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Hasan MK, Jeannine Brady L. Nucleic acid-binding KH domain proteins influence a spectrum of biological pathways including as part of membrane-localized complexes. J Struct Biol X 2024; 10:100106. [PMID: 39040530 PMCID: PMC11261784 DOI: 10.1016/j.yjsbx.2024.100106] [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: 02/23/2024] [Revised: 06/18/2024] [Accepted: 06/24/2024] [Indexed: 07/24/2024] Open
Abstract
K-Homology domain (KH domain) proteins bind single-stranded nucleic acids, influence protein-protein interactions of proteins that harbor them, and are found in all kingdoms of life. In concert with other functional protein domains KH domains contribute to a variety of critical biological activities, often within higher order machineries including membrane-localized protein complexes. Eukaryotic KH domain proteins are linked to developmental processes, morphogenesis, and growth regulation, and their aberrant expression is often associated with cancer. Prokaryotic KH domain proteins are involved in integral cellular activities including cell division and protein translocation. Eukaryotic and prokaryotic KH domains share structural features, but are differentiated based on their structural organizations. In this review, we explore the structure/function relationships of known examples of KH domain proteins, and highlight cases in which they function within or at membrane surfaces. We also summarize examples of KH domain proteins that influence bacterial virulence and pathogenesis. We conclude the article by discussing prospective research avenues that could be pursued to better investigate this largely understudied protein category.
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Affiliation(s)
- Md Kamrul Hasan
- Department of Oral Biology, University of Florida, Gainesville, FL 32610, USA
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - L. Jeannine Brady
- Department of Oral Biology, University of Florida, Gainesville, FL 32610, USA
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2
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Ojha R, Tantray I, Banerjee S, Rimal S, Thirunavukkarasu S, Srikris S, Chiu W, Mete U, Sharma A, Kakkar N, Lu B. Translation stalling induced mitochondrial entrapment of ribosomal quality control related proteins offers cancer cell vulnerability. RESEARCH SQUARE 2024:rs.3.rs-4899860. [PMID: 39315278 PMCID: PMC11419255 DOI: 10.21203/rs.3.rs-4899860/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Ribosome-associated quality control (RQC) monitors ribosomes for aberrant translation. While the role of RQC in neurodegenerative disease is beginning to be appreciated, its involvement in cancer is understudied. Here, we show a positive correlation between RQC proteins ABCE1 and ZNF598 and high-grade muscle-invasive bladder cancer. Translational stalling by the inhibitor emetine (EME) leads to increased mitochondrial localization of RQC factors including ABCE1, ZNF598, and NEMF, which are continuously imported into mitochondria facilitated by increased mitochondrial membrane potential caused by EME. This reduces the availability of these factors in the cytosol, compromising the effectiveness of RQC in handling stalled ribosomes in the cytosol and those associated with the mitochondrial outer membrane (MOM). Imported RQC factors form aggregates inside the mitochondria in a process we term stalling-induced mitochondrial stress (SIMS). ABCE1 plays a crucial role in maintaining mitochondrial health during SIMS. Notably, cancer stem cells (CSCs) exhibit increased expression of ABCE1 and consequently are more resistant to EME-induced mitochondrial dysfunction. This points to a potential mechanism of drug resistance by CSCs. Our study highlights the significance of mitochondrial entrapment of RQC factors such as ABCE1 in determining the fate of cancer cells versus CSCs. Targeting ABCE1 or other RQC factors in translational inhibition cancer therapy may help overcome drug resistance.
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3
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Gao Y, Kwan J, Orofino J, Burrone G, Mitra S, Fan TY, English J, Hekman R, Emili A, Lyons SM, Cardamone MD, Perissi V. Inhibition of K63 ubiquitination by G-Protein pathway suppressor 2 (GPS2) regulates mitochondria-associated translation. Pharmacol Res 2024; 207:107336. [PMID: 39094987 DOI: 10.1016/j.phrs.2024.107336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 07/29/2024] [Accepted: 07/29/2024] [Indexed: 08/04/2024]
Abstract
G-Protein Pathway Suppressor 2 (GPS2) is an inhibitor of non-proteolytic K63 ubiquitination mediated by the E2 ubiquitin-conjugating enzyme Ubc13. Previous studies have associated GPS2-mediated restriction of ubiquitination with the regulation of insulin signaling, inflammatory responses and mitochondria-nuclear communication across different tissues and cell types. However, a detailed understanding of the targets of GPS2/Ubc13 activity is lacking. Here, we have dissected the GPS2-regulated K63 ubiquitome in mouse embryonic fibroblasts and human breast cancer cells, unexpectedly finding an enrichment for proteins involved in RNA binding and translation on the outer mitochondrial membrane. Validation of selected targets of GPS2-mediated regulation, including the RNA-binding protein PABPC1 and translation factors RPS1, RACK1 and eIF3M, revealed a mitochondrial-specific strategy for regulating the translation of nuclear-encoded mitochondrial proteins via non-proteolytic ubiquitination. Removal of GPS2-mediated inhibition, either via genetic deletion or stress-induced nuclear translocation, promotes the import-coupled translation of selected mRNAs leading to the increased expression of an adaptive antioxidant program. In light of GPS2 role in nuclear-mitochondria communication, these findings reveal an exquisite regulatory network for modulating mitochondrial gene expression through spatially coordinated transcription and translation.
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Affiliation(s)
- Yuan Gao
- Department of Biochemistry and Cell Biology, Chobanian&Avedisian School of Medicine, Boston University, Boston, MA 02115, United States
| | - Julian Kwan
- Department of Biochemistry and Cell Biology, Chobanian&Avedisian School of Medicine, Boston University, Boston, MA 02115, United States; Center for Network and Systems Biology, Boston University, Boston, MA 02115, United States
| | - Joseph Orofino
- Department of Biochemistry and Cell Biology, Chobanian&Avedisian School of Medicine, Boston University, Boston, MA 02115, United States
| | - Giulia Burrone
- Department of Biochemistry and Cell Biology, Chobanian&Avedisian School of Medicine, Boston University, Boston, MA 02115, United States; Department of Computer Science, University of Torino, Torino, Italy; Department of Clinical and Biological Science, University of Torino, Torino, Italy; Graduate Program in Complex Systems for Quantitative Biomedicine, University of Torino, Torino, Italy
| | - Sahana Mitra
- Department of Biochemistry and Cell Biology, Chobanian&Avedisian School of Medicine, Boston University, Boston, MA 02115, United States
| | - Ting-Yu Fan
- Department of Biochemistry and Cell Biology, Chobanian&Avedisian School of Medicine, Boston University, Boston, MA 02115, United States
| | - Justin English
- Department of Biochemistry and Cell Biology, Chobanian&Avedisian School of Medicine, Boston University, Boston, MA 02115, United States; Graduate Program in Pharmacology and Experimental Therapeutics, Chobanian&Avedisian School of Medicine, Boston University, Boston, MA 02115, United States
| | - Ryan Hekman
- Department of Biochemistry and Cell Biology, Chobanian&Avedisian School of Medicine, Boston University, Boston, MA 02115, United States; Center for Network and Systems Biology, Boston University, Boston, MA 02115, United States
| | - Andrew Emili
- Department of Biochemistry and Cell Biology, Chobanian&Avedisian School of Medicine, Boston University, Boston, MA 02115, United States; Center for Network and Systems Biology, Boston University, Boston, MA 02115, United States; Biology Department, Boston University, Boston, MA 02115, United States
| | - Shawn M Lyons
- Department of Biochemistry and Cell Biology, Chobanian&Avedisian School of Medicine, Boston University, Boston, MA 02115, United States
| | - Maria Dafne Cardamone
- Department of Biochemistry and Cell Biology, Chobanian&Avedisian School of Medicine, Boston University, Boston, MA 02115, United States
| | - Valentina Perissi
- Department of Biochemistry and Cell Biology, Chobanian&Avedisian School of Medicine, Boston University, Boston, MA 02115, United States.
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4
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Chen S, Collart MA. Membrane-associated mRNAs: A Post-transcriptional Pathway for Fine-turning Gene Expression. J Mol Biol 2024; 436:168579. [PMID: 38648968 DOI: 10.1016/j.jmb.2024.168579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 04/14/2024] [Accepted: 04/16/2024] [Indexed: 04/25/2024]
Abstract
Gene expression is a fundamental and highly regulated process involving a series of tightly coordinated steps, including transcription, post-transcriptional processing, translation, and post-translational modifications. A growing number of studies have revealed an additional layer of complexity in gene expression through the phenomenon of mRNA subcellular localization. mRNAs can be organized into membraneless subcellular structures within both the cytoplasm and the nucleus, but they can also targeted to membranes. In this review, we will summarize in particular our knowledge on localization of mRNAs to organelles, focusing on important regulators and available techniques for studying organellar localization, and significance of this localization in the broader context of gene expression regulation.
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Affiliation(s)
- Siyu Chen
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Institute of Genetics and Genomics of Geneva, Geneva, Switzerland.
| | - Martine A Collart
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Institute of Genetics and Genomics of Geneva, Geneva, Switzerland.
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5
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Cai T, Zhang B, Reddy E, Wu Y, Tang Y, Mondal I, Wang J, Ho WS, Lu RO, Wu Z. The mitochondrial stress-induced protein carboxyl-terminal alanine and threonine tailing (msiCAT-tailing) promotes glioblastoma tumorigenesis by modulating mitochondrial functions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.15.594447. [PMID: 38798583 PMCID: PMC11118334 DOI: 10.1101/2024.05.15.594447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
The rapid and sustained proliferation in cancer cells requires accelerated protein synthesis. Accelerated protein synthesis and disordered cell metabolism in cancer cells greatly increase the risk of translation errors. ribosome-associated quality control (RQC) is a recently discovered mechanism for resolving ribosome collisions caused by frequent translation stalls. The role of the RQC pathway in cancer initiation and progression remains controversial and confusing. In this study, we investigated the pathogenic role of mitochondrial stress-induced protein carboxyl-terminal terminal alanine and threonine tailing (msiCAT-tailing) in glioblastoma (GBM), which is a specific RQC response to translational arrest on the outer mitochondrial membrane. We found that msiCAT-tailed mitochondrial proteins frequently exist in glioblastoma stem cells (GSCs). Ectopically expressed msiCAT-tailed mitochondrial ATP synthase F1 subunit alpha (ATP5α) protein increases the mitochondrial membrane potential and blocks mitochondrial permeability transition pore (MPTP) formation/opening. These changes in mitochondrial properties confer resistance to staurosporine (STS)-induced apoptosis in GBM cells. Therefore, msiCAT-tailing can promote cell survival and migration, while genetic and pharmacological inhibition of msiCAT-tailing can prevent the overgrowth of GBM cells. Highlights The RQC pathway is disturbed in glioblastoma (GBM) cellsmsiCAT-tailing on ATP5α elevates mitochondrial membrane potential and inhibits MPTP openingmsiCAT-tailing on ATP5α inhibits drug-induced apoptosis in GBM cellsInhibition of msiCAT-tailing impedes overall growth of GBM cells.
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6
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Sharma S, Fazal FM. Localization of RNAs to the mitochondria-mechanisms and functions. RNA (NEW YORK, N.Y.) 2024; 30:597-608. [PMID: 38448244 PMCID: PMC11098466 DOI: 10.1261/rna.079999.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 03/08/2024]
Abstract
The mammalian mitochondrial proteome comprises over 1000 proteins, with the majority translated from nuclear-encoded messenger RNAs (mRNAs). Mounting evidence suggests many of these mRNAs are localized to the outer mitochondrial membrane (OMM) in a pre- or cotranslational state. Upon reaching the mitochondrial surface, these mRNAs are locally translated to produce proteins that are cotranslationally imported into mitochondria. Here, we summarize various mechanisms cells use to localize RNAs, including transfer RNAs (tRNAs), to the OMM and recent technological advancements in the field to study these processes. While most early studies in the field were carried out in yeast, recent studies reveal RNA localization to the OMM and their regulation in higher organisms. Various factors regulate this localization process, including RNA sequence elements, RNA-binding proteins (RBPs), cytoskeletal motors, and translation machinery. In this review, we also highlight the role of RNA structures and modifications in mitochondrial RNA localization and discuss how these features can alter the binding properties of RNAs. Finally, in addition to RNAs related to mitochondrial function, RNAs involved in other cellular processes can also localize to the OMM, including those implicated in the innate immune response and piRNA biogenesis. As impairment of messenger RNA (mRNA) localization and regulation compromise mitochondrial function, future studies will undoubtedly expand our understanding of how RNAs localize to the OMM and investigate the consequences of their mislocalization in disorders, particularly neurodegenerative diseases, muscular dystrophies, and cancers.
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Affiliation(s)
- Surbhi Sharma
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, USA
- Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, Texas 77030, USA
| | - Furqan M Fazal
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, USA
- Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, Texas 77030, USA
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7
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Bao X, Jia H, Zhang X, Tian S, Zhao Y, Li X, Lin P, Ma C, Wang P, Song CP, Zhu X. Mapping of cytosol-facing organelle outer membrane proximity proteome by proximity-dependent biotinylation in living Arabidopsis cells. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:7-23. [PMID: 38261530 DOI: 10.1111/tpj.16641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/15/2023] [Accepted: 01/09/2024] [Indexed: 01/25/2024]
Abstract
The cytosol-facing outer membrane (OM) of organelles communicates with other cellular compartments to exchange proteins, metabolites, and signaling molecules. Cellular surveillance systems also target OM-resident proteins to control organellar homeostasis and ensure cell survival under stress. However, the OM proximity proteomes have never been mapped in plant cells since using traditional approaches to discover OM proteins and identify their dynamically interacting partners remains challenging. In this study, we developed an OM proximity labeling (OMPL) system using biotin ligase-mediated proximity biotinylation to identify the proximity proteins of the OMs of mitochondria, chloroplasts, and peroxisomes in living Arabidopsis (Arabidopsis thaliana) cells. Using this approach, we mapped the OM proximity proteome of these three organelles under normal conditions and examined the effects of the ultraviolet-B (UV-B) or high light (HL) stress on the abundances of OM proximity proteins. We demonstrate the power of this system with the discovery of cytosolic factors and OM receptor candidates potentially involved in local protein translation and translocation. The candidate proteins that are involved in mitochondrion-peroxisome, mitochondrion-chloroplast, or peroxisome-chloroplast contacts, and in the organellar quality control system are also proposed based on OMPL analysis. OMPL-generated OM proximity proteomes are valuable sources of candidates for functional validation and suggest directions for further investigation of important questions in cell biology.
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Affiliation(s)
- Xinyue Bao
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, 475004, China
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Huifang Jia
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, 475004, China
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Xiaoyan Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, 475004, China
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Sang Tian
- Institute of Advanced Biotechnology and School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yanming Zhao
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, 475004, China
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Xiangyun Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, 475004, China
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Ping Lin
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, 475004, China
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Chongyang Ma
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, 475004, China
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Pengcheng Wang
- Institute of Advanced Biotechnology and School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Chun-Peng Song
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, 475004, China
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Xiaohong Zhu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, 475004, China
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China
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8
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Tatara Y, Kasai S, Kokubu D, Tsujita T, Mimura J, Itoh K. Emerging Role of GCN1 in Disease and Homeostasis. Int J Mol Sci 2024; 25:2998. [PMID: 38474243 PMCID: PMC10931611 DOI: 10.3390/ijms25052998] [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: 01/29/2024] [Revised: 02/29/2024] [Accepted: 03/02/2024] [Indexed: 03/14/2024] Open
Abstract
GCN1 is recognized as a factor that is essential for the activation of GCN2, which is a sensor of amino acid starvation. This function is evolutionarily conserved from yeast to higher eukaryotes. However, recent studies have revealed non-canonical functions of GCN1 that are independent of GCN2, such as its participation in cell proliferation, apoptosis, and the immune response, beyond the borders of species. Although it is known that GCN1 and GCN2 interact with ribosomes to accomplish amino acid starvation sensing, recent studies have reported that GCN1 binds to disomes (i.e., ribosomes that collide each other), thereby regulating both the co-translational quality control and stress response. We propose that GCN1 regulates ribosome-mediated signaling by dynamically changing its partners among RWD domain-possessing proteins via unknown mechanisms. We recently demonstrated that GCN1 is essential for cell proliferation and whole-body energy regulation in mice. However, the manner in which ribosome-initiated signaling via GCN1 is related to various physiological functions warrants clarification. GCN1-mediated mechanisms and its interaction with other quality control and stress response signals should be important for proteostasis during aging and neurodegenerative diseases, and may be targeted for drug development.
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Affiliation(s)
- Yota Tatara
- Department of Stress Response Science, Biomedical Research Center, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki 036-8562, Aomori, Japan
| | - Shuya Kasai
- Department of Stress Response Science, Biomedical Research Center, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki 036-8562, Aomori, Japan
| | - Daichi Kokubu
- Diet and Well-Being Research Institute, KAGOME, Co., Ltd., 17 Nishitomiyama, Nasushiobara 329-2762, Tochigi, Japan
- Department of Vegetable Life Science, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki 036-8562, Aomori, Japan
| | - Tadayuki Tsujita
- Laboratory of Biochemistry, Department of Applied Biochemistry and Food Science, Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga City 840-8502, Saga, Japan;
| | - Junsei Mimura
- Department of Stress Response Science, Biomedical Research Center, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki 036-8562, Aomori, Japan
| | - Ken Itoh
- Department of Stress Response Science, Biomedical Research Center, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki 036-8562, Aomori, Japan
- Department of Vegetable Life Science, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki 036-8562, Aomori, Japan
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9
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Hees JT, Wanderoy S, Lindner J, Helms M, Murali Mahadevan H, Harbauer AB. Insulin signalling regulates Pink1 mRNA localization via modulation of AMPK activity to support PINK1 function in neurons. Nat Metab 2024; 6:514-530. [PMID: 38504131 PMCID: PMC10963278 DOI: 10.1038/s42255-024-01007-w] [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: 02/20/2023] [Accepted: 02/06/2024] [Indexed: 03/21/2024]
Abstract
Mitochondrial quality control failure is frequently observed in neurodegenerative diseases. The detection of damaged mitochondria by stabilization of PTEN-induced kinase 1 (PINK1) requires transport of Pink1 messenger RNA (mRNA) by tethering it to the mitochondrial surface. Here, we report that inhibition of AMP-activated protein kinase (AMPK) by activation of the insulin signalling cascade prevents Pink1 mRNA binding to mitochondria. Mechanistically, AMPK phosphorylates the RNA anchor complex subunit SYNJ2BP within its PDZ domain, a phosphorylation site that is necessary for its interaction with the RNA-binding protein SYNJ2. Notably, loss of mitochondrial Pink1 mRNA association upon insulin addition is required for PINK1 protein activation and its function as a ubiquitin kinase in the mitophagy pathway, thus placing PINK1 function under metabolic control. Induction of insulin resistance in vitro by the key genetic Alzheimer risk factor apolipoprotein E4 retains Pink1 mRNA at the mitochondria and prevents proper PINK1 activity, especially in neurites. Our results thus identify a metabolic switch controlling Pink1 mRNA localization and PINK1 activity via insulin and AMPK signalling in neurons and propose a mechanistic connection between insulin resistance and mitochondrial dysfunction.
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Affiliation(s)
- J Tabitha Hees
- TUM Medical Graduate Center, Technical University of Munich, Munich, Germany
- Max Planck Institute for Biological Intelligence, Martinsried, Germany
| | - Simone Wanderoy
- TUM Medical Graduate Center, Technical University of Munich, Munich, Germany
- Max Planck Institute for Biological Intelligence, Martinsried, Germany
| | - Jana Lindner
- Max Planck Institute for Biological Intelligence, Martinsried, Germany
| | - Marlena Helms
- Max Planck Institute for Biological Intelligence, Martinsried, Germany
| | - Hariharan Murali Mahadevan
- TUM Medical Graduate Center, Technical University of Munich, Munich, Germany
- Max Planck Institute for Biological Intelligence, Martinsried, Germany
| | - Angelika B Harbauer
- Max Planck Institute for Biological Intelligence, Martinsried, Germany.
- Technical University of Munich, Institute of Neuronal Cell Biology, Munich, Germany.
- Munich Cluster for Systems Neurology, Munich, Germany.
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10
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Wang Q, Bu C, Wang H, Zhang B, Chen Q, Shi D, Chi L. Distinct mechanisms underlying the therapeutic effects of low-molecular-weight heparin and chondroitin sulfate on Parkinson's disease. Int J Biol Macromol 2024; 262:129846. [PMID: 38296150 DOI: 10.1016/j.ijbiomac.2024.129846] [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: 08/17/2023] [Revised: 01/26/2024] [Accepted: 01/28/2024] [Indexed: 02/09/2024]
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder influenced by various factors, including age, genetics, and the environment. Current treatments provide symptomatic relief without impeding disease progression. Previous studies have demonstrated the therapeutic potential of exogenous heparin and chondroitin sulfate in PD. However, their therapeutic mechanisms and structure-activity relationships remain poorly understood. In this study, low-molecular-weight heparin (L-HP) and chondroitin sulfate (L-CS) exhibited favorable therapeutic effects in a mouse model of PD. Proteomics revealed that L-HP attenuated mitochondrial dysfunction through its antioxidant properties, whereas L-CS suppressed neuroinflammation by inhibiting platelet activation. Two glycosaminoglycan (GAG)-binding proteins, manganese superoxide dismutase (MnSOD2) and fibrinogen beta chain (FGB), were identified as potential targets of L-HP and L-CS, and we investigated their structure-activity relationships. The IdoA2S-GlcNS6S/GlcNAc6S unit in HP bound to SOD2, whereas the GlcA-GalNAc4S and GlcA-GalNAc4S6S units in CS preferred FGB. Furthermore, N-S and 2-O-S in L-HP, and 4-O-S, 6-O-S, and -COOH in L-CS contributed significantly to the binding process. These findings provide new insights and evidence for the development and use of glycosaminoglycan-based therapeutics for PD.
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Affiliation(s)
- Qingchi Wang
- National Glycoengineering Research Center and Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, 72 Binhai Rd, Qingdao 266200, China; Xianghu Laboratory, Hangzhou 311231, China
| | - Changkai Bu
- National Glycoengineering Research Center and Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, 72 Binhai Rd, Qingdao 266200, China
| | - Haoran Wang
- National Glycoengineering Research Center and Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, 72 Binhai Rd, Qingdao 266200, China
| | - Bin Zhang
- National Glycoengineering Research Center and Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, 72 Binhai Rd, Qingdao 266200, China
| | - Qingqing Chen
- National Glycoengineering Research Center and Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, 72 Binhai Rd, Qingdao 266200, China
| | - Deling Shi
- National Glycoengineering Research Center and Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, 72 Binhai Rd, Qingdao 266200, China
| | - Lianli Chi
- National Glycoengineering Research Center and Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, 72 Binhai Rd, Qingdao 266200, China.
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11
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Ip JY, Wijaya I, Lee LT, Lim Y, Teoh DEJ, Chan CSC, Cui L, Begley TJ, Dedon PC, Guo H. ROS-induced translational regulation-through spatiotemporal differences in codon recognition-is a key driver of brown adipogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.22.572954. [PMID: 38463965 PMCID: PMC10925207 DOI: 10.1101/2023.12.22.572954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The role of translational regulation in brown adipogenesis is relatively unknown. Localized translation of mRNAs encoding mitochondrial components enables swift mitochondrial responses, but whether this occurs during brown adipogenesis, which involves massive mitochondrial biogenesis, has not been explored. Here, we used ribosome profiling and RNA-Seq, coupled with cellular fractionation, to obtain spatiotemporal insights into translational regulation. During brown adipogenesis, a translation bias towards G/C-ending codons is triggered first in the mitochondrial vicinity by reactive oxygen species (ROS), which later spreads to the rest of the cell. This translation bias is induced through ROS modulating the activity of the tRNA modification enzyme, ELP3. Intriguingly, functionally relevant mRNAs, including those encoding ROS scavengers, benefit from this bias; in so doing, ROS-induced translation bias both fuels differentiation and concurrently minimizes oxidative damage. These ROS-induced changes could enable sustained mitochondrial biogenesis during brown adipogenesis, and explain in part, the molecular basis for ROS hormesis.
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12
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Geng J, Li S, Li Y, Wu Z, Bhurtel S, Rimal S, Khan D, Ohja R, Brandman O, Lu B. Stalled translation by mitochondrial stress upregulates a CNOT4-ZNF598 ribosomal quality control pathway important for tissue homeostasis. Nat Commun 2024; 15:1637. [PMID: 38388640 PMCID: PMC10883933 DOI: 10.1038/s41467-024-45525-3] [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: 01/17/2023] [Accepted: 01/26/2024] [Indexed: 02/24/2024] Open
Abstract
Translational control exerts immediate effect on the composition, abundance, and integrity of the proteome. Ribosome-associated quality control (RQC) handles ribosomes stalled at the elongation and termination steps of translation, with ZNF598 in mammals and Hel2 in yeast serving as key sensors of translation stalling and coordinators of downstream resolution of collided ribosomes, termination of stalled translation, and removal of faulty translation products. The physiological regulation of RQC in general and ZNF598 in particular in multicellular settings is underexplored. Here we show that ZNF598 undergoes regulatory K63-linked ubiquitination in a CNOT4-dependent manner and is upregulated upon mitochondrial stresses in mammalian cells and Drosophila. ZNF598 promotes resolution of stalled ribosomes and protects against mitochondrial stress in a ubiquitination-dependent fashion. In Drosophila models of neurodegenerative diseases and patient cells, ZNF598 overexpression aborts stalled translation of mitochondrial outer membrane-associated mRNAs, removes faulty translation products causal of disease, and improves mitochondrial and tissue health. These results shed lights on the regulation of ZNF598 and its functional role in mitochondrial and tissue homeostasis.
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Affiliation(s)
- Ji Geng
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Shuangxi Li
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Yu Li
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Zhihao Wu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Sunil Bhurtel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Suman Rimal
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Danish Khan
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Rani Ohja
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Onn Brandman
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Bingwei Lu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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13
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Ashraf D, Khan MR, Dawson TM, Dawson VL. Protein Translation in the Pathogenesis of Parkinson's Disease. Int J Mol Sci 2024; 25:2393. [PMID: 38397070 PMCID: PMC10888601 DOI: 10.3390/ijms25042393] [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: 01/04/2024] [Revised: 02/15/2024] [Accepted: 02/17/2024] [Indexed: 02/25/2024] Open
Abstract
In recent years, research into Parkinson's disease and similar neurodegenerative disorders has increasingly suggested that these conditions are synonymous with failures in proteostasis. However, the spotlight of this research has remained firmly focused on the tail end of proteostasis, primarily aggregation, misfolding, and degradation, with protein translation being comparatively overlooked. Now, there is an increasing body of evidence supporting a potential role for translation in the pathogenesis of PD, and its dysregulation is already established in other similar neurodegenerative conditions. In this paper, we consider how altered protein translation fits into the broader picture of PD pathogenesis, working hand in hand to compound the stress placed on neurons, until this becomes irrecoverable. We will also consider molecular players of interest, recent evidence that suggests that aggregates may directly influence translation in PD progression, and the implications for the role of protein translation in our development of clinically useful diagnostics and therapeutics.
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Affiliation(s)
- Daniyal Ashraf
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (D.A.); (M.R.K.)
- School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Box 111, Cambridge CB2 0SP, UK
| | - Mohammed Repon Khan
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (D.A.); (M.R.K.)
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130, USA
| | - Ted M. Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (D.A.); (M.R.K.)
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Valina L. Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (D.A.); (M.R.K.)
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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14
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Lewis BM, Cho CY, Her HL, Mizrahi O, Hunter T, Yeo GW. LARP4 is an RNA-binding protein that binds nuclear-encoded mitochondrial mRNAs to promote mitochondrial function. RNA (NEW YORK, N.Y.) 2024; 30:223-239. [PMID: 38164626 PMCID: PMC10870378 DOI: 10.1261/rna.079799.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 11/25/2023] [Indexed: 01/03/2024]
Abstract
Mitochondria-associated RNA-binding proteins (RBPs) have emerged as key contributors to mitochondrial biogenesis and homeostasis. With few examples known, we set out to identify RBPs that regulate nuclear-encoded mitochondrial mRNAs (NEMmRNAs). Our systematic analysis of RNA targets of 150 RBPs identified RBPs with a preference for binding NEMmRNAs, including LARP4, a La RBP family member. We show that LARP4's targets are particularly enriched in mRNAs that encode respiratory chain complex proteins (RCCPs) and mitochondrial ribosome proteins (MRPs) across multiple human cell lines. Through quantitative proteomics, we demonstrate that depletion of LARP4 leads to a significant reduction in RCCP and MRP protein levels. Furthermore, we show that LARP4 depletion reduces mitochondrial function, and that LARP4 re-expression rescues this phenotype. Our findings shed light on a novel function for LARP4 as an RBP that binds to and positively regulates NEMmRNAs to promote mitochondrial respiratory function.
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Affiliation(s)
- Benjamin M Lewis
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California 92037, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California 92037, USA
- Stem Cell Program, University of California San Diego, La Jolla, California 92037, USA
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Chae Yun Cho
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Hsuan-Lin Her
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California 92037, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California 92037, USA
- Stem Cell Program, University of California San Diego, La Jolla, California 92037, USA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, California 92037, USA
| | - Orel Mizrahi
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California 92037, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California 92037, USA
- Stem Cell Program, University of California San Diego, La Jolla, California 92037, USA
| | - Tony Hunter
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California 92037, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California 92037, USA
- Stem Cell Program, University of California San Diego, La Jolla, California 92037, USA
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15
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Cohen B, Golani-Armon A, Arava YS. Emerging implications for ribosomes in proximity to mitochondria. Semin Cell Dev Biol 2024; 154:123-130. [PMID: 36642616 DOI: 10.1016/j.semcdb.2023.01.003] [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: 04/29/2022] [Revised: 12/11/2022] [Accepted: 01/05/2023] [Indexed: 01/15/2023]
Abstract
Synthesis of all proteins in eukaryotic cells, apart from a few organellar proteins, is done by cytosolic ribosomes. Many of these ribosomes are localized in the vicinity of the functional site of their encoded protein, enabling local protein synthesis. Studies in various organisms and tissues revealed that such locally translating ribosomes are also present near mitochondria. Here, we provide a brief summary of evidence for localized translation near mitochondria, then present data suggesting that these localized ribosomes may enable local translational regulatory processes in response to mitochondria needs. Finally, we describe the involvement of such localized ribosomes in the quality control of protein synthesis and mitochondria. These emerging views suggest that ribosomes localized near mitochondria are a hub for a variety of activities with diverse implications on mitochondria physiology.
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Affiliation(s)
- Bar Cohen
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Adi Golani-Armon
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Yoav S Arava
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel.
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16
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Chen Y, Tang W, Huang X, An Y, Li J, Yuan S, Shan H, Zhang M. Mitophagy in intracerebral hemorrhage: a new target for therapeutic intervention. Neural Regen Res 2024; 19:316-323. [PMID: 37488884 PMCID: PMC10503626 DOI: 10.4103/1673-5374.379019] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 04/12/2023] [Accepted: 05/18/2023] [Indexed: 07/26/2023] Open
Abstract
Intracerebral hemorrhage is a life-threatening condition with a high fatality rate and severe sequelae. However, there is currently no treatment available for intracerebral hemorrhage, unlike for other stroke subtypes. Recent studies have indicated that mitochondrial dysfunction and mitophagy likely relate to the pathophysiology of intracerebral hemorrhage. Mitophagy, or selective autophagy of mitochondria, is an essential pathway to preserve mitochondrial homeostasis by clearing up damaged mitochondria. Mitophagy markedly contributes to the reduction of secondary brain injury caused by mitochondrial dysfunction after intracerebral hemorrhage. This review provides an overview of the mitochondrial dysfunction that occurs after intracerebral hemorrhage and the underlying mechanisms regarding how mitophagy regulates it, and discusses the new direction of therapeutic strategies targeting mitophagy for intracerebral hemorrhage, aiming to determine the close connection between mitophagy and intracerebral hemorrhage and identify new therapies to modulate mitophagy after intracerebral hemorrhage. In conclusion, although only a small number of drugs modulating mitophagy in intracerebral hemorrhage have been found thus far, most of which are in the preclinical stage and require further investigation, mitophagy is still a very valid and promising therapeutic target for intracerebral hemorrhage in the long run.
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Affiliation(s)
- Yiyang Chen
- Institute of Forensic Sciences, Suzhou Medical College, Soochow University, Suzhou, Jiangsu Province, China
- Shanghai Key Lab of Forensic Medicine, Key Lab of Forensic Science, Ministry of Justice (Academy of Forensic Science), Shanghai, China
| | - Wenxuan Tang
- Institute of Forensic Sciences, Suzhou Medical College, Soochow University, Suzhou, Jiangsu Province, China
| | - Xinqi Huang
- Institute of Forensic Sciences, Suzhou Medical College, Soochow University, Suzhou, Jiangsu Province, China
| | - Yumei An
- Institute of Forensic Sciences, Suzhou Medical College, Soochow University, Suzhou, Jiangsu Province, China
| | - Jiawen Li
- Institute of Forensic Sciences, Suzhou Medical College, Soochow University, Suzhou, Jiangsu Province, China
| | - Shengye Yuan
- Institute of Forensic Sciences, Suzhou Medical College, Soochow University, Suzhou, Jiangsu Province, China
| | - Haiyan Shan
- Department of Obstetrics and Gynecology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, Jiangsu Province, China
| | - Mingyang Zhang
- Institute of Forensic Sciences, Suzhou Medical College, Soochow University, Suzhou, Jiangsu Province, China
- Shanghai Key Lab of Forensic Medicine, Key Lab of Forensic Science, Ministry of Justice (Academy of Forensic Science), Shanghai, China
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17
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Collart MA, Audebert L, Bushell M. Roles of the CCR4-Not complex in translation and dynamics of co-translation events. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 15:e1827. [PMID: 38009591 PMCID: PMC10909573 DOI: 10.1002/wrna.1827] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 10/06/2023] [Accepted: 10/30/2023] [Indexed: 11/29/2023]
Abstract
The Ccr4-Not complex is a global regulator of mRNA metabolism in eukaryotic cells that is most well-known to repress gene expression. Delivery of the complex to mRNAs through a multitude of distinct mechanisms accelerates their decay, yet Ccr4-Not also plays an important role in co-translational processes, such as co-translational association of proteins and delivery of translating mRNAs to organelles. The recent structure of Not5 interacting with the translated ribosome has brought to light that embedded information within the codon sequence can be monitored by recruitment of the Ccr4-Not complex to elongating ribosomes. Thereby, the Ccr4-Not complex is empowered with regulatory decisions determining the fate of proteins being synthesized and their encoding mRNAs. This review will focus on the roles of the complex in translation and dynamics of co-translation events. This article is categorized under: Translation > Mechanisms Translation > Regulation.
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Affiliation(s)
- Martine A. Collart
- Department of Microbiology and Molecular MedicineInstitute of Genetics and Genomics Geneva, University of Geneva, Faculty of MedicineGenèveSwitzerland
| | - Léna Audebert
- Department of Microbiology and Molecular MedicineInstitute of Genetics and Genomics Geneva, University of Geneva, Faculty of MedicineGenèveSwitzerland
| | - Martin Bushell
- Cancer Research UK Beatson InstituteGlasgowUK
- School of Cancer Sciences, University of GlasgowGlasgowUK
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18
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Daskalaki I, Markaki M, Gkikas I, Tavernarakis N. Local coordination of mRNA storage and degradation near mitochondria modulates C. elegans ageing. EMBO J 2023; 42:e112446. [PMID: 37427543 PMCID: PMC10425844 DOI: 10.15252/embj.2022112446] [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: 08/23/2022] [Revised: 06/10/2023] [Accepted: 06/17/2023] [Indexed: 07/11/2023] Open
Abstract
Mitochondria are central regulators of healthspan and lifespan, yet the intricate choreography of multiple, tightly controlled steps regulating mitochondrial biogenesis remains poorly understood. Here, we uncover a pivotal role for specific elements of the 5'-3' mRNA degradation pathway in the regulation of mitochondrial abundance and function. We find that the mRNA degradation and the poly-A tail deadenylase CCR4-NOT complexes form distinct foci in somatic Caenorhabditis elegans cells that physically and functionally associate with mitochondria. Components of these two multi-subunit complexes bind transcripts of nuclear-encoded mitochondria-targeted proteins to regulate mitochondrial biogenesis during ageing in an opposite manner. In addition, we show that balanced degradation and storage of mitochondria-targeted protein mRNAs are critical for mitochondrial homeostasis, stress resistance and longevity. Our findings reveal a multifaceted role of mRNA metabolism in mitochondrial biogenesis and show that fine-tuning of mRNA turnover and local translation control mitochondrial abundance and promote longevity in response to stress and during ageing.
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Affiliation(s)
- Ioanna Daskalaki
- Institute of Molecular Biology and BiotechnologyFoundation for Research and Technology‐HellasHeraklionGreece
- Department of Biology, School of Sciences and EngineeringUniversity of CreteHeraklionGreece
| | - Maria Markaki
- Institute of Molecular Biology and BiotechnologyFoundation for Research and Technology‐HellasHeraklionGreece
| | - Ilias Gkikas
- Institute of Molecular Biology and BiotechnologyFoundation for Research and Technology‐HellasHeraklionGreece
| | - Nektarios Tavernarakis
- Institute of Molecular Biology and BiotechnologyFoundation for Research and Technology‐HellasHeraklionGreece
- Division of Basic Sciences, School of MedicineUniversity of CreteHeraklionGreece
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19
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Jang HJ, Lee YH, Dao T, Jo Y, Khim KW, Eom HJ, Lee JE, Song YJ, Choi SS, Park K, Ji H, Chae YC, Myung K, Kim H, Ryu D, Park NH, Park SH, Choi JH. Thrap3 promotes nonalcoholic fatty liver disease by suppressing AMPK-mediated autophagy. Exp Mol Med 2023; 55:1720-1733. [PMID: 37524868 PMCID: PMC10474030 DOI: 10.1038/s12276-023-01047-4] [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: 10/02/2022] [Revised: 03/14/2023] [Accepted: 04/30/2023] [Indexed: 08/02/2023] Open
Abstract
Autophagy functions in cellular quality control and metabolic regulation. Dysregulation of autophagy is one of the major pathogenic factors contributing to the progression of nonalcoholic fatty liver disease (NAFLD). Autophagy is involved in the breakdown of intracellular lipids and the maintenance of healthy mitochondria in NAFLD. However, the mechanisms underlying autophagy dysregulation in NAFLD remain unclear. Here, we demonstrate that the hepatic expression level of Thrap3 was significantly increased in NAFLD conditions. Liver-specific Thrap3 knockout improved lipid accumulation and metabolic properties in a high-fat diet (HFD)-induced NAFLD model. Furthermore, Thrap3 deficiency enhanced autophagy and mitochondrial function. Interestingly, Thrap3 knockout increased the cytosolic translocation of AMPK from the nucleus and enhanced its activation through physical interaction. The translocation of AMPK was regulated by direct binding with AMPK and the C-terminal domain of Thrap3. Our results indicate a role for Thrap3 in NAFLD progression and suggest that Thrap3 is a potential target for NAFLD treatment.
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Affiliation(s)
- Hyun-Jun Jang
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, 58245, Republic of Korea
| | - Yo Han Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Tam Dao
- Department of Molecular Cell Biology, Sungkyunkwan University (SKKU) School of Medicine, Suwon, 16419, Republic of Korea
| | - Yunju Jo
- Department of Molecular Cell Biology, Sungkyunkwan University (SKKU) School of Medicine, Suwon, 16419, Republic of Korea
| | - Keon Woo Khim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Hye-Jin Eom
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Ju Eun Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Yi Jin Song
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Sun Sil Choi
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Kieun Park
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Haneul Ji
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Young Chan Chae
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, 44919, Republic of Korea
| | - Hongtae Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Dongryeol Ryu
- Department of Molecular Cell Biology, Sungkyunkwan University (SKKU) School of Medicine, Suwon, 16419, Republic of Korea
| | - Neung Hwa Park
- Department of Internal Medicine, University of Ulsan College of Medicine, Ulsan University Hospital, Ulsan, 44033, Republic of Korea.
| | - Sung Ho Park
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
| | - Jang Hyun Choi
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
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20
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Meurant S, Mauclet L, Dieu M, Arnould T, Eyckerman S, Renard P. Endogenous TOM20 Proximity Labeling: A Swiss-Knife for the Study of Mitochondrial Proteins in Human Cells. Int J Mol Sci 2023; 24:ijms24119604. [PMID: 37298552 DOI: 10.3390/ijms24119604] [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: 04/20/2023] [Revised: 05/24/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023] Open
Abstract
Biotin-based proximity labeling approaches, such as BioID, have demonstrated their use for the study of mitochondria proteomes in living cells. The use of genetically engineered BioID cell lines enables the detailed characterization of poorly characterized processes such as mitochondrial co-translational import. In this process, translation is coupled to the translocation of the mitochondrial proteins, alleviating the energy cost typically associated with the post-translational import relying on chaperone systems. However, the mechanisms are still unclear with only few actors identified but none that have been described in mammals yet. We thus profiled the TOM20 proxisome using BioID, assuming that some of the identified proteins could be molecular actors of the co-translational import in human cells. The obtained results showed a high enrichment of RNA binding proteins close to the TOM complex. However, for the few selected candidates, we could not demonstrate a role in the mitochondrial co-translational import process. Nonetheless, we were able to demonstrate additional uses of our BioID cell line. Indeed, the experimental approach used in this study is thus proposed for the identification of mitochondrial co-translational import effectors and for the monitoring of protein entry inside mitochondria with a potential application in the prediction of mitochondrial protein half-life.
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Affiliation(s)
- Sébastien Meurant
- URBC, Namur Research Institute for Life Sciences (Narilis), University of Namur (UNamur), 5000 Namur, Belgium
| | - Lorris Mauclet
- URBC, Namur Research Institute for Life Sciences (Narilis), University of Namur (UNamur), 5000 Namur, Belgium
| | - Marc Dieu
- Mass Spectrometry Platform (MaSUN), Namur Research Institute for Life Sciences (Narilis), University of Namur (UNamur), 5000 Namur, Belgium
| | - Thierry Arnould
- URBC, Namur Research Institute for Life Sciences (Narilis), University of Namur (UNamur), 5000 Namur, Belgium
| | - Sven Eyckerman
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Patricia Renard
- URBC, Namur Research Institute for Life Sciences (Narilis), University of Namur (UNamur), 5000 Namur, Belgium
- Mass Spectrometry Platform (MaSUN), Namur Research Institute for Life Sciences (Narilis), University of Namur (UNamur), 5000 Namur, Belgium
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21
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Zhang Y, He J, Yang Z, Zheng H, Deng H, Luo Z, Sun Q, Sun Q. Preventative effect of TSPO ligands on mixed antibody-mediated rejection through a Mitochondria-mediated metabolic disorder. J Transl Med 2023; 21:295. [PMID: 37131248 PMCID: PMC10152746 DOI: 10.1186/s12967-023-04134-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/13/2023] [Indexed: 05/04/2023] Open
Abstract
BACKGROUND Immune-mediated rejection was the major cause of graft dysfunction. Although the advances in immunosuppressive agents have markedly reduced the incidence of T-cell-mediated rejection after transplantation. However, the incidence of antibody-mediated rejection (AMR) remains high. Donor-specific antibodies (DSAs) were considered the major mediators of allograft loss. Previously, we showed that treatment with 18-kDa translocator protein (TSPO) ligands inhibited the differentiation and effector functions of T cells and reduced the rejection observed after allogeneic skin transplantation in mice. This study we further investigate the effect of TSPO ligands on B cells and DSAs production in the recipients of mixed-AMR model. METHODS In vitro, we explored the effect of treatment with TSPO ligands on the activation, proliferation, and antibody production of B cells. Further, we established a heart-transplantation mixed-AMR model in rats. This model was treated with the TSPO ligands, FGIN1-27 or Ro5-4864, to investigate the role of ligands in preventing transplant rejection and DSAs production in vivo. As TSPO was the mitochondrial membrane transporters, we then investigated the TSPO ligands effect on mitochondrial-related metabolic ability of B cells as well as expression of downstream proteins. RESULTS In vitro studies, treatment with TSPO ligands inhibited the differentiation of B cells into CD138+CD27+ plasma cells; reduced antibodies, IgG and IgM, secretion of B cells; and suppressed the B cell activation and proliferation. In the mixed-AMR rat model, treatment with FGIN1-27 or Ro5-4864 attenuated DSA-mediated cardiac-allograft injury, prolonged graft survival, and reduced the numbers of B cells, including IgG+ secreting B cells, T cells and macrophages infiltrating in grafts. For the further mechanism exploration, treatment with TSPO ligands inhibited the metabolic ability of B cells by downregulating expression of pyruvate dehydrogenase kinase 1 and proteins in complexes I, II, and IV of the electron transport chain. CONCLUSIONS We clarified the mechanism of action of TSPO ligands on B-cell functions and provided new ideas and drug targets for the clinical treatment of postoperative AMR.
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Affiliation(s)
- Yannan Zhang
- Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Jiannan He
- Department of Urology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhe Yang
- Department of Urology, The First Affiliated Hospital of Shandong First Medical University, Jinan, China
| | - Haofeng Zheng
- Division of kidney Transplantation, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, 106 2nd road Zhongshan, Yuexiu District, Guangzhou, 510080, China
| | - Haoxiang Deng
- Division of kidney Transplantation, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, 106 2nd road Zhongshan, Yuexiu District, Guangzhou, 510080, China
| | - Zihuan Luo
- Division of kidney Transplantation, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, 106 2nd road Zhongshan, Yuexiu District, Guangzhou, 510080, China
| | - Qipeng Sun
- Division of kidney Transplantation, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, 106 2nd road Zhongshan, Yuexiu District, Guangzhou, 510080, China
| | - Qiquan Sun
- Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China.
- Division of kidney Transplantation, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, 106 2nd road Zhongshan, Yuexiu District, Guangzhou, 510080, China.
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22
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Geng J, Khaket TP, Pan J, Li W, Zhang Y, Ping Y, Cobos Sillero MI, Lu B. Deregulation of ER-mitochondria contact formation and mitochondrial calcium homeostasis mediated by VDAC in fragile X syndrome. Dev Cell 2023; 58:597-615.e10. [PMID: 37040696 PMCID: PMC10113018 DOI: 10.1016/j.devcel.2023.03.002] [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: 02/27/2022] [Revised: 07/31/2022] [Accepted: 03/06/2023] [Indexed: 04/13/2023]
Abstract
Loss of fragile X messenger ribonucleoprotein (FMRP) causes fragile X syndrome (FXS), the most prevalent form of inherited intellectual disability. Here, we show that FMRP interacts with the voltage-dependent anion channel (VDAC) to regulate the formation and function of endoplasmic reticulum (ER)-mitochondria contact sites (ERMCSs), structures that are critical for mitochondrial calcium (mito-Ca2+) homeostasis. FMRP-deficient cells feature excessive ERMCS formation and ER-to-mitochondria Ca2+ transfer. Genetic and pharmacological inhibition of VDAC or other ERMCS components restored synaptic structure, function, and plasticity and rescued locomotion and cognitive deficits of the Drosophila dFmr1 mutant. Expressing FMRP C-terminal domain (FMRP-C), which confers FMRP-VDAC interaction, rescued the ERMCS formation and mito-Ca2+ homeostasis defects in FXS patient iPSC-derived neurons and locomotion and cognitive deficits in Fmr1 knockout mice. These results identify altered ERMCS formation and mito-Ca2+ homeostasis as contributors to FXS and offer potential therapeutic targets.
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Affiliation(s)
- Ji Geng
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tejinder Pal Khaket
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jie Pan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Wen Li
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yan Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China; Shanghai Key Laboratory of Psychotic Disorders (No. 13dz2260500), Shanghai Mental Health Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Yong Ping
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China; Shanghai Key Laboratory of Psychotic Disorders (No. 13dz2260500), Shanghai Mental Health Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
| | | | - Bingwei Lu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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23
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Storkebaum E, Rosenblum K, Sonenberg N. Messenger RNA Translation Defects in Neurodegenerative Diseases. N Engl J Med 2023; 388:1015-1030. [PMID: 36920757 DOI: 10.1056/nejmra2215795] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Affiliation(s)
- Erik Storkebaum
- From the Molecular Neurobiology Laboratory, Donders Center for Neuroscience, Donders Institute for Brain, Cognition, and Behavior, and the Faculty of Science, Radboud University, Nijmegen, the Netherlands (E.S.); the Sagol Department of Neurobiology, Faculty of Natural Sciences, and the Center for Genetic Manipulation in the Brain, University of Haifa, Haifa, Israel (K.R.); and the Department of Biochemistry and Goodman Cancer Institute, McGill University, Montreal (N.S.)
| | - Kobi Rosenblum
- From the Molecular Neurobiology Laboratory, Donders Center for Neuroscience, Donders Institute for Brain, Cognition, and Behavior, and the Faculty of Science, Radboud University, Nijmegen, the Netherlands (E.S.); the Sagol Department of Neurobiology, Faculty of Natural Sciences, and the Center for Genetic Manipulation in the Brain, University of Haifa, Haifa, Israel (K.R.); and the Department of Biochemistry and Goodman Cancer Institute, McGill University, Montreal (N.S.)
| | - Nahum Sonenberg
- From the Molecular Neurobiology Laboratory, Donders Center for Neuroscience, Donders Institute for Brain, Cognition, and Behavior, and the Faculty of Science, Radboud University, Nijmegen, the Netherlands (E.S.); the Sagol Department of Neurobiology, Faculty of Natural Sciences, and the Center for Genetic Manipulation in the Brain, University of Haifa, Haifa, Israel (K.R.); and the Department of Biochemistry and Goodman Cancer Institute, McGill University, Montreal (N.S.)
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24
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Li J, Yang D, Li Z, Zhao M, Wang D, Sun Z, Wen P, Dai Y, Gou F, Ji Y, Zhao D, Yang L. PINK1/Parkin-mediated mitophagy in neurodegenerative diseases. Ageing Res Rev 2023; 84:101817. [PMID: 36503124 DOI: 10.1016/j.arr.2022.101817] [Citation(s) in RCA: 63] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 11/21/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022]
Abstract
Mitochondria play key roles in bioenergetics, metabolism, and signaling; therefore, stable mitochondrial function is essential for cell survival, particularly in energy-intensive neuronal cells. In neurodegenerative diseases, damaged mitochondria accumulate in neurons causing associated bioenergetics deficiency, impaired cell signaling, defective cytoplasmic calcium buffering, and other pathological changes. Mitochondrial quality control is an important mechanism to ensure the maintenance of mitochondrial health, homeostasis, and mitophagy, the latter of which is a pathway that delivers defective mitochondria to the lysosome for degradation. Defective mitophagy is thought to be responsible for the accumulation of damaged mitochondria, which leads to cellular dysfunction and/or death in neurodegenerative diseases. PINK1/Parkin mainly regulates ubiquitin-dependent mitophagy, which is crucial for many aspects of mitochondrial physiology, particularly the initiation of autophagic mechanisms. Therefore, in the present review, we summarize the current knowledge of the conventional mitophagy pathway, focusing on the molecular mechanisms underlying mitophagy dysregulation in prion disease and other age-related neurodegenerative diseases, especially in relation to the PINK1/Parkin pathway. Moreover, we list the inducers of mitophagy that possess neuroprotective effects, in addition to their mechanisms related to the PINK1/Parkin pathway. These mechanisms may provide potential interventions centered on the regulation of mitophagy and offer therapeutic strategies for the treatment of neurodegenerative diseases.
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Affiliation(s)
- Jie Li
- National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Dongming Yang
- National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Zhiping Li
- National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Mengyang Zhao
- National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Dongdong Wang
- National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Zhixin Sun
- National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Pei Wen
- National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Yuexin Dai
- National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Fengting Gou
- National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Yilan Ji
- National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Deming Zhao
- National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Lifeng Yang
- National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China.
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25
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Jeandard D, Smirnova A, Fasemore AM, Coudray L, Entelis N, Förstner K, Tarassov I, Smirnov A. CoLoC-seq probes the global topology of organelle transcriptomes. Nucleic Acids Res 2022; 51:e16. [PMID: 36537202 PMCID: PMC9943681 DOI: 10.1093/nar/gkac1183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Proper RNA localisation is essential for physiological gene expression. Various kinds of genome-wide approaches permit to comprehensively profile subcellular transcriptomes. Among them, cell fractionation methods, that couple RNase treatment of isolated organelles to the sequencing of protected transcripts, remain most widely used, mainly because they do not require genetic modification of the studied system and can be easily implemented in any cells or tissues, including in non-model species. However, they suffer from numerous false-positives since incompletely digested contaminant RNAs can still be captured and erroneously identified as resident transcripts. Here we introduce Controlled Level of Contamination coupled to deep sequencing (CoLoC-seq) as a new subcellular transcriptomics approach that efficiently bypasses this caveat. CoLoC-seq leverages classical enzymatic kinetics and tracks the depletion dynamics of transcripts in a gradient of an exogenously added RNase, with or without organellar membranes. By means of straightforward mathematical modelling, CoLoC-seq infers the localisation topology of RNAs and robustly distinguishes between genuinely resident, luminal transcripts and merely abundant surface-attached contaminants. Our generic approach performed well on human mitochondria and is in principle applicable to other membrane-bounded organelles, including plastids, compartments of the vacuolar system, extracellular vesicles, and viral particles.
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Affiliation(s)
| | | | | | - Léna Coudray
- UMR7156 – Génétique Moléculaire, Génomique, Microbiologie (GMGM), University of Strasbourg, CNRS, Strasbourg, F-67000, France
| | - Nina Entelis
- UMR7156 – Génétique Moléculaire, Génomique, Microbiologie (GMGM), University of Strasbourg, CNRS, Strasbourg, F-67000, France
| | - Konrad U Förstner
- ZB MED – Information Centre for Life Sciences, Cologne, D-50931, Germany,TH Köln – University of Applied Sciences, Faculty of Information Science and Communication Studies, Institute of Information Science, Cologne, D-50678, Germany
| | - Ivan Tarassov
- UMR7156 – Génétique Moléculaire, Génomique, Microbiologie (GMGM), University of Strasbourg, CNRS, Strasbourg, F-67000, France
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26
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ITCH deficiency clinical phenotype expansion and mitochondrial dysfunction. Mol Genet Metab Rep 2022; 33:100932. [PMID: 36338154 PMCID: PMC9634006 DOI: 10.1016/j.ymgmr.2022.100932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 10/20/2022] [Accepted: 10/22/2022] [Indexed: 11/07/2022] Open
Abstract
Autoimmune Disease, Multisystem, with Facial Dysmorphism (ADMFD) is an autosomal recessive disorder due to pathogenic variants in the ITCH gene. It is characterized by failure to thrive, dysmorphic facial features, developmental delay, and systemic autoimmunity that can manifest variably with autoimmune hepatitis, thyroiditis, and enteropathy, among other organ manifestations. It was originally described in 10 consanguineous Old Order Amish patients, and more recently in two patients of White British and Black German ethnicities. While the role of ITCH protein in apoptosis and inflammation has previously been characterized, a defect in cellular bioenergetics has not yet been reported in ITCH deficiency. Here we present a Caucasian female originally evaluated for possible mitochondrial respiratory chain deficiency, who ultimately was found to have two novel variants in ITCH with absence of ITCH protein in patient derived fibroblasts. Clinical studies of patient muscle showed mitochondrial DNA copy number of 57% compared to controls. Functional studies in skin fibroblasts revealed decreased activity of mitochondrial fatty acid oxidation and oxidative phosphorylation, and decreased overall ATP production. Our findings confirm mitochondrial energy dysfunction in a patient with ITCH deficiency offering the opportunity to assess alternative therapeutic options.
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27
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Liu S, Liu S, Jiang H. Multifaceted roles of mitochondrial stress responses under ETC dysfunction - repair, destruction and pathogenesis. FEBS J 2022; 289:6994-7013. [PMID: 34918460 DOI: 10.1111/febs.16323] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/08/2021] [Accepted: 12/15/2021] [Indexed: 01/13/2023]
Abstract
Electron transport chain (ETC) dysfunction is a common feature of mitochondrial diseases and induces severe cellular stresses, including mitochondrial membrane potential (Δψm ) reduction, mitochondrial matrix acidification, metabolic derangements and proteostatic stresses. Extensive studies of ETC dysfunction in yeast, Caenorhabditis elegans, cultured cells and mouse models have revealed multiple mitochondrial stress response pathways. Here, we summarise the current understanding of the triggers, sensors, signalling mechanisms and the functional outcomes of mitochondrial stress responses in different species. We highlight Δψm reduction as a major trigger of stress responses in different species, but the responses are species-specific and the outcomes are context-dependent. ETC dysfunction elicits a mitochondrial unfolded protein response (UPRmt ) to repair damaged mitochondria in C. elegans, and activates a global adaptive programme to maintain Δψm in yeast. Yeast and C. elegans responses are remarkably similar at the downstream responses, although they are activated by different signalling mechanisms. UPRmt generally protects ETC-defective worms, but its constitutive activation is toxic for wildtype worms and worms carrying mutant mtDNA. In contrast to lower organisms, ETC dysfunction in mammals mainly activates a mitochondrial integrated stress response (ISRmt ) to reprogramme metabolism and a PINK1-Parkin mitophagy pathway to degrade damaged mitochondria. Accumulating in vivo results suggest that the ATF4 branch of ISRmt exacerbates metabolic derangements to accelerate mitochondrial disease progression. The in vivo roles of mitophagy in mitochondrial diseases are also context-dependent. These results thus reveal the common and unique aspects of mitochondrial stress responses in different species and highlight their multifaceted roles in mitochondrial diseases.
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Affiliation(s)
- Shanshan Liu
- National Institute of Biological Sciences, Beijing, China.,Beijing Key Laboratory of Cell Biology for Animal Aging, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Siqi Liu
- National Institute of Biological Sciences, Beijing, China.,Beijing Key Laboratory of Cell Biology for Animal Aging, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Hui Jiang
- National Institute of Biological Sciences, Beijing, China.,Beijing Key Laboratory of Cell Biology for Animal Aging, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
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28
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Hees JT, Harbauer AB. Metabolic Regulation of Mitochondrial Protein Biogenesis from a Neuronal Perspective. Biomolecules 2022; 12:1595. [PMID: 36358945 PMCID: PMC9687362 DOI: 10.3390/biom12111595] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/24/2022] [Accepted: 10/26/2022] [Indexed: 09/29/2023] Open
Abstract
Neurons critically depend on mitochondria for ATP production and Ca2+ buffering. They are highly compartmentalized cells and therefore a finely tuned mitochondrial network constantly adapting to the local requirements is necessary. For neuronal maintenance, old or damaged mitochondria need to be degraded, while the functional mitochondrial pool needs to be replenished with freshly synthesized components. Mitochondrial biogenesis is known to be primarily regulated via the PGC-1α-NRF1/2-TFAM pathway at the transcriptional level. However, while transcriptional regulation of mitochondrial genes can change the global mitochondrial content in neurons, it does not explain how a morphologically complex cell such as a neuron adapts to local differences in mitochondrial demand. In this review, we discuss regulatory mechanisms controlling mitochondrial biogenesis thereby making a case for differential regulation at the transcriptional and translational level. In neurons, additional regulation can occur due to the axonal localization of mRNAs encoding mitochondrial proteins. Hitchhiking of mRNAs on organelles including mitochondria as well as contact site formation between mitochondria and endolysosomes are required for local mitochondrial biogenesis in axons linking defects in any of these organelles to the mitochondrial dysfunction seen in various neurological disorders.
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Affiliation(s)
- Jara Tabitha Hees
- TUM Medical Graduate Center, Technical University of Munich, 81675 Munich, Germany
- Max Planck Institute for Biological Intelligence, in Foundation, 82152 Planegg-Martinsried, Germany
| | - Angelika Bettina Harbauer
- Max Planck Institute for Biological Intelligence, in Foundation, 82152 Planegg-Martinsried, Germany
- Institute of Neuronal Cell Biology, Technical University of Munich, 80802 Munich, Germany
- Munich Cluster for Systems Neurology, 81377 Munich, Germany
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29
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Sen A, Cox RT. Loss of Drosophila Clueless differentially affects the mitochondrial proteome compared to loss of Sod2 and Pink1. Front Physiol 2022; 13:1004099. [DOI: 10.3389/fphys.2022.1004099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/11/2022] [Indexed: 11/13/2022] Open
Abstract
Mitochondria contain their own DNA, mitochondrial DNA, which encodes thirteen proteins. However, mitochondria require thousands of proteins encoded in the nucleus to carry out their many functions. Identifying the definitive mitochondrial proteome has been challenging as methods isolating mitochondrial proteins differ and different tissues and organisms may have specialized proteomes. Mitochondrial diseases arising from single gene mutations in nucleus encoded genes could affect the mitochondrial proteome, but deciphering which effects are due to loss of specific pathways or to accumulated general mitochondrial damage is difficult. To identify specific versus general effects, we have taken advantage of mutations in three Drosophila genes, clueless, Sod2, and Pink1, which are required for mitochondrial function through different pathways. We measured changes in each mutant’s mitochondrial proteome using quantitative tandem mass tag mass spectrometry. Our analysis identified protein classes that are unique to each mutant and those shared between them, suggesting that some changes in the mitochondrial proteome are due to general mitochondrial damage whereas others are gene specific. For example, clueless mutants had the greatest number of less and more abundant mitochondrial proteins whereas loss of all three genes increased stress and metabolism proteins. This study is the first to directly compare in vivo steady state levels of mitochondrial proteins by examining loss of three pathways critical for mitochondrial function. These data could be useful to understand disease etiology, and how mutations in genes critical for mitochondrial function cause specific mitochondrial proteomic changes as opposed to changes due to generalized mitochondrial damage.
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30
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Singh B, Avula K, Sufi SA, Parwin N, Das S, Alam MF, Samantaray S, Bankapalli L, Rani A, Poornima K, Prusty B, Mallick TP, Shaw SK, Dodia H, Kabi S, Pagad TT, Mohanty S, Syed GH. Defective Mitochondrial Quality Control during Dengue Infection Contributes to Disease Pathogenesis. J Virol 2022; 96:e0082822. [PMID: 36197108 PMCID: PMC9599662 DOI: 10.1128/jvi.00828-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 09/20/2022] [Indexed: 11/24/2022] Open
Abstract
Mitochondrial fitness is governed by mitochondrial quality control pathways comprising mitochondrial dynamics and mitochondrial-selective autophagy (mitophagy). Disruption of these processes has been implicated in many human diseases, including viral infections. Here, we report a comprehensive analysis of the effect of dengue infection on host mitochondrial homeostasis and its significance in dengue disease pathogenesis. Despite severe mitochondrial stress and injury, we observed that the pathways of mitochondrial quality control and mitochondrial biogenesis are paradoxically downregulated in dengue-infected human liver cells. This leads to the disruption of mitochondrial homeostasis and the onset of cellular injury and necrotic death in the infected cells. Interestingly, dengue promotes global autophagy but selectively disrupts mitochondrial-selective autophagy (mitophagy). Dengue downregulates the expression of PINK1 and Parkin, the two major proteins involved in tagging the damaged mitochondria for elimination through mitophagy. Mitophagy flux assays also suggest that Parkin-independent pathways of mitophagy are also inactive during dengue infection. Dengue infection also disrupts mitochondrial biogenesis by downregulating the master regulators PPARγ and PGC1α. Dengue-infected cells release mitochondrial damage-associated molecular patterns (mtDAMPs) such as mitochondrial DNA into the cytosol and extracellular milieu. Furthermore, the challenge of naive immune cells with culture supernatants from dengue-infected liver cells was sufficient to trigger proinflammatory signaling. In correlation with our in vitro observations, dengue patients have high levels of cell-free mitochondrial DNA in their blood in proportion to the degree of thrombocytopenia. Overall, our study shows how defective mitochondrial homeostasis in dengue-infected liver cells can drive dengue disease pathogenesis. IMPORTANCE Many viruses target host cell mitochondria to create a microenvironment conducive to viral dissemination. Dengue virus also exploits host cell mitochondria to facilitate its viral life cycle. Dengue infection of liver cells leads to severe mitochondrial injury and inhibition of proteins that regulate mitochondrial quality control and biogenesis, thereby disrupting mitochondrial homeostasis. A defect in mitochondrial quality control leads to the accumulation of damaged mitochondria and promotes cellular injury. This leads to the release of mitochondrial damage-associated molecular patterns (mt-DAMPs) into the cell cytoplasm and extracellular milieu. These mt-DAMPs activate the naive immune cells and trigger proinflammatory signaling, leading to the release of cytokines and chemokines, which may trigger systemic inflammation and contribute to dengue disease pathogenesis. In correlation with this, we observed high levels of cell-free mitochondrial DNA in dengue patient blood. This study provides insight into how the disruption of mitochondrial quality control in dengue-infected cells can trigger inflammation and drive dengue disease pathogenesis.
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Affiliation(s)
- Bharati Singh
- Institute of Life Sciences, Bhubaneswar, Odisha, India
- Kalinga Institute of Information and Technology, Bhubaneswar, Odisha, India
| | - Kiran Avula
- Institute of Life Sciences, Bhubaneswar, Odisha, India
- Regional Centre for Biotechnology, Faridabad, Haryana, India
| | | | - Nahid Parwin
- Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Sayani Das
- Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Mohd Faraz Alam
- Institute of Life Sciences, Bhubaneswar, Odisha, India
- Regional Centre for Biotechnology, Faridabad, Haryana, India
| | | | | | | | | | | | | | | | - Hiren Dodia
- Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Shobhitendu Kabi
- Department of Medicine, Institute of Medical Sciences & SUM Hospital, Bhubaneswar, Odisha, India
| | - Trupti T. Pagad
- Department of Medicine, Institute of Medical Sciences & SUM Hospital, Bhubaneswar, Odisha, India
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31
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Uszczynska-Ratajczak B, Sugunan S, Kwiatkowska M, Migdal M, Carbonell-Sala S, Sokol A, Winata CL, Chacinska A. Profiling subcellular localization of nuclear-encoded mitochondrial gene products in zebrafish. Life Sci Alliance 2022; 6:6/1/e202201514. [PMID: 36283702 PMCID: PMC9595208 DOI: 10.26508/lsa.202201514] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 09/30/2022] [Accepted: 10/04/2022] [Indexed: 11/08/2022] Open
Abstract
Most mitochondrial proteins are encoded by nuclear genes, synthetized in the cytosol and targeted into the organelle. To characterize the spatial organization of mitochondrial gene products in zebrafish (Danio rerio), we sequenced RNA from different cellular fractions. Our results confirmed the presence of nuclear-encoded mRNAs in the mitochondrial fraction, which in unperturbed conditions, are mainly transcripts encoding large proteins with specific properties, like transmembrane domains. To further explore the principles of mitochondrial protein compartmentalization in zebrafish, we quantified the transcriptomic changes for each subcellular fraction triggered by the chchd4a -/- mutation, causing the disorders in the mitochondrial protein import. Our results indicate that the proteostatic stress further restricts the population of transcripts on the mitochondrial surface, allowing only the largest and the most evolutionary conserved proteins to be synthetized there. We also show that many nuclear-encoded mitochondrial transcripts translated by the cytosolic ribosomes stay resistant to the global translation shutdown. Thus, vertebrates, in contrast to yeast, are not likely to use localized translation to facilitate synthesis of mitochondrial proteins under proteostatic stress conditions.
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Affiliation(s)
- Barbara Uszczynska-Ratajczak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland .,Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Sreedevi Sugunan
- ReMedy International Research Agenda Unit, University of Warsaw, Warsaw, Poland,International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Monika Kwiatkowska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland,Centre of New Technologies, University of Warsaw, Warsaw, Poland,International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Maciej Migdal
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Silvia Carbonell-Sala
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Anna Sokol
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany,Biomolecular Mass Spectrometry, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Cecilia L Winata
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Agnieszka Chacinska
- ReMedy International Research Agenda Unit, IMol Polish Academy of Sciences, Warsaw, Poland
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32
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Liu Y, Gu W. The complexity of p53-mediated metabolic regulation in tumor suppression. Semin Cancer Biol 2022; 85:4-32. [PMID: 33785447 PMCID: PMC8473587 DOI: 10.1016/j.semcancer.2021.03.010] [Citation(s) in RCA: 99] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/12/2021] [Accepted: 03/15/2021] [Indexed: 02/07/2023]
Abstract
Although the classic activities of p53 including induction of cell-cycle arrest, senescence, and apoptosis are well accepted as critical barriers to cancer development, accumulating evidence suggests that loss of these classic activities is not sufficient to abrogate the tumor suppression activity of p53. Numerous studies suggest that metabolic regulation contributes to tumor suppression, but the mechanisms by which it does so are not completely understood. Cancer cells rewire cellular metabolism to meet the energetic and substrate demands of tumor development. It is well established that p53 suppresses glycolysis and promotes mitochondrial oxidative phosphorylation through a number of downstream targets against the Warburg effect. The role of p53-mediated metabolic regulation in tumor suppression is complexed by its function to promote both cell survival and cell death under different physiological settings. Indeed, p53 can regulate both pro-oxidant and antioxidant target genes for complete opposite effects. In this review, we will summarize the roles of p53 in the regulation of glucose, lipid, amino acid, nucleotide, iron metabolism, and ROS production. We will highlight the mechanisms underlying p53-mediated ferroptosis, AKT/mTOR signaling as well as autophagy and discuss the complexity of p53-metabolic regulation in tumor development.
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Affiliation(s)
- Yanqing Liu
- Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, 1130 Nicholas Ave, New York, NY, 10032, USA
| | - Wei Gu
- Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, 1130 Nicholas Ave, New York, NY, 10032, USA; Department of Pathology and Cell Biology, Vagelos College of Physicians & Surgeons, Columbia University, 1130 Nicholas Ave, New York, NY, 10032, USA.
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33
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Lu B. Translational regulation by ribosome-associated quality control in neurodegenerative disease, cancer, and viral infection. Front Cell Dev Biol 2022; 10:970654. [PMID: 36187485 PMCID: PMC9515510 DOI: 10.3389/fcell.2022.970654] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/30/2022] [Indexed: 11/22/2022] Open
Abstract
Translational control at the initiation, elongation, and termination steps exerts immediate effects on the rate as well as the spatiotemporal dynamics of new protein synthesis, shaping the composition of the proteome. Translational control is particularly important for cells under stress as during viral infection or in disease conditions such as cancer and neurodegenerative diseases. Much has been learned about the control mechanisms acting at the translational initiation step under normal or pathological conditions. However, problems during the elongation or termination steps of translation can lead to ribosome stalling and ribosome collision, which will trigger ribosome-associated quality control (RQC) mechanism. Inadequate RQC may lead to the accumulation of faulty translation products that perturb protein homeostasis (proteostasis). Proteostasis signifies a cellular state in which the synthesis, folding, and degradation of proteins are maintained at a homeostatic state such that an intact proteome is preserved. Cellular capacity to preserve proteostasis declines with age, which is thought to contribute to age-related diseases. Proteostasis failure manifested as formation of aberrant protein aggregates, epitomized by the amyloid plaques in Alzheimer’s disease (AD), is a defining feature of neurodegenerative diseases. The root cause of the proteostasis failure and protein aggregation is still enigmatic. Here I will review recent studies supporting that faulty translation products resulting from inadequate RQC of translational stalling and ribosome collision during the translation of problematic mRNAs can be the root cause of proteostasis failure and may represent novel therapeutic targets for neurodegenerative diseases. I will also review evidence that translation regulation by RQC is operative in cancer cells and during viral infection. Better understanding of RQC mechanism may lead to novel therapeutic strategies against neurodegenerative diseases, cancer, and viral infections, including the ongoing COVID-19 pandemic.
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Arceo XG, Koslover EF, Zid BM, Brown AI. Mitochondrial mRNA localization is governed by translation kinetics and spatial transport. PLoS Comput Biol 2022; 18:e1010413. [PMID: 35984860 PMCID: PMC9432724 DOI: 10.1371/journal.pcbi.1010413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/31/2022] [Accepted: 07/19/2022] [Indexed: 11/24/2022] Open
Abstract
For many nuclear-encoded mitochondrial genes, mRNA localizes to the mitochondrial surface co-translationally, aided by the association of a mitochondrial targeting sequence (MTS) on the nascent peptide with the mitochondrial import complex. For a subset of these co-translationally localized mRNAs, their localization is dependent on the metabolic state of the cell, while others are constitutively localized. To explore the differences between these two mRNA types we developed a stochastic, quantitative model for MTS-mediated mRNA localization to mitochondria in yeast cells. This model includes translation, applying gene-specific kinetics derived from experimental data; and diffusion in the cytosol. Even though both mRNA types are co-translationally localized we found that the steady state number, or density, of ribosomes along an mRNA was insufficient to differentiate the two mRNA types. Instead, conditionally-localized mRNAs have faster translation kinetics which modulate localization in combination with changes to diffusive search kinetics across metabolic states. Our model also suggests that the MTS requires a maturation time to become competent to bind mitochondria. Our work indicates that yeast cells can regulate mRNA localization to mitochondria by controlling mitochondrial volume fraction (influencing diffusive search times) and gene translation kinetics (adjusting mRNA binding competence) without the need for mRNA-specific binding proteins. These results shed light on both global and gene-specific mechanisms that enable cells to alter mRNA localization in response to changing metabolic conditions.
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Affiliation(s)
- Ximena G. Arceo
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California, United States of America
| | - Elena F. Koslover
- Department of Physics, University of California, San Diego, La Jolla, California, United States of America
| | - Brian M. Zid
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California, United States of America
| | - Aidan I. Brown
- Department of Physics, Ryerson University, Toronto, Canada
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Different platforms for mitomiRs in mitochondria: Emerging facets in regulation of mitochondrial functions. Mitochondrion 2022; 66:67-73. [DOI: 10.1016/j.mito.2022.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 07/29/2022] [Accepted: 08/02/2022] [Indexed: 11/23/2022]
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Pekkurnaz G, Wang X. Mitochondrial heterogeneity and homeostasis through the lens of a neuron. Nat Metab 2022; 4:802-812. [PMID: 35817853 PMCID: PMC11151822 DOI: 10.1038/s42255-022-00594-w] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 05/23/2022] [Indexed: 12/12/2022]
Abstract
Mitochondria are vital organelles with distinct morphological features and functional properties. The dynamic network of mitochondria undergoes structural and functional adaptations in response to cell-type-specific metabolic demands. Even within the same cell, mitochondria can display wide diversity and separate into functionally distinct subpopulations. Mitochondrial heterogeneity supports unique subcellular functions and is crucial to polarized cells, such as neurons. The spatiotemporal metabolic burden within the complex shape of a neuron requires precisely localized mitochondria. By travelling great lengths throughout neurons and experiencing bouts of immobility, mitochondria meet distant local fuel demands. Understanding mitochondrial heterogeneity and homeostasis mechanisms in neurons provides a framework to probe their significance to many other cell types. Here, we put forth an outline of the multifaceted role of mitochondria in regulating neuronal physiology and cellular functions more broadly.
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Affiliation(s)
- Gulcin Pekkurnaz
- Neurobiology Department, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA.
| | - Xinnan Wang
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA.
- Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA, USA.
- Maternal & Child Health Research Institute, Stanford University School of Medicine, Stanford, CA, USA.
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Peng Y, Gavis ER. The Drosophila hnRNP F/H homolog Glorund recruits dFMRP to inhibit nanos translation elongation. Nucleic Acids Res 2022; 50:7067-7083. [PMID: 35699205 PMCID: PMC9262583 DOI: 10.1093/nar/gkac500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 05/24/2022] [Accepted: 05/27/2022] [Indexed: 12/24/2022] Open
Abstract
Translational control of maternal mRNAs generates spatial and temporal patterns of protein expression necessary to begin animal development. Translational repression of unlocalized nanos (nos) mRNA in late-stage Drosophila oocytes by the hnRNP F/H homolog, Glorund (Glo), is important for embryonic body patterning. While previous work has suggested that repression occurs at both the translation initiation and elongation phases, the molecular mechanism by which Glo regulates nos translation remains elusive. Here, we have identified the Drosophila fragile X mental retardation protein, dFMRP, as a Glo interaction partner with links to the translational machinery. Using an oocyte-based in vitro translation system, we confirmed that Glo regulates both initiation and elongation of a nos translational reporter and showed that dFMRP specifically represses translation elongation and promotes ribosome stalling. Furthermore, we combined mutational analysis and in vivo and in vitro binding assays to show that Glo's qRRM2 domain specifically and directly interacts with dFMRP. Our findings suggest that Glo regulates nos translation elongation by recruiting dFMRP and that Glo's RNA-binding domains can also function as protein-protein interaction interfaces critical for its regulatory functions. Additionally, they reveal a mechanism for targeting dFMRP to specific transcripts.
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Affiliation(s)
- Yingshi Peng
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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Huang Y, Wan Z, Tang Y, Xu J, Laboret B, Nallamothu S, Yang C, Liu B, Lu RO, Lu B, Feng J, Cao J, Hayflick S, Wu Z, Zhou B. Pantothenate kinase 2 interacts with PINK1 to regulate mitochondrial quality control via acetyl-CoA metabolism. Nat Commun 2022; 13:2412. [PMID: 35504872 PMCID: PMC9065001 DOI: 10.1038/s41467-022-30178-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 04/20/2022] [Indexed: 12/26/2022] Open
Abstract
Human neurodegenerative disorders often exhibit similar pathologies, suggesting a shared aetiology. Key pathological features of Parkinson's disease (PD) are also observed in other neurodegenerative diseases. Pantothenate Kinase-Associated Neurodegeneration (PKAN) is caused by mutations in the human PANK2 gene, which catalyzes the initial step of de novo CoA synthesis. Here, we show that fumble (fbl), the human PANK2 homolog in Drosophila, interacts with PINK1 genetically. fbl and PINK1 mutants display similar mitochondrial abnormalities, and overexpression of mitochondrial Fbl rescues PINK1 loss-of-function (LOF) defects. Dietary vitamin B5 derivatives effectively rescue CoA/acetyl-CoA levels and mitochondrial function, reversing the PINK1 deficiency phenotype. Mechanistically, Fbl regulates Ref(2)P (p62/SQSTM1 homolog) by acetylation to promote mitophagy, whereas PINK1 regulates fbl translation by anchoring mRNA molecules to the outer mitochondrial membrane. In conclusion, Fbl (or PANK2) acts downstream of PINK1, regulating CoA/acetyl-CoA metabolism to promote mitophagy, uncovering a potential therapeutic intervention strategy in PD treatment.
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Affiliation(s)
- Yunpeng Huang
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
| | - Zhihui Wan
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Department of Laboratory Medicine, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, 100026, China
| | - Yinglu Tang
- Department of Biological Sciences, Dedman College of Humanities and Sciences, Southern Methodist University, Dallas, TX, 75275, USA
| | - Junxuan Xu
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Bretton Laboret
- Department of Biological Sciences, Dedman College of Humanities and Sciences, Southern Methodist University, Dallas, TX, 75275, USA
| | - Sree Nallamothu
- Department of Biological Sciences, Dedman College of Humanities and Sciences, Southern Methodist University, Dallas, TX, 75275, USA
| | - Chenyu Yang
- Department of Statistical Science, Dedman College of Humanities and Sciences, Southern Methodist University, Dallas, TX, 75275, USA
| | - Boxiang Liu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Rongze Olivia Lu
- Department of Neurosurgery, Dell Medical School, University of Texas Austin, Austin, TX, 78712, USA
- Department of Neurological Surgery, Brain Tumor Center, University of California San Francisco, California, CA, 94143, USA
| | - Bingwei Lu
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Juan Feng
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China
| | - Jing Cao
- Department of Statistical Science, Dedman College of Humanities and Sciences, Southern Methodist University, Dallas, TX, 75275, USA
| | - Susan Hayflick
- Department of Molecular & Medical Genetics, Oregon Health and Science University, Portland, OR, 97201, USA
| | - Zhihao Wu
- Department of Biological Sciences, Dedman College of Humanities and Sciences, Southern Methodist University, Dallas, TX, 75275, USA.
| | - Bing Zhou
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
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Guatteo E, Berretta N, Monda V, Ledonne A, Mercuri NB. Pathophysiological Features of Nigral Dopaminergic Neurons in Animal Models of Parkinson's Disease. Int J Mol Sci 2022; 23:ijms23094508. [PMID: 35562898 PMCID: PMC9102081 DOI: 10.3390/ijms23094508] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/16/2022] [Accepted: 04/18/2022] [Indexed: 12/21/2022] Open
Abstract
The degeneration of nigral dopaminergic neurons is considered the hallmark of Parkinson’s disease (PD), and it is triggered by different factors, including mitochondrial dysfunction, Lewy body accumulation, neuroinflammation, excitotoxicity and metal accumulation. Despite the extensive literature devoted to unravelling the signalling pathways involved in neuronal degeneration, little is known about the functional impairments occurring in these cells during illness progression. Of course, it is not possible to obtain direct information on the properties of the dopaminergic cells in patients. However, several data are available in the literature reporting changes in the function of these cells in PD animal models. In the present manuscript, we focus on dopaminergic neuron functional properties and summarize shared or peculiar features of neuronal dysfunction in different PD animal models at different stages of the disease in an attempt to design a picture of the functional modifications occurring in nigral dopaminergic neurons during disease progression preceding their eventual death.
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Affiliation(s)
- Ezia Guatteo
- Department of Motor Science and Wellness, University of Naples Parthenope, 80133 Naples, Italy; (E.G.); (V.M.)
- Experimental Neurology Laboratory, IRCCS Santa Lucia Foundation, 00143 Rome, Italy;
| | - Nicola Berretta
- Experimental Neurology Laboratory, IRCCS Santa Lucia Foundation, 00143 Rome, Italy;
| | - Vincenzo Monda
- Department of Motor Science and Wellness, University of Naples Parthenope, 80133 Naples, Italy; (E.G.); (V.M.)
| | - Ada Ledonne
- Experimental Neurology Laboratory, IRCCS Santa Lucia Foundation, 00143 Rome, Italy;
- Correspondence: (A.L.); (N.B.M.)
| | - Nicola Biagio Mercuri
- Experimental Neurology Laboratory, IRCCS Santa Lucia Foundation, 00143 Rome, Italy;
- Department of Systems Medicine, University of Rome Tor Vergata, 00143 Rome, Italy
- Correspondence: (A.L.); (N.B.M.)
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A Poxvirus Decapping Enzyme Colocalizes with Mitochondria To Regulate RNA Metabolism and Translation and Promote Viral Replication. mBio 2022; 13:e0030022. [PMID: 35435699 PMCID: PMC9239241 DOI: 10.1128/mbio.00300-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Decapping enzymes remove the 5′ cap of eukaryotic mRNA, leading to accelerated RNA decay. They are critical in regulating RNA homeostasis and play essential roles in many cellular and life processes. They are encoded in many organisms and viruses, including vaccinia virus, which was used as the vaccine to eradicate smallpox. Vaccinia virus encodes two decapping enzymes, D9 and D10, that are necessary for efficient viral replication and pathogenesis. However, the underlying molecular mechanisms regulating vaccinia decapping enzymes’ functions are still largely elusive. Here, we demonstrated that vaccinia D10 almost exclusively colocalized with mitochondria. As mitochondria are highly mobile cellular organelles, colocalization of D10 with mitochondria can concentrate D10 locally and mobilize it to efficiently decap mRNAs. Mitochondria were barely observed in “viral factories,” where viral transcripts are produced, suggesting that mitochondrial colocalization provides a spatial mechanism to preferentially decap cellular mRNAs over viral mRNAs. We identified three amino acids at the N terminus of D10 that are required for D10’s mitochondrial colocalization. Loss of mitochondrial colocalization significantly impaired viral replication, reduced D10’s ability to remove the RNA 5′ cap during infection, and diminished D10’s gene expression shutoff and mRNA translation promotion abilities.
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Capera J, Navarro-Pérez M, Moen AS, Szabó I, Felipe A. The Mitochondrial Routing of the Kv1.3 Channel. Front Oncol 2022; 12:865686. [PMID: 35402277 PMCID: PMC8990977 DOI: 10.3389/fonc.2022.865686] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/02/2022] [Indexed: 12/19/2022] Open
Abstract
Voltage-gated potassium channels control neuronal excitability and cardiac action potentials. In addition, these proteins are involved in a myriad of cellular processes. The potassium channel Kv1.3 plays an essential role in the immune response mediated by leukocytes. Kv1.3 is functional both at the plasma membrane and the inner mitochondrial membrane. Plasma membrane Kv1.3 mediates cellular activation and proliferation, whereas mitochondrial Kv1.3 participates in cell survival and apoptosis. Therefore, this protein emerges as an important target in cancer therapies. Several forward-traffic motifs target the channel to the plasma membrane in a COPII-dependent manner. However, the mitochondrial import pathway for Kv1.3 is largely unknown. Here, we deciphered the mitochondrial routing of the mitoKv1.3 channel. Kv1.3 uses the TIM23 complex to translocate to the inner mitochondrial membrane. This mechanism is unconventional because the channel is a multimembrane spanning protein without a defined N-terminal presequence. We found that transmembrane domains cooperatively mediate Kv1.3 mitochondrial targeting and identified the cytosolic HSP70/HSP90 chaperone complex as a key regulator of the process. Our results provide insights into the mechanisms mediating the localization of Kv1.3 to mitochondrial membranes, further extending the knowledge of ion channel biogenesis and turnover in mitochondria.
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Affiliation(s)
- Jesusa Capera
- Molecular Physiology Laboratory, Dpt. de Bioquímica i Biomedicina Molecular, Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Spain.,Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom
| | - María Navarro-Pérez
- Molecular Physiology Laboratory, Dpt. de Bioquímica i Biomedicina Molecular, Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Spain
| | - Anne Stine Moen
- Molecular Physiology Laboratory, Dpt. de Bioquímica i Biomedicina Molecular, Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Spain
| | - Ildiko Szabó
- Department of Biology, University of Padova, Padova, Italy
| | - Antonio Felipe
- Molecular Physiology Laboratory, Dpt. de Bioquímica i Biomedicina Molecular, Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Spain
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Steady-State Levels of Miro1 Linked to Phosphorylation at Serine 156 and Mitochondrial Respiration in Dopaminergic Neurons. Cells 2022; 11:cells11081269. [PMID: 35455950 PMCID: PMC9032684 DOI: 10.3390/cells11081269] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/01/2022] [Accepted: 04/04/2022] [Indexed: 11/16/2022] Open
Abstract
Miro1 has emerged as an interesting target to study Parkinson’s disease-relevant pathways since it is a target of PINK1 and Parkin. Miro1 is a mitochondrial GTPase with the primary function of facilitating mitochondrial movement, and its knockout in mice is postnatally lethal. Here, we investigated the effect of the artificial RHOT1/Miro1 S156A mutation since it is a putative PINK1 phosphorylation site shown to be involved in Miro1 degradation and mitochondrial arrest during mitophagy. We gene-edited a homozygous phospho-null Miro1 S156A mutation in induced pluripotent stem cells to study the mutation in human dopaminergic neurons. This mutation causes a significant depletion of Miro1 steady-state protein levels and impairs further Miro1 degradation upon CCCP-induced mitophagy. However, mitochondrial mass measured by Tom20 protein levels, as well as mitochondrial area, are not affected in Miro1 S156A neurons. The mitochondria are slightly lengthened, which is in line with their increased turnover. Under basal conditions, we found no discernable effect of the mutation on mitochondrial movement in neurites. Interestingly, the S156A mutation leads to a significant reduction of mitochondrial oxygen consumption, which is accompanied by a depletion of OXPHOS complexes III and V. These effects are not mirrored by Miro1 knockdown in neuroblastoma cells, but they are observed upon differentiation. Undifferentiated Miro1 S156A neural precursor cells do not have decreased Miro1 levels nor OXPHOS complexes, suggesting that the effect of the mutation is tied to development. In mature dopaminergic neurons, the inhibition of Miro1 Ser156 phosphorylation elicits a mild loss of mitochondrial quality involving reduced mitochondrial membrane potential, which is sufficient to induce compensatory events involving OXPHOS. We suggest that the mechanism governing Miro1 steady-state levels depends on differentiation state and metabolic demand, thus underscoring the importance of this pathway in the pathobiology of Parkinson’s disease.
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Abstract
The brain is one of the most energetically demanding tissues in the human body, and mitochondrial pathology is strongly implicated in chronic neurodegenerative diseases. In contrast to acute brain injuries in which bioenergetics and cell death play dominant roles, studies modeling familial neurodegeneration implicate a more complex and nuanced relationship involving the entire mitochondrial life cycle. Recent literature on mitochondrial mechanisms in Parkinson's disease, Alzheimer's disease, frontotemporal dementia, Huntington's disease, and amyotrophic lateral sclerosis is reviewed with an emphasis on mitochondrial quality control, transport and synaptodendritic calcium homeostasis. Potential neuroprotective interventions include targeting the mitochondrial kinase PTEN-induced kinase 1 (PINK1), which plays a role in regulating not only multiple facets of mitochondrial biology, but also neuronal morphogenesis and dendritic arborization.
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Affiliation(s)
- Charleen T Chu
- Departments of Pathology and Ophthalmology, Pittsburgh Institute for Neurodegenerative Diseases, McGowan Institute for Regenerative Medicine, Center for Protein Conformational Diseases, Center for Neuroscience at the University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
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Cairrão F, Santos CC, Le Thomas A, Marsters S, Ashkenazi A, Domingos PM. Pumilio protects Xbp1 mRNA from regulated Ire1-dependent decay. Nat Commun 2022; 13:1587. [PMID: 35332141 PMCID: PMC8948244 DOI: 10.1038/s41467-022-29105-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 02/17/2022] [Indexed: 12/12/2022] Open
Abstract
The unfolded protein response (UPR) maintains homeostasis of the endoplasmic reticulum (ER). Residing in the ER membrane, the UPR mediator Ire1 deploys its cytoplasmic kinase-endoribonuclease domain to activate the key UPR transcription factor Xbp1 through non-conventional splicing of Xbp1 mRNA. Ire1 also degrades diverse ER-targeted mRNAs through regulated Ire1-dependent decay (RIDD), but how it spares Xbp1 mRNA from this decay is unknown. Here, we identify binding sites for the RNA-binding protein Pumilio in the 3'UTR Drosophila Xbp1. In the developing Drosophila eye, Pumilio binds both the Xbp1unspliced and Xbp1spliced mRNAs, but only Xbp1spliced is stabilized by Pumilio. Furthermore, Pumilio displays Ire1 kinase-dependent phosphorylation during ER stress, which is required for its stabilization of Xbp1spliced. hIRE1 can phosphorylate Pumilio directly, and phosphorylated Pumilio protects Xbp1spliced mRNA against RIDD. Thus, Ire1-mediated phosphorylation enables Pumilio to shield Xbp1spliced from RIDD. These results uncover an unexpected regulatory link between an RNA-binding protein and the UPR.
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Affiliation(s)
- Fátima Cairrão
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.
| | - Cristiana C Santos
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Adrien Le Thomas
- Cancer Immunology, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Scot Marsters
- Cancer Immunology, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Avi Ashkenazi
- Cancer Immunology, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Pedro M Domingos
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.
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Liu Q, Chang CE, Wooldredge AC, Fong B, Kennedy BK, Zhou C. Tom70-based transcriptional regulation of mitochondrial biogenesis and aging. eLife 2022; 11:e75658. [PMID: 35234609 PMCID: PMC8926401 DOI: 10.7554/elife.75658] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 03/01/2022] [Indexed: 11/13/2022] Open
Abstract
Mitochondrial biogenesis has two major steps: the transcriptional activation of nuclear genome-encoded mitochondrial proteins and the import of nascent mitochondrial proteins that are synthesized in the cytosol. These nascent mitochondrial proteins are aggregation-prone and can cause cytosolic proteostasis stress. The transcription factor-dependent transcriptional regulations and the TOM-TIM complex-dependent import of nascent mitochondrial proteins have been extensively studied. Yet, little is known regarding how these two steps of mitochondrial biogenesis coordinate with each other to avoid the cytosolic accumulation of these aggregation-prone nascent mitochondrial proteins. Here, we show that in budding yeast, Tom70, a conserved receptor of the TOM complex, moonlights to regulate the transcriptional activity of mitochondrial proteins. Tom70's transcription regulatory role is conserved in Drosophila. The dual roles of Tom70 in both transcription/biogenesis and import of mitochondrial proteins allow the cells to accomplish mitochondrial biogenesis without compromising cytosolic proteostasis. The age-related reduction of Tom70, caused by reduced biogenesis and increased degradation of Tom70, is associated with the loss of mitochondrial membrane potential, mtDNA, and mitochondrial proteins. While loss of Tom70 accelerates aging and age-related mitochondrial defects, overexpressing TOM70 delays these mitochondrial dysfunctions and extends the replicative lifespan. Our results reveal unexpected roles of Tom70 in mitochondrial biogenesis and aging.
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Affiliation(s)
- Qingqing Liu
- Buck Institute for Research on AgingNovatoUnited States
| | | | | | - Benjamin Fong
- Buck Institute for Research on AgingNovatoUnited States
| | - Brian K Kennedy
- Buck Institute for Research on AgingNovatoUnited States
- Healthy Longevity Programme, Yong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
- Centre for Healthy Longevity, National University Health SystemSingaporeSingapore
- Singapore Institute of Clinical Sciences, A(∗)STARSingaporeSingapore
| | - Chuankai Zhou
- Buck Institute for Research on AgingNovatoUnited States
- USC Leonard Davis School of Gerontology, University of Southern CaliforniaLos AngelesUnited States
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The potential inhibitory effect of ginsenoside Rh2 on mitophagy in UV-irradiated human dermal fibroblasts. J Ginseng Res 2022; 46:646-656. [PMID: 36090683 PMCID: PMC9459079 DOI: 10.1016/j.jgr.2022.02.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 01/27/2022] [Accepted: 02/03/2022] [Indexed: 11/30/2022] Open
Abstract
Background In addition to its use as a health food, ginseng is used in cosmetics and shampoo because of its extensive health benefits. The ginsenoside, Rh2, is a component of ginseng that inhibits tumor cell proliferation and differentiation, promotes insulin secretion, improves insulin sensitivity, and shows antioxidant effects. Methods The effects of Rh2 on cell survival, extracellular matrix (ECM) protein expression, and cell differentiation were examined. The antioxidant effects of Rh2 in UV-irradiated normal human dermal fibroblast (NHDF) cells were also examined. The effects of Rh2 on mitochondrial function, morphology, and mitophagy were investigated in UV-irradiated NHDF cells. Results Rh2 treatment promoted the proliferation of NHDF cells. Additionally, Rh2 increased the expression levels of ECM proteins and growth-associated immediate-early genes in ultraviolet (UV)-irradiated NHDF cells. Rh2 also affected antioxidant protein expression and increased total antioxidant capacity. Furthermore, treatment with Rh2 ameliorated the changes in mitochondrial morphology, induced the recovery of mitochondrial function, and inhibited the initiation of mitophagy in UV-irradiated NHDF cells. Conclusion Rh2 inhibits mitophagy and reinstates mitochondrial ATP production and membrane potential in NHDF cells damaged by UV exposure, leading to the recovery of ECM, cell proliferation, and antioxidant capacity.
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Xue J, Li G, Ji X, Liu ZH, Wang HL, Xiao G. Drosophila ZIP13 overexpression or transferrin1 RNAi influences the muscle degeneration of Pink1 RNAi by elevating iron levels in mitochondria. J Neurochem 2022; 160:540-555. [PMID: 35038358 DOI: 10.1111/jnc.15574] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 01/08/2022] [Accepted: 01/10/2022] [Indexed: 12/01/2022]
Abstract
Disruption of iron homeostasis in the brain of Parkinson's disease (PD) patients has been reported for many years, but the underlying mechanisms remain unclear. To investigate iron metabolism genes related to PTEN-induced kinase 1 (Pink1) and parkin (E3 ubiquitin ligase), two PD-associated proteins that function to coordinate mitochondrial turnover via induction of selective mitophagy, we conducted a genetic screen in Drosophila and found that altered expression of genes involved in iron metabolism, such as Drosophila ZIP13 (dZIP13) or transferrin1 (Tsf1), significantly influences the disease progression related to Pink1 but not parkin. Several phenotypes of Pink1 mutant and Pink1 RNAi but not parkin mutant were significantly rescued by overexpression (OE) of dZIP13 (dZIP13 OE) or silencing of Tsf1 (Tsf1 RNAi) in the flight muscles. The rescue effects of dZIP13 OE or Tsf1 RNAi were not exerted through mitochondrial disruption or mitophagy, instead, the iron levels in mitochondira were significantly increased, resulting in enhanced activity of enzymes participating in respiration and increased ATP synthesis. Consistently, the rescue effects of dZIP13 OE or Tsf1 RNAi on Pink1 RNAi can be inhibited by decreasing the iron levels in mitochondria through mitoferrin (dmfrn) RNAi. This study suggests that dZIP13, Tsf1 and dmfrn might act independently of parkin in a parallel pathway downstream of Pink1 by modulating respiration and indicates that manipulation of iron levels in mitochondria may provide a novel therapeutic strategy for PD associated with Pink1.
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Affiliation(s)
- Jinsong Xue
- Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes, College of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui, China
| | - Guangying Li
- Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes, College of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui, China
| | - Xiaowen Ji
- Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes, College of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui, China
| | - Zhi-Hua Liu
- Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes, College of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui, China
| | - Hui-Li Wang
- Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes, College of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui, China
| | - Guiran Xiao
- Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes, College of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui, China
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Hémono M, Haller A, Chicher J, Duchêne AM, Ngondo RP. The interactome of CLUH reveals its association to SPAG5 and its co-translational proximity to mitochondrial proteins. BMC Biol 2022; 20:13. [PMID: 35012549 PMCID: PMC8744257 DOI: 10.1186/s12915-021-01213-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 12/14/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Mitochondria require thousands of proteins to fulfill their essential function in energy production and other fundamental biological processes. These proteins are mostly encoded by the nuclear genome, translated in the cytoplasm before being imported into the organelle. RNA binding proteins (RBPs) are central players in the regulation of this process by affecting mRNA translation, stability, or localization. CLUH is an RBP recognizing specifically mRNAs coding for mitochondrial proteins, but its precise molecular function and interacting partners remain undiscovered in mammals. RESULTS Here we reveal for the first time CLUH interactome in mammalian cells. Using both co-IP and BioID proximity-labeling approaches, we identify novel molecular partners interacting stably or transiently with CLUH in HCT116 cells and mouse embryonic stem cells. We reveal stable RNA-independent interactions of CLUH with itself and with SPAG5 in cytosolic granular structures. More importantly, we uncover an unexpected proximity of CLUH to mitochondrial proteins and their cognate mRNAs in the cytosol. We show that this interaction occurs during the process of active translation and is dependent on CLUH TPR domain. CONCLUSIONS Overall, through the analysis of CLUH interactome, our study sheds a new light on CLUH molecular function by revealing new partners and by highlighting its link to the translation and subcellular localization of some mRNAs coding for mitochondrial proteins.
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Affiliation(s)
- Mickaële Hémono
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 12 rue du Général Zimmer, Strasbourg, 67084, France
| | - Alexandre Haller
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 12 rue du Général Zimmer, Strasbourg, 67084, France
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104, U 1258, 1 rue Laurent Fries, 67404, Illkirch, France
| | - Johana Chicher
- Plateforme protéomique Strasbourg Esplanade FR1589 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Anne-Marie Duchêne
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 12 rue du Général Zimmer, Strasbourg, 67084, France
| | - Richard Patryk Ngondo
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 12 rue du Général Zimmer, Strasbourg, 67084, France.
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Gasparski AN, Mason DE, Moissoglu K, Mili S. Regulation and outcomes of localized RNA translation. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1721. [PMID: 35166036 PMCID: PMC9787767 DOI: 10.1002/wrna.1721] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/18/2022] [Accepted: 01/22/2022] [Indexed: 12/31/2022]
Abstract
Spatial segregation of mRNAs in the cytoplasm of cells is a well-known biological phenomenon that is widely observed in diverse species spanning different kingdoms of life. In mammalian cells, localization of mRNAs has been documented and studied quite extensively in highly polarized cells, most notably in neurons, where localized mRNAs function to direct protein production at sites that are quite distant from the soma. Recent studies have strikingly revealed that a large proportion of the cellular transcriptome exhibits polarized distributions even in cells that lack an obvious need for long-range transport, such as fibroblasts or epithelial cells. This review focuses on emerging concepts regarding the functional outcomes of mRNA targeting in the cytoplasm of such cells. We also discuss regulatory mechanisms controlling these events, with an emphasis on the role of cell mechanics and the organization of the cytoskeleton. This article is categorized under: Translation > Regulation RNA Export and Localization > RNA Localization.
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Affiliation(s)
- Alexander N. Gasparski
- Laboratory of Cellular and Molecular Biology, Center for Cancer ResearchNational Cancer Institute, NIHBethesdaMarylandUSA
| | - Devon E. Mason
- Laboratory of Cellular and Molecular Biology, Center for Cancer ResearchNational Cancer Institute, NIHBethesdaMarylandUSA
| | - Konstadinos Moissoglu
- Laboratory of Cellular and Molecular Biology, Center for Cancer ResearchNational Cancer Institute, NIHBethesdaMarylandUSA
| | - Stavroula Mili
- Laboratory of Cellular and Molecular Biology, Center for Cancer ResearchNational Cancer Institute, NIHBethesdaMarylandUSA
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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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