1
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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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2
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Ma J, Dong D, Qi H, Li J, Yu H, Hu X, Sun L, Shen L. LARP1, an RNA-binding protein, participates in ovarian cancer cell survival by regulating mitochondrial oxidative phosphorylation in response to the influence of the PI3K/mTOR pathway. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167453. [PMID: 39111634 DOI: 10.1016/j.bbadis.2024.167453] [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: 12/07/2023] [Revised: 07/31/2024] [Accepted: 07/31/2024] [Indexed: 08/15/2024]
Abstract
Targeting the PI3K/mTOR pathway and modulating mitochondrial adaptation is expected to be a critical approach for cancer therapy. Although the regulation of mitochondria by the PI3K/mTOR pathway has been investigated, it is not well understood due to the complexity of its regulatory mechanisms. RNA-binding proteins (RBPs) selectively regulate gene expression through post-transcriptional modulation, playing a key role in cancer progression. LARP1, a downstream RBP of the mTOR pathway, is involved in mitochondria-mediated BCL-2 cell survival. Therefore, exploring the involvement of LARP1 in PI3K/mTOR-mediated translational regulation of mitochondria-associated proteins in ovarian cancer cells could help elucidate the role of mitochondria in the PI3K/mTOR pathway. We found that, unlike SKOV3 cells, the mitochondrial function of A2780 cells was not affected, which were insensitive to the dual PI3K/mTOR inhibitor PKI-402, suggesting that cell survival may be related to mitochondrial function. Knockdown of the LARP1 gene after PKI-402 treatment resulted in impaired mitochondrial function in A2780 cells, possibly due to decreased mRNA stability and reduced protein translation of the mitochondrial transcription initiation factor, TFB2M, and the respiratory chain complex II subunit, SDHB. LARP1 affects protein translation by binding to TFB2M mRNA, regulating mitochondrial DNA-encoded genes, or indirectly regulating the nuclear DNA-encoded SDHB gene, ultimately interfering with mitochondrial oxidative phosphorylation and leading to apoptosis. Therefore, LARP1 may be an important mediator in the PI3K/mTOR pathway for regulating mRNA translation and mitochondrial function. Targeting RBPs such as LARP1 downstream of the mTOR pathway may provide new insights and potential therapeutic approaches for ovarian cancer treatment.
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Affiliation(s)
- Jiaoyan Ma
- Key Laboratory of Pathobiology, Department of Pathophysiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Delu Dong
- Key Laboratory of Pathobiology, Department of Pathophysiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Hang Qi
- Key Laboratory of Pathobiology, Department of Pathophysiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Jiaxin Li
- Key Laboratory of Pathobiology, Department of Pathophysiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Huimei Yu
- Key Laboratory of Pathobiology, Department of Pathophysiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Xiaoqing Hu
- The First Bethune Hospital of Jilin University, Changchun 130021, China
| | - Liankun Sun
- Key Laboratory of Pathobiology, Department of Pathophysiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun 130021, China.
| | - Luyan Shen
- Key Laboratory of Pathobiology, Department of Pathophysiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun 130021, China.
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3
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Ahola S, Pazurek LA, Mayer F, Lampe P, Hermans S, Becker L, Amarie OV, Fuchs H, Gailus-Durner V, de Angelis MH, Riedel D, Nolte H, Langer T. Opa1 processing is dispensable in mouse development but is protective in mitochondrial cardiomyopathy. SCIENCE ADVANCES 2024; 10:eadp0443. [PMID: 39093974 PMCID: PMC11296347 DOI: 10.1126/sciadv.adp0443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 06/28/2024] [Indexed: 08/04/2024]
Abstract
Mitochondrial fusion and fission accompany adaptive responses to stress and altered metabolic demands. Inner membrane fusion and cristae morphogenesis depends on optic atrophy 1 (Opa1), which is expressed in different isoforms and is cleaved from a membrane-bound, long to a soluble, short form. Here, we have analyzed the physiological role of Opa1 isoforms and Opa1 processing by generating mouse lines expressing only one cleavable Opa1 isoform or a non-cleavable variant thereof. Our results show that expression of a single cleavable or non-cleavable Opa1 isoform preserves embryonic development and the health of adult mice. Opa1 processing is dispensable under metabolic and thermal stress but prolongs life span and protects against mitochondrial cardiomyopathy in OXPHOS-deficient Cox10-/- mice. Mechanistically, loss of Opa1 processing disturbs the balance between mitochondrial biogenesis and mitophagy, suppressing cardiac hypertrophic growth in Cox10-/- hearts. Our results highlight the critical regulatory role of Opa1 processing, mitochondrial dynamics, and metabolism for cardiac hypertrophy.
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Affiliation(s)
- Sofia Ahola
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | | | - Fiona Mayer
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Philipp Lampe
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Steffen Hermans
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Lore Becker
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Oana V Amarie
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Helmut Fuchs
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Valerie Gailus-Durner
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Martin Hrabe de Angelis
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Experimental Genetics, TUM School of Life Sciences, Technische Universität München, Freising, Germany
- German Center for Diabetes Research (DZD), 85764 Neuherberg
| | - Dietmar Riedel
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Hendrik Nolte
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Thomas Langer
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
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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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Zaninello M, Schlegel T, Nolte H, Pirzada M, Savino E, Barth E, Klein I, Wüstenberg H, Uddin T, Wolff L, Wirth B, Lehmann HC, Cioni JM, Langer T, Rugarli EI. CLUH maintains functional mitochondria and translation in motoneuronal axons and prevents peripheral neuropathy. SCIENCE ADVANCES 2024; 10:eadn2050. [PMID: 38809982 PMCID: PMC11135423 DOI: 10.1126/sciadv.adn2050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 04/24/2024] [Indexed: 05/31/2024]
Abstract
Transporting and translating mRNAs in axons is crucial for neuronal viability. Local synthesis of nuclear-encoded mitochondrial proteins protects long-lived axonal mitochondria from damage; however, the regulatory factors involved are largely unknown. We show that CLUH, which binds mRNAs encoding mitochondrial proteins, prevents peripheral neuropathy and motor deficits in the mouse. CLUH is enriched in the growth cone of developing spinal motoneurons and is required for their growth. The lack of CLUH affects the abundance of target mRNAs and the corresponding mitochondrial proteins more prominently in axons, leading to ATP deficits in the growth cone. CLUH interacts with ribosomal subunits, translation initiation, and ribosome recycling components and preserves axonal translation. Overexpression of the ribosome recycling factor ABCE1 rescues the mRNA and translation defects, as well as the growth cone size, in CLUH-deficient motoneurons. Thus, we demonstrate a role for CLUH in mitochondrial quality control and translational regulation in axons, which is essential for their development and long-term integrity and function.
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Affiliation(s)
- Marta Zaninello
- Institute for Genetics, University of Cologne, Cologne 50931, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne 50931, Germany
| | - Tim Schlegel
- Institute for Genetics, University of Cologne, Cologne 50931, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne 50931, Germany
| | - Hendrik Nolte
- Max Planck Institute for Biology of Ageing, Cologne 50931, Germany
| | - Mujeeb Pirzada
- Institute for Genetics, University of Cologne, Cologne 50931, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne 50931, Germany
| | - Elisa Savino
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Esther Barth
- Institute for Genetics, University of Cologne, Cologne 50931, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne 50931, Germany
| | - Ines Klein
- Department of Neurology, University of Cologne, Cologne 50931, Germany
| | - Hauke Wüstenberg
- Department of Neurology, University of Cologne, Cologne 50931, Germany
| | - Tesmin Uddin
- Institute for Genetics, University of Cologne, Cologne 50931, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne 50931, Germany
| | - Lisa Wolff
- Institute of Human Genetics, University of Cologne, Cologne 50931, Germany
| | - Brunhilde Wirth
- Institute for Genetics, University of Cologne, Cologne 50931, Germany
- Institute of Human Genetics, University of Cologne, Cologne 50931, Germany
- Center for Molecular Medicine (CMMC), University of Cologne, Cologne 50931, Germany
- Center for Rare Diseases Cologne (CESEK), University Hospital of Cologne, Cologne 50937, Germany
| | - Helmar C. Lehmann
- Department of Neurology, University of Cologne, Cologne 50931, Germany
| | - Jean-Michel Cioni
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Thomas Langer
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne 50931, Germany
- Max Planck Institute for Biology of Ageing, Cologne 50931, Germany
| | - Elena I. Rugarli
- Institute for Genetics, University of Cologne, Cologne 50931, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne 50931, Germany
- Center for Molecular Medicine (CMMC), University of Cologne, Cologne 50931, Germany
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6
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Suomalainen A, Nunnari J. Mitochondria at the crossroads of health and disease. Cell 2024; 187:2601-2627. [PMID: 38788685 DOI: 10.1016/j.cell.2024.04.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024]
Abstract
Mitochondria reside at the crossroads of catabolic and anabolic metabolism-the essence of life. How their structure and function are dynamically tuned in response to tissue-specific needs for energy, growth repair, and renewal is being increasingly understood. Mitochondria respond to intrinsic and extrinsic stresses and can alter cell and organismal function by inducing metabolic signaling within cells and to distal cells and tissues. Here, we review how the centrality of mitochondrial functions manifests in health and a broad spectrum of diseases and aging.
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Affiliation(s)
- Anu Suomalainen
- University of Helsinki, Stem Cells and Metabolism Program, Faculty of Medicine, Helsinki, Finland; HiLife, University of Helsinki, Helsinki, Finland; HUS Diagnostics, Helsinki University Hospital, Helsinki, Finland.
| | - Jodi Nunnari
- Altos Labs, Bay Area Institute, Redwood Shores, CA, USA.
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7
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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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8
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Schneider KL, Hao X, Keuenhof KS, Berglund LL, Fischbach A, Ahmadpour D, Chawla S, Gómez P, Höög JL, Widlund PO, Nyström T. Elimination of virus-like particles reduces protein aggregation and extends replicative lifespan in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 2024; 121:e2313538121. [PMID: 38527193 PMCID: PMC10998562 DOI: 10.1073/pnas.2313538121] [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: 08/07/2023] [Accepted: 02/04/2024] [Indexed: 03/27/2024] Open
Abstract
A major consequence of aging and stress, in yeast to humans, is an increased accumulation of protein aggregates at distinct sites within the cells. Using genetic screens, immunoelectron microscopy, and three-dimensional modeling in our efforts to elucidate the importance of aggregate annexation, we found that most aggregates in yeast accumulate near the surface of mitochondria. Further, we show that virus-like particles (VLPs), which are part of the retrotransposition cycle of Ty elements, are markedly enriched in these sites of protein aggregation. RNA interference-mediated silencing of Ty expression perturbed aggregate sequestration to mitochondria, reduced overall protein aggregation, mitigated toxicity of a Huntington's disease model, and expanded the replicative lifespan of yeast in a partially Hsp104-dependent manner. The results are in line with recent data demonstrating that VLPs might act as aging factors in mammals, including humans, and extend these findings by linking VLPs to a toxic accumulation of protein aggregates and raising the possibility that they might negatively influence neurological disease progression.
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Affiliation(s)
- K. L. Schneider
- Department of Microbiology and Immunology, Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health—AgeCap, University of Gothenburg, Gothenburg40530, Sweden
| | - X. Hao
- Department of Microbiology and Immunology, Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health—AgeCap, University of Gothenburg, Gothenburg40530, Sweden
| | - K. S. Keuenhof
- Department for Chemistry and Molecular Biology, University of Gothenburg, Gothenburg41390, Sweden
| | - L. L. Berglund
- Department for Chemistry and Molecular Biology, University of Gothenburg, Gothenburg41390, Sweden
| | - A. Fischbach
- Department of Microbiology and Immunology, Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health—AgeCap, University of Gothenburg, Gothenburg40530, Sweden
| | - D. Ahmadpour
- Department of Microbiology and Immunology, Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health—AgeCap, University of Gothenburg, Gothenburg40530, Sweden
| | - S. Chawla
- Department of Microbiology and Immunology, Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health—AgeCap, University of Gothenburg, Gothenburg40530, Sweden
| | - P. Gómez
- Department of Microbiology and Immunology, Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health—AgeCap, University of Gothenburg, Gothenburg40530, Sweden
| | - J. L. Höög
- Department for Chemistry and Molecular Biology, University of Gothenburg, Gothenburg41390, Sweden
| | - P. O. Widlund
- Department of Microbiology and Immunology, Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health—AgeCap, University of Gothenburg, Gothenburg40530, Sweden
| | - T. Nyström
- Department of Microbiology and Immunology, Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health—AgeCap, University of Gothenburg, Gothenburg40530, Sweden
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9
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Zhou Y, Ray PS, Zhu J, Stein F, Rettel M, Sekaran T, Sahadevan S, Perez-Perri JI, Roth EK, Myklebost O, Meza-Zepeda LA, von Deimling A, Fu C, Brosig AN, Boye K, Nathrath M, Blattmann C, Lehner B, Hentze MW, Kulozik AE. Systematic analysis of RNA-binding proteins identifies targetable therapeutic vulnerabilities in osteosarcoma. Nat Commun 2024; 15:2810. [PMID: 38561347 PMCID: PMC10984982 DOI: 10.1038/s41467-024-47031-y] [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: 01/29/2023] [Accepted: 03/18/2024] [Indexed: 04/04/2024] Open
Abstract
Osteosarcoma is the most common primary malignant bone tumor with a strong tendency to metastasize, limiting the prognosis of affected patients. Genomic, epigenomic and transcriptomic analyses have demonstrated the exquisite molecular complexity of this tumor, but have not sufficiently defined the underlying mechanisms or identified promising therapeutic targets. To systematically explore RNA-protein interactions relevant to OS, we define the RNA interactomes together with the full proteome and the transcriptome of cells from five malignant bone tumors (four osteosarcomata and one malignant giant cell tumor of the bone) and from normal mesenchymal stem cells and osteoblasts. These analyses uncover both systematic changes of the RNA-binding activities of defined RNA-binding proteins common to all osteosarcomata and individual alterations that are observed in only a subset of tumors. Functional analyses reveal a particular vulnerability of these tumors to translation inhibition and a positive feedback loop involving the RBP IGF2BP3 and the transcription factor Myc which affects cellular translation and OS cell viability. Our results thus provide insight into potentially clinically relevant RNA-binding protein-dependent mechanisms of osteosarcoma.
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Affiliation(s)
- Yang Zhou
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University and European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Partho Sarothi Ray
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University and European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Jianguo Zhu
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Frank Stein
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Mandy Rettel
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | - Sudeep Sahadevan
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | - Eva K Roth
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University and European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Ola Myklebost
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Leonardo A Meza-Zepeda
- Genomics Core Facility, Department of Core Facilities, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
| | - Chuli Fu
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Annika N Brosig
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University and European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Kjetil Boye
- Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Michaela Nathrath
- Department of Pediatrics and Children's Cancer Research Center, Technical University of Munich, School of Medicine, Munich, Germany
- Pediatric Hematology and Oncology, Klinikum Kassel, Kassel, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Olga Hospital, Stuttgart, Germany
| | - Claudia Blattmann
- Department of Pediatric Oncology, Hematology and Immunology, Olga Hospital, Stuttgart, Germany
| | - Burkhard Lehner
- Department of Orthopaedics, Trauma Surgery and Paraplegiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Matthias W Hentze
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University and European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
| | - Andreas E Kulozik
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University and European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany.
- Clinical Cooperation Unit Pediatric Leukemia, German Cancer Research Center (DKFZ) and Heidelberg University, Heidelberg, Germany.
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10
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Chakrabarty Y, Yang Z, Chen H, Chan DC. The HRI branch of the integrated stress response selectively triggers mitophagy. Mol Cell 2024; 84:1090-1100.e6. [PMID: 38340717 PMCID: PMC11062084 DOI: 10.1016/j.molcel.2024.01.016] [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: 12/16/2022] [Revised: 08/31/2023] [Accepted: 01/18/2024] [Indexed: 02/12/2024]
Abstract
To maintain mitochondrial homeostasis, damaged or excessive mitochondria are culled in coordination with the physiological state of the cell. The integrated stress response (ISR) is a signaling network that recognizes diverse cellular stresses, including mitochondrial dysfunction. Because the four ISR branches converge to common outputs, it is unclear whether mitochondrial stress detected by this network can regulate mitophagy, the autophagic degradation of mitochondria. Using a whole-genome screen, we show that the heme-regulated inhibitor (HRI) branch of the ISR selectively induces mitophagy. Activation of the HRI branch results in mitochondrial localization of phosphorylated eukaryotic initiation factor 2, which we show is sufficient to induce mitophagy. The HRI mitophagy pathway operates in parallel with the mitophagy pathway controlled by the Parkinson's disease related genes PINK1 and PARKIN and is mechanistically distinct. Therefore, HRI repurposes machinery that is normally used for translational initiation to trigger mitophagy in response to mitochondrial damage.
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Affiliation(s)
- Yogaditya Chakrabarty
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Zheng Yang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Hsiuchen Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - David C Chan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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11
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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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12
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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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13
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Ng AQE, Chan SN, Pek JW. Nutrient-dependent regulation of a stable intron modulates germline mitochondrial quality control. Nat Commun 2024; 15:1252. [PMID: 38341415 PMCID: PMC10858910 DOI: 10.1038/s41467-024-45651-y] [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: 02/08/2023] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
Mitochondria are inherited exclusively from the mothers and are required for the proper development of embryos. Hence, germline mitochondrial quality is highly regulated during oogenesis to ensure oocyte viability. How nutrient availability influences germline mitochondrial quality control is unclear. Here we find that fasting leads to the accumulation of mitochondrial clumps and oogenesis arrest in Drosophila. Fasting induces the downregulation of the DIP1-Clueless pathway, leading to an increase in the expression of a stable intronic sequence RNA called sisR-1. Mechanistically, sisR-1 localizes to the mitochondrial clumps to inhibit the poly-ubiquitination of the outer mitochondrial protein Porin/VDAC1, thereby suppressing p62-mediated mitophagy. Alleviation of the fasting-induced high sisR-1 levels by either sisR-1 RNAi or refeeding leads to mitophagy, the resumption of oogenesis and an improvement in oocyte quality. Thus, our study provides a possible mechanism by which fasting can improve oocyte quality by modulating the mitochondrial quality control pathway. Of note, we uncover that the sisR-1 response also regulates mitochondrial clumping and oogenesis during protein deprivation, heat shock and aging, suggesting a broader role for this mechanism in germline mitochondrial quality control.
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Affiliation(s)
- Annabel Qi En Ng
- Temasek Life Sciences Laboratory, 1 Research Link National University of Singapore, Singapore, 117604, Singapore
| | - Seow Neng Chan
- Temasek Life Sciences Laboratory, 1 Research Link National University of Singapore, Singapore, 117604, Singapore
| | - Jun Wei Pek
- Temasek Life Sciences Laboratory, 1 Research Link National University of Singapore, Singapore, 117604, Singapore.
- Department of Biological Sciences, National University of Singapore, 14 Science Drive, Singapore, 117543, Singapore.
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14
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Miano M, Bertola N, Grossi A, Dell’Orso G, Regis S, Rusmini M, Uva P, Vozzi D, Fioredda F, Palmisani E, Lupia M, Lanciotti M, Grilli F, Corsolini F, Arcuri L, Giarratana MC, Ceccherini I, Dufour C, Cappelli E, Ravera S. Impaired Mitochondrial Function and Marrow Failure in Patients Carrying a Variant of the SRSF4 Gene. Int J Mol Sci 2024; 25:2083. [PMID: 38396760 PMCID: PMC10888539 DOI: 10.3390/ijms25042083] [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: 12/12/2023] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Serine/arginine-rich splicing factors (SRSFs) are a family of proteins involved in RNA metabolism, including pre-mRNA constitutive and alternative splicing. The role of SRSF proteins in regulating mitochondrial activity has already been shown for SRSF6, but SRSF4 altered expression has never been reported as a cause of bone marrow failure. An 8-year-old patient admitted to the hematology unit because of leukopenia, lymphopenia, and neutropenia showed a missense variant of unknown significance of the SRSF4 gene (p.R235W) found via whole genome sequencing analysis and inherited from the mother who suffered from mild leuko-neutropenia. Both patients showed lower SRSF4 protein expression and altered mitochondrial function and energetic metabolism in primary lymphocytes and Epstein-Barr-virus (EBV)-immortalized lymphoblasts compared to healthy donor (HD) cells, which appeared associated with low mTOR phosphorylation and an imbalance in the proteins regulating mitochondrial biogenesis (i.e., CLUH) and dynamics (i.e., DRP1 and OPA1). Transfection with the wtSRSF4 gene restored mitochondrial function. In conclusion, this study shows that the described variant of the SRSF4 gene is pathogenetic and causes reduced SRSF4 protein expression, which leads to mitochondrial dysfunction. Since mitochondrial function is crucial for hematopoietic stem cell maintenance and some genetic bone marrow failure syndromes display mitochondrial defects, the SRSF4 mutation could have substantially contributed to the clinical phenotype of our patient.
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Affiliation(s)
- Maurizio Miano
- Haematology Unit, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (M.M.); (G.D.); (F.F.); (E.P.); (M.L.); (M.L.); (F.G.); (L.A.); (M.C.G.); (C.D.)
| | - Nadia Bertola
- Molecular Pathology Unit, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy;
| | - Alice Grossi
- Laboratory of Genetics and Genomics of Rare Diseases, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (A.G.); (M.R.); (I.C.)
| | - Gianluca Dell’Orso
- Haematology Unit, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (M.M.); (G.D.); (F.F.); (E.P.); (M.L.); (M.L.); (F.G.); (L.A.); (M.C.G.); (C.D.)
| | - Stefano Regis
- Laboratory of Clinical and Experimental Immunology, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy;
| | - Marta Rusmini
- Laboratory of Genetics and Genomics of Rare Diseases, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (A.G.); (M.R.); (I.C.)
| | - Paolo Uva
- Clinical Bioinformatics Unit, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy;
| | - Diego Vozzi
- Genomics Facility, Istituto Italiano di Tecnologia (IIT), 16163 Genoa, Italy;
| | - Francesca Fioredda
- Haematology Unit, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (M.M.); (G.D.); (F.F.); (E.P.); (M.L.); (M.L.); (F.G.); (L.A.); (M.C.G.); (C.D.)
| | - Elena Palmisani
- Haematology Unit, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (M.M.); (G.D.); (F.F.); (E.P.); (M.L.); (M.L.); (F.G.); (L.A.); (M.C.G.); (C.D.)
| | - Michela Lupia
- Haematology Unit, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (M.M.); (G.D.); (F.F.); (E.P.); (M.L.); (M.L.); (F.G.); (L.A.); (M.C.G.); (C.D.)
| | - Marina Lanciotti
- Haematology Unit, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (M.M.); (G.D.); (F.F.); (E.P.); (M.L.); (M.L.); (F.G.); (L.A.); (M.C.G.); (C.D.)
| | - Federica Grilli
- Haematology Unit, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (M.M.); (G.D.); (F.F.); (E.P.); (M.L.); (M.L.); (F.G.); (L.A.); (M.C.G.); (C.D.)
| | - Fabio Corsolini
- Laboratory for the Study of Inborn Errors of Metabolism (LABSIEM), Pediatric Clinic and Endocrinology, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy;
| | - Luca Arcuri
- Haematology Unit, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (M.M.); (G.D.); (F.F.); (E.P.); (M.L.); (M.L.); (F.G.); (L.A.); (M.C.G.); (C.D.)
| | - Maria Carla Giarratana
- Haematology Unit, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (M.M.); (G.D.); (F.F.); (E.P.); (M.L.); (M.L.); (F.G.); (L.A.); (M.C.G.); (C.D.)
| | - Isabella Ceccherini
- Laboratory of Genetics and Genomics of Rare Diseases, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (A.G.); (M.R.); (I.C.)
| | - Carlo Dufour
- Haematology Unit, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (M.M.); (G.D.); (F.F.); (E.P.); (M.L.); (M.L.); (F.G.); (L.A.); (M.C.G.); (C.D.)
| | - Enrico Cappelli
- Haematology Unit, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (M.M.); (G.D.); (F.F.); (E.P.); (M.L.); (M.L.); (F.G.); (L.A.); (M.C.G.); (C.D.)
| | - Silvia Ravera
- Department of Experimental Medicine, University of Genoa, 16132 Genoa, Italy;
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15
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Baker ZN, Forny P, Pagliarini DJ. Mitochondrial proteome research: the road ahead. Nat Rev Mol Cell Biol 2024; 25:65-82. [PMID: 37773518 DOI: 10.1038/s41580-023-00650-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2023] [Indexed: 10/01/2023]
Abstract
Mitochondria are multifaceted organelles with key roles in anabolic and catabolic metabolism, bioenergetics, cellular signalling and nutrient sensing, and programmed cell death processes. Their diverse functions are enabled by a sophisticated set of protein components encoded by the nuclear and mitochondrial genomes. The extent and complexity of the mitochondrial proteome remained unclear for decades. This began to change 20 years ago when, driven by the emergence of mass spectrometry-based proteomics, the first draft mitochondrial proteomes were established. In the ensuing decades, further technological and computational advances helped to refine these 'maps', with current estimates of the core mammalian mitochondrial proteome ranging from 1,000 to 1,500 proteins. The creation of these compendia provided a systemic view of an organelle previously studied primarily in a reductionist fashion and has accelerated both basic scientific discovery and the diagnosis and treatment of human disease. Yet numerous challenges remain in understanding mitochondrial biology and translating this knowledge into the medical context. In this Roadmap, we propose a path forward for refining the mitochondrial protein map to enhance its discovery and therapeutic potential. We discuss how emerging technologies can assist the detection of new mitochondrial proteins, reveal their patterns of expression across diverse tissues and cell types, and provide key information on proteoforms. We highlight the power of an enhanced map for systematically defining the functions of its members. Finally, we examine the utility of an expanded, functionally annotated mitochondrial proteome in a translational setting for aiding both diagnosis of mitochondrial disease and targeting of mitochondria for treatment.
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Affiliation(s)
- Zakery N Baker
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Patrick Forny
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
| | - David J Pagliarini
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
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16
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Singh S, Gaur A, Sharma RK, Kumari R, Prakash S, Kumari S, Chaudhary AD, Prasun P, Pant P, Hunkler H, Thum T, Jagavelu K, Bharati P, Hanif K, Chitkara P, Kumar S, Mitra K, Gupta SK. Musashi-2 causes cardiac hypertrophy and heart failure by inducing mitochondrial dysfunction through destabilizing Cluh and Smyd1 mRNA. Basic Res Cardiol 2023; 118:46. [PMID: 37923788 DOI: 10.1007/s00395-023-01016-y] [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: 03/03/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 11/06/2023]
Abstract
Regulation of RNA stability and translation by RNA-binding proteins (RBPs) is a crucial process altering gene expression. Musashi family of RBPs comprising Msi1 and Msi2 is known to control RNA stability and translation. However, despite the presence of MSI2 in the heart, its function remains largely unknown. Here, we aim to explore the cardiac functions of MSI2. We confirmed the presence of MSI2 in the adult mouse, rat heart, and neonatal rat cardiomyocytes. Furthermore, Msi2 was significantly enriched in the heart cardiomyocyte fraction. Next, using RNA-seq data and isoform-specific PCR primers, we identified Msi2 isoforms 1, 4, and 5, and two novel putative isoforms labeled as Msi2 6 and 7 to be expressed in the heart. Overexpression of Msi2 isoforms led to cardiac hypertrophy in cultured cardiomyocytes. Additionally, Msi2 exhibited a significant increase in a pressure-overload model of cardiac hypertrophy. We selected isoforms 4 and 7 to validate the hypertrophic effects due to their unique alternative splicing patterns. AAV9-mediated overexpression of Msi2 isoforms 4 and 7 in murine hearts led to cardiac hypertrophy, dilation, heart failure, and eventually early death, confirming a pathological function for Msi2. Using global proteomics, gene ontology, transmission electron microscopy, seahorse, and transmembrane potential measurement assays, increased MSI2 was found to cause mitochondrial dysfunction in the heart. Mechanistically, we identified Cluh and Smyd1 as direct downstream targets of Msi2. Overexpression of Cluh and Smyd1 inhibited Msi2-induced cardiac malfunction and mitochondrial dysfunction. Collectively, we show that Msi2 induces hypertrophy, mitochondrial dysfunction, and heart failure.
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Affiliation(s)
- Sandhya Singh
- Pharmacology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Lucknow, India, 226031
| | - Aakash Gaur
- Pharmacology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Lucknow, India, 226031
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Rakesh Kumar Sharma
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Division of Sophisticated Analytical Instrument Facility and Research, CSIR-Central Drug Research Institute, Lucknow, India
| | - Renu Kumari
- Pharmacology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Lucknow, India, 226031
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Shakti Prakash
- Pharmacology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Lucknow, India, 226031
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sunaina Kumari
- Pharmacology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Lucknow, India, 226031
| | - Ayushi Devendrasingh Chaudhary
- Pharmacology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Lucknow, India, 226031
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Pankaj Prasun
- Pharmacology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Lucknow, India, 226031
| | - Priyanka Pant
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Hannah Hunkler
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Hannover, Germany
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Hannover, Germany
- Fraunhofer Institute of Toxicology and Experimental Medicine, Hannover, Germany
| | - Kumaravelu Jagavelu
- Pharmacology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Lucknow, India, 226031
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Pragya Bharati
- Pharmacology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Lucknow, India, 226031
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Kashif Hanif
- Pharmacology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Lucknow, India, 226031
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Pragya Chitkara
- National Institute of Plant Genome Research, New Delhi, India
| | - Shailesh Kumar
- National Institute of Plant Genome Research, New Delhi, India
| | - Kalyan Mitra
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Division of Sophisticated Analytical Instrument Facility and Research, CSIR-Central Drug Research Institute, Lucknow, India
| | - Shashi Kumar Gupta
- Pharmacology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Lucknow, India, 226031.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
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17
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Roy S, Roy S, Mahata B, Pramanik J, Hennrich ML, Gavin AC, Teichmann SA. CLICK-chemoproteomics and molecular dynamics simulation reveals pregnenolone targets and their binding conformations in Th2 cells. Front Immunol 2023; 14:1229703. [PMID: 38022565 PMCID: PMC10644475 DOI: 10.3389/fimmu.2023.1229703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 10/05/2023] [Indexed: 12/01/2023] Open
Abstract
Pregnenolone (P5) is synthesized as the first bioactive steroid in the mitochondria from cholesterol. Clusters of differentiation 4 (CD4+) and Clusters of differentiation 8 (CD8+) immune cells synthesize P5 de novo; P5, in turn, play important role in immune homeostasis and regulation. However, P5's biochemical mode of action in immune cells is still emerging. We envisage that revealing the complete spectrum of P5 target proteins in immune cells would have multifold applications, not only in basic understanding of steroids biochemistry in immune cells but also in developing new therapeutic applications. We employed a CLICK-enabled probe to capture P5-binding proteins in live T helper cell type 2 (Th2) cells. Subsequently, using high-throughput quantitative proteomics, we identified the P5 interactome in CD4+ Th2 cells. Our study revealed P5's mode of action in CD4+ immune cells. We identified novel proteins from mitochondrial and endoplasmic reticulum membranes to be the primary mediators of P5's biochemistry in CD4+ and to concur with our earlier finding in CD8+ immune cells. Applying advanced computational algorithms and molecular simulations, we were able to generate near-native maps of P5-protein key molecular interactions. We showed bonds and interactions between key amino acids and P5, which revealed the importance of ionic bond, hydrophobic interactions, and water channels. We point out that our results can lead to designing of novel molecular therapeutics strategies.
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Affiliation(s)
- Sougata Roy
- Department of Biology, Ashoka University, Rajiv Gandhi Education City, Sonipat, Haryana, India
| | - Sudeep Roy
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czechia
| | - Bidesh Mahata
- Division of Immunology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Jhuma Pramanik
- Division of Immunology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Marco L. Hennrich
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, EMBL, Heidelberg, Germany
- Cellzome, a GlaxoSmithKline (GSK) company, Genomic Sciences, Pharma R&D, Heidelberg, Germany
| | - Anne-Claude Gavin
- Department for Cell Physiology and Metabolism, Centre Medical Universitaire, University of Geneva, Geneva, Switzerland
- Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Sarah A. Teichmann
- Cellular Genetics, Wellcome Sanger Institute, Cambridge, United Kingdom
- Theory of Condensed Matter, Cavendish Laboratory, Cambridge, United Kingdom
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18
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Avolio R, Agliarulo I, Criscuolo D, Sarnataro D, Auriemma M, De Lella S, Pennacchio S, Calice G, Ng MY, Giorgi C, Pinton P, Cooperman BS, Landriscina M, Esposito F, Matassa DS. Cytosolic and mitochondrial translation elongation are coordinated through the molecular chaperone TRAP1 for the synthesis and import of mitochondrial proteins. Genome Res 2023; 33:1242-1257. [PMID: 37487647 PMCID: PMC10547376 DOI: 10.1101/gr.277755.123] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 07/19/2023] [Indexed: 07/26/2023]
Abstract
A complex interplay between mRNA translation and cellular respiration has been recently unveiled, but its regulation in humans is poorly characterized in either health or disease. Cancer cells radically reshape both biosynthetic and bioenergetic pathways to sustain their aberrant growth rates. In this regard, we have shown that the molecular chaperone TRAP1 not only regulates the activity of respiratory complexes, behaving alternatively as an oncogene or a tumor suppressor, but also plays a concomitant moonlighting function in mRNA translation regulation. Herein, we identify the molecular mechanisms involved, showing that TRAP1 (1) binds both mitochondrial and cytosolic ribosomes, as well as translation elongation factors; (2) slows down translation elongation rate; and (3) favors localized translation in the proximity of mitochondria. We also provide evidence that TRAP1 is coexpressed in human tissues with the mitochondrial translational machinery, which is responsible for the synthesis of respiratory complex proteins. Altogether, our results show an unprecedented level of complexity in the regulation of cancer cell metabolism, strongly suggesting the existence of a tight feedback loop between protein synthesis and energy metabolism, based on the demonstration that a single molecular chaperone plays a role in both mitochondrial and cytosolic translation, as well as in mitochondrial respiration.
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Affiliation(s)
- Rosario Avolio
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples 80131, Italy
| | - Ilenia Agliarulo
- Institute of Experimental Endocrinology and Oncology "G. Salvatore"-IEOS, National Research Council of Italy (CNR), Naples 80131, Italy
| | - Daniela Criscuolo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples 80131, Italy
| | - Daniela Sarnataro
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples 80131, Italy
| | - Margherita Auriemma
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples 80131, Italy
| | - Sabrina De Lella
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples 80131, Italy
| | - Sara Pennacchio
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples 80131, Italy
| | - Giovanni Calice
- Laboratory of Preclinical and Translational Research, IRCCS, Referral Cancer Center of Basilicata, Rionero in Vulture 85028, Italy
| | - Martin Y Ng
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA
| | - Carlotta Giorgi
- Department of Medical Sciences, University of Ferrara, Ferrara 44121, Italy
| | - Paolo Pinton
- Department of Medical Sciences, University of Ferrara, Ferrara 44121, Italy
| | - Barry S Cooperman
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA
| | - Matteo Landriscina
- Institute of Experimental Endocrinology and Oncology "G. Salvatore"-IEOS, National Research Council of Italy (CNR), Naples 80131, Italy
- Department Medical and Surgical Science, University of Foggia, Foggia 71122, Italy
| | - Franca Esposito
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples 80131, Italy;
| | - Danilo Swann Matassa
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples 80131, Italy;
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19
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Ma J, Sun L, Gao W, Li Y, Dong D. RNA binding protein: coordinated expression between the nuclear and mitochondrial genomes in tumors. J Transl Med 2023; 21:512. [PMID: 37507746 PMCID: PMC10386658 DOI: 10.1186/s12967-023-04373-3] [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: 05/11/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Mitochondria are the only organelles regulated by two genomes. The coordinated translation of nuclear DNA (nDNA) and mitochondrial DNA (mtDNA), which together co-encode the subunits of the oxidative phosphorylation (OXPHOS) complex, is critical for determining the metabolic plasticity of tumor cells. RNA-binding protein (RBP) is a post-transcriptional regulatory factor that plays a pivotal role in determining the fate of mRNA. RBP rapidly and effectively reshapes the mitochondrial proteome in response to intracellular and extracellular stressors, mediating the cytoplasmic and mitochondrial translation balance to adjust mitochondrial respiratory capacity and provide energy for tumor cells to adapt to different environmental pressures and growth needs. This review highlights the ability of RBPs to use liquid-liquid phase separation (LLPS) as a platform for translation regulation, integrating nuclear-mitochondrial positive and retrograde signals to coordinate cross-department translation, reshape mitochondrial energy metabolism, and promote the development and survival of tumor cells.
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Affiliation(s)
- Jiaoyan Ma
- Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China
| | - Liankun Sun
- Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China
| | - Weinan Gao
- Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China
| | - Yang Li
- Department of Physiology, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China
| | - Delu Dong
- Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China.
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20
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Guerra RM, Pagliarini DJ. Coenzyme Q biochemistry and biosynthesis. Trends Biochem Sci 2023; 48:463-476. [PMID: 36702698 PMCID: PMC10106368 DOI: 10.1016/j.tibs.2022.12.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/19/2022] [Accepted: 12/30/2022] [Indexed: 01/26/2023]
Abstract
Coenzyme Q (CoQ) is a remarkably hydrophobic, redox-active lipid that empowers diverse cellular processes. Although most known for shuttling electrons between mitochondrial electron transport chain (ETC) complexes, the roles for CoQ are far more wide-reaching and ever-expanding. CoQ serves as a conduit for electrons from myriad pathways to enter the ETC, acts as a cofactor for biosynthetic and catabolic reactions, detoxifies damaging lipid species, and engages in cellular signaling and oxygen sensing. Many open questions remain regarding the biosynthesis, transport, and metabolism of CoQ, which hinders our ability to treat human CoQ deficiency. Here, we recount progress in filling these knowledge gaps, highlight unanswered questions, and underscore the need for novel tools to enable discoveries and improve the treatment of CoQ-related diseases.
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Affiliation(s)
- Rachel M Guerra
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - David J Pagliarini
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Departament of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA; Departament of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.
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21
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Multi-Omics Profiling of Hypertrophic Cardiomyopathy Reveals Altered Mechanisms in Mitochondrial Dynamics and Excitation-Contraction Coupling. Int J Mol Sci 2023; 24:ijms24054724. [PMID: 36902152 PMCID: PMC10002553 DOI: 10.3390/ijms24054724] [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: 01/21/2023] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
Hypertrophic cardiomyopathy is one of the most common inherited cardiomyopathies and a leading cause of sudden cardiac death in young adults. Despite profound insights into the genetics, there is imperfect correlation between mutation and clinical prognosis, suggesting complex molecular cascades driving pathogenesis. To investigate this, we performed an integrated quantitative multi-omics (proteomic, phosphoproteomic, and metabolomic) analysis to illuminate the early and direct consequences of mutations in myosin heavy chain in engineered human induced pluripotent stem-cell-derived cardiomyocytes relative to late-stage disease using patient myectomies. We captured hundreds of differential features, which map to distinct molecular mechanisms modulating mitochondrial homeostasis at the earliest stages of pathobiology, as well as stage-specific metabolic and excitation-coupling maladaptation. Collectively, this study fills in gaps from previous studies by expanding knowledge of the initial responses to mutations that protect cells against the early stress prior to contractile dysfunction and overt disease.
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22
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Ul Fatima N, Ananthanarayanan V. Mitochondrial movers and shapers: Recent insights into regulators of fission, fusion and transport. Curr Opin Cell Biol 2023; 80:102150. [PMID: 36580830 DOI: 10.1016/j.ceb.2022.102150] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 10/28/2022] [Accepted: 11/29/2022] [Indexed: 12/28/2022]
Abstract
Mitochondria are highly dynamic organelles that undergo rapid morphological adaptations influencing their number, transport, cellular distribution, and function, which in turn facilitate the integration of mitochondrial function with physiological changes in the cell. These mitochondrial dynamics are dependent on tightly regulated processes such as fission, fusion, and attachment to the cytoskeleton, and their defects are observed in various pathophysiological conditions including cancer, cardiovascular disease, and neurodegeneration. Various studies over the years have identified key molecular players and uncovered the mechanisms that mediate and regulate these processes and have highlighted their complexity and context-specificity. This review focuses on the recent studies that have contributed to the understanding of processes that influence mitochondrial morphology including fission, fusion, and transport in the cell.
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Affiliation(s)
- Nida Ul Fatima
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Australia.
| | - Vaishnavi Ananthanarayanan
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Australia.
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23
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Avolio R, Agliarulo I, Criscuolo D, Sarnataro D, Auriemma M, Pennacchio S, Calice G, Ng MY, Giorgi C, Pinton P, Cooperman B, Landriscina M, Esposito F, Matassa DS. Cytosolic and mitochondrial translation elongation are coordinated through the molecular chaperone TRAP1 for the synthesis and import of mitochondrial proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.19.524708. [PMID: 36712063 PMCID: PMC9882373 DOI: 10.1101/2023.01.19.524708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A complex interplay between mRNA translation and cellular respiration has been recently unveiled, but its regulation in humans is poorly characterized in either health or disease. Cancer cells radically reshape both biosynthetic and bioenergetic pathways to sustain their aberrant growth rates. In this regard, we have shown that the molecular chaperone TRAP1 not only regulates the activity of respiratory complexes, behaving alternatively as an oncogene or a tumor suppressor, but also plays a concomitant moonlighting function in mRNA translation regulation. Herein we identify the molecular mechanisms involved, demonstrating that TRAP1: i) binds both mitochondrial and cytosolic ribosomes as well as translation elongation factors, ii) slows down translation elongation rate, and iii) favors localized translation in the proximity of mitochondria. We also provide evidence that TRAP1 is coexpressed in human tissues with the mitochondrial translational machinery, which is responsible for the synthesis of respiratory complex proteins. Altogether, our results show an unprecedented level of complexity in the regulation of cancer cell metabolism, strongly suggesting the existence of a tight feedback loop between protein synthesis and energy metabolism, based on the demonstration that a single molecular chaperone plays a role in both mitochondrial and cytosolic translation, as well as in mitochondrial respiration.
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Affiliation(s)
- Rosario Avolio
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, 80131, Italy
| | - Ilenia Agliarulo
- Institute of Experimental Endocrinology and Oncology “G. Salvatore” - IEOS, National Research Council of Italy (CNR), Naples, 80131, Italy
| | - Daniela Criscuolo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, 80131, Italy
| | - Daniela Sarnataro
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, 80131, Italy
| | - Margherita Auriemma
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, 80131, Italy
| | - Sara Pennacchio
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, 80131, Italy
| | - Giovanni Calice
- Laboratory of Pre-clinical and Translational Research, IRCCS, Referral Cancer Center of Basilicata, Rionero in Vulture, 85028, Italy
| | - Martin Y. Ng
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Carlotta Giorgi
- Dept. of Medical Sciences, University of Ferrara, Ferrara, 44121, Italy
| | - Paolo Pinton
- Dept. of Medical Sciences, University of Ferrara, Ferrara, 44121, Italy
| | - Barry Cooperman
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Matteo Landriscina
- Institute of Experimental Endocrinology and Oncology “G. Salvatore” - IEOS, National Research Council of Italy (CNR), Naples, 80131, Italy
- Department Medical and Surgical Science, University of Foggia, Foggia, 71122, Italy
| | - Franca Esposito
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, 80131, Italy
| | - Danilo Swann Matassa
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, 80131, Italy
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24
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Jobst M, Kiss E, Gerner C, Marko D, Del Favero G. Activation of autophagy triggers mitochondrial loss and changes acetylation profile relevant for mechanotransduction in bladder cancer cells. Arch Toxicol 2023; 97:217-233. [PMID: 36214828 PMCID: PMC9816236 DOI: 10.1007/s00204-022-03375-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/05/2022] [Indexed: 01/19/2023]
Abstract
Bladder cells are constantly exposed to multiple xenobiotics and bioactive metabolites. In addition to this challenging chemical environment, they are also exposed to shear stress originating from urine and interstitial fluids. Hence, physiological function of bladder cells relies on a high biochemical and biomechanical adaptive competence, which, in turn, is largely supported via autophagy-related mechanisms. As a negative side of this plasticity, bladder cancer cells are known to adapt readily to chemotherapeutic programs. At the molecular level, autophagy was described to support resistance against pharmacological treatments and to contribute to the maintenance of cell structure and metabolic competence. In this study, we enhanced autophagy with rapamycin (1-100 nM) and assessed its effects on the motility of bladder cells, as well as the capability to respond to shear stress. We observed that rapamycin reduced cell migration and the mechanical-induced translocation potential of Krüppel-like transcription factor 2 (KLF2). These effects were accompanied by a rearrangement of cytoskeletal elements and mitochondrial loss. In parallel, intracellular acetylation levels were decreased. Mechanistically, inhibition of the NAD + -dependent deacetylase sirtuin-1 (SIRT1) with nicotinamide (NAM; 0.1-5 mM) restored acetylation levels hampered by rapamycin and cell motility. Taken together, we described the effects of rapamycin on cytoskeletal elements crucial for mechanotransduction and the dependency of these changes on the mitochondrial turnover caused by autophagy activation. Additionally, we could show that targeted metabolic intervention could revert the outcome of autophagy activation, reinforcing the idea that bladder cells can easily adapt to multiple xenobiotics and circumvent in this way the effects of single chemicals.
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Affiliation(s)
- Maximilian Jobst
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, Währingerstr. 38-40, 1090 Vienna, Austria
| | - Endre Kiss
- Core Facility Multimodal, Imaging, Faculty of Chemistry, University of Vienna, Währingerstr. 38-40, 1090 Vienna, Austria
| | - Christopher Gerner
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währingerstr. 38-40, 1090 Vienna, Austria ,Joint Metabolome Facility, University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Doris Marko
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, Währingerstr. 38-40, 1090 Vienna, Austria
| | - Giorgia Del Favero
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, Währingerstr. 38-40, 1090 Vienna, Austria ,Core Facility Multimodal, Imaging, Faculty of Chemistry, University of Vienna, Währingerstr. 38-40, 1090 Vienna, Austria
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25
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Bennett CF, Latorre-Muro P, Puigserver P. Mechanisms of mitochondrial respiratory adaptation. Nat Rev Mol Cell Biol 2022; 23:817-835. [PMID: 35804199 PMCID: PMC9926497 DOI: 10.1038/s41580-022-00506-6] [Citation(s) in RCA: 82] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/31/2022] [Indexed: 02/07/2023]
Abstract
Mitochondrial energetic adaptations encompass a plethora of conserved processes that maintain cell and organismal fitness and survival in the changing environment by adjusting the respiratory capacity of mitochondria. These mitochondrial responses are governed by general principles of regulatory biology exemplified by changes in gene expression, protein translation, protein complex formation, transmembrane transport, enzymatic activities and metabolite levels. These changes can promote mitochondrial biogenesis and membrane dynamics that in turn support mitochondrial respiration. The main regulatory components of mitochondrial energetic adaptation include: the transcription coactivator peroxisome proliferator-activated receptor-γ (PPARγ) coactivator 1α (PGC1α) and associated transcription factors; mTOR and endoplasmic reticulum stress signalling; TOM70-dependent mitochondrial protein import; the cristae remodelling factors, including mitochondrial contact site and cristae organizing system (MICOS) and OPA1; lipid remodelling; and the assembly and metabolite-dependent regulation of respiratory complexes. These adaptive molecular and structural mechanisms increase respiration to maintain basic processes specific to cell types and tissues. Failure to execute these regulatory responses causes cell damage and inflammation or senescence, compromising cell survival and the ability to adapt to energetically demanding conditions. Thus, mitochondrial adaptive cellular processes are important for physiological responses, including to nutrient availability, temperature and physical activity, and their failure leads to diseases associated with mitochondrial dysfunction such as metabolic and age-associated diseases and cancer.
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Affiliation(s)
- Christopher F Bennett
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Pedro Latorre-Muro
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Pere Puigserver
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
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26
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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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27
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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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28
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Hemono M, Salinas‐Giegé T, Roignant J, Vingadassalon A, Hammann P, Ubrig E, Ngondo P, Duchêne A. FRIENDLY (FMT) is an RNA binding protein associated with cytosolic ribosomes at the mitochondrial surface. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:309-321. [PMID: 36050837 PMCID: PMC9826127 DOI: 10.1111/tpj.15962] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 07/22/2022] [Accepted: 08/15/2022] [Indexed: 06/15/2023]
Abstract
The spatial organization of protein synthesis in the eukaryotic cell is essential for maintaining the integrity of the proteome and the functioning of the cell. Translation on free polysomes or on ribosomes associated with the endoplasmic reticulum has been studied for a long time. More recent data have revealed selective translation of mRNAs in other compartments, in particular at the surface of mitochondria. Although these processes have been described in many organisms, particularky in plants, the mRNA targeting and localized translation mechanisms remain poorly understood. Here, the Arabidopsis thaliana Friendly (FMT) protein is shown to be a cytosolic RNA binding protein that associates with cytosolic ribosomes at the surface of mitochondria. FMT knockout delays seedling development and causes mitochondrial clustering. The mutation also disrupts the mitochondrial proteome, as well as the localization of nuclear transcripts encoding mitochondrial proteins at the surface of mitochondria. These data indicate that FMT participates in the localization of mRNAs and their translation at the surface of mitochondria.
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Affiliation(s)
- Mickaele Hemono
- Institut de biologie moléculaire des plantes, UPR 2357 du CNRS, Université de Strasbourg12 rue du Général Zimmer67084Strasbourg CedexFrance
| | - Thalia Salinas‐Giegé
- Institut de biologie moléculaire des plantes, UPR 2357 du CNRS, Université de Strasbourg12 rue du Général Zimmer67084Strasbourg CedexFrance
| | - Jeanne Roignant
- Institut de biologie moléculaire des plantes, UPR 2357 du CNRS, Université de Strasbourg12 rue du Général Zimmer67084Strasbourg CedexFrance
| | - Audrey Vingadassalon
- Institut de biologie moléculaire des plantes, UPR 2357 du CNRS, Université de Strasbourg12 rue du Général Zimmer67084Strasbourg CedexFrance
- Université des Antilles, COVACHIM M2E (EA 3592), UFR SEN, Campus de FouilloleF‐97 110Pointe‐à‐PitreFrance
| | - Philippe Hammann
- Plateforme Protéomique Strasbourg‐EsplanadeInstitut de Biologie Moléculaire et CellulaireFR1589 du CNRS, 2 Allée Konrad Roentgen67084Strasbourg CedexFrance
| | - Elodie Ubrig
- Institut de biologie moléculaire des plantes, UPR 2357 du CNRS, Université de Strasbourg12 rue du Général Zimmer67084Strasbourg CedexFrance
| | - Patryk Ngondo
- Institut de biologie moléculaire des plantes, UPR 2357 du CNRS, Université de Strasbourg12 rue du Général Zimmer67084Strasbourg CedexFrance
- Institut de Biologie Moléculaire et Cellulaire, UPR 9002 du CNRS, Université de Strasbourg2 Allée Konrad Roentgen67 084Strasbourg CedexFrance
| | - Anne‐Marie Duchêne
- Institut de biologie moléculaire des plantes, UPR 2357 du CNRS, Université de Strasbourg12 rue du Général Zimmer67084Strasbourg CedexFrance
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29
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Gart E, van Duyvenvoorde W, Caspers MPM, van Trigt N, Snabel J, Menke A, Keijer J, Salic K, Morrison MC, Kleemann R. Intervention with isoleucine or valine corrects hyperinsulinemia and reduces intrahepatic diacylglycerols, liver steatosis, and inflammation in Ldlr-/-.Leiden mice with manifest obesity-associated NASH. FASEB J 2022; 36:e22435. [PMID: 35830259 DOI: 10.1096/fj.202200111r] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 06/08/2022] [Accepted: 06/21/2022] [Indexed: 11/11/2022]
Abstract
Non-alcoholic steatohepatitis (NASH) is associated with a disturbed metabolism in liver, insulin resistance, and excessive accumulation of ectopic fat. Branched-chain amino acids (BCAAs) may beneficially modulate hepatic lipids, however, it remains unclear whether individual BCAAs can attenuate already established NASH and associated oxidative-inflammatory stress. After a 26 weeks run-in on fast food diet (FFD), obese Ldlr-/-.Leiden mice were treated for another 12 weeks with either valine or isoleucine (3% of FFD) and then compared to FFD controls. Valine and isoleucine did not affect obesity, dyslipidemia, gut permeability, or fecal fatty acid excretion, but significantly reduced hyperinsulinemia. Valine and isoleucine reduced ALT, CK18-M30, and liver steatosis with a particularly pronounced suppression of the microvesicular component (-61% by valine and -71% by isoleucine). Both BCAAs decreased intrahepatic diacylglycerols and 4-hydroxynonenal immunoreactivity, a marker for oxidative stress-induced lipid peroxidation. Functional genomics analysis demonstrated that valine and isoleucine affected BCAA metabolism genes, deactivated master regulators of anabolic pathways related to steatosis (e.g., SREBPF1), and activated master regulators of mitochondrial biogenesis (e.g., PPARGC1A) and lipid catabolism (e.g., ACOX1, AMPK). This correction of critical metabolic pathways on gene expression level was accompanied by a significant decrease in histological liver inflammation, and suppression of FFD-stimulated cytokine and chemokine proteins KC/CXCL1, MCP-1/CCL2, and MIP-2/CXCL2 and their pathways. In conclusion, dietary intervention with either valine or isoleucine corrected liver diacylglycerols, gene expression of multiple metabolic processes, and reduced NASH histology with profound hepatoprotective effects on oxidative stress and inflammatory proteins.
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Affiliation(s)
- Eveline Gart
- Department of Metabolic Health Research, The Netherlands Organization for Applied Scientific Research (TNO), Leiden, the Netherlands.,Human and Animal Physiology, Wageningen University, Wageningen, The Netherlands
| | - Wim van Duyvenvoorde
- Department of Metabolic Health Research, The Netherlands Organization for Applied Scientific Research (TNO), Leiden, the Netherlands
| | - Martien P M Caspers
- Department of Microbiology and Systems Biology, The Netherlands Organization for Applied Scientific Research (TNO), Zeist, the Netherlands
| | - Nikki van Trigt
- Department of Metabolic Health Research, The Netherlands Organization for Applied Scientific Research (TNO), Leiden, the Netherlands
| | - Jessica Snabel
- Department of Metabolic Health Research, The Netherlands Organization for Applied Scientific Research (TNO), Leiden, the Netherlands
| | - Aswin Menke
- Department of Metabolic Health Research, The Netherlands Organization for Applied Scientific Research (TNO), Leiden, the Netherlands
| | - Jaap Keijer
- Human and Animal Physiology, Wageningen University, Wageningen, The Netherlands
| | - Kanita Salic
- Department of Metabolic Health Research, The Netherlands Organization for Applied Scientific Research (TNO), Leiden, the Netherlands
| | - Martine C Morrison
- Department of Metabolic Health Research, The Netherlands Organization for Applied Scientific Research (TNO), Leiden, the Netherlands.,Human and Animal Physiology, Wageningen University, Wageningen, The Netherlands
| | - Robert Kleemann
- Department of Metabolic Health Research, The Netherlands Organization for Applied Scientific Research (TNO), Leiden, the Netherlands.,Department of Vascular Surgery, Leiden University Medical Center, Leiden, the Netherlands
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30
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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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31
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Ralevski A, Apelt F, Olas JJ, Mueller-Roeber B, Rugarli EI, Kragler F, Horvath TL. Plant mitochondrial FMT and its mammalian homolog CLUH controls development and behavior in Arabidopsis and locomotion in mice. Cell Mol Life Sci 2022; 79:334. [PMID: 35652974 PMCID: PMC11071973 DOI: 10.1007/s00018-022-04382-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 05/15/2022] [Accepted: 05/16/2022] [Indexed: 11/26/2022]
Abstract
Mitochondria in animals are associated with development, as well as physiological and pathological behaviors. Several conserved mitochondrial genes exist between plants and higher eukaryotes. Yet, the similarities in mitochondrial function between plant and animal species is poorly understood. Here, we show that FMT (FRIENDLY MITOCHONDRIA) from Arabidopsis thaliana, a highly conserved homolog of the mammalian CLUH (CLUSTERED MITOCHONDRIA) gene family encoding mitochondrial proteins associated with developmental alterations and adult physiological and pathological behaviors, affects whole plant morphology and development under both stressed and normal growth conditions. FMT was found to regulate mitochondrial morphology and dynamics, germination, and flowering time. It also affects leaf expansion growth, salt stress responses and hyponastic behavior, including changes in speed of hyponastic movements. Strikingly, Cluh± heterozygous knockout mice also displayed altered locomotive movements, traveling for shorter distances and had slower average and maximum speeds in the open field test. These observations indicate that homologous mitochondrial genes may play similar roles and affect homologous functions in both plants and animals.
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Affiliation(s)
- Alexandra Ralevski
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, 06520, USA
- Yale Center for Molecular and Systems Metabolism, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Federico Apelt
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, 14476, Potsdam, Germany
| | - Justyna J Olas
- Department of Molecular Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476, Potsdam, Germany
| | - Bernd Mueller-Roeber
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, 14476, Potsdam, Germany
- Department of Molecular Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476, Potsdam, Germany
| | - Elena I Rugarli
- Department of Biology, Institute for Genetics, University of Cologne, Cologne, Germany
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Friedrich Kragler
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, 14476, Potsdam, Germany
| | - Tamas L Horvath
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, 06520, USA.
- Yale Center for Molecular and Systems Metabolism, Yale University School of Medicine, New Haven, CT, 06520, USA.
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT, 06520, USA.
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Schatton D, Di Pietro G, Szczepanowska K, Veronese M, Marx MC, Braunöhler K, Barth E, Müller S, Giavalisco P, Langer T, Trifunovic A, Rugarli EI. CLUH controls astrin-1 expression to couple mitochondrial metabolism to cell cycle progression. eLife 2022; 11:74552. [PMID: 35559794 PMCID: PMC9135405 DOI: 10.7554/elife.74552] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 05/12/2022] [Indexed: 11/24/2022] Open
Abstract
Proliferating cells undergo metabolic changes in synchrony with cell cycle progression and cell division. Mitochondria provide fuel, metabolites, and ATP during different phases of the cell cycle, however it is not completely understood how mitochondrial function and the cell cycle are coordinated. CLUH (clustered mitochondria homolog) is a post-transcriptional regulator of mRNAs encoding mitochondrial proteins involved in oxidative phosphorylation and several metabolic pathways. Here, we show a role of CLUH in regulating the expression of astrin, which is involved in metaphase to anaphase progression, centrosome integrity, and mTORC1 inhibition. We find that CLUH binds both the SPAG5 mRNA and its product astrin, and controls the synthesis and the stability of the full-length astrin-1 isoform. We show that CLUH interacts with astrin-1 specifically during interphase. Astrin-depleted cells show mTORC1 hyperactivation and enhanced anabolism. On the other hand, cells lacking CLUH show decreased astrin levels and increased mTORC1 signaling, but cannot sustain anaplerotic and anabolic pathways. In absence of CLUH, cells fail to grow during G1, and progress faster through the cell cycle, indicating dysregulated matching of growth, metabolism, and cell cycling. Our data reveal a role of CLUH in coupling growth signaling pathways and mitochondrial metabolism with cell cycle progression.
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Affiliation(s)
| | - Giada Di Pietro
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Karolina Szczepanowska
- Institute for Mitochondrial Diseases and Ageing, University of Cologne, Cologne, Germany
| | - Matteo Veronese
- Institute for Genetics, University of Cologne, Cologne, Germany
| | | | | | - Esther Barth
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Stefan Müller
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | | | - Thomas Langer
- Langer Department, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Aleksandra Trifunovic
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | - Elena I Rugarli
- Institute for Genetics, University of Cologne, Cologne, Germany
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33
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Fessler E, Krumwiede L, Jae LT. DELE1 tracks perturbed protein import and processing in human mitochondria. Nat Commun 2022; 13:1853. [PMID: 35388015 PMCID: PMC8986780 DOI: 10.1038/s41467-022-29479-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 03/11/2022] [Indexed: 12/15/2022] Open
Abstract
Protein homeostatic control of mitochondria is key to age-related diseases and organismal decline. However, it is unknown how the diverse types of stress experienced by mitochondria can be integrated and appropriately responded to in human cells. Here we identify perturbations in the ancient conserved processes of mitochondrial protein import and processing as sources of DELE1 activation: DELE1 is continuously sorted across both mitochondrial membranes into the matrix and detects different types of perturbations along the way. DELE1 molecules in transit can become licensed for mitochondrial release and stress signaling through proteolytic removal of N-terminal sorting signals. Import defects that occur at the mitochondrial surface allow DELE1 precursors to bind and activate downstream factor HRI without the need for cleavage. Genome-wide genetics reveal that DELE1 additionally responds to compromised presequence processing by the matrix proteases PITRM1 and MPP, which are mutated in neurodegenerative diseases. These mechanisms rationalize DELE1-dependent mitochondrial stress integration in the human system and may inform future therapies of neuropathies.
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Affiliation(s)
- Evelyn Fessler
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377, Munich, Germany.
| | - Luisa Krumwiede
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377, Munich, Germany
| | - Lucas T Jae
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377, Munich, Germany.
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34
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Yang H, Sibilla C, Liu R, Yun J, Hay BA, Blackstone C, Chan DC, Harvey RJ, Guo M. Clueless/CLUH regulates mitochondrial fission by promoting recruitment of Drp1 to mitochondria. Nat Commun 2022; 13:1582. [PMID: 35332133 PMCID: PMC8948191 DOI: 10.1038/s41467-022-29071-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 02/04/2022] [Indexed: 02/08/2023] Open
Abstract
Mitochondrial fission is critically important for controlling mitochondrial morphology, function, quality and transport. Drp1 is the master regulator driving mitochondrial fission, but exactly how Drp1 is regulated remains unclear. Here, we identified Drosophila Clueless and its mammalian orthologue CLUH as key regulators of Drp1. As with loss of drp1, depletion of clueless or CLUH results in mitochondrial elongation, while as with drp1 overexpression, clueless or CLUH overexpression leads to mitochondrial fragmentation. Importantly, drp1 overexpression rescues adult lethality, tissue disintegration and mitochondrial defects of clueless null mutants in Drosophila. Mechanistically, Clueless and CLUH promote recruitment of Drp1 to mitochondria from the cytosol. This involves CLUH binding to mRNAs encoding Drp1 receptors MiD49 and Mff, and regulation of their translation. Our findings identify a crucial role of Clueless and CLUH in controlling mitochondrial fission through regulation of Drp1. Drp1 is the master regulator of mitochondrial fission, which has important impact on cellular functions. Here, Yang et al identified evolutionarily conserved proteins Clueless and its homolog CLUH as key regulators of Drp1 that function via translation of Drp1 receptors MiD49 and Mff.
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Affiliation(s)
- Huan Yang
- Department of Neurology, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
| | - Caroline Sibilla
- Cell Biology Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA.,Department of Pharmacology, University College London School of Pharmacy, London, UK.,AstraZeneca PLC, Cambridge Biomedical Campus, Cambridge, UK
| | - Raymond Liu
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.,Department of Microbiology and Immunology, UCSF, San Francisco, CA, USA
| | - Jina Yun
- Department of Neurology, UCLA David Geffen School of Medicine, Los Angeles, CA, USA.,Genentech, Inc., South San Francisco, CA, USA
| | - Bruce A Hay
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Craig Blackstone
- Cell Biology Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA.,Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - David C Chan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Robert J Harvey
- School of Health and Behavioural Sciences, University of the Sunshine Coast, Sippy Downs, QLD, Australia.,Sunshine Coast Health Institute, Birtinya, QLD, Australia
| | - Ming Guo
- Department of Neurology, UCLA David Geffen School of Medicine, Los Angeles, CA, USA. .,Department of Molecular and Medical Pharmacology, UCLA David Geffen School of Medicine, Los Angeles, CA, USA. .,California NanoSystems Institute at UCLA, Los Angeles, CA, USA.
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35
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Vargas JNS, Sleigh JN, Schiavo G. Coupling axonal mRNA transport and local translation to organelle maintenance and function. Curr Opin Cell Biol 2022; 74:97-103. [PMID: 35220080 PMCID: PMC10477965 DOI: 10.1016/j.ceb.2022.01.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/14/2022] [Accepted: 01/22/2022] [Indexed: 12/14/2022]
Abstract
Neuronal homeostasis requires the transport of various organelles to distal compartments and defects in this process lead to neurological disorders. Although several mechanisms for the delivery of organelles to axons and dendrites have been elucidated, exactly how this process is orchestrated is not well-understood. In this review, we discuss the recent literature supporting a novel paradigm - the co-shuttling of mRNAs with different membrane-bound organelles. This model postulates that the tethering of ribonucleoprotein complexes to endolysosomes and mitochondria allows for the spatiotemporal coupling of organelle transport and the delivery of transcripts to axons. Subcellular translation of these "hitchhiking" transcripts may thus provide a proximal source of proteins required for the maintenance and function of organelles in axons.
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Affiliation(s)
- Jose Norberto S Vargas
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, UK; UCL Queen Square Motor Neuron Disease Centre, UCL Queen Square Institute of Neurology, University College London, London, UK; UK Dementia Research Institute, University College London, London, UK
| | - James N Sleigh
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, UK; UCL Queen Square Motor Neuron Disease Centre, UCL Queen Square Institute of Neurology, University College London, London, UK; UK Dementia Research Institute, University College London, London, UK
| | - Giampietro Schiavo
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, UK; UCL Queen Square Motor Neuron Disease Centre, UCL Queen Square Institute of Neurology, University College London, London, UK; UK Dementia Research Institute, University College London, London, UK.
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36
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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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37
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Bogorodskiy A, Okhrimenko I, Burkatovskii D, Jakobs P, Maslov I, Gordeliy V, Dencher NA, Gensch T, Voos W, Altschmied J, Haendeler J, Borshchevskiy V. Role of Mitochondrial Protein Import in Age-Related Neurodegenerative and Cardiovascular Diseases. Cells 2021; 10:3528. [PMID: 34944035 PMCID: PMC8699856 DOI: 10.3390/cells10123528] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/10/2021] [Accepted: 12/12/2021] [Indexed: 11/17/2022] Open
Abstract
Mitochondria play a critical role in providing energy, maintaining cellular metabolism, and regulating cell survival and death. To carry out these crucial functions, mitochondria employ more than 1500 proteins, distributed between two membranes and two aqueous compartments. An extensive network of dedicated proteins is engaged in importing and sorting these nuclear-encoded proteins into their designated mitochondrial compartments. Defects in this fundamental system are related to a variety of pathologies, particularly engaging the most energy-demanding tissues. In this review, we summarize the state-of-the-art knowledge about the mitochondrial protein import machinery and describe the known interrelation of its failure with age-related neurodegenerative and cardiovascular diseases.
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Affiliation(s)
- Andrey Bogorodskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia; (A.B.); (I.O.); (D.B.); (I.M.); (V.G.); (N.A.D.)
| | - Ivan Okhrimenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia; (A.B.); (I.O.); (D.B.); (I.M.); (V.G.); (N.A.D.)
| | - Dmitrii Burkatovskii
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia; (A.B.); (I.O.); (D.B.); (I.M.); (V.G.); (N.A.D.)
| | - Philipp Jakobs
- Environmentally-Induced Cardiovascular Degeneration, Central Institute of Clinical Chemistry and Laboratory Medicine, Medical Faculty, University Hospital and Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany; (P.J.); (J.A.); (J.H.)
| | - Ivan Maslov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia; (A.B.); (I.O.); (D.B.); (I.M.); (V.G.); (N.A.D.)
| | - Valentin Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia; (A.B.); (I.O.); (D.B.); (I.M.); (V.G.); (N.A.D.)
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, 38400 Grenoble, France
| | - Norbert A. Dencher
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia; (A.B.); (I.O.); (D.B.); (I.M.); (V.G.); (N.A.D.)
- Physical Biochemistry, Chemistry Department, Technical University of Darmstadt, 64289 Darmstadt, Germany
| | - Thomas Gensch
- Institute of Biological Information Processing (IBI-1: Molecular and Cellular Physiology), Forschungszentrum Jülich, 52428 Jülich, Germany;
| | - Wolfgang Voos
- Institute of Biochemistry and Molecular Biology (IBMB), Faculty of Medicine, University of Bonn, 53113 Bonn, Germany;
| | - Joachim Altschmied
- Environmentally-Induced Cardiovascular Degeneration, Central Institute of Clinical Chemistry and Laboratory Medicine, Medical Faculty, University Hospital and Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany; (P.J.); (J.A.); (J.H.)
- IUF—Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
| | - Judith Haendeler
- Environmentally-Induced Cardiovascular Degeneration, Central Institute of Clinical Chemistry and Laboratory Medicine, Medical Faculty, University Hospital and Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany; (P.J.); (J.A.); (J.H.)
| | - Valentin Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia; (A.B.); (I.O.); (D.B.); (I.M.); (V.G.); (N.A.D.)
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
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38
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Fernández-Alvarez AJ, Thomas MG, Pascual ML, Habif M, Pimentel J, Corbat AA, Pessoa JP, La Spina PE, Boscaglia L, Plessis A, Carmo-Fonseca M, Grecco HE, Casado M, Boccaccio GL. Smaug1 membrane-less organelles respond to AMPK/mTOR and affect mitochondrial function‡. J Cell Sci 2021; 135:273619. [PMID: 34859817 DOI: 10.1242/jcs.253591] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 11/15/2021] [Indexed: 11/20/2022] Open
Abstract
Smaug is a conserved translational regulator that binds numerous mRNAs, including nuclear transcripts that encode mitochondrial enzymes. Smaug orthologs form cytosolic membrane-less organelles (MLOs) in several organisms and cell types. We have performed single-molecule FISH assays that revealed that SDHB and UQCRC1 mRNAs associate with Smaug1 bodies in U2OS cells. Loss of function of Smaug1 and Smaug2 affected both mitochondrial respiration and morphology of the mitochondrial network. Phenotype rescue by Smaug1 transfection depends on the presence of its RNA binding domain. Moreover, we identified specific Smaug1 domains involved in MLO formation, and found that impaired Smaug1 MLO condensation correlates with mitochondrial defects. Mitochondrial Complex I inhibition by rotenone -but not strong mitochondrial uncoupling by CCCP- rapidly induced Smaug1 MLOs dissolution. Metformin and rapamycin elicited similar effects, which were blocked by pharmacological inhibition of AMPK. Finally, we found that Smaug1 MLO dissolution weakens the interaction with target mRNAs, thus enabling their release. We propose that mitochondrial respiration and the AMPK/mTOR balance controls the condensation and dissolution of Smaug1 MLOs, thus regulating nuclear mRNAs that encode key mitochondrial proteins.
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Affiliation(s)
- Ana J Fernández-Alvarez
- Fundación Instituto Leloir (FIL).,Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), C1405BWE Buenos Aires, Argentina
| | - María Gabriela Thomas
- Fundación Instituto Leloir (FIL).,Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), C1405BWE Buenos Aires, Argentina
| | - Malena L Pascual
- Fundación Instituto Leloir (FIL).,Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), C1405BWE Buenos Aires, Argentina
| | - Martín Habif
- Department of Physics, Facultad de Ciencias Exactas y Naturales (FCEN), University of Buenos Aires, and IFIBA, CONICET, C1428EHA Buenos Aires, Argentina
| | - Jerónimo Pimentel
- Fundación Instituto Leloir (FIL).,Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), C1405BWE Buenos Aires, Argentina
| | - Agustín A Corbat
- Department of Physics, Facultad de Ciencias Exactas y Naturales (FCEN), University of Buenos Aires, and IFIBA, CONICET, C1428EHA Buenos Aires, Argentina
| | - João P Pessoa
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Pablo E La Spina
- Fundación Instituto Leloir (FIL).,Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), C1405BWE Buenos Aires, Argentina
| | | | - Anne Plessis
- Institut Jacques Monod, CNRS, UMR 7592, University Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Hernán E Grecco
- Department of Physics, Facultad de Ciencias Exactas y Naturales (FCEN), University of Buenos Aires, and IFIBA, CONICET, C1428EHA Buenos Aires, Argentina
| | - Marta Casado
- Instituto de Biomedicina de Valencia, IBV-CSIC, Valencia 46010, Spain, and Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid 28029, Spain
| | - Graciela L Boccaccio
- Fundación Instituto Leloir (FIL).,Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), C1405BWE Buenos Aires, Argentina.,Department of Molecular and Cellular Biology and Physiology (FBMyC), Facultad de Ciencias Exactas y Naturales (FCEN), University of Buenos Aires, C1428EHA Buenos Aires, Argentina
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39
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Ravera S, Vigliarolo T, Bruno S, Morandi F, Marimpietri D, Sabatini F, Dagnino M, Petretto A, Bartolucci M, Muraca M, Biasin E, Haupt R, Zecca M, Fagioli F, Cilloni D, Podestà M, Frassoni F. Identification of Biochemical and Molecular Markers of Early Aging in Childhood Cancer Survivors. Cancers (Basel) 2021; 13:cancers13205214. [PMID: 34680366 PMCID: PMC8534026 DOI: 10.3390/cancers13205214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/12/2021] [Accepted: 10/14/2021] [Indexed: 12/30/2022] Open
Abstract
Simple Summary Childhood cancer survivors (CCS) display a higher risk of developing second malignant tumors and chronic diseases compared with aged-matched controls because of chemo/radiotherapy. This early frailty seems associated with accelerated cell aging, a process correlated with altered mitochondrial energy production. Therefore, this work aims to shed light on the mechanisms involved in chemo/radiotherapy-induced early aging, morbidities, and the risk of developing second tumors in CCS through a biochemical and molecular approach. The identification of crucial mechanisms involved in the CCS chemo/radiotherapy-related pathological conditions will allow identifying therapeutic targets to develop appropriate risk-based care and interventions, minimize morbidities, and maximize the quality of life in the cancer survivor population. Abstract Survival rates of childhood cancer patients have improved over the past four decades, although cancer treatments increase the risk of developing chronic diseases typical of aging. Thus, we aimed to identify molecular/metabolic cellular alterations responsible for early aging in childhood cancer survivors (CCS). Biochemical, proteomic, and molecular biology analyses were conducted on mononuclear cells (MNCs) isolated from peripheral blood of 196 CCS, the results being compared with those obtained on MNCs of 154 healthy subjects. CCS-MNCs showed inefficient oxidative phosphorylation associated with low energy status, and increased lipid peroxidation and lactate fermentation compared with age-matched normal controls. According to a mathematical model based on biochemical parameters, CCS-MNCs showed significantly higher metabolic ages than their real ages. The dysfunctional metabolism of CCS-MNCs is associated with lower expression levels of genes and proteins involved in mitochondrial biogenesis and metabolism regulation, such as CLUH, PGC1-alpha, and SIRT6 in CCS, not observed in the age-matched healthy or elderly subjects. In conclusion, our study identified some biochemical and molecular alterations possibly contributing to the pathophysiology of aging and metabolic deficiencies in CCS. These results identify new targets for pharmacological interventions to restore mitochondrial function, slowing down the aging-associated pathologies in CCS.
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Affiliation(s)
- Silvia Ravera
- Stem Cell Laboratory and Cell Therapy Center, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (T.V.); (F.M.); (D.M.); (F.S.); (M.D.); (M.P.); (F.F.)
- Department of Experimental Medicine, University of Genoa, 16132 Genoa, Italy;
- Correspondence: ; Tel.: +39-010-335-7871
| | - Tiziana Vigliarolo
- Stem Cell Laboratory and Cell Therapy Center, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (T.V.); (F.M.); (D.M.); (F.S.); (M.D.); (M.P.); (F.F.)
| | - Silvia Bruno
- Department of Experimental Medicine, University of Genoa, 16132 Genoa, Italy;
| | - Fabio Morandi
- Stem Cell Laboratory and Cell Therapy Center, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (T.V.); (F.M.); (D.M.); (F.S.); (M.D.); (M.P.); (F.F.)
| | - Danilo Marimpietri
- Stem Cell Laboratory and Cell Therapy Center, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (T.V.); (F.M.); (D.M.); (F.S.); (M.D.); (M.P.); (F.F.)
| | - Federica Sabatini
- Stem Cell Laboratory and Cell Therapy Center, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (T.V.); (F.M.); (D.M.); (F.S.); (M.D.); (M.P.); (F.F.)
| | - Monica Dagnino
- Stem Cell Laboratory and Cell Therapy Center, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (T.V.); (F.M.); (D.M.); (F.S.); (M.D.); (M.P.); (F.F.)
| | - Andrea Petretto
- Core Facilities-Clinical Proteomics and Metabolomics, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (A.P.); (M.B.)
| | - Martina Bartolucci
- Core Facilities-Clinical Proteomics and Metabolomics, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (A.P.); (M.B.)
| | - Monica Muraca
- Epidemiology and Biostatistics Unit and DOPO Clinic, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (M.M.); (R.H.)
| | - Eleonora Biasin
- Department of Pediatric Onco-Haematology, Regina Margherita Children’s Hospital, University of Turin, 10126 Turin, Italy; (E.B.); (F.F.)
| | - Riccardo Haupt
- Epidemiology and Biostatistics Unit and DOPO Clinic, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (M.M.); (R.H.)
| | - Marco Zecca
- Pediatric Hematology Oncology, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy;
| | - Franca Fagioli
- Department of Pediatric Onco-Haematology, Regina Margherita Children’s Hospital, University of Turin, 10126 Turin, Italy; (E.B.); (F.F.)
| | - Daniela Cilloni
- Department of Clinical and Biological Sciences, School of Medicine, University of Turin, 10124 Turin, Italy;
| | - Marina Podestà
- Stem Cell Laboratory and Cell Therapy Center, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (T.V.); (F.M.); (D.M.); (F.S.); (M.D.); (M.P.); (F.F.)
| | - Francesco Frassoni
- Stem Cell Laboratory and Cell Therapy Center, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (T.V.); (F.M.); (D.M.); (F.S.); (M.D.); (M.P.); (F.F.)
- Department of Clinical and Biological Sciences, School of Medicine, University of Turin, 10124 Turin, Italy;
- Department of Mathematics (DIMA), University of Genoa, 16146 Genoa, Italy
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40
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Sensing, signaling and surviving mitochondrial stress. Cell Mol Life Sci 2021; 78:5925-5951. [PMID: 34228161 PMCID: PMC8316193 DOI: 10.1007/s00018-021-03887-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 06/15/2021] [Accepted: 06/22/2021] [Indexed: 12/11/2022]
Abstract
Mitochondrial fidelity is a key determinant of longevity and was found to be perturbed in a multitude of disease contexts ranging from neurodegeneration to heart failure. Tight homeostatic control of the mitochondrial proteome is a crucial aspect of mitochondrial function, which is severely complicated by the evolutionary origin and resulting peculiarities of the organelle. This is, on one hand, reflected by a range of basal quality control factors such as mitochondria-resident chaperones and proteases, that assist in import and folding of precursors as well as removal of aggregated proteins. On the other hand, stress causes the activation of several additional mechanisms that counteract any damage that may threaten mitochondrial function. Countermeasures depend on the location and intensity of the stress and on a range of factors that are equipped to sense and signal the nature of the encountered perturbation. Defective mitochondrial import activates mechanisms that combat the accumulation of precursors in the cytosol and the import pore. To resolve proteotoxic stress in the organelle interior, mitochondria depend on nuclear transcriptional programs, such as the mitochondrial unfolded protein response and the integrated stress response. If organelle damage is too severe, mitochondria signal for their own destruction in a process termed mitophagy, thereby preventing further harm to the mitochondrial network and allowing the cell to salvage their biological building blocks. Here, we provide an overview of how different types and intensities of stress activate distinct pathways aimed at preserving mitochondrial fidelity.
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41
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Lashkevich KA, Dmitriev SE. mRNA Targeting, Transport and Local Translation in Eukaryotic Cells: From the Classical View to a Diversity of New Concepts. Mol Biol 2021; 55:507-537. [PMID: 34092811 PMCID: PMC8164833 DOI: 10.1134/s0026893321030080] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 02/26/2021] [Accepted: 03/12/2021] [Indexed: 12/28/2022]
Abstract
Spatial organization of protein biosynthesis in the eukaryotic cell has been studied for more than fifty years, thus many facts have already been included in textbooks. According to the classical view, mRNA transcripts encoding secreted and transmembrane proteins are translated by ribosomes associated with endoplasmic reticulum membranes, while soluble cytoplasmic proteins are synthesized on free polysomes. However, in the last few years, new data has emerged, revealing selective translation of mRNA on mitochondria and plastids, in proximity to peroxisomes and endosomes, in various granules and at the cytoskeleton (actin network, vimentin intermediate filaments, microtubules and centrosomes). There are also long-standing debates about the possibility of protein synthesis in the nucleus. Localized translation can be determined by targeting signals in the synthesized protein, nucleotide sequences in the mRNA itself, or both. With RNA-binding proteins, many transcripts can be assembled into specific RNA condensates and form RNP particles, which may be transported by molecular motors to the sites of active translation, form granules and provoke liquid-liquid phase separation in the cytoplasm, both under normal conditions and during cell stress. The translation of some mRNAs occurs in specialized "translation factories," assemblysomes, transperons and other structures necessary for the correct folding of proteins, interaction with functional partners and formation of oligomeric complexes. Intracellular localization of mRNA has a significant impact on the efficiency of its translation and presumably determines its response to cellular stress. Compartmentalization of mRNAs and the translation machinery also plays an important role in viral infections. Many viruses provoke the formation of specific intracellular structures, virus factories, for the production of their proteins. Here we review the current concepts of the molecular mechanisms of transport, selective localization and local translation of cellular and viral mRNAs, their effects on protein targeting and topogenesis, and on the regulation of protein biosynthesis in different compartments of the eukaryotic cell. Special attention is paid to new systems biology approaches, providing new cues to the study of localized translation.
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Affiliation(s)
- Kseniya A Lashkevich
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119234 Moscow, Russia.,Faculty of Bioengineering and Bioinformatics, Moscow State University, 119234 Moscow, Russia
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119234 Moscow, Russia.,Faculty of Bioengineering and Bioinformatics, Moscow State University, 119234 Moscow, Russia.,Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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42
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Nakamura S, Hagihara S, Otomo K, Ishida H, Hidema J, Nemoto T, Izumi M. Autophagy Contributes to the Quality Control of Leaf Mitochondria. PLANT & CELL PHYSIOLOGY 2021; 62:229-247. [PMID: 33355344 PMCID: PMC8112837 DOI: 10.1093/pcp/pcaa162] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 12/05/2020] [Indexed: 05/11/2023]
Abstract
In autophagy, cytoplasmic components of eukaryotic cells are transported to lysosomes or the vacuole for degradation. Autophagy is involved in plant tolerance to the photooxidative stress caused by ultraviolet B (UVB) radiation, but its roles in plant adaptation to UVB damage have not been fully elucidated. Here, we characterized organellar behavior in UVB-damaged Arabidopsis (Arabidopsis thaliana) leaves and observed the occurrence of autophagic elimination of dysfunctional mitochondria, a process termed mitophagy. Notably, Arabidopsis plants blocked in autophagy displayed increased leaf chlorosis after a 1-h UVB exposure compared to wild-type plants. We visualized autophagosomes by labeling with a fluorescent protein-tagged autophagosome marker, AUTOPHAGY8 (ATG8), and found that a 1-h UVB treatment led to increased formation of autophagosomes and the active transport of mitochondria into the central vacuole. In atg mutant plants, the mitochondrial population increased in UVB-damaged leaves due to the cytoplasmic accumulation of fragmented, depolarized mitochondria. Furthermore, we observed that autophagy was involved in the removal of depolarized mitochondria when mitochondrial function was disrupted by mutation of the FRIENDLY gene, which is required for proper mitochondrial distribution. Therefore, autophagy of mitochondria functions in response to mitochondrion-specific dysfunction as well as UVB damage. Together, these results indicate that autophagy is centrally involved in mitochondrial quality control in Arabidopsis leaves.
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Affiliation(s)
- Sakuya Nakamura
- Center for Sustainable Resource Science (CSRS), RIKEN, Wako, 351-0198 Japan
| | - Shinya Hagihara
- Center for Sustainable Resource Science (CSRS), RIKEN, Wako, 351-0198 Japan
| | - Kohei Otomo
- Exploratory Research Center on Life and Living Systems (ExCELLs), National Institute of Natural Sciences, Okazaki, 444-8787 Japan
- National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, 444-8787 Japan
- Department of Physiological Sciences, The Graduate University for Advanced Study (SOKENDAI), Hayama, 240-0193 Japan
- Research Institute for Electronic Science, Hokkaido University, Sapporo, 001-0020 Japan
| | - Hiroyuki Ishida
- Department of Applied Plant Science, Graduate School of Agricultural Sciences, Tohoku University, Sendai, 980-0845, Japan
| | - Jun Hidema
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577, Japan
| | - Tomomi Nemoto
- Exploratory Research Center on Life and Living Systems (ExCELLs), National Institute of Natural Sciences, Okazaki, 444-8787 Japan
- National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, 444-8787 Japan
- Department of Physiological Sciences, The Graduate University for Advanced Study (SOKENDAI), Hayama, 240-0193 Japan
- Research Institute for Electronic Science, Hokkaido University, Sapporo, 001-0020 Japan
| | - Masanori Izumi
- Center for Sustainable Resource Science (CSRS), RIKEN, Wako, 351-0198 Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, 322-0012 Japan
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43
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Jourdain AA, Begg BE, Mick E, Shah H, Calvo SE, Skinner OS, Sharma R, Blue SM, Yeo GW, Burge CB, Mootha VK. Loss of LUC7L2 and U1 snRNP subunits shifts energy metabolism from glycolysis to OXPHOS. Mol Cell 2021; 81:1905-1919.e12. [PMID: 33852893 PMCID: PMC8314041 DOI: 10.1016/j.molcel.2021.02.033] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 12/18/2020] [Accepted: 02/22/2021] [Indexed: 12/17/2022]
Abstract
Oxidative phosphorylation (OXPHOS) and glycolysis are the two major pathways for ATP production. The reliance on each varies across tissues and cell states, and can influence susceptibility to disease. At present, the full set of molecular mechanisms governing the relative expression and balance of these two pathways is unknown. Here, we focus on genes whose loss leads to an increase in OXPHOS activity. Unexpectedly, this class of genes is enriched for components of the pre-mRNA splicing machinery, in particular for subunits of the U1 snRNP. Among them, we show that LUC7L2 represses OXPHOS and promotes glycolysis by multiple mechanisms, including (1) splicing of the glycolytic enzyme PFKM to suppress glycogen synthesis, (2) splicing of the cystine/glutamate antiporter SLC7A11 (xCT) to suppress glutamate oxidation, and (3) secondary repression of mitochondrial respiratory supercomplex formation. Our results connect LUC7L2 expression and, more generally, the U1 snRNP to cellular energy metabolism.
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Affiliation(s)
- Alexis A Jourdain
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | | | - Eran Mick
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Hardik Shah
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sarah E Calvo
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Owen S Skinner
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Rohit Sharma
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Steven M Blue
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | | | - Vamsi K Mootha
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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44
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Ryan SL, Dave KA, Beard S, Gyimesi M, McTaggart M, Sahin KB, Molloy C, Gandhi NS, Boittier E, O'Leary CG, Shah ET, Bolderson E, Baird AM, Richard DJ, O'Byrne KJ, Adams MN. Identification of Proteins Deregulated by Platinum-Based Chemotherapy as Novel Biomarkers and Therapeutic Targets in Non-Small Cell Lung Cancer. Front Oncol 2021; 11:615967. [PMID: 33777753 PMCID: PMC7991912 DOI: 10.3389/fonc.2021.615967] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 01/19/2021] [Indexed: 12/24/2022] Open
Abstract
Platinum-based chemotherapy remains the cornerstone of treatment for most people with non-small cell lung cancer (NSCLC), either as adjuvant therapy in combination with a second cytotoxic agent or in combination with immunotherapy. Resistance to therapy, either in the form of primary refractory disease or evolutionary resistance, remains a significant issue in the treatment of NSCLC. Hence, predictive biomarkers and novel combinational strategies are required to improve the effectiveness and durability of treatment response 6for people with NSCLC. The aim of this study was to identify novel biomarkers and/or druggable proteins from deregulated protein networks within non-oncogene driven disease that are involved in the cellular response to cisplatin. Following exposure of NSCLC cells to cisplatin, in vitro quantitative mass spectrometry was applied to identify altered protein response networks. A total of 65 proteins were significantly deregulated following cisplatin exposure. These proteins were assessed to determine if they are druggable targets using novel machine learning approaches and to identify whether these proteins might serve as prognosticators of platinum therapy. Our data demonstrate novel candidates and drug-like molecules warranting further investigation to improve response to platinum agents in NSCLC.
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Affiliation(s)
- Sarah-Louise Ryan
- Faculty of Health, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Translational Research Institute, Queensland University of Technology, Woolloongabba, QLD, Australia
| | - Keyur A Dave
- Faculty of Health, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Translational Research Institute, Queensland University of Technology, Woolloongabba, QLD, Australia
| | - Sam Beard
- Faculty of Health, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Translational Research Institute, Queensland University of Technology, Woolloongabba, QLD, Australia
| | - Martina Gyimesi
- Faculty of Health, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Translational Research Institute, Queensland University of Technology, Woolloongabba, QLD, Australia
| | - Matthew McTaggart
- Faculty of Health, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Translational Research Institute, Queensland University of Technology, Woolloongabba, QLD, Australia
| | - Katherine B Sahin
- Faculty of Health, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Translational Research Institute, Queensland University of Technology, Woolloongabba, QLD, Australia
| | - Christopher Molloy
- Faculty of Health, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Translational Research Institute, Queensland University of Technology, Woolloongabba, QLD, Australia
| | - Neha S Gandhi
- Faculty of Science and Engineering, School of Chemistry and Physics, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Eric Boittier
- Faculty of Health, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Translational Research Institute, Queensland University of Technology, Woolloongabba, QLD, Australia
| | - Connor G O'Leary
- Faculty of Health, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Translational Research Institute, Queensland University of Technology, Woolloongabba, QLD, Australia.,Cancer Services, Princess Alexandra Hospital, Woolloongabba, QLD, Australia
| | - Esha T Shah
- Faculty of Health, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Translational Research Institute, Queensland University of Technology, Woolloongabba, QLD, Australia
| | - Emma Bolderson
- Faculty of Health, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Translational Research Institute, Queensland University of Technology, Woolloongabba, QLD, Australia
| | - Anne-Marie Baird
- Department of Clinical Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland.,Thoracic Oncology Research Group, Labmed Directorate, St. James's Hospital, Dublin, Ireland
| | - Derek J Richard
- Faculty of Health, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Translational Research Institute, Queensland University of Technology, Woolloongabba, QLD, Australia
| | - Kenneth J O'Byrne
- Faculty of Health, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Translational Research Institute, Queensland University of Technology, Woolloongabba, QLD, Australia.,Cancer Services, Princess Alexandra Hospital, Woolloongabba, QLD, Australia.,Thoracic Oncology Research Group, Labmed Directorate, St. James's Hospital, Dublin, Ireland
| | - Mark N Adams
- Faculty of Health, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Translational Research Institute, Queensland University of Technology, Woolloongabba, QLD, Australia
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45
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Villalba JM, Navas P. Regulation of coenzyme Q biosynthesis pathway in eukaryotes. Free Radic Biol Med 2021; 165:312-323. [PMID: 33549646 DOI: 10.1016/j.freeradbiomed.2021.01.055] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/22/2021] [Accepted: 01/30/2021] [Indexed: 12/21/2022]
Abstract
Coenzyme Q (CoQ, ubiquinone/ubiquinol) is a ubiquitous and unique molecule that drives electrons in mitochondrial respiratory chain and an obligatory step for multiple metabolic pathways in aerobic metabolism. Alteration of CoQ biosynthesis or its redox stage are causing mitochondrial dysfunctions as hallmark of heterogeneous disorders as mitochondrial/metabolic, cardiovascular, and age-associated diseases. Regulation of CoQ biosynthesis pathway is demonstrated to affect all steps of proteins production of this pathway, posttranslational modifications and protein-protein-lipid interactions inside mitochondria. There is a bi-directional relationship between CoQ and the epigenome in which not only the CoQ status determines the epigenetic regulation of many genes, but CoQ biosynthesis is also a target for epigenetic regulation, which adds another layer of complexity to the many pathways by which CoQ levels are regulated by environmental and developmental signals to fulfill its functions in eukaryotic aerobic metabolism.
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Affiliation(s)
- José Manuel Villalba
- Departamento de Biología Celular, Fisiología e Inmunología, Universidad de Córdoba, Campus de Excelencia Internacional Agroalimentario, ceiA3, Spain
| | - Plácido Navas
- Centro Andaluz de Biología del Desarrollo and CIBERER, Instituto de Salud Carlos III, Universidad Pablo de Olavide-CSIC-JA, Sevilla, 41013, Spain.
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46
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Ayabe H, Kawai N, Shibamura M, Fukao Y, Fujimoto M, Tsutsumi N, Arimura SI. FMT, a protein that affects mitochondrial distribution, interacts with translation-related proteins in Arabidopsis thaliana. PLANT CELL REPORTS 2021; 40:327-337. [PMID: 33385240 DOI: 10.1007/s00299-020-02634-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 11/06/2020] [Indexed: 06/12/2023]
Abstract
Two translation-related proteins are identified as FMT-interacting proteins. However, FMT, unlike mutants of other CLU genes in fly and human, has no clear impact on the accumulation of mitochondrial proteins. Organelle distribution is critical for effective metabolism and stress response and is controlled by various environmental factors. Clustered mitochondria (CLU) superfamily genes affect mitochondrial distribution and their disruptions cause mitochondria to cluster within a cell in various species including yeast, fly, mammals and Arabidopsis. In Arabidopsis thaliana, Friendly mitochondria (FMT) is a CLU gene that is required for normal mitochondrial distribution, but its molecular function is unclear. Here, we demonstrate that FMT interacts with some translation-related proteins (translation initiation factor eIFiso4G1 and glutamyl-tRNA synthetase OVA9), as well as itself. We also show FMT forms dynamic particles in the cytosol that sometimes move with mitochondria, and their movements are mainly controlled by actin filaments but also by microtubules. Similar results have been reported for animal CLU orthologs. However, an fmt mutant, unlike animal clu mutants, did not show any clear decrease of nuclear-encoded mitochondrial protein levels. This difference may reflect a functional divergence of FMT from other CLU superfamily genes.
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Affiliation(s)
- Hiroki Ayabe
- Graduate School of Agricultural & Life Sciences, University of Tokyo, Tokyo, Japan
| | - Narumi Kawai
- Graduate School of Agricultural & Life Sciences, University of Tokyo, Tokyo, Japan
| | - Mitsuhiro Shibamura
- Graduate School of Agricultural & Life Sciences, University of Tokyo, Tokyo, Japan
| | - Yoichiro Fukao
- Graduate School of Life Science, Ritsumeikan University, Shiga, Japan
| | - Masaru Fujimoto
- Graduate School of Agricultural & Life Sciences, University of Tokyo, Tokyo, Japan
| | - Nobuhiro Tsutsumi
- Graduate School of Agricultural & Life Sciences, University of Tokyo, Tokyo, Japan
| | - Shin-Ichi Arimura
- Graduate School of Agricultural & Life Sciences, University of Tokyo, Tokyo, Japan.
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47
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Tsuboi T, Leff J, Zid BM. Post-transcriptional control of mitochondrial protein composition in changing environmental conditions. Biochem Soc Trans 2020; 48:2565-2578. [PMID: 33245320 PMCID: PMC8108647 DOI: 10.1042/bst20200250] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/26/2020] [Accepted: 10/29/2020] [Indexed: 02/07/2023]
Abstract
In fluctuating environmental conditions, organisms must modulate their bioenergetic production in order to maintain cellular homeostasis for optimal fitness. Mitochondria are hubs for metabolite and energy generation. Mitochondria are also highly dynamic in their function: modulating their composition, size, density, and the network-like architecture in relation to the metabolic demands of the cell. Here, we review the recent research on the post-transcriptional regulation of mitochondrial composition focusing on mRNA localization, mRNA translation, protein import, and the role that dynamic mitochondrial structure may have on these gene expression processes. As mitochondrial structure and function has been shown to be very important for age-related processes, including cancer, metabolic disorders, and neurodegeneration, understanding how mitochondrial composition can be affected in fluctuating conditions can lead to new therapeutic directions to pursue.
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Affiliation(s)
- Tatsuhisa Tsuboi
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92023-0358, USA
| | - Jordan Leff
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92023-0358, USA
| | - Brian M. Zid
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92023-0358, USA
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48
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Chaanine AH, LeJemtel TH, Delafontaine P. Mitochondrial Pathobiology and Metabolic Remodeling in Progression to Overt Systolic Heart Failure. J Clin Med 2020; 9:jcm9113582. [PMID: 33172082 PMCID: PMC7694785 DOI: 10.3390/jcm9113582] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 11/02/2020] [Accepted: 11/04/2020] [Indexed: 12/04/2022] Open
Abstract
The mitochondria are mostly abundant in the heart, a beating organ of high- energy demands. Their function extends beyond being a power plant of the cell including redox balance, ion homeostasis and metabolism. They are dynamic organelles that are tethered to neighboring structures, especially the endoplasmic reticulum. Together, they constitute a functional unit implicated in complex physiological and pathophysiological processes. Their topology in the cell, the cardiac myocyte in particular, places them at the hub of signaling and calcium homeostasis, making them master regulators of cell survival or cell death. Perturbations in mitochondrial function play a central role in the pathophysiology of myocardial remodeling and progression of heart failure. In this minireview, we summarize important pathophysiological mechanisms, pertaining to mitochondrial morphology, dynamics and function, which take place in compensated hypertrophy and in progression to overt systolic heart failure. Published work in the last few years has expanded our understanding of these important mechanisms; a key prerequisite to identifying therapeutic strategies targeting mitochondrial dysfunction in heart failure.
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Affiliation(s)
- Antoine H. Chaanine
- Department of Medicine/Heart and Vascular Institute, Tulane University, New Orleans, LA 70112, USA; (T.H.L.); (P.D.)
- Department of Physiology, Tulane University, New Orleans, LA 70112, USA
- Correspondence: ; Tel.: +504-988-1612; Fax: +504-995-2771
| | - Thierry H. LeJemtel
- Department of Medicine/Heart and Vascular Institute, Tulane University, New Orleans, LA 70112, USA; (T.H.L.); (P.D.)
| | - Patrice Delafontaine
- Department of Medicine/Heart and Vascular Institute, Tulane University, New Orleans, LA 70112, USA; (T.H.L.); (P.D.)
- Department of Physiology, Tulane University, New Orleans, LA 70112, USA
- Department of Pharmacology, Tulane University, New Orleans, LA 70112, USA
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49
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Mitochondrial biogenesis in organismal senescence and neurodegeneration. Mech Ageing Dev 2020; 191:111345. [DOI: 10.1016/j.mad.2020.111345] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/17/2020] [Accepted: 08/27/2020] [Indexed: 12/19/2022]
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Trenkel VM, Boudry P, Verrez-Bagnis V, Lorance P. Methods for identifying and interpreting sex-linked SNP markers and carrying out sex assignment: application to thornback ray (Raja clavata). Mol Ecol Resour 2020; 20:1610-1619. [PMID: 32657500 DOI: 10.1111/1755-0998.13225] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 06/18/2020] [Accepted: 07/08/2020] [Indexed: 11/28/2022]
Abstract
Sex-determining modes remain unknown in numerous species, notably in fishes, in which a variety of modalities have been reported. Additionally, noninvasive individual sexing is problematic for species without external sex attributes or for early life stages, requiring cytogenetic or molecular analyses when sex chromosomes or sex-linked markers have been characterized. Genomics now provide a means to achieve this. Here, we review common sex-determination systems and corresponding statistical methods for identifying sex-linked genetic markers and their use for sex assignment, focusing on single nucleotide polymorphism (SNP) markers derived from reduced representation sequencing methods. We demonstrate the dependence of expected sex assignment error on the number of sex-linked SNPs and minor allele frequency. The application of three methods was made here: (a) identification of heterozygote excess in one sex, (b) FST outlier analysis between the two sexes and (c) neuronal net modelling. These methods were applied to a large SNP data set (4604 SNPs) for 1680 thornback rays (Raja clavata). Using method (a), nineteen putative sex-linked SNPs were identified. Comparison with the reference genome of a related species (Amblyraja radiata) indicated that all 19 SNPs are probably located on the same chromosome. These results suggest that thornback ray has a XX/XY sex-determination system. Method (b) identified eight SNPs probably located on different chromosomes. Method (a) led to the lowest sex assignment error among the three methods (4.2% error for females and 3.7% for males).
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Affiliation(s)
| | - Pierre Boudry
- CNRS, IRD, LEMAR, Ifremer, Univ Brest, Plouzané, France
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