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Kan KT, Wilcock J, Lu H. Role of Yme1 in mitochondrial protein homeostasis: from regulation of protein import, OXPHOS function to lipid synthesis and mitochondrial dynamics. Biochem Soc Trans 2024; 52:1539-1548. [PMID: 38864432 DOI: 10.1042/bst20240450] [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: 04/16/2024] [Revised: 05/29/2024] [Accepted: 05/30/2024] [Indexed: 06/13/2024]
Abstract
Mitochondria are essential organelles of eukaryotic cells and thus mitochondrial proteome is under constant quality control and remodelling. Yme1 is a multi-functional protein and subunit of the homo-hexametric complex i-AAA proteinase. Yme1 plays vital roles in the regulation of mitochondrial protein homeostasis and mitochondrial plasticity, ranging from substrate degradation to the regulation of protein functions involved in mitochondrial protein biosynthesis, energy production, mitochondrial dynamics, and lipid biosynthesis and signalling. In this mini review, we focus on discussing the current understanding of the roles of Yme1 in mitochondrial protein import via TIM22 and TIM23 pathways, oxidative phosphorylation complex function, as well as mitochondrial lipid biosynthesis and signalling, as well as a brief discussion of the role of Yme1 in modulating mitochondrial dynamics.
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Affiliation(s)
- Kwan Ting Kan
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester M13 9PT, U.K
| | - Joel Wilcock
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester M13 9PT, U.K
| | - Hui Lu
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester M13 9PT, U.K
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2
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Liu BH, Xu CZ, Liu Y, Lu ZL, Fu TL, Li GR, Deng Y, Luo GQ, Ding S, Li N, Geng Q. Mitochondrial quality control in human health and disease. Mil Med Res 2024; 11:32. [PMID: 38812059 PMCID: PMC11134732 DOI: 10.1186/s40779-024-00536-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 05/07/2024] [Indexed: 05/31/2024] Open
Abstract
Mitochondria, the most crucial energy-generating organelles in eukaryotic cells, play a pivotal role in regulating energy metabolism. However, their significance extends beyond this, as they are also indispensable in vital life processes such as cell proliferation, differentiation, immune responses, and redox balance. In response to various physiological signals or external stimuli, a sophisticated mitochondrial quality control (MQC) mechanism has evolved, encompassing key processes like mitochondrial biogenesis, mitochondrial dynamics, and mitophagy, which have garnered increasing attention from researchers to unveil their specific molecular mechanisms. In this review, we present a comprehensive summary of the primary mechanisms and functions of key regulators involved in major components of MQC. Furthermore, the critical physiological functions regulated by MQC and its diverse roles in the progression of various systemic diseases have been described in detail. We also discuss agonists or antagonists targeting MQC, aiming to explore potential therapeutic and research prospects by enhancing MQC to stabilize mitochondrial function.
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Affiliation(s)
- Bo-Hao Liu
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, China
- Department of Thoracic Surgery, First Hospital of Jilin University, Changchun, 130021, China
| | - Chen-Zhen Xu
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Yi Liu
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Zi-Long Lu
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Ting-Lv Fu
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Guo-Rui Li
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Yu Deng
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Guo-Qing Luo
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Song Ding
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Ning Li
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, China.
| | - Qing Geng
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, China.
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3
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Aloisio S, Satolli S, Bellini G, Lopriore P. Parkinsonism in complex neurogenetic disorders: lessons from hereditary dementias, adult-onset ataxias and spastic paraplegias. Neurol Sci 2023; 44:3379-3388. [PMID: 37648940 PMCID: PMC10495519 DOI: 10.1007/s10072-023-07044-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 08/22/2023] [Indexed: 09/01/2023]
Abstract
Parkinsonism is a syndrome characterized by bradykinesia in combination with either rest tremor, rigidity, or both. These features are the cardinal manifestations of Parkinson's disease, the most common cause of parkinsonism, and atypical parkinsonian disorders. However, parkinsonism can be a manifestation of complex neurological and neurodegenerative genetically determined disorders, which have a vast and heterogeneous motor and non-motor phenotypic features. Hereditary dementias, adult-onset ataxias and spastic paraplegias represent only few of this vast group of neurogenetic diseases. This review will provide an overview of parkinsonism's clinical features within adult-onset neurogenetic diseases which a neurologist could face with. Understanding parkinsonism and its characteristics in the context of the aforementioned neurological conditions may provide insights into pathophysiological mechanisms and have important clinical implications, including diagnostic and therapeutic aspects.
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Affiliation(s)
- Simone Aloisio
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Sara Satolli
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Fondazione Stella Maris, Pisa, Italy
| | - Gabriele Bellini
- Department of Clinical and Experimental Medicine, Neurological Institute, University of Pisa, Pisa, Italy
| | - Piervito Lopriore
- Department of Clinical and Experimental Medicine, Neurological Institute, University of Pisa, Pisa, Italy.
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4
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Brodsky MC, Olson RJ, Asumda FZ, Lopour MQ, Schimmenti LA, Klee EW. Identification of AFG3L2 dominant optic atrophy following reanalysis of clinical exome sequencing. Am J Ophthalmol Case Rep 2023; 30:101825. [PMID: 36974169 PMCID: PMC10038781 DOI: 10.1016/j.ajoc.2023.101825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 02/09/2023] [Accepted: 02/24/2023] [Indexed: 03/11/2023] Open
Abstract
Purpose To highlight the importance of the utility of clinical exome sequencing, and show how it led to the diagnosis of nonsyndromic autosomal dominant optic atrophy arising from an autosomal dominant variant in AFG3L2. Observations A healthy father and daughter of East African heritage experienced the onset of vision loss in the first decade of life due to optic atrophy. No additional neurologic or neuroimaging abnormalities were detected. Clinical exome sequencing was initially performed and provided a negative result. Reanalysis of the sequencing data revealed an autosomal dominant pathogenic variant in AFG3L2, c.1064C>T (p.Thr355Met), a gene that was recently identified to be associated with non-syndromic optic atrophy. This variant has previously been reported in a patient with optic atrophy, motor disturbances, and an abnormal brain MRI. Conclusions As the causes of dominant optic atrophy continue to expand, accurate genetic diagnosis is aided by an iterative reanalysis process for individuals and families when initial exome and genome testing does not provide an answer.
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Affiliation(s)
- Michael C. Brodsky
- Department of Ophthalmology, Mayo Clinic, Rochester, MN, United States
- Department of Neurology, Mayo Clinic, Rochester, MN, United States
- Corresponding author. Mayo Clinic, Department of Ophthalmology, 200 First St SW, Rochester, MN, 55905, United States.
| | - Rory J. Olson
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States
| | - Faizal Z. Asumda
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, United States
- Department of Pediatrics, Medical College of Georgia, Augusta University, Augusta, GA, United States
| | | | - Lisa A. Schimmenti
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, United States
- Department of Otorhinolaryngology, Mayo Clinic, Rochester, MN, United States
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
| | - Eric W. Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States
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5
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Peptidomics as a Tool to Assess the Cleavage of Wine Haze Proteins by Peptidases from Drosophila suzukii Larvae. Biomolecules 2023; 13:biom13030451. [PMID: 36979386 PMCID: PMC10046487 DOI: 10.3390/biom13030451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/20/2023] [Accepted: 02/23/2023] [Indexed: 03/06/2023] Open
Abstract
Thermolabile grape berry proteins such as thaumatin-like proteins (TLPs) and chitinases (CHIs) promote haze formation in bottled wines if not properly fined. As a natural grapevine pest, the spotted-wing fly Drosophila suzukii is a promising source of peptidases that break down grape berry proteins because the larvae develop and feed inside mature berries. Therefore, we produced recombinant TLP and CHI as model thermolabile wine haze proteins and applied a peptidomics strategy to investigate whether D. suzukii larval peptidases were able to digest them under acidic conditions (pH 3.5), which are typically found in winemaking practices. The activity of the novel peptidases was confirmed by mass spectrometry, and cleavage sites within the wine haze proteins were visualized in 3D protein models. The combination of recombinant haze proteins and peptidomics provides a valuable screening tool to identify optimal peptidases suitable for clarification processes in the winemaking industry.
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6
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Kumar A, Waingankar TP, D'Silva P. Functional crosstalk between the TIM22 complex and YME1 machinery maintains mitochondrial proteostasis and integrity. J Cell Sci 2023; 136:286750. [PMID: 36601773 DOI: 10.1242/jcs.260060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 12/13/2022] [Indexed: 01/06/2023] Open
Abstract
TIM22 pathway cargos are essential for sustaining mitochondrial homeostasis as an excess of these proteins leads to proteostatic stress and cell death. Yme1 is an inner membrane metalloprotease that regulates protein quality control with chaperone-like and proteolytic activities. Although the mitochondrial translocase and protease machinery are critical for organelle health, their functional association remains unexplored. The present study unravels a novel genetic connection between the TIM22 complex and YME1 machinery in Saccharomyces cerevisiae that is required for maintaining mitochondrial health. Our genetic analyses indicate that impairment in the TIM22 complex rescues the respiratory growth defects of cells without Yme1. Furthermore, Yme1 is essential for the stability of the TIM22 complex and regulates the proteostasis of TIM22 pathway substrates. Moreover, impairment in the TIM22 complex suppressed the mitochondrial structural and functional defects of Yme1-devoid cells. In summary, excessive levels of TIM22 pathway substrates could be one of the reasons for respiratory growth defects of cells lacking Yme1, and compromising the TIM22 complex can compensate for the imbalance in mitochondrial proteostasis caused by the loss of Yme1.
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Affiliation(s)
- Abhishek Kumar
- Department of Biochemistry, New Biological Sciences Building, Indian Institute of Science, C V Raman Avenue, Bangalore 560012, India
| | - Tejashree Pradip Waingankar
- Department of Biochemistry, New Biological Sciences Building, Indian Institute of Science, C V Raman Avenue, Bangalore 560012, India
| | - Patrick D'Silva
- Department of Biochemistry, New Biological Sciences Building, Indian Institute of Science, C V Raman Avenue, Bangalore 560012, India
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7
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Baker MJ, Crameri JJ, Thorburn DR, Frazier AE, Stojanovski D. Mitochondrial biology and dysfunction in secondary mitochondrial disease. Open Biol 2022; 12:220274. [PMID: 36475414 PMCID: PMC9727669 DOI: 10.1098/rsob.220274] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Mitochondrial diseases are a broad, genetically heterogeneous class of metabolic disorders characterized by deficits in oxidative phosphorylation (OXPHOS). Primary mitochondrial disease (PMD) defines pathologies resulting from mutation of mitochondrial DNA (mtDNA) or nuclear genes affecting either mtDNA expression or the biogenesis and function of the respiratory chain. Secondary mitochondrial disease (SMD) arises due to mutation of nuclear-encoded genes independent of, or indirectly influencing OXPHOS assembly and operation. Despite instances of novel SMD increasing year-on-year, PMD is much more widely discussed in the literature. Indeed, since the implementation of next generation sequencing (NGS) techniques in 2010, many novel mitochondrial disease genes have been identified, approximately half of which are linked to SMD. This review will consolidate existing knowledge of SMDs and outline discrete categories within which to better understand the diversity of SMD phenotypes. By providing context to the biochemical and molecular pathways perturbed in SMD, we hope to further demonstrate the intricacies of SMD pathologies outside of their indirect contribution to mitochondrial energy generation.
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Affiliation(s)
- Megan J. Baker
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Jordan J. Crameri
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3052, Australia
| | - David R. Thorburn
- Murdoch Children's Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, Parkville, Victoria 3052, Australia,Victorian Clinical Genetics Services, Royal Children's Hospital, Parkville, Victoria 3052, Australia
| | - Ann E. Frazier
- Murdoch Children's Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Diana Stojanovski
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3052, Australia
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8
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Hackett PT, Jia X, Li L, Ward DM. Posttranslational regulation of mitochondrial frataxin and identification of compounds that increase frataxin levels in Friedreich's ataxia. J Biol Chem 2022; 298:101982. [PMID: 35472330 PMCID: PMC9127368 DOI: 10.1016/j.jbc.2022.101982] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 04/18/2022] [Accepted: 04/19/2022] [Indexed: 11/18/2022] Open
Abstract
Friedreich's ataxia (FRDA) is a degenerative disease caused by a decrease in the mitochondrial protein frataxin (Fxn), which is involved in iron-sulfur cluster (ISC) synthesis. Diminutions in Fxn result in decreased ISC synthesis, increased mitochondrial iron accumulation, and impaired mitochondrial function. Here, we show that conditions that result in increased mitochondrial reactive oxygen species in yeast or mammalian cell culture give rise to increased turnover of Fxn but not of other ISC synthesis proteins. We demonstrate that the mitochondrial Lon protease is involved in Fxn degradation and that iron export through the mitochondrial metal transporter Mmt1 protects yeast Fxn from degradation. We also determined that when FRDA fibroblasts were grown in media containing elevated iron, mitochondrial reactive oxygen species increased and Fxn decreased compared to WT fibroblasts. Furthermore, we screened a library of FDA-approved compounds and identified 38 compounds that increased yeast Fxn levels, including the azole bifonazole, antiparasitic fipronil, antitumor compound dibenzoylmethane, antihypertensive 4-hydroxychalcone, and a nonspecific anion channel inhibitor 4,4-diisothiocyanostilbene-2,2-sulfonic acid. We show that top hits 4-hydroxychalcone and dibenzoylmethane increased mRNA levels of transcription factor nuclear factor erythroid 2-related factor 2 in FRDA patient-derived fibroblasts, as well as downstream antioxidant targets thioredoxin, glutathione reductase, and superoxide dismutase 2. Taken together, these findings reveal that FRDA progression may be in part due to oxidant-mediated decreases in Fxn and that some approved compounds may be effective in increasing mitochondrial Fxn in FRDA, delaying disease progression.
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Affiliation(s)
- Peter T Hackett
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Xuan Jia
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Liangtao Li
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Diane M Ward
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, Utah, USA.
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9
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Wachoski-Dark E, Zhao T, Khan A, Shutt TE, Greenway SC. Mitochondrial Protein Homeostasis and Cardiomyopathy. Int J Mol Sci 2022; 23:ijms23063353. [PMID: 35328774 PMCID: PMC8953902 DOI: 10.3390/ijms23063353] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 12/06/2022] Open
Abstract
Human mitochondrial disorders impact tissues with high energetic demands and can be associated with cardiac muscle disease (cardiomyopathy) and early mortality. However, the mechanistic link between mitochondrial disease and the development of cardiomyopathy is frequently unclear. In addition, there is often marked phenotypic heterogeneity between patients, even between those with the same genetic variant, which is also not well understood. Several of the mitochondrial cardiomyopathies are related to defects in the maintenance of mitochondrial protein homeostasis, or proteostasis. This essential process involves the importing, sorting, folding and degradation of preproteins into fully functional mature structures inside mitochondria. Disrupted mitochondrial proteostasis interferes with mitochondrial energetics and ATP production, which can directly impact cardiac function. An inability to maintain proteostasis can result in mitochondrial dysfunction and subsequent mitophagy or even apoptosis. We review the known mitochondrial diseases that have been associated with cardiomyopathy and which arise from mutations in genes that are important for mitochondrial proteostasis. Genes discussed include DnaJ heat shock protein family member C19 (DNAJC19), mitochondrial import inner membrane translocase subunit TIM16 (MAGMAS), translocase of the inner mitochondrial membrane 50 (TIMM50), mitochondrial intermediate peptidase (MIPEP), X-prolyl-aminopeptidase 3 (XPNPEP3), HtraA serine peptidase 2 (HTRA2), caseinolytic mitochondrial peptidase chaperone subunit B (CLPB) and heat shock 60-kD protein 1 (HSPD1). The identification and description of disorders with a shared mechanism of disease may provide further insights into the disease process and assist with the identification of potential therapeutics.
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Affiliation(s)
- Emily Wachoski-Dark
- Department of Cardiac Sciences, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada;
- Libin Cardiovascular Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Tian Zhao
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada;
| | - Aneal Khan
- Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada;
- Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
- M.A.G.I.C. Inc., Calgary, AB T2E 7Z4, Canada
| | - Timothy E. Shutt
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada;
- Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Correspondence: (T.E.S.); (S.C.G.)
| | - Steven C. Greenway
- Department of Cardiac Sciences, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada;
- Libin Cardiovascular Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada;
- Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada;
- Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
- Correspondence: (T.E.S.); (S.C.G.)
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10
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Bazylianska V, Sharma A, Chauhan H, Schneider B, Moszczynska A. Dopamine and Methamphetamine Differentially Affect Electron Transport Chain Complexes and Parkin in Rat Striatum: New Insight into Methamphetamine Neurotoxicity. Int J Mol Sci 2021; 23:ijms23010363. [PMID: 35008791 PMCID: PMC8745447 DOI: 10.3390/ijms23010363] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 01/24/2023] Open
Abstract
Methamphetamine (METH) is a highly abused psychostimulant that is neurotoxic to dopaminergic (DAergic) nerve terminals in the striatum and increases the risk of developing Parkinson’s disease (PD). In vivo, METH-mediated DA release, followed by DA-mediated oxidative stress and mitochondrial dysfunction in pre- and postsynaptic neurons, mediates METH neurotoxicity. METH-triggered oxidative stress damages parkin, a neuroprotective protein involved in PD etiology via its involvement in the maintenance of mitochondria. It is not known whether METH itself contributes to mitochondrial dysfunction and whether parkin regulates complex I, an enzymatic complex downregulated in PD. To determine this, we separately assessed the effects of METH or DA alone on electron transport chain (ETC) complexes and the protein parkin in isolated striatal mitochondria. We show that METH decreases the levels of selected complex I, II, and III subunits (NDUFS3, SDHA, and UQCRC2, respectively), whereas DA decreases the levels only of the NDUFS3 subunit in our preparations. We also show that the selected subunits are not decreased in synaptosomal mitochondria under similar experimental conditions. Finally, we found that parkin overexpression does not influence the levels of the NDUFS3 subunit in rat striatum. The presented results indicate that METH itself is a factor promoting dysfunction of striatal mitochondria; therefore, it is a potential drug target against METH neurotoxicity. The observed decreases in ETC complex subunits suggest that DA and METH decrease activities of the ETC complexes via oxidative damage to their subunits and that synaptosomal mitochondria may be somewhat “resistant” to DA- and METH-induced disruption in mitochondrial ETC complexes than perikaryal mitochondria. The results also suggest that parkin does not regulate NDUFS3 turnover in rat striatum.
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Affiliation(s)
- Viktoriia Bazylianska
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, MI 48201, USA; (V.B.); (A.S.); (H.C.)
| | - Akhil Sharma
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, MI 48201, USA; (V.B.); (A.S.); (H.C.)
| | - Heli Chauhan
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, MI 48201, USA; (V.B.); (A.S.); (H.C.)
| | - Bernard Schneider
- Brain Mind Institute, École Polytechnique Fédérale de Lausanne, School of Life Sciences, CH-1015 Lausanne, Switzerland;
| | - Anna Moszczynska
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, MI 48201, USA; (V.B.); (A.S.); (H.C.)
- Correspondence:
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11
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Zhao F, Zou MH. Role of the Mitochondrial Protein Import Machinery and Protein Processing in Heart Disease. Front Cardiovasc Med 2021; 8:749756. [PMID: 34651031 PMCID: PMC8505727 DOI: 10.3389/fcvm.2021.749756] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 08/26/2021] [Indexed: 12/12/2022] Open
Abstract
Mitochondria are essential organelles for cellular energy production, metabolic homeostasis, calcium homeostasis, cell proliferation, and apoptosis. About 99% of mammalian mitochondrial proteins are encoded by the nuclear genome, synthesized as precursors in the cytosol, and imported into mitochondria by mitochondrial protein import machinery. Mitochondrial protein import systems function not only as independent units for protein translocation, but also are deeply integrated into a functional network of mitochondrial bioenergetics, protein quality control, mitochondrial dynamics and morphology, and interaction with other organelles. Mitochondrial protein import deficiency is linked to various diseases, including cardiovascular disease. In this review, we describe an emerging class of protein or genetic variations of components of the mitochondrial import machinery involved in heart disease. The major protein import pathways, including the presequence pathway (TIM23 pathway), the carrier pathway (TIM22 pathway), and the mitochondrial intermembrane space import and assembly machinery, related translocases, proteinases, and chaperones, are discussed here. This review highlights the importance of mitochondrial import machinery in heart disease, which deserves considerable attention, and further studies are urgently needed. Ultimately, this knowledge may be critical for the development of therapeutic strategies in heart disease.
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Affiliation(s)
- Fujie Zhao
- Center for Molecular and Translational Medicine, Georgia State University, Atlanta, GA, United States
| | - Ming-Hui Zou
- Center for Molecular and Translational Medicine, Georgia State University, Atlanta, GA, United States
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12
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Proteomic analysis demonstrates the role of the quality control protease LONP1 in mitochondrial protein aggregation. J Biol Chem 2021; 297:101134. [PMID: 34461102 PMCID: PMC8503632 DOI: 10.1016/j.jbc.2021.101134] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 08/23/2021] [Accepted: 08/26/2021] [Indexed: 11/20/2022] Open
Abstract
The mitochondrial matrix protease LONP1 is an essential part of the organellar protein quality control system. LONP1 has been shown to be involved in respiration control and apoptosis. Furthermore, a reduction in LONP1 level correlates with aging. Up to now, the effects of a LONP1 defect were mostly studied by utilizing transient, siRNA-mediated knockdown approaches. We generated a new cellular model system for studying the impact of LONP1 on mitochondrial protein homeostasis by a CRISPR/Cas-mediated genetic knockdown (gKD). These cells showed a stable reduction of LONP1 along with a mild phenotype characterized by absent morphological differences and only small negative effects on mitochondrial functions under normal culture conditions. To assess the consequences of a permanent LONP1 depletion on the mitochondrial proteome, we analyzed the alterations of protein levels by quantitative mass spectrometry, demonstrating small adaptive changes, in particular with respect to mitochondrial protein biogenesis. In an additional proteomic analysis, we determined the temperature-dependent aggregation behavior of mitochondrial proteins and its dependence on a reduction of LONP1 activity, demonstrating the important role of the protease for mitochondrial protein homeostasis in mammalian cells. We identified a significant number of mitochondrial proteins that are affected by a reduced LONP1 activity especially with respect to their stress-induced solubility. Taken together, our results suggest a very good applicability of the LONP1 gKD cell line as a model system for human aging processes.
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13
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Positive DAT-SCAN in SPG7: a case report mimicking possible MSA-C. BMC Neurol 2021; 21:328. [PMID: 34433436 PMCID: PMC8386044 DOI: 10.1186/s12883-021-02345-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 08/04/2021] [Indexed: 11/10/2022] Open
Abstract
Background Spastic Paraplegia type 7 (SPG7) is one of the most common autosomal recessive Hereditary Spastic Paraplegias (HSP); Spastic Paraplegias (SPGs) can present as hereditary ataxias. However, ataxia is frequently the symptom of presentation of many other hereditary/sporadic disorders, such as Multiple system atrophy type C (MSA-C), an α-synuclein sporadic neurodegenerative disorder, in which cerebellar ataxia is one of the main clinical features. Dopamine Transporter imaging (DAT-SCAN), associated with clinical features, can be a helpful tool in order to distinguish MSA-C from other causes of ataxia. Case-presentation We present the case of a 70-year-old man with gait difficulties over a period of 3 years and frequent backward/lateral falls. He also reported urinary urge incontinence, but no symptoms that are compatible with orthostatic hypotension. On neurological examination he showed ataxic gait, spasticity in the left lower limb and trunk and limb ataxia, especially on the left side. Mild hypokinesia was found in all 4 limbs, especially in the left foot. MRI revealed atrophy of the cerebellar hemispheres and vermis. DAT-SCAN imaging revealed bilateral nigro-striatal degeneration, which was compatible with a diagnosis of possible MSA-C. Considering the atypical disease course (the patient walked without any support after 3 years), we carried out a genetic investigation for Ataxia, and a mutation in SPG7 was found. Conclusions DAT-SCAN imaging, evaluated together with the clinical findings, can be useful for differentiating MSA from other possible causes of adult-onset Ataxia. Indeed, patients with MSA-C generally show a decreased uptake of dopamine transporters in DAT-SCAN imaging. Ours is the first case reported in the literature of a patient with SPG7 mutation with nigrostriatal degeneration and a clinical presentation of a possible MSA-C. Performing genetic investigations in patients with an atypical disease course is important to avoid MSA-mimicries. Identifying the correct diagnosis is important not only for prognostic reasons, but also for possible future genetic therapies.
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Abstract
Maintaining mitochondrial health is essential for the survival and function of eukaryotic organisms. Misfunctioning mitochondria activate stress-responsive pathways to restore mitochondrial network homeostasis, remove damaged or toxic proteins, and eliminate damaged organelles via selective autophagy of mitochondria, a process termed mitophagy. Failure of these quality control pathways is implicated in the pathogenesis of Parkinson's disease and other neurodegenerative diseases. Impairment of mitochondrial quality control has been demonstrated to activate innate immune pathways, including inflammasome-mediated signaling and the antiviral cyclic GMP-AMP synthase (cGAS)/stimulator of interferon genes (STING)-regulated interferon response. Immune system malfunction is a common hallmark in many neurodegenerative diseases; however, whether inflammation suppresses or exacerbates disease pathology is still unclear. The goal of this review is to provide a historical overview of the field, describe mechanisms of mitochondrial quality control, and highlight recent advances on the emerging role of mitochondria in innate immunity and inflammation.
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Affiliation(s)
- Andrew T Moehlman
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA;
| | - Richard J Youle
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA;
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15
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Wang C, Wang Y, Shen L. Mitochondrial proteins in heart failure: The role of deacetylation by SIRT3. Pharmacol Res 2021; 172:105802. [PMID: 34363948 DOI: 10.1016/j.phrs.2021.105802] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 07/29/2021] [Accepted: 08/03/2021] [Indexed: 12/28/2022]
Abstract
Heart failure (HF) is still the leading cause of death worldwide, occurring with a variety of complex mechanisms. However, most intervention for HF do not directly target the pathological mechanisms underlying cell damage in failing cardiomyocytes. Mitochondria are involved in many physiological processes, which is an important guarantee for normal heart function. Mitochondrial dysfunction is considered to be the critical node of the development of HF. Strict modulation of the mitochondrial function can ameliorate the myocardial injury and protect cardiac function. Acetylation plays an important role in mitochondrial protein homeostasis, and SIRT3, the most important deacetylation protein in mitochondria, is involved in the maintenance of mitochondrial function. SIRT3 can delay the progression of HF by improving mitochondrial function. Herein we summarize the interaction between SIRT3 and proteins related to mitochondrial function including oxidative phosphorylation (OXPHOS), fatty acid oxidation (FAO), mitochondrial biosynthesis, mitochondrial quality control. In addition, we also sum up the effects of this interaction on HF and the research progress of treatments targeting SIRT3, so as to find potential HF therapeutic for clinical use in the future.
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Affiliation(s)
- Chunfang Wang
- Department of Internal Cardiovascular Medicine, The Second Xiangya Hospital, Central South University, 139 Middle Renming Road, Changsha, Hunan 410011, PR China.
| | - Yating Wang
- Department of Internal Cardiovascular Medicine, The Second Xiangya Hospital, Central South University, 139 Middle Renming Road, Changsha, Hunan 410011, PR China.
| | - Li Shen
- Department of Internal Cardiovascular Medicine, The Second Xiangya Hospital, Central South University, 139 Middle Renming Road, Changsha, Hunan 410011, PR China.
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16
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Li M, Thorne RF, Shi R, Zhang XD, Li J, Li J, Zhang Q, Wu M, Liu L. DDIT3 Directs a Dual Mechanism to Balance Glycolysis and Oxidative Phosphorylation during Glutamine Deprivation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2003732. [PMID: 34105294 PMCID: PMC8188220 DOI: 10.1002/advs.202003732] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 01/29/2021] [Indexed: 05/26/2023]
Abstract
Extracellular glutamine represents an important energy source for many cancer cells and its metabolism is intimately involved in maintaining redox homeostasis. The heightened metabolic activity within tumor tissues can result in glutamine deficiency, necessitating metabolic reprogramming responses. Here, dual mechanisms involving the stress-responsive transcription factor DDIT3 (DNA damage induced transcript 3) that establishes an interrelationship between glycolysis and mitochondrial respiration are revealed. DDIT3 is induced during glutamine deprivation to promote glycolysis and adenosine triphosphate production via suppression of the negative glycolytic regulator TIGAR. In concert, a proportion of the DDIT3 pool translocates to the mitochondria and suppresses oxidative phosphorylation through LONP1-mediated down-regulation of COQ9 and COX4. This in turn dampens the sustained levels of reactive oxygen species that follow glutamine withdrawal. Together these mechanisms constitute an adaptive survival mechanism permitting tumor cells to survive metabolic stress induced by glutamine starvation.
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Affiliation(s)
- Mingyue Li
- Heifei National Laboratory for Physical Sciences at the Microscale of USTCCAS Centre for Excellence in Molecular Cell Sciencethe First Affiliated Hospital of University of Science and Technology of ChinaHefeiAnhui230027China
| | - Rick Francis Thorne
- Translational Research InstituteHenan Provincial People's HospitalSchool of Clinical MedicineHenan UniversityZhengzhouHenan450003China
| | - Ronghua Shi
- Heifei National Laboratory for Physical Sciences at the Microscale of USTCCAS Centre for Excellence in Molecular Cell Sciencethe First Affiliated Hospital of University of Science and Technology of ChinaHefeiAnhui230027China
| | - Xu Dong Zhang
- Translational Research InstituteHenan Provincial People's HospitalSchool of Clinical MedicineHenan UniversityZhengzhouHenan450003China
| | - Jingmin Li
- Translational Research InstituteHenan Provincial People's HospitalSchool of Clinical MedicineHenan UniversityZhengzhouHenan450003China
- Harbin Medical University Cancer HospitalHarbinHeilongjiang150081China
| | - Jingtong Li
- Harbin Medical University Cancer HospitalHarbinHeilongjiang150081China
| | - Qingyuan Zhang
- Harbin Medical University Cancer HospitalHarbinHeilongjiang150081China
| | - Mian Wu
- Heifei National Laboratory for Physical Sciences at the Microscale of USTCCAS Centre for Excellence in Molecular Cell Sciencethe First Affiliated Hospital of University of Science and Technology of ChinaHefeiAnhui230027China
- Translational Research InstituteHenan Provincial People's HospitalSchool of Clinical MedicineHenan UniversityZhengzhouHenan450003China
| | - Lianxin Liu
- Heifei National Laboratory for Physical Sciences at the Microscale of USTCCAS Centre for Excellence in Molecular Cell Sciencethe First Affiliated Hospital of University of Science and Technology of ChinaHefeiAnhui230027China
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17
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Ramos JE, Jain RG, Powell CA, Dawson WO, Gowda S, Borovsky D, Shatters RG. Crowdsourced Identification of Potential Target Genes for CTV Induced Gene Silencing for Controlling the Citrus Greening Vector Diaphorina citri. Front Physiol 2021; 12:571826. [PMID: 33897443 PMCID: PMC8063116 DOI: 10.3389/fphys.2021.571826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 03/19/2021] [Indexed: 11/25/2022] Open
Abstract
Citrus Greening or Huanglongbing (HLB) is a disease of citrus, causing high reduction in citrus production and is transmitted by the Asian citrus psyllid Diaphorina citri Kuwayama vectoring a phloem-limited bacterium Candidatus Liberibacter sp. We report research results using crowdsourcing challenge strategy identifying potential gene targets in D. citri to control the insect using RNA interference (RNAi). From 63 submitted sequences, 43 were selected and tested by feeding them to D. citri using artificial diet assays. After feeding on artificial diet, the three most effective dsRNAs causing 30% mortality above control silenced genes expressing iron-sulfur cluster subunit of the mitochondrial electron transport chain complex (Rieske), heme iron-binding terminal oxidase enzyme (Cytochrome P450) and tetrahydrobiopterin (BH4) pathway enzyme (Pterin 4α-Carbinolamine Dehydratase). These sequences were cloned into a citrus phloem-limited virus (Citrus tristeza virus, CTV T36) expressing dsRNA against these target genes in citrus. The use of a viral mediated “para-transgenic” citrus plant system caused higher mortality to adult D. citri than what was observed using artificial diet, reaching 100% when detached citrus leaves with the engineered CTV expressing dsRNA were fed to adult D. citri. Using this approach, a virus-induced gene silencing (VIGS) can be used to test future transgenic cultivars before genetically engineering citrus. RNA Seq analysis after feeding D. citri CTV-RIE on infected leaves identified transcriptionally modified genes located upstream and downstream of the targeted RIE gene. These genes were annotated showing that many are associated with the primary function of the Rieske gene that was targeted by VIGS.
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Affiliation(s)
- John E Ramos
- U.S. Horticultural Research Laboratory (USDA-ARS), Fort Pierce, FL, United States
| | - Ritesh G Jain
- Indian River Research and Education Center, UF/IFAS, Fort Pierce, FL, United States
| | - Charles A Powell
- Indian River Research and Education Center, UF/IFAS, Fort Pierce, FL, United States
| | - William O Dawson
- Citrus Research and Education Center, UF/IFAS, Lake Alfred, FL, United States
| | - Siddarame Gowda
- Citrus Research and Education Center, UF/IFAS, Lake Alfred, FL, United States
| | - Dov Borovsky
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, United States
| | - Robert G Shatters
- U.S. Horticultural Research Laboratory (USDA-ARS), Fort Pierce, FL, United States
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18
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Sokolova I. Bioenergetics in environmental adaptation and stress tolerance of aquatic ectotherms: linking physiology and ecology in a multi-stressor landscape. J Exp Biol 2021; 224:224/Suppl_1/jeb236802. [PMID: 33627464 DOI: 10.1242/jeb.236802] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Energy metabolism (encompassing energy assimilation, conversion and utilization) plays a central role in all life processes and serves as a link between the organismal physiology, behavior and ecology. Metabolic rates define the physiological and life-history performance of an organism, have direct implications for Darwinian fitness, and affect ecologically relevant traits such as the trophic relationships, productivity and ecosystem engineering functions. Natural environmental variability and anthropogenic changes expose aquatic ectotherms to multiple stressors that can strongly affect their energy metabolism and thereby modify the energy fluxes within an organism and in the ecosystem. This Review focuses on the role of bioenergetic disturbances and metabolic adjustments in responses to multiple stressors (especially the general cellular stress response), provides examples of the effects of multiple stressors on energy intake, assimilation, conversion and expenditure, and discusses the conceptual and quantitative approaches to identify and mechanistically explain the energy trade-offs in multiple stressor scenarios, and link the cellular and organismal bioenergetics with fitness, productivity and/or ecological functions of aquatic ectotherms.
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Affiliation(s)
- Inna Sokolova
- Marine Biology Department, Institute of Biological Sciences, University of Rostock, 18059 Rostock, Germany .,Department of Maritime Systems, Interdisciplinary Faculty, University of Rostock, 18059 Rostock, Germany
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19
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Estiar MA, Yu E, Haj Salem I, Ross JP, Mufti K, Akçimen F, Leveille E, Spiegelman D, Ruskey JA, Asayesh F, Dagher A, Yoon G, Tarnopolsky M, Boycott KM, Dupre N, Dion PA, Suchowersky O, Trempe JF, Rouleau GA, Gan-Or Z. Evidence for Non-Mendelian Inheritance in Spastic Paraplegia 7. Mov Disord 2021; 36:1664-1675. [PMID: 33598982 DOI: 10.1002/mds.28528] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Although the typical inheritance of spastic paraplegia 7 is recessive, several reports have suggested that SPG7 variants may also cause autosomal dominant hereditary spastic paraplegia (HSP). OBJECTIVES We aimed to conduct an exome-wide genetic analysis on a large Canadian cohort of HSP patients and controls to examine the association of SPG7 and HSP. METHODS We analyzed 585 HSP patients from 372 families and 1175 controls, including 580 unrelated individuals. Whole-exome sequencing was performed on 400 HSP patients (291 index cases) and all 1175 controls. RESULTS The frequency of heterozygous pathogenic/likely pathogenic SPG7 variants (4.8%) among unrelated HSP patients was higher than among unrelated controls (1.7%; OR 2.88, 95% CI 1.24-6.66, P = 0.009). The heterozygous SPG7 p.(Ala510Val) variant was found in 3.7% of index patients versus 0.85% in unrelated controls (OR 4.42, 95% CI 1.49-13.07, P = 0.005). Similar results were obtained after including only genetically-undiagnosed patients. We identified four heterozygous SPG7 variant carriers with an additional pathogenic variant in known HSP genes, compared to zero in controls (OR 19.58, 95% CI 1.05-365.13, P = 0.0031), indicating potential digenic inheritance. We further identified four families with heterozygous variants in SPG7 and SPG7-interacting genes (CACNA1A, AFG3L2, and MORC2). Of these, there is especially compelling evidence for epistasis between SPG7 and AFG3L2. The p.(Ile705Thr) variant in AFG3L2 is located at the interface between hexamer subunits, in a hotspot of mutations associated with spinocerebellar ataxia type 28 that affect its proteolytic function. CONCLUSIONS Our results provide evidence for complex inheritance in SPG7-associated HSP, which may include recessive and possibly dominant and digenic/epistasis forms of inheritance. © 2021 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Mehrdad A Estiar
- Department of Human Genetics, McGill University, Montréal, Québec, Canada.,The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, Québec, Canada
| | - Eric Yu
- Department of Human Genetics, McGill University, Montréal, Québec, Canada.,The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, Québec, Canada
| | | | - Jay P Ross
- Department of Human Genetics, McGill University, Montréal, Québec, Canada.,The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, Québec, Canada
| | - Kheireddin Mufti
- Department of Human Genetics, McGill University, Montréal, Québec, Canada.,The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, Québec, Canada
| | - Fulya Akçimen
- Department of Human Genetics, McGill University, Montréal, Québec, Canada.,The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, Québec, Canada
| | - Etienne Leveille
- Faculty of Medicine, McGill University, Montréal, Québec, Canada
| | - Dan Spiegelman
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, Québec, Canada
| | - Jennifer A Ruskey
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, Québec, Canada
| | - Farnaz Asayesh
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, Québec, Canada
| | - Alain Dagher
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, Québec, Canada
| | - Grace Yoon
- Divisions of Neurology and Clinical and Metabolic Genetics, Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Mark Tarnopolsky
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Nicolas Dupre
- Neuroscience Axis, CHU de Québec, Université Laval, Québec City, Québec, Canada.,Department of Medicine, Faculty of Medicine, Université Laval, Québec City, Québec, Canada
| | - Patrick A Dion
- Department of Human Genetics, McGill University, Montréal, Québec, Canada.,The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, Québec, Canada.,Department of Neurology and Neurosurgery, McGill University, Montréal, Québec, Canada
| | - Oksana Suchowersky
- Departments of Medicine (Neurology) and Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Jean-Francois Trempe
- Department of Pharmacology & Therapeutics, McGill University, Montréal, Québec, Canada.,Centre de Recherche en Biologie Structurale, McGill University, Montréal, Québec, Canada
| | - Guy A Rouleau
- Department of Human Genetics, McGill University, Montréal, Québec, Canada.,The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, Québec, Canada.,Department of Neurology and Neurosurgery, McGill University, Montréal, Québec, Canada
| | - Ziv Gan-Or
- Department of Human Genetics, McGill University, Montréal, Québec, Canada.,The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, Québec, Canada.,Department of Neurology and Neurosurgery, McGill University, Montréal, Québec, Canada
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20
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Zia A, Farkhondeh T, Pourbagher-Shahri AM, Samarghandian S. The Roles of mitochondrial dysfunction and Reactive Oxygen Species in Aging and Senescence. Curr Mol Med 2021; 22:37-49. [PMID: 33602082 DOI: 10.2174/1566524021666210218112616] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 12/16/2020] [Accepted: 12/23/2020] [Indexed: 11/22/2022]
Abstract
The aging process deteriorates organs' function at different levels, causing its progressive decline to resist stress, damage, and disease. In addition to alterations in metabolic control and gene expression, the rate of aging has been connected with the generation of high amounts of Reactive Oxygen Species (ROS). The essential perspective in free radical biology is that reactive oxygen species (ROS) and free radicals are toxic, mostly cause direct biological damage to targets, and are thus a major cause of oxidative stress. Different enzymatic and non-enzymatic compounds in the cells have roles in neutralizing this toxicity. Oxidative damage in aging is mostly high in particular molecular targets, such as mitochondrial DNA and aconitase, and oxidative stress in mitochondria can cause tissue aging across intrinsic apoptosis. Mitochondria's function and morphology are impaired through aging, following a decrease in the membrane potential by an increase in peroxide generation and size of the organelles. Telomeres may be the significant trigger of replicative senescence. Oxidative stress accelerates telomere loss, whereas antioxidants slow it down. Oxidative stress is a crucial modulator of telomere shortening, and that telomere-driven replicative senescence is mainly a stress response. The age-linked mitochondrial DNA mutation and protein dysfunction aggregate in some organs like the brain and skeletal muscle, thus contributing considerably to these post-mitotic tissues' aging. The aging process is mostly due to accumulated damage done by harmful species in some macromolecules such proteins, DNA, and lipids. The degradation of non-functional, oxidized proteins is a crucial part of the antioxidant defenses of cells, in which the clearance of these proteins occurs through autophagy in the cells, which is known as mitophagy for mitochondria.
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Affiliation(s)
- Aliabbas Zia
- Department of Biochemistry, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran. Iran
| | - Tahereh Farkhondeh
- Medical Toxicology and Drug Abuse Research Center (MTDRC), Birjand University of Medical Sciences, Birjand. Iran
| | | | - Saeed Samarghandian
- Noncommunicable Diseases Research Center, Neyshabur University of Medical Sciences, Neyshabur. Iran
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21
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Zeng M, He Y, Du H, Yang J, Wan H. Output Regulation and Function Optimization of Mitochondria in Eukaryotes. Front Cell Dev Biol 2020; 8:598112. [PMID: 33330486 PMCID: PMC7718039 DOI: 10.3389/fcell.2020.598112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 10/26/2020] [Indexed: 12/23/2022] Open
Abstract
The emergence of endosymbiosis between aerobic alpha-proteobacterium and anaerobic eukaryotic cell precursors opened the chapter of eukaryotic evolution. Multiple functions of mitochondria originated from the ancient precursors of mitochondria and underwent remodeling in eukaryotic cells. Due to the dependence on mitochondrial functions, eukaryotic cells need to constantly adjust mitochondrial output based on energy demand and cellular stress. Meanwhile, eukaryotes conduct the metabolic cooperation between different cells through the involvement of mitochondria. Under some conditions, mitochondria might also be transferred to nearby cells to provide a protective mechanism. However, the endosymbiont relationship determines the existence of various types of mitochondrial injury, such as proteotoxic stress, mutational meltdown, oxidative injure, and immune activation caused by released mitochondrial contents. Eukaryotes have a repertoire of mitochondrial optimization processes, including various mitochondrial quality-control proteins, regulation of mitochondrial dynamics and activation of mitochondrial autophagy. When these quality-control processes fail, eukaryotic cells can activate apoptosis to intercept uncontrolled cell death, thereby minimizing the damage to extracellular tissue. In this review, we describe the intracellular and extracellular context-based regulation of mitochondrial output in eukaryotic cells, and introduce new findings on multifaceted quality-control processes to deal with mitochondrial defects.
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Affiliation(s)
- Miaolin Zeng
- College of Basic Medical Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yu He
- College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Haixia Du
- College of Basic Medical Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jiehong Yang
- College of Basic Medical Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Haitong Wan
- College of Basic Medical Science, Zhejiang Chinese Medical University, Hangzhou, China.,College of Life Science, Zhejiang Chinese Medical University, Hangzhou, China
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22
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Sulkshane P, Ram J, Glickman MH. Ubiquitination of Intramitochondrial Proteins: Implications for Metabolic Adaptability. Biomolecules 2020; 10:biom10111559. [PMID: 33207558 PMCID: PMC7697252 DOI: 10.3390/biom10111559] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 11/11/2020] [Accepted: 11/12/2020] [Indexed: 02/07/2023] Open
Abstract
Mitochondria are constantly subjected to stressful conditions due to their unique physiology and organization. The resulting damage leads to mitochondrial dysfunction, which underlies many pathophysiological conditions. Hence, constant surveillance is required to closely monitor mitochondrial health for sound maintenance of cellular metabolism and thus, for viability. In addition to internal mitochondrial chaperones and proteases, mitochondrial health is also governed by host cell protein quality control systems. The ubiquitin-proteasome system (UPS) and autophagy constitute the main pathways for removal of damaged or superfluous proteins in the cytosol, nucleus, and from certain organelles such as the Endoplasmic Reticulum (ER) and mitochondria. Although stress-induced ubiquitin-dependent degradation of mitochondrial outer membrane proteins has been widely studied, mechanisms of intramitochondrial protein ubiquitination has remained largely elusive due to the predominantly cytosolic nature of UPS components, separated from internal mitochondrial proteins by a double membrane. However, recent research has illuminated examples of intramitochondrial protein ubiquitination pathways and highlighted their importance under basal and stressful conditions. Owing to the dependence of mitochondria on the error-prone process of protein import from the cytosol, it is imperative that the cell eliminate any accumulated proteins in the event of mitochondrial protein import deficiency. Apparently, a significant portion of this activity involves ubiquitination in one way or another. In the present review article, following a brief introduction to mitochondrial protein quality control mechanisms, we discuss our recent understanding of intramitochondrial protein ubiquitination, its importance for basal function of mitochondria, metabolic implications, and possible therapeutic applications.
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Affiliation(s)
- Prasad Sulkshane
- Correspondence: (P.S.); (M.H.G.); Tel.: +972-58779-2319 (P.S.); +972-4-829-4552 (M.H.G.)
| | | | - Michael H Glickman
- Correspondence: (P.S.); (M.H.G.); Tel.: +972-58779-2319 (P.S.); +972-4-829-4552 (M.H.G.)
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23
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Abstract
Most mammals rely on chemosensory cues for individual recognition, which is essential to many aspects of social behavior, such as maternal bonding, mate recognition, and inbreeding avoidance. Both volatile molecules and nonvolatile peptides secreted by individual conspecifics are detected by olfactory sensory neurons in the olfactory epithelium and the vomeronasal organ. The pertinent cues used for individual recognition remain largely unidentified. Here we show that nonformylated, but not N-formylated, mitochondrially encoded peptides-that is, the nine N-terminal amino acids of NADH dehydrogenases 1 and 2-can be used to convey strain-specific information among individual mice. We demonstrate that these nonformylated peptides are sufficient to induce a strain-selective pregnancy block. We also observed that the pregnancy block by an unfamiliar peptide derived from a male of a different strain was prevented by a memory formed at the time of mating with that male. Our findings also demonstrate that pregnancy-blocking chemosignals in the urine are maternally inherited, as evidenced by the production of reciprocal sons from two inbred strains and our test of their urine's ability to block pregnancy. We propose that this link between polymorphic mitochondrial peptides and individual recognition provides the molecular means to communicate an individual's maternal lineage and strain.
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24
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Human CLPB forms ATP-dependent complexes in the mitochondrial intermembrane space. Int J Biochem Cell Biol 2020; 127:105841. [PMID: 32866687 DOI: 10.1016/j.biocel.2020.105841] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/22/2020] [Accepted: 08/24/2020] [Indexed: 02/07/2023]
Abstract
Human caseinolytic peptidase B protein homolog (CLPB), also known as suppressor of potassium transport defect 3 (SKD3), is a broadly-expressed member of the family of ATPases associated with diverse cellular activities (AAA+). Mutations in the human CLPB gene cause 3-methylglutaconic aciduria type VII. CLPB is upregulated in acute myeloid leukemia (AML), where it contributes to anti-cancer drug resistance. The biological function of CLPB in human cells and mechanistic links to the clinical phenotypes are currently unknown. Herein, subcellular fractionation of human HEK-293 and BT-549 cells showed that a single 57-kDa form of CLPB was present in the mitochondria and not in the cytosolic fraction. Immunofluorescence staining of HEK-293 and BT-549 cells with anti-CLPB antibody co-localized with the mitochondrial staining using a MitoTracker dye. In purified intact mitochondria, CLPB was protected against externally added proteinase K, but it was susceptible to degradation after disruption of the outer membrane, indicating that CLPB resides in the mitochondrial intermembrane space. Overexpressed CLPB, while properly trafficked to the mitochondria, appeared to form large clusters/aggregates that were resistant to extraction with non-ionic detergents and were readily visualized by immunofluorescence microscopy. Importantly, endogenous CLPB formed high molecular weight protein complexes in an ATP-dependent manner that were detected by blue native polyacrylamide gel electrophoresis. These results demonstrate that ATP induces a structural change in CLPB and controls its ability to self-associate or form complexes with other proteins in the intermembrane space of mitochondria.
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25
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Kovalinka T, Pánek T, Kováčová B, Horváth A. Orientation of FtsH protease homologs in Trypanosoma brucei inner mitochondrial membrane and its evolutionary implications. Mol Biochem Parasitol 2020; 238:111282. [DOI: 10.1016/j.molbiopara.2020.111282] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 04/10/2020] [Accepted: 05/07/2020] [Indexed: 12/18/2022]
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26
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Botham A, Coyaud E, Nirmalanandhan VS, Gronda M, Hurren R, Maclean N, St-Germain J, Mirali S, Laurent E, Raught B, Schimmer A. Global Interactome Mapping of Mitochondrial Intermembrane Space Proteases Identifies a Novel Function for HTRA2. Proteomics 2020; 19:e1900139. [PMID: 31617661 DOI: 10.1002/pmic.201900139] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 09/30/2019] [Indexed: 12/20/2022]
Abstract
A number of unique proteases localize to specific sub-compartments of the mitochondria, but the functions of these enzymes are poorly defined. Here, in vivo proximity-dependent biotinylation (BioID) is used to map the interactomes of seven proteases localized to the mitochondrial intermembrane space (IMS). In total, 802 high confidence proximity interactions with 342 unique proteins are identified. While all seven proteases co-localized with the IMS markers OPA1 and CLPB, 230 of the interacting partners are unique to just one or two protease bait proteins, highlighting the ability of BioID to differentiate unique interactomes within the confined space of the IMS. Notably, high-temperature requirement peptidase 2 (HTRA2) interacts with eight of 13 components of the mitochondrial intermembrane space bridging (MIB) complex, a multiprotein assembly essential for the maintenance of mitochondrial cristae structure. Knockdown of HTRA2 disrupts cristae in HEK 293 and OCI-AML2 cells, and leads to increased intracellular levels of the MIB subunit IMMT. Using a cell-free assay it is demonstrated that HTRA2 can degrade recombinant IMMT but not two other core MIB complex subunits, SAMM50 and CHCHD3. The IMS protease interactome thus represents a rich dataset that can be mined to uncover novel IMS protease biology.
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Affiliation(s)
- Aaron Botham
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, ON, Canada
| | - Etienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, ON, Canada
| | | | - Marcela Gronda
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, ON, Canada
| | - Rose Hurren
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, ON, Canada
| | - Neil Maclean
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, ON, Canada
| | - Jonathan St-Germain
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, ON, Canada
| | - Sara Mirali
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, ON, Canada.,Institute of Medical Science, University of Toronto, Toronto, M5G 1L7, ON, Canada
| | - Estelle Laurent
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, ON, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, ON, Canada
| | - Aaron Schimmer
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, ON, Canada.,Institute of Medical Science, University of Toronto, Toronto, M5G 1L7, ON, Canada
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27
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Sun Z, Lv J, Ji C, Liang H, Li S, Yang Z, Xu W, Zhang S, Lin X. Analysis of carotenoid profile changes and carotenogenic genes transcript levels in Rhodosporidium toruloides mutants from an optimized Agrobacterium tumefaciens-mediated transformation method. Biotechnol Appl Biochem 2020; 68:71-81. [PMID: 32017256 DOI: 10.1002/bab.1895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 01/30/2020] [Indexed: 11/09/2022]
Abstract
Rhodosporidium toruloides has been reported as a potential biotechnological microorganism to produce carotenoids. The most commonly used molecular and genetic manipulation methods based on Agrobacterium-mediated transformation (ATMT). However, this method was of relatively lower transformation efficiency. In this study, we optimized the ATMT method for R. toruloides on account of the promoter on T-DNA, the ratio of A. tumefaciens to R. toruloides NP11, acetosyringone concentration, cocultivation temperature and time, and a transformation efficiency of 2,369 cells per 105 recipient cells was obtained and was 24 times as that of the previous report. With this optimized method, four redder mutants and four yellower mutants were selected out with torularhodin and β-carotene production preference, respectively. The highest torularhodin production was 1,638.15 µg/g dry cell weight in A1-13. The yellower mutants were found to divert the metabolic flux from torularhodin and torulene to γ-carotene and β-carotene, and the proportion of γ-carotene and β-carotene were all over 92%. TAIL-PCR was carried out to found T-DNA insertion in these mutants, and insertion hotspot was found. RT-qPCR results showed that CTA1 genes in these mutants were closely related to the synthesis of total carotenoids, especially torularhodin, and was a potenial metabolic engineering site in the future.
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Affiliation(s)
- Zeping Sun
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, People's Republic of China
| | - Jing Lv
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, People's Republic of China
| | - Chaofan Ji
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, People's Republic of China
| | - Huipeng Liang
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, People's Republic of China
| | - Shengjie Li
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, People's Republic of China
| | - Zhaoxia Yang
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, People's Republic of China
| | - Wenhuan Xu
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, People's Republic of China
| | - Sufang Zhang
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, People's Republic of China
| | - Xinping Lin
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, People's Republic of China
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Abstract
Mitochondria are essential organelles in eukaryotes. Most mitochondrial proteins are encoded by the nuclear genome and translated in the cytosol. Nuclear-encoded mitochondrial proteins need to be imported, processed, folded, and assembled into their functional states. To maintain protein homeostasis (proteostasis), mitochondria are equipped with a distinct set of quality control machineries. Deficiencies in such systems lead to mitochondrial dysfunction, which is a hallmark of aging and many human diseases, such as neurodegenerative diseases, cardiovascular diseases, and cancer. In this review, we discuss the unique challenges and solutions of proteostasis in mitochondria. The import machinery coordinates with mitochondrial proteases and chaperones to maintain the mitochondrial proteome. Moreover, mitochondrial proteostasis depends on cytosolic protein quality control mechanisms during crises. In turn, mitochondria facilitate cytosolic proteostasis. Increasing evidence suggests that enhancing mitochondrial proteostasis may hold therapeutic potential to protect against protein aggregation-associated cellular defects.
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Affiliation(s)
- Linhao Ruan
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA; , , , , ,
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Yuhao Wang
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA; , , , , ,
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Xi Zhang
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA; , , , , ,
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Alexis Tomaszewski
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA; , , , , ,
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Joshua T McNamara
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA; , , , , ,
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Rong Li
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA; , , , , ,
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
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Ravanelli S, den Brave F, Hoppe T. Mitochondrial Quality Control Governed by Ubiquitin. Front Cell Dev Biol 2020; 8:270. [PMID: 32391359 PMCID: PMC7193050 DOI: 10.3389/fcell.2020.00270] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 03/30/2020] [Indexed: 12/15/2022] Open
Abstract
Mitochondria are essential organelles important for energy production, proliferation, and cell death. Biogenesis, homeostasis, and degradation of this organelle are tightly controlled to match cellular needs and counteract chronic stress conditions. Despite providing their own DNA, the vast majority of mitochondrial proteins are encoded in the nucleus, synthesized by cytosolic ribosomes, and subsequently imported into different mitochondrial compartments. The integrity of the mitochondrial proteome is permanently challenged by defects in folding, transport, and turnover of mitochondrial proteins. Therefore, damaged proteins are constantly sequestered from the outer mitochondrial membrane and targeted for proteasomal degradation in the cytosol via mitochondrial-associated degradation (MAD). Recent studies identified specialized quality control mechanisms important to decrease mislocalized proteins, which affect the mitochondrial import machinery. Interestingly, central factors of these ubiquitin-dependent pathways are shared with the ER-associated degradation (ERAD) machinery, indicating close collaboration between both tubular organelles. Here, we summarize recently described cellular stress response mechanisms, which are triggered by defects in mitochondrial protein import and quality control. Moreover, we discuss how ubiquitin-dependent degradation is integrated with cytosolic stress responses, particularly focused on the crosstalk between MAD and ERAD.
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Affiliation(s)
- Sonia Ravanelli
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | - Fabian den Brave
- Department of Molecular Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Thorsten Hoppe
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
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30
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Caporali L, Magri S, Legati A, Del Dotto V, Tagliavini F, Balistreri F, Nasca A, La Morgia C, Carbonelli M, Valentino ML, Lamantea E, Baratta S, Schöls L, Schüle R, Barboni P, Cascavilla ML, Maresca A, Capristo M, Ardissone A, Pareyson D, Cammarata G, Melzi L, Zeviani M, Peverelli L, Lamperti C, Marzoli SB, Fang M, Synofzik M, Ghezzi D, Carelli V, Taroni F. ATPase Domain AFG3L2 Mutations Alter OPA1 Processing and Cause Optic Neuropathy. Ann Neurol 2020; 88:18-32. [PMID: 32219868 PMCID: PMC7383914 DOI: 10.1002/ana.25723] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 03/12/2020] [Accepted: 03/20/2020] [Indexed: 12/21/2022]
Abstract
OBJECTIVE Dominant optic atrophy (DOA) is the most common inherited optic neuropathy, with a prevalence of 1:12,000 to 1:25,000. OPA1 mutations are found in 70% of DOA patients, with a significant number remaining undiagnosed. METHODS We screened 286 index cases presenting optic atrophy, negative for OPA1 mutations, by targeted next generation sequencing or whole exome sequencing. Pathogenicity and molecular mechanisms of the identified variants were studied in yeast and patient-derived fibroblasts. RESULTS Twelve cases (4%) were found to carry novel variants in AFG3L2, a gene that has been associated with autosomal dominant spinocerebellar ataxia 28 (SCA28). Half of cases were familial with a dominant inheritance, whereas the others were sporadic, including de novo mutations. Biallelic mutations were found in 3 probands with severe syndromic optic neuropathy, acting as recessive or phenotype-modifier variants. All the DOA-associated AFG3L2 mutations were clustered in the ATPase domain, whereas SCA28-associated mutations mostly affect the proteolytic domain. The pathogenic role of DOA-associated AFG3L2 mutations was confirmed in yeast, unraveling a mechanism distinct from that of SCA28-associated AFG3L2 mutations. Patients' fibroblasts showed abnormal OPA1 processing, with accumulation of the fission-inducing short forms leading to mitochondrial network fragmentation, not observed in SCA28 patients' cells. INTERPRETATION This study demonstrates that mutations in AFG3L2 are a relevant cause of optic neuropathy, broadening the spectrum of clinical manifestations and genetic mechanisms associated with AFG3L2 mutations, and underscores the pivotal role of OPA1 and its processing in the pathogenesis of DOA. ANN NEUROL 2020 ANN NEUROL 2020;88:18-32.
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Affiliation(s)
- Leonardo Caporali
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Italy
| | - Stefania Magri
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Andrea Legati
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Valentina Del Dotto
- Neurology Unit, Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Francesca Tagliavini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Italy
| | - Francesca Balistreri
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Alessia Nasca
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Chiara La Morgia
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Italy.,Neurology Unit, Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Michele Carbonelli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Italy
| | - Maria L Valentino
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Italy.,Neurology Unit, Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Eleonora Lamantea
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Silvia Baratta
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Ludger Schöls
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research and Center of Neurology, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases, Tübingen, Germany
| | - Rebecca Schüle
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research and Center of Neurology, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases, Tübingen, Germany
| | - Piero Barboni
- Studio Oculistico D'Azeglio, Bologna, Italy.,IRCCS Ospedale San Raffaele, Milan, Italy
| | | | - Alessandra Maresca
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Italy
| | - Mariantonietta Capristo
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Italy
| | - Anna Ardissone
- Unit of Child Neurology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Davide Pareyson
- Unit of Rare Neurodegenerative and Neurometabolic Diseases, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Gabriella Cammarata
- Neuro-Ophthalmology Center and Ocular Electrophysiology Laboratory, IRCCS Istituto Auxologico Italiano, Capitanio Hospital, Milan, Italy
| | - Lisa Melzi
- Neuro-Ophthalmology Center and Ocular Electrophysiology Laboratory, IRCCS Istituto Auxologico Italiano, Capitanio Hospital, Milan, Italy
| | - Massimo Zeviani
- Department of Neuroscience, University of Padua, Padua, Italy
| | - Lorenzo Peverelli
- Neurology Unit, Azienda Socio Sanitaria Territoriale Lodi, Ospedale Maggiore di Lodi, Lodi, Italy
| | - Costanza Lamperti
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Stefania B Marzoli
- Neuro-Ophthalmology Center and Ocular Electrophysiology Laboratory, IRCCS Istituto Auxologico Italiano, Capitanio Hospital, Milan, Italy
| | - Mingyan Fang
- Beijing Genomics Institute-Shenzhen, Shenzhen, China
| | - Matthis Synofzik
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research and Center of Neurology, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases, Tübingen, Germany
| | - Daniele Ghezzi
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy.,Department of Medical-Surgical Physiopathology and Transplantation, University of Milan, Milan, Italy
| | - Valerio Carelli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Italy.,Neurology Unit, Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Franco Taroni
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
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31
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AAA+ ATPases in Protein Degradation: Structures, Functions and Mechanisms. Biomolecules 2020; 10:biom10040629. [PMID: 32325699 PMCID: PMC7226402 DOI: 10.3390/biom10040629] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/21/2020] [Accepted: 03/30/2020] [Indexed: 12/28/2022] Open
Abstract
Adenosine triphosphatases (ATPases) associated with a variety of cellular activities (AAA+), the hexameric ring-shaped motor complexes located in all ATP-driven proteolytic machines, are involved in many cellular processes. Powered by cycles of ATP binding and hydrolysis, conformational changes in AAA+ ATPases can generate mechanical work that unfolds a substrate protein inside the central axial channel of ATPase ring for degradation. Three-dimensional visualizations of several AAA+ ATPase complexes in the act of substrate processing for protein degradation have been resolved at the atomic level thanks to recent technical advances in cryogenic electron microscopy (cryo-EM). Here, we summarize the resulting advances in structural and biochemical studies of AAA+ proteases in the process of proteolysis reactions, with an emphasis on cryo-EM structural analyses of the 26S proteasome, Cdc48/p97 and FtsH-like mitochondrial proteases. These studies reveal three highly conserved patterns in the structure–function relationship of AAA+ ATPase hexamers that were observed in the human 26S proteasome, thus suggesting common dynamic models of mechanochemical coupling during force generation and substrate translocation.
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32
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Kalvala AK, Khan I, Gundu C, Kumar A. An Overview on ATP Dependent and Independent Proteases Including an Anterograde to Retrograde Control on Mitochondrial Function; Focus on Diabetes and Diabetic Complications. Curr Pharm Des 2020; 25:2584-2594. [PMID: 31317835 DOI: 10.2174/1381612825666190718153901] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 07/12/2019] [Indexed: 12/17/2022]
Abstract
Mitochondria are the central power stations of the cell involved with a myriad of cell signalling pathways that contribute for whole health status of the cell. It is a well known fact that not only mitochondrial genome encodes for mitochondrial proteins but there are several other mitochondrial specific proteins encoded by nuclear genome which regulate plethora of cell catabolic and anabolic process. Anterograde pathways include nuclear gene encoded proteins and their specific transport into the mitochondria and regulation of mitochondrial homeostasis. The retrograde pathways include crosstalk between the mitochondria and cytoplasmic proteins. Indeed, ATP dependent and independent proteases are identified to be very critical in balancing anterograde to retrograde signalling and vice versa to maintain the cell viability or cell death. Different experimental studies conducted on silencing the genes of these proteases have shown embryonic lethality, cancer cells death, increased hepatic glucose output, insulin tolerance, increased protein exclusion bodies, mitochondrial dysfunction, and defect in mitochondrial biogenesis, increased inflammation, Apoptosis etc. These experimental studies included from eubacteria to eukaryotes. Hence, many lines of theories proposed these proteases are conservative from eubacteria to eukaryotes. However, the regulation of these proteases at gene level is not clearly understood and still research is warranted. In this review, we articulated the origin and regulation of these proteases and the cross talk between the nucleus and mitochondria vice versa, and highlighted the role of these proteases in diabetes and diabetic complications in human diseases.
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Affiliation(s)
- Anil Kumar Kalvala
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER)-Hyderabad, Bala Nagar, India
| | - Islauddin Khan
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER)-Hyderabad, Bala Nagar, India
| | - Chayanika Gundu
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER)-Hyderabad, Bala Nagar, India
| | - Ashutosh Kumar
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER)-Hyderabad, Bala Nagar, India
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33
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AIF meets the CHCHD4/Mia40-dependent mitochondrial import pathway. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165746. [PMID: 32105825 DOI: 10.1016/j.bbadis.2020.165746] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 02/19/2020] [Accepted: 02/20/2020] [Indexed: 02/06/2023]
Abstract
In the mitochondria of healthy cells, Apoptosis-Inducing factor (AIF) is required for the optimal functioning of the respiratory chain machinery, mitochondrial integrity, cell survival, and proliferation. In all analysed species, it was revealed that the downregulation or depletion of AIF provokes mainly the post-transcriptional loss of respiratory chain Complex I protein subunits. Recent progress in the field has revealed that AIF fulfils its mitochondrial pro-survival function by interacting physically and functionally with CHCHD4, the evolutionarily-conserved human homolog of yeast Mia40. The redox-regulated CHCHD4/Mia40-dependent import machinery operates in the intermembrane space of the mitochondrion and controls the import of a set of nuclear-encoded cysteine-motif carrying protein substrates. In addition to their participation in the biogenesis of specific respiratory chain protein subunits, CHCHD4/Mia40 substrates are also implicated in the control of redox regulation, antioxidant response, translation, lipid homeostasis and mitochondrial ultrastructure and dynamics. Here, we discuss recent insights on the AIF/CHCHD4-dependent protein import pathway and review current data concerning the CHCHD4/Mia40 protein substrates in metazoan. Recent findings and the identification of disease-associated mutations in AIF or in specific CHCHD4/Mia40 substrates have highlighted these proteins as potential therapeutic targets in a variety of human disorders.
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34
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Bozi LHM, Campos JC, Zambelli VO, Ferreira ND, Ferreira JCB. Mitochondrially-targeted treatment strategies. Mol Aspects Med 2019; 71:100836. [PMID: 31866004 DOI: 10.1016/j.mam.2019.100836] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 12/11/2019] [Accepted: 12/13/2019] [Indexed: 12/13/2022]
Abstract
Disruption of mitochondrial function is a common feature of inherited mitochondrial diseases (mitochondriopathies) and many other infectious and non-infectious diseases including viral, bacterial and protozoan infections, inflammatory and chronic pain, neurodegeneration, diabetes, obesity and cardiovascular diseases. Mitochondria therefore become an attractive target for developing new therapies. In this review we describe critical mechanisms involved in the maintenance of mitochondrial functionality and discuss strategies used to identify and validate mitochondrial targets in different diseases. We also highlight the most recent preclinical and clinical findings using molecules targeting mitochondrial bioenergetics, morphology, number, content and detoxification systems in common pathologies.
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Affiliation(s)
- Luiz H M Bozi
- Institute of Biomedical Sciences, University of Sao Paulo, Brazil
| | - Juliane C Campos
- Institute of Biomedical Sciences, University of Sao Paulo, Brazil
| | | | | | - Julio C B Ferreira
- Institute of Biomedical Sciences, University of Sao Paulo, Brazil; Department of Chemical and Systems Biology, School of Medicine, Stanford University, USA.
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35
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Youle RJ. Mitochondria-Striking a balance between host and endosymbiont. Science 2019; 365:365/6454/eaaw9855. [PMID: 31416937 DOI: 10.1126/science.aaw9855] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 07/24/2019] [Indexed: 12/11/2022]
Abstract
Mitochondria are organelles with their own genome that arose from α-proteobacteria living within single-celled Archaea more than a billion years ago. This step of endosymbiosis offered tremendous opportunities for energy production and metabolism and allowed the evolution of fungi, plants, and animals. However, less appreciated are the downsides of this endosymbiosis. Coordinating gene expression between the mitochondrial genomes and the nuclear genome is imprecise and can lead to proteotoxic stress. The clonal reproduction of mitochondrial DNA requires workarounds to avoid mutational meltdown. In metazoans that developed innate immune pathways to thwart bacterial and viral infections, mitochondrial components can cross-react with pathogen sensors and invoke inflammation. Here, I focus on the numerous and elegant quality control processes that compensate for or mitigate these challenges of endosymbiosis.
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Affiliation(s)
- Richard J Youle
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD 20892, USA.
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36
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The Role of Mitochondrial Stress in Muscle Wasting Following Severe Burn Trauma. J Burn Care Res 2019; 39:100-108. [PMID: 28448295 DOI: 10.1097/bcr.0000000000000553] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 02/26/2018] [Indexed: 11/26/2022]
Abstract
Increased resting metabolic rate and skeletal muscle wasting are hallmarks of the pathophysiological stress response to severe burn trauma. However, whether these two responses occur independently in burn patients or are in fact related remains unclear. In light of recent evidence demonstrating that increased proteolysis in skeletal muscle of burned patients is accompanied by mitochondrial hypermetabolism, oxidative stress, and protein damage; in this article, we discuss the evidence for a role for the mitochondrion in skeletal muscle wasting following severe burn trauma. In particular, we focus on the role of mitochondrial superoxide production in oxidative stress and subsequent proteolysis, and discuss the role of the mitochondrion as a signaling organelle resulting in protein catabolism in other cellular compartments following severe burn trauma.
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37
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Lualdi M, Ronci M, Zilocchi M, Corno F, Turilli ES, Sponchiado M, Aceto A, Alberio T, Fasano M. Exploring the Mitochondrial Degradome by the TAILS Proteomics Approach in a Cellular Model of Parkinson's Disease. Front Aging Neurosci 2019; 11:195. [PMID: 31417398 PMCID: PMC6685049 DOI: 10.3389/fnagi.2019.00195] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 07/15/2019] [Indexed: 12/11/2022] Open
Abstract
Parkinson’s disease (PD) is the second most frequent neurodegenerative disease worldwide and the availability of early biomarkers and novel biotargets represents an urgent medical need. The main pathogenetic hallmark of PD is the specific loss of nigral dopaminergic neurons, in which mitochondrial dysfunction plays a crucial role. Mitochondrial proteases are central to the maintenance of healthy mitochondria and they have recently emerged as drug targets. However, an exhaustive characterization of these enzymes and their targets is still lacking, due to difficulties in analyzing proteolytic fragments by bottom-up proteomics approaches. Here, we propose the “mitochondrial dimethylation-TAILS” strategy, which combines the isolation of mitochondria with the enrichment of N-terminal peptides to analyze the mitochondrial N-terminome. We applied this method in a cellular model of altered dopamine homeostasis in neuroblastoma SH-SY5Y cells, which recapitulates early steps of PD pathogenesis. The main aim was to identify candidate mitochondrial proteases aberrantly activated by dopamine dysregulation and their cleaved targets. The proposed degradomics workflow was able to improve the identification of mitochondrial proteins if compared to classical shotgun analysis. In detail, 40% coverage of the mitochondrial proteome was obtained, the sequences of the transit peptides of two mitochondrial proteins were unveiled, and a consensus cleavage sequence for proteases involved in the processing of mitochondrial proteins was depicted. Mass spectrometry proteomics data have been submitted to ProteomeXchange with the identifier PXD013900. Moreover, sixty-one N-terminal peptides whose levels were affected by dopamine treatment were identified. By an in-depth analysis of the proteolytic peptides included in this list, eleven mitochondrial proteins showed altered proteolytic processing. One of these proteins (i.e., the 39S ribosomal protein L49 – MRPL49) was cleaved by the neprilysin protease, already exploited in clinics as a biotarget. We eventually demonstrated a mitochondrial subcellular localization of neprilysin in human cells for the first time. Collectively, these results shed new light on mitochondrial dysfunction linked to dopamine imbalance in PD and opened up the possibility to explore the mitochondrial targets of neprilysin as candidate biomarkers.
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Affiliation(s)
- Marta Lualdi
- Department of Science and High Technology, University of Insubria, Busto Arsizio, Italy
| | - Maurizio Ronci
- Department of Pharmacy, University "G. D'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Mara Zilocchi
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, SK, Canada
| | - Federica Corno
- Department of Science and High Technology, University of Insubria, Busto Arsizio, Italy
| | - Emily S Turilli
- Department of Science and High Technology, University of Insubria, Busto Arsizio, Italy
| | - Mauro Sponchiado
- Department of Science and High Technology, University of Insubria, Busto Arsizio, Italy
| | - Antonio Aceto
- Department of Medical, Oral and Biotechnological Sciences, University "G. D'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Tiziana Alberio
- Department of Science and High Technology, University of Insubria, Busto Arsizio, Italy
| | - Mauro Fasano
- Department of Science and High Technology, University of Insubria, Busto Arsizio, Italy
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Sampaio-Marques B, Ludovico P. Linking cellular proteostasis to yeast longevity. FEMS Yeast Res 2019; 18:4970764. [PMID: 29800380 DOI: 10.1093/femsyr/foy043] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 04/12/2018] [Indexed: 12/19/2022] Open
Abstract
Proteostasis is a cellular housekeeping process that refers to the healthy maintenance of the cellular proteome that governs the fate of proteins from synthesis to degradation. Perturbations of proteostasis might result in protein dysfunction with consequent deleterious effects that can culminate in cell death. To deal with the loss of proteostasis, cells are supplied with a highly sophisticated and interconnected network that integrates as major players the molecular chaperones and the protein degradation pathways. It is well recognized that the ability of cells to maintain proteostasis declines during ageing, although the precise mechanisms are still elusive. Indeed, genetic or pharmacological enhancement of the proteostasis network has been shown to extend lifespan in a variety of ageing models. Therefore, an improved understanding of the interventions/mechanisms that contribute to cellular protein quality control will have a huge impact on the ageing field. This mini-review centers on the current knowledge about the major pathways that contribute for the maintenance of Saccharomyces cerevisiae proteostasis, with particular emphasis on the developments that highlight the multidimensional nature of the proteostasis network in the maintenance of proteostasis, as well as the age-dependent changes on this network.
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Affiliation(s)
- Belém Sampaio-Marques
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Paula Ludovico
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
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Orr AL, Kim C, Jimenez-Morales D, Newton BW, Johnson JR, Krogan NJ, Swaney DL, Mahley RW. Neuronal Apolipoprotein E4 Expression Results in Proteome-Wide Alterations and Compromises Bioenergetic Capacity by Disrupting Mitochondrial Function. J Alzheimers Dis 2019; 68:991-1011. [PMID: 30883359 PMCID: PMC6481541 DOI: 10.3233/jad-181184] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/21/2019] [Indexed: 12/13/2022]
Abstract
Apolipoprotein (apo) E4, the major genetic risk factor for Alzheimer's disease (AD), alters mitochondrial function and metabolism early in AD pathogenesis. When injured or stressed, neurons increase apoE synthesis. Because of its structural difference from apoE3, apoE4 undergoes neuron-specific proteolysis, generating fragments that enter the cytosol, interact with mitochondria, and cause neurotoxicity. However, apoE4's effect on mitochondrial respiration and metabolism is not understood in detail. Here we used biochemical assays and proteomic profiling to more completely characterize the effects of apoE4 on mitochondrial function and cellular metabolism in Neuro-2a neuronal cells stably expressing apoE4 or apoE3. Under basal conditions, apoE4 impaired respiration and increased glycolysis, but when challenged or stressed, apoE4-expressing neurons had 50% less reserve capacity to generate ATP to meet energy requirements than apoE3-expressing neurons. ApoE4 expression also decreased the NAD+/NADH ratio and increased the levels of reactive oxygen species and mitochondrial calcium. Global proteomic profiling revealed widespread changes in mitochondrial processes in apoE4 cells, including reduced levels of numerous respiratory complex subunits and major disruptions to all detected subunits in complex V (ATP synthase). Also altered in apoE4 cells were levels of proteins related to mitochondrial endoplasmic reticulum-associated membranes, mitochondrial fusion/fission, mitochondrial protein translocation, proteases, and mitochondrial ribosomal proteins. ApoE4-induced bioenergetic deficits led to extensive metabolic rewiring, but despite numerous cellular adaptations, apoE4-expressing neurons remained vulnerable to metabolic stress. Our results provide insights into potential molecular targets of therapies to correct apoE4-associated mitochondrial dysfunction and altered cellular metabolism.
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Affiliation(s)
- Adam L. Orr
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
- Present address: Helen & Robert Appel Alzheimer’s Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Chaeyoung Kim
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
| | - David Jimenez-Morales
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
- Present address: Department of Medicine, Division of Cardiovascular Medicine, Stanford University, CA, USA
| | - Billy W. Newton
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Jeffrey R. Johnson
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Nevan J. Krogan
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Quantitative Biosciences Institute, University of California, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Danielle L. Swaney
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Robert W. Mahley
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
- Department of Pathology and Medicine, University of California, San Francisco, CA, USA
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Loss of Mitochondrial AAA Proteases AFG3L2 and YME1L Impairs Mitochondrial Structure and Respiratory Chain Biogenesis. Int J Mol Sci 2018; 19:ijms19123930. [PMID: 30544562 PMCID: PMC6321463 DOI: 10.3390/ijms19123930] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 11/28/2018] [Accepted: 12/04/2018] [Indexed: 12/16/2022] Open
Abstract
Mitochondrial protein quality control is crucial for the maintenance of correct mitochondrial homeostasis. It is ensured by several specific mitochondrial proteases located across the various mitochondrial subcompartments. Here, we focused on characterization of functional overlap and cooperativity of proteolytic subunits AFG3L2 (AFG3 Like Matrix AAA Peptidase Subunit 2) and YME1L (YME1 like ATPase) of mitochondrial inner membrane AAA (ATPases Associated with diverse cellular Activities) complexes in the maintenance of mitochondrial structure and respiratory chain integrity. We demonstrate that loss of AFG3L2 and YME1L, both alone and in combination, results in diminished cell proliferation, fragmentation of mitochondrial reticulum, altered cristae morphogenesis, and defective respiratory chain biogenesis. The double AFG3L2/YME1L knockdown cells showed marked upregulation of OPA1 protein forms, with the most prominent increase in short OPA1 (optic atrophy 1). Loss of either protease led to marked elevation in OMA1 (OMA1 zinc metallopeptidase) (60 kDa) and severe reduction in the SPG7 (paraplegin) subunit of the m-AAA complex. Loss of the YME1L subunit led to an increased Drp1 level in mitochondrial fractions. While loss of YME1L impaired biogenesis and function of complex I, knockdown of AFG3L2 mainly affected the assembly and function of complex IV. Our results suggest cooperative and partly redundant functions of AFG3L2 and YME1L in the maintenance of mitochondrial structure and respiratory chain biogenesis and stress the importance of correct proteostasis for mitochondrial integrity.
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Mancini C, Hoxha E, Iommarini L, Brussino A, Richter U, Montarolo F, Cagnoli C, Parolisi R, Gondor Morosini DI, Nicolò V, Maltecca F, Muratori L, Ronchi G, Geuna S, Arnaboldi F, Donetti E, Giorgio E, Cavalieri S, Di Gregorio E, Pozzi E, Ferrero M, Riberi E, Casari G, Altruda F, Turco E, Gasparre G, Battersby BJ, Porcelli AM, Ferrero E, Brusco A, Tempia F. Mice harbouring a SCA28 patient mutation in AFG3L2 develop late-onset ataxia associated with enhanced mitochondrial proteotoxicity. Neurobiol Dis 2018; 124:14-28. [PMID: 30389403 DOI: 10.1016/j.nbd.2018.10.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 10/05/2018] [Accepted: 10/28/2018] [Indexed: 12/20/2022] Open
Abstract
Spinocerebellar ataxia 28 is an autosomal dominant neurodegenerative disorder caused by missense mutations affecting the proteolytic domain of AFG3L2, a major component of the mitochondrial m-AAA protease. However, little is known of the underlying pathogenetic mechanisms or how to treat patients with SCA28. Currently available Afg3l2 mutant mice harbour deletions that lead to severe, early-onset neurological phenotypes that do not faithfully reproduce the late-onset and slowly progressing SCA28 phenotype. Here we describe production and detailed analysis of a new knock-in murine model harbouring an Afg3l2 allele carrying the p.Met665Arg patient-derived mutation. Heterozygous mutant mice developed normally but adult mice showed signs of cerebellar ataxia detectable by beam test. Although cerebellar pathology was negative, electrophysiological analysis showed a trend towards increased spontaneous firing in Purkinje cells from heterozygous mutants with respect to wild-type controls. As homozygous mutants died perinatally with evidence of cardiac atrophy, for each genotype we generated mouse embryonic fibroblasts (MEFs) to investigate mitochondrial function. MEFs from mutant mice showed altered mitochondrial bioenergetics, with decreased basal oxygen consumption rate, ATP synthesis and mitochondrial membrane potential. Mitochondrial network formation and morphology was altered, with greatly reduced expression of fusogenic Opa1 isoforms. Mitochondrial alterations were also detected in cerebella of 18-month-old heterozygous mutants and may be a hallmark of disease. Pharmacological inhibition of de novo mitochondrial protein translation with chloramphenicol caused reversal of mitochondrial morphology in homozygous mutant MEFs, supporting the relevance of mitochondrial proteotoxicity for SCA28 pathogenesis and therapy development.
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Affiliation(s)
- Cecilia Mancini
- Department of Medical Sciences, University of Torino, Torino, Italy
| | - Eriola Hoxha
- Department of Neuroscience, University of Torino, Torino, Italy; Neuroscience Institute Cavalieri Ottolenghi (NICO), Orbassano, Italy
| | - Luisa Iommarini
- Department of Pharmacy and Biotechnologies (FABIT), University of Bologna, Bologna, Italy
| | | | - Uwe Richter
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Francesca Montarolo
- Department of Neuroscience, University of Torino, Torino, Italy; Neuroscience Institute Cavalieri Ottolenghi (NICO), Orbassano, Italy
| | - Claudia Cagnoli
- Department of Medical Sciences, University of Torino, Torino, Italy
| | - Roberta Parolisi
- Department of Neuroscience, University of Torino, Torino, Italy; Neuroscience Institute Cavalieri Ottolenghi (NICO), Orbassano, Italy
| | - Diana Iulia Gondor Morosini
- Department of Neuroscience, University of Torino, Torino, Italy; Neuroscience Institute Cavalieri Ottolenghi (NICO), Orbassano, Italy
| | - Valentina Nicolò
- Department of Neuroscience, University of Torino, Torino, Italy; Neuroscience Institute Cavalieri Ottolenghi (NICO), Orbassano, Italy
| | - Francesca Maltecca
- Università Vita-Salute San Raffaele, Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
| | - Luisa Muratori
- Neuroscience Institute Cavalieri Ottolenghi (NICO), Orbassano, Italy; Department of Clinical and Biological Sciences, University of Torino, Torino, Italy
| | - Giulia Ronchi
- Neuroscience Institute Cavalieri Ottolenghi (NICO), Orbassano, Italy; Department of Clinical and Biological Sciences, University of Torino, Torino, Italy
| | - Stefano Geuna
- Neuroscience Institute Cavalieri Ottolenghi (NICO), Orbassano, Italy; Department of Clinical and Biological Sciences, University of Torino, Torino, Italy
| | - Francesca Arnaboldi
- Department of Biomedical Sciences for Health, Università degli Studi di Milano, Milan, Italy
| | - Elena Donetti
- Department of Biomedical Sciences for Health, Università degli Studi di Milano, Milan, Italy
| | - Elisa Giorgio
- Department of Medical Sciences, University of Torino, Torino, Italy
| | - Simona Cavalieri
- Department of Medical Sciences, University of Torino, Torino, Italy
| | - Eleonora Di Gregorio
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Torino, Italy
| | - Elisa Pozzi
- Department of Medical Sciences, University of Torino, Torino, Italy
| | - Marta Ferrero
- Department of Medical Sciences, University of Torino, Torino, Italy
| | - Evelise Riberi
- Department of Public Health and Pediatrics, University of Torino, Torino, Italy
| | - Giorgio Casari
- Università Vita-Salute San Raffaele, Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
| | - Fiorella Altruda
- Molecular Biotechnology Center, Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Emilia Turco
- Molecular Biotechnology Center, Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Giuseppe Gasparre
- Department Medical and Surgical Sciences, Medical Genetics, University of Bologna, Bologna, Italy
| | | | - Anna Maria Porcelli
- Department of Pharmacy and Biotechnologies (FABIT), University of Bologna, Bologna, Italy
| | - Enza Ferrero
- Department of Medical Sciences, University of Torino, Torino, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Torino, Italy; Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Torino, Italy.
| | - Filippo Tempia
- Department of Neuroscience, University of Torino, Torino, Italy; Neuroscience Institute Cavalieri Ottolenghi (NICO), Orbassano, Italy
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Magri S, Fracasso V, Plumari M, Alfei E, Ghezzi D, Gellera C, Rusmini P, Poletti A, Di Bella D, Elia AE, Pantaleoni C, Taroni F. Concurrent AFG3L2 and SPG7 mutations associated with syndromic parkinsonism and optic atrophy with aberrant OPA1 processing and mitochondrial network fragmentation. Hum Mutat 2018; 39:2060-2071. [PMID: 30252181 DOI: 10.1002/humu.23658] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 09/03/2018] [Accepted: 09/22/2018] [Indexed: 01/26/2023]
Abstract
Mitochondrial dynamics and quality control are crucial for neuronal survival and their perturbation is a major cause of neurodegeneration. m-AAA complex is an ATP-dependent metalloprotease located in the inner mitochondrial membrane and involved in protein quality control. Mutations in the m-AAA subunits AFG3L2 and paraplegin are associated with autosomal dominant spinocerebellar ataxia (SCA28) and autosomal recessive hereditary spastic paraplegia (SPG7), respectively. We report a novel m-AAA-associated phenotype characterized by early-onset optic atrophy with spastic ataxia and L-dopa-responsive parkinsonism. The proband carried a de novo AFG3L2 heterozygous mutation (p.R468C) along with a heterozygous maternally inherited intragenic deletion of SPG7. Functional analysis in yeast demonstrated the pathogenic role of AFG3L2 p.R468C mutation shedding light on its pathogenic mechanism. Analysis of patient's fibroblasts showed an abnormal processing pattern of OPA1, a dynamin-related protein essential for mitochondrial fusion and responsible for most cases of hereditary optic atrophy. Consistently, assessment of mitochondrial morphology revealed a severe fragmentation of the mitochondrial network, not observed in SCA28 and SPG7 patients' cells. This case suggests that coincidental mutations in both components of the mitochondrial m-AAA protease may result in a complex phenotype and reveals a crucial role for OPA1 processing in the pathogenesis of neurodegenerative disease caused by m-AAA defects.
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Affiliation(s)
- Stefania Magri
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Valentina Fracasso
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Massimo Plumari
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Enrico Alfei
- Unit of Developmental Neurology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Daniele Ghezzi
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy.,Dipartimento di Fisiopatologia Medico-Chirurgica e dei Trapianti, Università degli Studi di Milano, Milan, Italy
| | - Cinzia Gellera
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Paola Rusmini
- Dipartimento di Scienze Farmacologiche e Biomolecolari (DiSFeB), Centro di Eccellenza sulle Malattie Neurodegenerative, Università degli Studi di Milano, Milan, Italy
| | - Angelo Poletti
- Dipartimento di Scienze Farmacologiche e Biomolecolari (DiSFeB), Centro di Eccellenza sulle Malattie Neurodegenerative, Università degli Studi di Milano, Milan, Italy
| | - Daniela Di Bella
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Antonio E Elia
- Unit of Neurology 1, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Chiara Pantaleoni
- Unit of Developmental Neurology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Franco Taroni
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
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43
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Kong L, Berg FJ. Identification of cholecystokinin tetrapeptide amide metabolites in liver microsomes of human, Rhesus Monkey, Sprague-Dawley rat and CD1 mouse using ultra-high performance liquid chromatography coupled to high resolution mass spectrometer. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1096:80-87. [PMID: 30149298 DOI: 10.1016/j.jchromb.2018.08.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 08/13/2018] [Accepted: 08/17/2018] [Indexed: 11/30/2022]
Abstract
Endogenous cholecystokinin tetrapeptide (CCK-4, Trp-Met-Asp-Phe-NH2) is a fragment derived from a larger peptide hormone, cholecystokinin (or gastrin). As a panicogenic agent, CCK-4 is commonly used in clinic settings to induce panic attacks for the study of new anxiolytic drugs. However, few studies on CCK-4 metabolism have been published to date. In the present study, we investigate the metabolism of CCK-4 in liver microsomes of human (HLM), Rhesus Monkey (RMLM), Sprague-Dawley rat (RLM) and CD1 mouse (MLM) using ultra-high performance liquid chromatography coupled to a high resolution mass spetrometer. Ten metabolites, inlcuding tryptophan (M1), tryptophan amide (M2), hydroxy metabolites (M3-M5), truncated peptides (M6-M9), and CCK-4 acid (M10), were identified and 8 of them were reported for the first time. The metabolic pattern of CCK-4 in HLM was distinctly different from these in RMLM, RLM, and MLM. M2 and M9 were the major metabolites in HLM and accounted for 19.8% and 13.4% of initial CCK-4, respectively. In contrast, M2 was the major metabolite in RMLM and accounted for 41.4%, whereas M6 was the major metabolite in RLM and account for 39.1%. Three major metabolites M2, M7 and M8 in MLM accounted for 22.6%, 17.9% and 17.8% of initial CCK-4, respectively. Chemical inhibition experiment showed that aminopeptidase and/or endopeptidase hydrolysis were the major metabolic pathways in human to generate these metabolites. We further showed that cytochrome P450 were also involved in the metabolism of CCK-4 via hydroxylation, but to a less extend. These findings provide valuable information for the metabolic processes of CCK-4 among various species and an important reference basis for its safety evaluation and rational clinical application.
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Affiliation(s)
- Li Kong
- Research and Technology Directorate, U. S. Army, Edgewood Chemical Biological Center (ECBC), Aberdeen Proving Ground, MD 21010-5424, United States.
| | - Frederic J Berg
- Research and Technology Directorate, U. S. Army, Edgewood Chemical Biological Center (ECBC), Aberdeen Proving Ground, MD 21010-5424, United States
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44
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Concepción-Acevedo J, Miller JC, Boucher MJ, Klingbeil MM. Cell cycle localization dynamics of mitochondrial DNA polymerase IC in African trypanosomes. Mol Biol Cell 2018; 29:2540-2552. [PMID: 30133333 PMCID: PMC6254582 DOI: 10.1091/mbc.e18-02-0127] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Trypanosoma brucei has a unique catenated mitochondrial DNA (mtDNA) network called kinetoplast DNA (kDNA). Replication of kDNA occurs once per cell cycle in near synchrony with nuclear S phase and requires the coordination of many proteins. Among these are three essential DNA polymerases (TbPOLIB, IC, and ID). Localization dynamics of these proteins with respect to kDNA replication stages and how they coordinate their functions during replication are not well understood. We previously demonstrated that TbPOLID undergoes dynamic localization changes that are coupled to kDNA replication events. Here, we report the localization of TbPOLIC, a second essential DNA polymerase, and demonstrate the accumulation of TbPOLIC foci at active kDNA replication sites (antipodal sites) during stage II of the kDNA duplication cycle. While TbPOLIC was undetectable by immunofluorescence during other cell cycle stages, steady-state protein levels measured by Western blot remained constant. TbPOLIC foci colocalized with the fraction of TbPOLID that localized to the antipodal sites. However, the partial colocalization of the two essential DNA polymerases suggests a highly dynamic environment at the antipodal sites to coordinate the trafficking of replication proteins during kDNA synthesis. These data indicate that cell cycle-dependent localization is a major regulatory mechanism for essential mtDNA polymerases during kDNA replication.
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Affiliation(s)
| | - Jonathan C Miller
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA 01003
| | - Michael J Boucher
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA 01003
| | - Michele M Klingbeil
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA 01003
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45
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Ding B, Martin DW, Rampello AJ, Glynn SE. Dissecting Substrate Specificities of the Mitochondrial AFG3L2 Protease. Biochemistry 2018; 57:4225-4235. [PMID: 29932645 DOI: 10.1021/acs.biochem.8b00565] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane. Identifying how AFG3L2 selects substrates from the diverse complement of matrix-localized proteins is essential for understanding mitochondrial protein biogenesis and quality control. Here, we create solubilized forms of AFG3L2 to examine the enzyme's substrate specificity mechanisms. We show that conserved residues within the presequence of the mitochondrial ribosomal protein, MrpL32, target the subunit to the protease for processing into a mature form. Moreover, these residues can act as a degron, delivering diverse model proteins to AFG3L2 for degradation. By determining the sequence of degradation products from multiple substrates using mass spectrometry, we construct a peptidase specificity profile that displays constrained product lengths and is dominated by the identity of the residue at the P1' position, with a strong preference for hydrophobic and small polar residues. This specificity profile is validated by examining the cleavage of both fluorogenic reporter peptides and full polypeptide substrates bearing different P1' residues. Together, these results demonstrate that AFG3L2 contains multiple modes of specificity, discriminating between potential substrates by recognizing accessible degron sequences and performing peptide bond cleavage at preferred patterns of residues within the compartmental chamber.
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46
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Puchades C, Rampello AJ, Shin M, Giuliano CJ, Wiseman RL, Glynn SE, Lander GC. Structure of the mitochondrial inner membrane AAA+ protease YME1 gives insight into substrate processing. Science 2018; 358:358/6363/eaao0464. [PMID: 29097521 DOI: 10.1126/science.aao0464] [Citation(s) in RCA: 149] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 09/25/2017] [Indexed: 12/20/2022]
Abstract
We present an atomic model of a substrate-bound inner mitochondrial membrane AAA+ quality control protease in yeast, YME1. Our ~3.4-angstrom cryo-electron microscopy structure reveals how the adenosine triphosphatases (ATPases) form a closed spiral staircase encircling an unfolded substrate, directing it toward the flat, symmetric protease ring. Three coexisting nucleotide states allosterically induce distinct positioning of tyrosines in the central channel, resulting in substrate engagement and translocation to the negatively charged proteolytic chamber. This tight coordination by a network of conserved residues defines a sequential, around-the-ring adenosine triphosphate hydrolysis cycle that results in stepwise substrate translocation. A hingelike linker accommodates the large-scale nucleotide-driven motions of the ATPase spiral relative to the planar proteolytic base. The translocation mechanism is likely conserved for other AAA+ ATPases.
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Affiliation(s)
- Cristina Puchades
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute HZ 175, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.,Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Anthony J Rampello
- Department of Biochemistry and Cell Biology, Stony Brook University, 450 Life Sciences Building, Stony Brook, NY 11794, USA
| | - Mia Shin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute HZ 175, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.,Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Christopher J Giuliano
- Department of Biochemistry and Cell Biology, Stony Brook University, 450 Life Sciences Building, Stony Brook, NY 11794, USA
| | - R Luke Wiseman
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Steven E Glynn
- Department of Biochemistry and Cell Biology, Stony Brook University, 450 Life Sciences Building, Stony Brook, NY 11794, USA.
| | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute HZ 175, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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47
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Leonov A, Arlia-Ciommo A, Bourque SD, Koupaki O, Kyryakov P, Dakik P, McAuley M, Medkour Y, Mohammad K, Di Maulo T, Titorenko VI. Specific changes in mitochondrial lipidome alter mitochondrial proteome and increase the geroprotective efficiency of lithocholic acid in chronologically aging yeast. Oncotarget 2018; 8:30672-30691. [PMID: 28410198 PMCID: PMC5458158 DOI: 10.18632/oncotarget.16766] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 03/20/2017] [Indexed: 02/07/2023] Open
Abstract
We have previously found that exogenously added lithocholic acid delays yeast chronological aging. We demonstrated that lithocholic acid enters the yeast cell, is sorted to mitochondria, resides in both mitochondrial membranes, changes the relative concentrations of different membrane phospholipids, triggers changes in the concentrations of many mitochondrial proteins, and alters some key aspects of mitochondrial functionality. We hypothesized that the lithocholic acid-driven changes in mitochondrial lipidome may have a causal role in the remodeling of mitochondrial proteome, which may in turn alter the functional state of mitochondria to create a mitochondrial pattern that delays yeast chronological aging. Here, we test this hypothesis by investigating how the ups1?, ups2? and psd1? mutations that eliminate enzymes involved in mitochondrial phospholipid metabolism influence the mitochondrial lipidome. We also assessed how these mutations affect the mitochondrial proteome, influence mitochondrial functionality and impinge on the efficiency of aging delay by lithocholic acid. Our findings provide evidence that 1) lithocholic acid initially creates a distinct pro-longevity pattern of mitochondrial lipidome by proportionally decreasing phosphatidylethanolamine and cardiolipin concentrations to maintain equimolar concentrations of these phospholipids, and by increasing phosphatidic acid concentration; 2) this pattern of mitochondrial lipidome allows to establish a specific, aging-delaying pattern of mitochondrial proteome; and 3) this pattern of mitochondrial proteome plays an essential role in creating a distinctive, geroprotective pattern of mitochondrial functionality.
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Affiliation(s)
- Anna Leonov
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | | | - Simon D Bourque
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Olivia Koupaki
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Pavlo Kyryakov
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Paméla Dakik
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Mélissa McAuley
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Younes Medkour
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Karamat Mohammad
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Tamara Di Maulo
- Department of Biology, Concordia University, Montreal, Quebec, Canada
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48
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Timón-Gómez A, Sanfeliu-Redondo D, Pascual-Ahuir A, Proft M. Regulation of the Stress-Activated Degradation of Mitochondrial Respiratory Complexes in Yeast. Front Microbiol 2018; 9:106. [PMID: 29441058 PMCID: PMC5797626 DOI: 10.3389/fmicb.2018.00106] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 01/17/2018] [Indexed: 02/05/2023] Open
Abstract
Repair and removal of damaged mitochondria is a key process for eukaryotic cell homeostasis. Here we investigate in the yeast model how different protein complexes of the mitochondrial electron transport chain are subject to specific degradation upon high respiration load and organelle damage. We find that the turnover of subunits of the electron transport complex I equivalent and complex III is preferentially stimulated upon high respiration rates. Particular mitochondrial proteases, but not mitophagy, are involved in this activated degradation. Further mitochondrial damage by valinomycin treatment of yeast cells triggers the mitophagic removal of the same respiratory complexes. This selective protein degradation depends on the mitochondrial fusion and fission apparatus and the autophagy adaptor protein Atg11, but not on the mitochondrial mitophagy receptor Atg32. Loss of autophagosomal protein function leads to valinomycin sensitivity and an overproduction of reactive oxygen species upon mitochondrial damage. A specific event in this selective turnover of electron transport chain complexes seems to be the association of Atg11 with the mitochondrial network, which can be achieved by overexpression of the Atg11 protein even in the absence of Atg32. Furthermore, the interaction of various Atg11 molecules via the C-terminal coil domain is specifically and rapidly stimulated upon mitochondrial damage and could therefore be an early trigger of selective mitophagy in response to the organelles dysfunction. Our work indicates that autophagic quality control upon mitochondrial damage operates in a selective manner.
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Affiliation(s)
- Alba Timón-Gómez
- Department of Molecular and Cellular Pathology and Therapy, Instituto de Biomedicina de Valencia-CSIC, Valencia, Spain.,Department of Biotechnology, Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València, Valencia, Spain
| | - David Sanfeliu-Redondo
- Department of Biotechnology, Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València, Valencia, Spain
| | - Amparo Pascual-Ahuir
- Department of Biotechnology, Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València, Valencia, Spain
| | - Markus Proft
- Department of Molecular and Cellular Pathology and Therapy, Instituto de Biomedicina de Valencia-CSIC, Valencia, Spain
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49
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Lee SR, Nilius B, Han J. Gaseous Signaling Molecules in Cardiovascular Function: From Mechanisms to Clinical Translation. Rev Physiol Biochem Pharmacol 2018; 174:81-156. [PMID: 29372329 DOI: 10.1007/112_2017_7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Carbon monoxide (CO), hydrogen sulfide (H2S), and nitric oxide (NO) constitute endogenous gaseous molecules produced by specific enzymes. These gases are chemically simple, but exert multiple effects and act through shared molecular targets to control both physiology and pathophysiology in the cardiovascular system (CVS). The gases act via direct and/or indirect interactions with each other in proteins such as heme-containing enzymes, the mitochondrial respiratory complex, and ion channels, among others. Studies of the major impacts of CO, H2S, and NO on the CVS have revealed their involvement in controlling blood pressure and in reducing cardiac reperfusion injuries, although their functional roles are not limited to these conditions. In this review, the basic aspects of CO, H2S, and NO, including their production and effects on enzymes, mitochondrial respiration and biogenesis, and ion channels are briefly addressed to provide insight into their biology with respect to the CVS. Finally, potential therapeutic applications of CO, H2S, and NO with the CVS are addressed, based on the use of exogenous donors and different types of delivery systems.
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Affiliation(s)
- Sung Ryul Lee
- Department of Convergence Biomedical Science, Cardiovascular and Metabolic Disease Center, College of Medicine, Inje University, Busan, Republic of Korea
| | - Bernd Nilius
- Laboratory of Ion Channel Research, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Jin Han
- National Research Laboratory for Mitochondrial Signaling, Department of Physiology, Department of Health Sciences and Technology, BK21 Plus Project Team, Cardiovascular and Metabolic Disease Center, Inje University, Busan, Republic of Korea.
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50
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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.
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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
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