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Nam KH, Ordureau A. How does the neuronal proteostasis network react to cellular cues? Biochem Soc Trans 2024; 52:581-592. [PMID: 38488108 DOI: 10.1042/bst20230316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 04/25/2024]
Abstract
Even though neurons are post-mitotic cells, they still engage in protein synthesis to uphold their cellular content balance, including for organelles, such as the endoplasmic reticulum or mitochondria. Additionally, they expend significant energy on tasks like neurotransmitter production and maintaining redox homeostasis. This cellular homeostasis is upheld through a delicate interplay between mRNA transcription-translation and protein degradative pathways, such as autophagy and proteasome degradation. When faced with cues such as nutrient stress, neurons must adapt by altering their proteome to survive. However, in many neurodegenerative disorders, such as Parkinson's disease, the pathway and processes for coping with cellular stress are impaired. This review explores neuronal proteome adaptation in response to cellular stress, such as nutrient stress, with a focus on proteins associated with autophagy, stress response pathways, and neurotransmitters.
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Affiliation(s)
- Ki Hong Nam
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, U.S.A
| | - Alban Ordureau
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, U.S.A
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DaRosa PA, Penchev I, Gumbin SC, Scavone F, Wąchalska M, Paulo JA, Ordureau A, Peter JJ, Kulathu Y, Harper JW, Becker T, Beckmann R, Kopito RR. UFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER. Nature 2024; 627:445-452. [PMID: 38383785 DOI: 10.1038/s41586-024-07073-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 01/15/2024] [Indexed: 02/23/2024]
Abstract
Reversible modification of target proteins by ubiquitin and ubiquitin-like proteins (UBLs) is widely used by eukaryotic cells to control protein fate and cell behaviour1. UFM1 is a UBL that predominantly modifies a single lysine residue on a single ribosomal protein, uL24 (also called RPL26), on ribosomes at the cytoplasmic surface of the endoplasmic reticulum (ER)2,3. UFM1 conjugation (UFMylation) facilitates the rescue of 60S ribosomal subunits (60S) that are released after ribosome-associated quality-control-mediated splitting of ribosomes that stall during co-translational translocation of secretory proteins into the ER3,4. Neither the molecular mechanism by which the UFMylation machinery achieves such precise target selection nor how this ribosomal modification promotes 60S rescue is known. Here we show that ribosome UFMylation in vivo occurs on free 60S and we present sequential cryo-electron microscopy snapshots of the heterotrimeric UFM1 E3 ligase (E3(UFM1)) engaging its substrate uL24. E3(UFM1) binds the L1 stalk, empty transfer RNA-binding sites and the peptidyl transferase centre through carboxy-terminal domains of UFL1, which results in uL24 modification more than 150 Å away. After catalysing UFM1 transfer, E3(UFM1) remains stably bound to its product, UFMylated 60S, forming a C-shaped clamp that extends all the way around the 60S from the transfer RNA-binding sites to the polypeptide tunnel exit. Our structural and biochemical analyses suggest a role for E3(UFM1) in post-termination release and recycling of the large ribosomal subunit from the ER membrane.
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Affiliation(s)
- Paul A DaRosa
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Ivan Penchev
- Department of Biochemistry, Gene Center, University of Munich, Munich, Germany
| | | | | | - Magda Wąchalska
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Alban Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joshua J Peter
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dundee, UK
| | - Yogesh Kulathu
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dundee, UK
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Thomas Becker
- Department of Biochemistry, Gene Center, University of Munich, Munich, Germany
| | - Roland Beckmann
- Department of Biochemistry, Gene Center, University of Munich, Munich, Germany.
| | - Ron R Kopito
- Department of Biology, Stanford University, Stanford, CA, USA.
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Goldsmith J, Ordureau A, Wade Harper J, Holzbaur EL. Brain-derived autophagosome profiling reveals the engulfment of nucleoid-enriched mitochondrial fragments by basal autophagy in neurons. Neuron 2024; 112:520. [PMID: 38330901 PMCID: PMC10935664 DOI: 10.1016/j.neuron.2024.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
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Paul S, Sarraf SA, Nam KH, Zavar L, DeFoor N, Biswas SR, Fritsch LE, Yaron TM, Johnson JL, Huntsman EM, Cantley LC, Ordureau A, Pickrell AM. NAK-associated protein 1/NAP1 activates TBK1 to ensure accurate mitosis and cytokinesis. J Cell Biol 2024; 223:e202303082. [PMID: 38059900 PMCID: PMC10702366 DOI: 10.1083/jcb.202303082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 10/03/2023] [Accepted: 11/10/2023] [Indexed: 12/08/2023] Open
Abstract
Subcellular location and activation of Tank Binding Kinase 1 (TBK1) govern precise progression through mitosis. Either loss of activated TBK1 or its sequestration from the centrosomes causes errors in mitosis and growth defects. Yet, what regulates its recruitment and activation on the centrosomes is unknown. We identified that NAK-associated protein 1 (NAP1) is essential for mitosis, binding to and activating TBK1, which both localize to centrosomes. Loss of NAP1 causes several mitotic and cytokinetic defects due to inactivation of TBK1. Our quantitative phosphoproteomics identified numerous TBK1 substrates that are not only confined to the centrosomes but are also associated with microtubules. Substrate motifs analysis indicates that TBK1 acts upstream of other essential cell cycle kinases like Aurora and PAK kinases. We also identified NAP1 as a TBK1 substrate phosphorylating NAP1 at S318 to promote its degradation by the ubiquitin proteasomal system. These data uncover an important distinct function for the NAP1-TBK1 complex during cell division.
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Affiliation(s)
- Swagatika Paul
- Graduate Program in Biomedical and Veterinary Sciences, Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA, USA
| | - Shireen A. Sarraf
- Biochemistry Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Ki Hong Nam
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Leila Zavar
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Nicole DeFoor
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Sahitya Ranjan Biswas
- Translational Biology, Medicine, and Health Graduate Program, Virginia Polytechnic Institute and State University, Roanoke, VA, USA
| | - Lauren E. Fritsch
- Translational Biology, Medicine, and Health Graduate Program, Virginia Polytechnic Institute and State University, Roanoke, VA, USA
| | - Tomer M. Yaron
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | | | - Emily M. Huntsman
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Lewis C. Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Alban Ordureau
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alicia M. Pickrell
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
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Watts ME, Giadone RM, Ordureau A, Holton KM, Harper JW, Rubin LL. Analyzing the ER stress response in ALS patient derived motor neurons identifies druggable neuroprotective targets. Front Cell Neurosci 2024; 17:1327361. [PMID: 38314348 PMCID: PMC10834640 DOI: 10.3389/fncel.2023.1327361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 12/15/2023] [Indexed: 02/06/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a degenerative motor neuron (MN) disease with severely limited treatment options. Identification of effective treatments has been limited in part by the lack of predictive animal models for complex human disorders. Here, we utilized pharmacologic ER stressors to exacerbate underlying sensitivities conferred by ALS patient genetics in induced pluripotent stem cell (iPSC)-derived motor neurons (MNs). In doing so, we found that thapsigargin and tunicamycin exposure recapitulated ALS-associated degeneration, and that we could rescue this degeneration via MAP4K4 inhibition (MAP4K4i). We subsequently identified mechanisms underlying MAP4K4i-mediated protection by performing phosphoproteomics on iPSC-derived MNs treated with ER stressors ±MAP4K4i. Through these analyses, we found JNK, PKC, and BRAF to be differentially modulated in MAP4K4i-protected MNs, and that inhibitors to these proteins could also rescue MN toxicity. Collectively, this study highlights the value of utilizing ER stressors in ALS patient MNs to identify novel druggable targets.
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Affiliation(s)
- Michelle E. Watts
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, United States
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, United States
| | - Richard M. Giadone
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, United States
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, United States
| | - Alban Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, MA, United States
| | - Kristina M. Holton
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, United States
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, United States
| | - J. Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA, United States
| | - Lee L. Rubin
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, United States
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, United States
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Morrone Parfitt G, Coccia E, Goldman C, Whitney K, Reyes R, Sarrafha L, Nam KH, Sohail S, Jones DR, Crary JF, Ordureau A, Blanchard J, Ahfeldt T. Disruption of lysosomal proteolysis in astrocytes facilitates midbrain organoid proteostasis failure in an early-onset Parkinson's disease model. Nat Commun 2024; 15:447. [PMID: 38200091 PMCID: PMC10781970 DOI: 10.1038/s41467-024-44732-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 01/02/2024] [Indexed: 01/12/2024] Open
Abstract
Accumulation of advanced glycation end products (AGEs) on biopolymers accompanies cellular aging and drives poorly understood disease processes. Here, we studied how AGEs contribute to development of early onset Parkinson's Disease (PD) caused by loss-of-function of DJ1, a protein deglycase. In induced pluripotent stem cell (iPSC)-derived midbrain organoid models deficient for DJ1 activity, we find that lysosomal proteolysis is impaired, causing AGEs to accumulate, α-synuclein (α-syn) phosphorylation to increase, and proteins to aggregate. We demonstrated these processes are at least partly driven by astrocytes, as DJ1 loss reduces their capacity to provide metabolic support and triggers acquisition of a pro-inflammatory phenotype. Consistently, in co-cultures, we find that DJ1-expressing astrocytes are able to reverse the proteolysis deficits of DJ1 knockout midbrain neurons. In conclusion, astrocytes' capacity to clear toxic damaged proteins is critical to preserve neuronal function and their dysfunction contributes to the neurodegeneration observed in a DJ1 loss-of-function PD model.
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Affiliation(s)
- Gustavo Morrone Parfitt
- Nash Family Department of Neuroscience at Mount Sinai, New York, NY, USA.
- Ronald M. Loeb Center for Alzheimer's Disease at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute at Mount Sinai, New York, NY, USA.
- Black Family Stem Cell Institute at Mount Sinai, New York, NY, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
- Department of Neuroscience, Genentech, Inc., South San Francisco, CA, 94080, USA.
| | - Elena Coccia
- Nash Family Department of Neuroscience at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease at Mount Sinai, New York, NY, USA
- Friedman Brain Institute at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute at Mount Sinai, New York, NY, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Camille Goldman
- Nash Family Department of Neuroscience at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease at Mount Sinai, New York, NY, USA
- Friedman Brain Institute at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute at Mount Sinai, New York, NY, USA
| | - Kristen Whitney
- Nash Family Department of Neuroscience at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease at Mount Sinai, New York, NY, USA
- Friedman Brain Institute at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular, and Cell-Based Medicine at Mount Sinai, New York, NY, USA
| | - Ricardo Reyes
- Nash Family Department of Neuroscience at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease at Mount Sinai, New York, NY, USA
- Friedman Brain Institute at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute at Mount Sinai, New York, NY, USA
| | - Lily Sarrafha
- Nash Family Department of Neuroscience at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease at Mount Sinai, New York, NY, USA
- Friedman Brain Institute at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute at Mount Sinai, New York, NY, USA
| | - Ki Hong Nam
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Soha Sohail
- Nash Family Department of Neuroscience at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease at Mount Sinai, New York, NY, USA
- Friedman Brain Institute at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute at Mount Sinai, New York, NY, USA
| | - Drew R Jones
- Metabolomics Core Resource Laboratory, NYU Langone Health, New York, NY, USA
| | - John F Crary
- Nash Family Department of Neuroscience at Mount Sinai, New York, NY, USA
- Friedman Brain Institute at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular, and Cell-Based Medicine at Mount Sinai, New York, NY, USA
| | - Alban Ordureau
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joel Blanchard
- Nash Family Department of Neuroscience at Mount Sinai, New York, NY, USA.
- Ronald M. Loeb Center for Alzheimer's Disease at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute at Mount Sinai, New York, NY, USA.
- Black Family Stem Cell Institute at Mount Sinai, New York, NY, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
| | - Tim Ahfeldt
- Nash Family Department of Neuroscience at Mount Sinai, New York, NY, USA.
- Ronald M. Loeb Center for Alzheimer's Disease at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute at Mount Sinai, New York, NY, USA.
- Black Family Stem Cell Institute at Mount Sinai, New York, NY, USA.
- Recursion Pharmaceuticals, Salt Lake City, UT, USA.
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7
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Park HM, Le L, Nguyen TT, Nam KH, Ordureau A, Lee JE, Nguyen TV. The CRL3 gigaxonin ubiquitin ligase-USP15 pathway governs the destruction of neurofilament proteins. Proc Natl Acad Sci U S A 2023; 120:e2306395120. [PMID: 37903270 PMCID: PMC10636361 DOI: 10.1073/pnas.2306395120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 09/20/2023] [Indexed: 11/01/2023] Open
Abstract
Giant axonal neuropathy (GAN) is caused by mutations in the GAN gene encoding for gigaxonin (GIG), which functions as an adaptor of the CUL3-RBX1-GIG (CRL3GIG) E3 ubiquitin ligase complex. The pathological hallmark of GAN is characterized by the accumulation of densely packed neurofilaments (NFs) in the axons. However, there are fundamental knowledge gaps in our understanding of the molecular mechanisms by which the ubiquitin-proteasome system controls the homeostasis of NF proteins. Recently, the deubiquitylating enzyme USP15 was reported to play a crucial role in regulating ubiquitylation and proteasomal degradation of CRL4CRBN substrate proteins. Here, we report that the CRL3GIG-USP15 pathway governs the destruction of NF proteins NEFL and INA. We identified a specific degron called NEFLL12 degron for CRL3GIG. Notably, mutations in the C-terminal Kelch domain of GIG, represented by L309R, R545C, and C570Y, disrupted the binding of GIG to NEFL and INA, leading to the accumulation of these NF proteins. This accounts for the loss-of-function mutations in GAN patients. In addition to regulating NFs, CRL3GIG also controls actin filaments by directly targeting actin-filament-binding regulatory proteins TPM1, TPM2, TAGLN, and CNN2 for proteasomal degradation. Thus, our findings broadly impact the field by providing fundamental mechanistic insights into regulating extremely long-lived NF proteins NEFL and INA by the CRL3GIG-USP15 pathway and offering previously unexplored therapeutic opportunities to treat GAN patients and other neurodegenerative diseases by explicitly targeting downstream substrates of CRL3GIG.
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Affiliation(s)
- Hyoung-Min Park
- Biometrology Group, Korea Research Institute of Standards and Science, Daejeon34113, Korea
| | - Ly Le
- Division of Quantum Simulation and Optimization, SandboxAQ, New York, NY10591
| | - Thao T. Nguyen
- Gehrke Proteomics Center, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO65211
| | - Ki Hong Nam
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Alban Ordureau
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - J. Eugene Lee
- Biometrology Group, Korea Research Institute of Standards and Science, Daejeon34113, Korea
| | - Thang Van Nguyen
- Center for Precision Medicine, Department of Medicine, University of Missouri, Columbia, MO65212
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Jordan VN, Ordureau A, An H. Identifying E3 Ligase Substrates With Quantitative Degradation Proteomics. Chembiochem 2023; 24:e202300108. [PMID: 37166757 PMCID: PMC10548883 DOI: 10.1002/cbic.202300108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 05/09/2023] [Accepted: 05/11/2023] [Indexed: 05/12/2023]
Abstract
Controlled protein degradation by the ubiquitin-proteasome pathway is critical for almost all cellular processes. E3 ubiquitin ligases are responsible for targeting proteins for ubiquitylation and subsequent proteasomal degradation with spatial and temporal precision. While studies have revealed various E3-substrate pairs involved in distinct biological processes, the complete substrate profiles of individual E3 ligases are largely unknown. Here we report a new approach to identify substrates of an E3 ligase for proteasomal degradation using unnatural amino acid incorporation pulse-chase proteomics (degradomics). Applying this approach, we determine the steady-state substrates of the C-terminal to LisH (CTLH) E3 ligase, a multi-component complex with poorly defined substrates. By comparing the proteome degradation profiles of active and inactive CTLH-expressing cells, we successfully identify previously known and new potential substrates of CTLH ligase. Altogether, degradomics can comprehensively identify degradation substrates of an E3 ligase, which can be adapted for other E3 ligases in various cellular contexts.
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Affiliation(s)
- Victoria N Jordan
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Tri-Institutional PhD Program of Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Alban Ordureau
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Heeseon An
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Tri-Institutional PhD Program of Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Department of Pharmacology, Weill Cornell Medical College, New York, NY, 10065, USA
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Yang N, Wang Y, Dai P, Li T, Zierhut C, Tan A, Zhang T, Xiang JZ, Ordureau A, Funabiki H, Chen Z, Deng L. Vaccinia E5 is a major inhibitor of the DNA sensor cGAS. Nat Commun 2023; 14:2898. [PMID: 37217469 PMCID: PMC10201048 DOI: 10.1038/s41467-023-38514-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 05/05/2023] [Indexed: 05/24/2023] Open
Abstract
The DNA sensor cyclic GMP-AMP synthase (cGAS) is critical in host antiviral immunity. Vaccinia virus (VACV) is a large cytoplasmic DNA virus that belongs to the poxvirus family. How vaccinia virus antagonizes the cGAS-mediated cytosolic DNA-sensing pathway is not well understood. In this study, we screened 80 vaccinia genes to identify potential viral inhibitors of the cGAS/Stimulator of interferon gene (STING) pathway. We discovered that vaccinia E5 is a virulence factor and a major inhibitor of cGAS. E5 is responsible for abolishing cGAMP production during vaccinia virus (Western Reserve strain) infection of dendritic cells. E5 localizes to the cytoplasm and nucleus of infected cells. Cytosolic E5 triggers ubiquitination of cGAS and proteasome-dependent degradation via interacting with cGAS. Deleting the E5R gene from the Modified vaccinia virus Ankara (MVA) genome strongly induces type I IFN production by dendritic cells (DCs) and promotes DC maturation, and thereby improves antigen-specific T cell responses.
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Affiliation(s)
- Ning Yang
- Dermatology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
| | - Yi Wang
- Dermatology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Peihong Dai
- Dermatology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Tuo Li
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Christian Zierhut
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY, 10065, USA
- The Institute of Cancer Research, London, SW3 6JB, UK
| | - Adrian Tan
- Genomic Resources Core Facility, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Tuo Zhang
- Genomic Resources Core Facility, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Jenny Zhaoying Xiang
- Genomic Resources Core Facility, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Alban Ordureau
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Hironori Funabiki
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY, 10065, USA
| | - Zhijian Chen
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Liang Deng
- Dermatology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
- Weill Cornell Medical College, New York, NY, 10065, USA.
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Chin RM, Rakhit R, Ditsworth D, Wang C, Bartholomeus J, Liu S, Mody A, Laishu A, Eastes A, Tai C, Kim RY, Li J, Hansberry S, Khasnavis S, Rafalski V, Herendeen D, Garda V, Phung J, de Roulet D, Ordureau A, Harper JW, Johnstone S, Stöhr J, Hertz NT. Pharmacological PINK1 activation ameliorates Pathology in Parkinson's Disease models. bioRxiv 2023:2023.02.14.528378. [PMID: 36824886 PMCID: PMC9949154 DOI: 10.1101/2023.02.14.528378] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
PINK1 loss-of-function mutations and exposure to mitochondrial toxins are causative for Parkinson's disease (PD) and Parkinsonism, respectively. We demonstrate that pathological α-synuclein deposition, the hallmark pathology of idiopathic PD, induces mitochondrial dysfunction and impairs mitophagy, driving accumulation of the PINK1 substrate pS65-Ubiquitin (pUb) in primary neurons and in vivo. We synthesized MTK458, a brain penetrant small molecule that binds to PINK1 and stabilizes an active heterocomplex, thereby increasing mitophagy. MTK458 mediates clearance of α-synuclein pathology in PFF seeding models in vitro and in vivo and reduces pUb. We developed an ultrasensitive assay to quantify pUb levels in plasma and observed an increase in pUb in PD subjects that correlates with disease progression, paralleling our observations in PD models. Our combined findings from preclinical PD models and patient biofluids suggest that pharmacological activation of PINK1 is worthy of further study as a therapeutic strategy for disease modification in PD. Highlights Discovery of a plasma Parkinson's Disease biomarker candidate, pS65-Ubiquitin (pUb)Plasma pUb levels correlate with disease status and progression in PD patients.Identification of a potent, brain penetrant PINK1 activator, MTK458MTK458 selectively activates PINK1 by stimulating dimerization and stabilization of the PINK1/TOM complexMTK458 drives clearance of α-synuclein pathology and normalizes pUb in in vivo Parkinson's models.
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11
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Fiesel FC, Fričová D, Hayes CS, Coban MA, Hudec R, Bredenberg JM, Broadway BJ, Markham BN, Yan T, Boneski PK, Fiorino G, Watzlawik JO, Hou X, McCarty AM, Lewis-Tuffin LJ, Zhong J, Madden BJ, Ordureau A, An H, Puschmann A, Wszolek ZK, Ross OA, Harper JW, Caulfield TR, Springer W. Substitution of PINK1 Gly411 modulates substrate receptivity and turnover. Autophagy 2022:1-22. [PMID: 36469690 DOI: 10.1080/15548627.2022.2151294] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The ubiquitin (Ub) kinase-ligase pair PINK1-PRKN mediates the degradation of damaged mitochondria by macroautophagy/autophagy (mitophagy). PINK1 surveils mitochondria and upon stress accumulates on the mitochondrial surface where it phosphorylates serine 65 of Ub to activate PRKN and to drive mitochondrial turnover. While loss of either PINK1 or PRKN is genetically linked to Parkinson disease (PD) and activating the pathway seems to have great therapeutic potential, there is no formal proof that stimulation of mitophagy is always beneficial. Here we used biochemical and cell biological methods to study single nucleotide variants in the activation loop of PINK1 to modulate the enzymatic function of this kinase. Structural modeling and in vitro kinase assays were used to investigate the molecular mechanism of the PINK1 variants. In contrast to the PD-linked PINK1G411S mutation that diminishes Ub kinase activity, we found that the PINK1G411A variant significantly boosted Ub phosphorylation beyond levels of PINK1 wild type. This resulted in augmented PRKN activation, mitophagy rates and increased viability after mitochondrial stress in midbrain-derived, gene-edited neurons. Mechanistically, the G411A variant stabilizes the kinase fold of PINK1 and transforms Ub to adopt the preferred, C-terminally retracted conformation for improved substrate turnover. In summary, we identify a critical role of residue 411 for substrate receptivity that may now be exploited for drug discovery to increase the enzymatic function of PINK1. The genetic substitution of Gly411 to Ala increases mitophagy and may be useful to confirm neuroprotection in vivo and might serve as a critical positive control during therapeutic development.Abbreviations: ATP: adenosine triphosphate; CCCP: carbonyl cyanide m-chlorophenyl hydrazone; Ub-CR: ubiquitin with C-terminally retracted tail; CTD: C-terminal domain (of PINK1); ELISA: enzyme-linked immunosorbent assay; HCI: high-content imaging; IB: immunoblot; IF: immunofluorescence; NPC: neuronal precursor cells; MDS: molecular dynamics simulation; PD: Parkinson disease; p-S65-Ub: ubiquitin phosphorylated at Ser65; RMSF: root mean scare fluctuation; TOMM: translocase of outer mitochondrial membrane; TVLN: ubiquitin with T66V and L67N mutation, mimics Ub-CR; Ub: ubiquitin; WT: wild-type.
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Affiliation(s)
- Fabienne C Fiesel
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.,Neuroscience PhD Program, Mayo Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, USA
| | | | - Caleb S Hayes
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Mathew A Coban
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, USA
| | - Roman Hudec
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | | | | | - Tingxiang Yan
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Paige K Boneski
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Gabriella Fiorino
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.,Neuroscience PhD Program, Mayo Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, USA
| | | | - Xu Hou
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Laura J Lewis-Tuffin
- Cytometry and Imaging Laboratory, Department of Research, Mayo Clinic, Jacksonville, FL, USA
| | - Jun Zhong
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Benjamin J Madden
- Proteomics Core, Medical Genome Facility, Mayo Clinic, Rochester, MN, USA
| | - Alban Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Heeseon An
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Andreas Puschmann
- Department of Neurology, Lund University, Skane University Hospital, Sweden
| | | | - Owen A Ross
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.,Neuroscience PhD Program, Mayo Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Thomas R Caulfield
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.,Neuroscience PhD Program, Mayo Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, USA.,Department of Neurosurgery, Mayo Clinic, Jacksonville, FL, USA
| | - Wolfdieter Springer
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.,Neuroscience PhD Program, Mayo Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, USA
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12
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Mazo G, Yang N, Wang Y, Li Z, Pan H, Hendrickson R, Ordureau A, Deng L. 554 Vaccinia immune evasion ankyrin-repeat/F-box protein WR199 mediates ubiquitination and proteasomal degradation of the DNA sensor cGAS. J Invest Dermatol 2022. [DOI: 10.1016/j.jid.2022.05.564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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13
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Nam KH, Ordureau A. Quantitative proteome remodeling characterization of two human reference pluripotent stem cell lines during neurogenesis and cardiomyogenesis. Proteomics 2022; 22:e2100246. [PMID: 35871287 PMCID: PMC10389174 DOI: 10.1002/pmic.202100246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 07/05/2022] [Accepted: 07/18/2022] [Indexed: 11/08/2022]
Abstract
Human pluripotent stem cells (PSCs) have become popular tools within the research community to study developmental and model diseases. While many induced-PSCs (iPSCs) from various genetic background sources are currently available, scientific advancement has been hampered by the considerable phenotypic variations observed between different iPSC lines. A recent collaborative effort selected a novel iPSC line to address this and encourage the adoption of a standardized iPSC line termed KOLF2.1J. Here, leveraging the multiplexing power of isobaric labeling, we systematically investigate, at the 10k proteome level, the relative protein abundance profiles of the KOLF2.1J reference iPSC line upon two distinct cell state differentiation trajectories. In addition, we side-by-side systematically compare this line with the H9 line, an established embryonically derived PSC line that we previously characterized. We noticed differences in the basal proteome of the two cell lines and highlighted the differentially expressed proteins. While the difference between the cell line's proteome subsisted upon differentiation, the global proteome remodeling trajectory was highly similar during the tested differentiation routes. We thus conclude that the KOLF2.1J line performs well at the proteome level upon the neuro and cardiomyogenesis differentiation protocol used. We believe this dataset will serve as a resource of value for the research community.
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Affiliation(s)
- Ki Hong Nam
- Cell Biology Program Sloan Kettering Institute Memorial Sloan Kettering Cancer Center New York New York 10065 USA
| | - Alban Ordureau
- Cell Biology Program Sloan Kettering Institute Memorial Sloan Kettering Cancer Center New York New York 10065 USA
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14
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Goldsmith J, Ordureau A, Harper JW, Holzbaur ELF. Brain-derived autophagosome profiling reveals the engulfment of nucleoid-enriched mitochondrial fragments by basal autophagy in neurons. Neuron 2022; 110:967-976.e8. [PMID: 35051374 PMCID: PMC8930448 DOI: 10.1016/j.neuron.2021.12.029] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 10/18/2021] [Accepted: 12/16/2021] [Indexed: 12/20/2022]
Abstract
Neurons depend on autophagy to maintain cellular homeostasis, and defects in autophagy are pathological hallmarks of neurodegenerative disease. To probe the role of basal autophagy in the maintenance of neuronal health, we isolated autophagic vesicles from mouse brain tissue and used proteomics to identify the major cargos engulfed within autophagosomes, validating our findings in rodent primary and human iPSC-derived neurons. Mitochondrial proteins were identified as a major cargo in the absence of mitophagy adaptors such as OPTN. We found that nucleoid-associated proteins are enriched compared with other mitochondrial components. In the axon, autophagic engulfment of nucleoid-enriched mitochondrial fragments requires the mitochondrial fission machinery Drp1. We proposed that localized Drp1-dependent fission of nucleoid-enriched fragments in proximity to the sites of autophagosome biogenesis enhances their capture. The resulting efficient autophagic turnover of nucleoids may prevent accumulation of mitochondrial DNA in the neuron, thus mitigating activation of proinflammatory pathways that contribute to neurodegeneration.
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Affiliation(s)
- Juliet Goldsmith
- Department of Physiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Alban Ordureau
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - J Wade Harper
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Erika L F Holzbaur
- Department of Physiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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15
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Welsh KA, Bolhuis DL, Nederstigt AE, Boyer J, Temple BRS, Bonacci T, Gu L, Ordureau A, Harper JW, Steimel JP, Zhang Q, Emanuele MJ, Harrison JS, Brown NG. Functional conservation and divergence of the helix-turn-helix motif of E2 ubiquitin-conjugating enzymes. EMBO J 2021; 41:e108823. [PMID: 34942047 PMCID: PMC8804933 DOI: 10.15252/embj.2021108823] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 11/22/2021] [Accepted: 11/25/2021] [Indexed: 02/05/2023] Open
Abstract
Polyubiquitination by E2 and E3 enzymes is crucial to cell cycle control, epigenetic regulation, and development. The hallmark of the E2 family is the ubiquitin (Ub)-conjugating (UBC) domain that forms a dynamic thioester conjugate with ubiquitin (E2~Ub). Numerous studies have focused on E2 surfaces, such as the N-terminal and crossover helices, that directly interact with an E3 or the conjugated ubiquitin to stabilize the active, "closed" state of the E2~Ub. However, it remains unclear how other E2 surfaces regulate ubiquitin transfer. Here, we demonstrate the helix-turn-helix (HTH) motif of the UBC tunes the intrinsic polyubiquitination activity through distinct functions in different E2s. Interestingly, the E2HTH motif is repurposed in UBE2S and UBE2R2 to interact with the conjugated or acceptor ubiquitin, respectively, modulating ubiquitin transfer. Furthermore, we propose that Anaphase-Promoting Complex/Cyclosome binding to the UBE2SHTH reduces the conformational space of the flexible E2~Ub, demonstrating an atypical E3-dependent activation mechanism. Altogether, we postulate the E2HTH motif evolved to provide new functionalities that can be harnessed by E3s and permits additional regulation to facilitate specific E2-E3-mediated polyubiquitination.
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Affiliation(s)
- Kaeli A Welsh
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Derek L Bolhuis
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Joshua Boyer
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Brenda R S Temple
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,R L Juliano Structural Bioinformatics Core Facility, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Thomas Bonacci
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Li Gu
- Department of Chemistry, University of the Pacific, Stockton, CA, USA
| | - Alban Ordureau
- Department of Cell Biology, Blavatnik Institute of Harvard Medical School, Boston, MA, USA
| | - J Wade Harper
- Department of Cell Biology, Blavatnik Institute of Harvard Medical School, Boston, MA, USA
| | - Joshua P Steimel
- Department of Mechanical Engineering, University of the Pacific, Stockton, CA, USA
| | - Qi Zhang
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael J Emanuele
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Joseph S Harrison
- Department of Chemistry, University of the Pacific, Stockton, CA, USA
| | - Nicholas G Brown
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA
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16
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Antico O, Ordureau A, Stevens M, Singh F, Nirujogi RS, Gierlinski M, Barini E, Rickwood ML, Prescott A, Toth R, Ganley IG, Harper JW, Muqit MMK. Global ubiquitylation analysis of mitochondria in primary neurons identifies endogenous Parkin targets following activation of PINK1. Sci Adv 2021; 7:eabj0722. [PMID: 34767452 PMCID: PMC8589319 DOI: 10.1126/sciadv.abj0722] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 09/21/2021] [Indexed: 05/16/2023]
Abstract
How activation of PINK1 and Parkin leads to elimination of damaged mitochondria by mitophagy is largely based on cell lines with few studies in neurons. Here, we have undertaken proteomic analysis of mitochondria from mouse neurons to identify ubiquitylated substrates of endogenous Parkin. Comparative analysis with human iNeuron datasets revealed a subset of 49 PINK1 activation–dependent diGLY sites in 22 proteins conserved across mouse and human systems. We use reconstitution assays to demonstrate direct ubiquitylation by Parkin in vitro. We also identified a subset of cytoplasmic proteins recruited to mitochondria that undergo PINK1 and Parkin independent ubiquitylation, indicating the presence of alternate ubiquitin E3 ligase pathways that are activated by mitochondrial depolarization in neurons. Last, we have developed an online resource to search for ubiquitin sites and enzymes in mitochondria of neurons, MitoNUb. These findings will aid future studies to understand Parkin activation in neuronal subtypes.
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Affiliation(s)
- Odetta Antico
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Alban Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Michael Stevens
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Francois Singh
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Raja S. Nirujogi
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Marek Gierlinski
- Data Analysis Group, Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Erica Barini
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Mollie L. Rickwood
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Alan Prescott
- Dundee Imaging Facility, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Rachel Toth
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Ian G. Ganley
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - J. Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Miratul M. K. Muqit
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
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17
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Ordureau A, Kraus F, Zhang J, An H, Park S, Ahfeldt T, Paulo JA, Harper JW. Temporal proteomics during neurogenesis reveals large-scale proteome and organelle remodeling via selective autophagy. Mol Cell 2021; 81:5082-5098.e11. [PMID: 34699746 DOI: 10.1016/j.molcel.2021.10.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/23/2021] [Accepted: 10/01/2021] [Indexed: 12/18/2022]
Abstract
Cell state changes are associated with proteome remodeling to serve newly emergent cell functions. Here, we show that NGN2-driven conversion of human embryonic stem cells to induced neurons (iNeurons) is associated with increased PINK1-independent mitophagic flux that is temporally correlated with metabolic reprogramming to support oxidative phosphorylation. Global multiplex proteomics during neurogenesis revealed large-scale remodeling of functional modules linked with pluripotency, mitochondrial metabolism, and proteostasis. Differentiation-dependent mitophagic flux required BNIP3L and its LC3-interacting region (LIR) motif, and BNIP3L also promoted mitophagy in dopaminergic neurons. Proteomic analysis of ATG12-/- iNeurons revealed accumulation of endoplasmic reticulum, Golgi, and mitochondria during differentiation, indicative of widespread organelle remodeling during neurogenesis. This work reveals broad organelle remodeling of membrane-bound organelles during NGN2-driven neurogenesis via autophagy, identifies BNIP3L's central role in programmed mitophagic flux, and provides a proteomic resource for elucidating how organelle remodeling and autophagy alter the proteome during changes in cell state.
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Affiliation(s)
- Alban Ordureau
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
| | - Felix Kraus
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Jiuchun Zhang
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Heeseon An
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Sookhee Park
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Tim Ahfeldt
- Nash Family Department of Neuroscience at Mount Sinai, New York, NY 10029, USA; Department of Neurology at Mount Sinai, New York, NY 10029, USA; Department of Cell, Developmental and Regenerative Biology at Mount Sinai, New York, NY 10029, USA; Ronald M. Loeb Center for Alzheimer's Disease at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute at Mount Sinai, New York, NY 10029, USA; Black Family Stem Cell Institute at Mount Sinai, New York, NY 10029, USA
| | - Joao A Paulo
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - J Wade Harper
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
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18
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Ordureau A, Yu Q, Bomgarden RD, Rogers JC, Harper JW, Gygi SP, Paulo JA. Super Heavy TMTpro Labeling Reagent: An Alternative and Higher-Charge-State-Amenable Stable-Isotope-Labeled TMTpro Variant. J Proteome Res 2021; 20:3009-3013. [PMID: 33689365 DOI: 10.1021/acs.jproteome.0c01056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Stable isotope labeling is a leading strategy for mass-spectrometry-based peptide quantification. Whereas TMTpro isobaric tagging can quantify up to 16 multiplexed samples in a single experiment, nonisobaric, yet chromatographically indistinguishable, variants of TMTpro reagents can be used in conjunction with the isobaric tag series for various peptide-targeting applications. Here we test the performance of two nonisobaric TMTpro variants, a stable-isotope-free TMTproZero tag and a nearly fully isotope-labeled "super-heavy" variant, shTMTpro, in a targeted assay for peptides of charge state 4+. We label each peptide with TMTproZero or Super Heavy TMTpro reagents and separately spike each peptide into a TMTpro16-labeled background (equal amount of peptide across all 16 channels). We observe that the expected 1:1 reporter ion ratio is distorted when a TMTproZero-labeled peptide is used; however, we note no such interference when shTMTpro substitutes the TMTproZero tag. Our data suggest that using the Super Heavy TMTpro reagent is an improvement over the TMTproZero reagent for the accurate quantification of high-charge-state peptides for trigger-based multiplexed assays.
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Affiliation(s)
- Alban Ordureau
- Department of Cell Biology, Blavatnik Institute of Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Qing Yu
- Department of Cell Biology, Blavatnik Institute of Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Ryan D Bomgarden
- Thermo Fisher Scientific, Rockford, Illinois 61105, United States
| | - John C Rogers
- Thermo Fisher Scientific, Rockford, Illinois 61105, United States
| | - J Wade Harper
- Department of Cell Biology, Blavatnik Institute of Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Steven P Gygi
- Department of Cell Biology, Blavatnik Institute of Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Joao A Paulo
- Department of Cell Biology, Blavatnik Institute of Harvard Medical School, Boston, Massachusetts 02115, United States
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19
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Najafov A, Luu HS, Mookhtiar AK, Mifflin L, Xia HG, Amin PP, Ordureau A, Wang H, Yuan J. RIPK1 Promotes Energy Sensing by the mTORC1 Pathway. Mol Cell 2020; 81:370-385.e7. [PMID: 33271062 DOI: 10.1016/j.molcel.2020.11.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 08/31/2020] [Accepted: 11/04/2020] [Indexed: 02/03/2023]
Abstract
The mechanisms of cellular energy sensing and AMPK-mediated mTORC1 inhibition are not fully delineated. Here, we discover that RIPK1 promotes mTORC1 inhibition during energetic stress. RIPK1 is involved in mediating the interaction between AMPK and TSC2 and facilitate TSC2 phosphorylation at Ser1387. RIPK1 loss results in a high basal mTORC1 activity that drives defective lysosomes in cells and mice, leading to accumulation of RIPK3 and CASP8 and sensitization to cell death. RIPK1-deficient cells are unable to cope with energetic stress and are vulnerable to low glucose levels and metformin. Inhibition of mTORC1 rescues the lysosomal defects and vulnerability to energetic stress and prolongs the survival of RIPK1-deficient neonatal mice. Thus, RIPK1 plays an important role in the cellular response to low energy levels and mediates AMPK-mTORC1 signaling. These findings shed light on the regulation of mTORC1 during energetic stress and unveil a point of crosstalk between pro-survival and pro-death pathways.
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Affiliation(s)
- Ayaz Najafov
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center, Harvard Medical School, Boston, MA 02115, USA.
| | - Hoang Son Luu
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Adnan K Mookhtiar
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Lauren Mifflin
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Hong-Guang Xia
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Palak P Amin
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Alban Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Huibing Wang
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Junying Yuan
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center, Harvard Medical School, Boston, MA 02115, USA.
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20
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McKenna MJ, Sim SI, Ordureau A, Wei L, Harper JW, Shao S, Park E. The endoplasmic reticulum P5A-ATPase is a transmembrane helix dislocase. Science 2020; 369:eabc5809. [PMID: 32973005 PMCID: PMC8053355 DOI: 10.1126/science.abc5809] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 07/28/2020] [Indexed: 01/28/2023]
Abstract
Organelle identity depends on protein composition. How mistargeted proteins are selectively recognized and removed from organelles is incompletely understood. Here, we found that the orphan P5A-adenosine triphosphatase (ATPase) transporter ATP13A1 (Spf1 in yeast) directly interacted with the transmembrane segment (TM) of mitochondrial tail-anchored proteins. P5A-ATPase activity mediated the extraction of mistargeted proteins from the endoplasmic reticulum (ER). Cryo-electron microscopy structures of Saccharomyces cerevisiae Spf1 revealed a large, membrane-accessible substrate-binding pocket that alternately faced the ER lumen and cytosol and an endogenous substrate resembling an α-helical TM. Our results indicate that the P5A-ATPase could dislocate misinserted hydrophobic helices flanked by short basic segments from the ER. TM dislocation by the P5A-ATPase establishes an additional class of P-type ATPase substrates and may correct mistakes in protein targeting or topogenesis.
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Affiliation(s)
- Michael J McKenna
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Sue Im Sim
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Alban Ordureau
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Lianjie Wei
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - J Wade Harper
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Sichen Shao
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
| | - Eunyong Park
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
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21
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Sinha NK, Ordureau A, Best K, Saba JA, Zinshteyn B, Sundaramoorthy E, Fulzele A, Garshott DM, Denk T, Thoms M, Paulo JA, Harper JW, Bennett EJ, Beckmann R, Green R. EDF1 coordinates cellular responses to ribosome collisions. eLife 2020; 9:e58828. [PMID: 32744497 PMCID: PMC7486125 DOI: 10.7554/elife.58828] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 08/02/2020] [Indexed: 12/11/2022] Open
Abstract
Translation of aberrant mRNAs induces ribosomal collisions, thereby triggering pathways for mRNA and nascent peptide degradation and ribosomal rescue. Here we use sucrose gradient fractionation combined with quantitative proteomics to systematically identify proteins associated with collided ribosomes. This approach identified Endothelial differentiation-related factor 1 (EDF1) as a novel protein recruited to collided ribosomes during translational distress. Cryo-electron microscopic analyses of EDF1 and its yeast homolog Mbf1 revealed a conserved 40S ribosomal subunit binding site at the mRNA entry channel near the collision interface. EDF1 recruits the translational repressors GIGYF2 and EIF4E2 to collided ribosomes to initiate a negative-feedback loop that prevents new ribosomes from translating defective mRNAs. Further, EDF1 regulates an immediate-early transcriptional response to ribosomal collisions. Our results uncover mechanisms through which EDF1 coordinates multiple responses of the ribosome-mediated quality control pathway and provide novel insights into the intersection of ribosome-mediated quality control with global transcriptional regulation.
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Affiliation(s)
- Niladri K Sinha
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Alban Ordureau
- Department of Cell Biology, Blavatnik Institute of Harvard Medical SchoolBostonUnited States
| | - Katharina Best
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität MünchenMunichGermany
| | - James A Saba
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Boris Zinshteyn
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Elayanambi Sundaramoorthy
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San DiegoSan DiegoUnited States
| | - Amit Fulzele
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San DiegoSan DiegoUnited States
| | - Danielle M Garshott
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San DiegoSan DiegoUnited States
| | - Timo Denk
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität MünchenMunichGermany
| | - Matthias Thoms
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität MünchenMunichGermany
| | - Joao A Paulo
- Department of Cell Biology, Blavatnik Institute of Harvard Medical SchoolBostonUnited States
| | - J Wade Harper
- Department of Cell Biology, Blavatnik Institute of Harvard Medical SchoolBostonUnited States
| | - Eric J Bennett
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San DiegoSan DiegoUnited States
| | - Roland Beckmann
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität MünchenMunichGermany
| | - Rachel Green
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of MedicineBaltimoreUnited States
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Ordureau A, Paulo JA, Zhang J, An H, Swatek KN, Cannon JR, Wan Q, Komander D, Harper JW. Global Landscape and Dynamics of Parkin and USP30-Dependent Ubiquitylomes in iNeurons during Mitophagic Signaling. Mol Cell 2020; 77:1124-1142.e10. [PMID: 32142685 PMCID: PMC7098486 DOI: 10.1016/j.molcel.2019.11.013] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 08/21/2019] [Accepted: 11/08/2019] [Indexed: 12/24/2022]
Abstract
The ubiquitin ligase Parkin, protein kinase PINK1, USP30 deubiquitylase, and p97 segregase function together to regulate turnover of damaged mitochondria via mitophagy, but our mechanistic understanding in neurons is limited. Here, we combine induced neurons (iNeurons) derived from embryonic stem cells with quantitative proteomics to reveal the dynamics and specificity of Parkin-dependent ubiquitylation under endogenous expression conditions. Targets showing elevated ubiquitylation in USP30−/− iNeurons are concentrated in components of the mitochondrial translocon, and the ubiquitylation kinetics of the vast majority of Parkin targets are unaffected, correlating with a modest kinetic acceleration in accumulation of pS65-Ub and mitophagic flux upon mitochondrial depolarization without USP30. Basally, ubiquitylated translocon import substrates accumulate, suggesting a quality control function for USP30. p97 was dispensable for Parkin ligase activity in iNeurons. This work provides an unprecedented quantitative landscape of the Parkin-modified ubiquitylome in iNeurons and reveals the underlying specificity of central regulatory elements in the pathway. Global phospho and ubiquitylome analysis of PINK1-Parkin pathway in iNeurons Dynamics and specificity of Parkin-mediated ubiquitylation revealed in iNeurons p97-mediated MFN turnover not required for Parkin substrate “gating” in iNeurons USP30 acts primarily on translocon and supports import quality control in iNeurons
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Affiliation(s)
- Alban Ordureau
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Jiuchun Zhang
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Heeseon An
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Kirby N Swatek
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany; Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Joe R Cannon
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Qiaoqiao Wan
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - David Komander
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; Ubiquitin Signalling Division, The Walter and Eliza Hall Institute for Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
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23
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An H, Ordureau A, Körner M, Paulo JA, Harper JW. Systematic quantitative analysis of ribosome inventory during nutrient stress. Nature 2020; 583:303-309. [PMID: 32612236 PMCID: PMC7351614 DOI: 10.1038/s41586-020-2446-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 05/07/2020] [Indexed: 12/14/2022]
Abstract
Mammalian cells reorganize their proteomes in response to nutrient stress through translational suppression and degradative mechanisms using the proteasome and autophagy systems1,2. Ribosomes are central targets of this response, as they are responsible for translation and subject to lysosomal turnover during nutrient stress3-5. The abundance of ribosomal (r)-proteins (around 6% of the proteome; 107 copies per cell)6,7 and their high arginine and lysine content has led to the hypothesis that they are selectively used as a source of basic amino acids during nutrient stress through autophagy4,7. However, the relative contributions of translational and degradative mechanisms to the control of r-protein abundance during acute stress responses is poorly understood, as is the extent to which r-proteins are used to generate amino acids when specific building blocks are limited7. Here, we integrate quantitative global translatome and degradome proteomics8 with genetically encoded Ribo-Keima5 and Ribo-Halo reporters to interrogate r-protein homeostasis with and without active autophagy. In conditions of acute nutrient stress, cells strongly suppress the translation of r-proteins, but, notably, r-protein degradation occurs largely through non-autophagic pathways. Simultaneously, the decrease in r-protein abundance is compensated for by a reduced dilution of pre-existing ribosomes and a reduction in cell volume, thereby maintaining the density of ribosomes within single cells. Withdrawal of basic or hydrophobic amino acids induces translational repression without differential induction of ribophagy, indicating that ribophagy is not used to selectively produce basic amino acids during acute nutrient stress. We present a quantitative framework that describes the contributions of biosynthetic and degradative mechanisms to r-protein abundance and proteome remodelling in conditions of nutrient stress.
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Affiliation(s)
- Heeseon An
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Alban Ordureau
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Maria Körner
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Biochemistry, University of Würzburg, Würzburg, Germany
| | - Joao A Paulo
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - J Wade Harper
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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24
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Jacoupy M, Hamon-Keromen E, Ordureau A, Erpapazoglou Z, Coge F, Corvol JC, Nosjean O, Mannoury la Cour C, Millan MJ, Boutin JA, Harper JW, Brice A, Guedin D, Gautier CA, Corti O. The PINK1 kinase-driven ubiquitin ligase Parkin promotes mitochondrial protein import through the presequence pathway in living cells. Sci Rep 2019; 9:11829. [PMID: 31413265 PMCID: PMC6694185 DOI: 10.1038/s41598-019-47352-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 05/28/2019] [Indexed: 01/05/2023] Open
Abstract
Most of over a thousand mitochondrial proteins are encoded by nuclear genes and must be imported from the cytosol. Little is known about the cytosolic events regulating mitochondrial protein import, partly due to the lack of appropriate tools for its assessment in living cells. We engineered an inducible biosensor for monitoring the main presequence-mediated import pathway with a quantitative, luminescence-based readout. This tool was used to explore the regulation of mitochondrial import by the PINK1 kinase-driven Parkin ubiquitin ligase, which is dysfunctional in autosomal recessive Parkinson's disease. We show that mitochondrial import was stimulated by Parkin, but not by disease-causing Parkin variants. This effect was dependent on Parkin activation by PINK1 and accompanied by an increase in the abundance of K11 ubiquitin chains on mitochondria and by ubiquitylation of subunits of the translocase of outer mitochondrial membrane. Mitochondrial import efficiency was abnormally low in cells from patients with PINK1- and PARK2-linked Parkinson's disease and was restored by phosphomimetic ubiquitin in cells with residual Parkin activity. Altogether, these findings uncover a role of ubiquitylation in mitochondrial import regulation and suggest that loss of this regulatory loop may underlie the pathophysiology of Parkinson's disease, providing novel opportunities for therapeutic intervention.
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Affiliation(s)
- M Jacoupy
- Inserm, U1127, F-75013, Paris, France.,CNRS, UMR 7225, F-75013, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, F-75013, Paris, France.,Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France
| | - E Hamon-Keromen
- Inserm, U1127, F-75013, Paris, France.,CNRS, UMR 7225, F-75013, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, F-75013, Paris, France.,Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France
| | - A Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Z Erpapazoglou
- Inserm, U1127, F-75013, Paris, France.,CNRS, UMR 7225, F-75013, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, F-75013, Paris, France.,Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France
| | - F Coge
- Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France.,Laboratoire de Chémogénétique Servier, F-75013, Paris, France.,Institut de Recherches Servier, Croissy-sur-Seine, France
| | - J-C Corvol
- Inserm, U1127, F-75013, Paris, France.,CNRS, UMR 7225, F-75013, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, F-75013, Paris, France.,Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France.,Assistance-Publique Hôpitaux de Paris, Inserm, CIC-1422, Department of Neurology, Hôpital Pitié-Salpêtrière, F-75013, Paris, France
| | - O Nosjean
- Institut de Recherches Servier, Croissy-sur-Seine, France
| | | | - M J Millan
- Institut de Recherches Servier, Croissy-sur-Seine, France
| | - J A Boutin
- Institut de Recherches Servier, Croissy-sur-Seine, France
| | - J W Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - A Brice
- Inserm, U1127, F-75013, Paris, France.,CNRS, UMR 7225, F-75013, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, F-75013, Paris, France.,Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France
| | - D Guedin
- Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France.,Laboratoire de Chémogénétique Servier, F-75013, Paris, France.,Institut de Recherches Servier, Croissy-sur-Seine, France
| | - C A Gautier
- Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France. .,Laboratoire de Chémogénétique Servier, F-75013, Paris, France. .,Institut de Recherches Servier, Croissy-sur-Seine, France.
| | - O Corti
- Inserm, U1127, F-75013, Paris, France. .,CNRS, UMR 7225, F-75013, Paris, France. .,Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, F-75013, Paris, France. .,Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France.
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25
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Gottlieb CD, Thompson ACS, Ordureau A, Harper JW, Kopito RR. Acute unfolding of a single protein immediately stimulates recruitment of ubiquitin protein ligase E3C (UBE3C) to 26S proteasomes. J Biol Chem 2019; 294:16511-16524. [PMID: 31375563 DOI: 10.1074/jbc.ra119.009654] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/16/2019] [Indexed: 01/26/2023] Open
Abstract
The intracellular accumulation of aggregated misfolded proteins is a cytopathological hallmark of neurodegenerative diseases. However, the functional relationship between protein misfolding or aggregation and the cellular proteostasis network that monitors and maintains proteome health is poorly understood. Previous studies have associated translational suppression and transcriptional remodeling with the appearance of protein aggregates, but whether these responses are induced by aggregates or their misfolded monomeric or oligomeric precursors remains unclear. Because aggregation in cells is rapid, nonlinear, and asynchronous, it has not been possible to deconvolve these kinetically linked processes to determine the earliest cellular responses to misfolded proteins. Upon removal of the synthetic, biologically inert ligand shield-1 (S1), AgDD, an engineered variant FK506-binding protein (FKBP1A), rapidly (t ½ ∼5 min) unfolds and self-associates, forming detergent-insoluble, microscopic cytoplasmic aggregates. Using global diglycine-capture (K-GG) proteomics, we found here that this solubility transition is associated with immediate increases in ubiquitylation of AgDD itself, along with that of endogenous proteins that are components of the ribosome and the 26S proteasome. We also found that the earliest cellular responses to acute S1 removal include recruitment of ubiquitin protein ligase E3C (UBE3C) to the 26S proteasome and ubiquitylation of two key proteasomal ubiquitin receptors, 26S proteasome regulatory subunit RPN10 (RPN10) and Rpn13 homolog (RPN13 or ADRM1). We conclude that these proteasomal responses are due to AgDD protein misfolding and not to the presence of detergent-insoluble aggregates.
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Affiliation(s)
- Colin D Gottlieb
- Department of Biology, Stanford University, Stanford, California 94305
| | | | - Alban Ordureau
- Department of Cell Biology, Blavatnik Institute of Harvard Medical School, Boston, Massachusetts 02115
| | - J Wade Harper
- Department of Cell Biology, Blavatnik Institute of Harvard Medical School, Boston, Massachusetts 02115
| | - Ron R Kopito
- Department of Biology, Stanford University, Stanford, California 94305
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26
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Najafov A, Mookhtiar AK, Luu HS, Ordureau A, Pan H, Amin PP, Li Y, Lu Q, Yuan J. TAM Kinases Promote Necroptosis by Regulating Oligomerization of MLKL. Mol Cell 2019; 75:457-468.e4. [DOI: 10.1016/j.molcel.2019.05.022] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 04/23/2019] [Accepted: 05/13/2019] [Indexed: 01/09/2023]
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27
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Heo JM, Ordureau A, Swarup S, Paulo JA, Shen K, Sabatini DM, Harper JW. RAB7A phosphorylation by TBK1 promotes mitophagy via the PINK-PARKIN pathway. Sci Adv 2018; 4:eaav0443. [PMID: 30627666 PMCID: PMC6314648 DOI: 10.1126/sciadv.aav0443] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 10/19/2018] [Indexed: 05/09/2023]
Abstract
Removal of damaged mitochondria is orchestrated by a pathway involving the PINK1 kinase and the PARKIN ubiquitin ligase. Ubiquitin chains assembled by PARKIN on the mitochondrial outer membrane recruit autophagy cargo receptors in complexes with TBK1 protein kinase. While TBK1 is known to phosphorylate cargo receptors to promote ubiquitin binding, it is unknown whether TBK1 phosphorylates other proteins to promote mitophagy. Using global quantitative proteomics, we identified S72 in RAB7A, a RAB previously linked with mitophagy, as a dynamic target of TBK1 upon mitochondrial depolarization. TBK1 directly phosphorylates RAB7AS72, but not several other RABs known to be phosphorylated on the homologous residue by LRRK2, in vitro, and this modification requires PARKIN activity in vivo. Interaction proteomics using nonphosphorylatable and phosphomimetic RAB7A mutants revealed loss of association of RAB7AS72E with RAB GDP dissociation inhibitor and increased association with the DENN domain-containing heterodimer FLCN-FNIP1. FLCN-FNIP1 is recruited to damaged mitochondria, and this process is inhibited in cells expressing RAB7AS72A. Moreover, nonphosphorylatable RAB7A failed to support efficient mitophagy, as well as recruitment of ATG9A-positive vesicles to damaged mitochondria. These data reveal a novel function for TBK1 in mitophagy, which parallels that of LRRK2-mediated phosphorylation of the homologous site in distinct RABs to control membrane trafficking.
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Affiliation(s)
- J.-M. Heo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - A. Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - S. Swarup
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - J. A. Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - K. Shen
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - D. M. Sabatini
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - J. W. Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
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28
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Ordureau A, Paulo JA, Zhang W, Ahfeldt T, Zhang J, Cohn EF, Hou Z, Heo JM, Rubin LL, Sidhu SS, Gygi SP, Harper JW. Dynamics of PARKIN-Dependent Mitochondrial Ubiquitylation in Induced Neurons and Model Systems Revealed by Digital Snapshot Proteomics. Mol Cell 2018; 70:211-227.e8. [PMID: 29656925 DOI: 10.1016/j.molcel.2018.03.012] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 02/21/2018] [Accepted: 03/08/2018] [Indexed: 11/24/2022]
Abstract
Flux through kinase and ubiquitin-driven signaling systems depends on the modification kinetics, stoichiometry, primary site specificity, and target abundance within the pathway, yet we rarely understand these parameters and their spatial organization within cells. Here we develop temporal digital snapshots of ubiquitin signaling on the mitochondrial outer membrane in embryonic stem cell-derived neurons, and we model HeLa cell systems upon activation of the PINK1 kinase and PARKIN ubiquitin ligase by proteomic counting of ubiquitylation and phosphorylation events. We define the kinetics and site specificity of PARKIN-dependent target ubiquitylation, and we demonstrate the power of this approach to quantify pathway modulators and to mechanistically define the role of PARKIN UBL phosphorylation in pathway activation in induced neurons. Finally, through modulation of pS65-Ub on mitochondria, we demonstrate that Ub hyper-phosphorylation is inhibitory to mitophagy receptor recruitment, indicating that pS65-Ub stoichiometry in vivo is optimized to coordinate PARKIN recruitment via pS65-Ub and mitophagy receptors via unphosphorylated chains.
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Affiliation(s)
- Alban Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Wei Zhang
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, and Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, ON M5S3E1, Canada
| | - Tim Ahfeldt
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02132, USA
| | - Jiuchun Zhang
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Erin F Cohn
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Zhonggang Hou
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Jin-Mi Heo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Lee L Rubin
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02132, USA
| | - Sachdev S Sidhu
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, and Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, ON M5S3E1, Canada
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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29
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30
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Menou A, Babeanu D, Paruit HN, Ordureau A, Guillard S, Chambellan A. Normal values of offline exhaled and nasal nitric oxide in healthy children and teens using chemiluminescence. J Breath Res 2017; 11:036008. [PMID: 28579561 DOI: 10.1088/1752-7163/aa76ef] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Nitric oxide (NO) can be used to detect respiratory or ciliary diseases. Fractional exhaled nitric oxide (FeNO) measurement can reflect ongoing eosinophilic airway inflammation and has a diagnostic utility as a test for asthma screening and follow-up while nasal nitric oxide (nNO) is a valuable screening tool for the diagnosis of primary ciliary dyskinesia. The possibility of collecting airway gas samples in an offline manner offers the advantage to extend these measures and improve the screening and management of these diseases, but normal values from healthy children and teens remain sparse. METHODS Samples were consecutively collected using the offline method for eNO and nNO chemiluminescence measurement in 88 and 31 healthy children and teens, respectively. Offline eNO measurement was also performed in 30 consecutive children with naïve asthma and/or respiratory allergy. RESULTS The normal offline eNO value was determined by the following regression equation -8.206 + 0.176 × height. The upper limit of the norm for the offline eNO value was 27.4 parts per billion (ppb). A separate analysis was performed in children, pre-teens and teens, for which offline eNO was 13.6 ± 4.7 ppb, 16.3 ± 13.7 ppb and 20.0 ± 7.2 ppb, respectively. The optimal cut-off value of the offline eNO to predict asthma or respiratory allergies was 23.3 ppb, with a sensitivity and specificity of 77% and 91%, respectively. Mean offline nNO was determined at 660 ppb with the lower limit of the norm at 197 ppb. CONCLUSION The use of offline eNO and nNO normal values should favour the widespread screening of respiratory diseases in children of school age in their usual environment.
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Affiliation(s)
- A Menou
- Faculte des Sciences, Université de Nantes, Nantes, France
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31
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Mohideen F, Paulo JA, Ordureau A, Gygi SP, Harper JW. Quantitative Phospho-proteomic Analysis of TNFα/NFκB Signaling Reveals a Role for RIPK1 Phosphorylation in Suppressing Necrotic Cell Death. Mol Cell Proteomics 2017; 16:1200-1216. [PMID: 28539327 DOI: 10.1074/mcp.m117.068189] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 04/24/2017] [Indexed: 12/19/2022] Open
Abstract
TNFα is a potent inducer of inflammation due to its ability to promote gene expression, in part via the NFκB pathway. Moreover, in some contexts, TNFα promotes Caspase-dependent apoptosis or RIPK1/RIPK3/MLKL-dependent necrosis. Engagement of the TNF Receptor Signaling Complex (TNF-RSC), which contains multiple kinase activities, promotes phosphorylation of several downstream components, including TAK1, IKKα/IKKβ, IκBα, and NFκB. However, immediate downstream phosphorylation events occurring in response to TNFα signaling are poorly understood at a proteome-wide level. Here we use Tandem Mass Tagging-based proteomics to quantitatively characterize acute TNFα-mediated alterations in the proteome and phosphoproteome with or without inhibition of the cIAP-dependent survival arm of the pathway with a SMAC mimetic. We identify and quantify over 8,000 phosphorylated peptides, among which are numerous known sites in the TNF-RSC, NFκB, and MAP kinase signaling systems, as well as numerous previously unrecognized phosphorylation events. Functional analysis of S320 phosphorylation in RIPK1 demonstrates a role for this event in suppressing its kinase activity, association with CASPASE-8 and FADD proteins, and subsequent necrotic cell death during inflammatory TNFα stimulation. This study provides a resource for further elucidation of TNFα-dependent signaling pathways.
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Affiliation(s)
- Firaz Mohideen
- From the ‡Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Joao A Paulo
- From the ‡Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Alban Ordureau
- From the ‡Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Steve P Gygi
- From the ‡Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - J Wade Harper
- From the ‡Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
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32
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Wang B, Jie Z, Joo D, Ordureau A, Liu P, Gan W, Guo J, Zhang J, North BJ, Dai X, Cheng X, Bian X, Zhang L, Harper JW, Sun SC, Wei W. TRAF2 and OTUD7B govern a ubiquitin-dependent switch that regulates mTORC2 signalling. Nature 2017; 545:365-369. [PMID: 28489822 DOI: 10.1038/nature22344] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 04/04/2017] [Indexed: 12/25/2022]
Abstract
The mechanistic target of rapamycin (mTOR) has a key role in the integration of various physiological stimuli to regulate several cell growth and metabolic pathways. mTOR primarily functions as a catalytic subunit in two structurally related but functionally distinct multi-component kinase complexes, mTOR complex 1 (mTORC1) and mTORC2 (refs 1, 2). Dysregulation of mTOR signalling is associated with a variety of human diseases, including metabolic disorders and cancer. Thus, both mTORC1 and mTORC2 kinase activity is tightly controlled in cells. mTORC1 is activated by both nutrients and growth factors, whereas mTORC2 responds primarily to extracellular cues such as growth-factor-triggered activation of PI3K signalling. Although both mTOR and GβL (also known as MLST8) assemble into mTORC1 and mTORC2 (refs 11, 12, 13, 14, 15), it remains largely unclear what drives the dynamic assembly of these two functionally distinct complexes. Here we show, in humans and mice, that the K63-linked polyubiquitination status of GβL dictates the homeostasis of mTORC2 formation and activation. Mechanistically, the TRAF2 E3 ubiquitin ligase promotes K63-linked polyubiquitination of GβL, which disrupts its interaction with the unique mTORC2 component SIN1 (refs 12, 13, 14) to favour mTORC1 formation. By contrast, the OTUD7B deubiquitinase removes polyubiquitin chains from GβL to promote GβL interaction with SIN1, facilitating mTORC2 formation in response to various growth signals. Moreover, loss of critical ubiquitination residues in GβL, by either K305R/K313R mutations or a melanoma-associated GβL(ΔW297) truncation, leads to elevated mTORC2 formation, which facilitates tumorigenesis, in part by activating AKT oncogenic signalling. In support of a physiologically pivotal role for OTUD7B in the activation of mTORC2/AKT signalling, genetic deletion of Otud7b in mice suppresses Akt activation and Kras-driven lung tumorigenesis in vivo. Collectively, our study reveals a GβL-ubiquitination-dependent switch that fine-tunes the dynamic organization and activation of the mTORC2 kinase under both physiological and pathological conditions.
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Affiliation(s)
- Bin Wang
- Department of Gastroenterology, Institute of Surgery Research, Daping Hospital, Third Military Medical University, Chongqing 400042, China.,Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Zuliang Jie
- Department of Immunology, The University of Texas MD Anderson Cancer Center, 7455 Fannin Street, Box 902, Houston, Texas 77030, USA
| | - Donghyun Joo
- Department of Immunology, The University of Texas MD Anderson Cancer Center, 7455 Fannin Street, Box 902, Houston, Texas 77030, USA
| | - Alban Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Pengda Liu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Wenjian Gan
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Jianping Guo
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Jinfang Zhang
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Brian J North
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Xiangpeng Dai
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Xuhong Cheng
- Department of Immunology, The University of Texas MD Anderson Cancer Center, 7455 Fannin Street, Box 902, Houston, Texas 77030, USA
| | - Xiuwu Bian
- Institute of Pathology and Southwest Cancer Center and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Lingqiang Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Collaborative Innovation Center for Cancer Medicine, Beijing 100850, China
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Shao-Cong Sun
- Department of Immunology, The University of Texas MD Anderson Cancer Center, 7455 Fannin Street, Box 902, Houston, Texas 77030, USA
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
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33
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Liu L, Michowski W, Inuzuka H, Shimizu K, Nihira NT, Chick JM, Li N, Geng Y, Meng AY, Ordureau A, Kołodziejczyk A, Ligon KL, Bronson RT, Polyak K, Harper JW, Gygi SP, Wei W, Sicinski P. G1 cyclins link proliferation, pluripotency and differentiation of embryonic stem cells. Nat Cell Biol 2017; 19:177-188. [PMID: 28192421 DOI: 10.1038/ncb3474] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 01/16/2017] [Indexed: 12/13/2022]
Abstract
Progression of mammalian cells through the G1 and S phases of the cell cycle is driven by the D-type and E-type cyclins. According to the current models, at least one of these cyclin families must be present to allow cell proliferation. Here, we show that several cell types can proliferate in the absence of all G1 cyclins. However, following ablation of G1 cyclins, embryonic stem (ES) cells attenuated their pluripotent characteristics, with the majority of cells acquiring the trophectodermal cell fate. We established that G1 cyclins, together with their associated cyclin-dependent kinases (CDKs), phosphorylate and stabilize the core pluripotency factors Nanog, Sox2 and Oct4. Treatment of murine ES cells, patient-derived glioblastoma tumour-initiating cells, or triple-negative breast cancer cells with a CDK inhibitor strongly decreased Sox2 and Oct4 levels. Our findings suggest that CDK inhibition might represent an attractive therapeutic strategy by targeting glioblastoma tumour-initiating cells, which depend on Sox2 to maintain their tumorigenic potential.
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Affiliation(s)
- Lijun Liu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Wojciech Michowski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Hiroyuki Inuzuka
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Kouhei Shimizu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Naoe Taira Nihira
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Joel M Chick
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Na Li
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Yan Geng
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Alice Y Meng
- Department of Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Alban Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Aleksandra Kołodziejczyk
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Keith L Ligon
- Department of Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02215, USA
| | - Roderick T Bronson
- Department of Biomedical Sciences, Tufts University Veterinary School, North Grafton, Massachusetts 01536, USA
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Piotr Sicinski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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34
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Brown NG, VanderLinden R, Watson ER, Weissmann F, Ordureau A, Wu KP, Zhang W, Yu S, Mercredi PY, Harrison JS, Davidson IF, Qiao R, Lu Y, Dube P, Brunner MR, Grace CRR, Miller DJ, Haselbach D, Jarvis MA, Yamaguchi M, Yanishevski D, Petzold G, Sidhu SS, Kuhlman B, Kirschner MW, Harper JW, Peters JM, Stark H, Schulman BA. Dual RING E3 Architectures Regulate Multiubiquitination and Ubiquitin Chain Elongation by APC/C. Cell 2016; 165:1440-1453. [PMID: 27259151 DOI: 10.1016/j.cell.2016.05.037] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 04/16/2016] [Accepted: 05/09/2016] [Indexed: 11/25/2022]
Abstract
Protein ubiquitination involves E1, E2, and E3 trienzyme cascades. E2 and RING E3 enzymes often collaborate to first prime a substrate with a single ubiquitin (UB) and then achieve different forms of polyubiquitination: multiubiquitination of several sites and elongation of linkage-specific UB chains. Here, cryo-EM and biochemistry show that the human E3 anaphase-promoting complex/cyclosome (APC/C) and its two partner E2s, UBE2C (aka UBCH10) and UBE2S, adopt specialized catalytic architectures for these two distinct forms of polyubiquitination. The APC/C RING constrains UBE2C proximal to a substrate and simultaneously binds a substrate-linked UB to drive processive multiubiquitination. Alternatively, during UB chain elongation, the RING does not bind UBE2S but rather lures an evolving substrate-linked UB to UBE2S positioned through a cullin interaction to generate a Lys11-linked chain. Our findings define mechanisms of APC/C regulation, and establish principles by which specialized E3-E2-substrate-UB architectures control different forms of polyubiquitination.
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Affiliation(s)
- Nicholas G Brown
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ryan VanderLinden
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Howard Hughes Medical Institute, Memphis, TN 38105, USA
| | - Edmond R Watson
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Florian Weissmann
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Alban Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Kuen-Phon Wu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Wei Zhang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
| | - Shanshan Yu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Peter Y Mercredi
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Joseph S Harrison
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Iain F Davidson
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Renping Qiao
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Ying Lu
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Prakash Dube
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Michael R Brunner
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Christy R R Grace
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Darcie J Miller
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - David Haselbach
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Marc A Jarvis
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Masaya Yamaguchi
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - David Yanishevski
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Georg Petzold
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Sachdev S Sidhu
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Marc W Kirschner
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria.
| | - Holger Stark
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
| | - Brenda A Schulman
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Howard Hughes Medical Institute, Memphis, TN 38105, USA.
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35
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Rose CM, Isasa M, Ordureau A, Prado MA, Beausoleil SA, Jedrychowski MP, Finley DJ, Harper JW, Gygi SP. Highly Multiplexed Quantitative Mass Spectrometry Analysis of Ubiquitylomes. Cell Syst 2016; 3:395-403.e4. [PMID: 27667366 DOI: 10.1016/j.cels.2016.08.009] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 06/21/2016] [Accepted: 08/05/2016] [Indexed: 12/26/2022]
Abstract
System-wide quantitative analysis of ubiquitylomes has proven to be a valuable tool for elucidating targets and mechanisms of the ubiquitin-driven signaling systems, as well as gaining insights into neurodegenerative diseases and cancer. Current mass spectrometry methods for ubiquitylome detection require large amounts of starting material and rely on stochastic data collection to increase replicate analyses. We describe a method compatible with cell line and tissue samples for large-scale quantification of 5,000-9,000 ubiquitylation forms across ten samples simultaneously. Using this method, we reveal site-specific ubiquitylation in mammalian brain and liver tissues, as well as in cancer cells undergoing proteasome inhibition. To demonstrate the power of the approach for signal-dependent ubiquitylation, we examined protein and ubiquitylation dynamics for mitochondria undergoing PARKIN- and PINK1-dependent mitophagy. This analysis revealed the largest collection of PARKIN- and PINK1-dependent ubiquitylation targets to date in a single experiment, and it also revealed a subset of proteins recruited to the mitochondria during mitophagy.
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Affiliation(s)
- Christopher M Rose
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Marta Isasa
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Alban Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Miguel A Prado
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | | | - Daniel J Finley
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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36
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Zhang W, Wu KP, Sartori MA, Kamadurai HB, Ordureau A, Jiang C, Mercredi PY, Murchie R, Hu J, Persaud A, Mukherjee M, Li N, Doye A, Walker JR, Sheng Y, Hao Z, Li Y, Brown KR, Lemichez E, Chen J, Tong Y, Harper JW, Moffat J, Rotin D, Schulman BA, Sidhu SS. System-Wide Modulation of HECT E3 Ligases with Selective Ubiquitin Variant Probes. Mol Cell 2016; 62:121-36. [PMID: 26949039 DOI: 10.1016/j.molcel.2016.02.005] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 01/23/2016] [Accepted: 02/03/2016] [Indexed: 11/20/2022]
Abstract
HECT-family E3 ligases ubiquitinate protein substrates to control virtually every eukaryotic process and are misregulated in numerous diseases. Nonetheless, understanding of HECT E3s is limited by a paucity of selective and potent modulators. To overcome this challenge, we systematically developed ubiquitin variants (UbVs) that inhibit or activate HECT E3s. Structural analysis of 6 HECT-UbV complexes revealed UbV inhibitors hijacking the E2-binding site and activators occupying a ubiquitin-binding exosite. Furthermore, UbVs unearthed distinct regulation mechanisms among NEDD4 subfamily HECTs and proved useful for modulating therapeutically relevant targets of HECT E3s in cells and intestinal organoids, and in a genetic screen that identified a role for NEDD4L in regulating cell migration. Our work demonstrates versatility of UbVs for modulating activity across an E3 family, defines mechanisms and provides a toolkit for probing functions of HECT E3s, and establishes a general strategy for systematic development of modulators targeting families of signaling proteins.
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Affiliation(s)
- Wei Zhang
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, ON M5S3E1, Canada
| | - Kuen-Phon Wu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Maria A Sartori
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, ON M5S3E1, Canada
| | - Hari B Kamadurai
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Alban Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Chong Jiang
- Program in Cell Biology, Hospital for Sick Children, and Department of Biochemistry, University of Toronto, Toronto, ON M5G 0A4, Canada
| | - Peter Y Mercredi
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ryan Murchie
- Program in Cell Biology, Hospital for Sick Children, and Department of Biochemistry, University of Toronto, Toronto, ON M5G 0A4, Canada
| | - Jicheng Hu
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G1L7, Canada
| | - Avinash Persaud
- Program in Cell Biology, Hospital for Sick Children, and Department of Biochemistry, University of Toronto, Toronto, ON M5G 0A4, Canada
| | - Manjeet Mukherjee
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Nan Li
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA
| | - Anne Doye
- Inserm U1065, Centre Méditerranéen de Médecine Moléculaire, C3M, Equipe Labellisée La Ligue Contre Le Cancer, Université de Nice-Sophia Antipolis, 151 Route St Antoine de Ginestière, BP 2 3194, 06204 Nice Cedex, France
| | - John R Walker
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G1L7, Canada
| | - Yi Sheng
- Department of Biology, York University, Toronto, Ontario M3J1P3, Canada
| | - Zhenyue Hao
- Campbell Family Cancer Research Institute, University Health Network, Toronto, ON M5G2C1, Canada
| | - Yanjun Li
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G1L7, Canada
| | - Kevin R Brown
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, ON M5S3E1, Canada
| | - Emmanuel Lemichez
- Inserm U1065, Centre Méditerranéen de Médecine Moléculaire, C3M, Equipe Labellisée La Ligue Contre Le Cancer, Université de Nice-Sophia Antipolis, 151 Route St Antoine de Ginestière, BP 2 3194, 06204 Nice Cedex, France
| | - Junjie Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA
| | - Yufeng Tong
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G1L7, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5G1L7, Canada
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Jason Moffat
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, ON M5S3E1, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Cir, Toronto, ON M5S1A8, Canada
| | - Daniela Rotin
- Program in Cell Biology, Hospital for Sick Children, and Department of Biochemistry, University of Toronto, Toronto, ON M5G 0A4, Canada
| | - Brenda A Schulman
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Howard Hughes Medical Institute, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| | - Sachdev S Sidhu
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, ON M5S3E1, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Cir, Toronto, ON M5S1A8, Canada.
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37
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Huttlin EL, Ting L, Bruckner RJ, Gebreab F, Gygi MP, Szpyt J, Tam S, Zarraga G, Colby G, Baltier K, Dong R, Guarani V, Vaites LP, Ordureau A, Rad R, Erickson BK, Wühr M, Chick J, Zhai B, Kolippakkam D, Mintseris J, Obar RA, Harris T, Artavanis-Tsakonas S, Sowa ME, De Camilli P, Paulo JA, Harper JW, Gygi SP. The BioPlex Network: A Systematic Exploration of the Human Interactome. Cell 2015; 162:425-440. [PMID: 26186194 DOI: 10.1016/j.cell.2015.06.043] [Citation(s) in RCA: 963] [Impact Index Per Article: 107.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 03/04/2015] [Accepted: 06/12/2015] [Indexed: 01/05/2023]
Abstract
Protein interactions form a network whose structure drives cellular function and whose organization informs biological inquiry. Using high-throughput affinity-purification mass spectrometry, we identify interacting partners for 2,594 human proteins in HEK293T cells. The resulting network (BioPlex) contains 23,744 interactions among 7,668 proteins with 86% previously undocumented. BioPlex accurately depicts known complexes, attaining 80%-100% coverage for most CORUM complexes. The network readily subdivides into communities that correspond to complexes or clusters of functionally related proteins. More generally, network architecture reflects cellular localization, biological process, and molecular function, enabling functional characterization of thousands of proteins. Network structure also reveals associations among thousands of protein domains, suggesting a basis for examining structurally related proteins. Finally, BioPlex, in combination with other approaches, can be used to reveal interactions of biological or clinical significance. For example, mutations in the membrane protein VAPB implicated in familial amyotrophic lateral sclerosis perturb a defined community of interactors.
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Affiliation(s)
- Edward L Huttlin
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Lily Ting
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Raphael J Bruckner
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Fana Gebreab
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Melanie P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - John Szpyt
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Stanley Tam
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Gabriela Zarraga
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Greg Colby
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Kurt Baltier
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Rui Dong
- Department of Cell Biology and Howard Hughes Medical Institute, Yale School of Medicine, New Haven, CT 06519, USA
| | - Virginia Guarani
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Alban Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Ramin Rad
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Brian K Erickson
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Martin Wühr
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Joel Chick
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Bo Zhai
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Deepak Kolippakkam
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Julian Mintseris
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Robert A Obar
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Biogen, Cambridge, MA 02142, USA
| | | | - Spyros Artavanis-Tsakonas
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Biogen, Cambridge, MA 02142, USA
| | - Mathew E Sowa
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Pietro De Camilli
- Department of Cell Biology and Howard Hughes Medical Institute, Yale School of Medicine, New Haven, CT 06519, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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38
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Pickrell AM, Huang CH, Kennedy SR, Ordureau A, Sideris DP, Hoekstra JG, Harper JW, Youle RJ. Endogenous Parkin Preserves Dopaminergic Substantia Nigral Neurons following Mitochondrial DNA Mutagenic Stress. Neuron 2015; 87:371-81. [PMID: 26182419 DOI: 10.1016/j.neuron.2015.06.034] [Citation(s) in RCA: 239] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 06/03/2015] [Accepted: 06/24/2015] [Indexed: 12/30/2022]
Abstract
Parkinson's disease (PD) is a neurodegenerative disease caused by the loss of dopaminergic neurons in the substantia nigra. PARK2 mutations cause early-onset forms of PD. PARK2 encodes an E3 ubiquitin ligase, Parkin, that can selectively translocate to dysfunctional mitochondria to promote their removal by autophagy. However, Parkin knockout (KO) mice do not display signs of neurodegeneration. To assess Parkin function in vivo, we utilized a mouse model that accumulates dysfunctional mitochondria caused by an accelerated generation of mtDNA mutations (Mutator mice). In the absence of Parkin, dopaminergic neurons in Mutator mice degenerated causing an L-DOPA reversible motor deficit. Other neuronal populations were unaffected. Phosphorylated ubiquitin was increased in the brains of Mutator mice, indicating PINK1-Parkin activation. Parkin loss caused mitochondrial dysfunction and affected the pathogenicity but not the levels of mtDNA somatic mutations. A systemic loss of Parkin synergizes with mitochondrial dysfunction causing dopaminergic neuron death modeling PD pathogenic processes.
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Affiliation(s)
- Alicia M Pickrell
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chiu-Hui Huang
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Scott R Kennedy
- Department of Pathology, University of Washington, Seattle, WA 98104, USA
| | - Alban Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Dionisia P Sideris
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jake G Hoekstra
- Department of Pathology, University of Washington, Seattle, WA 98104, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Richard J Youle
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA.
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Heo JM, Ordureau A, Paulo JA, Rinehart J, Harper JW. The PINK1-PARKIN Mitochondrial Ubiquitylation Pathway Drives a Program of OPTN/NDP52 Recruitment and TBK1 Activation to Promote Mitophagy. Mol Cell 2015; 60:7-20. [PMID: 26365381 DOI: 10.1016/j.molcel.2015.08.016] [Citation(s) in RCA: 585] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 08/12/2015] [Accepted: 08/19/2015] [Indexed: 12/22/2022]
Abstract
Damaged mitochondria are detrimental to cellular homeostasis. One mechanism for removal of damaged mitochondria involves the PINK1-PARKIN pathway, which poly-ubiquitylates damaged mitochondria to promote mitophagy. We report that assembly of ubiquitin chains on mitochondria triggers autophagy adaptor recruitment concomitantly with activation of the TBK1 kinase, which physically associates with OPTN, NDP52, and SQSTM1. TBK1 activation in HeLa cells requires OPTN and NDP52 and OPTN ubiquitin chain binding. In addition to the known role of S177 phosphorylation in OPTN on ATG8 recruitment, TBK1-dependent phosphorylation on S473 and S513 promotes ubiquitin chain binding in vitro as well as TBK1 activation, OPTN mitochondrial retention, and efficient mitophagy in vivo. These data reveal a self-reinforcing positive feedback mechanism that coordinates TBK1-dependent autophagy adaptor phosphorylation with the assembly of ubiquitin chains on mitochondria to facilitate efficient mitophagy, and mechanistically links genes mutated in Parkinson's disease and amyotrophic lateral sclerosis in a common selective autophagy pathway.
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Affiliation(s)
- Jin-Mi Heo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Alban Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Jesse Rinehart
- Department of Cellular & Molecular Physiology, Systems Biology Institute, Yale University School of Medicine, New Haven, CT 06520, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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40
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Abstract
Ubiquitin (UB)-driven signaling systems permeate biology, and are often integrated with other types of post-translational modifications (PTMs), including phosphorylation. Flux through such pathways is dictated by the fractional stoichiometry of distinct modifications and protein assemblies as well as the spatial organization of pathway components. Yet, we rarely understand the dynamics and stoichiometry of rate-limiting intermediates along a reaction trajectory. Here, we review how quantitative proteomic tools and enrichment strategies are being used to quantify UB-dependent signaling systems, and to integrate UB signaling with regulatory phosphorylation events, illustrated with the PINK1/PARKIN pathway. A key feature of ubiquitylation is that the identity of UB chain linkage types can control downstream processes. We also describe how proteomic and enzymological tools can be used to identify and quantify UB chain synthesis and linkage preferences. The emergence of sophisticated quantitative proteomic approaches will set a new standard for elucidating biochemical mechanisms of UB-driven signaling systems.
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Affiliation(s)
- Alban Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Christian Münch
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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41
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Cirulli ET, Lasseigne BN, Petrovski S, Sapp PC, Dion PA, Leblond CS, Couthouis J, Lu YF, Wang Q, Krueger BJ, Ren Z, Keebler J, Han Y, Levy SE, Boone BE, Wimbish JR, Waite LL, Jones AL, Carulli JP, Day-Williams AG, Staropoli JF, Xin WW, Chesi A, Raphael AR, McKenna-Yasek D, Cady J, Vianney de Jong JMB, Kenna KP, Smith BN, Topp S, Miller J, Gkazi A, Al-Chalabi A, van den Berg LH, Veldink J, Silani V, Ticozzi N, Shaw CE, Baloh RH, Appel S, Simpson E, Lagier-Tourenne C, Pulst SM, Gibson S, Trojanowski JQ, Elman L, McCluskey L, Grossman M, Shneider NA, Chung WK, Ravits JM, Glass JD, Sims KB, Van Deerlin VM, Maniatis T, Hayes SD, Ordureau A, Swarup S, Landers J, Baas F, Allen AS, Bedlack RS, Harper JW, Gitler AD, Rouleau GA, Brown R, Harms MB, Cooper GM, Harris T, Myers RM, Goldstein DB. Exome sequencing in amyotrophic lateral sclerosis identifies risk genes and pathways. Science 2015; 347:1436-41. [PMID: 25700176 DOI: 10.1126/science.aaa3650] [Citation(s) in RCA: 703] [Impact Index Per Article: 78.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating neurological disease with no effective treatment. We report the results of a moderate-scale sequencing study aimed at increasing the number of genes known to contribute to predisposition for ALS. We performed whole-exome sequencing of 2869 ALS patients and 6405 controls. Several known ALS genes were found to be associated, and TBK1 (the gene encoding TANK-binding kinase 1) was identified as an ALS gene. TBK1 is known to bind to and phosphorylate a number of proteins involved in innate immunity and autophagy, including optineurin (OPTN) and p62 (SQSTM1/sequestosome), both of which have also been implicated in ALS. These observations reveal a key role of the autophagic pathway in ALS and suggest specific targets for therapeutic intervention.
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Affiliation(s)
- Elizabeth T Cirulli
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC 27708, USA
| | | | - Slavé Petrovski
- Institute for Genomic Medicine, Columbia University, New York, NY 10032, USA
| | - Peter C Sapp
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Patrick A Dion
- Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Claire S Leblond
- Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Julien Couthouis
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yi-Fan Lu
- Institute for Genomic Medicine, Columbia University, New York, NY 10032, USA
| | - Quanli Wang
- Institute for Genomic Medicine, Columbia University, New York, NY 10032, USA
| | - Brian J Krueger
- Institute for Genomic Medicine, Columbia University, New York, NY 10032, USA
| | - Zhong Ren
- Institute for Genomic Medicine, Columbia University, New York, NY 10032, USA
| | | | - Yujun Han
- Duke University School of Medicine, Durham, NC 27708, USA
| | - Shawn E Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Braden E Boone
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Jack R Wimbish
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Lindsay L Waite
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Angela L Jones
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | | | | | | - Winnie W Xin
- Neurogenetics DNA Diagnostic Laboratory, Center for Human Genetics Research, Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Alessandra Chesi
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alya R Raphael
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Diane McKenna-Yasek
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Janet Cady
- Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - J M B Vianney de Jong
- Department of Genome Analysis, Academic Medical Center, Meibergdreef 9, 1105AZ Amsterdam, Netherlands
| | - Kevin P Kenna
- Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Republic of Ireland
| | - Bradley N Smith
- Department of Basic and Clinical Neuroscience, King's College London, Institute of Psychiatry, Psychology and Neuroscience, London SE5 8AF, UK
| | - Simon Topp
- Department of Basic and Clinical Neuroscience, King's College London, Institute of Psychiatry, Psychology and Neuroscience, London SE5 8AF, UK
| | - Jack Miller
- Department of Basic and Clinical Neuroscience, King's College London, Institute of Psychiatry, Psychology and Neuroscience, London SE5 8AF, UK
| | - Athina Gkazi
- Department of Basic and Clinical Neuroscience, King's College London, Institute of Psychiatry, Psychology and Neuroscience, London SE5 8AF, UK
| | | | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, King's College London, Institute of Psychiatry, Psychology and Neuroscience, London SE5 8AF, UK
| | - Leonard H van den Berg
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Centre Utrecht, 3508 GA Utrecht, Netherlands
| | - Jan Veldink
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Centre Utrecht, 3508 GA Utrecht, Netherlands
| | - Vincenzo Silani
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan 20149, Italy, and Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan 20122, Italy
| | - Nicola Ticozzi
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan 20149, Italy, and Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan 20122, Italy
| | - Christopher E Shaw
- Department of Basic and Clinical Neuroscience, King's College London, Institute of Psychiatry, Psychology and Neuroscience, London SE5 8AF, UK
| | | | - Stanley Appel
- Houston Methodist Hospital, Houston, TX 77030, USA, and Weill Cornell Medical College of Cornell University, New York, NY 10065, USA
| | - Ericka Simpson
- Houston Methodist Hospital, Houston, TX 77030, USA, and Weill Cornell Medical College of Cornell University, New York, NY 10065, USA
| | - Clotilde Lagier-Tourenne
- Ludwig Institute for Cancer Research and Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Stefan M Pulst
- Department of Neurology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Summer Gibson
- Department of Neurology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - John Q Trojanowski
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lauren Elman
- Department of Neurology, Penn ALS Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Leo McCluskey
- Department of Neurology, Penn ALS Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Murray Grossman
- Department of Neurology, Penn Frontotemporal Degeneration Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Neil A Shneider
- Department of Neurology, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
| | - Wendy K Chung
- Department of Pediatrics and Medicine, Columbia University, New York, NY 10032, USA
| | - John M Ravits
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jonathan D Glass
- Department of Neurology, Emory University, Atlanta, GA 30322, USA
| | - Katherine B Sims
- Neurogenetics DNA Diagnostic Laboratory, Center for Human Genetics Research, Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Vivianna M Van Deerlin
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Tom Maniatis
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10027, USA
| | - Sebastian D Hayes
- Biogen Idec, Cambridge, MA 02142, USA. Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Alban Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Sharan Swarup
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - John Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Frank Baas
- Department of Genome Analysis, Academic Medical Center, Meibergdreef 9, 1105AZ Amsterdam, Netherlands
| | - Andrew S Allen
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC 27708, USA
| | | | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Aaron D Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Guy A Rouleau
- Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Robert Brown
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Matthew B Harms
- Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University, New York, NY 10032, USA
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42
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Ordureau A, Sarraf S, Duda D, Heo JM, Jedrychowski M, Sviderskiy V, Olszewski J, Koerber J, Xie T, Beausoleil S, Wells J, Gygi S, Schulman B, Harper J. Quantitative Proteomics Reveal a Feedforward Model for Mitochondrial PARKIN Translocation and Ubiquitin Chain Synthesis. Mol Cell 2014. [DOI: 10.1016/j.molcel.2014.10.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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43
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Li N, Fassl A, Chick J, Inuzuka H, Li X, Mansour MR, Liu L, Wang H, King B, Shaik S, Gutierrez A, Ordureau A, Otto T, Kreslavsky T, Baitsch L, Bury L, Meyer CA, Ke N, Mulry KA, Kluk MJ, Roy M, Kim S, Zhang X, Geng Y, Zagozdzon A, Jenkinson S, Gale RE, Linch DC, Zhao JJ, Mullighan CG, Harper JW, Aster JC, Aifantis I, von Boehmer H, Gygi SP, Wei W, Look AT, Sicinski P. Cyclin C is a haploinsufficient tumour suppressor. Nat Cell Biol 2014; 16:1080-91. [PMID: 25344755 PMCID: PMC4235773 DOI: 10.1038/ncb3046] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 08/29/2014] [Indexed: 12/12/2022]
Abstract
Cyclin C was cloned as a growth-promoting G1 cyclin, and was also shown to regulate gene transcription. Here we report that in vivo cyclin C acts as a haploinsufficient tumour suppressor, by controlling Notch1 oncogene levels. Cyclin C activates an 'orphan' CDK19 kinase, as well as CDK8 and CDK3. These cyclin-C-CDK complexes phosphorylate the Notch1 intracellular domain (ICN1) and promote ICN1 degradation. Genetic ablation of cyclin C blocks ICN1 phosphorylation in vivo, thereby elevating ICN1 levels in cyclin-C-knockout mice. Cyclin C ablation or heterozygosity collaborates with other oncogenic lesions and accelerates development of T-cell acute lymphoblastic leukaemia (T-ALL). Furthermore, the cyclin C encoding gene CCNC is heterozygously deleted in a significant fraction of human T-ALLs, and these tumours express reduced cyclin C levels. We also describe point mutations in human T-ALL that render cyclin-C-CDK unable to phosphorylate ICN1. Hence, tumour cells may develop different strategies to evade inhibition by cyclin C.
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Affiliation(s)
- Na Li
- Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Anne Fassl
- Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Joel Chick
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Hiroyuki Inuzuka
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Xiaoyu Li
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, and Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Marc R. Mansour
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Division of Hematology/ Oncology, Children's Hospital, Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02215, USA
- Department of Haematology, University College London Cancer Institute, London WC1E 6BT, UK
| | - Lijun Liu
- Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Haizhen Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Bryan King
- Howard Hughes Medical Institute and Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
| | - Shavali Shaik
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Alejandro Gutierrez
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Division of Hematology/ Oncology, Children's Hospital, Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Alban Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Tobias Otto
- Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Taras Kreslavsky
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, and Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Lukas Baitsch
- Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Leah Bury
- Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Clifford A. Meyer
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02115, USA
| | - Nan Ke
- Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Kristin A. Mulry
- Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Michael J. Kluk
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Moni Roy
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Sunkyu Kim
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, USA
| | - Xiaowu Zhang
- Cell Signaling Technology, Inc., Danvers MA 01923, USA
| | - Yan Geng
- Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Agnieszka Zagozdzon
- Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Sarah Jenkinson
- Department of Haematology, University College London Cancer Institute, London WC1E 6BT, UK
| | - Rosemary E. Gale
- Department of Haematology, University College London Cancer Institute, London WC1E 6BT, UK
| | - David C. Linch
- Department of Haematology, University College London Cancer Institute, London WC1E 6BT, UK
| | - Jean J. Zhao
- Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Charles G. Mullighan
- Department of Pathology, St. Jude Research Hospital, Memphis, Tennessee 38105, USA
| | - J. Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Jon C. Aster
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Iannis Aifantis
- Howard Hughes Medical Institute and Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
| | - Harald von Boehmer
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, and Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - A. Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Division of Hematology/ Oncology, Children's Hospital, Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Piotr Sicinski
- Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02215, USA
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Ordureau A, Sarraf SA, Duda DM, Heo JM, Jedrychowski MP, Sviderskiy VO, Olszewski JL, Koerber JT, Xie T, Beausoleil SA, Wells JA, Gygi SP, Schulman BA, Harper JW. Quantitative proteomics reveal a feedforward mechanism for mitochondrial PARKIN translocation and ubiquitin chain synthesis. Mol Cell 2014; 56:360-375. [PMID: 25284222 DOI: 10.1016/j.molcel.2014.09.007] [Citation(s) in RCA: 490] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 08/18/2014] [Accepted: 08/28/2014] [Indexed: 01/20/2023]
Abstract
Phosphorylation is often used to promote protein ubiquitylation, yet we rarely understand quantitatively how ligase activation and ubiquitin (UB) chain assembly are integrated with phosphoregulation. Here we employ quantitative proteomics and live-cell imaging to dissect individual steps in the PINK1 kinase-PARKIN UB ligase mitochondrial control pathway disrupted in Parkinson's disease. PINK1 plays a dual role by phosphorylating PARKIN on its UB-like domain and poly-UB chains on mitochondria. PARKIN activation by PINK1 produces canonical and noncanonical UB chains on mitochondria, and PARKIN-dependent chain assembly is required for accumulation of poly-phospho-UB (poly-p-UB) on mitochondria. In vitro, PINK1 directly activates PARKIN's ability to assemble canonical and noncanonical UB chains and promotes association of PARKIN with both p-UB and poly-p-UB. Our data reveal a feedforward mechanism that explains how PINK1 phosphorylation of both PARKIN and poly-UB chains synthesized by PARKIN drives a program of PARKIN recruitment and mitochondrial ubiquitylation in response to mitochondrial damage.
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Affiliation(s)
- Alban Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Shireen A Sarraf
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - David M Duda
- Department of Structural Biology and Howard Hughes Medical Institute, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jin-Mi Heo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Vladislav O Sviderskiy
- Department of Structural Biology and Howard Hughes Medical Institute, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jennifer L Olszewski
- Department of Structural Biology and Howard Hughes Medical Institute, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - James T Koerber
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Tiao Xie
- Data and Imaging Analysis Core, Harvard Medical School, Boston, MA 02115, USA
| | | | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Brenda A Schulman
- Department of Structural Biology and Howard Hughes Medical Institute, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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45
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Affiliation(s)
- Alban Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - J Wade Harper
- 1] Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA. [2] Biogen-Idec, Cambridge, Massachusetts
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46
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Ordureau A, Enesa K, Nanda S, Le Francois B, Peggie M, Prescott A, Albert PR, Cohen P. DEAF1 is a Pellino1-interacting protein required for interferon production by Sendai virus and double-stranded RNA. J Biol Chem 2013; 288:24569-80. [PMID: 23846693 PMCID: PMC3750155 DOI: 10.1074/jbc.m113.479550] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Double-stranded (ds) RNA of viral origin, a ligand for Melanoma Differentiation-associated gene 5 (MDA5) and Toll-Like Receptor 3 (TLR3), induces the TANK-Binding Kinase 1 (TBK1)-dependent phosphorylation and activation of Interferon Regulatory Factor 3 (IRF3) and the E3 ubiquitin ligase Pellino1, which are required for interferon β (IFNβ) gene transcription. Here, we report that Pellino1 interacts with the transcription factor Deformed Epidermal Autoregulatory Factor 1 (DEAF1). The interaction is independent of the E3 ligase activity of Pellino1, but weakened by the phosphorylation of Pellino1. We show that DEAF1 binds to the IFNβ promoter and to IRF3 and IRF7, that it is required for the transcription of the IFNβ gene and IFNβ secretion in MEFs infected with Sendai virus or transfected with poly(I:C). DEAF1 is also needed for TLR3-dependent IFNβ production. Taken together, our results identify DEAF1 as a novel component of the signal transduction network by which dsRNA of viral origin stimulates IFNβ production.
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Affiliation(s)
- Alban Ordureau
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom
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Enesa K, Ordureau A, Smith H, Barford D, Cheung PCF, Patterson-Kane J, Arthur JSC, Cohen P. Pellino1 is required for interferon production by viral double-stranded RNA. J Biol Chem 2012; 287:34825-35. [PMID: 22902624 PMCID: PMC3464584 DOI: 10.1074/jbc.m112.367557] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 08/13/2012] [Indexed: 12/24/2022] Open
Abstract
Viral double-stranded RNA, a ligand for Toll-like Receptor 3 (TLR3) and the cytoplasmic RNA receptors RIG1 and MDA5, activate a signaling network in which the IKK-related protein kinase TBK1 phosphorylates the transcription factor Interferon Regulatory Factor 3 (IRF3) and the E3 ubiquitin ligase Pellino1. IRF3 then translocates to the nucleus where it stimulates transcription of the interferonβ (IFNβ) gene, but the function of Pellino1 in this pathway is unknown. Here, we report that myeloid cells and embryonic fibroblasts from knock-in mice expressing an E3 ligase-deficient mutant of Pellino1 produce reduced levels of IFNβ mRNA and secrete much less IFNβ in response to viral double-stranded RNA because the interaction of IRF3 with the IFNβ promoter is impaired. These results identify Pellino1 as a novel component of the signal transduction network by which viral double-stranded RNA stimulates IFNβ gene transcription.
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MESH Headings
- Active Transport, Cell Nucleus
- Animals
- Cell Nucleus/genetics
- Cell Nucleus/metabolism
- DEAD Box Protein 58
- DEAD-box RNA Helicases/genetics
- DEAD-box RNA Helicases/metabolism
- Embryo, Mammalian/cytology
- Embryo, Mammalian/metabolism
- Fibroblasts/cytology
- Fibroblasts/metabolism
- Gene Knock-In Techniques
- Interferon Regulatory Factor-3/genetics
- Interferon Regulatory Factor-3/metabolism
- Interferon-Induced Helicase, IFIH1
- Interferon-beta/biosynthesis
- Interferon-beta/genetics
- Mice
- Mice, Transgenic
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Promoter Regions, Genetic/physiology
- Protein Serine-Threonine Kinases/genetics
- Protein Serine-Threonine Kinases/metabolism
- RNA, Double-Stranded/genetics
- RNA, Double-Stranded/metabolism
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Signal Transduction/physiology
- Toll-Like Receptor 3/genetics
- Toll-Like Receptor 3/metabolism
- Transcription, Genetic/physiology
- Ubiquitin-Protein Ligases
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Affiliation(s)
| | | | | | - David Barford
- the Institute of Cancer Research, London SW36JB, United Kingdom
| | | | - Janet Patterson-Kane
- the Institute of Infection, Immunity, and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, G611QH, United Kingdom
| | | | - Philip Cohen
- From the MRC Protein Phosphorylation Unit and
- Scottish Institute for Cell Signaling, Sir James Black Centre, University of Dundee, DD15EH, United Kingdom
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Gleason CE, Ordureau A, Gourlay R, Arthur JSC, Cohen P. Polyubiquitin binding to optineurin is required for optimal activation of TANK-binding kinase 1 and production of interferon β. J Biol Chem 2011; 286:35663-35674. [PMID: 21862579 DOI: 10.1074/jbc.m111.267567] [Citation(s) in RCA: 135] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
TANK-binding kinase (TBK1) is essential for transcription of the interferon (IFN) β gene in response to lipopolysaccharide (LPS) and double-stranded RNA, but the molecular mechanisms that underlie the activation of TBK1 are incompletely understood. Previously, we identified the NF-κB essential modulator (NEMO)-related polyubiquitin-binding protein, optineurin (OPTN), as a novel binding partner of TBK1. To determine whether the ubiquitin-binding function of OPTN is involved in regulating TBK1 and IFNβ production, we generated a mouse in which wild-type optineurin was replaced by the polyubiquitin binding-defective mutant, OPTN(D477N/D477N). In this study, we found that LPS or poly(I:C)-induced TBK1 activity was significantly reduced in bone marrow-derived macrophage (BMDM) from OPTN(D477N/D477N) mice. Consistent with this, the phosphorylation of IFN regulatory factor 3 (IRF3) and the production of IFNβ mRNA and secretion were reduced. Stimulation of BMDMs with LPS triggered the phosphorylation of OPTN, which was reversed by phosphatase treatment and prevented by pharmacological inhibition of both the canonical IκB kinases (IKKα/β) and the IKK-related kinases (TBK1/IKKε). In contrast, LPS-stimulated phosphorylation of OPTN(D477N) was markedly reduced in BMDMs from OPTN(D477N/D477N) mice, and inhibition of the canonical IKKs alone prevented phosphorylation, providing further evidence that ubiquitin binding to OPTN contributes to LPS-induced TBK1 activation. TBK1 and IKKβ phosphorylated OPTN preferentially at Ser-177 and Ser-513, respectively, in vitro. In conclusion, our results suggest that OPTN binds to polyubiquitylated species formed in response to LPS and poly(I:C), enhancing the activation of TBK1 that is required for optimal phosphorylation of IRF3 and production of IFNβ.
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Affiliation(s)
- Catherine E Gleason
- Medical Research Council Protein Phosphorylation Unit, The Sir James Black Centre, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, United Kingdom
| | - Alban Ordureau
- Medical Research Council Protein Phosphorylation Unit, The Sir James Black Centre, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, United Kingdom
| | - Robert Gourlay
- Medical Research Council Protein Phosphorylation Unit, The Sir James Black Centre, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, United Kingdom
| | - J Simon C Arthur
- Medical Research Council Protein Phosphorylation Unit, The Sir James Black Centre, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, United Kingdom
| | - Philip Cohen
- Medical Research Council Protein Phosphorylation Unit, The Sir James Black Centre, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, United Kingdom.
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Nanda SK, Venigalla RKC, Ordureau A, Patterson-Kane JC, Powell DW, Toth R, Arthur JSC, Cohen P. Polyubiquitin binding to ABIN1 is required to prevent autoimmunity. ACTA ACUST UNITED AC 2011; 208:1215-28. [PMID: 21606507 PMCID: PMC3173241 DOI: 10.1084/jem.20102177] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The polyubiquitin-binding domain of ABIN1 limits TLR-induced MyD88 signaling to prevent spontaneous autoimmunity in mice. The protein ABIN1 possesses a polyubiquitin-binding domain homologous to that present in nuclear factor κB (NF-κB) essential modulator (NEMO), a component of the inhibitor of NF-κB (IκB) kinase (IKK) complex. To address the physiological significance of polyubiquitin binding, we generated knockin mice expressing the ABIN1[D485N] mutant instead of the wild-type (WT) protein. These mice developed all the hallmarks of autoimmunity, including spontaneous formation of germinal centers, isotype switching, and production of autoreactive antibodies. Autoimmunity was suppressed by crossing to MyD88−/− mice, demonstrating that toll-like receptor (TLR)–MyD88 signaling pathways are needed for the phenotype to develop. The B cells and myeloid cells of the ABIN1[D485N] mice showed enhanced activation of the protein kinases TAK, IKK-α/β, c-Jun N-terminal kinases, and p38α mitogen-activated protein kinase and produced more IL-6 and IL-12 than WT. The mutant B cells also proliferated more rapidly in response to TLR ligands. Our results indicate that the interaction of ABIN1 with polyubiquitin is required to limit the activation of TLR–MyD88 pathways and prevent autoimmunity.
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Affiliation(s)
- Sambit K Nanda
- Medical Research Council Protein Phosphorylation Unit, Sir James Black Centre, University of Dundee, Dundee DD1 5EH, Scotland, UK.
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