151
|
PTEN-L is a novel protein phosphatase for ubiquitin dephosphorylation to inhibit PINK1-Parkin-mediated mitophagy. Cell Res 2018; 28:787-802. [PMID: 29934616 PMCID: PMC6082900 DOI: 10.1038/s41422-018-0056-0] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 05/21/2018] [Accepted: 05/23/2018] [Indexed: 01/08/2023] Open
Abstract
Mitophagy is an important type of selective autophagy for specific elimination of damaged mitochondria. PTEN-induced putative kinase protein 1 (PINK1)-catalyzed phosphorylation of ubiquitin (Ub) plays a critical role in the onset of PINK1-Parkin-mediated mitophagy. Phosphatase and tensin homolog (PTEN)-long (PTEN-L) is a newly identified isoform of PTEN, with addition of 173 amino acids to its N-terminus. Here we report that PTEN-L is a novel negative regulator of mitophagy via its protein phosphatase activity against phosphorylated ubiquitin. We found that PTEN-L localizes at the outer mitochondrial membrane (OMM) and overexpression of PTEN-L inhibits, whereas deletion of PTEN-L promotes, mitophagy induced by various mitochondria-damaging agents. Mechanistically, PTEN-L is capable of effectively preventing Parkin mitochondrial translocation, reducing Parkin phosphorylation, maintaining its closed inactive conformation, and inhibiting its E3 ligase activity. More importantly, PTEN-L reduces the level of phosphorylated ubiquitin (pSer65-Ub) in vivo, and in vitro phosphatase assay confirms that PTEN-L dephosphorylates pSer65-Ub via its protein phosphatase activity, independently of its lipid phosphatase function. Taken together, our findings demonstrate a novel function of PTEN-L as a protein phosphatase for ubiquitin, which counteracts PINK1-mediated ubiquitin phosphorylation leading to blockage of the feedforward mechanisms in mitophagy induction and eventual suppression of mitophagy. Thus, understanding this novel function of PTEN-L provides a key missing piece in the molecular puzzle controlling mitophagy, a critical process in many important human diseases including neurodegenerative disorders such as Parkinson's disease.
Collapse
|
152
|
Marcassa E, Kallinos A, Jardine J, Rusilowicz-Jones EV, Martinez A, Kuehl S, Islinger M, Clague MJ, Urbé S. Dual role of USP30 in controlling basal pexophagy and mitophagy. EMBO Rep 2018; 19:embr.201745595. [PMID: 29895712 PMCID: PMC6030704 DOI: 10.15252/embr.201745595] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 05/15/2018] [Accepted: 05/18/2018] [Indexed: 12/20/2022] Open
Abstract
USP30 is an integral protein of the outer mitochondrial membrane that counteracts PINK1 and Parkin‐dependent mitophagy following acute mitochondrial depolarisation. Here, we use two distinct mitophagy reporter systems to reveal tonic suppression by USP30, of a PINK1‐dependent component of basal mitophagy in cells lacking detectable Parkin. We propose that USP30 acts upstream of PINK1 through modulation of PINK1‐substrate availability and thereby determines the potential for mitophagy initiation. We further show that a fraction of endogenous USP30 is independently targeted to peroxisomes where it regulates basal pexophagy in a PINK1‐ and Parkin‐independent manner. Thus, we reveal a critical role of USP30 in the clearance of the two major sources of ROS in mammalian cells and in the regulation of both a PINK1‐dependent and a PINK1‐independent selective autophagy pathway.
Collapse
Affiliation(s)
- Elena Marcassa
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Andreas Kallinos
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Jane Jardine
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Emma V Rusilowicz-Jones
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Aitor Martinez
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Sandra Kuehl
- Institute of Neuroanatomy, Centre for Biomedicine and Medical Technology Mannheim, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Markus Islinger
- Institute of Neuroanatomy, Centre for Biomedicine and Medical Technology Mannheim, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Michael J Clague
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Sylvie Urbé
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| |
Collapse
|
153
|
Encoding human serine phosphopeptides in bacteria for proteome-wide identification of phosphorylation-dependent interactions. Nat Biotechnol 2018; 36:638-644. [PMID: 29889213 PMCID: PMC6590076 DOI: 10.1038/nbt.4150] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 04/04/2018] [Indexed: 11/19/2022]
|
154
|
Abstract
Mutations in the E3 ubiquitin ligase parkin (PARK2, also known as PRKN) and the protein kinase PINK1 (also known as PARK6) are linked to autosomal-recessive juvenile parkinsonism (AR-JP)1,2; at the cellular level, these mutations cause defects in mitophagy, the process that organizes the destruction of damaged mitochondria3,4. Parkin is autoinhibited, and requires activation by PINK1, which phosphorylates Ser65 in ubiquitin and in the parkin ubiquitin-like (Ubl) domain. Parkin binds phospho-ubiquitin, which enables efficient parkin phosphorylation; however, the enzyme remains autoinhibited with an inaccessible active site5,6. It is unclear how phosphorylation of parkin activates the molecule. Here we follow the activation of full-length human parkin by hydrogen-deuterium exchange mass spectrometry, and reveal large-scale domain rearrangement in the activation process, during which the phospho-Ubl rebinds to the parkin core and releases the catalytic RING2 domain. A 1.8 Å crystal structure of phosphorylated human parkin reveals the binding site of the phospho-Ubl on the unique parkin domain (UPD), involving a phosphate-binding pocket lined by AR-JP mutations. Notably, a conserved linker region between Ubl and the UPD acts as an activating element (ACT) that contributes to RING2 release by mimicking RING2 interactions on the UPD, explaining further AR-JP mutations. Our data show how autoinhibition in parkin is resolved, and suggest a mechanism for how parkin ubiquitinates its substrates via an untethered RING2 domain. These findings open new avenues for the design of parkin activators for clinical use.
Collapse
|
155
|
Franco-Iborra S, Vila M, Perier C. Mitochondrial Quality Control in Neurodegenerative Diseases: Focus on Parkinson's Disease and Huntington's Disease. Front Neurosci 2018; 12:342. [PMID: 29875626 PMCID: PMC5974257 DOI: 10.3389/fnins.2018.00342] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 05/02/2018] [Indexed: 12/15/2022] Open
Abstract
In recent years, several important advances have been made in our understanding of the pathways that lead to cell dysfunction and death in Parkinson's disease (PD) and Huntington's disease (HD). Despite distinct clinical and pathological features, these two neurodegenerative diseases share critical processes, such as the presence of misfolded and/or aggregated proteins, oxidative stress, and mitochondrial anomalies. Even though the mitochondria are commonly regarded as the "powerhouses" of the cell, they are involved in a multitude of cellular events such as heme metabolism, calcium homeostasis, and apoptosis. Disruption of mitochondrial homeostasis and subsequent mitochondrial dysfunction play a key role in the pathophysiology of neurodegenerative diseases, further highlighting the importance of these organelles, especially in neurons. The maintenance of mitochondrial integrity through different surveillance mechanisms is thus critical for neuron survival. Mitochondria display a wide range of quality control mechanisms, from the molecular to the organellar level. Interestingly, many of these lines of defense have been found to be altered in neurodegenerative diseases such as PD and HD. Current knowledge and further elucidation of the novel pathways that protect the cell through mitochondrial quality control may offer unique opportunities for disease therapy in situations where ongoing mitochondrial damage occurs. In this review, we discuss the involvement of mitochondrial dysfunction in neurodegeneration with a special focus on the recent findings regarding mitochondrial quality control pathways, beyond the classical effects of increased production of reactive oxygen species (ROS) and bioenergetic alterations. We also discuss how disturbances in these processes underlie the pathophysiology of neurodegenerative disorders such as PD and HD.
Collapse
Affiliation(s)
- Sandra Franco-Iborra
- Vall d'Hebron Research Institute (VHIR)-Center for Networked Biomedical Research in Neurodegenerative Diseases (CIBERNED), Barcelona, Spain
| | - Miquel Vila
- Vall d'Hebron Research Institute (VHIR)-Center for Networked Biomedical Research in Neurodegenerative Diseases (CIBERNED), Barcelona, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona, Spain
- Department of Biochemistry and Molecular Biology, Autonomous University of Barcelona, Barcelona, Spain
| | - Celine Perier
- Vall d'Hebron Research Institute (VHIR)-Center for Networked Biomedical Research in Neurodegenerative Diseases (CIBERNED), Barcelona, Spain
| |
Collapse
|
156
|
Ryan TA, Tumbarello DA. Optineurin: A Coordinator of Membrane-Associated Cargo Trafficking and Autophagy. Front Immunol 2018; 9:1024. [PMID: 29867991 PMCID: PMC5962687 DOI: 10.3389/fimmu.2018.01024] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 04/24/2018] [Indexed: 12/13/2022] Open
Abstract
Optineurin is a multifunctional adaptor protein intimately involved in various vesicular trafficking pathways. Through interactions with an array of proteins, such as myosin VI, huntingtin, Rab8, and Tank-binding kinase 1, as well as via its oligomerisation, optineurin has the ability to act as an adaptor, scaffold, or signal regulator to coordinate many cellular processes associated with the trafficking of membrane-delivered cargo. Due to its diverse interactions and its distinct functions, optineurin is an essential component in a number of homeostatic pathways, such as protein trafficking and organelle maintenance. Through the binding of polyubiquitinated cargoes via its ubiquitin-binding domain, optineurin also serves as a selective autophagic receptor for the removal of a wide range of substrates. Alternatively, it can act in an ubiquitin-independent manner to mediate the clearance of protein aggregates. Regarding its disease associations, mutations in the optineurin gene are associated with glaucoma and have more recently been found to correlate with Paget’s disease of bone and amyotrophic lateral sclerosis (ALS). Indeed, ALS-associated mutations in optineurin result in defects in neuronal vesicular localisation, autophagosome–lysosome fusion, and secretory pathway function. More recent molecular and functional analysis has shown that it also plays a role in mitophagy, thus linking it to a number of other neurodegenerative conditions, such as Parkinson’s. Here, we review the role of optineurin in intracellular membrane trafficking, with a focus on autophagy, and describe how upstream signalling cascades are critical to its regulation. Current data and contradicting reports would suggest that optineurin is an important and selective autophagy receptor under specific conditions, whereby interplay, synergy, and functional redundancy with other receptors occurs. We will also discuss how dysfunction in optineurin-mediated pathways may lead to perturbation of critical cellular processes, which can drive the pathologies of number of diseases. Therefore, further understanding of optineurin function, its target specificity, and its mechanism of action will be critical in fully delineating its role in human disease.
Collapse
Affiliation(s)
- Thomas A Ryan
- Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - David A Tumbarello
- Biological Sciences, University of Southampton, Southampton, United Kingdom
| |
Collapse
|
157
|
Xu Y, Zhi F, Peng Y, Shao N, Khiati D, Balboni G, Yang Y, Xia Y. δ-Opioid Receptor Activation Attenuates Hypoxia/MPP +-Induced Downregulation of PINK1: a Novel Mechanism of Neuroprotection Against Parkinsonian Injury. Mol Neurobiol 2018; 56:252-266. [PMID: 29687347 DOI: 10.1007/s12035-018-1043-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 03/27/2018] [Indexed: 12/22/2022]
Abstract
There is emerging evidence suggesting that neurotoxic insults and hypoxic/ischemic injury are underlying causes of Parkinson's disease (PD). Since PTEN-induced kinase 1 (PINK1) dysfunction is involved in the molecular genesis of PD and since our recent studies have demonstrated that the δ-opioid receptor (DOR) induced neuroprotection against hypoxic and 1-methyl-4-phenyl-pyridimium (MPP+) insults, we sought to explore whether DOR protects neuronal cells from hypoxic and/or MPP+ injury via the regulation of PINK1-related pathways. Using highly differentiated rat PC12 cells exposed to either severe hypoxia (0.5-1% O2) for 24-48 h or varying concentrations of MPP+, we found that both hypoxic and MPP+ stress reduced the level of PINK1 expression, while incubation with the specific DOR agonist UFP-512 reversed this reduction and protected the cells from hypoxia and/or MPP+-induced injury. However, the DOR-mediated cytoprotection largely disappeared after knocking down PINK1 by PINK1 small interfering RNA. Moreover, we examined several important signaling molecules related to cell survival and apoptosis and found that DOR activation attenuated the hypoxic and/or MPP+-induced reduction in phosphorylated Akt and inhibited the activation of cleaved caspase-3, whereas PINK1 knockdown largely deprived the cell of the DOR-induced effects. Our novel data suggests a unique mechanism underlying DOR-mediated cytoprotection against hypoxic and MPP+ stress via a PINK1-mediated regulation of signaling.
Collapse
Affiliation(s)
- Yuan Xu
- Department of Neurosurgery, The First People's Hospital of Changzhou, Changzhou, Jiangsu, China.,Modern Medical Research Center, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - Feng Zhi
- Department of Neurosurgery, The First People's Hospital of Changzhou, Changzhou, Jiangsu, China.,Modern Medical Research Center, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - Ya Peng
- Department of Neurosurgery, The First People's Hospital of Changzhou, Changzhou, Jiangsu, China
| | - Naiyuan Shao
- Department of Neurosurgery, The First People's Hospital of Changzhou, Changzhou, Jiangsu, China
| | - Dhiaedin Khiati
- Royal College of Surgeons of Ireland - Medical University of Bahrain, Busaiteen, Bahrain
| | - Gianfranco Balboni
- Department of Life and Environment Sciences, University of Cagliari, Cagliari, Italy
| | - Yilin Yang
- Department of Neurosurgery, The First People's Hospital of Changzhou, Changzhou, Jiangsu, China. .,Modern Medical Research Center, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China.
| | - Ying Xia
- Shanghai Key Laboratory of Acupuncture Mechanism and Acupoint Function, Fudan University, Shanghai, China.
| |
Collapse
|
158
|
McLelland GL, Goiran T, Yi W, Dorval G, Chen CX, Lauinger ND, Krahn AI, Valimehr S, Rakovic A, Rouiller I, Durcan TM, Trempe JF, Fon EA. Mfn2 ubiquitination by PINK1/parkin gates the p97-dependent release of ER from mitochondria to drive mitophagy. eLife 2018; 7:32866. [PMID: 29676259 PMCID: PMC5927771 DOI: 10.7554/elife.32866] [Citation(s) in RCA: 249] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 04/19/2018] [Indexed: 12/23/2022] Open
Abstract
Despite their importance as signaling hubs, the function of mitochondria-ER contact sites in mitochondrial quality control pathways remains unexplored. Here we describe a mechanism by which Mfn2, a mitochondria-ER tether, gates the autophagic turnover of mitochondria by PINK1 and parkin. Mitochondria-ER appositions are destroyed during mitophagy, and reducing mitochondria-ER contacts increases the rate of mitochondrial degradation. Mechanistically, parkin/PINK1 catalyze a rapid burst of Mfn2 phosphoubiquitination to trigger p97-dependent disassembly of Mfn2 complexes from the outer mitochondrial membrane, dissociating mitochondria from the ER. We additionally demonstrate that a major portion of the facilitatory effect of p97 on mitophagy is epistatic to Mfn2 and promotes the availability of other parkin substrates such as VDAC1. Finally, we reconstitute the action of these factors on Mfn2 and VDAC1 ubiquitination in a cell-free assay. We show that mitochondria-ER tethering suppresses mitophagy and describe a parkin-/PINK1-dependent mechanism that regulates the destruction of mitochondria-ER contact sites.
Collapse
Affiliation(s)
- Gian-Luca McLelland
- McGill Parkinson Program, Montreal Neurological Institute, McGill University, Montreal, Canada.,Neurodegenerative Diseases Group, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Thomas Goiran
- McGill Parkinson Program, Montreal Neurological Institute, McGill University, Montreal, Canada.,Neurodegenerative Diseases Group, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Wei Yi
- McGill Parkinson Program, Montreal Neurological Institute, McGill University, Montreal, Canada.,Neurodegenerative Diseases Group, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Geneviève Dorval
- McGill Parkinson Program, Montreal Neurological Institute, McGill University, Montreal, Canada.,Neurodegenerative Diseases Group, Montreal Neurological Institute, McGill University, Montreal, Canada.,iPSC-CRISPR Platform, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Carol X Chen
- McGill Parkinson Program, Montreal Neurological Institute, McGill University, Montreal, Canada.,Neurodegenerative Diseases Group, Montreal Neurological Institute, McGill University, Montreal, Canada.,iPSC-CRISPR Platform, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Nadine D Lauinger
- McGill Parkinson Program, Montreal Neurological Institute, McGill University, Montreal, Canada.,Neurodegenerative Diseases Group, Montreal Neurological Institute, McGill University, Montreal, Canada.,iPSC-CRISPR Platform, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Andrea I Krahn
- McGill Parkinson Program, Montreal Neurological Institute, McGill University, Montreal, Canada.,Neurodegenerative Diseases Group, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Sepideh Valimehr
- Department of Anatomy & Cell Biology, McGill University, Montreal, Canada
| | | | - Isabelle Rouiller
- Department of Anatomy & Cell Biology, McGill University, Montreal, Canada
| | - Thomas M Durcan
- McGill Parkinson Program, Montreal Neurological Institute, McGill University, Montreal, Canada.,Neurodegenerative Diseases Group, Montreal Neurological Institute, McGill University, Montreal, Canada.,iPSC-CRISPR Platform, Montreal Neurological Institute, McGill University, Montreal, Canada
| | | | - Edward A Fon
- McGill Parkinson Program, Montreal Neurological Institute, McGill University, Montreal, Canada.,Neurodegenerative Diseases Group, Montreal Neurological Institute, McGill University, Montreal, Canada.,iPSC-CRISPR Platform, Montreal Neurological Institute, McGill University, Montreal, Canada
| |
Collapse
|
159
|
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: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [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.
Collapse
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.
| |
Collapse
|
160
|
Abstract
Complex signaling cascades are difficult to study in vitro without phosphorylated proteins. Here, we describe a technique for the routine production of recombinant phosphoproteins by directly incorporating phosphoserine as a nonstandard amino acid. This protocol utilizes an optimized phosphoserine orthogonal translation system and an engineered strain of E. coli containing no genomic amber codons. This approach has been used to generate a variety of phosphorylated proteins to understand the role of protein phosphorylation in cell signaling.
Collapse
|
161
|
Morris G, Puri BK, Walder K, Berk M, Stubbs B, Maes M, Carvalho AF. The Endoplasmic Reticulum Stress Response in Neuroprogressive Diseases: Emerging Pathophysiological Role and Translational Implications. Mol Neurobiol 2018; 55:8765-8787. [PMID: 29594942 PMCID: PMC6208857 DOI: 10.1007/s12035-018-1028-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 03/20/2018] [Indexed: 02/07/2023]
Abstract
The endoplasmic reticulum (ER) is the main cellular organelle involved in protein synthesis, assembly and secretion. Accumulating evidence shows that across several neurodegenerative and neuroprogressive diseases, ER stress ensues, which is accompanied by over-activation of the unfolded protein response (UPR). Although the UPR could initially serve adaptive purposes in conditions associated with higher cellular demands and after exposure to a range of pathophysiological insults, over time the UPR may become detrimental, thus contributing to neuroprogression. Herein, we propose that immune-inflammatory, neuro-oxidative, neuro-nitrosative, as well as mitochondrial pathways may reciprocally interact with aberrations in UPR pathways. Furthermore, ER stress may contribute to a deregulation in calcium homoeostasis. The common denominator of these pathways is a decrease in neuronal resilience, synaptic dysfunction and even cell death. This review also discusses how mechanisms related to ER stress could be explored as a source for novel therapeutic targets for neurodegenerative and neuroprogressive diseases. The design of randomised controlled trials testing compounds that target aberrant UPR-related pathways within the emerging framework of precision psychiatry is warranted.
Collapse
Affiliation(s)
- Gerwyn Morris
- Tir Na Nog, Bryn Road seaside 87, Llanelli, Wales, SA15 2LW, UK
- IMPACT Strategic Research Centre, School of Medicine, Deakin University, Geelong, Australia
| | - Basant K Puri
- Department of Medicine, Imperial College London, Hammersmith Hospital, London, England, W12 0HS, UK.
| | - Ken Walder
- The Centre for Molecular and Medical Research, School of Medicine, Deakin University, P.O. Box 291, Geelong, 3220, Australia
| | - Michael Berk
- IMPACT Strategic Research Centre, School of Medicine, Deakin University, Geelong, Australia
- Department of Psychiatry, University of Melbourne, Melbourne, Australia
- Orygen, the National Centre of Excellence in Youth Mental Health, Parkville, Australia
- Centre for Youth Mental Health, University of Melbourne, Melbourne, Australia
- Florey Institute for Neuroscience and Mental Health, Melbourne, Australia
| | - Brendon Stubbs
- Physiotherapy Department, South London and Maudsley NHS Foundation Trust, London, UK
- Health Service and Population Research Department, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- Faculty of Health, Social Care and Education, Anglia Ruskin University, Chelmsford, UK
| | - Michael Maes
- IMPACT Strategic Research Centre, School of Medicine, Deakin University, Geelong, Australia
- Department of Psychiatry, Chulalongkorn University, Bangkok, Thailand
| | - André F Carvalho
- Department of Psychiatry, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Centre for Addiction & Mental Health (CAMH), Toronto, ON, Canada
| |
Collapse
|
162
|
Peker N, Donipadi V, Sharma M, McFarlane C, Kambadur R. Loss of Parkin impairs mitochondrial function and leads to muscle atrophy. Am J Physiol Cell Physiol 2018; 315:C164-C185. [PMID: 29561660 DOI: 10.1152/ajpcell.00064.2017] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Parkinson's disease is a neurodegenerative disease characterized by tremors, muscle stiffness, and muscle weakness. Molecular genetic analysis has confirmed that mutations in PARKIN and PINK1 genes, which play major roles in mitochondrial quality control and mitophagy, are frequently associated with Parkinson's disease. PARKIN is an E3 ubiquitin ligase that translocates to mitochondria during loss of mitochondrial membrane potential to increase mitophagy. Although muscle dysfunction is noted in Parkinson's disease, little is known about the involvement of PARKIN in the muscle phenotype of Parkinson's disease. In this study, we report that the mitochondrial uncoupler CCCP promotes PINK1/PARKIN-mediated mitophagy in myogenic C2C12 cells. As a result of this excess mitophagy, we show that CCCP treatment of myotubes leads to the development of myotube atrophy in vitro. Surprisingly, we also found that siRNA-mediated knockdown of Parkin results in impaired mitochondrial turnover. In addition, knockdown of Parkin led to myotubular atrophy in vitro. Consistent with these in vitro results, Parkin knockout muscles showed impaired mitochondrial function and smaller myofiber area, suggesting that Parkin function is required for post-natal skeletal muscle growth and development.
Collapse
Affiliation(s)
- Nesibe Peker
- School of Biological Sciences, Nanyang Technological University , Singapore
| | - Vinay Donipadi
- Cell and Molecular Biology Group, Singapore Institute for Clinical Sciences , Singapore
| | - Mridula Sharma
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore , Singapore
| | - Craig McFarlane
- Cell and Molecular Biology Group, Singapore Institute for Clinical Sciences , Singapore
| | - Ravi Kambadur
- School of Biological Sciences, Nanyang Technological University , Singapore
| |
Collapse
|
163
|
Aguirre JD, Dunkerley KM, Lam R, Rusal M, Shaw GS. Impact of altered phosphorylation on loss of function of juvenile Parkinsonism-associated genetic variants of the E3 ligase parkin. J Biol Chem 2018. [PMID: 29530980 PMCID: PMC5925814 DOI: 10.1074/jbc.ra117.000605] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Autosomal recessive juvenile Parkinsonism (ARJP) is an inherited neurodegenerative disease in which 50% of affected individuals harbor mutations in the gene encoding the E3 ligase parkin. Parkin regulates the mitochondrial recycling pathway, which is induced by oxidative stress. In its native state, parkin is auto-inhibited by its N-terminal ubiquitin-like (Ubl) domain, which blocks the binding site for an incoming E2∼ubiquitin conjugate, needed for parkin's ubiquitination activity. Parkin is activated via phosphorylation of Ser-65 in its Ubl domain by PTEN-induced putative kinase 1 (PINK1) and a ubiquitin molecule phosphorylated at a position equivalent to Ser-65 in parkin. Here we have examined the underlying molecular mechanism of phosphorylation of parkin's Ubl domain carrying ARJP-associated substitutions and how altered phosphorylation modulates parkin activation and ubiquitination. We found that three substitutions in the Ubl domain (G12R, R33Q, and R42P) significantly decrease PINK1's ability to phosphorylate the Ubl domain. We noted that two basic loss-of-function substitutions (R33Q and R42P) are close to acidic patches in the proposed PINK1–parkin interface, indicating that ionic interactions at this site may be important for efficient parkin phosphorylation. Increased auto-ubiquitination with unique ubiquitin chain patterns was observed for two other Ubl domain substitutions (G12R and T55I), suggesting that these substitutions, along with phosphorylation, increase parkin degradation. Moreover, Ubl domain phosphorylation decreased its affinity for the potential effector protein ataxin-3, which edits ubiquitin chain building by parkin. Overall, our work provides a framework for the mechanisms of parkin's loss-of-function, indicating an interplay between ARJP-associated substitutions and phosphorylation of its Ubl domain.
Collapse
Affiliation(s)
- Jacob D Aguirre
- From the Department of Biochemistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Karen M Dunkerley
- From the Department of Biochemistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Rica Lam
- From the Department of Biochemistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Michele Rusal
- From the Department of Biochemistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Gary S Shaw
- From the Department of Biochemistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
| |
Collapse
|
164
|
Anzell AR, Maizy R, Przyklenk K, Sanderson TH. Mitochondrial Quality Control and Disease: Insights into Ischemia-Reperfusion Injury. Mol Neurobiol 2018; 55:2547-2564. [PMID: 28401475 PMCID: PMC5636654 DOI: 10.1007/s12035-017-0503-9] [Citation(s) in RCA: 252] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 03/20/2017] [Indexed: 12/28/2022]
Abstract
Mitochondria are key regulators of cell fate during disease. They control cell survival via the production of ATP that fuels cellular processes and, conversely, cell death via the induction of apoptosis through release of pro-apoptotic factors such as cytochrome C. Therefore, it is essential to have stringent quality control mechanisms to ensure a healthy mitochondrial network. Quality control mechanisms are largely regulated by mitochondrial dynamics and mitophagy. The processes of mitochondrial fission (division) and fusion allow for damaged mitochondria to be segregated and facilitate the equilibration of mitochondrial components such as DNA, proteins, and metabolites. The process of mitophagy are responsible for the degradation and recycling of damaged mitochondria. These mitochondrial quality control mechanisms have been well studied in chronic and acute pathologies such as Parkinson's disease, Alzheimer's disease, stroke, and acute myocardial infarction, but less is known about how these two processes interact and contribute to specific pathophysiologic states. To date, evidence for the role of mitochondrial quality control in acute and chronic disease is divergent and suggests that mitochondrial quality control processes can serve both survival and death functions depending on the disease state. This review aims to provide a synopsis of the molecular mechanisms involved in mitochondrial quality control, to summarize our current understanding of the complex role that mitochondrial quality control plays in the progression of acute vs chronic diseases and, finally, to speculate on the possibility that targeted manipulation of mitochondrial quality control mechanisms may be exploited for the rationale design of novel therapeutic interventions.
Collapse
Affiliation(s)
- Anthony R Anzell
- Department of Emergency Medicine, Wayne State University School of Medicine, Detroit, MI, 48201, USA
- Cardiovascular Research Institute, Wayne State University School of Medicine, Detroit, MI, 48201, USA
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Rita Maizy
- Department of Emergency Medicine, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Karin Przyklenk
- Department of Emergency Medicine, Wayne State University School of Medicine, Detroit, MI, 48201, USA
- Cardiovascular Research Institute, Wayne State University School of Medicine, Detroit, MI, 48201, USA
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Thomas H Sanderson
- Department of Emergency Medicine, Wayne State University School of Medicine, Detroit, MI, 48201, USA.
- Cardiovascular Research Institute, Wayne State University School of Medicine, Detroit, MI, 48201, USA.
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI, 48201, USA.
| |
Collapse
|
165
|
Heidelberger JB, Voigt A, Borisova ME, Petrosino G, Ruf S, Wagner SA, Beli P. Proteomic profiling of VCP substrates links VCP to K6-linked ubiquitylation and c-Myc function. EMBO Rep 2018; 19:embr.201744754. [PMID: 29467282 DOI: 10.15252/embr.201744754] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 01/17/2018] [Accepted: 01/26/2018] [Indexed: 12/20/2022] Open
Abstract
Valosin-containing protein (VCP) is an evolutionarily conserved ubiquitin-dependent ATPase that mediates the degradation of proteins through the ubiquitin-proteasome pathway. Despite the central role of VCP in the regulation of protein homeostasis, identity and nature of its cellular substrates remain poorly defined. Here, we combined chemical inhibition of VCP and quantitative ubiquitin remnant profiling to assess the effect of VCP inhibition on the ubiquitin-modified proteome and to probe the substrate spectrum of VCP in human cells. We demonstrate that inhibition of VCP perturbs cellular ubiquitylation and increases ubiquitylation of a different subset of proteins compared to proteasome inhibition. VCP inhibition globally upregulates K6-linked ubiquitylation that is dependent on the HECT-type ubiquitin E3 ligase HUWE1. We report ~450 putative VCP substrates, many of which function in nuclear processes, including gene expression, DNA repair and cell cycle. Moreover, we identify that VCP regulates the level and activity of the transcription factor c-Myc.
Collapse
Affiliation(s)
| | - Andrea Voigt
- Institute of Molecular Biology (IMB), Mainz, Germany
| | | | | | - Stefanie Ruf
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Sebastian A Wagner
- Department of Medicine, Hematology/Oncology, Goethe University School of Medicine, Frankfurt, Germany
| | - Petra Beli
- Institute of Molecular Biology (IMB), Mainz, Germany
| |
Collapse
|
166
|
Yamano K, Wang C, Sarraf SA, Münch C, Kikuchi R, Noda NN, Hizukuri Y, Kanemaki MT, Harper W, Tanaka K, Matsuda N, Youle RJ. Endosomal Rab cycles regulate Parkin-mediated mitophagy. eLife 2018; 7:e31326. [PMID: 29360040 PMCID: PMC5780041 DOI: 10.7554/elife.31326] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 01/11/2018] [Indexed: 11/13/2022] Open
Abstract
Damaged mitochondria are selectively eliminated by mitophagy. Parkin and PINK1, gene products mutated in familial Parkinson's disease, play essential roles in mitophagy through ubiquitination of mitochondria. Cargo ubiquitination by E3 ubiquitin ligase Parkin is important to trigger selective autophagy. Although autophagy receptors recruit LC3-labeled autophagic membranes onto damaged mitochondria, how other essential autophagy units such as ATG9A-integrated vesicles are recruited remains unclear. Here, using mammalian cultured cells, we demonstrate that RABGEF1, the upstream factor of the endosomal Rab GTPase cascade, is recruited to damaged mitochondria via ubiquitin binding downstream of Parkin. RABGEF1 directs the downstream Rab proteins, RAB5 and RAB7A, to damaged mitochondria, whose associations are further regulated by mitochondrial Rab-GAPs. Furthermore, depletion of RAB7A inhibited ATG9A vesicle assembly and subsequent encapsulation of the mitochondria by autophagic membranes. These results strongly suggest that endosomal Rab cycles on damaged mitochondria are a crucial regulator of mitophagy through assembling ATG9A vesicles.
Collapse
Affiliation(s)
- Koji Yamano
- Ubiquitin ProjectTokyo Metropolitan Institute of Medical ScienceTokyoJapan
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaUnited States
| | - Chunxin Wang
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaUnited States
| | - Shireen A Sarraf
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaUnited States
| | - Christian Münch
- Department of Cell BiologyHarvard Medical SchoolBostonUnited States
- Institute of Biochemistry IISchool of Medicine, Goethe UniversityFrankfurtGermany
| | - Reika Kikuchi
- Ubiquitin ProjectTokyo Metropolitan Institute of Medical ScienceTokyoJapan
| | | | - Yohei Hizukuri
- Institute for Frontier Life and Medical SciencesKyoto UniversityKyotoJapan
| | - Masato T Kanemaki
- Division of Molecular Cell EngineeringNational Institute of Genetics, Research Organization of Information and SystemsMishimaJapan
- Department of GeneticsSOKENDAIMishimaJapan
- Division of Molecular Cell EngineeringNational Institute of Genetics, ROISMishimaJapan
| | - Wade Harper
- Department of Cell BiologyHarvard Medical SchoolBostonUnited States
| | - Keiji Tanaka
- Laboratory of Protein MetabolismTokyo Metropolitan Institute of Medical ScienceTokyoJapan
| | - Noriyuki Matsuda
- Ubiquitin ProjectTokyo Metropolitan Institute of Medical ScienceTokyoJapan
| | - Richard J Youle
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaUnited States
| |
Collapse
|
167
|
Harper JW, Ordureau A, Heo JM. Building and decoding ubiquitin chains for mitophagy. Nat Rev Mol Cell Biol 2018; 19:93-108. [DOI: 10.1038/nrm.2017.129] [Citation(s) in RCA: 323] [Impact Index Per Article: 53.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
|
168
|
Abstract
The ubiquitin proteasome system can arguably affect all cellular proteins with few exceptions. In addition to regulating many pathways such as cell cycle progression, inflammation, gene expression, DNA repair, and vesicle trafficking-to just name a few-ubiquitination can occur to any nascent or newly translated protein that misfolds. In the past years, substantial progress has been achieved in advancing our global understanding of the ubiquitinome-the ensemble of ubiquitinated proteins within a cell-using mass spectrometry-based proteomics. Notably, over 50,000 conjugation sites have now been reported. In this review, we discuss recent proteomics methods used to expand our knowledge of the ubiquitin proteasome system through the identification of ubiquitination sites, poly-ubiquitin chain types, and E3 ubiquitin ligase substrates.
Collapse
Affiliation(s)
- Amalia Rose
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Thibault Mayor
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada.
| |
Collapse
|
169
|
Zimmermann M, Reichert AS. How to get rid of mitochondria: crosstalk and regulation of multiple mitophagy pathways. Biol Chem 2017; 399:29-45. [PMID: 28976890 DOI: 10.1515/hsz-2017-0206] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 09/08/2017] [Indexed: 02/06/2023]
Abstract
Mitochondria are indispensable cellular organelles providing ATP and numerous other essential metabolites to ensure cell survival. Reactive oxygen species (ROS), which are formed as side reactions during oxidative phosphorylation or by external agents, induce molecular damage in mitochondrial proteins, lipids/membranes and DNA. To cope with this and other sorts of organellar stress, a multi-level quality control system exists to maintain cellular homeostasis. One critical level of mitochondrial quality control is the removal of damaged mitochondria by mitophagy. This process utilizes parts of the general autophagy machinery, e.g. for the formation of autophagosomes but also employs mitophagy-specific factors. Depending on the proteins utilized mitophagy is divided into receptor-mediated and ubiquitin-mediated mitophagy. So far, at least seven receptor proteins are known to be required for mitophagy under different experimental conditions. In contrast to receptor-mediated pathways, the Pink-Parkin-dependent pathway is currently the best characterized ubiquitin-mediated pathway. Recently two additional ubiquitin-mediated pathways with distinctive similarities and differences were unraveled. We will summarize the current state of knowledge about these multiple pathways, explain their mechanism, and describe the regulation and crosstalk between these pathways. Finally, we will review recent evidence for the evolutionary conservation of ubiquitin-mediated mitophagy pathways.
Collapse
Affiliation(s)
- Marcel Zimmermann
- Institute of Biochemistry and Molecular Biology I, Medical Faculty, Heinrich Heine University, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | - Andreas S Reichert
- Institute of Biochemistry and Molecular Biology I, Medical Faculty, Heinrich Heine University, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| |
Collapse
|
170
|
Abstract
Ubiquitination is a widespread post-translational modification that controls multiple steps in autophagy, a major lysosome-mediated intracellular degradation pathway. A variety of ubiquitin chains are attached as selective labels on protein aggregates and dysfunctional organelles, thus promoting their autophagy-dependent degradation. Moreover, ubiquitin modification of autophagy regulatory components is essential to positively or negatively regulate autophagy flux in both non-selective and selective pathways. We review the current findings that elucidate the components, timing, and kinetics of the multivalent role of ubiquitin signals in control of amplitude and selectivity of autophagy pathways as well as their impact on the development of human diseases.
Collapse
Affiliation(s)
- Paolo Grumati
- From the Institute of Biochemistry II, Goethe University Frankfurt-Medical Faculty, University Hospital, 60590 Frankfurt am Main and
| | - Ivan Dikic
- From the Institute of Biochemistry II, Goethe University Frankfurt-Medical Faculty, University Hospital, 60590 Frankfurt am Main and .,the Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt-Riedberg Campus, 60438 Frankfurt am Main, Germany
| |
Collapse
|
171
|
Lee S, Tumolo JM, Ehlinger AC, Jernigan KK, Qualls-Histed SJ, Hsu PC, McDonald WH, Chazin WJ, MacGurn JA. Ubiquitin turnover and endocytic trafficking in yeast are regulated by Ser57 phosphorylation of ubiquitin. eLife 2017; 6:29176. [PMID: 29130884 PMCID: PMC5706963 DOI: 10.7554/elife.29176] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 11/10/2017] [Indexed: 11/30/2022] Open
Abstract
Despite its central role in protein degradation little is known about the molecular mechanisms that sense, maintain, and regulate steady state concentration of ubiquitin in the cell. Here, we describe a novel mechanism for regulation of ubiquitin homeostasis that is mediated by phosphorylation of ubiquitin at the Ser57 position. We find that loss of Ppz phosphatase activity leads to defects in ubiquitin homeostasis that are at least partially attributable to elevated levels of Ser57 phosphorylated ubiquitin. Phosphomimetic mutation at the Ser57 position of ubiquitin conferred increased rates of endocytic trafficking and ubiquitin turnover. These phenotypes are associated with bypass of recognition by endosome-localized deubiquitylases - including Doa4 which is critical for regulation of ubiquitin recycling. Thus, ubiquitin homeostasis is significantly impacted by the rate of ubiquitin flux through the endocytic pathway and by signaling pathways that converge on ubiquitin itself to determine whether it is recycled or degraded in the vacuole.
Collapse
Affiliation(s)
- Sora Lee
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, United States
| | - Jessica M Tumolo
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, United States
| | - Aaron C Ehlinger
- Department of Biochemistry, Vanderbilt University, Nashville, United States
| | - Kristin K Jernigan
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, United States
| | - Susan J Qualls-Histed
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, United States
| | - Pi-Chiang Hsu
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, United States
| | - W Hayes McDonald
- Department of Biochemistry, Vanderbilt University, Nashville, United States.,Mass Spectrometry Research Center, Vanderbilt University, Nashville, United States
| | - Walter J Chazin
- Department of Biochemistry, Vanderbilt University, Nashville, United States
| | - Jason A MacGurn
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, United States
| |
Collapse
|
172
|
Kwon YT, Ciechanover A. The Ubiquitin Code in the Ubiquitin-Proteasome System and Autophagy. Trends Biochem Sci 2017; 42:873-886. [DOI: 10.1016/j.tibs.2017.09.002] [Citation(s) in RCA: 374] [Impact Index Per Article: 53.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 09/05/2017] [Accepted: 09/07/2017] [Indexed: 12/14/2022]
|
173
|
Ottis P, Toure M, Cromm PM, Ko E, Gustafson JL, Crews CM. Assessing Different E3 Ligases for Small Molecule Induced Protein Ubiquitination and Degradation. ACS Chem Biol 2017; 12:2570-2578. [PMID: 28767222 DOI: 10.1021/acschembio.7b00485] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proteolysis targeting chimera (PROTAC) technology, the recruitment of E3 ubiquitin ligases to induce the degradation of a protein target, is rapidly impacting chemical biology, as well as modern drug development. Here, we explore the universality of this approach by evaluating different E3 ubiquitin ligases, engineered in their substrate binding domains to accept a recruiting ligand. Five out of six E3 ligases were found to be amenable to recruitment for target degradation. Taking advantage of the tight spatiotemporal control of inducing ubiquitination on a preselected target in living cells, we focused on two of the engineered E3 ligases, βTRCP and parkin, to unravel their ubiquitination characteristics in comparison with the PROTAC-recruited endogenous E3 ligases VHL and cereblon.
Collapse
Affiliation(s)
- Philipp Ottis
- Department
of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, United States
| | - Momar Toure
- Department
of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, United States
| | - Philipp M. Cromm
- Department
of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, United States
| | - Eunhwa Ko
- Department
of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, United States
| | - Jeffrey L. Gustafson
- Department
of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, United States
| | - Craig M. Crews
- Department
of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, United States
- Department
of Chemistry, Yale University, New Haven, Connecticut, United States
- Department
of Pharmacology, Yale University, New Haven, Connecticut, United States
| |
Collapse
|
174
|
Superoxide drives progression of Parkin/PINK1-dependent mitophagy following translocation of Parkin to mitochondria. Cell Death Dis 2017; 8:e3097. [PMID: 29022898 PMCID: PMC5680585 DOI: 10.1038/cddis.2017.463] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 07/05/2017] [Accepted: 07/24/2017] [Indexed: 11/13/2022]
Abstract
Reactive oxygen species (ROS) and mitophagy are profoundly implicated in the pathogenesis of neurodegenerative diseases, such as Parkinson’s disease (PD). Several studies have suggested that ROS are not involved in mitochondrial translocation of Parkin which primes mitochondria for autophagic elimination. However, whether ROS play a role in the execution of mitophagy is unknown. In the present study, we show that carbonyl cyanide m-chlorophenylhydrazone (CCCP) treatment induced both mitochondrial depolarization and generation of ROS that were needed for the mitophagy process. Cells failed to proceed to complete mitophagy if CCCP treatment was discontinued even after recruitment of Parkin and autophagy machinery to mitochondria. Notably, treatment of pro-oxidant was able to replace CCCP treatment to take mitophagy forward, while it alone was insufficient to induce translocation of Parkin to mitochondria or autophagic clearance of mitochondria. In addition, an SOD mimetic that attenuated the superoxide level suppressed mitophagy, while an SOD inhibitor accumulated cellular superoxide and promoted mitophagy. Furthermore, blockage of the p38 signaling pathway inhibited mitophagy induced by ROS, suggesting that it may contribute to the activation of ROS-mediated mitophagy. Together, our study sheds light on the link between ROS and mitophagy at a molecular level, and suggests the therapeutic potential of regulating mitophagy through the superoxide–p38–mitophagy axis.
Collapse
|
175
|
Structural basis for specific cleavage of Lys6-linked polyubiquitin chains by USP30. Nat Struct Mol Biol 2017; 24:911-919. [PMID: 28945247 DOI: 10.1038/nsmb.3469] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 08/17/2017] [Indexed: 12/21/2022]
Abstract
Parkin ubiquitin (Ub) ligase (also known as PARK2) ubiquitinates damaged mitochondria for their clearance and quality control. USP30 deubiquitinase opposes parkin-mediated Ub-chain formation on mitochondria by preferentially cleaving Lys6-linked Ub chains. Here, we report the crystal structure of zebrafish USP30 in complex with a Lys6-linked diubiquitin (diUb or Ub2) at 1.87-Å resolution. The distal Ub-recognition mechanism of USP30 is similar to those of other USP family members, whereas Phe4 and Thr12 of the proximal Ub are recognized by a USP30-specific surface. Structure-based mutagenesis showed that the interface with the proximal Ub is critical for the specific cleavage of Lys6-linked Ub chains, together with the noncanonical catalytic triad composed of Cys-His-Ser. The structural findings presented here reveal a mechanism for Lys6-linkage-specific deubiquitination.
Collapse
|
176
|
Gersch M, Gladkova C, Schubert AF, Michel MA, Maslen S, Komander D. Mechanism and regulation of the Lys6-selective deubiquitinase USP30. Nat Struct Mol Biol 2017; 24:920-930. [PMID: 28945249 PMCID: PMC5757785 DOI: 10.1038/nsmb.3475] [Citation(s) in RCA: 153] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 08/30/2017] [Indexed: 12/24/2022]
Abstract
Damaged mitochondria undergo mitophagy, a specialized form of autophagy that is initiated by the protein kinase PINK1 and the ubiquitin E3 ligase Parkin. Ubiquitin-specific protease USP30 antagonizes Parkin-mediated ubiquitination events on mitochondria and is a key negative regulator of mitophagy. Parkin and USP30 both show a preference for assembly or disassembly, respectively, of Lys6-linked polyubiquitin, a chain type that has not been well studied. Here we report crystal structures of human USP30 bound to monoubiquitin and Lys6-linked diubiquitin, which explain how USP30 achieves Lys6-linkage preference through unique ubiquitin binding interfaces. We assess the interplay between USP30, PINK1 and Parkin and show that distally phosphorylated ubiquitin chains impair USP30 activity. Lys6-linkage-specific affimers identify numerous mitochondrial substrates for this modification, and we show that USP30 regulates Lys6-polyubiquitinated TOM20. Our work provides insights into the architecture, activity and regulation of USP30, which will aid drug design against this and related enzymes.
Collapse
Affiliation(s)
- Malte Gersch
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | | | | | - Martin A Michel
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Sarah Maslen
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - David Komander
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| |
Collapse
|
177
|
Mass spectrometry techniques for studying the ubiquitin system. Biochem Soc Trans 2017; 45:1137-1148. [PMID: 28939693 DOI: 10.1042/bst20170091] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 08/07/2017] [Accepted: 08/10/2017] [Indexed: 11/17/2022]
Abstract
Post-translational control of proteins through covalent attachment of ubiquitin plays important roles in all eukaryotic cell functions. The ubiquitin system in humans consists of 2 E1, 35 E2 and >600 E3 ubiquitin ligases as well as hundreds of deubiquitylases, which reverse ubiquitin attachment. Moreover, there are hundreds of proteins with ubiquitin-binding domains that bind one of the eight possible polyubiquitin chains. Dysfunction of the ubiquitin system is associated with many diseases such as cancer, autoimmunity and neurodegeneration, demonstrating the importance of ubiquitylation. Therefore, enzymes of the ubiquitin system are considered highly attractive drug targets. In recent years, mass spectrometry (MS)-based techniques have become increasingly important in the deciphering of the ubiquitin system. This short review addresses the state-of-the-art MS techniques for the identification of ubiquitylated proteins and their ubiquitylation sites. We also discuss the identification and quantitation of ubiquitin chain topologies and highlight how the activity of enzymes in the ubiquitin pathway can be measured. Finally, we present current MS tools that can be used for drug discovery in the ubiquitin space.
Collapse
|
178
|
Michel MA, Swatek KN, Hospenthal MK, Komander D. Ubiquitin Linkage-Specific Affimers Reveal Insights into K6-Linked Ubiquitin Signaling. Mol Cell 2017; 68:233-246.e5. [PMID: 28943312 PMCID: PMC5640506 DOI: 10.1016/j.molcel.2017.08.020] [Citation(s) in RCA: 136] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 07/13/2017] [Accepted: 08/22/2017] [Indexed: 12/30/2022]
Abstract
Several ubiquitin chain types have remained unstudied, mainly because tools and techniques to detect these posttranslational modifications are scarce. Linkage-specific antibodies have shaped our understanding of the roles and dynamics of polyubiquitin signals but are available for only five out of eight linkage types. We here characterize K6- and K33-linkage-specific "affimer" reagents as high-affinity ubiquitin interactors. Crystal structures of affimers bound to their cognate chain types reveal mechanisms of specificity and a K11 cross-reactivity in the K33 affimer. Structure-guided improvements yield superior affinity reagents suitable for western blotting, confocal fluorescence microscopy and pull-down applications. This allowed us to identify RNF144A and RNF144B as E3 ligases that assemble K6-, K11-, and K48-linked polyubiquitin in vitro. A protocol to enrich K6-ubiquitinated proteins from cells identifies HUWE1 as a main E3 ligase for this chain type, and we show that mitofusin-2 is modified with K6-linked polyubiquitin in a HUWE1-dependent manner.
Collapse
Affiliation(s)
- Martin A Michel
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Kirby N Swatek
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Manuela K Hospenthal
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - David Komander
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
| |
Collapse
|
179
|
Yang A, Cho K, Park HS. Chemical biology approaches for studying posttranslational modifications. RNA Biol 2017; 15:427-440. [PMID: 28901832 DOI: 10.1080/15476286.2017.1360468] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Posttranslational modification (PTM) is a key mechanism for regulating diverse protein functions, and thus critically affects many essential biological processes. Critical for systematic study of the effects of PTMs is the ability to obtain recombinant proteins with defined and homogenous modifications. To this end, various synthetic and chemical biology approaches, including genetic code expansion and protein chemical modification methods, have been developed. These methods have proven effective for generating site-specific authentic modifications or structural mimics, and have demonstrated their value for in vitro and in vivo functional studies of diverse PTMs. This review will discuss recent advances in chemical biology strategies and their application to various PTM studies.
Collapse
Affiliation(s)
- Aerin Yang
- a Department of Chemistry , Korea Advanced Institute of Science and Technology , 291 Daehak-ro, Yuseong-gu , Daejeon , Republic of Korea
| | - Kyukwang Cho
- a Department of Chemistry , Korea Advanced Institute of Science and Technology , 291 Daehak-ro, Yuseong-gu , Daejeon , Republic of Korea
| | - Hee-Sung Park
- a Department of Chemistry , Korea Advanced Institute of Science and Technology , 291 Daehak-ro, Yuseong-gu , Daejeon , Republic of Korea
| |
Collapse
|
180
|
Abstract
Host anti-viral innate-immune signalling pathways are regulated by a variety of post-translation modifications including ubiquitination, which is critical to regulate various signalling pathways for synthesis of anti-viral molecules. A homeostasis of host immune responses, induced due to viral infection and further ubiquitination, is maintained by the action of deubiquitinases (DUB). Infecting viruses utilize the process of deubiquitination for tricking host immune system wherein viral DUBs compete with host DUBs for inhibition of innate-immune anti-viral signalling pathways, which instead of maintaining an immune homeostasis bring about virus-mediated pathogenesis. This suggests that viruses co-evolve with their hosts to acquire similar machinery for tricking immune surveillance and establishing infection.
Collapse
Affiliation(s)
- Puja Kumari
- a Department of Biological Sciences, Laboratory of Immunology and Infectious Disease Biology , Indian Institute of Science Education and Research (IISER) Bhopal , Bhopal , India
| | - Himanshu Kumar
- a Department of Biological Sciences, Laboratory of Immunology and Infectious Disease Biology , Indian Institute of Science Education and Research (IISER) Bhopal , Bhopal , India
| |
Collapse
|
181
|
O'Mealey GB, Plafker KS, Berry WL, Janknecht R, Chan JY, Plafker SM. A PGAM5-KEAP1-Nrf2 complex is required for stress-induced mitochondrial retrograde trafficking. J Cell Sci 2017; 130:3467-3480. [PMID: 28839075 DOI: 10.1242/jcs.203216] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 08/20/2017] [Indexed: 12/12/2022] Open
Abstract
The Nrf2 transcription factor is a master regulator of the cellular anti-stress response. A population of the transcription factor associates with the mitochondria through a complex with KEAP1 and the mitochondrial outer membrane histidine phosphatase, PGAM5. To determine the function of this mitochondrial complex, we knocked down each component and assessed mitochondrial morphology and distribution. We discovered that depletion of Nrf2 or PGAM5, but not KEAP1, inhibits mitochondrial retrograde trafficking induced by proteasome inhibition. Mechanistically, this disrupted motility results from aberrant degradation of Miro2, a mitochondrial GTPase that links mitochondria to microtubules. Rescue experiments demonstrate that this Miro2 degradation involves the KEAP1-cullin-3 E3 ubiquitin ligase and the proteasome. These data are consistent with a model in which an intact complex of PGAM5-KEAP1-Nrf2 preserves mitochondrial motility by suppressing dominant-negative KEAP1 activity. These data further provide a mechanistic explanation for how age-dependent declines in Nrf2 expression impact mitochondrial motility and induce functional deficits commonly linked to neurodegeneration.
Collapse
Affiliation(s)
- Gary B O'Mealey
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73118, USA.,Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73118, USA
| | - Kendra S Plafker
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73118, USA
| | - William L Berry
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73118, USA
| | - Ralf Janknecht
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73118, USA
| | - Jefferson Y Chan
- Department of Pathology, University of Irvine School of Medicine, Irvine, CA 92697, USA
| | - Scott M Plafker
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73118, USA
| |
Collapse
|
182
|
Wong YK, Zhang J, Hua ZC, Lin Q, Shen HM, Wang J. Recent advances in quantitative and chemical proteomics for autophagy studies. Autophagy 2017; 13:1472-1486. [PMID: 28820289 DOI: 10.1080/15548627.2017.1313944] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Macroautophagy/autophagy is an evolutionarily well-conserved cellular degradative process with important biological functions that is closely implicated in health and disease. In recent years, quantitative mass spectrometry-based proteomics and chemical proteomics have emerged as important tools for the study of autophagy, through large-scale unbiased analysis of the proteome or through highly specific and accurate analysis of individual proteins of interest. At present, a variety of approaches have been successfully applied, including (i) expression and interaction proteomics for the study of protein post-translational modifications, (ii) investigating spatio-temporal dynamics of protein synthesis and degradation, and (iii) direct determination of protein activity and profiling molecular targets in the autophagic process. In this review, we attempted to provide an overview of principles and techniques relevant to the application of quantitative and chemical proteomics methods to autophagy, and outline the current landscape as well as future outlook of these methods in autophagy research.
Collapse
Affiliation(s)
- Yin-Kwan Wong
- a Department of Physiology, Yong Loo Lin School of Medicine , National University of Singapore , Singapore
| | - Jianbin Zhang
- b Department of Oncology, Clinical Research Institute , Zhejiang Provincial People's Hospital , Hangzhou , China
| | - Zi-Chun Hua
- c Changzhou High-Tech Research Institute of Nanjing University and the State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences , Nanjing University , Nanjing , China
| | - Qingsong Lin
- d Department of Biological Sciences , National University of Singapore , Singapore
| | - Han-Ming Shen
- a Department of Physiology, Yong Loo Lin School of Medicine , National University of Singapore , Singapore.,e NUS Graduate School for Integrative Sciences and Engineering , National University of Singapore , Singapore
| | - Jigang Wang
- a Department of Physiology, Yong Loo Lin School of Medicine , National University of Singapore , Singapore.,c Changzhou High-Tech Research Institute of Nanjing University and the State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences , Nanjing University , Nanjing , China
| |
Collapse
|
183
|
Torres-Odio S, Key J, Hoepken HH, Canet-Pons J, Valek L, Roller B, Walter M, Morales-Gordo B, Meierhofer D, Harter PN, Mittelbronn M, Tegeder I, Gispert S, Auburger G. Progression of pathology in PINK1-deficient mouse brain from splicing via ubiquitination, ER stress, and mitophagy changes to neuroinflammation. J Neuroinflammation 2017; 14:154. [PMID: 28768533 PMCID: PMC5541666 DOI: 10.1186/s12974-017-0928-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 07/26/2017] [Indexed: 12/18/2022] Open
Abstract
Background PINK1 deficiency causes the autosomal recessive PARK6 variant of Parkinson’s disease. PINK1 activates ubiquitin by phosphorylation and cooperates with the downstream ubiquitin ligase PARKIN, to exert quality control and control autophagic degradation of mitochondria and of misfolded proteins in all cell types. Methods Global transcriptome profiling of mouse brain and neuron cultures were assessed in protein-protein interaction diagrams and by pathway enrichment algorithms. Validation by quantitative reverse transcriptase polymerase chain reaction and immunoblots was performed, including human neuroblastoma cells and patient primary skin fibroblasts. Results In a first approach, we documented Pink1-deleted mice across the lifespan regarding brain mRNAs. The expression changes were always subtle, consistently affecting “intracellular membrane-bounded organelles”. Significant anomalies involved about 250 factors at age 6 weeks, 1300 at 6 months, and more than 3500 at age 18 months in the cerebellar tissue, including Srsf10, Ube3a, Mapk8, Creb3, and Nfkbia. Initially, mildly significant pathway enrichment for the spliceosome was apparent. Later, highly significant networks of ubiquitin-mediated proteolysis and endoplasmic reticulum protein processing occurred. Finally, an enrichment of neuroinflammation factors appeared, together with profiles of bacterial invasion and MAPK signaling changes—while mitophagy had minor significance. Immunohistochemistry showed pronounced cellular response of Iba1-positive microglia and GFAP-positive astrocytes; brain lipidomics observed increases of ceramides as neuroinflammatory signs at old age. In a second approach, we assessed PINK1 deficiency in the presence of a stressor. Marked dysregulations of microbial defense factors Ifit3 and Rsad2 were consistently observed upon five analyses: (1) Pink1−/− primary neurons in the first weeks after brain dissociation, (2) aged Pink1−/− midbrain with transgenic A53T-alpha-synuclein overexpression, (3) human neuroblastoma cells with PINK1-knockdown and murine Pink1−/− embryonal fibroblasts undergoing acute starvation, (4) triggering mitophagy in these cells with trifluoromethoxy carbonylcyanide phenylhydrazone (FCCP), and (5) subjecting them to pathogenic RNA-analogue poly(I:C). The stress regulation of MAVS, RSAD2, DDX58, IFIT3, IFIT1, and LRRK2 was PINK1 dependent. Dysregulation of some innate immunity genes was also found in skin fibroblast cells from PARK6 patients. Conclusions Thus, an individual biomarker with expression correlating to progression was not identified. Instead, more advanced disease stages involved additional pathways. Hence, our results identify PINK1 deficiency as an early modulator of innate immunity in neurons, which precedes late stages of neuroinflammation during alpha-synuclein spreading. Electronic supplementary material The online version of this article (doi:10.1186/s12974-017-0928-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Sylvia Torres-Odio
- Experimental Neurology, Goethe University Medical School, 60590, Frankfurt am Main, Germany
| | - Jana Key
- Experimental Neurology, Goethe University Medical School, 60590, Frankfurt am Main, Germany
| | - Hans-Hermann Hoepken
- Experimental Neurology, Goethe University Medical School, 60590, Frankfurt am Main, Germany
| | - Júlia Canet-Pons
- Experimental Neurology, Goethe University Medical School, 60590, Frankfurt am Main, Germany
| | - Lucie Valek
- Institute of Clinical Pharmacology, Goethe University Medical School, 60590, Frankfurt am Main, Germany
| | - Bastian Roller
- Edinger-Institute (Institute of Neurology), Goethe University Medical School, 60590, Frankfurt am Main, Germany
| | - Michael Walter
- Institute for Medical Genetics, Eberhard-Karls-University of Tuebingen, 72076, Tuebingen, Germany
| | - Blas Morales-Gordo
- Department of Neurology, University Hospital San Cecilio, 18012, Granada, Spain
| | - David Meierhofer
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195, Berlin, Germany
| | - Patrick N Harter
- Edinger-Institute (Institute of Neurology), Goethe University Medical School, 60590, Frankfurt am Main, Germany
| | - Michel Mittelbronn
- Edinger-Institute (Institute of Neurology), Goethe University Medical School, 60590, Frankfurt am Main, Germany.,Luxembourg Centre of Neuropathology (LCNP), Luxembourg, Luxembourg.,Department of Pathology, Laboratoire National de Santé, Dudelange, Luxembourg.,Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg, Luxembourg.,Department of Oncology, Luxembourg Institute of Health, NORLUX Neuro-Oncology Laboratory, Luxembourg, Luxembourg
| | - Irmgard Tegeder
- Institute of Clinical Pharmacology, Goethe University Medical School, 60590, Frankfurt am Main, Germany
| | - Suzana Gispert
- Experimental Neurology, Goethe University Medical School, 60590, Frankfurt am Main, Germany
| | - Georg Auburger
- Experimental Neurology, Goethe University Medical School, 60590, Frankfurt am Main, Germany.
| |
Collapse
|
184
|
Park S, Foote PK, Krist DT, Rice SE, Statsyuk AV. UbMES and UbFluor: Novel probes for ring-between-ring (RBR) E3 ubiquitin ligase PARKIN. J Biol Chem 2017; 292:16539-16553. [PMID: 28710279 DOI: 10.1074/jbc.m116.773200] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Revised: 07/03/2017] [Indexed: 12/30/2022] Open
Abstract
Ring-between-ring (RBR) E3 ligases have been implicated in autoimmune disorders and neurodegenerative diseases. The functions of many RBR E3s are poorly defined, and their regulation is complex, involving post-translational modifications and allosteric regulation with other protein partners. The functional complexity of RBRs, coupled with the complexity of the native ubiquitination reaction that requires ATP and E1 and E2 enzymes, makes it difficult to study these ligases for basic research and therapeutic purposes. To address this challenge, we developed novel chemical probes, ubiquitin C-terminal fluorescein thioesters UbMES and UbFluor, to qualitatively and quantitatively assess the activity of the RBR E3 ligase PARKIN in a simple experimental setup and in real time using fluorescence polarization. First, we confirmed that PARKIN does not require an E2 enzyme for substrate ubiquitination, lysine selection, and polyubiquitin chain formation. Second, we confirmed that UbFluor quantitatively detects naturally occurring activation states of PARKIN caused by Ser65 phosphorylation (pPARKIN) and phosphorylated ubiquitin (pUb). Third, we showed that both pUb and the ubiquitin-accepting substrate contribute to maximal pPARKIN ubiquitin conjugation turnover. pUb enhances the transthiolation step, whereas the substrate clears the pPARKIN∼Ub thioester intermediate. Finally, we established that UbFluor can quantify activation or inhibition of PARKIN by structural mutations. These results demonstrate the feasibility of using UbFluor for quantitative studies of the biochemistry of RBR E3s and for high-throughput screening of small-molecule activators or inhibitors of PARKIN and other RBR E3 ligases.
Collapse
Affiliation(s)
- Sungjin Park
- From the Department of Cell and Molecular Biology, Northwestern University, Chicago, Illinois 60611
| | - Peter K Foote
- the Chemistry of Life Processes Institute, Department of Chemistry, Northwestern University, Evanston, Illinois 60208, and
| | - David T Krist
- the Chemistry of Life Processes Institute, Department of Chemistry, Northwestern University, Evanston, Illinois 60208, and
| | - Sarah E Rice
- From the Department of Cell and Molecular Biology, Northwestern University, Chicago, Illinois 60611
| | - Alexander V Statsyuk
- the Chemistry of Life Processes Institute, Department of Chemistry, Northwestern University, Evanston, Illinois 60208, and .,the Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, Texas 77204-5037
| |
Collapse
|
185
|
George S, Wang SM, Bi Y, Treidlinger M, Barber KR, Shaw GS, O'Donoghue P. Ubiquitin phosphorylated at Ser57 hyper-activates parkin. Biochim Biophys Acta Gen Subj 2017; 1861:3038-3046. [PMID: 28689991 DOI: 10.1016/j.bbagen.2017.06.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 06/26/2017] [Indexed: 11/28/2022]
Abstract
Malfunction of the ubiquitin (Ub) E3 ligase, parkin, leads to defects in mitophagy and protein quality control linked to Parkinson's disease. Parkin activity is stimulated by phosphorylation of Ub at Ser65 (pUbS65). Since the upstream kinase is only known for Ser65 (PINK1), the biochemical function of other phosphorylation sites on Ub remain largely unknown. We used fluorescently labelled and site-specifically phosphorylated Ub substrates to quantitatively relate the position and stoichiometry of Ub phosphorylation to parkin activation. Fluorescence measurements show that pUbS65-stimulated parkin is 5-fold more active than auto-inhibited and un-stimulated parkin, which catalyzes a basal level of auto-ubiquitination. We consistently observed a low but detectable level of parkin activity with pUbS12. Strikingly, pUbS57 hyper-activates parkin, and our data demonstrate that parkin is able to selectively synthesize poly-pUbS57 chains, even when 90% of the Ub in the reaction is un-phosphorylated. We further found that parkin ubiquitinates its physiological substrate Miro-1 with chains solely composed of pUbS65 and more efficiently with pUbS57 chains. Parkin hyper-activation by pUbS57 demonstrates the first PINK1-independent route to active parkin, revealing the roles of multiple ubiquitin phosphorylation sites in governing parkin stimulation and catalytic activity. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.
Collapse
Affiliation(s)
- Susanna George
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Sabrina M Wang
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Yumin Bi
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Margot Treidlinger
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Kathryn R Barber
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Gary S Shaw
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada; Department of Chemistry, The University of Western Ontario, London, ON N6A 5C1, Canada.
| | - Patrick O'Donoghue
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada; Department of Chemistry, The University of Western Ontario, London, ON N6A 5C1, Canada.
| |
Collapse
|
186
|
Abstract
Autophagy and the ubiquitin-proteasome system are the two major quality control pathways responsible for cellular homeostasis. As such, they provide protection against age-associated changes and a plethora of human diseases. Ubiquitination is utilized as a degradation signal by both systems, albeit in different ways, to mark cargoes for proteasomal and lysosomal degradation. Both systems intersect and communicate at multiple points to coordinate their actions in proteostasis and organelle homeostasis. This review summarizes molecular details of how proteasome and autophagy pathways are functionally interconnected in cells and indicates common principles and nodes of communication that can be therapeutically exploited.
Collapse
Affiliation(s)
- Ivan Dikic
- Institute of Biochemistry II, School of Medicine, Goethe University, 60598 Frankfurt am Main, Germany; .,Buchmann Institute for Molecular Life Sciences, Goethe University, 60438 Frankfurt am Main, Germany
| |
Collapse
|
187
|
Abstract
Ubiquitylation is essential for signal transduction as well as cell division and differentiation in all eukaryotes. Substrate modifications range from a single ubiquitin molecule to complex polymeric chains, with different types of ubiquitylation often eliciting distinct outcomes. The recent identification of novel chain topologies has improved our understanding of how ubiquitylation establishes precise communication within cells. Here, we discuss how the increasing complexity of ubiquitylation is employed to ensure robust and faithful signal transduction in eukaryotic cells.
Collapse
|
188
|
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] [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.
Collapse
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
| |
Collapse
|
189
|
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: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [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.
Collapse
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
| |
Collapse
|
190
|
Kumar A, Chaugule VK, Condos TEC, Barber KR, Johnson C, Toth R, Sundaramoorthy R, Knebel A, Shaw GS, Walden H. Parkin-phosphoubiquitin complex reveals cryptic ubiquitin-binding site required for RBR ligase activity. Nat Struct Mol Biol 2017; 24:475-483. [PMID: 28414322 PMCID: PMC5420311 DOI: 10.1038/nsmb.3400] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 03/16/2017] [Indexed: 12/20/2022]
Abstract
RING-between-RING (RBR) E3 ligases are a class of ubiquitin ligases distinct from RING or HECT E3 ligases. An important RBR ligase is Parkin, mutations in which lead to early-onset hereditary Parkinsonism. Parkin and other RBR ligases share a catalytic RBR module but are usually autoinhibited and activated via distinct mechanisms. Recent insights into Parkin regulation predict large, unknown conformational changes during Parkin activation. However, current data on active RBR ligases reflect the absence of regulatory domains. Therefore, it remains unclear how individual RBR ligases are activated, and whether they share a common mechanism. We now report the crystal structure of a human Parkin-phosphoubiquitin complex, which shows that phosphoubiquitin binding induces movement in the 'in-between RING' (IBR) domain to reveal a cryptic ubiquitin-binding site. Mutation of this site negatively affects Parkin's activity. Furthermore, ubiquitin binding promotes cooperation between Parkin molecules, which suggests a role for interdomain association in the RBR ligase mechanism.
Collapse
Affiliation(s)
- Atul Kumar
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences University of Dundee, Dundee, UK
| | - Viduth K Chaugule
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences University of Dundee, Dundee, UK
| | - Tara E C Condos
- Department of Biochemistry, Schulich School of Medicine and
Dentistry, University of Western Ontario, London, ON, Canada
| | - Kathryn R Barber
- Department of Biochemistry, Schulich School of Medicine and
Dentistry, University of Western Ontario, London, ON, Canada
| | - Clare Johnson
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences University of Dundee, Dundee, UK
| | - Rachel Toth
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences University of Dundee, Dundee, UK
| | | | - Axel Knebel
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences University of Dundee, Dundee, UK
| | - Gary S Shaw
- Department of Biochemistry, Schulich School of Medicine and
Dentistry, University of Western Ontario, London, ON, Canada
| | - Helen Walden
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences University of Dundee, Dundee, UK
| |
Collapse
|
191
|
McWilliams TG, Muqit MM. PINK1 and Parkin: emerging themes in mitochondrial homeostasis. Curr Opin Cell Biol 2017; 45:83-91. [PMID: 28437683 DOI: 10.1016/j.ceb.2017.03.013] [Citation(s) in RCA: 232] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 02/22/2017] [Accepted: 03/22/2017] [Indexed: 12/23/2022]
Abstract
The Parkinson's disease (PD)-associated protein kinase, PTEN-induced putative kinase1 (PINK1), and ubiquitin E3 ligase Parkin, function in a common signalling pathway known to regulate mitochondrial network homeostasis and quality control, including mitophagy. The multistep activation of this pathway, as well as an unexpected convergence between the post-translational modifications of ubiquitylation and phosphorylation, has added breadth to our understanding of cellular damage responses during human disease. In concert with these new insights in signal transduction, unique modalities and signatures of vertebrate mitophagy have been unravelled in vivo for the very first time. The cell biology of mammalian mitophagy, and the roles of PINK1-Parkin signalling in vivo have emerged to be more complex than previously thought.
Collapse
Affiliation(s)
- Thomas G McWilliams
- MRC Protein Phosphorylation and Ubiquitylation Unit, The Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Miratul Mk Muqit
- MRC Protein Phosphorylation and Ubiquitylation Unit, The Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK; School of Medicine, University of Dundee, Dundee DD1 9SY, UK.
| |
Collapse
|
192
|
Ubiquitin and Parkinson's disease through the looking glass of genetics. Biochem J 2017; 474:1439-1451. [PMID: 28408429 PMCID: PMC5390927 DOI: 10.1042/bcj20160498] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Revised: 02/20/2017] [Accepted: 02/20/2017] [Indexed: 12/12/2022]
Abstract
Biochemical alterations found in the brains of Parkinson's disease (PD) patients indicate that cellular stress is a major driver of dopaminergic neuronal loss. Oxidative stress, mitochondrial dysfunction, and ER stress lead to impairment of the homeostatic regulation of protein quality control pathways with a consequent increase in protein misfolding and aggregation and failure of the protein degradation machinery. Ubiquitin signalling plays a central role in protein quality control; however, prior to genetic advances, the detailed mechanisms of how impairment in the ubiquitin system was linked to PD remained mysterious. The discovery of mutations in the α-synuclein gene, which encodes the main protein misfolded in PD aggregates, together with mutations in genes encoding ubiquitin regulatory molecules, including PTEN-induced kinase 1 (PINK1), Parkin, and FBX07, has provided an opportunity to dissect out the molecular basis of ubiquitin signalling disruption in PD, and this knowledge will be critical for developing novel therapeutic strategies in PD that target the ubiquitin system.
Collapse
|
193
|
Ke S, Zhou T, Yang P, Wang Y, Zhang P, Chen K, Ren L, Ye S. Gold nanoparticles enhance TRAIL sensitivity through Drp1-mediated apoptotic and autophagic mitochondrial fission in NSCLC cells. Int J Nanomedicine 2017; 12:2531-2551. [PMID: 28408823 PMCID: PMC5383076 DOI: 10.2147/ijn.s129274] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Although tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) and its agonistic receptors have been identified as highly promising antitumor agents preferentially eliminating cancer cells with minimal damage, the emergence of TRAIL resistance in most cancers may contribute to therapeutic failure. Thus, there is an urgent need for new approaches to overcome TRAIL resistance. Gold nanoparticles (AuNPs) are one of the most promising nanomaterials that show immense antitumor potential via targeting various cellular and molecular processes; however, the effects of AuNPs on TRAIL sensitivity in cancer cells remain unclear. In this study, we found that AuNPs combined with TRAIL exhibited a greater potency in promoting apoptosis in non-small-cell lung cancer (NSCLC) cells compared with TRAIL alone, suggesting that AuNPs sensitize cancer cells to TRAIL. Further experiments demonstrated that the combination of TRAIL and AuNPs was more effective in causing excessive mitochondrial fragmentation in cancer cells accompanied by a dramatic increase in mitochondrial recruitment of dynamin-related protein 1 (Drp1), mitochondrial dysfunctions, and enhancement of autophagy induction. Small interfering RNA (siRNA) silencing of Drp1 or inhibition of autophagy could effectively alleviate apoptosis in cells exposed to TRAIL combined with AuNPs. In vivo studies revealed that AuNPs augmented TRAIL sensitivity in tumor-bearing mice. Our data indicated that AuNPs potentiate apoptotic response to TRAIL in NSCLC cells through Drp1-dependent mitochondrial fission, and TRAIL combined with AuNPs can be a potential chemotherapeutic strategy for the treatment of NSCLC.
Collapse
Affiliation(s)
- Sunkui Ke
- Department of Thoracic Surgery, Zhongshan Hospital of Xiamen University
| | - Tong Zhou
- Department of Biomaterials, College of Materials, Xiamen University
| | - Peiyan Yang
- Department of Surgery, First Affiliated Hospital of Xiamen University, Xiamen University, Xiamen, People’s Republic of China
| | - Yange Wang
- Department of Biomaterials, College of Materials, Xiamen University
| | - Peng Zhang
- Department of Biomaterials, College of Materials, Xiamen University
| | - Keman Chen
- Department of Biomaterials, College of Materials, Xiamen University
| | - Lei Ren
- Department of Biomaterials, College of Materials, Xiamen University
| | - Shefang Ye
- Department of Biomaterials, College of Materials, Xiamen University
| |
Collapse
|
194
|
Tang MY, Vranas M, Krahn AI, Pundlik S, Trempe JF, Fon EA. Structure-guided mutagenesis reveals a hierarchical mechanism of Parkin activation. Nat Commun 2017; 8:14697. [PMID: 28276439 PMCID: PMC5347139 DOI: 10.1038/ncomms14697] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 01/24/2017] [Indexed: 01/12/2023] Open
Abstract
Parkin and PINK1 function in a common pathway to clear damaged mitochondria. Parkin exists in an auto-inhibited conformation stabilized by multiple interdomain interactions. The binding of PINK1-generated phospho-ubiquitin and the phosphorylation of the ubiquitin-like (Ubl) domain of Parkin at Ser65 release its auto-inhibition, but how and when these events take place in cells remain to be defined. Here we show that mutations that we designed to activate Parkin by releasing the Repressor Element of Parkin (REP) domain, or by disrupting the interface between the RING0:RING2 domains, can completely rescue mutations in the Parkin Ubl that are defective in mitochondrial autophagy. Using a FRET reporter assay we show that Parkin undergoes a conformational change upon phosphorylation that can be mimicked by mutating Trp403 in the REP. We propose a hierarchical model whereby pUb binding on mitochondria enables Parkin phosphorylation, which, in turn, leads to REP removal, E3 ligase activation and mitophagy. Parkin and PINK1 are involved in damaged mitochondria clearance; however the sequence of events of Parkin activation is not clear. Here, the authors show that binding to phospho-ubiquitin on mitochondria enables Parkin phosphorylation, which allows Repressor Element of Parkin removal, E3 ligase activation and mitophagy.
Collapse
Affiliation(s)
- Matthew Y Tang
- McGill Parkinson Program, Neurodegenerative Diseases Group, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montréal, Québec, Canada H3A 2B4
| | - Marta Vranas
- Groupe de Recherche Axé sur la Structure des Protéines, Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada H3G 1Y6
| | - Andrea I Krahn
- McGill Parkinson Program, Neurodegenerative Diseases Group, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montréal, Québec, Canada H3A 2B4
| | - Shayal Pundlik
- McGill Parkinson Program, Neurodegenerative Diseases Group, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montréal, Québec, Canada H3A 2B4
| | - Jean-François Trempe
- Groupe de Recherche Axé sur la Structure des Protéines, Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada H3G 1Y6
| | - Edward A Fon
- McGill Parkinson Program, Neurodegenerative Diseases Group, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montréal, Québec, Canada H3A 2B4
| |
Collapse
|
195
|
Fiorese CJ, Haynes CM. Integrating the UPR mt into the mitochondrial maintenance network. Crit Rev Biochem Mol Biol 2017; 52:304-313. [PMID: 28276702 DOI: 10.1080/10409238.2017.1291577] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Mitochondrial function is central to many different processes in the cell, from oxidative phosphorylation to the synthesis of iron-sulfur clusters. Therefore, mitochondrial dysfunction underlies a diverse array of diseases, from neurodegenerative diseases to cancer. Stress can be communicated to the cytosol and nucleus from the mitochondria through many different signals, and in response the cell can effect everything from transcriptional to post-transcriptional responses to protect the mitochondrial network. How these responses are coordinated have only recently begun to be understood. In this review, we explore how the cell maintains mitochondrial function, focusing on the mitochondrial unfolded protein response (UPRmt), a transcriptional response that can activate a wide array of programs to repair and restore mitochondrial function.
Collapse
Affiliation(s)
- Christopher J Fiorese
- a Department of Molecular Cell and Cancer Biology , University of Massachusetts Medical School , Worcester , MA , USA.,b BCMB Allied Program , Weill Cornell Medical College , New York , NY , USA
| | - Cole M Haynes
- a Department of Molecular Cell and Cancer Biology , University of Massachusetts Medical School , Worcester , MA , USA.,b BCMB Allied Program , Weill Cornell Medical College , New York , NY , USA
| |
Collapse
|
196
|
Clague MJ, Urbé S. Integration of cellular ubiquitin and membrane traffic systems: focus on deubiquitylases. FEBS J 2017; 284:1753-1766. [PMID: 28064438 PMCID: PMC5484354 DOI: 10.1111/febs.14007] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 12/29/2016] [Accepted: 01/06/2017] [Indexed: 12/17/2022]
Abstract
The cell is comprised of integrated multilevel protein networks or systems. The ubiquitin, protein homeostasis and membrane trafficking systems are highly integrated. Here, we look at the influence of reversible ubiquitylation on membrane trafficking and organelle dynamics. We review the regulation of endocytic sorting, selective autophagy and the secretory pathway by ubiquitin signals, with a particular focus on detailing the contribution of deubiquitylating enzymes.
Collapse
Affiliation(s)
- Michael J Clague
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, UK
| | - Sylvie Urbé
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, UK
| |
Collapse
|
197
|
Keck F, Brooks-Faulconer T, Lark T, Ravishankar P, Bailey C, Salvador-Morales C, Narayanan A. Altered mitochondrial dynamics as a consequence of Venezuelan Equine encephalitis virus infection. Virulence 2017; 8:1849-1866. [PMID: 28075229 DOI: 10.1080/21505594.2016.1276690] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Mitochondria are sentinel organelles that are impacted by various forms of cellular stress, including viral infections. While signaling events associated with mitochondria, including those activated by pathogen associated molecular patterns (PAMPs), are widely studied, alterations in mitochondrial distribution and changes in mitochondrial dynamics are also beginning to be associated with cellular insult. Cells of neuronal origin have been demonstrated to display remarkable alterations in several instances, including neurodegenerative disorders. Venezuelan Equine Encephalitis Virus (VEEV) is a New World alphavirus that infects neuronal cells and contributes to an encephalitic phenotype. We demonstrate that upon infection by the vaccine strain of VEEV (TC-83), astrocytoma cells experience a robust drop in mitochondrial activity, which corresponds with an increased accumulation of reactive oxygen species (ROS) in an infection-dependent manner. Infection status also corresponds with a prominent perinuclear accumulation of mitochondria. Cellular enzymatic machinery, including PINK1 and Parkin, appears to be enriched in mitochondrial fractions as compared with uninfected cells, which is indicative of mitochondrial damage. Dynamin related protein 1 (Drp1), a protein that is associated with mitochondrial fission, demonstrated a modest enrichment in mitochondrial fractions of infected cells. Treatment with an inhibitor of mitochondrial fission, Mdivi-1, led to a decrease in caspase cleavage, suggesting that mitochondrial fission was likely to contribute to apoptosis of infected cells. Finally, our data demonstrate that mitophagy ensues in infected cells. In combination, our data suggest that VEEV infection results in significant changes in the mitochondrial landscape that may influence pathological outcomes in the infected cell.
Collapse
Affiliation(s)
- Forrest Keck
- a National Center for Biodefense and Infectious Diseases, School of Systems Biology, George Mason University , Manassas , VA , USA
| | - Taryn Brooks-Faulconer
- a National Center for Biodefense and Infectious Diseases, School of Systems Biology, George Mason University , Manassas , VA , USA
| | - Tyler Lark
- a National Center for Biodefense and Infectious Diseases, School of Systems Biology, George Mason University , Manassas , VA , USA
| | | | - Charles Bailey
- a National Center for Biodefense and Infectious Diseases, School of Systems Biology, George Mason University , Manassas , VA , USA
| | | | - Aarthi Narayanan
- a National Center for Biodefense and Infectious Diseases, School of Systems Biology, George Mason University , Manassas , VA , USA
| |
Collapse
|
198
|
Barodia SK, Creed RB, Goldberg MS. Parkin and PINK1 functions in oxidative stress and neurodegeneration. Brain Res Bull 2016; 133:51-59. [PMID: 28017782 DOI: 10.1016/j.brainresbull.2016.12.004] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 12/07/2016] [Accepted: 12/15/2016] [Indexed: 12/12/2022]
Abstract
Loss-of-function mutations in the genes encoding Parkin and PINK1 are causally linked to autosomal recessive Parkinson's disease (PD). Parkin, an E3 ubiquitin ligase, and PINK1, a mitochondrial-targeted kinase, function together in a common pathway to remove dysfunctional mitochondria by autophagy. Presumably, deficiency for Parkin or PINK1 impairs mitochondrial autophagy and thereby increases oxidative stress due to the accumulation of dysfunctional mitochondria that release reactive oxygen species. Parkin and PINK1 likely have additional functions that may be relevant to the mechanisms by which mutations in these genes cause neurodegeneration, such as regulating inflammation, apoptosis, or dendritic morphogenesis. Here we briefly review what is known about functions of Parkin and PINK1 related to oxidative stress and neurodegeneration.
Collapse
Affiliation(s)
- Sandeep K Barodia
- Center for Neurodegeneration and Experimental Therapeutics, Department of Neurology, The University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - Rose B Creed
- Center for Neurodegeneration and Experimental Therapeutics, Department of Neurology, The University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - Matthew S Goldberg
- Center for Neurodegeneration and Experimental Therapeutics, Department of Neurology, The University of Alabama at Birmingham, Birmingham, AL 35294, United States; Department of Neurobiology, The University of Alabama at Birmingham, Birmingham, AL 35294, United States.
| |
Collapse
|
199
|
Callegari S, Oeljeklaus S, Warscheid B, Dennerlein S, Thumm M, Rehling P, Dudek J. Phospho-ubiquitin-PARK2 complex as a marker for mitophagy defects. Autophagy 2016; 13:201-211. [PMID: 27846363 DOI: 10.1080/15548627.2016.1254852] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The E3 ubiquitin ligase PARK2 and the mitochondrial protein kinase PINK1 are required for the initiation of mitochondrial damage-induced mitophagy. Together, PARK2 and PINK1 generate a phospho-ubiquitin signal on outer mitochondrial membrane proteins that triggers recruitment of the autophagy machinery. This paper describes the detection of a defined 500-kDa phospho-ubiquitin-rich PARK2 complex that accumulates on mitochondria upon treatment with the membrane uncoupler CCCP. Formation of this complex is dependent on the presence of PINK1 and is absent in mutant forms of PARK2, whereby mitophagy is also arrested. These results signify a functional signaling complex that is essential for the progression of mitophagy. The visualization of the PARK2 signaling complex represents a novel marker for this critical step in mitophagy and can be used to monitor mitophagy progression in PARK2 mutants and to uncover additional upstream factors required for PARK2-mediated mitophagy signaling.
Collapse
Affiliation(s)
- Sylvie Callegari
- a Department of Cellular Biochemistry , University Medical Center Göttingen , Göttingen , Germany
| | - Silke Oeljeklaus
- b University of Freiburg , Department of Biochemistry and Functional Proteomics , Institute of Biology II, Faculty of Biology , Freiburg , Germany
| | - Bettina Warscheid
- b University of Freiburg , Department of Biochemistry and Functional Proteomics , Institute of Biology II, Faculty of Biology , Freiburg , Germany.,c University of Freiburg, BIOSS Center for Biological Signaling Studies , Freiburg , Germany
| | - Sven Dennerlein
- a Department of Cellular Biochemistry , University Medical Center Göttingen , Göttingen , Germany
| | - Michael Thumm
- a Department of Cellular Biochemistry , University Medical Center Göttingen , Göttingen , Germany
| | - Peter Rehling
- a Department of Cellular Biochemistry , University Medical Center Göttingen , Göttingen , Germany.,d Max Planck Institute for Biophysical Chemistry , Göttingen , Germany
| | - Jan Dudek
- a Department of Cellular Biochemistry , University Medical Center Göttingen , Göttingen , Germany
| |
Collapse
|
200
|
Bingol B, Sheng M. Mechanisms of mitophagy: PINK1, Parkin, USP30 and beyond. Free Radic Biol Med 2016; 100:210-222. [PMID: 27094585 DOI: 10.1016/j.freeradbiomed.2016.04.015] [Citation(s) in RCA: 209] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/15/2016] [Accepted: 04/15/2016] [Indexed: 12/16/2022]
Abstract
Mitochondrial quality control is central for maintaining a healthy population of mitochondria. Two Parkinson's disease genes, mitochondrial kinase PINK1 and ubiquitin ligase Parkin, degrade damaged mitochondria though mitophagy. In this pathway, PINK1 senses mitochondrial damage and activates Parkin by phosphorylating Parkin and ubiquitin. Activated Parkin then builds ubiquitin chains on damaged mitochondria to tag them for degradation in lysosomes. USP30 deubiquitinase acts as a brake on mitophagy by opposing Parkin-mediated ubiquitination. Human genetic data point to a role for mitophagy defects in neurodegenerative diseases. This review highlights the molecular mechanisms of the mitophagy pathway and the recent advances in the understanding of mitophagy in vivo.
Collapse
Affiliation(s)
- Baris Bingol
- Department of Neuroscience, Genentech Inc, South San Francisco, CA 94080, USA.
| | - Morgan Sheng
- Department of Neuroscience, Genentech Inc, South San Francisco, CA 94080, USA
| |
Collapse
|