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Martin-Solana E, Casado-Zueras L, Torres TE, Goya GF, Fernandez-Fernandez MR, Fernandez JJ. Disruption of the mitochondrial network in a mouse model of Huntington's disease visualized by in-tissue multiscale 3D electron microscopy. Acta Neuropathol Commun 2024; 12:88. [PMID: 38840253 PMCID: PMC11151585 DOI: 10.1186/s40478-024-01802-2] [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: 04/04/2024] [Accepted: 05/27/2024] [Indexed: 06/07/2024] Open
Abstract
Huntington's disease (HD) is an inherited neurodegenerative disorder caused by an expanded CAG repeat in the coding sequence of huntingtin protein. Initially, it predominantly affects medium-sized spiny neurons (MSSNs) of the corpus striatum. No effective treatment is still available, thus urging the identification of potential therapeutic targets. While evidence of mitochondrial structural alterations in HD exists, previous studies mainly employed 2D approaches and were performed outside the strictly native brain context. In this study, we adopted a novel multiscale approach to conduct a comprehensive 3D in situ structural analysis of mitochondrial disturbances in a mouse model of HD. We investigated MSSNs within brain tissue under optimal structural conditions utilizing state-of-the-art 3D imaging technologies, specifically FIB/SEM for the complete imaging of neuronal somas and Electron Tomography for detailed morphological examination, and image processing-based quantitative analysis. Our findings suggest a disruption of the mitochondrial network towards fragmentation in HD. The network of interlaced, slim and long mitochondria observed in healthy conditions transforms into isolated, swollen and short entities, with internal cristae disorganization, cavities and abnormally large matrix granules.
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Affiliation(s)
- Eva Martin-Solana
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | | | - Teobaldo E Torres
- Advanced Microscopy Laboratory, University of Zaragoza, Zaragoza, Spain
- Instituto de Nanociencia y Materiales de Aragon (INMA), CSIC-Universidad de Zaragoza, 50018, Zaragoza, Spain
- Department of Condensed Matter Physics, University of Zaragoza, Zaragoza, Spain
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Gerardo F Goya
- Instituto de Nanociencia y Materiales de Aragon (INMA), CSIC-Universidad de Zaragoza, 50018, Zaragoza, Spain
- Department of Condensed Matter Physics, University of Zaragoza, Zaragoza, Spain
| | | | - Jose-Jesus Fernandez
- Spanish National Research Council (CSIC, CINN), Health Research Institute of Asturias (ISPA), 33011, Oviedo, Spain.
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2
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Key J, Gispert S, Auburger G. Knockout Mouse Studies Show That Mitochondrial CLPP Peptidase and CLPX Unfoldase Act in Matrix Condensates near IMM, as Fast Stress Response in Protein Assemblies for Transcript Processing, Translation, and Heme Production. Genes (Basel) 2024; 15:694. [PMID: 38927630 PMCID: PMC11202940 DOI: 10.3390/genes15060694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
LONP1 is the principal AAA+ unfoldase and bulk protease in the mitochondrial matrix, so its deletion causes embryonic lethality. The AAA+ unfoldase CLPX and the peptidase CLPP also act in the matrix, especially during stress periods, but their substrates are poorly defined. Mammalian CLPP deletion triggers infertility, deafness, growth retardation, and cGAS-STING-activated cytosolic innate immunity. CLPX mutations impair heme biosynthesis and heavy metal homeostasis. CLPP and CLPX are conserved from bacteria to humans, despite their secondary role in proteolysis. Based on recent proteomic-metabolomic evidence from knockout mice and patient cells, we propose that CLPP acts on phase-separated ribonucleoprotein granules and CLPX on multi-enzyme condensates as first-aid systems near the inner mitochondrial membrane. Trimming within assemblies, CLPP rescues stalled processes in mitoribosomes, mitochondrial RNA granules and nucleoids, and the D-foci-mediated degradation of toxic double-stranded mtRNA/mtDNA. Unfolding multi-enzyme condensates, CLPX maximizes PLP-dependent delta-transamination and rescues malformed nascent peptides. Overall, their actions occur in granules with multivalent or hydrophobic interactions, separated from the aqueous phase. Thus, the role of CLPXP in the matrix is compartment-selective, as other mitochondrial peptidases: MPPs at precursor import pores, m-AAA and i-AAA at either IMM face, PARL within the IMM, and OMA1/HTRA2 in the intermembrane space.
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Affiliation(s)
| | | | - Georg Auburger
- Experimental Neurology, Clinic of Neurology, University Hospital, Goethe University Frankfurt, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (J.K.); (S.G.)
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3
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Nesterov SV, Ilyinsky NS, Plokhikh KS, Manuylov VD, Chesnokov YM, Vasilov RG, Kuznetsova IM, Turoverov KK, Gordeliy VI, Fonin AV, Uversky VN. Order wrapped in chaos: On the roles of intrinsically disordered proteins and RNAs in the arrangement of the mitochondrial enzymatic machines. Int J Biol Macromol 2024; 267:131455. [PMID: 38588835 DOI: 10.1016/j.ijbiomac.2024.131455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 04/10/2024]
Abstract
The analysis of cryo-electron tomography images of human and rat mitochondria revealed that the mitochondrial matrix is at least as crowded as the cytosol. To mitigate the crowding effects, metabolite transport in the mitochondria primarily occurs through the intermembrane space, which is significantly less crowded. The scientific literature largely ignores how enzyme systems and metabolite transport are organized in the crowded environment of the mitochondrial matrix. Under crowded conditions, multivalent interactions carried out by disordered protein regions (IDRs), may become extremely important. We analyzed the human mitochondrial proteome to determine the presence and physiological significance of IDRs. Despite mitochondrial proteins being generally more ordered than cytosolic or overall proteome proteins, disordered regions plays a significant role in certain mitochondrial compartments and processes. Even in highly ordered enzyme systems, there are proteins with long IDRs. Some IDRs act as binding elements between highly ordered subunits, while the roles of others are not yet established. Mitochondrial systems, like their bacterial ancestors, rely less on IDRs and more on RNA for LLPS compartmentalization. More evolutionarily advanced subsystems that enable mitochondria-cell interactions contain more IDRs. The study highlights the crucial and often overlooked role played by IDRs and non-coding RNAs in mitochondrial organization.
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Affiliation(s)
- Semen V Nesterov
- National Research Center "Kurchatov Institute", Moscow 123182, Russia; Moscow Institute of Physics and Techonology, Dolgoprudny, Moscow Region 141701, Russia; Institute of Cytology, Russian Academy of Sciences, Saint Petersburg 194064, Russia.
| | - Nikolay S Ilyinsky
- Moscow Institute of Physics and Techonology, Dolgoprudny, Moscow Region 141701, Russia.
| | | | - Vladimir D Manuylov
- Moscow Institute of Physics and Techonology, Dolgoprudny, Moscow Region 141701, Russia
| | - Yuriy M Chesnokov
- National Research Center "Kurchatov Institute", Moscow 123182, Russia
| | - Raif G Vasilov
- National Research Center "Kurchatov Institute", Moscow 123182, Russia
| | - Irina M Kuznetsova
- Institute of Cytology, Russian Academy of Sciences, Saint Petersburg 194064, Russia
| | | | - Valentin I Gordeliy
- Institut de Biologie Structurale Jean-Pierre Ebel, Université Grenoble Alpes-Commissariat à l'Energie Atomique et aux Energies Alternatives-CNRS, 38027 Grenoble, France
| | - Alexander V Fonin
- Institute of Cytology, Russian Academy of Sciences, Saint Petersburg 194064, Russia
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., MDC07, Tampa, FL 33612, USA.
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4
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Leisten ED, Woods AC, Wong YC. Super-resolution microscopy: Insights into mitochondria-lysosome crosstalk in health and disease. J Cell Biol 2023; 222:e202305032. [PMID: 37917024 PMCID: PMC10621667 DOI: 10.1083/jcb.202305032] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Abstract
Live super-resolution microscopy has allowed for new insights into recently identified mitochondria-lysosome contact sites, which mediate crosstalk between mitochondria and lysosomes, including co-regulation of Rab7 GTP hydrolysis and Drp1 GTP hydrolysis. Here, we highlight recent findings and future perspectives on this dynamic pathway and its roles in health and disease.
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Affiliation(s)
- Eric D. Leisten
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Abby C. Woods
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Yvette C. Wong
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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5
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Rey T, Tábara LC, Prudent J, Minczuk M. mtFociCounter for automated single-cell mitochondrial nucleoid quantification and reproducible foci analysis. Nucleic Acids Res 2023; 51:e107. [PMID: 37850644 PMCID: PMC10681798 DOI: 10.1093/nar/gkad864] [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] [Received: 05/16/2023] [Revised: 09/13/2023] [Accepted: 10/01/2023] [Indexed: 10/19/2023] Open
Abstract
Mitochondrial DNA (mtDNA) encodes the core subunits for OXPHOS, essential in near-all eukaryotes. Packed into distinct foci (nucleoids) inside mitochondria, the number of mtDNA copies differs between cell-types and is affected in several human diseases. Currently, common protocols estimate per-cell mtDNA-molecule numbers by sequencing or qPCR from bulk samples. However, this does not allow insight into cell-to-cell heterogeneity and can mask phenotypical sub-populations. Here, we present mtFociCounter, a single-cell image analysis tool for reproducible quantification of nucleoids and other foci. mtFociCounter is a light-weight, open-source freeware and overcomes current limitations to reproducible single-cell analysis of mitochondrial foci. We demonstrate its use by analysing 2165 single fibroblasts, and observe a large cell-to-cell heterogeneity in nucleoid numbers. In addition, mtFociCounter quantifies mitochondrial content and our results show good correlation (R = 0.90) between nucleoid number and mitochondrial area, and we find nucleoid density is less variable than nucleoid numbers in wild-type cells. Finally, we demonstrate mtFociCounter readily detects differences in foci-numbers upon sample treatment, and applies to Mitochondrial RNA Granules and superresolution microscopy. mtFociCounter provides a versatile solution to reproducibly quantify cellular foci in single cells and our results highlight the importance of accounting for cell-to-cell variance and mitochondrial context in mitochondrial foci analysis.
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Affiliation(s)
- Timo Rey
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Luis Carlos Tábara
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Julien Prudent
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Michal Minczuk
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
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6
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Toledo PL, Gianotti AR, Vazquez DS, Ermácora MR. Protein nanocondensates: the next frontier. Biophys Rev 2023; 15:515-530. [PMID: 37681092 PMCID: PMC10480383 DOI: 10.1007/s12551-023-01105-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 07/21/2023] [Indexed: 09/09/2023] Open
Abstract
Over the past decade, myriads of studies have highlighted the central role of protein condensation in subcellular compartmentalization and spatiotemporal organization of biological processes. Conceptually, protein condensation stands at the highest level in protein structure hierarchy, accounting for the assembly of bodies ranging from thousands to billions of molecules and for densities ranging from dense liquids to solid materials. In size, protein condensates range from nanocondensates of hundreds of nanometers (mesoscopic clusters) to phase-separated micron-sized condensates. In this review, we focus on protein nanocondensation, a process that can occur in subsaturated solutions and can nucleate dense liquid phases, crystals, amorphous aggregates, and fibers. We discuss the nanocondensation of proteins in the light of general physical principles and examine the biophysical properties of several outstanding examples of nanocondensation. We conclude that protein nanocondensation cannot be fully explained by the conceptual framework of micron-scale biomolecular condensation. The evolution of nanocondensates through changes in density and order is currently under intense investigation, and this should lead to the development of a general theoretical framework, capable of encompassing the full range of sizes and densities found in protein condensates.
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Affiliation(s)
- Pamela L. Toledo
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876, Bernal, Buenos Aires, Argentina
- Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Alejo R. Gianotti
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876, Bernal, Buenos Aires, Argentina
- Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Diego S. Vazquez
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876, Bernal, Buenos Aires, Argentina
- Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Mario R. Ermácora
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876, Bernal, Buenos Aires, Argentina
- Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Bernal, Argentina
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7
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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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8
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Sun CL, Van Gilst M, Crowder CM. Hypoxia-induced mitochondrial stress granules. Cell Death Dis 2023; 14:448. [PMID: 37468471 PMCID: PMC10356818 DOI: 10.1038/s41419-023-05988-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 07/10/2023] [Accepted: 07/12/2023] [Indexed: 07/21/2023]
Abstract
Perturbations of mitochondrial proteostasis have been associated with aging, neurodegenerative diseases, and recently with hypoxic injury. While examining hypoxia-induced mitochondrial protein aggregation in C. elegans, we found that sublethal hypoxia, sodium azide, or heat shock-induced abundant ethidium bromide staining mitochondrial granules that preceded evidence of protein aggregation. Genetic manipulations that reduce cellular and organismal hypoxic death block the formation of these mitochondrial stress granules (mitoSG). Knockdown of mitochondrial nucleoid proteins also blocked the formation of mitoSG by a mechanism distinct from the mitochondrial unfolded protein response. Lack of the major mitochondrial matrix protease LONP-1 resulted in the constitutive formation of mitoSG without external stress. Ethidium bromide-staining RNA-containing mitochondrial granules were also observed in rat cardiomyocytes treated with sodium azide, a hypoxia mimetic. Mitochondrial stress granules are an early mitochondrial pathology controlled by LONP and the nucleoid, preceding hypoxia-induced protein aggregation.
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Affiliation(s)
- Chun-Ling Sun
- Department of Anesthesiology and Pain Medicine, University of Washington School of Medicine, Seattle, Washington, 98109, USA
- Mitochondrial and Metabolism Center, University of Washington School of Medicine, Seattle, Washington, 98109, USA
| | - Marc Van Gilst
- Department of Anesthesiology and Pain Medicine, University of Washington School of Medicine, Seattle, Washington, 98109, USA
- Mitochondrial and Metabolism Center, University of Washington School of Medicine, Seattle, Washington, 98109, USA
| | - C Michael Crowder
- Department of Anesthesiology and Pain Medicine, University of Washington School of Medicine, Seattle, Washington, 98109, USA.
- Mitochondrial and Metabolism Center, University of Washington School of Medicine, Seattle, Washington, 98109, USA.
- Department of Genome Science, University of Washington School of Medicine, Seattle, Washington, 98109, USA.
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9
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Chukrallah LG, Snyder EM. Modern tools applied to classic structures: Approaches for mammalian male germ cell RNA granule research. Andrology 2023; 11:872-883. [PMID: 36273399 DOI: 10.1111/andr.13320] [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: 07/29/2022] [Revised: 09/20/2022] [Accepted: 10/10/2022] [Indexed: 11/28/2022]
Abstract
First reported in the 1800s, germ cell granules are small nonmembrane bound RNA-rich regions of the cytoplasm. These sites of critical RNA processing and storage in the male germ cell are essential for proper differentiation and development and are present in a wide range of species from Caenorhabditis elegans through mammals. Initially characterized by light and electron microscopy, more modern techniques such as immunofluorescence and genetic models have played a major role in expanding our understanding of the composition of these structures. While these methods have given light to potential granule functions, much work remains to be done. The current expansion of imaging technologies and omics-scale analyses to germ cell granule research will drive the field forward considerably. Many of these methods, both current and upcoming, have considerable caveats and limitations that necessitate a holistic approach to the study of germ granules. By combining and balancing different techniques, the field is poised to elucidate the nature of these critical structures.
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Affiliation(s)
- Lauren G Chukrallah
- Department of Animal Science, Rutgers, the State University of New Jersey, New Brunswick, New Jersey, USA
| | - Elizabeth M Snyder
- Department of Animal Science, Rutgers, the State University of New Jersey, New Brunswick, New Jersey, USA
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10
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Zhou Q, Wang Y, Lu Z, He C, Li L, You M, Wang L, Cao T, Zhao Y, Li Q, Mou A, Shu W, He H, Zhao Z, Liu D, Zhu Z, Gao P, Yan Z. Cx43 acts as a mitochondrial calcium regulator that promotes obesity by inducing the polarization of macrophages in adipose tissue. Cell Signal 2023; 105:110606. [PMID: 36681290 DOI: 10.1016/j.cellsig.2023.110606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/12/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023]
Abstract
Metabolic reprogramming of macrophages initiates the polarization of pro-inflammatory macrophages that exacerbates adipocyte dysfunction and obesity. The imbalance of mitochondrial Ca2+ homeostasis impairs mitochondrial function and promotes inflammation. Connexin 43 (Cx43), a ubiquitous gap junction protein, has been demonstrated to regulate intracellular Ca2+ homeostasis. Here we explored whether macrophage Cx43 affects the obesity process by regulating the polarization of macrophage. HFD treatment induced obesity and exacerbated macrophages infiltration with upregulation of macrophages Cx43. Macrophage-specific knockout of Cx43 reduced HFD-induced obesity by alleviating inflammation in adipose tissue, with less pro-inflammatory M1 macrophage infiltration. Consistently, inhibition or knockdown of Cx43 improved palmitic acid (PA) induced mitochondrial dysfunction, as indicated by improved oxidative phosphorylation (OXPHOS), reduced formation of mitochondria-associated membranes (MAM) and mitochondrial Ca2+ overload. Mechanistically, Cx43 interacted with the mitochondrial Ca2+ uniporter (MCU) and knockdown of Cx43 alleviated PA-induced succinate dehydrogenase (SDH) oxidation by lowering MCU-mediated mitochondrial Ca2+ uptake, which then, promoting the polarization of pro-inflammatory M1 macrophages. Thus, this study identified Cx43 as a mitochondrial Ca2+ regulator that aggravates obesity via promoting macrophages polarized to M1 pro-inflammatory phenotype and suggests that Cx43 might be a promising therapeutic target antagonizing obesity.
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Affiliation(s)
- Qing Zhou
- Department of Hypertension and Endocrinology, Center for Hypertension and Metabolic Diseases, Daping Hospital, Army Medical University, and Chongqing Institute of Hypertension, Chongqing, China
| | - Yuyan Wang
- School of Medicine, Chongqing University, Chongqing, China
| | - Zongshi Lu
- Department of Hypertension and Endocrinology, Center for Hypertension and Metabolic Diseases, Daping Hospital, Army Medical University, and Chongqing Institute of Hypertension, Chongqing, China
| | - Chengkang He
- Department of Hypertension and Endocrinology, Center for Hypertension and Metabolic Diseases, Daping Hospital, Army Medical University, and Chongqing Institute of Hypertension, Chongqing, China
| | - Li Li
- Department of Hypertension and Endocrinology, Center for Hypertension and Metabolic Diseases, Daping Hospital, Army Medical University, and Chongqing Institute of Hypertension, Chongqing, China
| | - Mei You
- Department of Hypertension and Endocrinology, Center for Hypertension and Metabolic Diseases, Daping Hospital, Army Medical University, and Chongqing Institute of Hypertension, Chongqing, China
| | - Lijuan Wang
- Department of Hypertension and Endocrinology, Center for Hypertension and Metabolic Diseases, Daping Hospital, Army Medical University, and Chongqing Institute of Hypertension, Chongqing, China
| | - Tingbing Cao
- Department of Hypertension and Endocrinology, Center for Hypertension and Metabolic Diseases, Daping Hospital, Army Medical University, and Chongqing Institute of Hypertension, Chongqing, China
| | - Yu Zhao
- Department of Hypertension and Endocrinology, Center for Hypertension and Metabolic Diseases, Daping Hospital, Army Medical University, and Chongqing Institute of Hypertension, Chongqing, China
| | - Qiang Li
- Department of Hypertension and Endocrinology, Center for Hypertension and Metabolic Diseases, Daping Hospital, Army Medical University, and Chongqing Institute of Hypertension, Chongqing, China
| | - Aidi Mou
- Department of Hypertension and Endocrinology, Center for Hypertension and Metabolic Diseases, Daping Hospital, Army Medical University, and Chongqing Institute of Hypertension, Chongqing, China
| | - Wentao Shu
- Department of Hypertension and Endocrinology, Center for Hypertension and Metabolic Diseases, Daping Hospital, Army Medical University, and Chongqing Institute of Hypertension, Chongqing, China
| | - Hongbo He
- Department of Hypertension and Endocrinology, Center for Hypertension and Metabolic Diseases, Daping Hospital, Army Medical University, and Chongqing Institute of Hypertension, Chongqing, China
| | - Zhigang Zhao
- Department of Hypertension and Endocrinology, Center for Hypertension and Metabolic Diseases, Daping Hospital, Army Medical University, and Chongqing Institute of Hypertension, Chongqing, China
| | - Daoyan Liu
- Department of Hypertension and Endocrinology, Center for Hypertension and Metabolic Diseases, Daping Hospital, Army Medical University, and Chongqing Institute of Hypertension, Chongqing, China
| | - Zhiming Zhu
- Department of Hypertension and Endocrinology, Center for Hypertension and Metabolic Diseases, Daping Hospital, Army Medical University, and Chongqing Institute of Hypertension, Chongqing, China.
| | - Peng Gao
- Department of Hypertension and Endocrinology, Center for Hypertension and Metabolic Diseases, Daping Hospital, Army Medical University, and Chongqing Institute of Hypertension, Chongqing, China.
| | - Zhencheng Yan
- Department of Hypertension and Endocrinology, Center for Hypertension and Metabolic Diseases, Daping Hospital, Army Medical University, and Chongqing Institute of Hypertension, Chongqing, China.
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11
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Schäfer JA, Sutandy FXR, Münch C. Omics-based approaches for the systematic profiling of mitochondrial biology. Mol Cell 2023; 83:911-926. [PMID: 36931258 DOI: 10.1016/j.molcel.2023.02.015] [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: 11/11/2022] [Revised: 02/06/2023] [Accepted: 02/14/2023] [Indexed: 03/18/2023]
Abstract
Mitochondria are essential for cellular functions such as metabolism and apoptosis. They dynamically adapt to the changing environmental demands by adjusting their protein, nucleic acid, metabolite, and lipid contents. In addition, the mitochondrial components are modulated on different levels in response to changes, including abundance, activity, and interaction. A wide range of omics-based approaches has been developed to be able to explore mitochondrial adaptation and how mitochondrial function is compromised in disease contexts. Here, we provide an overview of the omics methods that allow us to systematically investigate the different aspects of mitochondrial biology. In addition, we show examples of how these methods have provided new biological insights. The emerging use of these toolboxes provides a more comprehensive understanding of the processes underlying mitochondrial function.
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Affiliation(s)
- Jasmin Adriana Schäfer
- Institute of Biochemistry II, Goethe University Frankfurt, Theodor-Stern-Kai 7, Haus 75, 60590 Frankfurt am Main, Germany
| | - F X Reymond Sutandy
- Institute of Biochemistry II, Goethe University Frankfurt, Theodor-Stern-Kai 7, Haus 75, 60590 Frankfurt am Main, Germany
| | - Christian Münch
- Institute of Biochemistry II, Goethe University Frankfurt, Theodor-Stern-Kai 7, Haus 75, 60590 Frankfurt am Main, Germany.
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12
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Wu GH, Smith-Geater C, Galaz-Montoya JG, Gu Y, Gupte SR, Aviner R, Mitchell PG, Hsu J, Miramontes R, Wang KQ, Geller NR, Hou C, Danita C, Joubert LM, Schmid MF, Yeung S, Frydman J, Mobley W, Wu C, Thompson LM, Chiu W. CryoET reveals organelle phenotypes in huntington disease patient iPSC-derived and mouse primary neurons. Nat Commun 2023; 14:692. [PMID: 36754966 PMCID: PMC9908936 DOI: 10.1038/s41467-023-36096-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 01/13/2023] [Indexed: 02/10/2023] Open
Abstract
Huntington's disease (HD) is caused by an expanded CAG repeat in the huntingtin gene, yielding a Huntingtin protein with an expanded polyglutamine tract. While experiments with patient-derived induced pluripotent stem cells (iPSCs) can help understand disease, defining pathological biomarkers remains challenging. Here, we used cryogenic electron tomography to visualize neurites in HD patient iPSC-derived neurons with varying CAG repeats, and primary cortical neurons from BACHD, deltaN17-BACHD, and wild-type mice. In HD models, we discovered sheet aggregates in double membrane-bound organelles, and mitochondria with distorted cristae and enlarged granules, likely mitochondrial RNA granules. We used artificial intelligence to quantify mitochondrial granules, and proteomics experiments reveal differential protein content in isolated HD mitochondria. Knockdown of Protein Inhibitor of Activated STAT1 ameliorated aberrant phenotypes in iPSC- and BACHD neurons. We show that integrated ultrastructural and proteomic approaches may uncover early HD phenotypes to accelerate diagnostics and the development of targeted therapeutics for HD.
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Affiliation(s)
- Gong-Her Wu
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, 94305, USA
| | - Charlene Smith-Geater
- Department of Psychiatry & Human Behavior University of California Irvine, Irvine, CA, 92697, USA
| | - Jesús G Galaz-Montoya
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, 94305, USA
| | - Yingli Gu
- Department of Neurosciences, University of California San Diego, La Jolla, CA, 92037-0662, USA
| | - Sanket R Gupte
- Department of Computer Science, Stanford University, Stanford, CA, 94305, USA
| | - Ranen Aviner
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Patrick G Mitchell
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, USA
| | - Joy Hsu
- Department of Computer Science, Stanford University, Stanford, CA, 94305, USA
| | - Ricardo Miramontes
- Department of Memory Impairment and Neurological Disorders, University of California Irvine, Irvine, CA, 92697, USA
| | - Keona Q Wang
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, 96267, USA
| | - Nicolette R Geller
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, 96267, USA
| | - Cathy Hou
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, 94305, USA
| | - Cristina Danita
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, 94305, USA
| | - Lydia-Marie Joubert
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, USA
| | - Michael F Schmid
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, USA
| | - Serena Yeung
- Department of Computer Science, Stanford University, Stanford, CA, 94305, USA.,Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.,Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - William Mobley
- Department of Neurosciences, University of California San Diego, La Jolla, CA, 92037-0662, USA
| | - Chengbiao Wu
- Department of Neurosciences, University of California San Diego, La Jolla, CA, 92037-0662, USA
| | - Leslie M Thompson
- Department of Psychiatry & Human Behavior University of California Irvine, Irvine, CA, 92697, USA. .,Department of Memory Impairment and Neurological Disorders, University of California Irvine, Irvine, CA, 92697, USA. .,Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, 96267, USA. .,Sue & Bill Gross Stem Cell Research Center, University of California Irvine, Irvine, CA, 96267, USA. .,Department of Biological Chemistry, University of California Irvine, Irvine, CA, 92617, USA.
| | - Wah Chiu
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, 94305, USA. .,Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, USA. .,Department of Microbiology and Immunology, Stanford University, Stanford, CA, 94305, USA.
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13
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Zhorabek F, Abesekara MS, Liu J, Dai X, Huang J, Chau Y. Construction of multiphasic membraneless organelles towards spontaneous spatial segregation and directional flow of biochemical reactions. Chem Sci 2023; 14:801-811. [PMID: 36755726 PMCID: PMC9890938 DOI: 10.1039/d2sc05438h] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/29/2022] [Indexed: 01/15/2023] Open
Abstract
Many intracellular membraneless organelles (MLOs) appear to adapt a hierarchical multicompartment organization for efficient coordination of highly complex reaction networks. Recapitulating such an internal architecture in biomimetic platforms is, therefore, an important step to facilitate the functional understanding of MLOs and to enable the design of advanced microreactors. Herein, we present a modular bottom-up approach for building synthetic multiphasic condensates using a set of engineered multivalent polymer-oligopeptide hybrids. These hybrid constructs exhibit dynamic phase separation behaviour generating membraneless droplets with a subdivided interior featuring distinct chemical and physical properties, whereby a range of functional biomolecules can be spontaneously enriched and spatially segregated. The platform also attains separated confinement of transcription and translation reactions in proximal compartments, while allowing inter-compartment communication via a directional flow of reactants. With advanced structural and functional features attained, this system can be of great value as a MLO model and as a cell-free system for multiplex chemical biosynthesis.
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Affiliation(s)
- Fariza Zhorabek
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology Clear Water Bay, Kowloon Hong Kong SAR China
| | - Manisha Sandupama Abesekara
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology Clear Water Bay, Kowloon Hong Kong SAR China
| | - Jianhui Liu
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology Clear Water Bay, Kowloon Hong Kong SAR China
| | - Xin Dai
- Department of Chemistry, Hong Kong University of Science and TechnologyClear Water Bay, KowloonHong Kong SARChina
| | - Jinqing Huang
- Department of Chemistry, Hong Kong University of Science and TechnologyClear Water Bay, KowloonHong Kong SARChina
| | - Ying Chau
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology Clear Water Bay, Kowloon Hong Kong SAR China
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14
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Sahayasheela VJ, Yu Z, Hidaka T, Pandian GN, Sugiyama H. Mitochondria and G-quadruplex evolution: an intertwined relationship. Trends Genet 2023; 39:15-30. [PMID: 36414480 PMCID: PMC9772288 DOI: 10.1016/j.tig.2022.10.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/27/2022] [Accepted: 10/27/2022] [Indexed: 11/21/2022]
Abstract
G-quadruplexes (G4s) are non-canonical structures formed in guanine (G)-rich sequences through stacked G tetrads by Hoogsteen hydrogen bonding. Several studies have demonstrated the existence of G4s in the genome of various organisms, including humans, and have proposed that G4s have a regulatory role in various cellular functions. However, little is known regarding the dissemination of G4s in mitochondria. In this review, we report the observation that the number of potential G4-forming sequences in the mitochondrial genome increases with the evolutionary complexity of different species, suggesting that G4s have a beneficial role in higher-order organisms. We also discuss the possible function of G4s in mitochondrial (mt)DNA and long noncoding (lnc)RNA and their role in various biological processes.
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Affiliation(s)
- Vinodh J Sahayasheela
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Zutao Yu
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Takuya Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Ganesh N Pandian
- Institute for Integrated Cell-Material Science (WPI-iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan; Institute for Integrated Cell-Material Science (WPI-iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan.
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15
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Feric M, Sarfallah A, Dar F, Temiakov D, Pappu RV, Misteli T. Mesoscale structure-function relationships in mitochondrial transcriptional condensates. Proc Natl Acad Sci U S A 2022; 119:e2207303119. [PMID: 36191226 PMCID: PMC9565167 DOI: 10.1073/pnas.2207303119] [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: 04/28/2022] [Accepted: 09/09/2022] [Indexed: 12/14/2022] Open
Abstract
In live cells, phase separation is thought to organize macromolecules into membraneless structures known as biomolecular condensates. Here, we reconstituted transcription in condensates from purified mitochondrial components using optimized in vitro reaction conditions to probe the structure-function relationships of biomolecular condensates. We find that the core components of the mt-transcription machinery form multiphasic, viscoelastic condensates in vitro. Strikingly, the rates of condensate-mediated transcription are substantially lower than in solution. The condensate-mediated decrease in transcriptional rates is associated with the formation of vesicle-like structures that are driven by the production and accumulation of RNA during transcription. The generation of RNA alters the global phase behavior and organization of transcription components within condensates. Coarse-grained simulations of mesoscale structures at equilibrium show that the components stably assemble into multiphasic condensates and that the vesicles formed in vitro are the result of dynamical arrest. Overall, our findings illustrate the complex phase behavior of transcribing, multicomponent condensates, and they highlight the intimate, bidirectional interplay of structure and function in transcriptional condensates.
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Affiliation(s)
- Marina Feric
- National Cancer Institute, NIH, Bethesda, MD 20892
- National Institute of General Medical Sciences, NIH, Bethesda, MD 20892
| | - Azadeh Sarfallah
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107
| | - Furqan Dar
- Department of Physics, Washington University in St. Louis, St. Louis, MO 63130
- Department of Biomedical Engineering, Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63130
| | - Dmitry Temiakov
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107
| | - Rohit V. Pappu
- Department of Biomedical Engineering, Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63130
| | - Tom Misteli
- National Cancer Institute, NIH, Bethesda, MD 20892
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16
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Werner E, Gokhale A, Ackert M, Xu C, Wen Z, Roberts AM, Roberts BR, Vrailas-Mortimer A, Crocker A, Faundez V. The mitochondrial RNA granule modulates manganese-dependent cell toxicity. Mol Biol Cell 2022; 33:ar108. [PMID: 35921164 DOI: 10.1091/mbc.e22-03-0096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Prolonged manganese exposure causes manganism, a neurodegenerative movement disorder. The identity of adaptive and nonadaptive cellular processes targeted by manganese remains mostly unexplored. Here we study mechanisms engaged by manganese in genetic cellular models known to increase susceptibility to manganese exposure, the plasma membrane manganese efflux transporter SLC30A10 and the mitochondrial Parkinson's gene PARK2. We found that SLC30A10 and PARK2 mutations as well as manganese exposure compromised the mitochondrial RNA granule composition and function, resulting in disruption of mitochondrial transcript processing. These RNA granule defects led to impaired assembly and function of the mitochondrial respiratory chain. Notably, cells that survived a cytotoxic manganese challenge had impaired RNA granule function, thus suggesting that this granule phenotype was adaptive. CRISPR gene editing of subunits of the mitochondrial RNA granule, FASTKD2 or DHX30, as well as pharmacological inhibition of mitochondrial transcription-translation, were protective rather than deleterious for survival of cells acutely exposed to manganese. Similarly, adult Drosophila mutants with defects in the mitochondrial RNA granule component scully were safeguarded from manganese-induced mortality. We conclude that impairment of the mitochondrial RNA granule function is a protective mechanism for acute manganese toxicity.
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Affiliation(s)
- E Werner
- Department of Cell Biology, Emory University, Atlanta, GA 30322
| | - A Gokhale
- Department of Cell Biology, Emory University, Atlanta, GA 30322
| | - M Ackert
- School of Biological Sciences, Illinois State University, Normal, IL 617901
| | - C Xu
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA 30322
| | - Z Wen
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA 30322
| | - A M Roberts
- Department of Biochemistry, Emory University, Atlanta, GA 30322
| | - B R Roberts
- Department of Biochemistry, Emory University, Atlanta, GA 30322
| | - A Vrailas-Mortimer
- School of Biological Sciences, Illinois State University, Normal, IL 617901
| | - A Crocker
- Program in Neuroscience, Middlebury College, Middlebury, VT 05753
| | - V Faundez
- Department of Cell Biology, Emory University, Atlanta, GA 30322
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17
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Zhu X, Xie X, Das H, Tan BG, Shi Y, Al-Behadili A, Peter B, Motori E, Valenzuela S, Posse V, Gustafsson CM, Hällberg BM, Falkenberg M. Non-coding 7S RNA inhibits transcription via mitochondrial RNA polymerase dimerization. Cell 2022; 185:2309-2323.e24. [PMID: 35662414 DOI: 10.1016/j.cell.2022.05.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 04/05/2022] [Accepted: 05/05/2022] [Indexed: 12/19/2022]
Abstract
The mitochondrial genome encodes 13 components of the oxidative phosphorylation system, and altered mitochondrial transcription drives various human pathologies. A polyadenylated, non-coding RNA molecule known as 7S RNA is transcribed from a region immediately downstream of the light strand promoter in mammalian cells, and its levels change rapidly in response to physiological conditions. Here, we report that 7S RNA has a regulatory function, as it controls levels of mitochondrial transcription both in vitro and in cultured human cells. Using cryo-EM, we show that POLRMT dimerization is induced by interactions with 7S RNA. The resulting POLRMT dimer interface sequesters domains necessary for promoter recognition and unwinding, thereby preventing transcription initiation. We propose that the non-coding 7S RNA molecule is a component of a negative feedback loop that regulates mitochondrial transcription in mammalian cells.
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Affiliation(s)
- Xuefeng Zhu
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, 405 30 Gothenburg, Sweden
| | - Xie Xie
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, 405 30 Gothenburg, Sweden
| | - Hrishikesh Das
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Benedict G Tan
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, 405 30 Gothenburg, Sweden
| | - Yonghong Shi
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, 405 30 Gothenburg, Sweden
| | - Ali Al-Behadili
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, 405 30 Gothenburg, Sweden
| | - Bradley Peter
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, 405 30 Gothenburg, Sweden
| | - Elisa Motori
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), 50931 Cologne, Germany; Institute of Biochemistry, University of Cologne, Zülpicher Str. 47, 50674 Cologne, Germany
| | - Sebastian Valenzuela
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, 405 30 Gothenburg, Sweden
| | - Viktor Posse
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, 405 30 Gothenburg, Sweden
| | - Claes M Gustafsson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, 405 30 Gothenburg, Sweden
| | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden.
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, 405 30 Gothenburg, Sweden.
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18
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Viscomi C, Soriano ME. Molecular Research on Mitochondrial Dysfunction. Int J Mol Sci 2022; 23:ijms23126845. [PMID: 35743286 PMCID: PMC9224555 DOI: 10.3390/ijms23126845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 06/16/2022] [Indexed: 11/26/2022] Open
Affiliation(s)
- Carlo Viscomi
- Department of Biomedical Sciences, University of Padova, 35121 Padova, Italy;
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19
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Feric M, Misteli T. Function moves biomolecular condensates in phase space. Bioessays 2022; 44:e2200001. [PMID: 35243657 PMCID: PMC9277701 DOI: 10.1002/bies.202200001] [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: 01/03/2022] [Revised: 02/19/2022] [Accepted: 02/22/2022] [Indexed: 11/08/2022]
Abstract
Phase separation underlies the formation of biomolecular condensates. We hypothesize the cellular processes that occur within condensates shape their structural features. We use the example of transcription to discuss structure-function relationships in condensates. Various types of transcriptional condensates have been reported across the evolutionary spectrum in the cell nucleus as well as in mitochondrial and bacterial nucleoids. In vitro and in vivo observations suggest that transcriptional activity of condensates influences their supramolecular structure, which in turn affects their function. Condensate organization thus becomes driven by differences in miscibility among the DNA and proteins of the transcription machinery and the RNA transcripts they generate. These considerations are in line with the notion that cellular processes shape the structural properties of condensates, leading to a dynamic, mutual interplay between structure and function in the cell.
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Affiliation(s)
- Marina Feric
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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20
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Organization and expression of the mammalian mitochondrial genome. Nat Rev Genet 2022; 23:606-623. [PMID: 35459860 DOI: 10.1038/s41576-022-00480-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2022] [Indexed: 02/07/2023]
Abstract
The mitochondrial genome encodes core subunits of the respiratory chain that drives oxidative phosphorylation and is, therefore, essential for energy conversion. Advances in high-throughput sequencing technologies and cryoelectron microscopy have shed light on the structure and organization of the mitochondrial genome and revealed unique mechanisms of mitochondrial gene regulation. New animal models of impaired mitochondrial protein synthesis have shown how the coordinated regulation of the cytoplasmic and mitochondrial translation machineries ensures the correct assembly of the respiratory chain complexes. These new technologies and disease models are providing a deeper understanding of mitochondrial genome organization and expression and of the diseases caused by impaired energy conversion, including mitochondrial, neurodegenerative, cardiovascular and metabolic diseases. They also provide avenues for the development of treatments for these conditions.
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21
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Eaglesfield R, Tokatlidis K. Targeting and Insertion of Membrane Proteins in Mitochondria. Front Cell Dev Biol 2022; 9:803205. [PMID: 35004695 PMCID: PMC8740019 DOI: 10.3389/fcell.2021.803205] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/09/2021] [Indexed: 01/26/2023] Open
Abstract
Mitochondrial membrane proteins play an essential role in all major mitochondrial functions. The respiratory complexes of the inner membrane are key for the generation of energy. The carrier proteins for the influx/efflux of essential metabolites to/from the matrix. Many other inner membrane proteins play critical roles in the import and processing of nuclear encoded proteins (∼99% of all mitochondrial proteins). The outer membrane provides another lipidic barrier to nuclear-encoded protein translocation and is home to many proteins involved in the import process, maintenance of ionic balance, as well as the assembly of outer membrane components. While many aspects of the import and assembly pathways of mitochondrial membrane proteins have been elucidated, many open questions remain, especially surrounding the assembly of the respiratory complexes where certain highly hydrophobic subunits are encoded by the mitochondrial DNA and synthesised and inserted into the membrane from the matrix side. This review will examine the various assembly pathways for inner and outer mitochondrial membrane proteins while discussing the most recent structural and biochemical data examining the biogenesis process.
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Affiliation(s)
- Ross Eaglesfield
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, University Avenue, Scotland, United Kingdom
| | - Kostas Tokatlidis
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, University Avenue, Scotland, United Kingdom
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22
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Friedman JR. Mitochondria from the Outside in: The Relationship Between Inter-Organelle Crosstalk and Mitochondrial Internal Organization. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2022; 5:10.1177/25152564221133267. [PMID: 36329759 PMCID: PMC9629538 DOI: 10.1177/25152564221133267] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A fundamental role of membrane-bound organelles is the compartmentalization and organization of cellular processes. Mitochondria perform an immense number of metabolic chemical reactions and to efficiently regulate these, the organelle organizes its inner membrane into distinct morphological domains, including its characteristic cristae membranes. In recent years, a structural feature of increasing apparent importance is the inter-connection between the mitochondrial exterior and other organelles at membrane contact sites (MCSs). Mitochondria form MCSs with almost every other organelle in the cell, including the endoplasmic reticulum, lipid droplets, and lysosomes, to coordinate global cellular metabolism with mitochondrial metabolism. However, these MCSs not only facilitate the transport of metabolites between organelles, but also directly impinge on the physical shape and functional organization inside mitochondria. In this review, we highlight recent advances in our understanding of how physical connections between other organelles and mitochondria both directly and indirectly influence the internal architecture of mitochondria.
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Affiliation(s)
- Jonathan R Friedman
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
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23
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Grochowska J, Czerwinska J, Borowski LS, Szczesny RJ. Mitochondrial RNA, a new trigger of the innate immune system. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1690. [PMID: 34498404 DOI: 10.1002/wrna.1690] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 02/06/2023]
Abstract
Mitochondria play a pivotal role in numerous cellular processes. One of them is regulation of the innate immune pathway. In this instance, mitochondria function in two different aspects of regulatory mechanisms. First, mitochondria are part of the antiviral signaling cascade that is triggered in the cytoplasm and transmitted to effector proteins through mitochondria-localized proteins. Second, mitochondria can become an endogenous source of innate immune stimuli. Under some pathophysiological conditions, mitochondria release to the cytoplasm immunogenic factors, such as mitochondrial nucleic acids. Here, we focus on immunogenic mitochondrial double-stranded RNA (mt-dsRNA) and its origin and metabolism. We discuss factors that are responsible for regulating mt-dsRNA and its escape from mitochondria, emphasizing the contribution of polynucleotide phosphorylase (PNPase, PNPT1). Finally, we review current knowledge of the role of PNPase in human health and disease. This article is categorized under: RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Joanna Grochowska
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland
| | - Jolanta Czerwinska
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland
| | - Lukasz S Borowski
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
| | - Roman J Szczesny
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland
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24
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Xavier VJ, Martinou JC. RNA Granules in the Mitochondria and Their Organization under Mitochondrial Stresses. Int J Mol Sci 2021; 22:9502. [PMID: 34502411 PMCID: PMC8431320 DOI: 10.3390/ijms22179502] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 08/25/2021] [Accepted: 08/27/2021] [Indexed: 12/25/2022] Open
Abstract
The human mitochondrial genome (mtDNA) regulates its transcription products in specialised and distinct ways as compared to nuclear transcription. Thanks to its mtDNA mitochondria possess their own set of tRNAs, rRNAs and mRNAs that encode a subset of the protein subunits of the electron transport chain complexes. The RNA regulation within mitochondria is organised within specialised, membraneless, compartments of RNA-protein complexes, called the Mitochondrial RNA Granules (MRGs). MRGs were first identified to contain nascent mRNA, complexed with many proteins involved in RNA processing and maturation and ribosome assembly. Most recently, double-stranded RNA (dsRNA) species, a hybrid of the two complementary mRNA strands, were found to form granules in the matrix of mitochondria. These RNA granules are therefore components of the mitochondrial post-transcriptional pathway and as such play an essential role in mitochondrial gene expression. Mitochondrial dysfunctions in the form of, for example, RNA processing or RNA quality control defects, or inhibition of mitochondrial fission, can cause the loss or the aberrant accumulation of these RNA granules. These findings underline the important link between mitochondrial maintenance and the efficient expression of its genome.
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Affiliation(s)
| | - Jean-Claude Martinou
- Department of Cell Biology, Faculty of Sciences, University of Geneva, 1205 Geneva, Switzerland;
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25
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Nesterov SV, Ilyinsky NS, Uversky VN. Liquid-liquid phase separation as a common organizing principle of intracellular space and biomembranes providing dynamic adaptive responses. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1868:119102. [PMID: 34293345 DOI: 10.1016/j.bbamcr.2021.119102] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/13/2021] [Accepted: 07/18/2021] [Indexed: 02/07/2023]
Abstract
This work is devoted to the phenomenon of liquid-liquid phase separation (LLPS), which has come to be recognized as fundamental organizing principle of living cells. We distinguish separation processes with different dimensions. Well-known 3D-condensation occurs in aqueous solution and leads to membraneless organelle (MLOs) formation. 2D-films may be formed near membrane surfaces and lateral phase separation (membrane rafts) occurs within the membranes themselves. LLPS may also occur on 1D structures like DNA and the cyto- and nucleoskeleton. Phase separation provides efficient transport and sorting of proteins and metabolites, accelerates the assembly of metabolic and signaling complexes, and mediates stress responses. In this work, we propose a model in which the processes of polymerization (1D structures), phase separation in membranes (2D structures), and LLPS in the volume (3D structures) influence each other. Disordered proteins and whole condensates may provide membrane raft separation or polymerization of specific proteins. On the other hand, 1D and 2D structures with special composition or embedded IDRs can nucleate condensates. We hypothesized that environmental change may trigger a LLPS which can propagate within the cell interior moving along the cytoskeleton or as an autowave. New phase propagation quickly and using a low amount of energy adjusts cell signaling and metabolic systems to new demands. Cumulatively, the interconnected phase separation phenomena in different dimensions represent a previously unexplored system of intracellular communication and regulation which cannot be ignored when considering both physiological and pathological cell processes.
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Affiliation(s)
- Semen V Nesterov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny 141700, Russia; Kurchatov Complex of NBICS-Technologies, National Research Center Kurchatov Institute, Moscow 123182, Russia.
| | - Nikolay S Ilyinsky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny 141700, Russia
| | - Vladimir N Uversky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny 141700, Russia; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., MDC07, Tampa, FL 33612, USA.
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26
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Fare CM, Villani A, Drake LE, Shorter J. Higher-order organization of biomolecular condensates. Open Biol 2021; 11:210137. [PMID: 34129784 PMCID: PMC8205532 DOI: 10.1098/rsob.210137] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
A guiding principle of biology is that biochemical reactions must be organized in space and time. One way this spatio-temporal organization is achieved is through liquid–liquid phase separation (LLPS), which generates biomolecular condensates. These condensates are dynamic and reactive, and often contain a complex mixture of proteins and nucleic acids. In this review, we discuss how underlying physical and chemical processes generate internal condensate architectures. We then outline the diverse condensate architectures that are observed in biological systems. Finally, we discuss how specific condensate organization is critical for specific biological functions.
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Affiliation(s)
- Charlotte M Fare
- Department of Biochemistry and Biophysics, and.,Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | | | - James Shorter
- Department of Biochemistry and Biophysics, and.,Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
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27
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Driscoll RK, Krasniewski LK, Cockey SG, Yang JH, Piao Y, Lehrmann E, Zhang Y, Michel M, Noh JH, Cui CY, Gorospe M. GRSF1 deficiency in skeletal muscle reduces endurance in aged mice. Aging (Albany NY) 2021; 13:14557-14570. [PMID: 34078750 PMCID: PMC8221292 DOI: 10.18632/aging.203151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 05/27/2021] [Indexed: 12/14/2022]
Abstract
GRSF1 is a mitochondrial RNA-binding protein important for maintaining mitochondrial function. We found that GRSF1 is highly expressed in cultured skeletal myoblasts differentiating into myotubes. To understand the physiological function of GRSF1 in vivo, we generated mice in which GRSF1 was specifically ablated in skeletal muscle. The conditional knockout mice (Grsf1cKO) appeared normal until 7-9 months of age. Importantly, however, a reduction of muscle endurance compared to wild-type controls was observed in 16- to 18-month old Grsf1cKO mice. Transcriptomic analysis revealed more than 200 mRNAs differentially expressed in Grsf1cKO muscle at this age. Notably, mRNAs encoding proteins involved in mitochondrial function, inflammation, and ion transport, including Mgarp, Cxcl10, Nfkb2, and Sln mRNAs, were significantly elevated in aged Grsf1cKO muscle. Our findings suggest that GRSF1 deficiency exacerbates the functional decline of aged skeletal muscle, likely through multiple downstream effector proteins.
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Affiliation(s)
- Riley K. Driscoll
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Linda K. Krasniewski
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Samuel G. Cockey
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Jen-Hao Yang
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Yulan Piao
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Elin Lehrmann
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Yongqing Zhang
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Marc Michel
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Ji Heon Noh
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
- Department of Biochemistry, Chungnam National University, Daejeon, Korea
| | - Chang-Yi Cui
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
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28
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Distinct fission signatures predict mitochondrial degradation or biogenesis. Nature 2021; 593:435-439. [PMID: 33953403 DOI: 10.1038/s41586-021-03510-6] [Citation(s) in RCA: 296] [Impact Index Per Article: 98.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 03/31/2021] [Indexed: 02/08/2023]
Abstract
Mitochondrial fission is a highly regulated process that, when disrupted, can alter metabolism, proliferation and apoptosis1-3. Dysregulation has been linked to neurodegeneration3,4, cardiovascular disease3 and cancer5. Key components of the fission machinery include the endoplasmic reticulum6 and actin7, which initiate constriction before dynamin-related protein 1 (DRP1)8 binds to the outer mitochondrial membrane via adaptor proteins9-11, to drive scission12. In the mitochondrial life cycle, fission enables both biogenesis of new mitochondria and clearance of dysfunctional mitochondria through mitophagy1,13. Current models of fission regulation cannot explain how those dual fates are decided. However, uncovering fate determinants is challenging, as fission is unpredictable, and mitochondrial morphology is heterogeneous, with ultrastructural features that are below the diffraction limit. Here, we used live-cell structured illumination microscopy to capture mitochondrial dynamics. By analysing hundreds of fissions in African green monkey Cos-7 cells and mouse cardiomyocytes, we discovered two functionally and mechanistically distinct types of fission. Division at the periphery enables damaged material to be shed into smaller mitochondria destined for mitophagy, whereas division at the midzone leads to the proliferation of mitochondria. Both types are mediated by DRP1, but endoplasmic reticulum- and actin-mediated pre-constriction and the adaptor MFF govern only midzone fission. Peripheral fission is preceded by lysosomal contact and is regulated by the mitochondrial outer membrane protein FIS1. These distinct molecular mechanisms explain how cells independently regulate fission, leading to distinct mitochondrial fates.
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A549 cells contain enlarged mitochondria with independently functional clustered mtDNA nucleoids. PLoS One 2021; 16:e0249047. [PMID: 33765066 PMCID: PMC7993880 DOI: 10.1371/journal.pone.0249047] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 03/10/2021] [Indexed: 11/19/2022] Open
Abstract
Mitochondria are commonly viewed as highly elongated organelles with regularly spaced mtDNA genomes organized as compact nucleoids that generate the local transcripts essential for production of mitochondrial ribosomes and key components of the respiratory chain. In contrast, A549 human lung carcinoma cells frequently contain apparently swollen mitochondria harboring multiple discrete mtDNA nucleoids and RNA processing granules in a contiguous matrix compartment. While this seemingly aberrant mitochondrial morphology is akin to “mito-bulbs” previously described in cells exposed to a variety of genomic stressors, it occurs in A549 cells under typical culture conditions. We provide a detailed confocal and super-resolution microscopic investigation of the incidence of such mito-bulbs in A549 cells. Most mito-bulbs appear stable, engage in active replication and transcription, and maintain respiration but feature an elevated oxidative environment. High concentrations of glucose and/or L-glutamine in growth media promote a greater incidence of mito-bulbs. Furthermore, we demonstrate that treatment of A549 cells with TGFβ suppresses the formation of mito-bulbs while treatment with a specific TGFβ pathway inhibitor substantially increases incidence. This striking heterogeneity of mitochondrial form and function may play an important role in a variety of diseases involving mitochondrial dysfunction.
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