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An H, Zhou B, Hayakawa K, Durán Laforet V, Park JH, Nakamura Y, Mandeville ET, Liu N, Guo S, Yu Z, Shi J, Wu D, Li W, Lo EH, Ji X. ATF5-Mediated Mitochondrial Unfolded Protein Response (UPR mt) Protects Neurons Against Oxygen-Glucose Deprivation and Cerebral Ischemia. Stroke 2024; 55:1904-1913. [PMID: 38913800 DOI: 10.1161/strokeaha.123.045550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 05/09/2024] [Indexed: 06/26/2024]
Abstract
BACKGROUND The mitochondrial unfolded protein response (UPRmt) is an evolutionarily conserved mitochondrial response that is critical for maintaining mitochondrial and energetic homeostasis under cellular stress after tissue injury and disease. Here, we ask whether UPRmt may be a potential therapeutic target for ischemic stroke. METHODS We performed the middle cerebral artery occlusion and oxygen-glucose deprivation models to mimic ischemic stroke in vivo and in vitro, respectively. Oligomycin and meclizine were used to trigger the UPRmt. We used 2,3,5-triphenyltetrazolium chloride staining, behavioral tests, and Nissl staining to evaluate cerebral injury in vivo. The Cell Counting Kit-8 assay and the Calcein AM Assay Kit were conducted to test cerebral injury in vitro. RESULTS Inducing UPRmt with oligomycin protected neuronal cultures against oxygen-glucose deprivation. UPRmt could also be triggered with meclizine, and this Food and Drug Administration-approved drug also protected neurons against oxygen-glucose deprivation. Blocking UPRmt with siRNA against activating transcription factor 5 eliminated the neuroprotective effects of meclizine. In a mouse model of focal cerebral ischemia, pretreatment with meclizine was able to induce UPRmt in vivo, which reduced infarction and improved neurological outcomes. CONCLUSIONS These findings suggest that the UPRmt is important in maintaining the survival of neurons facing ischemic/hypoxic stress. The UPRmt mechanism may provide a new therapeutic avenue for ischemic stroke.
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Affiliation(s)
- Hong An
- Department of Neurology, Beijing Chaoyang Hospital, Capital Medical University, China (H.A.)
- Neuroprotection Research Laboratories, Departments of Radiology and Neurology, Massachusetts General Hospital, Harvard Medical School, Boston (H.A., K.H., V.D.L., J.-H.P., Y.N., E.T.M., S.G., Z.Y., J.S., D.W., W.L., E.H.L.)
- Cerebrovascular and Neuroscience Research Institute, Xuanwu Hospital, Capital Medical University, Beijing, China (H.A., J.S., D.W., X.J.)
| | - Bing Zhou
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University, China (B.Z.)
| | - Kazuhide Hayakawa
- Neuroprotection Research Laboratories, Departments of Radiology and Neurology, Massachusetts General Hospital, Harvard Medical School, Boston (H.A., K.H., V.D.L., J.-H.P., Y.N., E.T.M., S.G., Z.Y., J.S., D.W., W.L., E.H.L.)
| | - Violeta Durán Laforet
- Neuroprotection Research Laboratories, Departments of Radiology and Neurology, Massachusetts General Hospital, Harvard Medical School, Boston (H.A., K.H., V.D.L., J.-H.P., Y.N., E.T.M., S.G., Z.Y., J.S., D.W., W.L., E.H.L.)
- Unidad de Investigación Neurovascular, Departamento de Farmacología, Facultad de Medicina, Universidad Complutense de Madrid (UCM), Instituto de Investigación Hospital 12 de Octubre, Spain (V.D.L.)
| | - Ji-Hyun Park
- Neuroprotection Research Laboratories, Departments of Radiology and Neurology, Massachusetts General Hospital, Harvard Medical School, Boston (H.A., K.H., V.D.L., J.-H.P., Y.N., E.T.M., S.G., Z.Y., J.S., D.W., W.L., E.H.L.)
| | - Yoshihiko Nakamura
- Neuroprotection Research Laboratories, Departments of Radiology and Neurology, Massachusetts General Hospital, Harvard Medical School, Boston (H.A., K.H., V.D.L., J.-H.P., Y.N., E.T.M., S.G., Z.Y., J.S., D.W., W.L., E.H.L.)
- Department of Emergency and Critical Care Medicine, Fukuoka University Hospital, Japan (Y.N.)
| | - Emiri T Mandeville
- Neuroprotection Research Laboratories, Departments of Radiology and Neurology, Massachusetts General Hospital, Harvard Medical School, Boston (H.A., K.H., V.D.L., J.-H.P., Y.N., E.T.M., S.G., Z.Y., J.S., D.W., W.L., E.H.L.)
| | - Ning Liu
- Clinical Neuroscience Research Center, Department of Neurosurgery and Neurology, Tulane University School of Medicine, New Orleans, LA (N.L.)
| | - Shuzhen Guo
- Neuroprotection Research Laboratories, Departments of Radiology and Neurology, Massachusetts General Hospital, Harvard Medical School, Boston (H.A., K.H., V.D.L., J.-H.P., Y.N., E.T.M., S.G., Z.Y., J.S., D.W., W.L., E.H.L.)
| | - Zhanyang Yu
- Neuroprotection Research Laboratories, Departments of Radiology and Neurology, Massachusetts General Hospital, Harvard Medical School, Boston (H.A., K.H., V.D.L., J.-H.P., Y.N., E.T.M., S.G., Z.Y., J.S., D.W., W.L., E.H.L.)
| | - Jingfei Shi
- Neuroprotection Research Laboratories, Departments of Radiology and Neurology, Massachusetts General Hospital, Harvard Medical School, Boston (H.A., K.H., V.D.L., J.-H.P., Y.N., E.T.M., S.G., Z.Y., J.S., D.W., W.L., E.H.L.)
- Cerebrovascular and Neuroscience Research Institute, Xuanwu Hospital, Capital Medical University, Beijing, China (H.A., J.S., D.W., X.J.)
| | - Di Wu
- Neuroprotection Research Laboratories, Departments of Radiology and Neurology, Massachusetts General Hospital, Harvard Medical School, Boston (H.A., K.H., V.D.L., J.-H.P., Y.N., E.T.M., S.G., Z.Y., J.S., D.W., W.L., E.H.L.)
- Cerebrovascular and Neuroscience Research Institute, Xuanwu Hospital, Capital Medical University, Beijing, China (H.A., J.S., D.W., X.J.)
| | - Wenlu Li
- Neuroprotection Research Laboratories, Departments of Radiology and Neurology, Massachusetts General Hospital, Harvard Medical School, Boston (H.A., K.H., V.D.L., J.-H.P., Y.N., E.T.M., S.G., Z.Y., J.S., D.W., W.L., E.H.L.)
| | - Eng H Lo
- Neuroprotection Research Laboratories, Departments of Radiology and Neurology, Massachusetts General Hospital, Harvard Medical School, Boston (H.A., K.H., V.D.L., J.-H.P., Y.N., E.T.M., S.G., Z.Y., J.S., D.W., W.L., E.H.L.)
| | - Xunming Ji
- Cerebrovascular and Neuroscience Research Institute, Xuanwu Hospital, Capital Medical University, Beijing, China (H.A., J.S., D.W., X.J.)
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing, China (X.J.)
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2
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Moisoi N. Mitochondrial proteases modulate mitochondrial stress signalling and cellular homeostasis in health and disease. Biochimie 2024:S0300-9084(24)00141-X. [PMID: 38906365 DOI: 10.1016/j.biochi.2024.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 05/16/2024] [Accepted: 06/17/2024] [Indexed: 06/23/2024]
Abstract
Maintenance of mitochondrial homeostasis requires a plethora of coordinated quality control and adaptations' mechanisms in which mitochondrial proteases play a key role. Their activation or loss of function reverberate beyond local mitochondrial biochemical and metabolic remodelling into coordinated cellular pathways and stress responses that feedback onto the mitochondrial functionality and adaptability. Mitochondrial proteolysis modulates molecular and organellar quality control, metabolic adaptations, lipid homeostasis and regulates transcriptional stress responses. Defective mitochondrial proteolysis results in disease conditions most notably, mitochondrial diseases, neurodegeneration and cancer. Here, it will be discussed how mitochondrial proteases and mitochondria stress signalling impact cellular homeostasis and determine the cellular decision to survive or die, how these processes may impact disease etiopathology, and how modulation of proteolysis may offer novel therapeutic strategies.
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Affiliation(s)
- Nicoleta Moisoi
- Leicester School of Pharmacy, Leicester Institute for Pharmaceutical Health and Social Care Innovations, Faculty of Health and Life Sciences, De Montfort University, The Gateway, Hawthorn Building 1.03, LE1 9BH, Leicester, UK.
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3
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Moretti-Horten DN, Peselj C, Taskin AA, Myketin L, Schulte U, Einsle O, Drepper F, Luzarowski M, Vögtle FN. Synchronized assembly of the oxidative phosphorylation system controls mitochondrial respiration in yeast. Dev Cell 2024; 59:1043-1057.e8. [PMID: 38508182 DOI: 10.1016/j.devcel.2024.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/19/2024] [Accepted: 02/28/2024] [Indexed: 03/22/2024]
Abstract
Control of protein stoichiometry is essential for cell function. Mitochondrial oxidative phosphorylation (OXPHOS) presents a complex stoichiometric challenge as the ratio of the electron transport chain (ETC) and ATP synthase must be tightly controlled, and assembly requires coordinated integration of proteins encoded in the nuclear and mitochondrial genome. How correct OXPHOS stoichiometry is achieved is unknown. We identify the Mitochondrial Regulatory hub for respiratory Assembly (MiRA) platform, which synchronizes ETC and ATP synthase biogenesis in yeast. Molecularly, this is achieved by a stop-and-go mechanism: the uncharacterized protein Mra1 stalls complex IV assembly. Two "Go" signals are required for assembly progression: binding of the complex IV assembly factor Rcf2 and Mra1 interaction with an Atp9-translating mitoribosome induce Mra1 degradation, allowing synchronized maturation of complex IV and the ATP synthase. Failure of the stop-and-go mechanism results in cell death. MiRA controls OXPHOS assembly, ensuring correct stoichiometry of protein machineries encoded by two different genomes.
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Affiliation(s)
- Daiana N Moretti-Horten
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Carlotta Peselj
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Asli Aras Taskin
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Lisa Myketin
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Uwe Schulte
- Institute of Physiology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Oliver Einsle
- Institut für Biochemie, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Friedel Drepper
- CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; Biochemistry & Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Marcin Luzarowski
- Core Facility for Mass Spectrometry and Proteomics, Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - F-Nora Vögtle
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; Network Aging Research, Heidelberg University, 69120 Heidelberg, Germany.
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4
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Dissecting the molecular mechanisms of mitochondrial import and maturation of peroxiredoxins from yeast and mammalian cells. Biophys Rev 2022; 13:983-994. [PMID: 35059022 DOI: 10.1007/s12551-021-00899-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 11/01/2021] [Indexed: 12/26/2022] Open
Abstract
Peroxiredoxins (Prxs) are cysteine-based peroxidases that play a central role in keeping the H2O2 at physiological levels. Eukaryotic cells express different Prxs isoforms, which differ in their subcellular locations and substrate specificities. Mitochondrial Prxs are synthesized in the cytosol as precursor proteins containing N-terminal cleavable presequences that act as mitochondrial targeting signals. Due to the fact that presequence controls the import of the vast majority of mitochondrial matrix proteins, the mitochondrial Prxs were initially predicted to be localized exclusively in the matrix. However, recent studies showed that mitochondrial Prxs are also targeted to the intermembrane space by mechanisms that remain poorly understood. While in yeast the IMP complex can translocate Prx1 to the intermembrane space, the maturation of yeast Prx1 and mammalian Prdx3 and Prdx5 in the matrix has been associated with sequential cleavages of the presequence by MPP and Oct1/MIP proteases. In this review, we describe the state of the art of the molecular mechanisms that control the mitochondrial import and maturation of Prxs of yeast and human cells. Once mitochondria are considered the major intracellular source of H2O2, understanding the mitochondrial Prx biogenesis pathways is essential to increase our knowledge about the H2O2-dependent cellular signaling, which is relevant to the pathophysiology of some human diseases.
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5
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Heidorn-Czarna M, Maziak A, Janska H. Protein Processing in Plant Mitochondria Compared to Yeast and Mammals. FRONTIERS IN PLANT SCIENCE 2022; 13:824080. [PMID: 35185991 PMCID: PMC8847149 DOI: 10.3389/fpls.2022.824080] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 01/12/2022] [Indexed: 05/02/2023]
Abstract
Limited proteolysis, called protein processing, is an essential post-translational mechanism that controls protein localization, activity, and in consequence, function. This process is prevalent for mitochondrial proteins, mainly synthesized as precursor proteins with N-terminal sequences (presequences) that act as targeting signals and are removed upon import into the organelle. Mitochondria have a distinct and highly conserved proteolytic system that includes proteases with sole function in presequence processing and proteases, which show diverse mitochondrial functions with limited proteolysis as an additional one. In virtually all mitochondria, the primary processing of N-terminal signals is catalyzed by the well-characterized mitochondrial processing peptidase (MPP). Subsequently, a second proteolytic cleavage occurs, leading to more stabilized residues at the newly formed N-terminus. Lately, mitochondrial proteases, intermediate cleavage peptidase 55 (ICP55) and octapeptidyl protease 1 (OCT1), involved in proteolytic cleavage after MPP and their substrates have been described in the plant, yeast, and mammalian mitochondria. Mitochondrial proteins can also be processed by removing a peptide from their N- or C-terminus as a maturation step during insertion into the membrane or as a regulatory mechanism in maintaining their function. This type of limited proteolysis is characteristic for processing proteases, such as IMP and rhomboid proteases, or the general mitochondrial quality control proteases ATP23, m-AAA, i-AAA, and OMA1. Identification of processing protease substrates and defining their consensus cleavage motifs is now possible with the help of large-scale quantitative mass spectrometry-based N-terminomics, such as combined fractional diagonal chromatography (COFRADIC), charge-based fractional diagonal chromatography (ChaFRADIC), or terminal amine isotopic labeling of substrates (TAILS). This review summarizes the current knowledge on the characterization of mitochondrial processing peptidases and selected N-terminomics techniques used to uncover protease substrates in the plant, yeast, and mammalian mitochondria.
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6
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Abstract
Mitochondria play a central role in the pathophysiological processes of acute ischemic stroke. Disruption of the cerebral blood flow during acute ischemic stroke interrupts oxygen and glucose delivery, leading to the dysfunction of mitochondrial oxidative phosphorylation and cellular bioenergetic stress. Cells can respond to such stress by activating mitochondrial quality control mechanisms, including the mitochondrial unfolded protein response, mitochondrial fission and fusion, mitophagy, mitochondrial biogenesis, and intercellular mitochondrial transfer. Collectively, these adaptive response strategies contribute to retaining the integrity and function of the mitochondrial network, thereby helping to recover the homeostasis of the neurovascular unit. In this review, we focus on mitochondrial quality control mechanisms occurring in acute ischemic stroke. A better understanding of how these regulatory pathways work in maintaining mitochondrial homeostasis will provide a rationale for developing innovative neuroprotectants when these mechanisms fail in acute ischemic stroke.
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Affiliation(s)
- Hong An
- Department of Neurology and China-America Institute of Neuroscience, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Bing Zhou
- Department of Neurology and China-America Institute of Neuroscience, Xuanwu Hospital, Capital Medical University, Beijing, China.,Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University, Beijing, China.,Interdisciplinary Innovation Institute of Medicine and Engineering Interdisciplinary, Beihang University, Beijing, China
| | - Xunming Ji
- Department of Neurology and China-America Institute of Neuroscience, Xuanwu Hospital, Capital Medical University, Beijing, China.,Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University, Beijing, China.,Interdisciplinary Innovation Institute of Medicine and Engineering Interdisciplinary, Beihang University, Beijing, China.,Department of Neurosurgery, 71044Xuanwu Hospital, Xuanwu Hospital, Capital Medical University, Beijing, China
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7
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Duran L, López JM, Avalos JL. ¡Viva la mitochondria!: harnessing yeast mitochondria for chemical production. FEMS Yeast Res 2021; 20:5863938. [PMID: 32592388 DOI: 10.1093/femsyr/foaa037] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 06/12/2020] [Indexed: 12/11/2022] Open
Abstract
The mitochondria, often referred to as the powerhouse of the cell, offer a unique physicochemical environment enriched with a distinct set of enzymes, metabolites and cofactors ready to be exploited for metabolic engineering. In this review, we discuss how the mitochondrion has been engineered in the traditional sense of metabolic engineering or completely bypassed for chemical production. We then describe the more recent approach of harnessing the mitochondria to compartmentalize engineered metabolic pathways, including for the production of alcohols, terpenoids, sterols, organic acids and other valuable products. We explain the different mechanisms by which mitochondrial compartmentalization benefits engineered metabolic pathways to boost chemical production. Finally, we discuss the key challenges that need to be overcome to expand the applicability of mitochondrial engineering and reach the full potential of this emerging field.
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Affiliation(s)
- Lisset Duran
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - José Montaño López
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - José L Avalos
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
- Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ 08544, USA
- Princeton Environmental Institute, Princeton University, Princeton, NJ 08544, USA
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8
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Abstract
All living organisms depend on tightly regulated cellular networks to control biological functions. Proteolysis is an important irreversible post-translational modification that regulates most, if not all, cellular processes. Proteases are a large family of enzymes that perform hydrolysis of protein substrates, leading to protein activation or degradation. The 473 known and 90 putative human proteases are divided into 5 main mechanistic groups: metalloproteases, serine proteases, cysteine proteases, threonine proteases, and aspartic acid proteases. Proteases are fundamental to all biological systems, and when dysregulated they profoundly influence disease progression. Inhibiting proteases has led to effective therapies for viral infections, cardiovascular disorders, and blood coagulation just to name a few. Between 5 and 10% of all pharmaceutical targets are proteases, despite limited knowledge about their biological roles. More than 50% of all human proteases have no known substrates. We present here a comprehensive list of all current known human proteases. We also present current and novel biochemical tools to characterize protease functions in vitro, in vivo, and ex vivo. These tools make it achievable to define both beneficial and detrimental activities of proteases in health and disease.
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Affiliation(s)
- Longxiang Wang
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Kimberly Main
- Department of Physiology & Pharmacology, University of Calgary, Calgary, AB T2N 1N4, Canada.,McCaig Institute for Bone & Joint Health, University of Calgary, Calgary, AB T2N 1N4, Canada.,Hotchkiss Brain Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Henry Wang
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Olivier Julien
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Antoine Dufour
- Department of Physiology & Pharmacology, University of Calgary, Calgary, AB T2N 1N4, Canada.,McCaig Institute for Bone & Joint Health, University of Calgary, Calgary, AB T2N 1N4, Canada.,Hotchkiss Brain Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
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9
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Gomez-Fabra Gala M, Vögtle FN. Mitochondrial proteases in human diseases. FEBS Lett 2021; 595:1205-1222. [PMID: 33453058 DOI: 10.1002/1873-3468.14039] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 12/15/2022]
Abstract
Mitochondria contain more than 1000 different proteins, including several proteolytic enzymes. These mitochondrial proteases form a complex system that performs limited and terminal proteolysis to build the mitochondrial proteome, maintain, and control its functions or degrade mitochondrial proteins and peptides. During protein biogenesis, presequence proteases cleave and degrade mitochondrial targeting signals to obtain mature functional proteins. Processing by proteases also exerts a regulatory role in modulation of mitochondrial functions and quality control enzymes degrade misfolded, aged, or superfluous proteins. Depending on their different functions and substrates, defects in mitochondrial proteases can affect the majority of the mitochondrial proteome or only a single protein. Consequently, mutations in mitochondrial proteases have been linked to several human diseases. This review gives an overview of the components and functions of the mitochondrial proteolytic machinery and highlights the pathological consequences of dysfunctional mitochondrial protein processing and turnover.
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Affiliation(s)
- Maria Gomez-Fabra Gala
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Germany.,Faculty of Biology, University of Freiburg, Germany.,Spemann Graduate School of Biology and Medicine, University of Freiburg, Germany
| | - Friederike-Nora Vögtle
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Germany.,CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, Germany
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10
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Friedl J, Knopp MR, Groh C, Paz E, Gould SB, Herrmann JM, Boos F. More than just a ticket canceller: the mitochondrial processing peptidase tailors complex precursor proteins at internal cleavage sites. Mol Biol Cell 2020; 31:2657-2668. [PMID: 32997570 PMCID: PMC8734313 DOI: 10.1091/mbc.e20-08-0524] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/21/2020] [Accepted: 09/25/2020] [Indexed: 11/11/2022] Open
Abstract
Most mitochondrial proteins are synthesized as precursors that carry N-terminal presequences. After they are imported into mitochondria, these targeting signals are cleaved off by the mitochondrial processing peptidase (MPP). Using the mitochondrial tandem protein Arg5,6 as a model substrate, we demonstrate that MPP has an additional role in preprotein maturation, beyond the removal of presequences. Arg5,6 is synthesized as a polyprotein precursor that is imported into mitochondria and subsequently separated into two distinct enzymes. This internal processing is performed by MPP, which cleaves the Arg5,6 precursor at its N-terminus and at an internal site. The peculiar organization of Arg5,6 is conserved across fungi and reflects the polycistronic arginine operon in prokaryotes. MPP cleavage sites are also present in other mitochondrial fusion proteins from fungi, plants, and animals. Hence, besides its role as a "ticket canceller" for removal of presequences, MPP exhibits a second conserved activity as an internal processing peptidase for complex mitochondrial precursor proteins.
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Affiliation(s)
- Jana Friedl
- Cell Biology, Technische Universität Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Michael R. Knopp
- Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Carina Groh
- Cell Biology, Technische Universität Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Eyal Paz
- Departments of Biochemistry and Molecular Biology, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Sven B. Gould
- Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Johannes M. Herrmann
- Cell Biology, Technische Universität Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Felix Boos
- Cell Biology, Technische Universität Kaiserslautern, 67663 Kaiserslautern, Germany
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11
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Hofsetz E, Demir F, Szczepanowska K, Kukat A, Kizhakkedathu JN, Trifunovic A, Huesgen PF. The Mouse Heart Mitochondria N Terminome Provides Insights into ClpXP-Mediated Proteolysis. Mol Cell Proteomics 2020; 19:1330-1345. [PMID: 32467259 PMCID: PMC8014998 DOI: 10.1074/mcp.ra120.002082] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/24/2020] [Indexed: 12/29/2022] Open
Abstract
The mammalian mitochondrial proteome consists of more than 1100 annotated proteins and their proteostasis is regulated by only a few ATP-dependent protease complexes. Technical advances in protein mass spectrometry allowed for detailed description of the mitoproteome from different species and tissues and their changes under specific conditions. However, protease-substrate relations within mitochondria are still poorly understood. Here, we combined Terminal Amine Isotope Labeling of Substrates (TAILS) N termini profiling of heart mitochondria proteomes isolated from wild type and Clpp-/- mice with a classical substrate-trapping screen using FLAG-tagged proteolytically active and inactive CLPP variants to identify new ClpXP substrates in mammalian mitochondria. Using TAILS, we identified N termini of more than 200 mitochondrial proteins. Expected N termini confirmed sequence determinants for mitochondrial targeting signal (MTS) cleavage and subsequent N-terminal processing after import, but the majority were protease-generated neo-N termini mapping to positions within the proteins. Quantitative comparison revealed widespread changes in protein processing patterns, including both strong increases or decreases in the abundance of specific neo-N termini, as well as an overall increase in the abundance of protease-generated neo-N termini in CLPP-deficient mitochondria that indicated altered mitochondrial proteostasis. Based on the combination of altered processing patterns, protein accumulation and stabilization in CLPP-deficient mice and interaction with CLPP, we identified OAT, HSPA9 and POLDIP2 and as novel bona fide ClpXP substrates. Finally, we propose that ClpXP participates in the cooperative degradation of UQCRC1. Together, our data provide the first landscape of the heart mitochondria N terminome and give further insights into regulatory and assisted proteolysis mediated by ClpXP.
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Affiliation(s)
- Eduard Hofsetz
- Institute for Mitochondrial Diseases and Aging at CECAD Research Centre, and Center for Molecular Medicine Cologne (CMMC), Medical Faculty, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), Cologne, Germany, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany
| | - Fatih Demir
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Germany
| | - Karolina Szczepanowska
- Institute for Mitochondrial Diseases and Aging at CECAD Research Centre, and Center for Molecular Medicine Cologne (CMMC), Medical Faculty, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), Cologne, Germany, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany
| | - Alexandra Kukat
- Institute for Mitochondrial Diseases and Aging at CECAD Research Centre, and Center for Molecular Medicine Cologne (CMMC), Medical Faculty, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), Cologne, Germany, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany
| | - Jayachandran N Kizhakkedathu
- Centre for Blood Research, School of Biomedical Engineering, Department of Pathology & Laboratory Medicine, Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Aleksandra Trifunovic
- Institute for Mitochondrial Diseases and Aging at CECAD Research Centre, and Center for Molecular Medicine Cologne (CMMC), Medical Faculty, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), Cologne, Germany, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany.
| | - Pitter F Huesgen
- Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), Cologne, Germany, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany; Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Germany; Institute for Biochemistry, Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne, Germany.
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12
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Abstract
Mitochondria are essential organelles of eukaryotic cells. They consist of hundreds of different proteins that exhibit crucial activities in respiration, catabolic metabolism and the synthesis of amino acids, lipids, heme and iron-sulfur clusters. With the exception of a handful of hydrophobic mitochondrially encoded membrane proteins, all these proteins are synthesized on cytosolic ribosomes, targeted to receptors on the mitochondrial surface, and transported across or inserted into the outer and inner mitochondrial membrane before they are folded and assembled into their final native structure. This review article provides a comprehensive overview of the mechanisms and components of the mitochondrial protein import systems with a particular focus on recent developments in the field.
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Affiliation(s)
- Katja G Hansen
- Cell Biology, University of Kaiserslautern, Erwin-Schrödinger-Strasse 13, 67663, Kaiserslautern, Germany
| | - Johannes M Herrmann
- Cell Biology, University of Kaiserslautern, Erwin-Schrödinger-Strasse 13, 67663, Kaiserslautern, Germany.
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13
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Poveda-Huertes D, Matic S, Marada A, Habernig L, Licheva M, Myketin L, Gilsbach R, Tosal-Castano S, Papinski D, Mulica P, Kretz O, Kücükköse C, Taskin AA, Hein L, Kraft C, Büttner S, Meisinger C, Vögtle FN. An Early mtUPR: Redistribution of the Nuclear Transcription Factor Rox1 to Mitochondria Protects against Intramitochondrial Proteotoxic Aggregates. Mol Cell 2020; 77:180-188.e9. [PMID: 31630969 PMCID: PMC6941230 DOI: 10.1016/j.molcel.2019.09.026] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 08/20/2019] [Accepted: 09/23/2019] [Indexed: 11/29/2022]
Abstract
The mitochondrial proteome is built mainly by import of nuclear-encoded precursors, which are targeted mostly by cleavable presequences. Presequence processing upon import is essential for proteostasis and survival, but the consequences of dysfunctional protein maturation are unknown. We find that impaired presequence processing causes accumulation of precursors inside mitochondria that form aggregates, which escape degradation and unexpectedly do not cause cell death. Instead, cells survive via activation of a mitochondrial unfolded protein response (mtUPR)-like pathway that is triggered very early after precursor accumulation. In contrast to classical stress pathways, this immediate response maintains mitochondrial protein import, membrane potential, and translation through translocation of the nuclear HMG-box transcription factor Rox1 to mitochondria. Rox1 binds mtDNA and performs a TFAM-like function pivotal for transcription and translation. Induction of early mtUPR provides a reversible stress model to mechanistically dissect the initial steps in mtUPR pathways with the stressTFAM Rox1 as the first line of defense.
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Affiliation(s)
- Daniel Poveda-Huertes
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Stanka Matic
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Adinarayana Marada
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Lukas Habernig
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Mariya Licheva
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Lisa Myketin
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Ralf Gilsbach
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Sergi Tosal-Castano
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Daniel Papinski
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, 1030 Vienna, Austria
| | - Patrycja Mulica
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Oliver Kretz
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany; Department of Medicine IV, Medical Center and Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Cansu Kücükköse
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Asli Aras Taskin
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Lutz Hein
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Claudine Kraft
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Sabrina Büttner
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden; Institute for Molecular Biosciences, University of Graz, 8010 Graz, Austria
| | - Chris Meisinger
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
| | - F-Nora Vögtle
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
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14
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Vögtle FN, Brändl B, Larson A, Pendziwiat M, Friederich MW, White SM, Basinger A, Kücükköse C, Muhle H, Jähn JA, Keminer O, Helbig KL, Delto CF, Myketin L, Mossmann D, Burger N, Miyake N, Burnett A, van Baalen A, Lovell MA, Matsumoto N, Walsh M, Yu HC, Shinde DN, Stephani U, Van Hove JLK, Müller FJ, Helbig I. Mutations in PMPCB Encoding the Catalytic Subunit of the Mitochondrial Presequence Protease Cause Neurodegeneration in Early Childhood. Am J Hum Genet 2018; 102:557-573. [PMID: 29576218 PMCID: PMC5985287 DOI: 10.1016/j.ajhg.2018.02.014] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 02/19/2018] [Indexed: 12/21/2022] Open
Abstract
Mitochondrial disorders causing neurodegeneration in childhood are genetically heterogeneous, and the underlying genetic etiology remains unknown in many affected individuals. We identified biallelic variants in PMPCB in individuals of four families including one family with two affected siblings with neurodegeneration and cerebellar atrophy. PMPCB encodes the catalytic subunit of the essential mitochondrial processing protease (MPP), which is required for maturation of the majority of mitochondrial precursor proteins. Mitochondria isolated from two fibroblast cell lines and induced pluripotent stem cells derived from one affected individual and differentiated neuroepithelial stem cells showed reduced PMPCB levels and accumulation of the processing intermediate of frataxin, a sensitive substrate for MPP dysfunction. Introduction of the identified PMPCB variants into the homologous S. cerevisiae Mas1 protein resulted in a severe growth and MPP processing defect leading to the accumulation of mitochondrial precursor proteins and early impairment of the biogenesis of iron-sulfur clusters, which are indispensable for a broad range of crucial cellular functions. Analysis of biopsy materials of an affected individual revealed changes and decreased activity in iron-sulfur cluster-containing respiratory chain complexes and dysfunction of mitochondrial and cytosolic Fe-S cluster-dependent enzymes. We conclude that biallelic mutations in PMPCB cause defects in MPP proteolytic activity leading to dysregulation of iron-sulfur cluster biogenesis and triggering a complex neurological phenotype of neurodegeneration in early childhood.
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Affiliation(s)
- F-Nora Vögtle
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg 79104, Germany.
| | - Björn Brändl
- Department of Psychiatry and Psychotherapy, University Hospital Schleswig Holstein, Kiel 24105, Germany
| | - Austin Larson
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado, Aurora, CO 80045, USA
| | - Manuela Pendziwiat
- Department of Neuropediatrics, Christian-Albrechts-University of Kiel, Kiel 24105, Germany
| | - Marisa W Friederich
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado, Aurora, CO 80045, USA
| | - Susan M White
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Alice Basinger
- Cook Children's Physician Network, Department of Genetics, Fort Worth, TX 76102, USA
| | - Cansu Kücükköse
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg 79104, Germany; Faculty of Biology, University of Freiburg, Freiburg 79104, Germany
| | - Hiltrud Muhle
- Department of Neuropediatrics, Christian-Albrechts-University of Kiel, Kiel 24105, Germany
| | - Johanna A Jähn
- Department of Neuropediatrics, Christian-Albrechts-University of Kiel, Kiel 24105, Germany
| | - Oliver Keminer
- Fraunhofer-Institut für Molekularbiologie und Angewandte Ökologie IME, ScreeningPort, Hamburg 22525, Germany
| | - Katherine L Helbig
- Division of Neurology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Carolyn F Delto
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg 97080, Germany
| | - Lisa Myketin
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg 79104, Germany
| | - Dirk Mossmann
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg 79104, Germany
| | - Nils Burger
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg 79104, Germany
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Audrey Burnett
- Cook Children's Physician Network, Department of Genetics, Fort Worth, TX 76102, USA
| | - Andreas van Baalen
- Department of Neuropediatrics, Christian-Albrechts-University of Kiel, Kiel 24105, Germany
| | - Mark A Lovell
- Department of Pathology, University of Colorado, Aurora, CO 80045, USA
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Maie Walsh
- Adult Genetic Medicine, Royal Melbourne Hospital, Melbourne, VIC 3052, Australia
| | - Hung-Chun Yu
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado, Aurora, CO 80045, USA
| | - Deepali N Shinde
- Division of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Ulrich Stephani
- Department of Neuropediatrics, Christian-Albrechts-University of Kiel, Kiel 24105, Germany
| | - Johan L K Van Hove
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado, Aurora, CO 80045, USA
| | - Franz-Josef Müller
- Department of Psychiatry and Psychotherapy, University Hospital Schleswig Holstein, Kiel 24105, Germany; Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
| | - Ingo Helbig
- Department of Neuropediatrics, Christian-Albrechts-University of Kiel, Kiel 24105, Germany; Division of Neurology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
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15
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Kunze M. Predicting Peroxisomal Targeting Signals to Elucidate the Peroxisomal Proteome of Mammals. Subcell Biochem 2018; 89:157-199. [PMID: 30378023 DOI: 10.1007/978-981-13-2233-4_7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Peroxisomes harbor a plethora of proteins, but the peroxisomal proteome as the entirety of all peroxisomal proteins is still unknown for mammalian species. Computational algorithms can be used to predict the subcellular localization of proteins based on their amino acid sequence and this method has been amply used to forecast the intracellular fate of individual proteins. However, when applying such algorithms systematically to all proteins of an organism the prediction of its peroxisomal proteome in silico should be possible. Therefore, a reliable detection of peroxisomal targeting signals (PTS ) acting as postal codes for the intracellular distribution of the encoding protein is crucial. Peroxisomal proteins can utilize different routes to reach their destination depending on the type of PTS. Accordingly, independent prediction algorithms have been developed for each type of PTS, but only those for type-1 motifs (PTS1) have so far reached a satisfying predictive performance. This is partially due to the low number of peroxisomal proteins limiting the power of statistical analyses and partially due to specific properties of peroxisomal protein import, which render functional PTS motifs inactive in specific contexts. Moreover, the prediction of the peroxisomal proteome is limited by the high number of proteins encoded in mammalian genomes, which causes numerous false positive predictions even when using reliable algorithms and buries the few yet unidentified peroxisomal proteins. Thus, the application of prediction algorithms to identify all peroxisomal proteins is currently ineffective as stand-alone method, but can display its full potential when combined with other methods.
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Affiliation(s)
- Markus Kunze
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna, Vienna, Austria.
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16
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Tholey A, Becker A. Top-down proteomics for the analysis of proteolytic events - Methods, applications and perspectives. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:2191-2199. [PMID: 28711385 DOI: 10.1016/j.bbamcr.2017.07.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 07/07/2017] [Accepted: 07/09/2017] [Indexed: 02/06/2023]
Abstract
Mass spectrometry based proteomics is an indispensable tool for almost all research areas relevant for the understanding of proteolytic processing, ranging from the identification of substrates, products and cleavage sites up to the analysis of structural features influencing protease activity. The majority of methods for these studies are based on bottom-up proteomics performing analysis at peptide level. As this approach is characterized by a number of pitfalls, e.g. loss of molecular information, there is an ongoing effort to establish top-down proteomics, performing separation and MS analysis both at intact protein level. We briefly introduce major approaches of bottom-up proteomics used in the field of protease research and highlight the shortcomings of these methods. We then discuss the present state-of-the-art of top-down proteomics. Together with the discussion of known challenges we show the potential of this approach and present a number of successful applications of top-down proteomics in protease research. This article is part of a Special Issue entitled: Proteolysis as a Regulatory Event in Pathophysiology edited by Stefan Rose-John.
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Affiliation(s)
- Andreas Tholey
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.
| | - Alexander Becker
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
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17
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Taskin AA, Kücükköse C, Burger N, Mossmann D, Meisinger C, Vögtle FN. The novel mitochondrial matrix protease Ste23 is required for efficient presequence degradation and processing. Mol Biol Cell 2017; 28:997-1002. [PMID: 28228553 PMCID: PMC5391191 DOI: 10.1091/mbc.e16-10-0732] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 02/08/2017] [Accepted: 02/13/2017] [Indexed: 11/15/2022] Open
Abstract
Approximately 70% of mitochondrial precursor proteins are imported from the cytosol via N-terminal presequences, which are cleaved upon exposure to the mitochondrial processing protease MPP in the matrix. Cleaved presequence peptides then need to be efficiently degraded, and impairment of this clearance step, for example, by amyloid β peptides, causes feedback inhibition of MPP, leading ultimately to accumulation of immature precursor proteins within mitochondria. Degradation of mitochondrial peptides is performed by Cym1 in yeast and its homologue, PreP, in humans. Here we identify the novel mitochondrial matrix protease Ste23 in yeast, a homologue of human insulin-degrading enzyme, which is required for efficient peptide degradation. Ste23 and Cym1 tightly cooperate to ensure the correct functioning of the essential presequence processing machinery.
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Affiliation(s)
- Asli Aras Taskin
- Institute of Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Cansu Kücükköse
- Institute of Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Nils Burger
- Institute of Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Dirk Mossmann
- Institute of Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Chris Meisinger
- Institute of Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - F-Nora Vögtle
- Institute of Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
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18
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Braun RJ, Zerbes RM, Steinberg F, Gris D, Dumit VI. Threading Granules in Freiburg. 2 nd International Symposium on "One Mitochondrion, Many Diseases - Biological and Molecular Perspectives", a FRIAS Junior Researcher Conference, Freiburg im Breisgau, Germany, March 9 th/10 th, 2016. MICROBIAL CELL 2016; 3:565-568. [PMID: 28357325 PMCID: PMC5349212 DOI: 10.15698/mic2016.11.540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Altered mitochondrial activities play an important role in many different human
disorders, including cancer and neurodegeneration. At the Freiburg Institute of
Advanced Studies (FRIAS) Junior Researcher Conference “One Mitochondrion, Many
Diseases - Biological and Molecular Perspectives” (University of Freiburg,
Freiburg, Germany), junior and experienced researches discussed common and
distinct mechanisms of mitochondrial contributions to various human
disorders.
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Affiliation(s)
- Ralf J Braun
- Institute of Cell Biology, University of Bayreuth, 95440 Bayreuth, Germany
| | - Ralf M Zerbes
- Institute for Biochemistry and Molecular Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Florian Steinberg
- ZBSA Center for Biological Systems Analysis, AG Steinberg, University of Freiburg, 79104 Freiburg, Germany
| | - Denis Gris
- Program of Immunology, Department of Pediatrics, CR-CHUS, Faculty of Medicine and Health Sciences, University of Sherbrooke, Sherbrooke, QC, Canada
| | - Verónica I Dumit
- ZBSA Center for Biological Systems Analysis, Core Facility Proteomics, University of Freiburg, 79104 Freiburg, Germany
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19
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Eldomery MK, Akdemir ZC, Vögtle FN, Charng WL, Mulica P, Rosenfeld JA, Gambin T, Gu S, Burrage LC, Al Shamsi A, Penney S, Jhangiani SN, Zimmerman HH, Muzny DM, Wang X, Tang J, Medikonda R, Ramachandran PV, Wong LJ, Boerwinkle E, Gibbs RA, Eng CM, Lalani SR, Hertecant J, Rodenburg RJ, Abdul-Rahman OA, Yang Y, Xia F, Wang MC, Lupski JR, Meisinger C, Sutton VR. MIPEP recessive variants cause a syndrome of left ventricular non-compaction, hypotonia, and infantile death. Genome Med 2016; 8:106. [PMID: 27799064 PMCID: PMC5088683 DOI: 10.1186/s13073-016-0360-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 09/26/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mitochondrial presequence proteases perform fundamental functions as they process about 70 % of all mitochondrial preproteins that are encoded in the nucleus and imported posttranslationally. The mitochondrial intermediate presequence protease MIP/Oct1, which carries out precursor processing, has not yet been established to have a role in human disease. METHODS Whole exome sequencing was performed on four unrelated probands with left ventricular non-compaction (LVNC), developmental delay (DD), seizures, and severe hypotonia. Proposed pathogenic variants were confirmed by Sanger sequencing or array comparative genomic hybridization. Functional analysis of the identified MIP variants was performed using the model organism Saccharomyces cerevisiae as the protein and its functions are highly conserved from yeast to human. RESULTS Biallelic single nucleotide variants (SNVs) or copy number variants (CNVs) in MIPEP, which encodes MIP, were present in all four probands, three of whom had infantile/childhood death. Two patients had compound heterozygous SNVs (p.L582R/p.L71Q and p.E602*/p.L306F) and one patient from a consanguineous family had a homozygous SNV (p.K343E). The fourth patient, identified through the GeneMatcher tool, a part of the Matchmaker Exchange Project, was found to have inherited a paternal SNV (p.H512D) and a maternal CNV (1.4-Mb deletion of 13q12.12) that includes MIPEP. All amino acids affected in the patients' missense variants are highly conserved from yeast to human and therefore S. cerevisiae was employed for functional analysis (for p.L71Q, p.L306F, and p.K343E). The mutations p.L339F (human p.L306F) and p.K376E (human p.K343E) resulted in a severe decrease of Oct1 protease activity and accumulation of non-processed Oct1 substrates and consequently impaired viability under respiratory growth conditions. The p.L83Q (human p.L71Q) failed to localize to the mitochondria. CONCLUSIONS Our findings reveal for the first time the role of the mitochondrial intermediate peptidase in human disease. Loss of MIP function results in a syndrome which consists of LVNC, DD, seizures, hypotonia, and cataracts. Our approach highlights the power of data exchange and the importance of an interrelationship between clinical and research efforts for disease gene discovery.
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Affiliation(s)
- Mohammad K Eldomery
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zeynep C Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - F-Nora Vögtle
- Institute of Biochemistry and Molecular Biology, ZBMZ and BIOSS Centre for Biological Signalling Studies and Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany
| | - Wu-Lin Charng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Patrycja Mulica
- Institute of Biochemistry and Molecular Biology, ZBMZ and BIOSS Centre for Biological Signalling Studies and Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Shen Gu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Lindsay C Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Texas Children's Hospital, Houston, TX, 77030, USA
| | - Aisha Al Shamsi
- Department of Pediatrics, Tawam Hospital, Al Ain, 15258, United Arab Emirates
| | - Samantha Penney
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Holly H Zimmerman
- Department of Pediatrics, University of Mississippi Medical Center, 2500N State St, Jackson, MS, 39216, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Xia Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jia Tang
- Medical Genetics Center, Jiang Men Maternity and Childhealth Care Hospital, Jiang Men, 529000, China
| | - Ravi Medikonda
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Prasanna V Ramachandran
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Huffington Center on Aging, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Lee-Jun Wong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Texas Children's Hospital, Houston, TX, 77030, USA
| | - Jozef Hertecant
- Department of Pediatrics, Tawam Hospital, Al Ain, 15258, United Arab Emirates
| | - Richard J Rodenburg
- Radboud Center for Mitochondrial Medicine, Department of Pediatrics, RadboudUMC, 6500HB, Nijmegen, Netherlands
| | - Omar A Abdul-Rahman
- Department of Pediatrics, University of Mississippi Medical Center, 2500N State St, Jackson, MS, 39216, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Meng C Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Huffington Center on Aging, Baylor College of Medicine, Houston, TX, 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Texas Children's Hospital, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Chris Meisinger
- Institute of Biochemistry and Molecular Biology, ZBMZ and BIOSS Centre for Biological Signalling Studies and Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany
| | - V Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA. .,Texas Children's Hospital, Houston, TX, 77030, USA.
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The versatility of the mitochondrial presequence processing machinery: cleavage, quality control and turnover. Cell Tissue Res 2016; 367:73-81. [DOI: 10.1007/s00441-016-2492-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 08/06/2016] [Accepted: 08/10/2016] [Indexed: 12/12/2022]
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Solari FA, Mattheij NJA, Burkhart JM, Swieringa F, Collins PW, Cosemans JMEM, Sickmann A, Heemskerk JWM, Zahedi RP. Combined Quantification of the Global Proteome, Phosphoproteome, and Proteolytic Cleavage to Characterize Altered Platelet Functions in the Human Scott Syndrome. Mol Cell Proteomics 2016; 15:3154-3169. [PMID: 27535140 PMCID: PMC5054341 DOI: 10.1074/mcp.m116.060368] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Indexed: 11/19/2022] Open
Abstract
The Scott syndrome is a very rare and likely underdiagnosed bleeding disorder associated with mutations in the gene encoding anoctamin-6. Platelets from Scott patients are impaired in various Ca2+-dependent responses, including phosphatidylserine exposure, integrin closure, intracellular protein cleavage, and cytoskeleton-dependent morphological changes. Given the central role of anoctamin-6 in the platelet procoagulant response, we used quantitative proteomics to understand the underlying molecular mechanisms and the complex phenotypic changes in Scott platelets compared with control platelets. Therefore, we applied an iTRAQ-based multi-pronged strategy to quantify changes in (1) the global proteome, (2) the phosphoproteome, and (3) proteolytic events between resting and stimulated Scott and control platelets. Our data indicate a limited number of proteins with decreased (70) or increased (64) expression in Scott platelets, among those we confirmed the absence of anoctamin-6 and the strong up-regulation of aquaporin-1 by parallel reaction monitoring. The quantification of 1566 phosphopeptides revealed major differences between Scott and control platelets after stimulation with thrombin/convulxin or ionomycin. In Scott platelets, phosphorylation levels of proteins regulating cytoskeletal or signaling events were increased. Finally, we quantified 1596 N-terminal peptides in activated Scott and control platelets, 180 of which we identified as calpain-regulated, whereas a distinct set of 23 neo-N termini was caspase-regulated. In Scott platelets, calpain-induced cleavage of cytoskeleton-linked and signaling proteins was downregulated, in accordance with an increased phosphorylation state. Thus, multipronged proteomic profiling of Scott platelets provides detailed insight into their protection against detrimental Ca2+-dependent changes that are normally associated with phosphatidylserine exposure.
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Affiliation(s)
- Fiorella A Solari
- From the ‡Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany
| | - Nadine J A Mattheij
- §Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
| | - Julia M Burkhart
- From the ‡Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany
| | - Frauke Swieringa
- §Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
| | - Peter W Collins
- ¶Arthur Bloom Haemophilia Centre, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Judith M E M Cosemans
- §Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
| | - Albert Sickmann
- From the ‡Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany; ‖Medizinisches Proteom-Center, Ruhr-University Bochum, Bochum, Germany; **Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, UK
| | - Johan W M Heemskerk
- §Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands;
| | - René P Zahedi
- From the ‡Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany;
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