1
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Owens DDG, Maitland MER, Khalili Yazdi A, Song X, Reber V, Schwalm MP, Machado RAC, Bauer N, Wang X, Szewczyk MM, Dong C, Dong A, Loppnau P, Calabrese MF, Dowling MS, Lee J, Montgomery JI, O'Connell TN, Subramanyam C, Wang F, Adamson EC, Schapira M, Gstaiger M, Knapp S, Vedadi M, Min J, Lajoie GA, Barsyte-Lovejoy D, Owen DR, Schild-Poulter C, Arrowsmith CH. A chemical probe to modulate human GID4 Pro/N-degron interactions. Nat Chem Biol 2024:10.1038/s41589-024-01618-0. [PMID: 38773330 DOI: 10.1038/s41589-024-01618-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 04/12/2024] [Indexed: 05/23/2024]
Abstract
The C-terminal to LisH (CTLH) complex is a ubiquitin ligase complex that recognizes substrates with Pro/N-degrons via its substrate receptor Glucose-Induced Degradation 4 (GID4), but its function and substrates in humans remain unclear. Here, we report PFI-7, a potent, selective and cell-active chemical probe that antagonizes Pro/N-degron binding to human GID4. Use of PFI-7 in proximity-dependent biotinylation and quantitative proteomics enabled the identification of GID4 interactors and GID4-regulated proteins. GID4 interactors are enriched for nucleolar proteins, including the Pro/N-degron-containing RNA helicases DDX21 and DDX50. We also identified a distinct subset of proteins whose cellular levels are regulated by GID4 including HMGCS1, a Pro/N-degron-containing metabolic enzyme. These data reveal human GID4 Pro/N-degron targets regulated through a combination of degradative and nondegradative functions. Going forward, PFI-7 will be a valuable research tool for investigating CTLH complex biology and facilitating development of targeted protein degradation strategies that highjack CTLH E3 ligase activity.
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Affiliation(s)
- Dominic D G Owens
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Matthew E R Maitland
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Robarts Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
- Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
- Don Rix Protein Identification Facility, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | | | - Xiaosheng Song
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Viviane Reber
- Institute of Molecular Systems Biology at ETH Zurich, Zurich, Switzerland
| | - Martin P Schwalm
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Frankfurt am Main, Germany
- Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Frankfurt am Main, Germany
| | - Raquel A C Machado
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Nicolas Bauer
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Frankfurt am Main, Germany
- Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Frankfurt am Main, Germany
| | - Xu Wang
- Robarts Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | | | - Cheng Dong
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Aiping Dong
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Peter Loppnau
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | | | | | - Jisun Lee
- Development and Medical, Pfizer Worldwide Research, Groton, CT, USA
| | | | | | | | - Feng Wang
- Development and Medical, Pfizer Worldwide Research, Groton, CT, USA
| | - Ella C Adamson
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Matthias Gstaiger
- Institute of Molecular Systems Biology at ETH Zurich, Zurich, Switzerland
| | - Stefan Knapp
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Frankfurt am Main, Germany
- Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Frankfurt am Main, Germany
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Gilles A Lajoie
- Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
- Don Rix Protein Identification Facility, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Dafydd R Owen
- Development and Medical, Pfizer Worldwide Research, Groton, CT, USA
| | - Caroline Schild-Poulter
- Robarts Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
- Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
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2
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Chrustowicz J, Sherpa D, Li J, Langlois CR, Papadopoulou EC, Vu DT, Hehl LA, Karayel Ö, Beier V, von Gronau S, Müller J, Prabu JR, Mann M, Kleiger G, Alpi AF, Schulman BA. Multisite phosphorylation dictates selective E2-E3 pairing as revealed by Ubc8/UBE2H-GID/CTLH assemblies. Mol Cell 2024; 84:293-308.e14. [PMID: 38113892 PMCID: PMC10843684 DOI: 10.1016/j.molcel.2023.11.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 10/29/2023] [Accepted: 11/21/2023] [Indexed: 12/21/2023]
Abstract
Ubiquitylation is catalyzed by coordinated actions of E3 and E2 enzymes. Molecular principles governing many important E3-E2 partnerships remain unknown, including those for RING-family GID/CTLH E3 ubiquitin ligases and their dedicated E2, Ubc8/UBE2H (yeast/human nomenclature). GID/CTLH-Ubc8/UBE2H-mediated ubiquitylation regulates biological processes ranging from yeast metabolic signaling to human development. Here, cryoelectron microscopy (cryo-EM), biochemistry, and cell biology reveal this exquisitely specific E3-E2 pairing through an unconventional catalytic assembly and auxiliary interactions 70-100 Å away, mediated by E2 multisite phosphorylation. Rather than dynamic polyelectrostatic interactions reported for other ubiquitylation complexes, multiple Ubc8/UBE2H phosphorylation sites within acidic CK2-targeted sequences specifically anchor the E2 C termini to E3 basic patches. Positions of phospho-dependent interactions relative to the catalytic domains correlate across evolution. Overall, our data show that phosphorylation-dependent multivalency establishes a specific E3-E2 partnership, is antagonistic with dephosphorylation, rigidifies the catalytic centers within a flexing GID E3-substrate assembly, and facilitates substrate collision with ubiquitylation active sites.
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Affiliation(s)
- Jakub Chrustowicz
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Dawafuti Sherpa
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Jerry Li
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, NV 89154, USA
| | - Christine R Langlois
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Eleftheria C Papadopoulou
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany; Technical University of Munich, School of Natural Sciences, Munich 85748, Germany
| | - D Tung Vu
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Laura A Hehl
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany; Technical University of Munich, School of Natural Sciences, Munich 85748, Germany
| | - Özge Karayel
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Viola Beier
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Susanne von Gronau
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Judith Müller
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - J Rajan Prabu
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Gary Kleiger
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, NV 89154, USA
| | - Arno F Alpi
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany; Technical University of Munich, School of Natural Sciences, Munich 85748, Germany.
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3
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Kong KYE, Shankar S, Rühle F, Khmelinskii A. Orphan quality control by an SCF ubiquitin ligase directed to pervasive C-degrons. Nat Commun 2023; 14:8363. [PMID: 38102142 PMCID: PMC10724198 DOI: 10.1038/s41467-023-44096-z] [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: 08/11/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023] Open
Abstract
Selective protein degradation typically involves substrate recognition via short linear motifs known as degrons. Various degrons can be found at protein termini from bacteria to mammals. While N-degrons have been extensively studied, our understanding of C-degrons is still limited. Towards a comprehensive understanding of eukaryotic C-degron pathways, here we perform an unbiased survey of C-degrons in budding yeast. We identify over 5000 potential C-degrons by stability profiling of random peptide libraries and of the yeast C‑terminome. Combining machine learning, high-throughput mutagenesis and genetic screens reveals that the SCF ubiquitin ligase targets ~40% of degrons using a single F-box substrate receptor Das1. Although sequence-specific, Das1 is highly promiscuous, recognizing a variety of C-degron motifs. By screening for full-length substrates, we implicate SCFDas1 in degradation of orphan protein complex subunits. Altogether, this work highlights the variety of C-degron pathways in eukaryotes and uncovers how an SCF/C-degron pathway of broad specificity contributes to proteostasis.
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Affiliation(s)
| | | | - Frank Rühle
- Institute of Molecular Biology (IMB), Mainz, Germany
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4
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van Gen Hassend PM, Pottikkadavath A, Delto C, Kuhn M, Endres M, Schönemann L, Schindelin H. RanBP9 controls the oligomeric state of CTLH complex assemblies. J Biol Chem 2023; 299:102869. [PMID: 36621627 PMCID: PMC9932110 DOI: 10.1016/j.jbc.2023.102869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 01/07/2023] Open
Abstract
The CTLH (C-terminal to lissencephaly-1 homology motif) complex is a multisubunit RING E3 ligase with poorly defined substrate specificity and flexible subunit composition. Two key subunits, muskelin and Wdr26, specify two alternative CTLH complexes that differ in quaternary structure, thereby allowing the E3 ligase to presumably target different substrates. With the aid of different biophysical and biochemical techniques, we characterized CTLH complex assembly pathways, focusing not only on Wdr26 and muskelin but also on RanBP9, Twa1, and Armc8β subunits, which are critical to establish the scaffold of this E3 ligase. We demonstrate that the ability of muskelin to tetramerize and the assembly of Wdr26 into dimers define mutually exclusive oligomerization modules that compete with nanomolar affinity for RanBP9 binding. The remaining scaffolding subunits, Armc8β and Twa1, strongly interact with each other and with RanBP9, again with nanomolar affinity. Our data demonstrate that RanBP9 organizes subunit assembly and prevents higher order oligomerization of dimeric Wdr26 and the Armc8β-Twa1 heterodimer through its tight binding. Combined, our studies define alternative assembly pathways of the CTLH complex and elucidate the role of RanBP9 in governing differential oligomeric assemblies, thereby advancing our mechanistic understanding of CTLH complex architectures.
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Affiliation(s)
- Pia Maria van Gen Hassend
- Julius-Maximilians-Universität Würzburg, Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute of Structural Biology, Würzburg, Germany
| | - Aparna Pottikkadavath
- Julius-Maximilians-Universität Würzburg, Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute of Structural Biology, Würzburg, Germany
| | - Carolyn Delto
- Julius-Maximilians-Universität Würzburg, Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute of Structural Biology, Würzburg, Germany
| | - Monika Kuhn
- Julius-Maximilians-Universität Würzburg, Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute of Structural Biology, Würzburg, Germany
| | - Michelle Endres
- Julius-Maximilians-Universität Würzburg, Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute of Structural Biology, Würzburg, Germany
| | - Lars Schönemann
- Julius-Maximilians-Universität Würzburg, Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute of Structural Biology, Würzburg, Germany
| | - Hermann Schindelin
- Julius-Maximilians-Universität Würzburg, Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute of Structural Biology, Würzburg, Germany.
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5
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Kong KYE, Reinbold C, Knop M, Khmelinskii A. Building yeast libraries to dissect terminal degrons with fluorescent timers. Methods Enzymol 2023. [PMID: 37532405 DOI: 10.1016/bs.mie.2023.02.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
Selective degradation of unnecessary or abnormal proteins by the ubiquitin-proteasome system is an essential part of proteostasis. Ubiquitin ligases recognize substrates of selective protein degradation and modify them with polyubiquitin chains, which mark them for proteasomal degradation. Substrate recognition by ubiquitin ligases often involves degradation signals or degrons, which are typically short linear motifs found in intrinsically disordered regions, e.g., at protein termini. However, specificity in selective protein degradation is generally not well understood, as for most ubiquitin ligases no degrons have been identified thus far. To address this limitation, high-throughput mutagenesis approaches, such as multiplexed protein stability (MPS) profiling, have been developed, enabling systematic surveys of degrons in vivo or allowing to define degron motifs recognized by different ubiquitin ligases. In MPS profiling, thousands of short peptides can be assessed in parallel for their ability to trigger degradation of a fluorescent timer reporter. Here, we describe common types of libraries used to identify and dissect degrons located at protein termini using MPS profiling in budding yeast, and provide protocols for their construction.
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6
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Rödl S, den Brave F, Räschle M, Kizmaz B, Lenhard S, Groh C, Becker H, Zimmermann J, Morgan B, Richling E, Becker T, Herrmann JM. The metabolite-controlled ubiquitin conjugase Ubc8 promotes mitochondrial protein import. Life Sci Alliance 2022; 6:6/1/e202201526. [PMID: 36253107 PMCID: PMC9579816 DOI: 10.26508/lsa.202201526] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 09/30/2022] [Accepted: 09/30/2022] [Indexed: 11/26/2022] Open
Abstract
Mitochondria play a key role in cellular energy metabolism. Transitions between glycolytic and respiratory conditions induce considerable adaptations of the cellular proteome. These metabolism-dependent changes are particularly pronounced for the protein composition of mitochondria. Here, we show that the yeast cytosolic ubiquitin conjugase Ubc8 plays a crucial role in the remodeling process when cells transition from respiratory to fermentative conditions. Ubc8 is a conserved and well-studied component of the catabolite control system that is known to regulate the stability of gluconeogenic enzymes. Unexpectedly, we found that Ubc8 also promotes the assembly of the translocase of the outer membrane of mitochondria (TOM) and increases the levels of its cytosol-exposed receptor subunit Tom22. Ubc8 deficiency results in compromised protein import into mitochondria and reduced steady-state levels of mitochondrial proteins. Our observations show that Ubc8, which is controlled by the prevailing metabolic conditions, promotes the switch from glucose synthesis to glucose usage in the cytosol and induces the biogenesis of the mitochondrial TOM machinery to improve mitochondrial protein import during phases of metabolic transition.
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Affiliation(s)
- Saskia Rödl
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Fabian den Brave
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Markus Räschle
- Molecular Genetics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Büsra Kizmaz
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Svenja Lenhard
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Carina Groh
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Hanna Becker
- Food Chemistry, University of Kaiserslautern, Kaiserslautern, Germany
| | - Jannik Zimmermann
- Biochemistry, Center for Human and Molecular Biology (ZHMB), Saarland University, Saarbrücken, Germany
| | - Bruce Morgan
- Biochemistry, Center for Human and Molecular Biology (ZHMB), Saarland University, Saarbrücken, Germany
| | - Elke Richling
- Food Chemistry, University of Kaiserslautern, Kaiserslautern, Germany
| | - Thomas Becker
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
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7
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Chana CK, Maisonneuve P, Posternak G, Grinberg NGA, Poirson J, Ona SM, Ceccarelli DF, Mader P, St-Cyr DJ, Pau V, Kurinov I, Tang X, Deng D, Cui W, Su W, Kuai L, Soll R, Tyers M, Röst HL, Batey RA, Taipale M, Gingras AC, Sicheri F. Discovery and Structural Characterization of Small Molecule Binders of the Human CTLH E3 Ligase Subunit GID4. J Med Chem 2022; 65:12725-12746. [PMID: 36117290 PMCID: PMC9574856 DOI: 10.1021/acs.jmedchem.2c00509] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Targeted protein
degradation (TPD) strategies exploit bivalent
small molecules to bridge substrate proteins to an E3 ubiquitin ligase
to induce substrate degradation. Few E3s have been explored as degradation
effectors due to a dearth of E3-binding small molecules. We show that
genetically induced recruitment to the GID4 subunit of the CTLH E3
complex induces protein degradation. An NMR-based fragment screen
followed by structure-guided analog elaboration identified two binders
of GID4, 16 and 67, with Kd values of 110 and 17 μM in vitro. A parallel DNA-encoded library (DEL) screen identified five binders
of GID4, the best of which, 88, had a Kd of 5.6 μM in vitro and an EC50 of 558 nM in cells with strong selectivity for GID4. X-ray
co-structure determination revealed the basis for GID4–small
molecule interactions. These results position GID4-CTLH as an E3 for
TPD and provide candidate scaffolds for high-affinity moieties that
bind GID4.
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Affiliation(s)
- Chetan K Chana
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario M5G 1X5, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Pierre Maisonneuve
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario M5G 1X5, Canada
| | - Ganna Posternak
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario M5G 1X5, Canada
| | - Nicolas G A Grinberg
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Juline Poirson
- Donnelly Centre for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Samara M Ona
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Derek F Ceccarelli
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario M5G 1X5, Canada
| | - Pavel Mader
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario M5G 1X5, Canada
| | | | - Victor Pau
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario M5G 1X5, Canada
| | - Igor Kurinov
- Department of Chemistry and Chemical Biology, Cornell University, NE-CAT, Argonne, Illinois 60439, United States
| | - Xiaojing Tang
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario M5G 1X5, Canada
| | - Dongjing Deng
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Weiren Cui
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Wenji Su
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Letian Kuai
- WuXi AppTec, 55 Cambridge Parkway, 8th Floor, Cambridge, Massachusetts 02142, United States
| | - Richard Soll
- WuXi AppTec, 55 Cambridge Parkway, 8th Floor, Cambridge, Massachusetts 02142, United States
| | - Mike Tyers
- Institute for Research in Immunology and Cancer, University of Montréal, Québec H3C 3J7, Canada
| | - Hannes L Röst
- Donnelly Centre for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario M5S 2E4, Canada
| | - Robert A Batey
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Mikko Taipale
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Donnelly Centre for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario M5G 1X5, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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8
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Crystal structure of the Ate1 arginyl-tRNA-protein transferase and arginylation of N-degron substrates. Proc Natl Acad Sci U S A 2022; 119:e2209597119. [PMID: 35878037 PMCID: PMC9351520 DOI: 10.1073/pnas.2209597119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
N-degron pathways are proteolytic systems that target proteins bearing N-terminal (Nt) degradation signals (degrons) called N-degrons. Nt-Arg of a protein is among Nt-residues that can be recognized as destabilizing ones by the Arg/N-degron pathway. A proteolytic cleavage of a protein can generate Arg at the N terminus of a resulting C-terminal (Ct) fragment either directly or after Nt-arginylation of that Ct-fragment by the Ate1 arginyl-tRNA-protein transferase (R-transferase), which uses Arg-tRNAArg as a cosubstrate. Ate1 can Nt-arginylate Nt-Asp, Nt-Glu, and oxidized Nt-Cys* (Cys-sulfinate or Cys-sulfonate) of proteins or short peptides. Ate1 genes of fungi, animals, and plants have been cloned decades ago, but a three-dimensional structure of Ate1 remained unknown. A detailed mechanism of arginylation is unknown as well. We describe here the crystal structure of the Ate1 R-transferase from the budding yeast Kluyveromyces lactis. The 58-kDa R-transferase comprises two domains that recognize, together, an acidic Nt-residue of an acceptor substrate, the Arg residue of Arg-tRNAArg, and a 3'-proximal segment of the tRNAArg moiety. The enzyme's active site is located, at least in part, between the two domains. In vitro and in vivo arginylation assays with site-directed Ate1 mutants that were suggested by structural results yielded inferences about specific binding sites of Ate1. We also analyzed the inhibition of Nt-arginylation activity of Ate1 by hemin (Fe3+-heme), and found that hemin induced the previously undescribed disulfide-mediated oligomerization of Ate1. Together, these results advance the understanding of R-transferase and the Arg/N-degron pathway.
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9
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Langlois CR, Beier V, Karayel O, Chrustowicz J, Sherpa D, Mann M, Schulman BA. A GID E3 ligase assembly ubiquitinates an Rsp5 E3 adaptor and regulates plasma membrane transporters. EMBO Rep 2022; 23:e53835. [PMID: 35437932 PMCID: PMC9171410 DOI: 10.15252/embr.202153835] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 03/22/2022] [Accepted: 03/30/2022] [Indexed: 11/25/2022] Open
Abstract
Cells rapidly remodel their proteomes to align their cellular metabolism to environmental conditions. Ubiquitin E3 ligases enable this response, by facilitating rapid and reversible changes to protein stability, localization, or interaction partners. In Saccharomyces cerevisiae, the GID E3 ligase regulates the switch from gluconeogenic to glycolytic conditions through induction and incorporation of the substrate receptor subunit Gid4, which promotes the degradation of gluconeogenic enzymes. Here, we show an alternative substrate receptor, Gid10, which is induced in response to changes in temperature, osmolarity, and nutrient availability, regulates the ART‐Rsp5 ubiquitin ligase pathway, a component of plasma membrane quality control. Proteomic studies reveal that the levels of the adaptor protein Art2 are elevated upon GID10 deletion. A crystal structure shows the basis for Gid10‐Art2 interactions, and we demonstrate that Gid10 directs a GID E3 ligase complex to ubiquitinate Art2. Our data suggest that the GID E3 ligase affects Art2‐dependent amino acid transport. This study reveals GID as a system of E3 ligases with metabolic regulatory functions outside of glycolysis and gluconeogenesis, controlled by distinct stress‐specific substrate receptors.
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Affiliation(s)
- Christine R Langlois
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Viola Beier
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ozge Karayel
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jakub Chrustowicz
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Dawafuti Sherpa
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
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10
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Qiao S, Lee CW, Sherpa D, Chrustowicz J, Cheng J, Duennebacke M, Steigenberger B, Karayel O, Vu DT, von Gronau S, Mann M, Wilfling F, Schulman BA. Cryo-EM structures of Gid12-bound GID E3 reveal steric blockade as a mechanism inhibiting substrate ubiquitylation. Nat Commun 2022; 13:3041. [PMID: 35650207 PMCID: PMC9160049 DOI: 10.1038/s41467-022-30803-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 05/19/2022] [Indexed: 11/09/2022] Open
Abstract
Protein degradation, a major eukaryotic response to cellular signals, is subject to numerous layers of regulation. In yeast, the evolutionarily conserved GID E3 ligase mediates glucose-induced degradation of fructose-1,6-bisphosphatase (Fbp1), malate dehydrogenase (Mdh2), and other gluconeogenic enzymes. "GID" is a collection of E3 ligase complexes; a core scaffold, RING-type catalytic core, and a supramolecular assembly module together with interchangeable substrate receptors select targets for ubiquitylation. However, knowledge of additional cellular factors directly regulating GID-type E3s remains rudimentary. Here, we structurally and biochemically characterize Gid12 as a modulator of the GID E3 ligase complex. Our collection of cryo-EM reconstructions shows that Gid12 forms an extensive interface sealing the substrate receptor Gid4 onto the scaffold, and remodeling the degron binding site. Gid12 also sterically blocks a recruited Fbp1 or Mdh2 from the ubiquitylation active sites. Our analysis of the role of Gid12 establishes principles that may more generally underlie E3 ligase regulation.
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Affiliation(s)
- Shuai Qiao
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany.,Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, 322000, Zhejiang, China
| | - Chia-Wei Lee
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany.,Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany.,Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Dawafuti Sherpa
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Jakub Chrustowicz
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Jingdong Cheng
- Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, University of Fudan, 200032, Shanghai, China
| | - Maximilian Duennebacke
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Barbara Steigenberger
- Mass Spectrometry Core Facility, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Ozge Karayel
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Duc Tung Vu
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Susanne von Gronau
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Florian Wilfling
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany.,Mechanisms of Cellular Quality Control, Max Planck Institute of Biophysics, 60438, Frankfurt am Main, Germany
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany.
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11
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Structural and Functional Insights into GID/CTLH E3 Ligase Complexes. Int J Mol Sci 2022; 23:ijms23115863. [PMID: 35682545 PMCID: PMC9180843 DOI: 10.3390/ijms23115863] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/18/2022] [Accepted: 05/20/2022] [Indexed: 11/29/2022] Open
Abstract
Multi-subunit E3 ligases facilitate ubiquitin transfer by coordinating various substrate receptor subunits with a single catalytic center. Small molecules inducing targeted protein degradation have exploited such complexes, proving successful as therapeutics against previously undruggable targets. The C-terminal to LisH (CTLH) complex, also called the glucose-induced degradation deficient (GID) complex, is a multi-subunit E3 ligase complex highly conserved from Saccharomyces cerevisiae to humans, with roles in fundamental pathways controlling homeostasis and development in several species. However, we are only beginning to understand its mechanistic basis. Here, we review the literature of the CTLH complex from all organisms and place previous findings on individual subunits into context with recent breakthroughs on its structure and function.
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12
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Cowan AD, Ciulli A. Driving E3 Ligase Substrate Specificity for Targeted Protein Degradation: Lessons from Nature and the Laboratory. Annu Rev Biochem 2022; 91:295-319. [PMID: 35320687 DOI: 10.1146/annurev-biochem-032620-104421] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Methods to direct the degradation of protein targets with proximity-inducing molecules that coopt the cellular degradation machinery are advancing in leaps and bounds, and diverse modalities are emerging. The most used and well-studied approach is to hijack E3 ligases of the ubiquitin-proteasome system. E3 ligases use specific molecular recognition to determine which proteins in the cell are ubiquitinated and degraded. This review focuses on the structural determinants of E3 ligase recruitment of natural substrates and neo-substrates obtained through monovalent molecular glues and bivalent proteolysis-targeting chimeras. We use structures to illustrate the different types of substrate recognition and assess the basis for neo-protein-protein interactions in ternary complex structures. The emerging structural and mechanistic complexity is reflective of the diverse physiological roles of protein ubiquitination. This molecular insight is also guiding the application of structure-based design approaches to the development of new and existing degraders as chemical tools and therapeutics. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Angus D Cowan
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, United Kingdom;
| | - Alessio Ciulli
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, United Kingdom;
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13
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Sherpa D, Chrustowicz J, Schulman BA. How the ends signal the end: Regulation by E3 ubiquitin ligases recognizing protein termini. Mol Cell 2022; 82:1424-1438. [PMID: 35247307 PMCID: PMC9098119 DOI: 10.1016/j.molcel.2022.02.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/18/2022] [Accepted: 02/01/2022] [Indexed: 12/31/2022]
Abstract
Specificity of eukaryotic protein degradation is determined by E3 ubiquitin ligases and their selective binding to protein motifs, termed "degrons," in substrates for ubiquitin-mediated proteolysis. From the discovery of the first substrate degron and the corresponding E3 to a flurry of recent studies enabled by modern systems and structural methods, it is clear that many regulatory pathways depend on E3s recognizing protein termini. Here, we review the structural basis for recognition of protein termini by E3s and how this recognition underlies biological regulation. Diverse E3s evolved to harness a substrate's N and/or C terminus (and often adjacent residues as well) in a sequence-specific manner. Regulation is achieved through selective activation of E3s and also through generation of degrons at ribosomes or by posttranslational means. Collectively, many E3 interactions with protein N and C termini enable intricate control of protein quality and responses to cellular signals.
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Affiliation(s)
- Dawafuti Sherpa
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Bavaria, Germany
| | - Jakub Chrustowicz
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Bavaria, Germany
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Bavaria, Germany.
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14
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Crystal structure of yeast Gid10 in complex with Pro/N-degron. Biochem Biophys Res Commun 2021; 582:86-92. [PMID: 34695755 DOI: 10.1016/j.bbrc.2021.10.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 10/03/2021] [Indexed: 11/22/2022]
Abstract
The cellular glucose level has to be tightly regulated by a variety of cellular processes. One of them is the degradation of gluconeogenic enzymes such as Fbp1, Icl1, Mdh2, and Pck1 by GID (glucose-induced degradation deficient) E3 ubiquitin ligase. The Gid4 component of the GID ligase complex is responsible for recognizing the N-terminal proline residue of the target substrates under normal conditions. However, an alternative N-recognin Gid10 controls the degradation process under stressed conditions. Although Gid10 shares a high sequence similarity with Gid4, their substrate specificities are quite different. Here, we report the structure of Gid10 from Saccharomyces cerevisiae in complex with Pro/N-degron, Pro-Tyr-Ile-Thr, which is almost identical to the sequence of the natural substrate Art2. Although Gid10 shares many structural features with the Gid4 protein from yeast and humans, the current structure explains the unique structural difference for the preference of bulky hydrophobic residue at the second position of Pro/N-degron. Therefore, this study provides a fundamental basis for understanding of the structural diversity and substrate specificity of recognition components in the GID E3 ligase complex involved in the Pro/N-degron pathway.
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15
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Chrustowicz J, Sherpa D, Teyra J, Loke MS, Popowicz GM, Basquin J, Sattler M, Prabu JR, Sidhu SS, Schulman BA. Multifaceted N-Degron Recognition and Ubiquitylation by GID/CTLH E3 Ligases. J Mol Biol 2021; 434:167347. [PMID: 34767800 DOI: 10.1016/j.jmb.2021.167347] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/02/2021] [Accepted: 11/02/2021] [Indexed: 12/22/2022]
Abstract
N-degron E3 ubiquitin ligases recognize specific residues at the N-termini of substrates. Although molecular details of N-degron recognition are known for several E3 ligases, the range of N-terminal motifs that can bind a given E3 substrate binding domain remains unclear. Here, we discovered capacity of Gid4 and Gid10 substrate receptor subunits of yeast "GID"/human "CTLH" multiprotein E3 ligases to tightly bind a wide range of N-terminal residues whose recognition is determined in part by the downstream sequence context. Screening of phage displaying peptide libraries with exposed N-termini identified novel consensus motifs with non-Pro N-terminal residues binding Gid4 or Gid10 with high affinity. Structural data reveal that conformations of flexible loops in Gid4 and Gid10 complement sequences and folds of interacting peptides. Together with analysis of endogenous substrate degrons, the data show that degron identity, substrate domains harboring targeted lysines, and varying E3 ligase higher-order assemblies combinatorially determine efficiency of ubiquitylation and degradation.
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Affiliation(s)
- Jakub Chrustowicz
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany. https://twitter.com/chrustowicz_j
| | - Dawafuti Sherpa
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany. https://twitter.com/dawafutisherpa
| | - Joan Teyra
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Mun Siong Loke
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Grzegorz M Popowicz
- Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Germany
| | - Jerome Basquin
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Michael Sattler
- Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Germany
| | - J Rajan Prabu
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany. https://twitter.com/rajanprabu
| | - Sachdev S Sidhu
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.
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16
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Aminopeptidases trim Xaa-Pro proteins, initiating their degradation by the Pro/N-degron pathway. Proc Natl Acad Sci U S A 2021; 118:2115430118. [PMID: 34663735 DOI: 10.1073/pnas.2115430118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/12/2021] [Indexed: 12/26/2022] Open
Abstract
N-degron pathways are proteolytic systems that recognize proteins bearing N-terminal (Nt) degradation signals (degrons) called N-degrons. Our previous work identified Gid4 as a recognition component (N-recognin) of the Saccharomyces cerevisiae proteolytic system termed the proline (Pro)/N-degron pathway. Gid4 is a subunit of the oligomeric glucose-induced degradation (GID) ubiquitin ligase. Gid4 targets proteins through the binding to their Nt-Pro residue. Gid4 is also required for degradation of Nt-Xaa-Pro (Xaa is any amino acid residue) proteins such as Nt-[Ala-Pro]-Aro10 and Nt-[Ser-Pro]-Pck1, with Pro at position 2. Here, we show that specific aminopeptidases function as components of the Pro/N-degron pathway by removing Nt-Ala or Nt-Ser and yielding Nt-Pro, which can be recognized by Gid4-GID. Nt-Ala is removed by the previously uncharacterized aminopeptidase Fra1. The enzymatic activity of Fra1 is shown to be essential for the GID-dependent degradation of Nt-[Ala-Pro]-Aro10. Fra1 can also trim Nt-[Ala-Pro-Pro-Pro] (stopping immediately before the last Pro) and thereby can target for degradation a protein bearing this Nt sequence. Nt-Ser is removed largely by the mitochondrial/cytosolic/nuclear aminopeptidase Icp55. These advances are relevant to eukaryotes from fungi to animals and plants, as Fra1, Icp55, and the GID ubiquitin ligase are conserved in evolution. In addition to discovering the mechanism of targeting of Xaa-Pro proteins, these insights have also expanded the diversity of substrates of the Pro/N-degron pathway.
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17
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Kong KYE, Fischer B, Meurer M, Kats I, Li Z, Rühle F, Barry JD, Kirrmaier D, Chevyreva V, San Luis BJ, Costanzo M, Huber W, Andrews BJ, Boone C, Knop M, Khmelinskii A. Timer-based proteomic profiling of the ubiquitin-proteasome system reveals a substrate receptor of the GID ubiquitin ligase. Mol Cell 2021; 81:2460-2476.e11. [PMID: 33974913 PMCID: PMC8189435 DOI: 10.1016/j.molcel.2021.04.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 03/15/2021] [Accepted: 04/19/2021] [Indexed: 01/01/2023]
Abstract
Selective protein degradation by the ubiquitin-proteasome system (UPS) is involved in all cellular processes. However, the substrates and specificity of most UPS components are not well understood. Here we systematically characterized the UPS in Saccharomyces cerevisiae. Using fluorescent timers, we determined how loss of individual UPS components affects yeast proteome turnover, detecting phenotypes for 76% of E2, E3, and deubiquitinating enzymes. We exploit this dataset to gain insights into N-degron pathways, which target proteins carrying N-terminal degradation signals. We implicate Ubr1, an E3 of the Arg/N-degron pathway, in targeting mitochondrial proteins processed by the mitochondrial inner membrane protease. Moreover, we identify Ylr149c/Gid11 as a substrate receptor of the glucose-induced degradation-deficient (GID) complex, an E3 of the Pro/N-degron pathway. Our results suggest that Gid11 recognizes proteins with N-terminal threonines, expanding the specificity of the GID complex. This resource of potential substrates and relationships between UPS components enables exploring functions of selective protein degradation.
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Affiliation(s)
| | - Bernd Fischer
- Computational Genome Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthias Meurer
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Ilia Kats
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Zhaoyan Li
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Frank Rühle
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Joseph D Barry
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Daniel Kirrmaier
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany; Cell Morphogenesis and Signal Transduction, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Veronika Chevyreva
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Bryan-Joseph San Luis
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Michael Costanzo
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Wolfgang Huber
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Brenda J Andrews
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Charles Boone
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Michael Knop
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany; Cell Morphogenesis and Signal Transduction, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany.
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18
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Sherpa D, Chrustowicz J, Qiao S, Langlois CR, Hehl LA, Gottemukkala KV, Hansen FM, Karayel O, von Gronau S, Prabu JR, Mann M, Alpi AF, Schulman BA. GID E3 ligase supramolecular chelate assembly configures multipronged ubiquitin targeting of an oligomeric metabolic enzyme. Mol Cell 2021; 81:2445-2459.e13. [PMID: 33905682 PMCID: PMC8189437 DOI: 10.1016/j.molcel.2021.03.025] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 02/17/2021] [Accepted: 03/17/2021] [Indexed: 12/31/2022]
Abstract
How are E3 ubiquitin ligases configured to match substrate quaternary structures? Here, by studying the yeast GID complex (mutation of which causes deficiency in glucose-induced degradation of gluconeogenic enzymes), we discover supramolecular chelate assembly as an E3 ligase strategy for targeting an oligomeric substrate. Cryoelectron microscopy (cryo-EM) structures show that, to bind the tetrameric substrate fructose-1,6-bisphosphatase (Fbp1), two minimally functional GID E3s assemble into the 20-protein Chelator-GIDSR4, which resembles an organometallic supramolecular chelate. The Chelator-GIDSR4 assembly avidly binds multiple Fbp1 degrons so that multiple Fbp1 protomers are simultaneously ubiquitylated at lysines near the allosteric and substrate binding sites. Importantly, key structural and biochemical features, including capacity for supramolecular assembly, are preserved in the human ortholog, the CTLH E3. Based on our integrative structural, biochemical, and cell biological data, we propose that higher-order E3 ligase assembly generally enables multipronged targeting, capable of simultaneously incapacitating multiple protomers and functionalities of oligomeric substrates.
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Affiliation(s)
- Dawafuti Sherpa
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Jakub Chrustowicz
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Shuai Qiao
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Christine R Langlois
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Laura A Hehl
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Karthik Varma Gottemukkala
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Fynn M Hansen
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Ozge Karayel
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Susanne von Gronau
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - J Rajan Prabu
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Arno F Alpi
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany.
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19
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Tying up loose ends: the N-degron and C-degron pathways of protein degradation. Biochem Soc Trans 2021; 48:1557-1567. [PMID: 32627813 PMCID: PMC7458402 DOI: 10.1042/bst20191094] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/11/2020] [Accepted: 06/15/2020] [Indexed: 12/13/2022]
Abstract
Selective protein degradation by the ubiquitin-proteasome system (UPS) is thought to be governed primarily by the recognition of specific motifs — degrons — present in substrate proteins. The ends of proteins — the N- and C-termini – have unique properties, and an important subset of protein–protein interactions involve the recognition of free termini. The first degrons to be discovered were located at the extreme N-terminus of proteins, a finding which initiated the study of the N-degron (formerly N-end rule) pathways, but only in the last few years has it emerged that a diverse set of C-degron pathways target analogous degron motifs located at the extreme C-terminus of proteins. In this minireview we summarise the N-degron and C-degron pathways currently known to operate in human cells, focussing primarily on those that have been discovered in recent years. In each case we describe the cellular machinery responsible for terminal degron recognition, and then consider some of the functional roles of terminal degron pathways. Altogether, a broad spectrum of E3 ubiquitin ligases mediate the recognition of a diverse array of terminal degron motifs; these degradative pathways have the potential to influence a wide variety of cellular functions.
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20
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Hiragi K, Nishio K, Moriyama S, Hamaguchi T, Mizoguchi A, Yonekura K, Tani K, Mizushima T. Structural insights into the targeting specificity of ubiquitin ligase for S. cerevisiae isocitrate lyase but not C. albicans isocitrate lyase. J Struct Biol 2021; 213:107748. [PMID: 34033899 DOI: 10.1016/j.jsb.2021.107748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 11/17/2022]
Abstract
In Saccharomyces cerevisiae, the glyoxylate cycle is controlled through the posttranslational regulation of its component enzymes, such as isocitrate lyase (ICL), which catalyzes the first unique step of the cycle. The ICL of S.cerevisiae (ScIcl1) is tagged for proteasomal degradation through ubiquitination by a multisubunit ubiquitin ligase (the glucose-induced degradation-deficient (GID) complex), whereas that of the pathogenic yeast Candida albicans (CaIcl1) escapes this process. However, the reason for the ubiquitin targeting specificity of the GID complex for ScIcl1 and not for CaIcl1 is unclear. To gain some insight into this, in this study, the crystal structures of apo ScIcl1 and CaIcl1 in complex with formate and the cryogenic electron microscopy structure of apo CaIcl1 were determined at a resolution of 2.3, 2.7, and 2.6 Å, respectively. A comparison of the various structures suggests that the orientation of N-terminal helix α1 in S.cerevisiae is likely key to repositioning of ubiquitination sites and contributes to the distinction found in C. albicans ubiquitin evasion mechanism. This finding gives us a better understanding of the molecular mechanism of ubiquitin-dependent ScIcl1 degradation and could serve as a theoretical basis for the research and development of anti-C. albicans drugs based on the concept of CaIcl1 ubiquitination.
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Affiliation(s)
- Keito Hiragi
- Graduate School of Science, University of Hyogo, 2167 Shosha, Himeji 671-2280, Japan
| | - Kazuya Nishio
- Graduate School of Science, University of Hyogo, 2167 Shosha, Himeji 671-2280, Japan
| | - Shu Moriyama
- Graduate School of Science, University of Hyogo, 2167 Shosha, Himeji 671-2280, Japan
| | - Tasuku Hamaguchi
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Akira Mizoguchi
- Graduate School of Medicine, Mie University, 2-174 Edobashi Tsu, Mie 514-8507, Japan
| | - Koji Yonekura
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan; Advanced Electron Microscope Development Unit, RIKEN-JEOL Collaboration Center, RIKEN Baton Zone Program, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan; Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira Aoba-ku, Sendai 980-8577, Japan
| | - Kazutoshi Tani
- Graduate School of Medicine, Mie University, 2-174 Edobashi Tsu, Mie 514-8507, Japan
| | - Tsunehiro Mizushima
- Graduate School of Science, University of Hyogo, 2167 Shosha, Himeji 671-2280, Japan.
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Karayel O, Michaelis AC, Mann M, Schulman BA, Langlois CR. DIA-based systems biology approach unveils E3 ubiquitin ligase-dependent responses to a metabolic shift. Proc Natl Acad Sci U S A 2020; 117:32806-32815. [PMID: 33288721 PMCID: PMC7768684 DOI: 10.1073/pnas.2020197117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The yeast Saccharomyces cerevisiae is a powerful model system for systems-wide biology screens and large-scale proteomics methods. Nearly complete proteomics coverage has been achieved owing to advances in mass spectrometry. However, it remains challenging to scale this technology for rapid and high-throughput analysis of the yeast proteome to investigate biological pathways on a global scale. Here we describe a systems biology workflow employing plate-based sample preparation and rapid, single-run, data-independent mass spectrometry analysis (DIA). Our approach is straightforward, easy to implement, and enables quantitative profiling and comparisons of hundreds of nearly complete yeast proteomes in only a few days. We evaluate its capability by characterizing changes in the yeast proteome in response to environmental perturbations, identifying distinct responses to each of them and providing a comprehensive resource of these responses. Apart from rapidly recapitulating previously observed responses, we characterized carbon source-dependent regulation of the GID E3 ligase, an important regulator of cellular metabolism during the switch between gluconeogenic and glycolytic growth conditions. This unveiled regulatory targets of the GID ligase during a metabolic switch. Our comprehensive yeast system readout pinpointed effects of a single deletion or point mutation in the GID complex on the global proteome, allowing the identification and validation of targets of the GID E3 ligase. Moreover, this approach allowed the identification of targets from multiple cellular pathways that display distinct patterns of regulation. Although developed in yeast, rapid whole-proteome-based readouts can serve as comprehensive systems-level assays in all cellular systems.
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Affiliation(s)
- Ozge Karayel
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - André C Michaelis
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany;
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Christine R Langlois
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
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22
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The Role of Deubiquitinating Enzymes in the Various Forms of Autophagy. Int J Mol Sci 2020; 21:ijms21124196. [PMID: 32545524 PMCID: PMC7352190 DOI: 10.3390/ijms21124196] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 12/20/2022] Open
Abstract
Deubiquitinating enzymes (DUBs) have an essential role in several cell biological processes via removing the various ubiquitin patterns as posttranslational modification forms from the target proteins. These enzymes also contribute to the normal cytoplasmic ubiquitin pool during the recycling of this molecule. Autophagy, a summary name of the lysosome dependent self-degradative processes, is necessary for maintaining normal cellular homeostatic equilibrium. Numerous forms of autophagy are known depending on how the cellular self-material is delivered into the lysosomal lumen. In this review we focus on the colorful role of DUBs in autophagic processes and discuss the mechanistic contribution of these molecules to normal cellular homeostasis via the possible regulation forms of autophagic mechanisms.
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23
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Elfiky AA, Ismail AM, Elshemey WM. Recognition of gluconeogenic enzymes; Icl1, Fbp1, and Mdh2 by Gid4 ligase: A molecular docking study. J Mol Recognit 2020; 33:e2831. [DOI: 10.1002/jmr.2831] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/03/2019] [Accepted: 12/04/2019] [Indexed: 02/03/2023]
Affiliation(s)
- Abdo A. Elfiky
- Biophysics Department, Faculty of ScienceCairo University Giza Egypt
- College of Applied Medical SciencesUniversity of Al‐Jouf Sakaka Saudi Arabia
| | - Alaa M. Ismail
- Biophysics Department, Faculty of ScienceCairo University Giza Egypt
| | - Wael M. Elshemey
- Biophysics Department, Faculty of ScienceCairo University Giza Egypt
- Department of Physics, Faculty of ScienceIslamic University in Madinah Medina Saudi Arabia
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24
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QTL mapping of modelled metabolic fluxes reveals gene variants impacting yeast central carbon metabolism. Sci Rep 2020; 10:2162. [PMID: 32034164 PMCID: PMC7005809 DOI: 10.1038/s41598-020-57857-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 12/21/2019] [Indexed: 11/08/2022] Open
Abstract
The yeast Saccharomyces cerevisiae is an attractive industrial microorganism for the production of foods and beverages as well as for various bulk and fine chemicals, such as biofuels or fragrances. Building blocks for these biosyntheses are intermediates of yeast central carbon metabolism (CCM), whose intracellular availability depends on balanced single reactions that form metabolic fluxes. Therefore, efficient product biosynthesis is influenced by the distribution of these fluxes. We recently demonstrated great variations in CCM fluxes between yeast strains of different origins. However, we have limited understanding of flux modulation and the genetic basis of flux variations. In this study, we investigated the potential of quantitative trait locus (QTL) mapping to elucidate genetic variations responsible for differences in metabolic flux distributions (fQTL). Intracellular metabolic fluxes were estimated by constraint-based modelling and used as quantitative phenotypes, and differences in fluxes were linked to genomic variations. Using this approach, we detected four fQTLs that influence metabolic pathways. The molecular dissection of these QTLs revealed two allelic gene variants, PDB1 and VID30, contributing to flux distribution. The elucidation of genetic determinants influencing metabolic fluxes, as reported here for the first time, creates new opportunities for the development of strains with optimized metabolite profiles for various applications.
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25
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Interconversion between Anticipatory and Active GID E3 Ubiquitin Ligase Conformations via Metabolically Driven Substrate Receptor Assembly. Mol Cell 2020; 77:150-163.e9. [DOI: 10.1016/j.molcel.2019.10.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/04/2019] [Accepted: 10/08/2019] [Indexed: 12/20/2022]
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26
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Liu H, Ding J, Köhnlein K, Urban N, Ori A, Villavicencio-Lorini P, Walentek P, Klotz LO, Hollemann T, Pfirrmann T. The GID ubiquitin ligase complex is a regulator of AMPK activity and organismal lifespan. Autophagy 2019; 16:1618-1634. [PMID: 31795790 PMCID: PMC8386601 DOI: 10.1080/15548627.2019.1695399] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The AMP-activated protein kinase (AMPK) regulates cellular energy homeostasis by sensing the metabolic status of the cell. AMPK is regulated by phosphorylation and dephosphorylation as a result of changing AMP/ATP levels and by removal of inhibitory ubiquitin residues by USP10. In this context, we identified the GID-complex, an evolutionarily conserved ubiquitin-ligase-complex (E3), as a negative regulator of AMPK activity. Our data show that the GID-complex targets AMPK for ubiquitination thereby altering its activity. Cells depleted of GID-subunits mimic a state of starvation as shown by increased AMPK activity and macroautophagic/autophagic flux as well as reduced MTOR activation. Consistently, gid-genes knockdown in C. elegans results in increased organismal lifespan. This study may contribute to understand metabolic disorders such as type 2 diabetes mellitus and morbid obesity and implements alternative therapeutic approaches to alter AMPK activity.
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Affiliation(s)
- Huaize Liu
- Institute of Physiological Chemistry, Martin-Luther University Halle-Wittenberg , Halle, Germany
| | - Jie Ding
- Institute of Physiological Chemistry, Martin-Luther University Halle-Wittenberg , Halle, Germany
| | - Karl Köhnlein
- Institute of Nutritional Sciences, Friedrich Schiller University Jena , Jena, Germany
| | - Nadine Urban
- Institute of Nutritional Sciences, Friedrich Schiller University Jena , Jena, Germany
| | - Alessandro Ori
- Leibniz Institute on Aging, Fritz Lipmann Institute (FLI) , Jena, Germany
| | | | - Peter Walentek
- Division of Genetics, Genomics and Development, Molecular and Cell Biology Department, University of California at Berkeley , Berkeley, USA.,Internal Medicine IV, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg , Germany.,CIBSS - Center for Integrative Biological Signalling Studies, Albert Ludwigs University , Freiburg, Germany
| | - Lars-Oliver Klotz
- Institute of Nutritional Sciences, Friedrich Schiller University Jena , Jena, Germany
| | - Thomas Hollemann
- Institute of Physiological Chemistry, Martin-Luther University Halle-Wittenberg , Halle, Germany
| | - Thorsten Pfirrmann
- Institute of Physiological Chemistry, Martin-Luther University Halle-Wittenberg , Halle, Germany
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27
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The mammalian CTLH complex is an E3 ubiquitin ligase that targets its subunit muskelin for degradation. Sci Rep 2019; 9:9864. [PMID: 31285494 PMCID: PMC6614414 DOI: 10.1038/s41598-019-46279-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 06/17/2019] [Indexed: 12/15/2022] Open
Abstract
The multi-subunit C-terminal to LisH (CTLH) complex is the mammalian homologue of the yeast Gid E3 ubiquitin ligase complex. In this study, we investigated the human CTLH complex and characterized its E3 ligase activity. We confirm that the complex immunoprecipitated from human cells comprises RanBPM, ARMC8 α/β, muskelin, WDR26, GID4 and the RING domain proteins RMND5A and MAEA. We find that loss of expression of individual subunits compromises the stability of other complex members and that MAEA and RMND5A protein levels are interdependent. Using in vitro ubiquitination assays, we demonstrate that the CTLH complex has E3 ligase activity which is dependent on RMND5A and MAEA. We report that the complex can pair with UBE2D1, UBE2D2 and UBE2D3 E2 enzymes and that recombinant RMND5A mediates K48 and K63 poly-ubiquitin chains. Finally, we show a proteasome-dependent increase in the protein levels of CTLH complex member muskelin in RMND5A KO cells. Furthermore, muskelin ubiquitination is dependent on RMND5A, suggesting that it may be a target of the complex. Overall, we further the characterization of the CTLH complex as an E3 ubiquitin ligase complex in human cells and reveal a potential autoregulation mechanism.
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28
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Kumar S, Masison DC. Hsp70-nucleotide exchange factor (NEF) Fes1 has non-NEF roles in degradation of gluconeogenic enzymes and cell wall integrity. PLoS Genet 2019; 15:e1008219. [PMID: 31242183 PMCID: PMC6615629 DOI: 10.1371/journal.pgen.1008219] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 07/09/2019] [Accepted: 05/28/2019] [Indexed: 12/03/2022] Open
Abstract
Fes1 is a conserved armadillo repeat-containing Hsp70 nucleotide exchange factor important for growth at high temperature, proteasomal protein degradation and prion propagation. Depleting or mutating Fes1 induces a stress response and causes defects in these processes that are ascribed solely to disruption of Fes1 regulation of Hsp70. Here, we find Fes1 was essential for degradation of gluconeogenic enzymes by the vacuole import and degradation (Vid) pathway and for cell wall integrity (CWI), which is crucial for growth at high temperature. Unexpectedly, Fes1 mutants defective in physical or functional interaction with Hsp70 retained activities that support Vid and CWI. Fes1 and the Fes1 mutants bound to the Vid substrate Fbp1 in vitro and captured Slt2, a signaling kinase that regulates CWI, from cell lysates. Our data show that the armadillo domain of Fes1 binds proteins other than Hsp70, that Fes1 has important Hsp70-independent roles in the cell, and that major growth defects caused by depleting Fes1 are due to loss of these functions rather than to loss of Hsp70 regulation. We uncovered diverse functions of Fes1 beyond its defined role in regulating Hsp70, which points to possible multi-functionality among its conserved counterparts in other organisms or organelles. Fes1, a yeast homolog of human nucleotide exchange factor HspBP1, binds and regulates Hsp70, a universally conserved protein that helps maintain health of proteins in cells. Fes1 is believed to function only by helping Hsp70 release ADP and substrates and cells lacking Fes1 are sick. We find Fes1 is essential for protein degradation by a vacuolar pathway (Vid) and for cell wall integrity (CWI), and it interacts with a Vid substrate and a regulator of CWI. Fes1 mutants that cannot regulate Hsp70 can still support Vid and CWI, interact with proteins involved in these processes and restore cell health. Thus, Fes1 binds proteins other than Hsp70 and has important functions beyond regulating Hsp70 that are needed for optimal cell fitness.
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Affiliation(s)
- Shailesh Kumar
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Daniel C. Masison
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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29
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Liu H, Pfirrmann T. The Gid-complex: an emerging player in the ubiquitin ligase league. Biol Chem 2019; 400:1429-1441. [DOI: 10.1515/hsz-2019-0139] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 02/20/2019] [Indexed: 12/16/2022]
Abstract
Abstract
The Saccharomyces cerevisiae Gid-complex is a highly evolutionary conserved ubiquitin ligase with at least seven protein subunits. Here, we review our knowledge about the yeast Gid-complex as an important regulator of glucose metabolism, specifically targeting key enzymes of gluconeogenesis for degradation. Furthermore, we summarize existing data about the individual subunits, the topology and possible substrate recognition mechanisms and compare the striking similarities, but also differences, between the yeast complex and its vertebrate counterpart. Present data is summarized to give an overview about cellular processes regulated by the vertebrate GID-complex that range from cell cycle regulation, primary cilia function to the regulation of energy homeostasis. In conclusion, the vertebrate GID-complex evolved as a versatile ubiquitin ligase complex with functions beyond the regulation of glucose metabolism.
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Affiliation(s)
- Huaize Liu
- Martin Luther University Halle-Wittenberg , Institute of Physiological Chemistry , Hollystr. 1 , D-06114 Halle , Germany
| | - Thorsten Pfirrmann
- Martin Luther University Halle-Wittenberg , Institute of Physiological Chemistry , Hollystr. 1 , D-06114 Halle , Germany
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30
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Kats I, Khmelinskii A, Kschonsak M, Huber F, Knieß RA, Bartosik A, Knop M. Mapping Degradation Signals and Pathways in a Eukaryotic N-terminome. Mol Cell 2019; 70:488-501.e5. [PMID: 29727619 DOI: 10.1016/j.molcel.2018.03.033] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 01/26/2018] [Accepted: 03/27/2018] [Indexed: 01/01/2023]
Abstract
Most eukaryotic proteins are N-terminally acetylated. This modification can be recognized as a signal for selective protein degradation (degron) by the N-end rule pathways. However, the prevalence and specificity of such degrons in the proteome are unclear. Here, by systematically examining how protein turnover is affected by N-terminal sequences, we perform a comprehensive survey of degrons in the yeast N-terminome. We find that approximately 26% of nascent protein N termini encode cryptic degrons. These degrons exhibit high hydrophobicity and are frequently recognized by the E3 ubiquitin ligase Doa10, suggesting a role in protein quality control. In contrast, N-terminal acetylation rarely functions as a degron. Surprisingly, we identify two pathways where N-terminal acetylation has the opposite function and blocks protein degradation through the E3 ubiquitin ligase Ubr1. Our analysis highlights the complexity of N-terminal degrons and argues that hydrophobicity, not N-terminal acetylation, is the predominant feature of N-terminal degrons in nascent proteins.
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Affiliation(s)
- Ilia Kats
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Anton Khmelinskii
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Marc Kschonsak
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Florian Huber
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Robert A Knieß
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Anna Bartosik
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Michael Knop
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany; Deutsches Krebsforschungszentrum (DKFZ), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
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31
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Menssen R, Bui K, Wolf DH. Regulation of the Gid ubiquitin ligase recognition subunit Gid4. FEBS Lett 2018; 592:3286-3294. [DOI: 10.1002/1873-3468.13229] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 08/08/2018] [Accepted: 08/15/2018] [Indexed: 11/05/2022]
Affiliation(s)
- Ruth Menssen
- Department of Biochemistry Institute of Biochemistry and Technical Biochemistry Stuttgart University Germany
| | - Kim Bui
- Department of Biochemistry Institute of Biochemistry and Technical Biochemistry Stuttgart University Germany
| | - Dieter H. Wolf
- Department of Biochemistry Institute of Biochemistry and Technical Biochemistry Stuttgart University Germany
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32
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Leal-Esteban LC, Rothé B, Fortier S, Isenschmid M, Constam DB. Role of Bicaudal C1 in renal gluconeogenesis and its novel interaction with the CTLH complex. PLoS Genet 2018; 14:e1007487. [PMID: 29995892 PMCID: PMC6056059 DOI: 10.1371/journal.pgen.1007487] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 07/23/2018] [Accepted: 06/13/2018] [Indexed: 01/06/2023] Open
Abstract
Altered glucose and lipid metabolism fuel cystic growth in polycystic kidneys, but the cause of these perturbations is unclear. Renal cysts also associate with mutations in Bicaudal C1 (Bicc1) or in its self-polymerizing sterile alpha motif (SAM). Here, we found that Bicc1 maintains normoglycemia and the expression of the gluconeogenic enzymes FBP1 and PEPCK in kidneys. A proteomic screen revealed that Bicc1 interacts with the C-Terminal to Lis-Homology domain (CTLH) complex. Since the orthologous Gid complex in S. cerevisae targets FBP1 and PEPCK for degradation, we mapped the topology among CTLH subunits and found that SAM-mediated binding controls Bicc1 protein levels, whereas Bicc1 inhibited the accumulation of several CTLH subunits. Under the conditions analyzed, Bicc1 increased FBP1 protein levels independently of the CTLH complex. Besides linking Bicc1 to cell metabolism, our findings reveal new layers of complexity in the regulation of renal gluconeogenesis compared to lower eukaryotes. Polycystic kidney diseases (PKD) are incurable inherited chronic disorders marked by fluid-filled cysts that frequently cause renal failure. A glycolytic metabolism reminiscent of cancerous cells accelerates cystic growth, but the mechanism underlying such metabolic re-wiring is poorly understood. PKD-like cystic kidneys also develop in mice that lack the RNA-binding protein Bicaudal-C (Bicc1), and mutations in a single copy of human BICC1 associate with renal cystic dysplasia. Here, we report that Bicc1 regulates renal gluconeogenesis. A screen for interacting factors revealed that Bicc1 binds the C-Terminal to Lis-Homology domain (CTLH) complex, which in lower eukaryotes mediates degradation of gluconeogenic enzymes. By contrast, Bicc1 and the mammalian CTLH complex regulated each other, and Bicc1 stimulated the accumulation of the rate-limiting gluconeogenic enzyme even in cells depleted of CTLH subunits. Our finding that Bicc1 is required for normoglycemia implies that renal gluconeogenesis may be important to inhibit cyst formation.
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Affiliation(s)
- Lucia Carolina Leal-Esteban
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland
| | - Benjamin Rothé
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland
| | - Simon Fortier
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland
| | - Manuela Isenschmid
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland
| | - Daniel B. Constam
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland
- * E-mail:
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33
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Dissmeyer N, Rivas S, Graciet E. Life and death of proteins after protease cleavage: protein degradation by the N-end rule pathway. THE NEW PHYTOLOGIST 2018; 218:929-935. [PMID: 28581033 DOI: 10.1111/nph.14619] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 04/04/2017] [Indexed: 06/07/2023]
Abstract
UNLABELLED Contents Summary 929 I. INTRODUCTION conservation and diversity of N-end rule pathways 929 II. Defensive functions of the N-end rule pathway in plants 930 III. Proteases and degradation by the N-end rule pathway 930 IV. New proteomics approaches for the identification of N-end rule substrates 932 V. Concluding remarks 932 Acknowledgements 934 References 934 SUMMARY: The N-end rule relates the stability of a protein to the identity of its N-terminal residue and some of its modifications. Since its discovery in the 1980s, the repertoire of N-terminal degradation signals has expanded, leading to a diversity of N-end rule pathways. Although some of these newly discovered N-end rule pathways remain largely unexplored in plants, recent discoveries have highlighted roles of N-end rule-mediated protein degradation in plant defense against pathogens and in cell proliferation during organ growth. Despite this progress, a bottleneck remains the proteome-wide identification of N-end rule substrates due to the prerequisite for endoproteolytic cleavage and technical limitations. Here, we discuss the recent diversification of N-end rule pathways and their newly discovered functions in plant defenses, stressing the role of proteases. We expect that novel proteomics techniques (N-terminomics) will be essential for substrate identification. We review these methods, their limitations and future developments.
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Affiliation(s)
- Nico Dissmeyer
- Independent Junior Research Group on Protein Recognition and Degradation, Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, Halle (Saale), D-06120, Germany
- ScienceCampus Halle - Plant-based Bioeconomy, Betty-Heimann-Strasse 3, Halle (Saale), D-06120, Germany
| | - Susana Rivas
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, 31 326, France
| | - Emmanuelle Graciet
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
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34
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Wang Z, Zhang H, Liu C, Xing J, Chen XL. A Deubiquitinating Enzyme Ubp14 Is Required for Development, Stress Response, Nutrient Utilization, and Pathogenesis of Magnaporthe oryzae. Front Microbiol 2018; 9:769. [PMID: 29720973 PMCID: PMC5915541 DOI: 10.3389/fmicb.2018.00769] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Accepted: 04/04/2018] [Indexed: 02/02/2023] Open
Abstract
Ubiquitination is an essential protein modification in eukaryotic cells, which is reversible. Deubiquitinating enzymes (DUBs) catalyze deubiquitination process to reverse ubiquitination, maintain ubiquitin homeostasis or promote protein degradation by recycling ubiquitins. In order to investigate effects of deubiquitination process in plant pathogenic fungus Magnaporthe oryzae, we generated deletion mutants of MoUBP14. Ortholog of MoUbp14 was reported to play general roles in ubiquitin-mediated protein degradation in Saccharomyces cerevisiae. The ΔMoubp14 mutant lost its pathogenicity and was severely reduced in mycelial growth, sporulation, carbon source utilization, and increased in sensitivity to distinct stresses. The mutant was blocked in penetration, which could due to defect in turgor generation. It is also blocked in invasive growth, which could due to reduction in stress tolerance and nutrient utilization. Deletion of UBP14 also led to accumulation of free polyubiquitin chains. Pulldown assay identified some proteins related to carbohydrate metabolism and stress response may putatively interact with MoUbp14, including two key rate-limiting enzymes of gluconeogenesis, MoFbp1 and MoPck1. These two proteins were degraded when the glucose was supplied to M. oryzae grown in low glucose media for a short period of time (∼12 h), and this process required MoUbp14. In summary, pleiotropic phenotypes of the deletion mutants indicated that MoUbp14 is required for different developments and pathogenicity of M. oryzae.
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Affiliation(s)
- Zhao Wang
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hong Zhang
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Caiyun Liu
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Junjie Xing
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
| | - Xiao-Lin Chen
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.,State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
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35
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Eldeeb MA, Leitao LCA, Fahlman RP. Emerging branches of the N-end rule pathways are revealing the sequence complexities of N-termini dependent protein degradation. Biochem Cell Biol 2017; 96:289-294. [PMID: 29253354 DOI: 10.1139/bcb-2017-0274] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The N-end rule links the identity of the N-terminal amino acid of a protein to its in vivo half-life, as some N-terminal residues confer metabolic instability to a protein via their recognition by the cellular machinery that targets them for degradation. Since its discovery, the N-end rule has generally been defined as set of rules of whether an N-terminal residue is stabilizing or not. However, recent studies are revealing that the N-terminal code of amino acids conferring protein instability is more complex than previously appreciated, as recent investigations are revealing that the identity of adjoining downstream residues can also influence the metabolic stability of N-end rule substrate. This is exemplified by the recent discovery of a new branch of N-end rule pathways that target proteins bearing N-terminal proline. In addition, recent investigations are demonstrating that the molecular machinery in N-termini dependent protein degradation may also target proteins for lysosomal degradation, in addition to proteasome-dependent degradation. Herein, we describe some of the recent advances in N-end rule pathways and discuss some of the implications regarding the emerging additional sequence requirements.
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Affiliation(s)
- Mohamed A Eldeeb
- a Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.,b Department of Chemistry, Faculty of Science, Cairo University, Giza, Cairo, Egypt
| | - Luana C A Leitao
- a Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Richard P Fahlman
- a Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.,c Department of Oncology, University of Alberta, Edmonton, AB T6G 2H7, Canada
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Dougan DA. Pro(moting) the Turnover of Gluconeogenic Enzymes by a New Branch of the N-end Rule Pathway. Trends Biochem Sci 2017; 42:330-332. [DOI: 10.1016/j.tibs.2017.03.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 03/24/2017] [Indexed: 12/19/2022]
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Stein K, Winters C, Chiang HL. Vps15p regulates the distribution of cup-shaped organelles containing the major eisosome protein Pil1p to the extracellular fraction required for endocytosis of extracellular vesicles carrying metabolic enzymes. Biol Cell 2017; 109:190-209. [PMID: 28248428 DOI: 10.1111/boc.201600060] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 02/20/2017] [Accepted: 02/23/2017] [Indexed: 11/30/2022]
Abstract
BACKGROUND INFORMATION Exosomes are small vesicles secreted from virtually every cell from bacteria to humans. Saccharomyces cerevisiae is a model system to study trafficking of small vesicles in response to changes in the environment. When yeast cells are grown in low glucose, vesicles carrying gluconeogenic enzymes are present as free vesicles and aggregated clusters in the cytoplasm. These vesicles are also secreted into the periplasm and account for more than 90% of total extracellular organelles, while less than 10% are larger 100-300 nm structures with unknown functions. When glucose is added to glucose-starved cells, secreted vesicles are endocytosed and then targeted to the vacuole. Recent secretomic studies indicated that more than 300 proteins involved in diverse biological functions are secreted during glucose starvation and endocytosed during glucose re-feeding. We hypothesised that extracellular vesicles are internalised using novel mechanisms independent of clathrin-mediated endocytosis. RESULTS Our results showed that vesicles carrying metabolic enzymes were endocytosed at a fast rate, whereas vesicles carrying the heat shock protein Ssa1p were endocytosed at a slow rate. The PI3K regulator Vps15p is critical for the fast internalisation of extracellular vesicles. VPS15 regulates the distribution of the 100-300 nm organelles that contain the major eisosome protein Pil1p to the extracellular fraction. These Pil1p-containing structures were purified and showed unique cup-shape with their centres deeper than the peripheries. In the absence of VPS15, PIL1 or when PIL1 was mutated, the 100-300 nm structures were not observed in the extracellular fraction and the rapid internalisation of vesicles was impaired. CONCLUSIONS We conclude that VPS15 regulates the distribution of the 100-300 nm Pil1p-containing organelles to the extracellular fraction required for fast endocytosis of vesicles carrying metabolic enzymes. This work provides the first evidence showing that Pil1p displayed unique distribution patterns in the intracellular and extracellular fractions. This work also demonstrates that endocytosis of vesicles is divided into a fast and a slow pathway. The fast pathway is the predominant pathway and is used by vesicles carrying metabolic enzymes. Cup-shaped Pil1p-containing structures are critical for the rapid endocytosis of vesicles into the cytoplasm. SIGNIFICANCE This work provides the first evidence showing that Pil1p displayed unique distribution patterns in the intracellular and extracellular fractions. This work also demonstrates that endocytosis of vesicles is divided into a fast and a slow pathway. The fast pathway is the predominant pathway and is used by vesicles carrying metabolic enzymes. Cup-shaped Pil1p-containing structures are critical for the rapid endocytosis of vesicles into the cytoplasm.
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Affiliation(s)
- Kathryn Stein
- Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, PA, 17033, USA
| | - Chelsea Winters
- Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, PA, 17033, USA
| | - Hui-Ling Chiang
- Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, PA, 17033, USA
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Ben-Nissan G, Belov ME, Morgenstern D, Levin Y, Dym O, Arkind G, Lipson C, Makarov AA, Sharon M. Triple-Stage Mass Spectrometry Unravels the Heterogeneity of an Endogenous Protein Complex. Anal Chem 2017; 89:4708-4715. [PMID: 28345864 DOI: 10.1021/acs.analchem.7b00518] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Protein complexes often represent an ensemble of different assemblies with distinct functions and regulation. This increased complexity is enabled by the variety of protein diversification mechanisms that exist at every step of the protein biosynthesis pathway, such as alternative splicing and post transcriptional and translational modifications. The resulting variation in subunits can generate compositionally distinct protein assemblies. These different forms of a single protein complex may comprise functional variances that enable response and adaptation to varying cellular conditions. Despite the biological importance of this layer of complexity, relatively little is known about the compositional heterogeneity of protein complexes, mostly due to technical barriers of studying such closely related species. Here, we show that native mass spectrometry (MS) offers a way to unravel this inherent heterogeneity of protein assemblies. Our approach relies on the advanced Orbitrap mass spectrometer capable of multistage MS analysis across all levels of protein organization. Specifically, we have implemented a two-step fragmentation process in the inject flatapole device, which was converted to a linear ion trap, and can now probe the intact protein complex assembly, through its constituent subunits, to the primary sequence of each protein. We demonstrate our approach on the yeast homotetrameric FBP1 complex, the rate-limiting enzyme in gluconeogenesis. We show that the complex responds differently to changes in growth conditions by tuning phosphorylation dynamics. Our methodology deciphers, on a single instrument and in a single measurement, the stoichiometry, kinetics, and exact position of modifications, contributing to the exposure of the multilevel diversity of protein complexes.
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Affiliation(s)
- Gili Ben-Nissan
- Department of Biomolecular Sciences, Weizmann Institute of Science , Rehovot 7610001, Israel
| | | | - David Morgenstern
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science , Rehovot 7610001, Israel
| | - Yishai Levin
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science , Rehovot 7610001, Israel
| | - Orly Dym
- Israel Structural Proteomics Center, Weizmann Institute of Science , Rehovot 7610001, Israel
| | - Galina Arkind
- Department of Biomolecular Sciences, Weizmann Institute of Science , Rehovot 7610001, Israel
| | - Carni Lipson
- Department of Biomolecular Sciences, Weizmann Institute of Science , Rehovot 7610001, Israel
| | | | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science , Rehovot 7610001, Israel
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Ghanem A, Kitanovic A, Holzwarth J, Wölfl S. Mutational analysis of fructose-1,6-bis-phosphatase FBP1 indicates partially independent functions in gluconeogenesis and sensitivity to genotoxic stress. MICROBIAL CELL 2017; 4:52-63. [PMID: 28357389 PMCID: PMC5349122 DOI: 10.15698/mic2017.02.557] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fructose-1,6-bisphosphatase (FBP1) is a key enzyme in the
evolutionary conserved pathway of gluconeogenesis. We had shown in an earlier
study that FBP1 is involved in the response and sensitivity to
methyl-methanesulfonate (MMS)-induced DNA damage in yeast. In the work presented
here we performed an alanine screen mutational analysis of several evolutionary
conserved amino acid residues of FBP1, which were selected
based on conserved residues and structural studies of mammalian and yeast
homologues of FBP1. Mutants were examined for enzymatic
activity, and yeast cells expressing these mutants were tested for growth on
non-fermentable and MMS-containing media. The results obtained support predicted
vital roles of several residues for enzymatic activity and led to the
identification of residues indispensable for the MMS-sensitizing effect. Despite
an overlap between these two properties, careful analysis revealed two
mutations, Asn75 and His324, which decouple the enzymatic activity and the
MMS-sensitizing effect, indicating two distinctive biological activities linked
in this key gluconeogenesis enzyme.
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Affiliation(s)
- Ali Ghanem
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
| | - Ana Kitanovic
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
| | - Jinda Holzwarth
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
| | - Stefan Wölfl
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
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Chen SJ, Wu X, Wadas B, Oh JH, Varshavsky A. An N-end rule pathway that recognizes proline and destroys gluconeogenic enzymes. Science 2017; 355:eaal3655. [PMID: 28126757 PMCID: PMC5457285 DOI: 10.1126/science.aal3655] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 12/14/2016] [Indexed: 01/07/2023]
Abstract
Cells synthesize glucose if deprived of it, and destroy gluconeogenic enzymes upon return to glucose-replete conditions. We found that the Gid4 subunit of the ubiquitin ligase GID in the yeast Saccharomyces cerevisiae targeted the gluconeogenic enzymes Fbp1, Icl1, and Mdh2 for degradation. Gid4 recognized the N-terminal proline (Pro) residue and the ~5-residue-long adjacent sequence motifs. Pck1, the fourth gluconeogenic enzyme, contains Pro at position 2; Gid4 directly or indirectly recognized Pro at position 2 of Pck1, contributing to its targeting. These and related results identified Gid4 as the recognition component of the GID-based proteolytic system termed the Pro/N-end rule pathway. Substrates of this pathway include gluconeogenic enzymes that bear either the N-terminal Pro residue or a Pro at position 2, together with adjacent sequence motifs.
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Affiliation(s)
- Shun-Jia Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Xia Wu
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Brandon Wadas
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Jang-Hyun Oh
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Alexander Varshavsky
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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Childers DS, Raziunaite I, Mol Avelar G, Mackie J, Budge S, Stead D, Gow NAR, Lenardon MD, Ballou ER, MacCallum DM, Brown AJP. The Rewiring of Ubiquitination Targets in a Pathogenic Yeast Promotes Metabolic Flexibility, Host Colonization and Virulence. PLoS Pathog 2016; 12:e1005566. [PMID: 27073846 PMCID: PMC4830568 DOI: 10.1371/journal.ppat.1005566] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 03/21/2016] [Indexed: 11/19/2022] Open
Abstract
Efficient carbon assimilation is critical for microbial growth and pathogenesis. The environmental yeast Saccharomyces cerevisiae is “Crabtree positive”, displaying a rapid metabolic switch from the assimilation of alternative carbon sources to sugars. Following exposure to sugars, this switch is mediated by the transcriptional repression of genes (carbon catabolite repression) and the turnover (catabolite inactivation) of enzymes involved in the assimilation of alternative carbon sources. The pathogenic yeast Candida albicans is Crabtree negative. It has retained carbon catabolite repression mechanisms, but has undergone posttranscriptional rewiring such that gluconeogenic and glyoxylate cycle enzymes are not subject to ubiquitin-mediated catabolite inactivation. Consequently, when glucose becomes available, C. albicans can continue to assimilate alternative carbon sources alongside the glucose. We show that this metabolic flexibility promotes host colonization and virulence. The glyoxylate cycle enzyme isocitrate lyase (CaIcl1) was rendered sensitive to ubiquitin-mediated catabolite inactivation in C. albicans by addition of a ubiquitination site. This mutation, which inhibits lactate assimilation in the presence of glucose, reduces the ability of C. albicans cells to withstand macrophage killing, colonize the gastrointestinal tract and cause systemic infections in mice. Interestingly, most S. cerevisiae clinical isolates we examined (67%) have acquired the ability to assimilate lactate in the presence of glucose (i.e. they have become Crabtree negative). These S. cerevisiae strains are more resistant to macrophage killing than Crabtree positive clinical isolates. Moreover, Crabtree negative S. cerevisiae mutants that lack Gid8, a key component of the Glucose-Induced Degradation complex, are more resistant to macrophage killing and display increased virulence in immunocompromised mice. Thus, while Crabtree positivity might impart a fitness advantage for yeasts in environmental niches, the more flexible carbon assimilation strategies offered by Crabtree negativity enhance the ability of yeasts to colonize and infect the mammalian host. Most yeast species occupy environmental niches, but some infect humans. All species must assimilate carbon to grow and colonize their niche, but carbon source availability differs significantly between niches. The environmental yeast Saccharomyces cerevisiae is thought to have evolved under conditions of sugar feast and famine because it has evolved mechanisms to exploit energetically favourable sugars first, and then switch to using alternative carbon sources. These mechanisms depend on catabolite inactivation—the degradation of enzymes involved in the assimilation of alternative carbon sources when glucose is present. In the pathogenic yeast Candida albicans, which has evolved in sugar-poor host niches, these enzymes are not subject to catabolite inactivation. Consequently, C. albicans can simultaneously exploit sugars and alternative carbon sources. We demonstrate that this metabolic flexibility promotes resistance to macrophage killing, gut colonization, and the ability to cause systemic infection. We also show that many S. cerevisiae clinical isolates have lost catabolite inactivation, and hence can simultaneously assimilate sugars and alternative carbon sources. The disruption of catabolite inactivation in S. cerevisiae renders it more resistant to phagocytic killing, and more virulent. We conclude that virulence is enhanced by metabolic flexibility.
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Affiliation(s)
- Delma S. Childers
- Aberdeen Fungal Group, School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, United Kingdom
| | - Ingrida Raziunaite
- Aberdeen Fungal Group, School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, United Kingdom
| | - Gabriela Mol Avelar
- Aberdeen Fungal Group, School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, United Kingdom
| | - Joanna Mackie
- Aberdeen Fungal Group, School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, United Kingdom
| | - Susan Budge
- Aberdeen Fungal Group, School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, United Kingdom
| | - David Stead
- Aberdeen Fungal Group, School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, United Kingdom
| | - Neil A. R. Gow
- Aberdeen Fungal Group, School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, United Kingdom
| | - Megan D. Lenardon
- Aberdeen Fungal Group, School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, United Kingdom
| | - Elizabeth R. Ballou
- Aberdeen Fungal Group, School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, United Kingdom
| | - Donna M. MacCallum
- Aberdeen Fungal Group, School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, United Kingdom
| | - Alistair J. P. Brown
- Aberdeen Fungal Group, School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, United Kingdom
- * E-mail:
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Lee KE, Heo JE, Kim JM, Hwang CS. N-Terminal Acetylation-Targeted N-End Rule Proteolytic System: The Ac/N-End Rule Pathway. Mol Cells 2016; 39:169-78. [PMID: 26883906 PMCID: PMC4794598 DOI: 10.14348/molcells.2016.2329] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 01/11/2016] [Accepted: 01/14/2016] [Indexed: 12/12/2022] Open
Abstract
Although Nα-terminal acetylation (Nt-acetylation) is a pervasive protein modification in eukaryotes, its general functions in a majority of proteins are poorly understood. In 2010, it was discovered that Nt-acetylation creates a specific protein degradation signal that is targeted by a new class of the N-end rule proteolytic system, called the Ac/N-end rule pathway. Here, we review recent advances in our understanding of the mechanism and biological functions of the Ac/N-end rule pathway, and its crosstalk with the Arg/N-end rule pathway (the classical N-end rule pathway).
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Affiliation(s)
- Kang-Eun Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 790–784,
Korea
| | - Ji-Eun Heo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 790–784,
Korea
| | - Jeong-Mok Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 790–784,
Korea
| | - Cheol-Sang Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 790–784,
Korea
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43
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Giardina BJ, Chiang HL. The key gluconeogenic enzyme fructose-1,6-bisphosphatase is secreted during prolonged glucose starvation and is internalized following glucose re-feeding via the non-classical secretory and internalizing pathways in Saccharomyces cerevisiae. PLANT SIGNALING & BEHAVIOR 2013; 8:24936. [PMID: 23673352 PMCID: PMC3999075 DOI: 10.4161/psb.24936] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 05/03/2013] [Accepted: 05/04/2013] [Indexed: 06/02/2023]
Abstract
In Saccharomyces cerevisia, the key gluconeogenic enzyme fructose-1,6-bisphosphatase is secreted into the periplasm during prolonged glucose starvation and is internalized into Vid/endosomes following glucose re-feeding. Fructose-1,6-bisphosphatase does not contain signal sequences required for the classical secretory and endocytic pathways. Hence, the secretion and internalization are mediated via the non-classical pathways.
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44
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Giardina BJ, Dunton D, Chiang HL. Vid28 protein is required for the association of vacuole import and degradation (Vid) vesicles with actin patches and the retention of Vid vesicle proteins in the intracellular fraction. J Biol Chem 2013; 288:11636-48. [PMID: 23393132 DOI: 10.1074/jbc.m112.419895] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Gluconeogenic enzymes are induced when Saccharomyces cerevisiae are starved of glucose. However, when glucose is added to prolonged starved cells, these enzymes are degraded in the vacuole via the vacuole import and degradation (Vid) pathway. The Vid pathway is linked to the nonclassical secretory and internalizing pathways. In prolonged starved cells, substantial amounts of the key gluconeogenic enzyme fructose-1,6-bisphosphatase (FBPase) are in the extracellular fraction (periplasm). However, when glucose is added to glucose-starved cells, levels of extracellular FBPase decrease rapidly. Ultrastructural studies indicate that FBPase is in Vid/endosomes following glucose addition, suggesting that FBPase is internalized in response to glucose refeeding. Under the same conditions, the majority of Vid vesicle proteins are in the intracellular fraction. In yeast, actin polymerization is involved in endocytosis. Vid vesicles associate with actin patches initially, and they dissociate later. Here, we show that VID28 plays a critical role in the association of Vid vesicles with actin patches and the retention of Vid vesicle proteins in the intracellular fraction. Vid28p was distributed to Vid vesicles and interacted with other Vid vesicle proteins. Vid28p contains an Armadillo (ARM) domain required for FBPase degradation. When VID28 was deleted or when the ARM domain was mutated, Vid vesicles failed to co-localize with actin patches, and Vid vesicle proteins appeared in the extracellular fraction. We suggest that the ARM domain is required for the association of Vid vesicles with actin patches and the retention of Vid vesicle proteins in the intracellular fraction.
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Affiliation(s)
- Bennett J Giardina
- Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, USA
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45
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The evolutionary rewiring of ubiquitination targets has reprogrammed the regulation of carbon assimilation in the pathogenic yeast Candida albicans. mBio 2012; 3:mBio.00495-12. [PMID: 23232717 PMCID: PMC3520108 DOI: 10.1128/mbio.00495-12] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Microbes must assimilate carbon to grow and colonize their niches. Transcript profiling has suggested that Candida albicans, a major pathogen of humans, regulates its carbon assimilation in an analogous fashion to the model yeast Saccharomyces cerevisiae, repressing metabolic pathways required for the use of alterative nonpreferred carbon sources when sugars are available. However, we show that there is significant dislocation between the proteome and transcriptome in C. albicans. Glucose triggers the degradation of the ICL1 and PCK1 transcripts in C. albicans, yet isocitrate lyase (Icl1) and phosphoenolpyruvate carboxykinase (Pck1) are stable and are retained. Indeed, numerous enzymes required for the assimilation of carboxylic and fatty acids are not degraded in response to glucose. However, when expressed in C. albicans, S. cerevisiae Icl1 (ScIcl1) is subjected to glucose-accelerated degradation, indicating that like S. cerevisiae, this pathogen has the molecular apparatus required to execute ubiquitin-dependent catabolite inactivation. C. albicans Icl1 (CaIcl1) lacks analogous ubiquitination sites and is stable under these conditions, but the addition of a ubiquitination site programs glucose-accelerated degradation of CaIcl1. Also, catabolite inactivation is slowed in C. albicans ubi4 cells. Ubiquitination sites are present in gluconeogenic and glyoxylate cycle enzymes from S. cerevisiae but absent from their C. albicans homologues. We conclude that evolutionary rewiring of ubiquitination targets has meant that following glucose exposure, C. albicans retains key metabolic functions, allowing it to continue to assimilate alternative carbon sources. This metabolic flexibility may be critical during infection, facilitating the rapid colonization of dynamic host niches containing complex arrays of nutrients. Pathogenic microbes must assimilate a range of carbon sources to grow and colonize their hosts. Current views about carbon assimilation in the pathogenic yeast Candida albicans are strongly influenced by the Saccharomyces cerevisiae paradigm in which cells faced with choices of nutrients first use energetically favorable sugars, degrading enzymes required for the assimilation of less favorable alternative carbon sources. We show that this is not the case in C. albicans because there has been significant evolutionary rewiring of the molecular signals that promote enzyme degradation in response to glucose. As a result, this major pathogen of humans retains enzymes required for the utilization of physiologically relevant carbon sources such as lactic acid and fatty acids, allowing it to continue to use these host nutrients even when glucose is available. This phenomenon probably enhances efficient colonization of host niches where sugars are only transiently available.
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Menssen R, Schweiggert J, Schreiner J, Kusevic D, Reuther J, Braun B, Wolf DH. Exploring the topology of the Gid complex, the E3 ubiquitin ligase involved in catabolite-induced degradation of gluconeogenic enzymes. J Biol Chem 2012; 287:25602-14. [PMID: 22645139 DOI: 10.1074/jbc.m112.363762] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
In the yeast Saccharomyces cerevisiae, key regulatory enzymes of gluconeogenesis such as fructose-1,6-bisphosphatase are degraded via the ubiquitin proteasome system when cells are replenished with glucose. Polyubiquitination is carried out by the Gid complex, a multisubunit ubiquitin ligase that consists of seven different Gid (glucose-induced degradation-deficient) proteins. Under gluconeogenic conditions the E3 ligase is composed of six subunits (Gid1/Vid30, Gid2/Rmd5, Gid5/Vid28, Gid7, Gid8, and Gid9/Fyv10). Upon the addition of glucose the regulatory subunit Gid4/Vid24 appears, binds to the Gid complex, and triggers ubiquitination of fructose-1,6-bisphosphatase. All seven proteins are essential for this process; however, nothing is known about the arrangement of the subunits in the complex. Interestingly, each Gid protein possesses several remarkable motifs (e.g. SPRY, LisH, CTLH domains) that may play a role in protein-protein interaction. We, therefore, generated altered versions of individual Gid proteins by deleting or mutating these domains and performed co-immunoprecipitation experiments to analyze the interaction between distinct subunits. Thus, we were able to create an initial model of the topology of this unusual E3 ubiquitin ligase.
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Affiliation(s)
- Ruth Menssen
- Institut für Biochemie, Universität Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
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47
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Alibhoy AA, Giardina BJ, Dunton DD, Chiang HL. Vid30 is required for the association of Vid vesicles and actin patches in the vacuole import and degradation pathway. Autophagy 2012; 8:29-46. [PMID: 22082961 DOI: 10.4161/auto.8.1.18104] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
When Saccharomyces cerevisiae is starved of glucose, the gluconeogenic enzymes fructose-1,6-bisphosphatase (FBPase), malate dehydrogenase (MDH2), isocitrate lyase (Icl1) and phosphoenolpyruvate carboxykinase (Pck1) are induced. However, when glucose is added to prolonged starved cells, these enzymes are degraded in the vacuole via the vacuole import and degradation (Vid) pathway. Recent evidence suggests that the Vid pathway merges with the endocytic pathway at actin patches where endocytic vesicles are formed. The convergence of the Vid pathway with the endocytic pathway allows cells to remove intracellular and extracellular proteins simultaneously. However, the genes that regulate this step of the convergence have not been identified previously. Here we show that VID30 plays a critical role for the association of Vid vesicles and actin patches. Vid30 is constitutively expressed and interacts with Vid vesicle proteins Vid24 and Sec28 but not with the cargo protein FBPase. In the absence of SEC28 or VID24, Vid30 association with actin patches was prolonged. In cells lacking the VID30 gene, FBPase and Vid24 were not localized to actin patches, suggesting that Vid30 has a role in the association of Vid vesicles and actin patches. Vid30 contains a LisH and a CTLH domain, both of which are required for FBPase degradation. When these domains were deleted, FBPase trafficking to the vacuole was impaired. We suggest that Vid30 also has a role in the Vid pathway at a later step in a process that is mediated by the LisH and CTLH domains.
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Affiliation(s)
- Abbas A Alibhoy
- Department of Cellular and Molecular Physiology, Penn State University, College of Medicine, Hershey, PA, USA
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Alibhoy AA, Chiang HL. Vacuole import and degradation pathway: Insights into a specialized autophagy pathway. World J Biol Chem 2011; 2:239-45. [PMID: 22125667 PMCID: PMC3224871 DOI: 10.4331/wjbc.v2.i11.239] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Revised: 08/30/2011] [Accepted: 11/06/2011] [Indexed: 02/05/2023] Open
Abstract
Glucose deprivation induces the synthesis of pivotal gluconeogenic enzymes such as fructose-1,6-bisphosphatase, malate dehydrogenase, phosphoenolpyruvate carboxykinase and isocitrate lyase in Saccharomyces cerevisiae. However, following glucose replenishment, these gluconeogenic enzymes are inactivated and degraded. Studies have characterized the mechanisms by which these enzymes are inactivated in response to glucose. The site of degradation of these proteins has also been ascertained to be dependent on the duration of starvation. Glucose replenishment of short-term starved cells results in these proteins being degraded in the proteasome. In contrast, addition of glucose to cells starved for a prolonged period results in these proteins being degraded in the vacuole. In the vacuole dependent pathway, these proteins are sequestered in specialized vesicles termed vacuole import and degradation (Vid). These vesicles converge with the endocytic pathway and deliver their cargo to the vacuole for degradation. Recent studies have identified that internalization, as mediated by actin polymerization, is essential for delivery of cargo proteins to the vacuole for degradation. In addition, components of the target of rapamycin complex 1 interact with cargo proteins during glucose starvation. Furthermore, Tor1p dissociates from cargo proteins following glucose replenishment. Future studies will be needed to elaborate on the importance of internalization at the plasma membrane and the subsequent import of cargo proteins into Vid vesicles in the vacuole dependent degradation pathway.
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Affiliation(s)
- Abbas A Alibhoy
- Abbas A Alibhoy, Hui-Ling Chiang, Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, PA 17033, United States
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Braun B, Pfirrmann T, Menssen R, Hofmann K, Scheel H, Wolf DH. Gid9, a second RING finger protein contributes to the ubiquitin ligase activity of the Gid complex required for catabolite degradation. FEBS Lett 2011; 585:3856-61. [PMID: 22044534 DOI: 10.1016/j.febslet.2011.10.038] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Revised: 10/20/2011] [Accepted: 10/23/2011] [Indexed: 10/15/2022]
Abstract
The two major antagonistic pathways of carbon metabolism in cells, glycolysis and gluconeogenesis, are tightly regulated. In the eukaryotic model organism Saccharomyces cerevisiae the switch from gluconeogenesis to glycolysis is brought about by proteasomal degradation of the gluconeogenic enzyme fructose-1,6-bisphosphatase. The ubiquitin ligase responsible for polyubiquitylation of fructose-1,6-bisphosphatase is the Gid complex. This complex consists of seven subunits of which subunit Gid2/Rmd5 contains a RING finger domain providing E3 ligase activity. Here we identify an additional subunit containing a degenerated RING finger, Gid9/Fyv10. This subunit binds to Gid2/Rmd5. A mutation in the degenerated RING finger of Gid9/Fyv10 abolishes polyubiquitylation and degradation of three enzymes specific for gluconeogenesis.
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Affiliation(s)
- Bernhard Braun
- Institut für Biochemie, Universität Stuttgart, Stuttgart, Germany
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Juretschke J, Menssen R, Sickmann A, Wolf DH. The Hsp70 chaperone Ssa1 is essential for catabolite induced degradation of the gluconeogenic enzyme fructose-1,6-bisphosphatase. Biochem Biophys Res Commun 2010; 397:447-52. [DOI: 10.1016/j.bbrc.2010.05.123] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Accepted: 05/23/2010] [Indexed: 01/17/2023]
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