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Rüttermann M, Koci M, Lill P, Geladas ED, Kaschani F, Klink BU, Erdmann R, Gatsogiannis C. Structure of the peroxisomal Pex1/Pex6 ATPase complex bound to a substrate. Nat Commun 2023; 14:5942. [PMID: 37741838 PMCID: PMC10518020 DOI: 10.1038/s41467-023-41640-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 09/12/2023] [Indexed: 09/25/2023] Open
Abstract
The double-ring AAA+ ATPase Pex1/Pex6 is required for peroxisomal receptor recycling and is essential for peroxisome formation. Pex1/Pex6 mutations cause severe peroxisome associated developmental disorders. Despite its pathophysiological importance, mechanistic details of the heterohexamer are not yet available. Here, we report cryoEM structures of Pex1/Pex6 from Saccharomyces cerevisiae, with an endogenous protein substrate trapped in the central pore of the catalytically active second ring (D2). Pairs of Pex1/Pex6(D2) subdomains engage the substrate via a staircase of pore-1 loops with distinct properties. The first ring (D1) is catalytically inactive but undergoes significant conformational changes resulting in alternate widening and narrowing of its pore. These events are fueled by ATP hydrolysis in the D2 ring and disengagement of a "twin-seam" Pex1/Pex6(D2) heterodimer from the staircase. Mechanical forces are propagated in a unique manner along Pex1/Pex6 interfaces that are not available in homo-oligomeric AAA-ATPases. Our structural analysis reveals the mechanisms of how Pex1 and Pex6 coordinate to achieve substrate translocation.
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Affiliation(s)
- Maximilian Rüttermann
- Institute for Medical Physics and Biophysics, University Münster, Münster, Germany
- Center for Soft Nanoscience (SoN), University Münster, Münster, Germany
| | - Michelle Koci
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Pascal Lill
- Institute for Medical Physics and Biophysics, University Münster, Münster, Germany
- Center for Soft Nanoscience (SoN), University Münster, Münster, Germany
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Ermis Dionysios Geladas
- Institute for Medical Physics and Biophysics, University Münster, Münster, Germany
- Center for Soft Nanoscience (SoN), University Münster, Münster, Germany
| | - Farnusch Kaschani
- Analytics Core Facility Essen, Center of Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Björn Udo Klink
- Institute for Medical Physics and Biophysics, University Münster, Münster, Germany
- Center for Soft Nanoscience (SoN), University Münster, Münster, Germany
| | - Ralf Erdmann
- Institute for Biochemistry and Pathobiochemistry, Department of Systems Biochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Christos Gatsogiannis
- Institute for Medical Physics and Biophysics, University Münster, Münster, Germany.
- Center for Soft Nanoscience (SoN), University Münster, Münster, Germany.
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
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2
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Ott J, Sehr J, Schmidt N, Schliebs W, Erdmann R. Comparison of human PEX knockout cell lines suggests a dual role of PEX1 in peroxisome biogenesis. Biol Chem 2023; 404:209-219. [PMID: 36534601 DOI: 10.1515/hsz-2022-0223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022]
Abstract
For the biogenesis and maintenance of peroxisomes several proteins, called peroxins, are essential. Malfunctions of these proteins lead to severe diseases summarized as peroxisome biogenesis disorders. The different genetic background of patient-derived cell lines and the residual expression of mutated PEX genes impede analysis of the whole spectrum of cellular functions of affected peroxins. To overcome these difficulties, we have generated a selected PEX knockout resource of HEK T-REx293 cells using the CRISPR/Cas9 technique. Comparative analyses of whole cell lysates revealed PEX-KO specific alterations in the steady-state level of peroxins and variations in the import efficacy of matrix proteins with a Type 2 peroxisomal targeting signal. One of the observed differences concerned PEX1 as in the complete absence of the protein, the number of peroxisomal ghosts is significantly increased. Upon expression of PEX1, import competence and abundance of peroxisomes was adjusted to the level of normal HEK cells. In contrast, expression of an alternatively spliced PEX1 isoform lacking 321 amino acids of the N-terminal region failed to rescue the peroxisomal import defects but reduced the number of peroxisomal vesicles. All in all, the data suggest a novel 'moonlighting' function of human PEX1 in the regulation of pre-peroxisomal vesicles.
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Affiliation(s)
- Julia Ott
- Department of Systems Biochemistry, Institute for Biochemistry and Pathobiochemistry, Ruhr University Bochum, D-44780 Bochum, Germany
| | - Jessica Sehr
- Department of Systems Biochemistry, Institute for Biochemistry and Pathobiochemistry, Ruhr University Bochum, D-44780 Bochum, Germany
| | - Nadine Schmidt
- Department of Systems Biochemistry, Institute for Biochemistry and Pathobiochemistry, Ruhr University Bochum, D-44780 Bochum, Germany
| | - Wolfgang Schliebs
- Department of Systems Biochemistry, Institute for Biochemistry and Pathobiochemistry, Ruhr University Bochum, D-44780 Bochum, Germany
| | - Ralf Erdmann
- Department of Systems Biochemistry, Institute for Biochemistry and Pathobiochemistry, Ruhr University Bochum, D-44780 Bochum, Germany
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3
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Carmichael RE, Schrader M. Determinants of Peroxisome Membrane Dynamics. Front Physiol 2022; 13:834411. [PMID: 35185625 PMCID: PMC8853631 DOI: 10.3389/fphys.2022.834411] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/12/2022] [Indexed: 11/13/2022] Open
Abstract
Organelles within the cell are highly dynamic entities, requiring dramatic morphological changes to support their function and maintenance. As a result, organelle membranes are also highly dynamic, adapting to a range of topologies as the organelle changes shape. In particular, peroxisomes—small, ubiquitous organelles involved in lipid metabolism and reactive oxygen species homeostasis—display a striking plasticity, for example, during the growth and division process by which they proliferate. During this process, the membrane of an existing peroxisome elongates to form a tubule, which then constricts and ultimately undergoes scission to generate new peroxisomes. Dysfunction of this plasticity leads to diseases with developmental and neurological phenotypes, highlighting the importance of peroxisome dynamics for healthy cell function. What controls the dynamics of peroxisomal membranes, and how this influences the dynamics of the peroxisomes themselves, is just beginning to be understood. In this review, we consider how the composition, biophysical properties, and protein-lipid interactions of peroxisomal membranes impacts on their dynamics, and in turn on the biogenesis and function of peroxisomes. In particular, we focus on the effect of the peroxin PEX11 on the peroxisome membrane, and its function as a major regulator of growth and division. Understanding the roles and regulation of peroxisomal membrane dynamics necessitates a multidisciplinary approach, encompassing knowledge across a range of model species and a number of fields including lipid biochemistry, biophysics and computational biology. Here, we present an integrated overview of our current understanding of the determinants of peroxisome membrane dynamics, and reflect on the outstanding questions still remaining to be solved.
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Affiliation(s)
- Ruth E Carmichael
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Michael Schrader
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, United Kingdom
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4
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VCP/p97 regulates Beclin-1-dependent autophagy initiation. Nat Chem Biol 2021; 17:448-455. [PMID: 33510452 DOI: 10.1038/s41589-020-00726-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 12/18/2020] [Indexed: 01/30/2023]
Abstract
Autophagy is an essential cellular process that removes harmful protein species, and autophagy upregulation may be able to protect against neurodegeneration and various pathogens. Here, we have identified the essential protein VCP/p97 (VCP, valosin-containing protein) as a novel regulator of autophagosome biogenesis, where VCP regulates autophagy induction in two ways, both dependent on Beclin-1. Utilizing small-molecule inhibitors of VCP ATPase activity, we show that VCP stabilizes Beclin-1 levels by promoting the deubiquitinase activity of ataxin-3 towards Beclin-1. VCP also regulates the assembly and activity of the Beclin-1-containing phosphatidylinositol-3-kinase (PI3K) complex I, thus regulating the production of PI(3)P, a key signaling lipid responsible for the recruitment of downstream autophagy factors. A decreased level of VCP, or inhibition of its ATPase activity, impairs starvation-induced production of PI(3)P and limits downstream recruitment of WIPI2, ATG16L and LC3, thereby decreasing autophagosome formation, illustrating an important role for VCP in early autophagy initiation.
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5
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Reglinski K, Steinfort-Effelsberg L, Sezgin E, Klose C, Platta HW, Girzalsky W, Eggeling C, Erdmann R. Fluidity and Lipid Composition of Membranes of Peroxisomes, Mitochondria and the ER From Oleic Acid-Induced Saccharomyces cerevisiae. Front Cell Dev Biol 2020; 8:574363. [PMID: 33195209 PMCID: PMC7658010 DOI: 10.3389/fcell.2020.574363] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 10/05/2020] [Indexed: 01/08/2023] Open
Abstract
The maintenance of a fluid lipid bilayer is key for organelle function and cell viability. Given the critical role of lipid compositions in determining membrane properties and organelle identity, it is clear that cells must have elaborate mechanism for membrane maintenance during adaptive responses to environmental conditions. Emphasis of the presented study is on peroxisomes, oleic acid-inducible organelles that are essential for the growth of yeast under conditions of oleic acid as single carbon source. Here, we isolated peroxisomes, mitochondria and ER from oleic acid-induced Saccharomyces cerevisiae and determined the lipid composition of their membranes using shotgun lipidomics and compared it to lipid ordering using fluorescence microscopy. In comparison to mitochondrial and ER membranes, the peroxisomal membranes were slightly more disordered and characterized by a distinct enrichment of phosphaditylinositol, indicating an important role of this phospholipid in peroxisomal membrane associated processes.
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Affiliation(s)
- Katharina Reglinski
- Leibniz-Institute of Photonic Technologies, Jena, Germany
- Institute of Applied Optics and Biophysics, Friedrich-Schiller University Jena, Jena, Germany
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- University Hospital Jena, Jena, Germany
| | | | - Erdinc Sezgin
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Science for Life Laboratory, Department of Women’s and Children’s Health, Karolinska Institutet, Solna, Sweden
| | | | - Harald W. Platta
- Biochemistry of Intracelluar Transport, Ruhr-University Bochum, Bochum, Germany
| | - Wolfgang Girzalsky
- Systems Biochemistry, Medical Faculty, Ruhr-University Bochum, Bochum, Germany
| | - Christian Eggeling
- Leibniz-Institute of Photonic Technologies, Jena, Germany
- Institute of Applied Optics and Biophysics, Friedrich-Schiller University Jena, Jena, Germany
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Jena Center for Soft Matter (JCSM), Jena, Germany
| | - Ralf Erdmann
- Systems Biochemistry, Medical Faculty, Ruhr-University Bochum, Bochum, Germany
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6
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Schwerter DP, Grimm I, Platta HW, Erdmann R. ATP-driven processes of peroxisomal matrix protein import. Biol Chem 2017; 398:607-624. [PMID: 27977397 DOI: 10.1515/hsz-2016-0293] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 12/11/2016] [Indexed: 12/13/2022]
Abstract
In peroxisomal matrix protein import two processes directly depend on the binding and hydrolysis of ATP, both taking place at the late steps of the peroxisomal import cycle. First, ATP hydrolysis is required to initiate a ubiquitin-transfer cascade to modify the import (co-)receptors. These receptors display a dual localization in the cytosol and at the peroxisomal membrane, whereas only the membrane bound fraction receives the ubiquitin modification. The second ATP-dependent process of the import cycle is carried out by the two AAA+-proteins Pex1p and Pex6p. These ATPases form a heterohexameric complex, which is recruited to the peroxisomal import machinery by the membrane anchor protein Pex15p. The Pex1p/Pex6p complex recognizes the ubiquitinated import receptors, pulls them out of the membrane and releases them into the cytosol. There the deubiquitinated receptors are provided for further rounds of import. ATP binding and hydrolysis are required for Pex1p/Pex6p complex formation and receptor export. In this review, we summarize the current knowledge on the peroxisomal import cascade. In particular, we will focus on the ATP-dependent processes, which are so far best understood in the model organism Saccharomyces cerevisiae.
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Affiliation(s)
- Daniel P Schwerter
- Abteilung für Systembiochemie, Institut für Biochemie und Pathobiochemie, Medizinische Fakultät der Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum
| | - Immanuel Grimm
- Abteilung für Systembiochemie, Institut für Biochemie und Pathobiochemie, Medizinische Fakultät der Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum
| | - Harald W Platta
- Biochemie Intrazellulärer Transportprozesse, Medizinische Fakultät der Ruhr-Universität Bochum, D-44780 Bochum
| | - Ralf Erdmann
- Abteilung für Systembiochemie, Institut für Biochemie und Pathobiochemie, Medizinische Fakultät der Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum
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7
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Deciphering the roles of phosphoinositide lipids in phagolysosome biogenesis. Commun Integr Biol 2016; 9:e1174798. [PMID: 27489580 PMCID: PMC4951175 DOI: 10.1080/19420889.2016.1174798] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 03/29/2016] [Accepted: 03/31/2016] [Indexed: 01/01/2023] Open
Abstract
Professional phagocytes engulf microbial invaders into plasma membrane-derived phagosomes. These mature into microbicidal phagolysosomes, leading to killing of the ingested microbe. Phagosome maturation involves sequential fusion of the phagosome with early endosomes, late endosomes, and the main degradative compartments in cells, lysosomes. Some bacterial pathogens manipulate the phosphoinositide (PIP) composition of phagosome membranes and are not delivered to phagolysosomes, pointing at a role of PIPs in phagosome maturation. This hypothesis is supported by comprehensive microscopic studies. Recently, cell-free reconstitution of fusion between phagosomes and endo(lyso)somes identified phosphatidylinositol 4-phosphate [PI(4)P] and phosphatidylinositol 3-phosphate [PI(3)P] as key regulators of phagolysosome biogenesis. Here, we describe the emerging roles of PIPs in phagosome maturation and we present tools to study PIP involvement in phagosome trafficking using intact cells or purified compartments.
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8
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Barthelme D, Sauer RT. Origin and Functional Evolution of the Cdc48/p97/VCP AAA+ Protein Unfolding and Remodeling Machine. J Mol Biol 2015; 428:1861-9. [PMID: 26608813 DOI: 10.1016/j.jmb.2015.11.015] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 11/03/2015] [Accepted: 11/16/2015] [Indexed: 01/25/2023]
Abstract
The AAA+ Cdc48 ATPase (alias p97 or VCP) is a key player in multiple ubiquitin-dependent cell signaling, degradation, and quality control pathways. Central to these broad biological functions is the ability of Cdc48 to interact with a large number of adaptor proteins and to remodel macromolecular proteins and their complexes. Different models have been proposed to explain how Cdc48 might couple ATP hydrolysis to forcible unfolding, dissociation, or remodeling of cellular clients. In this review, we provide an overview of possible mechanisms for substrate unfolding/remodeling by this conserved and essential AAA+ protein machine and their adaption and possible biological function throughout evolution.
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Affiliation(s)
- Dominik Barthelme
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Max Planck Institute for Infection Biology, Berlin 10117, Germany
| | - Robert T Sauer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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9
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Grimm I, Erdmann R, Girzalsky W. Role of AAA(+)-proteins in peroxisome biogenesis and function. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1863:828-37. [PMID: 26453804 DOI: 10.1016/j.bbamcr.2015.10.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 09/30/2015] [Accepted: 10/03/2015] [Indexed: 11/16/2022]
Abstract
Mutations in the PEX1 gene, which encodes a protein required for peroxisome biogenesis, are the most common cause of the Zellweger spectrum diseases. The recognition that Pex1p shares a conserved ATP-binding domain with p97 and NSF led to the discovery of the extended family of AAA+-type ATPases. So far, four AAA+-type ATPases are related to peroxisome function. Pex6p functions together with Pex1p in peroxisome biogenesis, ATAD1/Msp1p plays a role in membrane protein targeting and a member of the Lon-family of proteases is associated with peroxisomal quality control. This review summarizes the current knowledge on the AAA+-proteins involved in peroxisome biogenesis and function.
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Affiliation(s)
- Immanuel Grimm
- Abteilung für Systembiochemie, Medizinische Fakultät der Ruhr-Universität Bochum, D-44780 Bochum, Germany
| | - Ralf Erdmann
- Abteilung für Systembiochemie, Medizinische Fakultät der Ruhr-Universität Bochum, D-44780 Bochum, Germany.
| | - Wolfgang Girzalsky
- Abteilung für Systembiochemie, Medizinische Fakultät der Ruhr-Universität Bochum, D-44780 Bochum, Germany.
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10
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Cdc48: a swiss army knife of cell biology. JOURNAL OF AMINO ACIDS 2013; 2013:183421. [PMID: 24167726 PMCID: PMC3791797 DOI: 10.1155/2013/183421] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 07/29/2013] [Accepted: 08/12/2013] [Indexed: 12/13/2022]
Abstract
Cdc48 (also called VCP and p97) is an abundant protein that plays essential regulatory functions in a broad array of cellular processes. Working with various cofactors, Cdc48 utilizes its ATPase activity to promote the assembly and disassembly of protein complexes. Here, we review key biological functions and regulation of Cdc48 in ubiquitin-related events. Given the broad employment of Cdc48 in cell biology and its intimate ties to human diseases (e.g., amyotrophic lateral sclerosis), studies of Cdc48 will bring significant insights into the mechanism and function of ubiquitin in health and diseases.
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11
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Iwaya N, Akiyama K, Goda N, Tenno T, Fujiwara Y, Hamada D, Ikura T, Shirakawa M, Hiroaki H. Effect of Ca2+ on the microtubule-severing enzyme p60-katanin. Insight into the substrate-dependent activation mechanism. FEBS J 2012; 279:1339-52. [PMID: 22325007 DOI: 10.1111/j.1742-4658.2012.08528.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Katanin p60 (p60-katanin) is a microtubule (MT)-severing enzyme and its activity is regulated by the p80 subunit (adaptor-p80). p60-katanin consists of an N-terminal domain, followed by a single ATPase associated with various cellular activities (AAA) domain. We have previously shown that the N-terminal domain serves as the binding site for MT, the substrate of p60-katanin. In this study, we show that the same domain shares another interface with the C-terminal domain of adaptor-p80. We further show that Ca(2+) ions inhibit the MT-severing activity of p60-katanin, whereas the MT-binding activity is preserved in the presence of Ca(2+). In detail, the basal ATPase activity of p60-katanin is stimulated twofold by both MTs and the C-terminal domain of adaptor-p80, whereas Ca(2+) reduces elevated ATPase activity to the basal level. We identify the Ca(2+) -binding site at the end of helix 2 of the N-terminal domain, which is different from the MT-binding interface. On the basis of these observations, we propose a speculative model in which spatial rearrangement of the N-terminal domain relative to the C-terminal AAA domain may be important for productive ATP hydrolysis towards MT-severing. Our model can explain how Ca(2+) regulates both severing and ATP hydrolysis activity, because the Ca(2+) -binding site on the N-terminal domain moves close to the AAA domain during MT severing.
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Affiliation(s)
- Naoko Iwaya
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan
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12
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Grimm I, Saffian D, Platta HW, Erdmann R. The AAA-type ATPases Pex1p and Pex6p and their role in peroxisomal matrix protein import in Saccharomyces cerevisiae. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2012; 1823:150-8. [DOI: 10.1016/j.bbamcr.2011.09.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 09/02/2011] [Accepted: 09/03/2011] [Indexed: 12/25/2022]
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13
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Fujiki Y, Nashiro C, Miyata N, Tamura S, Okumoto K. New insights into dynamic and functional assembly of the AAA peroxins, Pex1p and Pex6p, and their membrane receptor Pex26p in shuttling of PTS1-receptor Pex5p during peroxisome biogenesis. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2011; 1823:145-9. [PMID: 22079764 DOI: 10.1016/j.bbamcr.2011.10.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Revised: 10/24/2011] [Accepted: 10/24/2011] [Indexed: 01/25/2023]
Abstract
Peroxisome is a single-membrane organelle in eukaryotes. The functional importance of peroxisomes in humans is highlighted by peroxisome-deficient peroxisome biogenesis disorders such as Zellweger syndrome. Two AAA peroxins, Pex1p and Pex6p, are encoded by PEX1 and PEX6, the causal genes for PBDs of complementation groups 1 and 4, respectively. PEX26 responsible for peroxisome biogenesis disorders of complementation group 8 codes for C-tail-anchored type-II membrane peroxin Pex26p, the recruiter of Pex1p-Pex6p complexes to peroxisomes. Pex1p is targeted to peroxisomes in a manner dependent on ATP hydrolysis, while Pex6p targeting requires ATP but not its hydrolysis. Pex1p and Pex6p are most likely regulated in their peroxisomal localization onto Pex26p via conformational changes by ATPase cycle. Pex5p is the cytosolic receptor for peroxisome matrix proteins with peroxisome targeting signal type-1 and shuttles between the cytosol and peroxisomes. AAA peroxins are involved in the export from peroxisomes of Pex5p. Pex5p is ubiquitinated at the conserved cysteine11 in a form associated with peroxisomes. Pex5p with a mutation of the cysteine11 to alanine, termed Pex5p-C11A, abrogates peroxisomal import of proteins harboring peroxisome targeting signals 1 and 2 in wild-type cells. Pex5p-C11A is imported into peroxisomes but not exported, hence suggesting an essential role of the cysteine residue in the export of Pex5p.
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Affiliation(s)
- Yukio Fujiki
- Department of Biology, Faculty of Sciences, Kyushu University Graduate School, Fukuoka 812-8581, Japan.
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14
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Fujiwara Y, Fujiwara KI, Goda N, Iwaya N, Tenno T, Shirakawa M, Hiroaki H. Structure and function of the N-terminal nucleolin binding domain of nuclear valosin-containing protein-like 2 (NVL2) harboring a nucleolar localization signal. J Biol Chem 2011; 286:21732-41. [PMID: 21474449 PMCID: PMC3122229 DOI: 10.1074/jbc.m110.174680] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Revised: 02/28/2011] [Indexed: 11/06/2022] Open
Abstract
The N-terminal regions of AAA-ATPases (ATPase associated with various cellular activities) often contain a domain that defines the distinct functions of the enzymes, such as substrate specificity and subcellular localization. As described herein, we have determined the solution structure of an N-terminal unique domain isolated from nuclear valosin-containing protein (VCP)-like protein 2 (NVL2(UD)). NVL2(UD) contains three α helices with an organization resembling that of a winged helix motif, whereas a pair of β-strands is missing. The structure is unique and distinct from those of other known type II AAA-ATPases, such as VCP. Consequently, we identified nucleolin from a HeLa cell extract as a binding partner of this domain. Nucleolin contains a long (∼300 amino acids) intrinsically unstructured region, followed by the four tandem RNA recognition motifs and the C-terminal glycine/arginine-rich domain. Binding analyses revealed that NVL2(UD) potentially binds to any of the combinations of two successive RNA binding domains in the presence of RNA. Furthermore, NVL2(UD) has a characteristic loop, in which the key basic residues RRKR are exposed to the solvent at the edge of the molecule. The mutation study showed that these residues are necessary and sufficient for nucleolin-RNA complex binding as well as nucleolar localization. Based on the observations presented above, we propose that NVL2 serves as an unfoldase for the nucleolin-RNA complex. As inferred from its RNA dependence and its ATPase activity, NVL2 might facilitate the dissociation and recycling of nucleolin, thereby promoting efficient ribosome biogenesis.
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Affiliation(s)
- Yoshie Fujiwara
- From the Division of Structural Biology, Graduate School of Medicine, and
- the Global Center of Excellence Program for Integrative Membrane Biology, Kobe University, 7-5-1 Kusunokicho, Chuo-ku, Kobe, Hyogo 650-0017, Japan
- the Institute for Bioinformatics Research and Development, Japan Science and Technology Agency, Kawaguchi Center Building, 4-1-8, Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Ken-ichiro Fujiwara
- the Field of Supramolecular Biology, International Graduate School of Arts and Sciences, Yokohama City University, 1-7-29 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Shionogi Research Laboratories, Shionogi & Co., Ltd., 5-12-4 Sagisu, Fukushima-ku, Osaka 553-0002, Japan, and
| | - Natsuko Goda
- From the Division of Structural Biology, Graduate School of Medicine, and
- the Institute for Bioinformatics Research and Development, Japan Science and Technology Agency, Kawaguchi Center Building, 4-1-8, Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Naoko Iwaya
- From the Division of Structural Biology, Graduate School of Medicine, and
- the Institute for Bioinformatics Research and Development, Japan Science and Technology Agency, Kawaguchi Center Building, 4-1-8, Honcho, Kawaguchi, Saitama 332-0012, Japan
- the Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Takeshi Tenno
- From the Division of Structural Biology, Graduate School of Medicine, and
- the Global Center of Excellence Program for Integrative Membrane Biology, Kobe University, 7-5-1 Kusunokicho, Chuo-ku, Kobe, Hyogo 650-0017, Japan
| | - Masahiro Shirakawa
- the Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Hidekazu Hiroaki
- From the Division of Structural Biology, Graduate School of Medicine, and
- the Global Center of Excellence Program for Integrative Membrane Biology, Kobe University, 7-5-1 Kusunokicho, Chuo-ku, Kobe, Hyogo 650-0017, Japan
- the Institute for Bioinformatics Research and Development, Japan Science and Technology Agency, Kawaguchi Center Building, 4-1-8, Honcho, Kawaguchi, Saitama 332-0012, Japan
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15
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Requirements for the catalytic cycle of the N-ethylmaleimide-Sensitive Factor (NSF). BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2011; 1823:159-71. [PMID: 21689688 DOI: 10.1016/j.bbamcr.2011.06.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Revised: 05/23/2011] [Accepted: 06/06/2011] [Indexed: 12/23/2022]
Abstract
The N-ethylmaleimide-Sensitive Factor (NSF) was one of the initial members of the ATPases Associated with various cellular Activities Plus (AAA(+)) family. In this review, we discuss what is known about the mechanism of NSF action and how that relates to the mechanisms of other AAA(+) proteins. Like other family members, NSF binds to a protein complex (i.e., SNAP-SNARE complex) and utilizes ATP hydrolysis to affect the conformations of that complex. SNAP-SNARE complex disassembly is essential for SNARE recycling and sustained membrane trafficking. NSF is a homo-hexamer; each protomer is composed of an N-terminal domain, NSF-N, and two adjacent AAA-domains, NSF-D1 and NSF-D2. Mutagenesis analysis has established specific roles for many of the structural elements of NSF-D1, the catalytic ATPase domain, and NSF-N, the SNAP-SNARE binding domain. Hydrodynamic analysis of NSF, labeled with (Ni(2+)-NTA)(2)-Cy3, detected conformational differences in NSF, in which the ATP-bound conformation appears more compact than the ADP-bound form. This indicates that NSF undergoes significant conformational changes as it progresses through its ATP-hydrolysis cycle. Incorporating these data, we propose a sequential mechanism by which NSF uses NSF-N and NSF-D1 to disassemble SNAP-SNARE complexes. We also illustrate how analytical centrifugation might be used to study other AAA(+) proteins.
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16
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Nashiro C, Kashiwagi A, Matsuzaki T, Tamura S, Fujiki Y. Recruiting mechanism of the AAA peroxins, Pex1p and Pex6p, to Pex26p on the peroxisomal membrane. Traffic 2011; 12:774-88. [PMID: 21362118 DOI: 10.1111/j.1600-0854.2011.01182.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A peroxisomal C-tail-anchored type-II membrane protein, Pex26p, recruits AAA ATPase Pex1p-Pex6p complexes to peroxisomes. We herein attempted to gain mechanistic insight into Pex26p function. Pex26pΔ33-40 truncated in amino-acid residues at 33-40 abolishes the recruiting of Pex1p-Pex6p complex to peroxisomes and fails to complement the impaired phenotype of pex26 CHO cell mutant ZP167, thereby suggesting that peroxisomal localization of Pex1p and Pex6p is indispensable for the transport of matrix proteins. In in vitro transport assay using semipermeabilized CHO cells, Pex1p is targeted to peroxisomes in a manner dependent on ATP hydrolysis, while Pex6p targeting requires ATP but not its hydrolysis. This finding is confirmed by the assay using Walker-motif mutants. Transport of Pex1p and Pex6p is temperature-dependent. In vitro binding assays with glutathione-S-transferase-fused Pex26p, Pex1p and Pex6p bind to Pex26p in a manner dependent on ATP binding but not ATP hydrolysis. These results suggest that ATP hydrolysis is required for stable localization of Pex1p to peroxisomes, but not for binding to Pex26p. Moreover, Pex1p and Pex6p are altered to a more compact conformation upon binding to ATP, as verified by limited proteolysis. Taken together, Pex1p and Pex6p are most likely regulated in their peroxisomal localization onto Pex26p via conformational changes by the ATPase cycle.
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Affiliation(s)
- Chika Nashiro
- Graduate School of Systems Life Sciences, Kyushu University, Fukuoka 812-8581, Japan
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17
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Fu H, Lin YL, Fatimababy AS. Proteasomal recognition of ubiquitylated substrates. TRENDS IN PLANT SCIENCE 2010; 15:375-86. [PMID: 20399133 DOI: 10.1016/j.tplants.2010.03.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2009] [Revised: 03/10/2010] [Accepted: 03/18/2010] [Indexed: 05/08/2023]
Abstract
Ubiquitin/26S proteasome-mediated proteolysis controls the half-life of numerous critical regulatory proteins and is an intimate regulatory component for nearly all aspects of cellular processes. In addition to ubiquitin conjugation, an additional level of substrate specificity is regulated at the step of proteasomal recognition of ubiquitylated substrates, which serves as an important mechanistic and regulatory component to connect the substrate from the conjugation machinery to the 26S proteasome. In this review, we discuss current knowledge and future challenges relevant to understanding the mechanism, regulation, functions and substrate specificity of proteasomal recognition mediated by a multitude of ubiquitin receptors. The mechanistic details of major recognition pathways for ubiquitylated substrates are clearly divergent within and across species, which implies functional differentiation.
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Affiliation(s)
- Hongyong Fu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan 115, ROC.
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18
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Slade PG, Williams MV, Brahmbhatt V, Dash A, Wishnok JS, Tannenbaum SR. Proteins modified by the lipid peroxidation aldehyde 9,12-dioxo-10(E)-dodecenoic acid in MCF7 breast cancer cells. Chem Res Toxicol 2010; 23:557-67. [PMID: 20131800 DOI: 10.1021/tx9002808] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The hydroperoxide of linoleic acid (13-HPODE) degrades to 9,12-dioxo-10(E)-dodecenoic acid (DODE), which readily modifies proteins. This study identified the major proteins in MCF7 cells modified by DODE. To reduce false positives, three methods were used to identify DODE-modified proteins. First, cells were treated with a synthetically biotinylated 13-HPODE (13-HPODE-biotin). Modified proteins were enriched by neutravidin affinity and identified by two-dimensional liquid chromatography--tandem mass spectrometry (2D LC-MS/MS). Second, cells were treated with native 13-HPODE. Protein carbonyls were biotinylated with an aldehyde reactive probe, and modified proteins were enriched by neutravidin affinity and identified by 2D LC-MS/MS. Third, using a newly developed DODE antibody, DODE-modified proteins were located by 2D sodium dodecyl sulfate--polyacrylamide gel electrophoresis and Western blot and identified by in-gel digestion and LC-MS/MS. Analysis of the proteins characterized by all three methods revealed a significant overlap and identified 32 primary proteins modified by DODE in MCF7 cells. These results demonstrated the feasibility for the cellular formation of DODE protein-carbonyl adducts that may be future indicators of oxidative stress.
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Affiliation(s)
- Peter G Slade
- Department of Biological Engineering and Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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19
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Zhao C, Matveeva EA, Ren Q, Whiteheart SW. Dissecting the N-ethylmaleimide-sensitive factor: required elements of the N and D1 domains. J Biol Chem 2009; 285:761-72. [PMID: 19887446 DOI: 10.1074/jbc.m109.056739] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
N-Ethylmaleimide-sensitive factor (NSF) is a homo-hexameric member of the AAA(+) (ATPases associated with various cellular activities plus) family. It plays an essential role in most intracellular membrane trafficking through its binding to and disassembly of soluble NSF attachment protein (SNAP) receptor (SNARE) complexes. Each NSF protomer contains an N-terminal domain (NSF-N) and two AAA domains, a catalytic NSF-D1 and a structural NSF-D2. This study presents detailed mutagenesis analyses of NSF-N and NSF-D1, dissecting their roles in ATP hydrolysis, SNAP.SNARE binding, and complex disassembly. Our results show that a positively charged surface on NSF-N, bounded by Arg(67) and Lys(105), and the conserved residues in the central pore of NSF-D1 (Tyr(296) and Gly(298)) are involved in SNAP.SNARE binding but not basal ATP hydrolysis. Mutagenesis of Sensor 1 (Thr(373)-Arg(375)), Sensor 2 (Glu(440)-Glu(442)), and Arginine Fingers (Arg(385) and Arg(388)) in NSF-D1 shows that each region plays a discrete role. Sensor 1 is important for basal ATPase activity and nucleotide binding. Sensor 2 plays a role in ATP- and SNAP-dependent SNARE complex binding and disassembly but does so in cis and not through inter-protomer interactions. Arginine Fingers are important for SNAP.SNARE complex-stimulated ATPase activity and complex disassembly. Mutants at these residues have a dominant-negative phenotype in cells, suggesting that Arginine Fingers function in trans via inter-protomer interactions. Taken together, these data establish functional roles for many of the structural elements of the N domain and of the D1 ATP-binding site of NSF.
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Affiliation(s)
- Chunxia Zhao
- Department of Molecular and Cellular Biochemistry, University of Kentucky Medical Center, Lexington, Kentucky 40536-0509, USA
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20
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New ATPase regulators--p97 goes to the PUB. Int J Biochem Cell Biol 2009; 41:2380-8. [PMID: 19497384 DOI: 10.1016/j.biocel.2009.05.017] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2009] [Revised: 05/26/2009] [Accepted: 05/26/2009] [Indexed: 01/10/2023]
Abstract
The conserved eukaryotic AAA-type ATPase complex, known as p97 or VCP in mammals and Cdc48 in yeast, is involved in a number of cellular pathways, including fusion of homotypic membranes, protein degradation, and activation of membrane-bound transcription factors. Most likely, p97 is directed to this broad spectrum of cellular functions through its binding to specific cofactors. More than 20 different p97 cofactors have been described to date and our understanding of their cellular functions is rapidly expanding. Common to these proteins is their intimate connection with the ubiquitin system. Recently, a small, conserved family of proteins, containing PUB domains, was found to function as p97 adaptors. Intriguingly, their association with p97 is regulated by tyrosine phosphorylation, suggesting that they act as a relay between signalling pathways and p97 functions. Here we give an overview of the currently known PUB-domain proteins and other p97-interacting proteins.
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21
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Gitcho MA, Strider J, Carter D, Taylor-Reinwald L, Forman MS, Goate AM, Cairns NJ. VCP mutations causing frontotemporal lobar degeneration disrupt localization of TDP-43 and induce cell death. J Biol Chem 2009; 284:12384-98. [PMID: 19237541 PMCID: PMC2673306 DOI: 10.1074/jbc.m900992200] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2009] [Indexed: 11/06/2022] Open
Abstract
Frontotemporal lobar degeneration (FTLD) with inclusion body myopathy and Paget disease of bone is a rare, autosomal dominant disorder caused by mutations in the VCP (valosin-containing protein) gene. The disease is characterized neuropathologically by frontal and temporal lobar atrophy, neuron loss and gliosis, and ubiquitin-positive inclusions (FTLD-U), which are distinct from those seen in other sporadic and familial FTLD-U entities. The major component of the ubiquitinated inclusions of FTLD with VCP mutation is TDP-43 (TAR DNA-binding protein of 43 kDa). TDP-43 proteinopathy links sporadic amyotrophic lateral sclerosis, sporadic FTLD-U, and most familial forms of FTLD-U. Understanding the relationship between individual gene defects and pathologic TDP-43 will facilitate the characterization of the mechanisms leading to neurodegeneration. Using cell culture models, we have investigated the role of mutant VCP in intracellular trafficking, proteasomal function, and cell death and demonstrate that mutations in the VCP gene 1) alter localization of TDP-43 between the nucleus and cytosol, 2) decrease proteasome activity, 3) induce endoplasmic reticulum stress, 4) increase markers of apoptosis, and 5) impair cell viability. These results suggest that VCP mutation-induced neurodegeneration is mediated by several mechanisms.
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Affiliation(s)
- Michael A Gitcho
- Alzheimer's Disease Research Center and the Department of Neurology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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22
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The AAA peroxins Pex1p and Pex6p function as dislocases for the ubiquitinated peroxisomal import receptor Pex5p. Biochem Soc Trans 2008; 36:99-104. [DOI: 10.1042/bst0360099] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The discovery of the peroxisomal ATPase Pex1p triggered the beginning of the research on AAA (ATPase associated with various cellular activities) proteins and the genetic dissection of peroxisome biogenesis. Peroxisomes are virtually ubiquitous organelles, which are connected to diverse cellular functions. The highly diverse and adaptive character of peroxisomes is accomplished by modulation of their enzyme content, which is mediated by dynamically operating protein-import machineries. The import of matrix proteins into the peroxisomal lumen has been described as the ATP-consuming step, but the corresponding reaction, as well as the ATPase responsible, had been obscure for nearly 15 years. Recent work using yeast and human fibroblast cells has identified the peroxisomal AAA proteins Pex1p and Pex6p as mechano-enzymes and core components of a complex which dislocates the cycling import receptor Pex5p from the peroxisomal membrane back to the cytosol. This AAA-mediated process is regulated by the ubiquitination status of the receptor. Pex4p [Ubc10p (ubiquitin-conjugating enzyme 10)]-catalysed mono-ubiquitination of Pex5p primes the receptor for recycling, thereby enabling further rounds of matrix protein import, whereas Ubc4p-catalysed polyubiquitination targets Pex5p to proteasomal degradation.
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23
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Tucker PA, Sallai L. The AAA+ superfamily--a myriad of motions. Curr Opin Struct Biol 2007; 17:641-52. [PMID: 18023171 DOI: 10.1016/j.sbi.2007.09.012] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2007] [Revised: 09/13/2007] [Accepted: 09/28/2007] [Indexed: 11/19/2022]
Abstract
ATPases associated with various cellular activities are aptly named. They are the engines that drive processes such as protein degradation, protein refolding, sigma(54)-dependent transcriptional activation, DNA helicase activity, DNA replication initiation, and cellular cargo transport. Recent structural information derived from biochemical studies, electron microscopy (EM), small-angle X-ray scattering (SAXS), and X-ray crystallography are beginning to show how, at an atomic level, some of these systems use the conformational changes generated during the ATP hydrolysis cycle. Structural highlights in the processes mentioned are provided by work on ClpX and p97, ClpB, PspF and NtrC, RuvBL1, DnaA and the papillomavirus E1 initiator protein and dynein. The results emphasize the versatility of the AAA+ core domain.
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Affiliation(s)
- Paul A Tucker
- EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, D22603 Hamburg, Germany.
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24
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Raasi S, Wolf DH. Ubiquitin receptors and ERAD: a network of pathways to the proteasome. Semin Cell Dev Biol 2007; 18:780-91. [PMID: 17942349 DOI: 10.1016/j.semcdb.2007.09.008] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2007] [Revised: 08/22/2007] [Accepted: 09/05/2007] [Indexed: 10/22/2022]
Abstract
The elimination of misfolded proteins, known as protein quality control, is an essential cellular process. Removal of misfolded proteins from the secretory pathway depends on their recognition in the endoplasmic reticulum (ER) followed by their retrograde transport into the cytosol for degradation. The AAA-ATPase Cdc48/p97 facilitates the translocation of misfolded ER-proteins into the cytosol. Cdc48/p97 can dock onto the ER-membrane via direct interaction with ER-membrane proteins and/or indirectly via its substrate-recruiting cofactors, which interact with the ubiquitylated substrates at the membrane. This tight interaction in conjunction with the conformational changes induced upon ATP hydrolysis within Cdc48/p97 is thought to provide the driving force for the translocation reaction. Subsequently, a series of protein-protein interactions between the Cdc48/p97 complex, its cofactors, and the ubiquitylated substrates is instrumental for the proper delivery of the ER substrates to the proteasome. These protein-protein interactions are governed mainly by ubiquitin-fold and ubiquitin-binding domains.
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Affiliation(s)
- Shahri Raasi
- Fachbereich Biologie, Universitaet Konstanz, Universitaetsstrasse 10, 78457 Konstanz, Germany.
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