1
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Breckel CA, Johnson ZM, Hickey CM, Hochstrasser M. Yeast 26S proteasome nuclear import is coupled to nucleus-specific degradation of the karyopherin adaptor protein Sts1. Sci Rep 2024; 14:2048. [PMID: 38267508 PMCID: PMC10808114 DOI: 10.1038/s41598-024-52352-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 01/16/2024] [Indexed: 01/26/2024] Open
Abstract
In eukaryotes, the ubiquitin-proteasome system is an essential pathway for protein degradation and cellular homeostasis. 26S proteasomes concentrate in the nucleus of budding yeast Saccharomyces cerevisiae due to the essential import adaptor protein Sts1 and the karyopherin-α protein Srp1. Here, we show that Sts1 facilitates proteasome nuclear import by recruiting proteasomes to the karyopherin-α/β heterodimer. Following nuclear transport, the karyopherin proteins are likely separated from Sts1 through interaction with RanGTP in the nucleus. RanGTP-induced release of Sts1 from the karyopherin proteins initiates Sts1 proteasomal degradation in vitro. Sts1 undergoes karyopherin-mediated nuclear import in the absence of proteasome interaction, but Sts1 degradation in vivo is only observed when proteasomes successfully localize to the nucleus. Sts1 appears to function as a proteasome import factor during exponential growth only, as it is not found in proteasome storage granules (PSGs) during prolonged glucose starvation, nor does it appear to contribute to the rapid nuclear reimport of proteasomes following glucose refeeding and PSG dissipation. We propose that Sts1 acts as a single-turnover proteasome nuclear import factor by recruiting karyopherins for transport and undergoing subsequent RanGTP-initiated ubiquitin-independent proteasomal degradation in the nucleus.
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Affiliation(s)
- Carolyn Allain Breckel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Zane M Johnson
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Christopher M Hickey
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
- Arvinas, Inc., 5 Science Park, New Haven, CT, USA
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06520, USA.
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2
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Pispa J, Mikkonen E, Arpalahti L, Jin C, Martínez-Fernández C, Cerón J, Holmberg CI. AKIR-1 regulates proteasome subcellular function in Caenorhabditis elegans. iScience 2023; 26:107886. [PMID: 37767001 PMCID: PMC10520889 DOI: 10.1016/j.isci.2023.107886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 07/07/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Polyubiquitinated proteins are primarily degraded by the ubiquitin-proteasome system (UPS). Proteasomes are present both in the cytoplasm and nucleus. Here, we investigated mechanisms coordinating proteasome subcellular localization and activity in a multicellular organism. We identified the nuclear protein-encoding gene akir-1 as a proteasome regulator in a genome-wide Caenorhabditis elegans RNAi screen. We demonstrate that depletion of akir-1 causes nuclear accumulation of endogenous polyubiquitinated proteins in intestinal cells, concomitant with slower in vivo proteasomal degradation in this subcellular compartment. Remarkably, akir-1 is essential for nuclear localization of proteasomes both in oocytes and intestinal cells but affects differentially the subcellular distribution of polyubiquitinated proteins. We further reveal that importin ima-3 genetically interacts with akir-1 and influences nuclear localization of a polyubiquitin-binding reporter. Our study shows that the conserved AKIR-1 is an important regulator of the subcellular function of proteasomes in a multicellular organism, suggesting a role for AKIR-1 in proteostasis maintenance.
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Affiliation(s)
- Johanna Pispa
- Department of Biochemistry and Developmental Biology, Medicum, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Elisa Mikkonen
- Department of Biochemistry and Developmental Biology, Medicum, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Leena Arpalahti
- Department of Biochemistry and Developmental Biology, Medicum, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Congyu Jin
- Department of Anatomy, Medicum, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Carmen Martínez-Fernández
- Modeling Human Diseases in C. elegans Group, Genes, Diseases, and Therapies Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Julián Cerón
- Modeling Human Diseases in C. elegans Group, Genes, Diseases, and Therapies Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Carina I. Holmberg
- Department of Biochemistry and Developmental Biology, Medicum, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
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3
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Sontag EM, Morales-Polanco F, Chen JH, McDermott G, Dolan PT, Gestaut D, Le Gros MA, Larabell C, Frydman J. Nuclear and cytoplasmic spatial protein quality control is coordinated by nuclear-vacuolar junctions and perinuclear ESCRT. Nat Cell Biol 2023; 25:699-713. [PMID: 37081164 DOI: 10.1038/s41556-023-01128-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 03/14/2023] [Indexed: 04/22/2023]
Abstract
Effective protein quality control (PQC), essential for cellular health, relies on spatial sequestration of misfolded proteins into defined inclusions. Here we reveal the coordination of nuclear and cytoplasmic spatial PQC. Cytoplasmic misfolded proteins concentrate in a cytoplasmic juxtanuclear quality control compartment, while nuclear misfolded proteins sequester into an intranuclear quality control compartment (INQ). Particle tracking reveals that INQ and the juxtanuclear quality control compartment converge to face each other across the nuclear envelope at a site proximal to the nuclear-vacuolar junction marked by perinuclear ESCRT-II/III protein Chm7. Strikingly, convergence at nuclear-vacuolar junction contacts facilitates VPS4-dependent vacuolar clearance of misfolded cytoplasmic and nuclear proteins, the latter entailing extrusion of nuclear INQ into the vacuole. Finding that nuclear-vacuolar contact sites are cellular hubs of spatial PQC to facilitate vacuolar clearance of nuclear and cytoplasmic inclusions highlights the role of cellular architecture in proteostasis maintenance.
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Affiliation(s)
- Emily M Sontag
- Department of Biology, Stanford University, Stanford, CA, USA.
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA.
| | | | - Jian-Hua Chen
- Department of Anatomy, School of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Gerry McDermott
- Department of Anatomy, School of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Patrick T Dolan
- Department of Biology, Stanford University, Stanford, CA, USA
- Quantitative Virology and Evolution Unit, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Daniel Gestaut
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Mark A Le Gros
- Department of Anatomy, School of Medicine, University of California San Francisco, San Francisco, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Carolyn Larabell
- Department of Anatomy, School of Medicine, University of California San Francisco, San Francisco, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, CA, USA.
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4
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van der Zanden SY, Jongsma MLM, Neefjes ACM, Berlin I, Neefjes J. Maintaining soluble protein homeostasis between nuclear and cytoplasmic compartments across mitosis. Trends Cell Biol 2023; 33:18-29. [PMID: 35778326 DOI: 10.1016/j.tcb.2022.06.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/23/2022] [Accepted: 06/06/2022] [Indexed: 12/27/2022]
Abstract
The nuclear envelope (NE) is central to the architecture of eukaryotic cells, both as a physical barrier separating the nucleus from the cytoplasm and as gatekeeper of selective transport between them. However, in open mitosis, the NE fragments to allow for spindle formation and segregation of chromosomes, resulting in intermixing of nuclear and cytoplasmic soluble fractions. Recent studies have shed new light on the mechanisms driving reinstatement of soluble proteome homeostasis following NE reformation in daughter cells. Here, we provide an overview of how mitotic cells confront this challenge to ensure continuity of basic cellular functions across generations and elaborate on the implications for the proteasome - a macromolecular machine that functions in both cytoplasmic and nuclear compartments.
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Affiliation(s)
- Sabina Y van der Zanden
- Department of Cell and Chemical Biology, ONCODE Institute, Leiden University Medical Center LUMC, 2333, ZC, Leiden, The Netherlands
| | - Marlieke L M Jongsma
- Department of Cell and Chemical Biology, ONCODE Institute, Leiden University Medical Center LUMC, 2333, ZC, Leiden, The Netherlands
| | - Anna C M Neefjes
- Department of Cell and Chemical Biology, ONCODE Institute, Leiden University Medical Center LUMC, 2333, ZC, Leiden, The Netherlands
| | - Ilana Berlin
- Department of Cell and Chemical Biology, ONCODE Institute, Leiden University Medical Center LUMC, 2333, ZC, Leiden, The Netherlands.
| | - Jacques Neefjes
- Department of Cell and Chemical Biology, ONCODE Institute, Leiden University Medical Center LUMC, 2333, ZC, Leiden, The Netherlands.
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5
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Enenkel C, Kang RW, Wilfling F, Ernst OP. Intracellular localization of the proteasome in response to stress conditions. J Biol Chem 2022; 298:102083. [PMID: 35636514 PMCID: PMC9218506 DOI: 10.1016/j.jbc.2022.102083] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 05/13/2022] [Accepted: 05/16/2022] [Indexed: 12/15/2022] Open
Abstract
The ubiquitin–proteasome system fulfills an essential role in regulating protein homeostasis by spatially and temporally controlling proteolysis in an ATP- and ubiquitin-dependent manner. However, the localization of proteasomes is highly variable under diverse cellular conditions. In yeast, newly synthesized proteasomes are primarily localized to the nucleus during cell proliferation. Yeast proteasomes are transported into the nucleus through the nuclear pore either as immature subcomplexes or as mature enzymes via adapter proteins Sts1 and Blm10, while in mammalian cells, postmitotic uptake of proteasomes into the nucleus is mediated by AKIRIN2, an adapter protein essentially required for nuclear protein degradation. Stressful growth conditions and the reversible halt of proliferation, that is quiescence, are associated with a decline in ATP and the reorganization of proteasome localization. Cellular stress leads to proteasome accumulation in membraneless granules either in the nucleus or in the cytoplasm. In quiescence, yeast proteasomes are sequestered in an ubiquitin-dependent manner into motile and reversible proteasome storage granules in the cytoplasm. In cancer cells, upon amino acid deprivation, heat shock, osmotic stress, oxidative stress, or the inhibition of either proteasome activity or nuclear export, reversible proteasome foci containing polyubiquitinated substrates are formed by liquid–liquid phase separation in the nucleus. In this review, we summarize recent literature revealing new links between nuclear transport, ubiquitin signaling, and the intracellular organization of proteasomes during cellular stress conditions.
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Affiliation(s)
- Cordula Enenkel
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
| | - Ryu Won Kang
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Florian Wilfling
- Mechanisms of Cellular Quality Control, Max-Planck-Institute of Biophysics, Frankfurt, Germany
| | - Oliver P Ernst
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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6
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Guo X. Localized Proteasomal Degradation: From the Nucleus to Cell Periphery. Biomolecules 2022; 12:biom12020229. [PMID: 35204730 PMCID: PMC8961600 DOI: 10.3390/biom12020229] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 01/25/2022] [Accepted: 01/27/2022] [Indexed: 12/31/2022] Open
Abstract
The proteasome is responsible for selective degradation of most cellular proteins. Abundantly present in the cell, proteasomes not only diffuse in the cytoplasm and the nucleus but also associate with the chromatin, cytoskeleton, various membranes and membraneless organelles/condensates. How and why the proteasome gets to these specific subcellular compartments remains poorly understood, although increasing evidence supports the hypothesis that intracellular localization may have profound impacts on the activity, substrate accessibility and stability/integrity of the proteasome. In this short review, I summarize recent advances on the functions, regulations and targeting mechanisms of proteasomes, especially those localized to the nuclear condensates and membrane structures of the cell, and I discuss the biological significance thereof in mediating compartmentalized protein degradation.
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Affiliation(s)
- Xing Guo
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China;
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Hangzhou 310058, China
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7
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Emerging Connections between Nuclear Pore Complex Homeostasis and ALS. Int J Mol Sci 2022; 23:ijms23031329. [PMID: 35163252 PMCID: PMC8835831 DOI: 10.3390/ijms23031329] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/17/2022] [Accepted: 01/20/2022] [Indexed: 12/26/2022] Open
Abstract
Developing effective treatments for neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) requires understanding of the underlying pathomechanisms that contribute to the motor neuron loss that defines the disease. As it causes the largest fraction of familial ALS cases, considerable effort has focused on hexanucleotide repeat expansions in the C9ORF72 gene, which encode toxic repeat RNA and dipeptide repeat (DPR) proteins. Both the repeat RNA and DPRs interact with and perturb multiple elements of the nuclear transport machinery, including shuttling nuclear transport receptors, the Ran GTPase and the nucleoporin proteins (nups) that build the nuclear pore complex (NPC). Here, we consider recent work that describes changes to the molecular composition of the NPC in C9ORF72 model and patient neurons in the context of quality control mechanisms that function at the nuclear envelope (NE). For example, changes to NPC structure may be caused by the dysregulation of a conserved NE surveillance pathway mediated by the endosomal sorting complexes required for the transport protein, CHMP7. Thus, these studies are introducing NE and NPC quality control pathways as key elements in a pathological cascade that leads to C9ORF72 ALS, opening entirely new experimental avenues and possibilities for targeted therapeutic intervention.
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8
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Chen X, Walters KJ. Nuclear destruction: A suicide mission by AKIRIN2 brings intact proteasomes into the nucleus. Mol Cell 2022; 82:13-14. [PMID: 34995507 PMCID: PMC11218005 DOI: 10.1016/j.molcel.2021.11.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
de Almeida et al. (2021) developed a temporally controlled CRISPR-Cas9 screen to identify mechanisms controlling MYC levels and discovered that intact proteasomes are imported into the nucleus by AKIRIN2 binding to proteasomes at one end and a nuclear import receptor at the other.
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Affiliation(s)
- Xiang Chen
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Kylie J Walters
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.
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9
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Flagg MP, Wangeline MA, Holland SR, Duttke SH, Benner C, Neal S, Hampton RY. Inner-nuclear-membrane-associated degradation employs Dfm1-independent retrotranslocation and alleviates misfolded transmembrane-protein toxicity. Mol Biol Cell 2021; 32:521-537. [PMID: 33566711 PMCID: PMC8101470 DOI: 10.1091/mbc.e20-11-0720] [Citation(s) in RCA: 3] [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: 11/17/2020] [Revised: 01/27/2021] [Accepted: 02/03/2021] [Indexed: 11/11/2022] Open
Abstract
Before their delivery to and degradation by the 26S proteasome, misfolded transmembrane proteins of the endoplasmic reticulum (ER) and inner-nuclear membrane (INM) must be extracted from lipid bilayers. This extraction process, known as retrotranslocation, requires both quality-control E3 ubiquitin ligases and dislocation factors that diminish the energetic cost of dislodging the transmembrane segments of a protein. Recently, we showed that retrotranslocation of all ER transmembrane proteins requires the Dfm1 rhomboid pseudoprotease. However, we did not investigate whether Dfm1 also mediated retrotranslocation of transmembrane substrates in the INM, which is contiguous with the ER but functionally separated from it by nucleoporins. Here, we show that canonical retrotranslocation occurs during INM-associated degradation (INMAD) but proceeds independently of Dfm1. Despite this independence, ER-associated degradation (ERAD)-M and INMAD cooperate to mitigate proteotoxicity. We show a novel misfolded-transmembrane-protein toxicity that elicits genetic suppression, demonstrating the cell's ability to tolerate a toxic burden of misfolded transmembrane proteins without functional INMAD or ERAD-M. This strikingly contrasted the suppression of the dfm1Δ null, which leads to the resumption of ERAD-M through HRD-complex remodeling. Thus, we conclude that INM retrotranslocation proceeds through a novel, private channel that can be studied by virtue of its role in alleviating membrane-associated proteotoxicity.
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Affiliation(s)
- Matthew P. Flagg
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Margaret A. Wangeline
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Sarah R. Holland
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Sascha H. Duttke
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093
| | - Christopher Benner
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093
| | - Sonya Neal
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Randolph Y. Hampton
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
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10
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Abstract
The 26S proteasome is the most complex ATP-dependent protease machinery, of ~2.5 MDa mass, ubiquitously found in all eukaryotes. It selectively degrades ubiquitin-conjugated proteins and plays fundamentally indispensable roles in regulating almost all major aspects of cellular activities. To serve as the sole terminal "processor" for myriad ubiquitylation pathways, the proteasome evolved exceptional adaptability in dynamically organizing a large network of proteins, including ubiquitin receptors, shuttle factors, deubiquitinases, AAA-ATPase unfoldases, and ubiquitin ligases, to enable substrate selectivity and processing efficiency and to achieve regulation precision of a vast diversity of substrates. The inner working of the 26S proteasome is among the most sophisticated, enigmatic mechanisms of enzyme machinery in eukaryotic cells. Recent breakthroughs in three-dimensional atomic-level visualization of the 26S proteasome dynamics during polyubiquitylated substrate degradation elucidated an extensively detailed picture of its functional mechanisms, owing to progressive methodological advances associated with cryogenic electron microscopy (cryo-EM). Multiple sites of ubiquitin binding in the proteasome revealed a canonical mode of ubiquitin-dependent substrate engagement. The proteasome conformation in the act of substrate deubiquitylation provided insights into how the deubiquitylating activity of RPN11 is enhanced in the holoenzyme and is coupled to substrate translocation. Intriguingly, three principal modes of coordinated ATP hydrolysis in the heterohexameric AAA-ATPase motor were discovered to regulate intermediate functional steps of the proteasome, including ubiquitin-substrate engagement, deubiquitylation, initiation of substrate translocation and processive substrate degradation. The atomic dissection of the innermost working of the 26S proteasome opens up a new era in our understanding of the ubiquitin-proteasome system and has far-reaching implications in health and disease.
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Affiliation(s)
- Youdong Mao
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, 02215, Massachusetts, USA. .,School of Physics, Center for Quantitative Biology, Peking University, Beijing, 100871, China.
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11
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Okeke E, Chen L, Madura K. The Cellular Location of Rad23, a Polyubiquitin Chain-Binding Protein, Plays a Key Role in Its Interaction with Substrates of the Proteasome. J Mol Biol 2020; 432:2388-2404. [PMID: 32147457 DOI: 10.1016/j.jmb.2020.03.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 02/28/2020] [Accepted: 03/02/2020] [Indexed: 11/30/2022]
Abstract
Well-studied structural motifs in Rad23 have been shown to bind polyubiquitin chains and the proteasome. These domains are predicted to enable Rad23 to transport polyubiquitylated (polyUb) substrates to the proteasome (Chen and Madura, 2002 [1]). The validation of this model, however, has been hindered by the lack of specific physiological substrates of Rad23. We report here that Rad23 can bind Ho-endonuclease (Ho-endo), a nuclear protein that initiates mating-type switching in Saccharomyces cerevisiae. We observed that the degradation of Ho-endo required export from the nucleus, in agreement with a previous report (Kaplun et al., 2003 [2]), and suggests that Rad23 can traffic proteins out of the nucleus. In agreement, the subcellular distribution of Rad23 is noticeably altered in genetic mutants that disrupt nucleocytoplasmic trafficking. Significantly, the location of Rad23 affected its binding to polyUb substrates. Mutations in nuclear export stabilized substrates, and caused accumulation in the nucleus. Importantly, Rad23 also accumulated in the nucleus in an export mutant, and bound to higher levels of polyUb proteins. In contrast, Rad23 is localized in the cytosol in rna1-1, a nucleocytoplasmic transport mutant, and it forms reduced binding to polyUb substrates. These and other studies indicate that substrates that are conjugated to polyubiquitin chains in the nucleus may rely on an export-dependent mechanism to be degraded by the proteasome. The evolutionary conservation of Rad23 and similar substrate-trafficking proteins predicts an important role for export in the turnover of nuclear proteins.
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Affiliation(s)
- Evelyn Okeke
- Department of Pharmacology - SPH 383, Robert Wood Johnson Medical School, Rutgers University, 683 Hoes Lane, Piscataway, NJ 08854, USA
| | - Li Chen
- Department of Pharmacology - SPH 383, Robert Wood Johnson Medical School, Rutgers University, 683 Hoes Lane, Piscataway, NJ 08854, USA
| | - Kiran Madura
- Department of Pharmacology - SPH 383, Robert Wood Johnson Medical School, Rutgers University, 683 Hoes Lane, Piscataway, NJ 08854, USA.
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12
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Budenholzer L, Breckel C, Hickey CM, Hochstrasser M. The Sts1 nuclear import adapter uses a non-canonical bipartite nuclear localization signal and is directly degraded by the proteasome. J Cell Sci 2020; 133:jcs.236158. [PMID: 32041904 DOI: 10.1242/jcs.236158] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 01/27/2020] [Indexed: 02/06/2023] Open
Abstract
The proteasome is an essential regulator of protein homeostasis. In yeast and many mammalian cells, proteasomes strongly concentrate in the nucleus. Sts1 from the yeast Saccharomyces cerevisiae is an essential protein linked to proteasome nuclear localization. Here, we show that Sts1 contains a non-canonical bipartite nuclear localization signal (NLS) important for both nuclear localization of Sts1 itself and the proteasome. Sts1 binds the karyopherin-α import receptor (Srp1) stoichiometrically, and this requires the NLS. The NLS is essential for viability, and over-expressed Sts1 with an inactive NLS interferes with 26S proteasome import. The Sts1-Srp1 complex binds preferentially to fully assembled 26S proteasomes in vitro Sts1 is itself a rapidly degraded 26S proteasome substrate; notably, this degradation is ubiquitin independent in cells and in vitro and is inhibited by Srp1 binding. Mutants of Sts1 are stabilized, suggesting that its degradation is tightly linked to its role in localizing proteasomes to the nucleus. We propose that Sts1 normally promotes nuclear import of fully assembled proteasomes and is directly degraded by proteasomes without prior ubiquitylation following karyopherin-α release in the nucleus.
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Affiliation(s)
- Lauren Budenholzer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Carolyn Breckel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Christopher M Hickey
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA .,Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT 06520, USA
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13
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Marshall RS, Vierstra RD. Dynamic Regulation of the 26S Proteasome: From Synthesis to Degradation. Front Mol Biosci 2019; 6:40. [PMID: 31231659 PMCID: PMC6568242 DOI: 10.3389/fmolb.2019.00040] [Citation(s) in RCA: 141] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 05/09/2019] [Indexed: 01/12/2023] Open
Abstract
All eukaryotes rely on selective proteolysis to control the abundance of key regulatory proteins and maintain a healthy and properly functioning proteome. Most of this turnover is catalyzed by the 26S proteasome, an intricate, multi-subunit proteolytic machine. Proteasomes recognize and degrade proteins first marked with one or more chains of poly-ubiquitin, the addition of which is actuated by hundreds of ligases that individually identify appropriate substrates for ubiquitylation. Subsequent proteasomal digestion is essential and influences a myriad of cellular processes in species as diverse as plants, fungi and humans. Importantly, dysfunction of 26S proteasomes is associated with numerous human pathologies and profoundly impacts crop performance, thus making an understanding of proteasome dynamics critically relevant to almost all facets of human health and nutrition. Given this widespread significance, it is not surprising that sophisticated mechanisms have evolved to tightly regulate 26S proteasome assembly, abundance and activity in response to demand, organismal development and stress. These include controls on transcription and chaperone-mediated assembly, influences on proteasome localization and activity by an assortment of binding proteins and post-translational modifications, and ultimately the removal of excess or damaged particles via autophagy. Intriguingly, the autophagic clearance of damaged 26S proteasomes first involves their modification with ubiquitin, thus connecting ubiquitylation and autophagy as key regulatory events in proteasome quality control. This turnover is also influenced by two distinct biomolecular condensates that coalesce in the cytoplasm, one attracting damaged proteasomes for autophagy, and the other reversibly storing proteasomes during carbon starvation to protect them from autophagic clearance. In this review, we describe the current state of knowledge regarding the dynamic regulation of 26S proteasomes at all stages of their life cycle, illustrating how protein degradation through this proteolytic machine is tightly controlled to ensure optimal growth, development and longevity.
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Affiliation(s)
- Richard S Marshall
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
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14
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Serrano-Bueno G, Madroñal JM, Manzano-López J, Muñiz M, Pérez-Castiñeira JR, Hernández A, Serrano A. Nuclear proteasomal degradation of Saccharomyces cerevisiae inorganic pyrophosphatase Ipp1p, a nucleocytoplasmic protein whose stability depends on its subcellular localization. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:1019-1033. [DOI: 10.1016/j.bbamcr.2019.02.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 02/13/2019] [Accepted: 02/26/2019] [Indexed: 12/29/2022]
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15
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Wendler P, Enenkel C. Nuclear Transport of Yeast Proteasomes. Front Mol Biosci 2019; 6:34. [PMID: 31157235 PMCID: PMC6532418 DOI: 10.3389/fmolb.2019.00034] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 04/26/2019] [Indexed: 11/13/2022] Open
Abstract
Proteasomes are key proteases in regulating protein homeostasis. Their holo-enzymes are composed of 40 different subunits which are arranged in a proteolytic core (CP) flanked by one to two regulatory particles (RP). Proteasomal proteolysis is essential for the degradation of proteins which control time-sensitive processes like cell cycle progression and stress response. In dividing yeast and human cells, proteasomes are primarily nuclear suggesting that proteasomal proteolysis is mainly required in the nucleus during cell proliferation. In yeast, which have a closed mitosis, proteasomes are imported into the nucleus as immature precursors via the classical import pathway. During quiescence, the reversible absence of proliferation induced by nutrient depletion or growth factor deprivation, proteasomes move from the nucleus into the cytoplasm. In the cytoplasm of quiescent yeast, proteasomes are dissociated into CP and RP and stored in membrane-less cytoplasmic foci, named proteasome storage granules (PSGs). With the resumption of growth, PSGs clear and mature proteasomes are transported into the nucleus by Blm10, a conserved 240 kDa protein and proteasome-intrinsic import receptor. How proteasomes are exported from the nucleus into the cytoplasm is unknown.
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Affiliation(s)
- Petra Wendler
- Institut für Biochemie und Biologie, Universität Potsdam, Potsdam, Germany
| | - Cordula Enenkel
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
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16
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Patrolling the nucleus: inner nuclear membrane-associated degradation. Curr Genet 2019; 65:1099-1106. [PMID: 31020383 PMCID: PMC6744382 DOI: 10.1007/s00294-019-00971-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 12/13/2022]
Abstract
Protein quality control and transport are important for the integrity of organelles such as the endoplasmic reticulum, but it is largely unknown how protein homeostasis is regulated at the nuclear envelope (NE) despite the connection between NE protein function and human disease. Elucidating mechanisms that regulate the NE proteome is key to understanding nuclear processes such as gene expression, DNA replication and repair as NE components, particularly proteins at the inner nuclear membrane (INM), are involved in the maintenance of nuclear structure, nuclear positioning and chromosome organization. Nuclear pore complexes control the entry and exit of proteins in and out of the nucleus, restricting movement across the nuclear membrane based on protein size, or the size of the extraluminal-facing domain of a transmembrane protein, providing one level of INM proteome regulation. Research in budding yeast has identified a protein quality control system that targets mislocalized and misfolded proteins at the INM. Here, we review what is known about INM-associated degradation, including recent evidence suggesting that it not only targets mislocalized or misfolded proteins, but also contributes to homeostasis of resident INM proteins.
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17
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Abstract
This study compares the native structures of cytosolic and nuclear proteasomes, visualized directly within cells. The assembly states and functional states of proteasomes in each compartment were similar, indicating comparable levels of proteolytic activity per proteasome. Nuclear proteasomes were tethered to two different sites at the nuclear pore complex (NPC): the inner nuclear membrane and the NPC basket. Structural analysis revealed mechanistic details of the two tethering interactions. These results present direct evidence that proteasomes bind at NPCs, establishing a cellular hub for protein degradation at the gateway between the nucleus and cytoplasm. This work demonstrates how cryo-electron tomography can reveal biological mechanisms by directly observing the interactions between molecular complexes within the native cellular environment. The partitioning of cellular components between the nucleus and cytoplasm is the defining feature of eukaryotic life. The nuclear pore complex (NPC) selectively gates the transport of macromolecules between these compartments, but it is unknown whether surveillance mechanisms exist to reinforce this function. By leveraging in situ cryo-electron tomography to image the native cellular environment of Chlamydomonas reinhardtii, we observed that nuclear 26S proteasomes crowd around NPCs. Through a combination of subtomogram averaging and nanometer-precision localization, we identified two classes of proteasomes tethered via their Rpn9 subunits to two specific NPC locations: binding sites on the NPC basket that reflect its eightfold symmetry and more abundant binding sites at the inner nuclear membrane that encircle the NPC. These basket-tethered and membrane-tethered proteasomes, which have similar substrate-processing state frequencies as proteasomes elsewhere in the cell, are ideally positioned to regulate transcription and perform quality control of both soluble and membrane proteins transiting the NPC.
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18
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Pantazopoulou M, Boban M, Foisner R, Ljungdahl PO. Cdc48 and Ubx1 participate in a pathway associated with the inner nuclear membrane that governs Asi1 degradation. J Cell Sci 2016; 129:3770-3780. [PMID: 27566164 DOI: 10.1242/jcs.189332] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 08/18/2016] [Indexed: 01/04/2023] Open
Abstract
The nuclear envelope is a barrier comprising outer and inner membranes that separate the cytoplasm from the nucleoplasm. The two membranes have different physical characteristics and protein compositions. The processes governing the stability of inner nuclear membrane (INM) proteins are not well characterized. In Saccharomyces cerevisiae, the INM Asi1-Asi3 complex, principally composed of integral membrane proteins Asi1 and Asi3, is an E3 ubiquitin ligase. In addition to its well-documented function in endoplasmic reticulum (ER)-associated degradation, the Doa10 E3 ubiquitin ligase complex partially localizes to the INM. The Asi1-Asi3 and Doa10 complexes define independent INM-associated degradation (INMAD) pathways that target discrete sets of nuclear substrates for proteasomal degradation. Here, we report that Asi1 is rapidly turned over (t1/2≤30 min). Its turnover depends on ubiquitin-mediated degradation by nucleus-localized proteasomes, exhibiting a clear requirement for the E2 ubiquitin-conjugating enzyme Ubc7, Cue1 and the AAA ATPase Cdc48 and co-factor Ubx1. Asi1 turnover occurs largely independently of the Asi1-Asi3 or Doa10 complexes, indicating that it is subject to quality control at the INM in a manner distinct from that of the characterized INMAD pathways.
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Affiliation(s)
- Marina Pantazopoulou
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm SE-106 91, Sweden
| | - Mirta Boban
- University of Zagreb, School of Medicine, Croatian Institute for Brain Research, Šalata 12, Zagreb 10000, Croatia
| | - Roland Foisner
- Max F. Perutz Laboratories, Department of Medical Biochemistry, Medical University of Vienna, Dr. Bohr-Gasse 9, Vienna A-1030, Austria
| | - Per O Ljungdahl
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm SE-106 91, Sweden
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19
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Yedidi RS, Fatehi AK, Enenkel C. Proteasome dynamics between proliferation and quiescence stages of Saccharomyces cerevisiae. Crit Rev Biochem Mol Biol 2016; 51:497-512. [PMID: 27677933 DOI: 10.1080/10409238.2016.1230087] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The ubiquitin-proteasome system (UPS) plays a critical role in cellular protein homeostasis and is required for the turnover of short-lived and unwanted proteins, which are targeted by poly-ubiquitination for degradation. Proteasome is the key protease of UPS and consists of multiple subunits, which are organized into a catalytic core particle (CP) and a regulatory particle (RP). In Saccharomyces cerevisiae, proteasome holo-enzymes are engaged in degrading poly-ubiquitinated substrates and are mostly localized in the nucleus during cell proliferation. While in quiescence, the RP and CP are sequestered into motile and reversible storage granules in the cytoplasm, called proteasome storage granules (PSGs). The reversible nature of PSGs allows the proteasomes to be transported back into the nucleus upon exit from quiescence. Nuclear import of RP and CP through nuclear pores occurs via the canonical pathway that includes the importin-αβ heterodimer and takes advantage of the Ran-GTP gradient across the nuclear membrane. Dependent on the growth stage, either inactive precursor complexes or mature holo-enzymes are imported into the nucleus. The present review discusses the dynamics of proteasomes including their assembly, nucleo-cytoplasmic transport during proliferation and the sequestration of proteasomes into PSGs during quiescence. [Formula: see text].
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Affiliation(s)
| | | | - Cordula Enenkel
- a Department of Biochemistry , University of Toronto , Toronto , Canada
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20
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Ren Y, Zhao P, Liu J, Yuan Y, Cheng Q, Zuo Y, Qian L, Liu C, Guo T, Zhang L, Wang X, Qian G, Li L, Ge J, Dai J, Xiong S, Zheng H. Deubiquitinase USP2a Sustains Interferons Antiviral Activity by Restricting Ubiquitination of Activated STAT1 in the Nucleus. PLoS Pathog 2016; 12:e1005764. [PMID: 27434509 PMCID: PMC4951015 DOI: 10.1371/journal.ppat.1005764] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 06/22/2016] [Indexed: 11/29/2022] Open
Abstract
STAT1 is a critical transcription factor for regulating host antiviral defenses. STAT1 activation is largely dependent on phosphorylation at tyrosine 701 site of STAT1 (pY701-STAT1). Understanding how pY701-STAT1 is regulated by intracellular signaling remains a major challenge. Here we find that pY701-STAT1 is the major form of ubiquitinated-STAT1 induced by interferons (IFNs). While total STAT1 remains relatively stable during the early stages of IFNs signaling, pY701-STAT1 can be rapidly downregulated by the ubiquitin-proteasome system. Moreover, ubiquitinated pY701-STAT1 is located predominantly in the nucleus, and inhibiting nuclear import of pY701-STAT1 significantly blocks ubiquitination and downregulation of pY701-STAT1. Furthermore, we reveal that the deubiquitinase USP2a translocates into the nucleus and binds to pY701-STAT1, and inhibits K48-linked ubiquitination and degradation of pY701-STAT1. Importantly, USP2a sustains IFNs-induced pY701-STAT1 levels, and enhances all three classes of IFNs- mediated signaling and antiviral activity. To our knowledge, this is the first identified deubiquitinase that targets activated pY701-STAT1. These findings uncover a positive mechanism by which IFNs execute efficient antiviral signaling and function, and may provide potential targets for improving IFNs-based antiviral therapy. Phosphorylated STAT1 at tyrosine 701 site (pY701-STAT1) is critical for regulating many cellular functions including antiviral immunity. Maintaining sufficient pY701-STAT1 levels in the nucleus is essential to sustain efficient interferons (IFNs) signaling and antiviral functions. Therefore, it is important to clarify how pY701-STAT1 levels are positively regulated in the nucleus. Here, we demonstrated for the first time that IFNs-induced pY701-STAT1 largely raised STAT1 ubiquitination, and ubiquitinated-pY701-STAT1 is located predominantly in the nucleus and regulated by proteasome-dependent degradation. In IFNs signaling, the deubiquitinase USP2a translocates into the nucleus and binds to pY701-STAT1. USP2a positively regulates pY701-STAT1 levels through inhibiting its K48-linked ubiquitination and degradation. Importantly, USP2a sustains all three classes of IFNs-mediated signaling and antiviral function. Our studies uncover an important positive mechanism in the nucleus by which IFNs can execute efficient antiviral signaling and functions.
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Affiliation(s)
- Ying Ren
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Peng Zhao
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Jin Liu
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Yukang Yuan
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Qiao Cheng
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Yibo Zuo
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Liping Qian
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Chang Liu
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Tingting Guo
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Liting Zhang
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Xiaofang Wang
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Guanghui Qian
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Lemin Li
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Jun Ge
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Jianfeng Dai
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Sidong Xiong
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
- Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Jiangsu, China
- * E-mail: (SX); (HZ)
| | - Hui Zheng
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
- Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Jiangsu, China
- * E-mail: (SX); (HZ)
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21
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Dang FW, Chen L, Madura K. Catalytically Active Proteasomes Function Predominantly in the Cytosol. J Biol Chem 2016; 291:18765-77. [PMID: 27417138 DOI: 10.1074/jbc.m115.712406] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Indexed: 12/18/2022] Open
Abstract
The ubiquitin/proteasome pathway is a well characterized system for degrading intracellular proteins, although many aspects remain poorly understood. There is, for instance, a conspicuous lack of understanding of the site(s) where nuclear proteins are degraded because the subcellular distribution of peptidase activity has not been investigated systematically. Although nuclear proteins could be degraded by importing proteasomes into the nucleus, it is also evident that some nuclear proteins are degraded only after export to cytosolic proteasomes. Proteasomes and substrates are mobile, and consequently, the sites of degradation might not be static. We sought to identify the location of proteasomes to provide more conclusive evidence on the sites of protein degradation. We report that catalytically active proteasomes exist almost exclusively in the cytosol. The resulting lack of nuclear peptidase activity suggests that little, if any, degradation occurs in the nucleus. These and other studies suggest that the export of proteolytic substrates could define an important regulatory step in the degradation of nuclear proteins by cytosolic proteasomes.
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Affiliation(s)
- Francis Wang Dang
- From the Department of Pharmacology, Robert Wood Johnson Medical School-Rutgers University, Piscataway, New Jersey 08854
| | - Li Chen
- From the Department of Pharmacology, Robert Wood Johnson Medical School-Rutgers University, Piscataway, New Jersey 08854
| | - Kiran Madura
- From the Department of Pharmacology, Robert Wood Johnson Medical School-Rutgers University, Piscataway, New Jersey 08854
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22
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Smith N, Adle DJ, Zhao M, Qin X, Kim H, Lee J. Endoplasmic Reticulum-associated Degradation of Pca1p, a Polytopic Protein, via Interaction with the Proteasome at the Membrane. J Biol Chem 2016; 291:15082-92. [PMID: 27226596 DOI: 10.1074/jbc.m116.726265] [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] [Received: 03/07/2016] [Indexed: 11/06/2022] Open
Abstract
Endoplasmic reticulum-associated degradation (ERAD) plays a critical role in the destruction of terminally misfolded proteins at the secretory pathway. The system also regulates expression levels of several proteins such as Pca1p, a cadmium exporter in yeast. To gain better insight into the mechanisms underlying ERAD of Pca1p and other polytopic proteins by the proteasome in the cytosol, our study determined the roles for the molecular factors of ERAD in dislodging Pca1p from the endoplasmic reticulum (ER). Inactivation of the 20S proteasome leads to accumulation of ubiquitinated Pca1p in the ER membrane, suggesting a role for the proteasome in extraction of Pca1p from the ER. Pca1p formed a complex with the proteasome at the membrane in a Doa10p E3 ligase-dependent manner. Cdc48p is required for recruiting the proteasome to Pca1p. Although the Ufd2p E4 ubiquitin chain extension enzyme is involved in efficient degradation of Pca1p, Ufd2p-deficient cells did not affect the formation of a complex between Pca1p and the proteasome. Two other polytopic membrane proteins undergoing ERAD, Ste6*p and Hmg2p, also displayed the same outcomes observed for Pca1p. However, poly-ubiquitinated Cpy1*p, a luminal ERAD substrate, was detected in the cytosol independent of proteolytic activities of the proteasome. These results indicate that extraction and degradation of polytopic membrane proteins at the ER is a coupled event. This mechanism would relieve the cost of exposed hydrophobic domains in the cytosol during ERAD.
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Affiliation(s)
- Nathan Smith
- From the Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska, 68588-0664 and
| | - David J Adle
- From the Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska, 68588-0664 and
| | - Miaoyun Zhao
- From the Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska, 68588-0664 and
| | - Xiaojuan Qin
- From the Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska, 68588-0664 and the College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China 200234
| | - Heejeong Kim
- From the Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska, 68588-0664 and
| | - Jaekwon Lee
- From the Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska, 68588-0664 and
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23
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N-Myristoylation of the Rpt2 subunit of the yeast 26S proteasome is implicated in the subcellular compartment-specific protein quality control system. J Proteomics 2015; 130:33-41. [PMID: 26344132 DOI: 10.1016/j.jprot.2015.08.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 08/14/2015] [Accepted: 08/27/2015] [Indexed: 12/14/2022]
Abstract
Ubiquitination is the posttranslational modification of a protein by covalent attachment of ubiquitin. Controlled proteolysis via the ubiquitin-proteasome system (\UPS) alleviates cellular stress by clearing misfolded proteins. In budding yeast, UPS within the nucleus degrades the nuclear proteins as well as proteins imported from the cytoplasm. While the predominantly nuclear localization of the yeast proteasome is maintained by the importin-mediated transport, N-myristoylation of the proteasome subunit Rpt2 was indicated to cause dynamic nucleo-cytoplasmic localization of proteasomes. Here, we quantitatively analyzed the ubiquitinated peptides using anti-K-ε-GG antibody in yeast cell lines with or without a mutation in the N-myristoylation site of Rpt2 and detected upregulated ubiquitination of proteins with nucleo-cytoplasmic localizations in the mutant strains. Moreover, both the protein and ubiquitinated peptide levels of two Hsp70 family chaperones involved in the nuclear import of misfolded proteins, Ssa and Sse1, were elevated in the mutant strains, whereas levels of an Hsp70 family chaperone involved in the nuclear export, Ssb, were reduced. Taken together, our results indicate that N-myristoylation of Rpt2 is involved in controlled proteolysis via regulation of the nucleo-cytoplasmic localization of the yeast proteasome.
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24
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Burcoglu J, Zhao L, Enenkel C. Nuclear Import of Yeast Proteasomes. Cells 2015; 4:387-405. [PMID: 26262643 PMCID: PMC4588042 DOI: 10.3390/cells4030387] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 06/28/2015] [Indexed: 01/16/2023] Open
Abstract
Proteasomes are highly conserved protease complexes responsible for the degradation of aberrant and short-lived proteins. In highly proliferating yeast and mammalian cells, proteasomes are predominantly nuclear. During quiescence and cell cycle arrest, proteasomes accumulate in granules in close proximity to the nuclear envelope/ER. With prolonged quiescence in yeast, these proteasome granules pinch off as membraneless organelles, and migrate as stable entities through the cytoplasm. Upon exit from quiescence, the proteasome granules clear and the proteasomes are rapidly transported into the nucleus, a process reflecting the dynamic nature of these multisubunit complexes. Due to the scarcity of studies on the nuclear transport of mammalian proteasomes, we summarised the current knowledge on the nuclear import of yeast proteasomes. This pathway uses canonical nuclear localisation signals within proteasomal subunits and Srp1/Kap95, and the canonical import receptor, named importin/karyopherin αβ. Blm10, a conserved 240 kDa protein, which is structurally related to Kap95, provides an alternative import pathway. Two models exist upon which either inactive precursor complexes or active holo-enzymes serve as the import cargo. Here, we reconcile both models and suggest that the import of inactive precursor complexes predominates in dividing cells, while the import of mature enzymes mainly occurs upon exit from quiescence.
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Affiliation(s)
- Julianne Burcoglu
- Biochemistry Department, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Liang Zhao
- Biochemistry Department, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Cordula Enenkel
- Biochemistry Department, University of Toronto, Toronto, ON M5S 1A8, Canada.
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25
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Lucena R, Dephoure N, Gygi SP, Kellogg DR, Tallada VA, Daga RR, Jimenez J. Nucleocytoplasmic transport in the midzone membrane domain controls yeast mitotic spindle disassembly. ACTA ACUST UNITED AC 2015; 209:387-402. [PMID: 25963819 PMCID: PMC4427787 DOI: 10.1083/jcb.201412144] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
During anaphase B, Imp1-mediated transport of the AAA-ATPase Cdc48 protein at the membrane domain surrounding the mitotic spindle midzone promotes spindle midzone dissolution in fission yeast. During each cell cycle, the mitotic spindle is efficiently assembled to achieve chromosome segregation and then rapidly disassembled as cells enter cytokinesis. Although much has been learned about assembly, how spindles disassemble at the end of mitosis remains unclear. Here we demonstrate that nucleocytoplasmic transport at the membrane domain surrounding the mitotic spindle midzone, here named the midzone membrane domain (MMD), is essential for spindle disassembly in Schizosaccharomyces pombe cells. We show that, during anaphase B, Imp1-mediated transport of the AAA-ATPase Cdc48 protein at the MMD allows this disassembly factor to localize at the spindle midzone, thereby promoting spindle midzone dissolution. Our findings illustrate how a separate membrane compartment supports spindle disassembly in the closed mitosis of fission yeast.
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Affiliation(s)
- Rafael Lucena
- Centro Andaluz de Biología del Desarrollo. Universidad Pablo de Olavide/Consejo Superior de Investigaciones Cientificas, 41013 Sevilla, Spain Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064
| | - Noah Dephoure
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Steve P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Douglas R Kellogg
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064
| | - Victor A Tallada
- Centro Andaluz de Biología del Desarrollo. Universidad Pablo de Olavide/Consejo Superior de Investigaciones Cientificas, 41013 Sevilla, Spain
| | - Rafael R Daga
- Centro Andaluz de Biología del Desarrollo. Universidad Pablo de Olavide/Consejo Superior de Investigaciones Cientificas, 41013 Sevilla, Spain
| | - Juan Jimenez
- Centro Andaluz de Biología del Desarrollo. Universidad Pablo de Olavide/Consejo Superior de Investigaciones Cientificas, 41013 Sevilla, Spain
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26
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Abstract
The ubiquitin-proteasome system is the major degradation pathway for short-lived proteins in eukaryotic cells. Targets of the ubiquitin-proteasome-system are proteins regulating a broad range of cellular processes including cell cycle progression, gene expression, the quality control of proteostasis and the response to geno- and proteotoxic stress. Prior to degradation, the proteasomal substrate is marked with a poly-ubiquitin chain. The key protease of the ubiquitin system is the proteasome. In dividing cells, proteasomes exist as holo-enzymes composed of regulatory and core particles. The regulatory complex confers ubiquitin-recognition and ATP dependence on proteasomal protein degradation. The catalytic sites are located in the proteasome core particle. Proteasome holo-enzymes are predominantly nuclear suggesting a major requirement for proteasomal proteolysis in the nucleus. In cell cycle arrested mammalian or quiescent yeast cells, proteasomes deplete from the nucleus and accumulate in granules at the nuclear envelope (NE) / endoplasmic reticulum ( ER) membranes. In prolonged quiescence, proteasome granules drop off the nuclear envelopeNE / ER membranes and migrate as droplet-like entitiesstable organelles throughout the cytoplasm, as thoroughly investigated in yeast. When quiescence yeast cells are allowed to resume growth, proteasome granules clear and proteasomes are rapidly imported into the nucleus. Here, we summarize our knowledge about the enigmatic structure of proteasome storage granules and the trafficking of proteasomes and their substrates between the cyto- and nucleoplasm. Most of our current knowledge is based on studies in yeast. Their translation to mammalian cells promises to provide keen insight into protein degradation in non-dividing cells, which comprise the majority of our body’s cells.
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Affiliation(s)
- Maisha Chowdhury
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Cordula Enenkel
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
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27
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Abstract
The ubiquitin-proteasome system is the major degradation pathway for short-lived proteins in eukaryotic cells. Targets of the ubiquitin-proteasome-system are proteins regulating a broad range of cellular processes including cell cycle progression, gene expression, the quality control of proteostasis and the response to geno- and proteotoxic stress. Prior to degradation, the proteasomal substrate is marked with a poly-ubiquitin chain. The key protease of the ubiquitin system is the proteasome. In dividing cells, proteasomes exist as holo-enzymes composed of regulatory and core particles. The regulatory complex confers ubiquitin-recognition and ATP dependence on proteasomal protein degradation. The catalytic sites are located in the proteasome core particle. Proteasome holo-enzymes are predominantly nuclear suggesting a major requirement for proteasomal proteolysis in the nucleus. In cell cycle arrested mammalian or quiescent yeast cells, proteasomes deplete from the nucleus and accumulate in granules at the nuclear envelope (NE) / endoplasmic reticulum ( ER) membranes. In prolonged quiescence, proteasome granules drop off the nuclear envelopeNE / ER membranes and migrate as droplet-like entitiesstable organelles throughout the cytoplasm, as thoroughly investigated in yeast. When quiescence yeast cells are allowed to resume growth, proteasome granules clear and proteasomes are rapidly imported into the nucleus. Here, we summarize our knowledge about the enigmatic structure of proteasome storage granules and the trafficking of proteasomes and their substrates between the cyto- and nucleoplasm. Most of our current knowledge is based on studies in yeast. Their translation to mammalian cells promises to provide keen insight into protein degradation in non-dividing cells, which comprise the majority of our body's cells.
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Affiliation(s)
- Maisha Chowdhury
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Cordula Enenkel
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
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28
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Abstract
The proper folding of proteins is continuously challenged by intrinsic and extrinsic stresses, and the accumulation of toxic misfolded proteins is associated with many human diseases. Eukaryotic cells have evolved a complex network of protein quality control pathways to protect the proteome, and these pathways are specialized for each subcellular compartment. While many details have been elucidated for how the cytosol and endoplasmic reticulum counteract proteotoxic stress, relatively little is known about the pathways protecting the nucleus from protein misfolding. Proper maintenance of nuclear proteostasis has important implications in preserving genomic integrity, as well as for aging and disease. Here, we offer a conceptual framework for how proteostasis is maintained in this organelle. We define the particular requirements that must be considered for the nucleus to manage proteotoxic stress, summarize the known and implicated pathways of nuclear protein quality control, and identify the unresolved questions in the field.
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Affiliation(s)
- Yoko Shibata
- Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, IL 60208, USA
| | - Richard I Morimoto
- Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, IL 60208, USA.
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29
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Enenkel C. Nuclear transport of yeast proteasomes. Biomolecules 2014; 4:940-55. [PMID: 25333764 PMCID: PMC4279164 DOI: 10.3390/biom4040940] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 08/18/2014] [Accepted: 09/26/2014] [Indexed: 12/25/2022] Open
Abstract
Proteasomes are conserved protease complexes enriched in the nuclei of dividing yeast cells, a major site for protein degradation. If yeast cells do not proliferate and transit to quiescence, metabolic changes result in the dissociation of proteasomes into proteolytic core and regulatory complexes and their sequestration into motile cytosolic proteasome storage granuli. These granuli rapidly clear with the resumption of growth, releasing the stored proteasomes, which relocalize back to the nucleus to promote cell cycle progression. Here, I report on three models of how proteasomes are transported from the cytoplasm into the nucleus of yeast cells. The first model applies for dividing yeast and is based on the canonical pathway using classical nuclear localization sequences of proteasomal subcomplexes and the classical import receptor importin/karyopherin αβ. The second model applies for quiescent yeast cells, which resume growth and use Blm10, a HEAT-like repeat protein structurally related to karyopherin β, for nuclear import of proteasome core particles. In the third model, the fully-assembled proteasome is imported into the nucleus. Our still marginal knowledge about proteasome dynamics will inspire the discussion on how protein degradation by proteasomes may be regulated in different cellular compartments of dividing and quiescent eukaryotic cells.
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Affiliation(s)
- Cordula Enenkel
- Department of Biochemistry, University of Toronto, Medical Sciences Building, 1 King's College Circle, Toronto, ON M5S 1A8, Canada.
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Chen L, Madura K. Yeast importin-α (Srp1) performs distinct roles in the import of nuclear proteins and in targeting proteasomes to the nucleus. J Biol Chem 2014; 289:32339-32352. [PMID: 25274630 DOI: 10.1074/jbc.m114.582023] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Srp1 (importin-α) can translocate proteins that contain a nuclear localization signal (NLS) into the nucleus. The loss of Srp1 is lethal, although several temperature-sensitive mutants have been described. Among these mutants, srp1-31 displays the characteristic nuclear import defect of importin-α mutants, whereas srp1-49 shows a defect in protein degradation. We characterized these and additional srp1 mutants to determine whether distinct mechanisms were required for intracellular proteolysis and the import of NLS-containing proteins. We determined that srp1 mutants that failed to import NLS-containing proteins (srp1-31 and srp1-55) successfully localized proteasomes to the nucleus. In contrast, srp1 mutants that did not target proteasomes to the nucleus (srp1-49 and srp1-E402Q) were able to import NLS-containing proteins. The proteasome targeting defect of specific srp1 mutants caused stabilization of nuclear substrates and overall accumulation of multiubiquitylated proteins. Co-expression of a member of each class of srp1 mutants corrected both the proteasome localization defect and the import of NLS-containing proteins. These findings indicate that the targeting of proteasomes to the nucleus occurs by a mechanism distinct from the Srp1-mediated import of nuclear proteins.
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Affiliation(s)
- Li Chen
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey 08854
| | - Kiran Madura
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey 08854.
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Boban M, Pantazopoulou M, Schick A, Ljungdahl PO, Foisner R. A nuclear ubiquitin-proteasome pathway targets the inner nuclear membrane protein Asi2 for degradation. J Cell Sci 2014; 127:3603-13. [PMID: 24928896 DOI: 10.1242/jcs.153163] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The nuclear envelope consists of inner and outer nuclear membranes. Whereas the outer membrane is an extension of the endoplasmic reticulum, the inner nuclear membrane (INM) represents a unique membranous environment containing specific proteins. The mechanisms of integral INM protein degradation are unknown. Here, we investigated the turnover of Asi2, an integral INM protein in Saccharomyces cerevisiae. We report that Asi2 is degraded by the proteasome independently of the vacuole and that it exhibited a half-life of ∼45 min. Asi2 exhibits enhanced stability in mutants lacking the E2 ubiquitin conjugating enzymes Ubc6 or Ubc7, or the E3 ubiquitin ligase Doa10. Consistent with these data, Asi2 is post-translationally modified by poly-ubiquitylation in a Ubc7- and Doa10-dependent manner. Importantly Asi2 degradation is significantly reduced in a sts1-2 mutant that fails to accumulate proteasomes in the nucleus, indicating that Asi2 is degraded in the nucleus. Our results reveal a molecular pathway that affects the stability of integral proteins of the inner nuclear membrane and indicate that Asi2 is subject to protein quality control in the nucleus.
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Affiliation(s)
- Mirta Boban
- Max F. Perutz Laboratories, Department of Medical Biochemistry, Medical University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria
| | - Marina Pantazopoulou
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Anna Schick
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Per O Ljungdahl
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Roland Foisner
- Max F. Perutz Laboratories, Department of Medical Biochemistry, Medical University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria
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Abstract
The ubiquitin/proteasome system has been characterized extensively, although the site of nuclear substrate turnover has not been established definitively. We report here that two well-characterized nuclear proteins are stabilized in nuclear export mutants in Saccharomyces cerevisiae. The requirement for nuclear export defines a new regulatory step in intracellular proteolysis.
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Pack CG, Yukii H, Toh-e A, Kudo T, Tsuchiya H, Kaiho A, Sakata E, Murata S, Yokosawa H, Sako Y, Baumeister W, Tanaka K, Saeki Y. Quantitative live-cell imaging reveals spatio-temporal dynamics and cytoplasmic assembly of the 26S proteasome. Nat Commun 2014; 5:3396. [PMID: 24598877 DOI: 10.1038/ncomms4396] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Accepted: 02/06/2014] [Indexed: 01/15/2023] Open
Abstract
The 26S proteasome is a 2.5-MDa multisubunit protease complex that degrades polyubiquitylated proteins. Although its functions and structure have been extensively characterized, little is known about its dynamics in living cells. Here, we investigate the absolute concentration, spatio-temporal dynamics and complex formation of the proteasome in living cells using fluorescence correlation spectroscopy. We find that the 26S proteasome complex is highly mobile, and that almost all proteasome subunits throughout the cell are stably incorporated into 26S proteasomes. The interaction between 19S and 20S particles is stable even in an importin-α mutant, suggesting that the 26S proteasome is assembled in the cytoplasm. Furthermore, a genetically stabilized 26S proteasome mutant is able to enter the nucleus. These results suggest that the 26S proteasome completes its assembly process in the cytoplasm and translocates into the nucleus through the nuclear pore complex as a holoenzyme.
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Affiliation(s)
- Chan-Gi Pack
- Cellular Informatics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Haruka Yukii
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo 156-8506, Japan
| | - Akio Toh-e
- Medical Mycology Center, Chiba University, 1-8-1 Inohana, Chiba 260-8673, Japan
| | - Tai Kudo
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo 156-8506, Japan
| | - Hikaru Tsuchiya
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo 156-8506, Japan
| | - Ai Kaiho
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo 156-8506, Japan
| | - Eri Sakata
- Department of Molecular Structural Biology, Max-Planck-Institute of Biochemistry, 82152 Martinsried, Germany
| | - Shigeo Murata
- Laboratory of Protein Metabolism, Graduate School of Pharmaceutical Sciences, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hideyoshi Yokosawa
- Department of Medicinal Biochemistry, School of Pharmacy, Aichi Gakuin University, 1-100 Kusumoto-cho, Chikusa-ku, Nagoya 464-8650, Japan
| | - Yasushi Sako
- Cellular Informatics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max-Planck-Institute of Biochemistry, 82152 Martinsried, Germany
| | - Keiji Tanaka
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo 156-8506, Japan
| | - Yasushi Saeki
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo 156-8506, Japan
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Ha SW, Ju D, Xie Y. Nuclear import factor Srp1 and its associated protein Sts1 couple ribosome-bound nascent polypeptides to proteasomes for cotranslational degradation. J Biol Chem 2013; 289:2701-10. [PMID: 24338021 DOI: 10.1074/jbc.m113.524926] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cotranslational protein degradation plays an important role in protein quality control and proteostasis. Although ubiquitylation has been suggested to signal cotranslational degradation of nascent polypeptides, cotranslational ubiquitylation occurs at a low level, suggesting the existence of an alternative route for delivery of nascent polypeptides to the proteasome. Here we report that the nuclear import factor Srp1 (also known as importin α or karyopherin α) is required for ubiquitin-independent cotranslational degradation of the transcription factor Rpn4. We further demonstrate that cotranslational protein degradation is generally impaired in the srp1-49 mutant. Srp1 binds nascent polypeptides emerging from the ribosome. The association of proteasomes with polysomes is weakened in srp1-49. The interaction between Srp1 and the proteasome is mediated by Sts1, a multicopy suppressor of srp1-49. The srp1-49 and sts1-2 mutants are hypersensitive to stressors that promote protein misfolding, underscoring the physiological function of Srp1 and Sts1 in degradation of misfolded nascent polypeptides. This study unveils a previously unknown role for Srp1 and Sts1 in cotranslational protein degradation and suggests a novel model whereby Srp1 and Sts1 cooperate to couple proteasomes to ribosome-bound nascent polypeptides.
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Affiliation(s)
- Seung-Wook Ha
- From the Karmanos Cancer Institute, Department of Oncology, and Department of Pathology, Wayne State University School of Medicine, Detroit, Michigan 48201
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35
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Chien CY, Chen RH. Cdc48 chaperone and adaptor Ubx4 distribute the proteasome in the nucleus for anaphase proteolysis. J Biol Chem 2013; 288:37180-91. [PMID: 24225956 DOI: 10.1074/jbc.m113.513598] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The cell cycle transition is driven by abrupt degradation of key regulators. While ubiquitylation of these proteins has been extensively studied, the requirement for the proteolytic step is less understood. By analyzing the cell cycle function of Cdc48 in the budding yeast Saccharomyces cerevisiae, we found that double mutations in Cdc48 and its adaptor Ubx4 cause mitotic arrest with sustained Clb2 and Cdc20 proteins that are normally degraded in anaphase. The phenotype is neither caused by spindle checkpoint activation nor a defect in the assembly or the activity of the ubiquitylation machinery and the proteasome. Interestingly, the 26S proteasome is mislocalized into foci, which are colocalized with nuclear envelope anchor Sts1 in cdc48-3 ubx4 cells. Moreover, genetic analysis reveals that ubx4 deletion mutant dies in the absence of Rpn4, a transcriptional activator for proteasome subunits, and the proteasome chaperone Ump1, indicating that an optimal level of the proteasome is required for survival. Overexpression of Rpn4 indeed can rescue cell growth and anaphase proteolysis in cdc48-3 ubx4 cells. Biochemical analysis further shows that Ubx4 interacts with the proteasome. Our data propose that Cdc48-Ubx4 acts on the proteasome and uses the chaperone activity to promote its nuclear distribution, thereby optimizing the proteasome level for efficient degradation of mitotic regulators.
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Affiliation(s)
- Chen-Ying Chien
- From the Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 114, Taiwan and
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Weberruss MH, Savulescu AF, Jando J, Bissinger T, Harel A, Glickman MH, Enenkel C. Blm10 facilitates nuclear import of proteasome core particles. EMBO J 2013; 32:2697-707. [PMID: 23982732 DOI: 10.1038/emboj.2013.192] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 08/02/2013] [Indexed: 01/12/2023] Open
Abstract
Short-lived proteins are degraded by proteasome complexes, which contain a proteolytic core particle (CP) but differ in the number of regulatory particles (RPs) and activators. A recently described member of conserved proteasome activators is Blm10. Blm10 contains 32 HEAT-like modules and is structurally related to the nuclear import receptor importin/karyopherin β. In proliferating yeast, RP-CP assemblies are primarily nuclear and promote cell division. During quiescence, RP-CP assemblies dissociate and CP and RP are sequestered into motile cytosolic proteasome storage granuli (PSG). Here, we show that CP sequestration into PSG depends on Blm10, whereas RP sequestration into PSG is independent of Blm10. PSG rapidly clear upon the resumption of cell proliferation and proteasomes are relocated into the nucleus. Thereby, Blm10 facilitates nuclear import of CP. Blm10-bound CP serves as an import receptor-cargo complex, as Blm10 mediates the interaction with FG-rich nucleoporins and is dissociated from the CP by Ran-GTP. Thus, Blm10 represents the first CP-dedicated nuclear import receptor in yeast.
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Affiliation(s)
- Marion H Weberruss
- 1] Department of Biochemistry, University of Toronto, One King's College Circle, Toronto, Ontario, Canada [2] Institute of Biochemistry, University of Stuttgart, Stuttgart, Germany
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Tsuchiya H, Arai N, Tanaka K, Saeki Y. Cytoplasmic proteasomes are not indispensable for cell growth in Saccharomyces cerevisiae. Biochem Biophys Res Commun 2013; 436:372-6. [DOI: 10.1016/j.bbrc.2013.05.105] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 05/24/2013] [Indexed: 01/08/2023]
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Proteasome dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1843:39-46. [PMID: 23545412 DOI: 10.1016/j.bbamcr.2013.03.023] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 03/20/2013] [Accepted: 03/22/2013] [Indexed: 01/06/2023]
Abstract
Proteasomes are highly conserved multisubunit protease complexes and occur in the cyto- and nucleoplasm of eukaryotic cells. In dividing cells proteasomes exist as holoenzymes and primarily localize in the nucleus. During quiescence they dissociate into proteolytic core and regulatory complexes and are sequestered into motile cytosolic clusters. Proteasome clusters rapidly clear upon the exit from quiescence, where proteasome core and regulatory complexes reassemble and localize to the nucleus again. The mechanisms underlying proteasome transport and assembly are not yet understood. Here, I summarize our present knowledge about nuclear transport and assembly of proteasomes in yeast and project our studies in this eukaryotic model organism to the mammalian cell system. This article is part of a Special Issue entitled: Ubiquitin-Proteasome System. Guest Editors: Thomas Sommer and Dieter H. Wolf.
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Kimura A, Kato Y, Hirano H. N-myristoylation of the Rpt2 subunit regulates intracellular localization of the yeast 26S proteasome. Biochemistry 2012; 51:8856-66. [PMID: 23102099 DOI: 10.1021/bi3007862] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The 26S proteasome is a large, complex multisubunit protease involved in protein quality control and other critical processes in eukaryotes. More than 110 post-translational modification (PTM) sites have been identified by a mass spectrometry of the 26S proteasome of Saccharomyces cerevisiae and are predicted to be implicated in the dynamic regulation of proteasomal functions. Here, we report that the N-myristoylation of the Rpt2 subunit controls the intracellular localization of the 26S proteasome. While proteasomes were mainly localized in the nucleus in normal cells, mutation of the N-myristoylation site of Rpt2 caused diffusion of the nuclear proteasome into the cytoplasm, where it formed aggregates. In mutant cells, the level of accumulation of cytoplasmic proteasomes was significantly increased in the nonproliferating state. Although the molecular assembly and peptidase activity of the 26S proteasome were totally unchanged in the nonmyristoylated mutants of Rpt2, an increased level of accumulation of polyubiquitinated proteins and a severe growth defect were observed in mutant cells induced for protein misfolding. In addition, polyubiquitinated protein and the nuclear protein Gcn4 tended not to colocalize with the proteasome in normal and mutant cells. Our results suggest that N-myristoylation is involved in regulating the proper intracellular distribution of proteasome activity by controlling the nuclear localization of the 26S proteasome.
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Affiliation(s)
- Ayuko Kimura
- Advanced Medical Research Center, Yokohama City University, Fukuura 3-9, Kanazawa, Yokohama 236-0004, Japan
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