data suggest that cargo ubiquitination mediated by UBC-13 plays an important role in maintaining the functionally distinct subdomains to ensure efficient cargo segregation on endosomes.
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Affiliation(s)
- Junbing Zhang
- College of Life Science, Beijing Normal University, Beijing 100875, China.,National Institute of Biological Sciences, Beijing 102206, China.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinchao Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Anne Norris
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854
| | - Barth D Grant
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854
| | - Xiaochen Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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33
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YOD1 attenuates neurogenic proteotoxicity through its deubiquitinating activity. Neurobiol Dis 2018; 112:14-23. [PMID: 29330040 DOI: 10.1016/j.nbd.2018.01.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 12/04/2017] [Accepted: 01/08/2018] [Indexed: 11/21/2022] Open
Abstract
Ubiquitination, a fundamental post-translational modification of intracellular proteins, is enzymatically reversed by deubiquitinase enzymes (deubiquitinases). >90 deubiquitinases have been identified. One of these enzymes, YOD1, possesses deubiquitinase activity and is similar to ovarian tumor domain-containing protein 1, which is associated with regulation of the endoplasmic reticulum (ER)-associated degradation pathway. Indeed, YOD1 is reported to be involved in the ER stress response induced by mislocalization of unfolded proteins in mammalian cells. However, it has remained unclear whether YOD1 is associated with pathophysiological conditions such as mitochondrial damage, impaired proteostasis, and neurodegeneration. We demonstrated that YOD1 possesses deubiquitinating activity and exhibits preference for K48- and K63-linked ubiquitin. Furthermore, YOD1 expression levels increased as a result of various stress conditions. We demonstrated that the neurogenic proteins that cause Huntington disease and Parkinson's disease induced upregulation of YOD1 level. We observed that YOD1 reduced disease cytotoxicity through efficient degradation of mutant proteins, whereas this activity was abolished by catalytically inactive YOD1. Additionally, YOD1 localized to Lewy bodies in Parkinson's disease patients. Collectively, these data suggest that the deubiquitinase YOD1 contributes to pathogenesis of neurodegenerative disease by decreasing ubiquitination of abnormal proteins and their subsequent degradation.
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34
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Juan T, Fürthauer M. Biogenesis and function of ESCRT-dependent extracellular vesicles. Semin Cell Dev Biol 2017; 74:66-77. [PMID: 28807885 DOI: 10.1016/j.semcdb.2017.08.022] [Citation(s) in RCA: 271] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 08/04/2017] [Accepted: 08/07/2017] [Indexed: 12/18/2022]
Abstract
From bacteria to humans, cells secrete a large variety of membrane-bound extracellular vesicles. Only relatively recently has it however started to become clear that the exovesicular transport of proteins and RNAs is important for normal physiology and numerous pathological conditions. Extracellular vesicles can be formed through the release of the intralumenal vesicles of multivesicular endosomes as so-called exosomes, or through direct, ectosomal, budding from the cell surface. Through their ability to promote the bending of membranes away from the cytoplasm, the components of the Endosomal Sorting Complex Required for Transport (ESCRT) have been implicated in both exo- and ectosomal biogenesis. Studies of the ESCRT machinery may therefore provide important insights into the formation and function of extracellular vesicles. In the present review, we first describe the cell biological mechanisms through which ESCRT components contribute to the biogenesis of different types of extracellular vesicles. We then discuss how recent functional studies have started to uncover important roles of ESCRT-dependent extracellular vesicles in a wide variety of processes, including the transport of developmental signaling molecules and embryonic morphogenesis, the regulation of social behavior and host-pathogen interactions, as well as the etiology and progression of neurodegenerative pathologies and cancer.
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Affiliation(s)
- Thomas Juan
- Université Côte d'Azur, CNRS, Inserm, iBV, France
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35
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Zhu L, Jorgensen JR, Li M, Chuang YS, Emr SD. ESCRTs function directly on the lysosome membrane to downregulate ubiquitinated lysosomal membrane proteins. eLife 2017; 6:e26403. [PMID: 28661397 PMCID: PMC5507667 DOI: 10.7554/elife.26403] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 06/23/2017] [Indexed: 11/23/2022] Open
Abstract
The lysosome plays an important role in maintaining cellular nutrient homeostasis. Regulation of nutrient storage can occur by the ubiquitination of certain transporters that are then sorted into the lysosome lumen for degradation. To better understand the underlying mechanism of this process, we performed genetic screens to identify components of the sorting machinery required for vacuole membrane protein degradation. These screens uncovered genes that encode a ubiquitin ligase complex, components of the PtdIns 3-kinase complex, and the ESCRT machinery. We developed a novel ubiquitination system, Rapamycin-Induced Degradation (RapiDeg), to test the sorting defects caused by these mutants. These tests revealed that ubiquitinated vacuole membrane proteins recruit ESCRTs to the vacuole surface, where they mediate cargo sorting and direct cargo delivery into the vacuole lumen. Our findings demonstrate that the ESCRTs can function at both the late endosome and the vacuole membrane to mediate cargo sorting and intra-luminal vesicle formation.
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Affiliation(s)
- Lu Zhu
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, United States
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States
| | - Jeff R Jorgensen
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, United States
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States
| | - Ming Li
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, United States
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, United States
| | - Ya-Shan Chuang
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, United States
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States
| | - Scott D Emr
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, United States
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36
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Buono RA, Leier A, Paez-Valencia J, Pennington J, Goodman K, Miller N, Ahlquist P, Marquez-Lago TT, Otegui MS. ESCRT-mediated vesicle concatenation in plant endosomes. J Cell Biol 2017; 216:2167-2177. [PMID: 28592443 PMCID: PMC5496621 DOI: 10.1083/jcb.201612040] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 04/06/2017] [Accepted: 05/01/2017] [Indexed: 11/23/2022] Open
Abstract
ESCRT proteins play essential functions by remodeling cellular membranes. Buono et al. report on a novel ESCRT-dependent mechanism in plant endosomes that leads to sequential concatenation of vesicle buds by temporally uncoupling membrane constriction from membrane fission. During this process, ESCRT-III proteins remain inside endosomes after intralumenal vesicle release. Ubiquitinated plasma membrane proteins (cargo) are delivered to endosomes and sorted by endosomal sorting complex required for transport (ESCRT) machinery into endosome intralumenal vesicles (ILVs) for degradation. In contrast to the current model that postulates that ILVs form individually from inward budding of the endosomal limiting membrane, plant ILVs form as networks of concatenated vesicle buds by a novel vesiculation mechanism. We ran computational simulations based on experimentally derived diffusion coefficients of an ESCRT cargo protein and electron tomograms of Arabidopsis thaliana endosomes to measure cargo escape from budding ILVs. We found that 50% of the ESCRT cargo would escape from a single budding profile in 5–20 ms and from three concatenated ILVs in 80–200 ms. These short cargo escape times predict the need for strong diffusion barriers in ILVs. Consistent with a potential role as a diffusion barrier, we find that the ESCRT-III protein SNF7 remains associated with ILVs and is delivered to the vacuole for degradation.
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Affiliation(s)
- Rafael Andrade Buono
- Department of Botany, University of Wisconsin-Madison, Madison, WI.,R.M. Bock Laboratories of Cell and Molecular Biology, University of Wisconsin-Madison, Madison, WI
| | - André Leier
- Informatics Institute, School of Medicine, University of Alabama at Birmingham, Birmingham, AL.,Department of Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Julio Paez-Valencia
- Department of Botany, University of Wisconsin-Madison, Madison, WI.,R.M. Bock Laboratories of Cell and Molecular Biology, University of Wisconsin-Madison, Madison, WI
| | | | - Kaija Goodman
- Department of Botany, University of Wisconsin-Madison, Madison, WI.,R.M. Bock Laboratories of Cell and Molecular Biology, University of Wisconsin-Madison, Madison, WI
| | - Nathan Miller
- Department of Botany, University of Wisconsin-Madison, Madison, WI
| | - Paul Ahlquist
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI.,Departments of Oncology, University of Wisconsin-Madison, Madison, WI.,Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI.,Howard Hughes Medical Institute, Chevy Chase, MD.,Morgridge Institute for Research, Madison, WI
| | - Tatiana T Marquez-Lago
- Informatics Institute, School of Medicine, University of Alabama at Birmingham, Birmingham, AL.,Department of Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Marisa S Otegui
- Department of Botany, University of Wisconsin-Madison, Madison, WI .,R.M. Bock Laboratories of Cell and Molecular Biology, University of Wisconsin-Madison, Madison, WI.,Department of Genetics, University of Wisconsin-Madison, Madison, WI
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37
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MacDonald C, Winistorfer S, Pope RM, Wright ME, Piper RC. Enzyme reversal to explore the function of yeast E3 ubiquitin-ligases. Traffic 2017; 18:465-484. [PMID: 28382714 DOI: 10.1111/tra.12485] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Revised: 03/31/2017] [Accepted: 03/31/2017] [Indexed: 12/27/2022]
Abstract
The covalent attachment of ubiquitin onto proteins can elicit a variety of downstream consequences. Attachment is mediated by a large array of E3 ubiquitin ligases, each thought be subject to regulatory control and to have a specific repertoire of substrates. Assessing the biological roles of ligases, and in particular, identifying their biologically relevant substrates has been a persistent yet challenging question. In this study, we describe tools that may help achieve both of these goals. We describe a strategy whereby the activity of a ubiquitin ligase has been enzymatically reversed, accomplished by fusing it to a catalytic domain of an exogenous deubiquitinating enzyme. We present a library of 72 "anti-ligases" that appear to work in a dominant-negative fashion to stabilize their cognate substrates against ubiquitin-dependent proteasomal and lysosomal degradation. We then used the ligase-deubiquitinating enzyme (DUb) library to screen for E3 ligases involved in post-Golgi/endosomal trafficking. We identify ligases previously implicated in these pathways (Rsp5 and Tul1), in addition to ligases previously localized to endosomes (Pib1 and Vps8). We also document an optimized workflow for isolating and analyzing the "ubiquitome" of yeast, which can be used with mass spectrometry to identify substrates perturbed by expression of particular ligase-DUb fusions.
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Affiliation(s)
- Chris MacDonald
- Molecular Physiology and Biophysics, University of Iowa, Iowa City, Iowa
| | | | - Robert M Pope
- Proteomics Facility, University of Iowa, Iowa City, Iowa
| | - Michael E Wright
- Molecular Physiology and Biophysics, University of Iowa, Iowa City, Iowa
| | - Robert C Piper
- Molecular Physiology and Biophysics, University of Iowa, Iowa City, Iowa
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38
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Abstract
Newly synthesized transmembrane proteins undergo a series of steps to ensure that only the required amount of correctly folded protein is localized to the membrane. The regulation of protein quality and its abundance at the membrane are often controlled by ubiquitination, a multistep enzymatic process that results in the attachment of ubiquitin, or chains of ubiquitin to the target protein. Protein ubiquitination acts as a signal for sorting, trafficking, and the removal of membrane proteins via endocytosis, a process through which multiple ubiquitin ligases are known to specifically regulate the functions of a number of ion channels, transporters, and signaling receptors. Endocytic removal of these proteins through ubiquitin-dependent endocytosis provides a way to rapidly downregulate the physiological outcomes, and defects in such controls are directly linked to human pathologies. Recent evidence suggests that ubiquitination is also involved in the shedding of membranes and associated proteins as extracellular vesicles, thereby not only controlling the cell surface levels of some membrane proteins, but also their potential transport to neighboring cells. In this review, we summarize the mechanisms and functions of ubiquitination of membrane proteins and provide specific examples of ubiquitin-dependent regulation of membrane proteins.
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Affiliation(s)
- Natalie Foot
- Centre for Cancer Biology, University of South Australia, Adelaide, Australia
| | - Tanya Henshall
- Centre for Cancer Biology, University of South Australia, Adelaide, Australia
| | - Sharad Kumar
- Centre for Cancer Biology, University of South Australia, Adelaide, Australia
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39
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Johnson N, West M, Odorizzi G. Regulation of yeast ESCRT-III membrane scission activity by the Doa4 ubiquitin hydrolase. Mol Biol Cell 2017; 28:661-672. [PMID: 28057764 PMCID: PMC5328624 DOI: 10.1091/mbc.e16-11-0761] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 12/15/2016] [Accepted: 12/30/2016] [Indexed: 11/23/2022] Open
Abstract
Doa4 is the ubiquitin hydrolase in yeast that deubiquitinates transmembrane proteins sorted by ESCRTs. Results support a model for bidirectional regulation between Doa4 and the ESCRT-III complex. ESCRT-III executes membrane scission during the budding of intralumenal vesicles (ILVs) at endosomes. The scission mechanism is unknown but appears to be linked to the cycle of assembly and disassembly of ESCRT-III complexes at membranes. Regulating this cycle is therefore expected to be important for determining the timing of ESCRT-III–mediated membrane scission. We show that in Saccharomyces cerevisiae, ESCRT-III complexes are stabilized and ILV membrane scission is delayed by Doa4, which is the ubiquitin hydrolase that deubiquitinates transmembrane proteins sorted as cargoes into ILVs. These results suggest a mechanism to delay ILV budding while cargoes undergo deubiquitination. We further show that deubiquitination of ILV cargoes is inhibited via Doa4 binding to Vps20, which is the subunit of ESCRT-III that initiates assembly of the complex. Current models suggest that ESCRT-III complexes surround ubiquitinated cargoes to trap them at the site of ILV budding while the cargoes undergo deubiquitination. Thus our results also propose a mechanism to prevent the onset of ILV cargo deubiquitination at the initiation of ESCRT-III complex assembly.
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Affiliation(s)
- Natalie Johnson
- Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309
| | - Matt West
- Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309
| | - Greg Odorizzi
- Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309
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40
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Abstract
Sorting internalized proteins and lipids back to the cell surface controls the supply of molecules throughout the cell and regulates integral membrane protein activity at the surface. One central process in mammalian cells is the transit of cargo from endosomes back to the plasma membrane (PM) directly, along a route that bypasses retrograde movement to the Golgi. Despite recognition of this pathway for decades we are only beginning to understand the machinery controlling this overall process. The budding yeastSaccharomyces cerevisiae, a stalwart genetic system, has been routinely used to identify fundamental proteins and their modes of action in conserved trafficking pathways. However, the study of cell surface recycling from endosomes in yeast is hampered by difficulties that obscure visualization of the pathway. Here we briefly discuss how recycling is likely a more prevalent process in yeast than is widely appreciated and how tools might be built to better study the pathway.
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41
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Wolters N, Amerik A. Inactivation of the VID27 gene prevents suppression of the doa4 degradation defect in doa4Δ did3Δ double mutant. Biochem Biophys Res Commun 2016; 482:1341-1345. [PMID: 27939891 DOI: 10.1016/j.bbrc.2016.12.038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 12/06/2016] [Indexed: 11/30/2022]
Abstract
Ubiquitination is a key regulatory mechanism that affects numerous cellular processes. This modification is reversible. Deubiquitinating enzymes (DUBs) remove the ubiquitin tag from modified proteins. DUB Doa4 is involved in deubiquitination of conjugates at the late endosome/pre vacuolar compartment. A genetic screen led to isolation of seven extragenic suppressors of the doa4 phenotypic abnormalities. Remarkably, cloned Doa4-independent degradation (DID) genes encode the class E vacuolar protein-sorting factors involved in membrane protein trafficking. Here we provide evidence that inactivation of Vid27 (vacuolar import and degradation) prevents suppression of the doa4 phenotype by did3 mutation. Vid27 is a cytoplasmic protein essential for delivery of fructose-1,6-bisphosphatase into VID vesicles. Thus, our data revealed another connection between Doa4 and vacuolar protein sorting.
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Affiliation(s)
- Nazia Wolters
- Department of Pharmacology, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT, 06030, USA
| | - Alexander Amerik
- Department of Pharmacology, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT, 06030, USA; Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygin Street, Moscow, 119991, Russian Federation.
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42
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Mallawaaratchy DM, Hallal S, Russell B, Ly L, Ebrahimkhani S, Wei H, Christopherson RI, Buckland ME, Kaufman KL. Comprehensive proteome profiling of glioblastoma-derived extracellular vesicles identifies markers for more aggressive disease. J Neurooncol 2016; 131:233-244. [PMID: 27770278 PMCID: PMC5306193 DOI: 10.1007/s11060-016-2298-3] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 10/09/2016] [Indexed: 11/24/2022]
Abstract
Extracellular vesicles (EVs) play key roles in glioblastoma (GBM) biology and represent novel sources of biomarkers that are detectable in the peripheral circulation. Despite this notionally non-invasive approach to assess GBM tumours in situ, a comprehensive GBM EV protein signature has not been described. Here, EVs secreted by six GBM cell lines were isolated and analysed by quantitative high-resolution mass spectrometry. Overall, 844 proteins were identified in the GBM EV proteome, of which 145 proteins were common to EVs secreted by all cell lines examined; included in the curated EV compendium (Vesiclepedia_559; http://microvesicles.org). Levels of 14 EV proteins significantly correlated with cell invasion (invadopodia production; r2 > 0.5, p < 0.05), including several proteins that interact with molecules responsible for regulating invadopodia formation. Invadopodia, actin-rich membrane protrusions with proteolytic activity, are associated with more aggressive disease and are sites of EV release. Gene levels corresponding to invasion-related EV proteins showed that five genes (annexin A1, actin-related protein 3, integrin-β1, insulin-like growth factor 2 receptor and programmed cell death 6-interacting protein) were significantly higher in GBM tumours compared to normal brain in silico, with common functions relating to actin polymerisation and endosomal sorting. We also show that Cavitron Ultrasonic Surgical Aspirator (CUSA) washings are a novel source of brain tumour-derived EVs, demonstrated by particle tracking analysis, TEM and proteome profiling. Quantitative proteomics corroborated the high levels of proposed invasion-related proteins in EVs enriched from a GBM compared to low-grade astrocytoma tumour. Large-scale clinical follow-up of putative biomarkers, particularly the proposed survival marker annexin A1, is warranted.
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Affiliation(s)
- Duthika M Mallawaaratchy
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Susannah Hallal
- Discipline of Pathology, Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia.,Brain and Mind Centre, The University of Sydney, Camperdown, NSW, 2050, Australia
| | - Ben Russell
- Discipline of Pathology, Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia.,Brain and Mind Centre, The University of Sydney, Camperdown, NSW, 2050, Australia
| | - Linda Ly
- Brain and Mind Centre, The University of Sydney, Camperdown, NSW, 2050, Australia
| | - Saeideh Ebrahimkhani
- Discipline of Pathology, Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia.,Brain and Mind Centre, The University of Sydney, Camperdown, NSW, 2050, Australia
| | - Heng Wei
- Brain and Mind Centre, The University of Sydney, Camperdown, NSW, 2050, Australia.,Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, NSW, 2050, Australia
| | - Richard I Christopherson
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Michael E Buckland
- Discipline of Pathology, Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia.,Brain and Mind Centre, The University of Sydney, Camperdown, NSW, 2050, Australia.,Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, NSW, 2050, Australia
| | - Kimberley L Kaufman
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia. .,Brain and Mind Centre, The University of Sydney, Camperdown, NSW, 2050, Australia. .,Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, NSW, 2050, Australia.
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43
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MacDonald C, Stamnes MA, Katzmann DJ, Piper RC. Tetraspan cargo adaptors usher GPI-anchored proteins into multivesicular bodies. Cell Cycle 2016; 14:3673-8. [PMID: 26505929 DOI: 10.1080/15384101.2015.1100773] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Ubiquitinated membrane proteins are sorted into intralumenal endosomal vesicles on their way for degradation in lysosomes. Here we summarize the discovery of the Cos proteins, which work to organize and segregate ubiquitinated cargo prior to its incorporation into intralumenal vesicles of the multivesicular body (MVB). Importantly, cargoes such as GPI-anchored proteins (GPI-APs) that cannot undergo ubiquitination, rely entirely on Cos proteins for sorting into intralumenal vesicles using the same pathway that depends on ESCRTs and ubiquitin ligases that typical polytopic membrane proteins do. Here we show Cos proteins provide functions as not only adaptor proteins for ubiquitin ligases, but also as cargo carriers that can physically usher a variety of other proteins into the MVB pathway. We then discuss the significance of this new sorting model and the broader implications for this cargo adaptor mechanism, whereby yeast Cos proteins, and their likely animal analogs, provide a ubiquitin sorting signal in trans to enable sorting of a membrane protein network into intralumenal vesicles.
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Affiliation(s)
- Chris MacDonald
- a Molecular Physiology and Biophysics; University of Iowa ; Iowa City , IA USA
| | - Mark A Stamnes
- a Molecular Physiology and Biophysics; University of Iowa ; Iowa City , IA USA
| | - David J Katzmann
- b Biochemistry and Molecular Biology; Mayo Clinic College of Medicine ; Rochester , MN USA
| | - Robert C Piper
- a Molecular Physiology and Biophysics; University of Iowa ; Iowa City , IA USA
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44
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A novel TP53 pathway influences the HGS-mediated exosome formation in colorectal cancer. Sci Rep 2016; 6:28083. [PMID: 27312428 PMCID: PMC4911576 DOI: 10.1038/srep28083] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 05/31/2016] [Indexed: 01/16/2023] Open
Abstract
Tumor-derived exosomes are important for cell-cell communication. However, the role of TP53 in the control of exosome production in colorectal cancer (CRC) is controversial and unclear. The features of exosomes secreted from HCT116 TP53-wild type (WT), TP53-knockout (KO) and constructed TP53 (R273H)-mutant (MT) cells were assessed. The exosomes from the MT and KO cells exhibited significantly reduced sizes compared with the WT cells. A comprehensive proteomic analysis of exosomal proteins was performed using the isobaric tag for relative and absolute quantitation (iTRAQ)-2D-LC-MS/MS strategy. A total of 3437 protein groups with ≥2 matched peptides were identified. Specifically, hepatocyte growth factor-regulated tyrosine kinase substrate (HGS) was consistently down-regulated in the exosomes from the MT and KO cells. Functional studies demonstrated that low HGS levels were responsible for the decreased exosome size. TP53 regulated HGS expression and thus HGS-dependent exosome formation. Furthermore, the HGS expression was gradually increased concomitant with CRC carcinogenesis and was an independent poor prognostic factor. In conclusion, a novel HGS-dependent TP53 mechanism in exosome formation was identified in CRC. HGS may serve as a novel prognostic biomarker and a candidate target for therapeutic interventions.
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45
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Huber LA, Teis D. Lysosomal signaling in control of degradation pathways. Curr Opin Cell Biol 2016; 39:8-14. [PMID: 26827287 DOI: 10.1016/j.ceb.2016.01.006] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 01/11/2016] [Accepted: 01/13/2016] [Indexed: 12/16/2022]
Abstract
Autophagy mediates the (non-)selective bulk degradation of cytoplasm, protein aggregates, damaged organelles and certain pathogens. The endosomal membrane system uses multivesicular bodies (MVBs) to selectively deliver ubiquitinated membrane proteins together with extracellular components into lysosomes. Microautophagy (MA) and chaperone-mediated autophagy (CMA) additionally contribute to the selective delivery of cargo into lysosomes. The coordinated function of these lysosomal degradation pathways is essential to maintain cellular homeostasis. Their activity is controlled by mTOR (mammalian target of rapamycin) signaling and thus coupled to metabolic processes during cell growth. Here, we will discuss how TORC1 on lysosomes and TORC2 at the plasma membrane coordinate the different membrane biogenesis pathways with cargo selection, vesicle transport and fusion with lysosomes in response to intracellular and extracellular cues.
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Affiliation(s)
- Lukas A Huber
- Division of Cell Biology, Biocenter, Medical University of Innsbruck, Austria
| | - David Teis
- Division of Cell Biology, Biocenter, Medical University of Innsbruck, Austria.
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46
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MacDonald C, Payne JA, Aboian M, Smith W, Katzmann DJ, Piper RC. A family of tetraspans organizes cargo for sorting into multivesicular bodies. Dev Cell 2015; 33:328-42. [PMID: 25942624 DOI: 10.1016/j.devcel.2015.03.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 01/22/2015] [Accepted: 03/04/2015] [Indexed: 12/11/2022]
Abstract
The abundance of cell-surface membrane proteins is regulated by internalization and delivery into intralumenal vesicles (ILVs) of multivesicular bodies (MVBs). Many cargoes are ubiquitinated, allowing access to an ESCRT-dependent pathway into MVBs. Yet how nonubiquitinated proteins, such as glycosylphosphatidylinositol-anchored proteins, enter MVBs is unclear, supporting the possibility of mechanistically distinct ILV biogenesis pathways. Here we show that a family of highly ubiquitinated tetraspan Cos proteins provides a Ub signal in trans, allowing sorting of nonubiquitinated MVB cargo into the canonical ESCRT- and Ub-dependent pathway. Cos proteins create discrete endosomal subdomains that concentrate Ub cargo prior to their envelopment into ILVs, and the activity of Cos proteins is required not only for efficient sorting of canonical Ub cargo but also for sorting nonubiquitinated cargo into MVBs. Expression of these proteins increases during nutrient stress through an NAD(+)/Sir2-dependent mechanism that in turn accelerates the downregulation of a broad range of cell-surface proteins.
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Affiliation(s)
- Chris MacDonald
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA 52242, USA
| | - Johanna A Payne
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Mariam Aboian
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA; Department of Radiology and Biomedical Imaging, University of California San Francisco School of Medicine, San Francisco, CA 94143, USA
| | - William Smith
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA 52242, USA
| | - David J Katzmann
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.
| | - Robert C Piper
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA 52242, USA.
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47
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Liu Z, Gong Z, Jiang WX, Yang J, Zhu WK, Guo DC, Zhang WP, Liu ML, Tang C. Lys63-linked ubiquitin chain adopts multiple conformational states for specific target recognition. eLife 2015; 4. [PMID: 26090905 PMCID: PMC4507786 DOI: 10.7554/elife.05767] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 06/18/2015] [Indexed: 12/16/2022] Open
Abstract
A polyubiquitin comprises multiple covalently linked ubiquitins and recognizes myriad targets. Free or bound to ligands, polyubiquitins are found in different arrangements of ubiquitin subunits. To understand the structural basis for polyubiquitin quaternary plasticity and to explore the target recognition mechanism, we characterize the conformational space of Lys63-linked diubiquitin (K63-Ub2). Refining against inter-subunit paramagnetic NMR data, we show that free K63-Ub2 exists as a dynamic ensemble comprising multiple closed and open quaternary states. The quaternary dynamics enables K63-Ub2 to be specifically recognized in a variety of signaling pathways. When binding to a target protein, one of the preexisting quaternary states is selected and stabilized. A point mutation that shifts the equilibrium between the different states modulates the binding affinities towards K63-Ub2 ligands. This conformational selection mechanism at the quaternary level may be used by polyubiquitins of different lengths and linkages for target recognition.
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Affiliation(s)
- Zhu Liu
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, China
| | - Zhou Gong
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, China
| | - Wen-Xue Jiang
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, China
| | - Ju Yang
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, China
| | - Wen-Kai Zhu
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, China
| | - Da-Chuan Guo
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, China
| | - Wei-Ping Zhang
- Department of Pharmacology and Institute of Neuroscience, Zhejiang University School of Medicine, Hangzhou, China
| | - Mai-Li Liu
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, China
| | - Chun Tang
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, China
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48
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MacDonald C, Piper RC. Puromycin- and methotrexate-resistance cassettes and optimized Cre-recombinase expression plasmids for use in yeast. Yeast 2015; 32:423-38. [PMID: 25688547 DOI: 10.1002/yea.3069] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 02/03/2015] [Accepted: 02/07/2015] [Indexed: 11/07/2022] Open
Abstract
Here we expand the set of tools for genetically manipulating Saccharomyces cerevisiae. We show that puromycin-resistance can be achieved in yeast through expression of a bacterial puromycin-resistance gene optimized to the yeast codon bias, which in turn serves as an easy-to-use dominant genetic marker suitable for gene disruption. We have constructed a similar DNA cassette expressing yeast codon-optimized mutant human dihydrofolate reductase (DHFR), which confers resistance to methotrexate and can also be used as a dominant selectable marker. Both of these drug-resistant marker cassettes are flanked by loxP sites, allowing for their excision from the genome following expression of Cre-recombinase. Finally, we have created a series of plasmids for low-level constitutive expression of Cre-recombinase in yeast that allows for efficient excision of loxP-flanked markers.
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Affiliation(s)
- Chris MacDonald
- Department of Molecular Physiology and Biophysics, University of Iowa, IA, USA
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49
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Silva GM, Finley D, Vogel C. K63 polyubiquitination is a new modulator of the oxidative stress response. Nat Struct Mol Biol 2015; 22:116-23. [PMID: 25622294 PMCID: PMC4318705 DOI: 10.1038/nsmb.2955] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 12/12/2014] [Indexed: 12/21/2022]
Abstract
Ubiquitination is a post-translational modification that signals multiple processes, including protein degradation, trafficking and DNA repair. Polyubiquitin accumulates globally during the oxidative stress response, and this has been mainly attributed to increased ubiquitin conjugation and perturbations in protein degradation. Here we show that the unconventional Lys63 (K63)-linked polyubiquitin accumulates in the yeast Saccharomyces cerevisiae in a highly sensitive and regulated manner as a result of exposure to peroxides. We demonstrate that hydrogen peroxide inhibits the deubiquitinating enzyme Ubp2, leading to accumulation of K63 conjugates assembled by the Rad6 ubiquitin conjugase and the Bre1 ubiquitin ligase. Using linkage-specific isolation methods and stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative proteomics, we identified >100 new K63-polyubiquitinated targets, which were substantially enriched in ribosomal proteins. Finally, we demonstrate that impairment of K63 ubiquitination during oxidative stress affects polysome stability and protein expression, rendering cells more sensitive to stress, and thereby reveal a new redox-regulatory role for this modification.
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Affiliation(s)
- Gustavo M. Silva
- Center for Genomics and Systems Biology, New York University, New York, New York, USA
| | - Daniel Finley
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Christine Vogel
- Center for Genomics and Systems Biology, New York University, New York, New York, USA
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50
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Mageswaran SK, Johnson NK, Odorizzi G, Babst M. Constitutively active ESCRT-II suppresses the MVB-sorting phenotype of ESCRT-0 and ESCRT-I mutants. Mol Biol Cell 2014; 26:554-68. [PMID: 25501366 PMCID: PMC4310745 DOI: 10.1091/mbc.e14-10-1469] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
This study is a step toward understanding the minimal requirements for MVB biogenesis and for ESCRT machinery in this process. Early ESCRT complexes (ESCRT-0 and -I) seem to have redundant functions in cargo sorting. Furthermore, vesicle formation seems to require cargo sorting in addition to late ESCRT machinery. The endosomal sorting complex required for transport (ESCRT) protein complexes function at the endosome in the formation of intraluminal vesicles (ILVs) containing cargo proteins destined for the vacuolar/lysosomal lumen. The early ESCRTs (ESCRT-0 and -I) are likely involved in cargo sorting, whereas ESCRT-III and Vps4 function to sever the neck of the forming ILVs. ESCRT-II links these functions by initiating ESCRT-III formation in an ESCRT-I–regulated manner. We identify a constitutively active mutant of ESCRT-II that partially suppresses the phenotype of an ESCRT-I or ESCRT-0 deletion strain, suggesting that these early ESCRTs are not essential and have redundant functions. However, the ESCRT-III/Vps4 system alone is not sufficient for ILV formation but requires cargo sorting mediated by one of the early ESCRTs.
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Affiliation(s)
- Shrawan Kumar Mageswaran
- Center for Cell and Genome Science and Department of Biology, University of Utah, Salt Lake City, UT 84112
| | - Natalie K Johnson
- Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, Boulder, CO 80309
| | - Greg Odorizzi
- Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, Boulder, CO 80309
| | - Markus Babst
- Center for Cell and Genome Science and Department of Biology, University of Utah, Salt Lake City, UT 84112
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