1
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Box JM, Higgins ME, Stuart RA. Importance of conserved hydrophobic pocket region in yeast mitoribosomal mL44 protein for mitotranslation and transcript preference. J Biol Chem 2024; 300:107519. [PMID: 38950860 PMCID: PMC11345376 DOI: 10.1016/j.jbc.2024.107519] [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: 01/23/2024] [Revised: 06/14/2024] [Accepted: 06/19/2024] [Indexed: 07/03/2024] Open
Abstract
The mitochondrial ribosome (mitoribosome) is responsible for the synthesis of key oxidative phosphorylation subunits encoded by the mitochondrial genome. Defects in mitoribosomal function therefore can have serious consequences for the bioenergetic capacity of the cell. Mutation of the conserved mitoribosomal mL44 protein has been directly linked to childhood cardiomyopathy and progressive neurophysiology issues. To further explore the functional significance of the mL44 protein in supporting mitochondrial protein synthesis, we have performed a mutagenesis study of the yeast mL44 homolog, the MrpL3/mL44 protein. We specifically investigated the conserved hydrophobic pocket region of the MrpL3/mL44 protein, where the known disease-related residue in the human mL44 protein (L156R) is located. While our findings identify a number of residues in this region critical for MrpL3/mL44's ability to support the assembly of translationally active mitoribosomes, the introduction of the disease-related mutation into the equivalent position in the yeast protein (residue A186) was found to not have a major impact on function. The human and yeast mL44 proteins share many similarities in sequence and structure; however results presented here indicate that these two proteins have diverged somewhat in evolution. Finally, we observed that mutation of the MrpL3/mL44 does not impact the translation of all mitochondrial encoded proteins equally, suggesting the mitochondrial translation system may exhibit a transcript hierarchy and prioritization.
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Affiliation(s)
- Jodie M Box
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, USA
| | - Margo E Higgins
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, USA
| | - Rosemary A Stuart
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, USA.
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2
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Demircan N, Sonmez MC, Akyol TY, Ozgur R, Turkan I, Dietz KJ, Uzilday B. Alternative electron sinks in chloroplasts and mitochondria of halophytes as a safety valve for controlling ROS production during salinity. PHYSIOLOGIA PLANTARUM 2024; 176:e14397. [PMID: 38894507 DOI: 10.1111/ppl.14397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 05/07/2024] [Accepted: 05/12/2024] [Indexed: 06/21/2024]
Abstract
Electron flow through the electron transport chain (ETC) is essential for oxidative phosphorylation in mitochondria and photosynthesis in chloroplasts. Electron fluxes depend on environmental parameters, e.g., ionic and osmotic conditions and endogenous factors, and this may cause severe imbalances. Plants have evolved alternative sinks to balance the reductive load on the electron transport chains in order to avoid overreduction, generation of reactive oxygen species (ROS), and to cope with environmental stresses. These sinks act primarily as valves for electron drainage and secondarily as regulators of tolerance-related metabolism, utilizing the excess reductive energy. High salinity is an environmental stressor that stimulates the generation of ROS and oxidative stress, which affects growth and development by disrupting the redox homeostasis of plants. While glycophytic plants are sensitive to high salinity, halophytic plants tolerate, grow, and reproduce at high salinity. Various studies have examined the ETC systems of glycophytic plants, however, information about the state and regulation of ETCs in halophytes under non-saline and saline conditions is scarce. This review focuses on alternative electron sinks in chloroplasts and mitochondria of halophytic plants. In cases where information on halophytes is lacking, we examined the available knowledge on the relationship between alternative sinks and gradual salinity resilience of glycophytes. To this end, transcriptional responses of involved components of photosynthetic and respiratory ETCs were compared between the glycophyte Arabidopsis thaliana and the halophyte Schrenkiella parvula, and the time-courses of these transcripts were examined in A. thaliana. The observed regulatory patterns are discussed in the context of reactive molecular species formation in halophytes and glycophytes.
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Affiliation(s)
- Nil Demircan
- Department of Biology, Faculty of Science, Ege University, Izmir, Türkiye
| | | | - Turgut Yigit Akyol
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Rengin Ozgur
- Department of Biology, Faculty of Science, Ege University, Izmir, Türkiye
| | - Ismail Turkan
- Department of Soil and Plant Nutrition, Faculty of Agricultural Sciences and Technologies, Yasar University, İzmir, Türkiye
| | - Karl-Josef Dietz
- Faculty of Biology, Department of Biochemistry and Physiology of Plants, University of Bielefeld, Bielefeld, Germany
| | - Baris Uzilday
- Department of Biology, Faculty of Science, Ege University, Izmir, Türkiye
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3
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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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4
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Sharma S, Yang J, Favate J, Shah P, Kiledjian M. NADcapPro and circNC: methods for accurate profiling of NAD and non-canonical RNA caps in eukaryotes. Commun Biol 2023; 6:406. [PMID: 37055518 PMCID: PMC10101982 DOI: 10.1038/s42003-023-04774-6] [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: 12/19/2022] [Accepted: 03/28/2023] [Indexed: 04/15/2023] Open
Abstract
Accurate identification of NAD-capped RNAs is essential for delineating their generation and biological function. Previous transcriptome-wide methods used to classify NAD-capped RNAs in eukaryotes contain inherent limitations that have hindered the accurate identification of NAD caps from eukaryotic RNAs. In this study, we introduce two orthogonal methods to identify NAD-capped RNAs more precisely. The first, NADcapPro, uses copper-free click chemistry and the second is an intramolecular ligation-based RNA circularization, circNC. Together, these methods resolve the limitations of previous methods and allowed us to discover unforeseen features of NAD-capped RNAs in budding yeast. Contrary to previous reports, we find that 1) cellular NAD-RNAs can be full-length and polyadenylated transcripts, 2) transcription start sites for NAD-capped and canonical m7G-capped RNAs can be different, and 3) NAD caps can be added subsequent to transcription initiation. Moreover, we uncovered a dichotomy of NAD-RNAs in translation where they are detected with mitochondrial ribosomes but minimally on cytoplasmic ribosomes indicating their propensity to be translated in mitochondria.
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Affiliation(s)
- Sunny Sharma
- Department of Cell Biology and Neurosciences, Rutgers University, Piscataway, NJ, USA.
| | - Jun Yang
- Department of Cell Biology and Neurosciences, Rutgers University, Piscataway, NJ, USA
| | - John Favate
- Department of Genetics, Rutgers University, Piscataway, NJ, USA
| | - Premal Shah
- Department of Genetics, Rutgers University, Piscataway, NJ, USA
| | - Megerditch Kiledjian
- Department of Cell Biology and Neurosciences, Rutgers University, Piscataway, NJ, USA.
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5
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Xu L, Li Y, Wei Z, Bai R, Gao G, Sun W, Jiang X, Wang J, Li X, Pi Y. Chenodeoxycholic Acid (CDCA) Promoted Intestinal Epithelial Cell Proliferation by Regulating Cell Cycle Progression and Mitochondrial Biogenesis in IPEC-J2 Cells. Antioxidants (Basel) 2022; 11:antiox11112285. [PMID: 36421471 PMCID: PMC9687205 DOI: 10.3390/antiox11112285] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 11/19/2022] Open
Abstract
Chenodeoxycholic acid (CDCA), a primary bile acid (BA), has been demonstrated to play an important role as a signaling molecule in various physiological functions. However, the role of CDCA in regulating intestinal epithelial cell (IEC) function remains largely unknown. Herein, porcine intestinal epithelial cells (IPEC-J2) were used as an in vitro model to investigate the effects of CDCA on IEC proliferation and explore the underlying mechanisms. IPEC-J2 cells were treated with CDCA, and flow cytometry and transcriptome analysis were adopted to investigate the effects and potential molecular mechanisms of CDCA on the proliferation of IECs. Our results indicated that adding 50 μmol/L of CDCA in the media significantly increased the proliferation of IPEC-J2 cells. In addition, CDCA treatment also hindered cell apoptosis, increased the proportion of G0/G1 phase cells in the cell cycle progression, reduced intracellular ROS, and MDA levels, and increased mitochondrial membrane potential, antioxidation enzyme activity (T-AOC and CAT), and intracellular ATP level (p < 0.05). RNA-seq results showed that CDCA significantly upregulated the expression of genes related to cell cycle progression (Cyclin-dependent kinase 1 (CDK1), cyclin G2 (CCNG2), cell-cycle progression gene 1 (CCPG1), Bcl-2 interacting protein 5 (BNIP5), etc.) and downregulated the expression of genes related to mitochondrial biogenesis (ND1, ND2, COX3, ATP6, etc.). Further KEGG pathway enrichment analysis showed that CDCA significantly enriched the signaling pathways of DNA replication, cell cycle, and p53. Collectively, this study demonstrated that CDCA could promote IPEC-J2 proliferation by regulating cell cycle progression and mitochondrial function. These findings provide a new strategy for promoting the intestinal health of pigs by regulating intestinal BA metabolism.
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Affiliation(s)
- Lei Xu
- Key Laboratory of Feed Biotechnology of Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yanpin Li
- Key Laboratory of Feed Biotechnology of Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zixi Wei
- Key Laboratory of Feed Biotechnology of Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Rong Bai
- Key Laboratory of Feed Biotechnology of Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Department of Business Economics, Wageningen University, 6700 EW Wageningen, The Netherlands
| | - Ge Gao
- Key Laboratory of Feed Biotechnology of Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wenjuan Sun
- Key Laboratory of Feed Biotechnology of Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xianren Jiang
- Key Laboratory of Feed Biotechnology of Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Junjun Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xilong Li
- Key Laboratory of Feed Biotechnology of Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Correspondence: (X.L.); (Y.P.); Tel.: +86-010-82108134 (X.L.)
| | - Yu Pi
- Key Laboratory of Feed Biotechnology of Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Correspondence: (X.L.); (Y.P.); Tel.: +86-010-82108134 (X.L.)
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6
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Wu GJ, Cherng YG, Chen JT, Chang CC, Liu SH, Chen RM. Genistein Triggers Translocation of Estrogen Receptor-Alpha in Mitochondria to Induce Expressions of ATP Synthesis-Associated Genes and Improves Energy Production and Osteoblast Maturation. THE AMERICAN JOURNAL OF CHINESE MEDICINE 2021; 49:901-923. [PMID: 33853499 DOI: 10.1142/s0192415x21500439] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Our previous study showed that estrogen can induce mitochondrial adenosine triphosphate (ATP) synthesis-associated gene expressions and osteoblast maturation. Genistein, a phytoestrogenic isoflavone that is widely found in various foods and traditional herb products, is beneficial for osteogenesis by selectively triggering estrogen receptor alpha (ER[Formula: see text] expression. In this study, we further investigated the mechanisms of genistein-induced energy production and osteoblast activation. Exposure of rat calvarial osteoblasts and human U-2 OS cells to genistein triggered osteoblast activation without affecting cell survival. Treatment with genistein time-dependently induced ER[Formula: see text] mRNA and protein expressions in rat calvarial osteoblasts. Analyses by confocal microscopy and immunoblotting showed that genistein stimulated translocation of ER[Formula: see text] from the cytoplasm to mitochondria. Subsequently, expressions of mitochondrial cytochrome c oxidase (COX) I and II mRNAs and proteins in primary rat osteoblasts were induced after exposure to genistein. Knocking-down ER[Formula: see text] concurrently inhibited genistein-induced COX I and II mRNA expressions. In addition, mitochondrial complex enzyme activities, the mitochondrial membrane potential, and cellular ATP levels in rat calvarial osteoblasts were time-dependently augmented by genistein. Suppressing ER[Formula: see text] expression instantaneously lowered genistein-induced enhancements of mitochondrial energy production and osteoblast activation. Effects of genistein on ER[Formula: see text] translocation, COX I and II mRNA expressions, ATP synthesis, and osteoblast activation were further confirmed in human U-2 OS cells. This study showed that genistein can stimulate energy production and consequent osteoblast activation via inducing ER[Formula: see text]-mediated mitochondrial ATP synthesis-linked gene expressions.
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Affiliation(s)
- Gong-Jhe Wu
- Department of Anesthesiology, Shin Kong Wu Ho-Su Memorial Hospital, Taipei, Taiwan.,Department of Anesthesiology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Yih-Giun Cherng
- Department of Anesthesiology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Jui-Tai Chen
- Department of Anesthesiology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Chuen-Chau Chang
- Department of Anesthesiology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Anesthesiology and Health Policy Research Center, Taipei Medical University Hospital, Taipei Medical University, Taipei, Taiwan
| | - Shing-Hwa Liu
- Cell Physiology and Molecular Image Research Center, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan.,Institute of Toxicology, College of Medicine National Taiwan University Taipei, Taiwan
| | - Ruei-Ming Chen
- Anesthesiology and Health Policy Research Center, Taipei Medical University Hospital, Taipei Medical University, Taipei, Taiwan.,Cell Physiology and Molecular Image Research Center, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan.,Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan.,TMU Research Center of Cancer Translational Medicine, Taipei, Taiwan
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7
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Gonçalves AM, Pereira-Santos AR, Esteves AR, Cardoso SM, Empadinhas N. The Mitochondrial Ribosome: A World of Opportunities for Mitochondrial Dysfunction Toward Parkinson's Disease. Antioxid Redox Signal 2021; 34:694-711. [PMID: 32098485 DOI: 10.1089/ars.2019.7997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Significance: Mitochondrial ribosomes (mitoribosomes) are organelles that translate mitochondrial messenger RNA in the matrix and, in mammals, have evolved to translate 13 polypeptides of the pathway that performs oxidative phosphorylation (OXPHOS). Although a number of devastating diseases result from defects in this mitochondrial translation apparatus, most are associated with genetic mutations and little is known about allelopathic defects caused by antibiotics, toxins, or nonproteinogenic amino acids. Recent Advances: The levels of mitochondrial ribosomal subunits 12S and 16S ribosomal RNA (rRNA) in cells/tissues from patients carrying mutations in these genes have been associated with alterations in mitochondrial translation efficiency and with impaired OXPHOS activities, as well as with the severity of clinical phenotypes. In recent decades, important studies revealed a prominent role of mitochondrial dysfunction in Parkinson's disease (PD); however, the involvement of mitoribosomes remains largely unknown. Critical Issues: Considering that mitoribosomal structure and function can determine the efficiency of OXPHOS and that an impaired mitochondrial respiratory chain is a common finding in PD, we argue that the mitoribosome may be key to disease onset and progression. With this review, we comprehensively integrate the available knowledge on the composition, assembly, and role of the mitoribosome in mitochondrial efficiency, reflecting on its possible involvement in the etiopathogenesis of this epidemic disease as an appealing research avenue. Future Directions: If a direct correlation between mitoribosome failure and PD pathology is demonstrated, these mitochondrial organelles will provide valuable early clinical markers and potentially attractive targets for the development of innovative PD-directed therapeutic agents.
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Affiliation(s)
- Ana Mafalda Gonçalves
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Ana Raquel Pereira-Santos
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Ana Raquel Esteves
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Sandra M Cardoso
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Nuno Empadinhas
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,IIIUC-Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
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8
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Balbi C, Costa A, Barile L, Bollini S. Message in a Bottle: Upgrading Cardiac Repair into Rejuvenation. Cells 2020; 9:cells9030724. [PMID: 32183455 PMCID: PMC7140681 DOI: 10.3390/cells9030724] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/05/2020] [Accepted: 03/12/2020] [Indexed: 12/12/2022] Open
Abstract
Ischaemic cardiac disease is associated with a loss of cardiomyocytes and an intrinsic lack of myocardial renewal. Recent work has shown that the heart retains limited cardiomyocyte proliferation, which remains inefficient when facing pathological conditions. While broadly active in the neonatal mammalian heart, this mechanism becomes quiescent soon after birth, suggesting loss of regenerative potential with maturation into adulthood. A key question is whether this temporary regenerative window can be enhanced via appropriate stimulation and further extended. Recently the search for novel therapeutic approaches for heart disease has centred on stem cell biology. The “paracrine effect” has been proposed as a promising strategy to boost endogenous reparative and regenerative mechanisms from within the cardiac tissue by exploiting the modulatory potential of soluble stem cell-secreted factors. As such, growing interest has been specifically addressed towards stem/progenitor cell-secreted extracellular vesicles (EVs), which can be easily isolated in vitro from cell-conditioned medium. This review will provide a comprehensive overview of the current paradigm on cardiac repair and regeneration, with a specific focus on the role and mechanism(s) of paracrine action of EVs from cardiac stromal progenitors as compared to exogenous stem cells in order to discuss the optimal choice for future therapy. In addition, the challenges to overcoming translational EV biology from bench to bedside for future cardiac regenerative medicine will be discussed.
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Affiliation(s)
- Carolina Balbi
- Laboratory of Cellular and Molecular Cardiology, Cardiocentro Ticino Foundation, 6900 Lugano, Switzerland;
| | - Ambra Costa
- Regenerative Medicine Laboratory, Dept. of Experimental Medicine (DIMES), University of Genova, 16132 Genova, Italy;
| | - Lucio Barile
- Laboratory for Cardiovascular Theranostics, Cardiocentro Ticino Foundation, 6900 Lugano, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, 6900 Lugano, Switzerland
- Correspondence: (L.B.); (S.B.)
| | - Sveva Bollini
- Regenerative Medicine Laboratory, Dept. of Experimental Medicine (DIMES), University of Genova, 16132 Genova, Italy;
- Correspondence: (L.B.); (S.B.)
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9
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Assembly of Mitochondrial Complex I Requires the Low-Complexity Protein AMC1 in Chlamydomonas reinhardtii. Genetics 2020; 214:895-911. [PMID: 32075865 DOI: 10.1534/genetics.120.303029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 02/05/2020] [Indexed: 11/18/2022] Open
Abstract
Complex I is the first enzyme involved in the mitochondrial electron transport chain. With >40 subunits of dual genetic origin, the biogenesis of complex I is highly intricate and poorly understood. We used Chlamydomonas reinhardtii as a model system to reveal factors involved in complex I biogenesis. Two insertional mutants, displaying a complex I assembly defect characterized by the accumulation of a 700 kDa subcomplex, were analyzed. Genetic analyses showed these mutations were allelic and mapped to the gene AMC1 (Cre16.g688900) encoding a low-complexity protein of unknown function. The complex I assembly and activity in the mutant was restored by complementation with the wild-type gene, confirming AMC1 is required for complex I biogenesis. The N terminus of AMC1 targets a reporter protein to yeast mitochondria, implying that AMC1 resides and functions in the Chlamydomonas mitochondria. Accordingly, in both mutants, loss of AMC1 function results in decreased abundance of the mitochondrial nd4 transcript, which encodes the ND4 membrane subunit of complex I. Loss of ND4 in a mitochondrial nd4 mutant is characterized by a membrane arm assembly defect, similar to that exhibited by loss of AMC1. These results suggest AMC1 is required for the production of mitochondrially-encoded complex I subunits, specifically ND4. We discuss the possible modes of action of AMC1 in mitochondrial gene expression and complex I biogenesis.
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10
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Li G, Qin Y. Mitochondrial translation factor EF4 regulates oxidative phosphorylation complexes and the production of ROS. Free Radic Res 2019; 52:1250-1255. [PMID: 30693836 DOI: 10.1080/10715762.2018.1479063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Mitochondrial translation system executes the biosynthesis of mitochondrial DNA encoded polypeptides that are the core subunits of oxidative phosphorylation complexes. Recently, we reported that elongation factor 4 (EF4) is a key quality control factor in bacterial and mitochondrial translation regulating tRNA translocation and modulating cellular responses via a direct cross-talk with cytoplasmic translation machinery. Here, we made a brief review on mtEF4-regulated mitochondrial translation, respiratory chain biogenesis and the production of reactive oxygen species (ROS). We will discuss the influence of mtEF4 on the electron transport chain, especially at respiratory chain complex IV, which could result in cytochrome c peroxidase formation, electron leakage from electron transport chain and ROS increase.
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Affiliation(s)
- Guichen Li
- a Key Laboratory of RNA Biology , Institute of Biophysics, Chinese Academy of Sciences , Chaoyang District , Beijing , China
| | - Yan Qin
- a Key Laboratory of RNA Biology , Institute of Biophysics, Chinese Academy of Sciences , Chaoyang District , Beijing , China.,b University of Chinese Academy of Sciences , Beijing , China
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11
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Bouchez C, Devin A. Mitochondrial Biogenesis and Mitochondrial Reactive Oxygen Species (ROS): A Complex Relationship Regulated by the cAMP/PKA Signaling Pathway. Cells 2019; 8:cells8040287. [PMID: 30934711 PMCID: PMC6523352 DOI: 10.3390/cells8040287] [Citation(s) in RCA: 140] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/15/2019] [Accepted: 03/20/2019] [Indexed: 12/23/2022] Open
Abstract
Mitochondrial biogenesis is a complex process. It requires the contribution of both the nuclear and the mitochondrial genomes and therefore cross talk between the nucleus and mitochondria. Cellular energy demand can vary by great length and it is now well known that one way to adjust adenosine triphosphate (ATP) synthesis to energy demand is through modulation of mitochondrial content in eukaryotes. The knowledge of actors and signals regulating mitochondrial biogenesis is thus of high importance. Here, we review the regulation of mitochondrial biogenesis both in yeast and in mammalian cells through mitochondrial reactive oxygen species.
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Affiliation(s)
- Cyrielle Bouchez
- Université Bordeaux, IBGC, UMR 5095, 33077 Bordeaux cedex, France.
- Institut de Biochimie et Génétique Cellulaires, CNRS UMR 5095, 1, rue Camille Saint Saëns, 33077 Bordeaux Cedex, France.
| | - Anne Devin
- Université Bordeaux, IBGC, UMR 5095, 33077 Bordeaux cedex, France.
- Institut de Biochimie et Génétique Cellulaires, CNRS UMR 5095, 1, rue Camille Saint Saëns, 33077 Bordeaux Cedex, France.
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12
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Ogunbona OB, Claypool SM. Emerging Roles in the Biogenesis of Cytochrome c Oxidase for Members of the Mitochondrial Carrier Family. Front Cell Dev Biol 2019; 7:3. [PMID: 30766870 PMCID: PMC6365663 DOI: 10.3389/fcell.2019.00003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 01/10/2019] [Indexed: 12/11/2022] Open
Abstract
The mitochondrial carrier family (MCF) is a group of transport proteins that are mostly localized to the inner mitochondrial membrane where they facilitate the movement of various solutes across the membrane. Although these carriers represent potential targets for therapeutic application and are repeatedly associated with human disease, research on the MCF has not progressed commensurate to their physiologic and pathophysiologic importance. Many of the 53 MCF members in humans are orphans and lack known transport substrates. Even for the relatively well-studied members of this family, such as the ADP/ATP carrier and the uncoupling protein, there exist fundamental gaps in our understanding of their biological roles including a clear rationale for the existence of multiple isoforms. Here, we briefly review this important family of mitochondrial carriers, provide a few salient examples of their diverse metabolic roles and disease associations, and then focus on an emerging link between several distinct MCF members, including the ADP/ATP carrier, and cytochrome c oxidase biogenesis. As the ADP/ATP carrier is regarded as the paradigm of the entire MCF, its newly established role in regulating translation of the mitochondrial genome highlights that we still have a lot to learn about these metabolite transporters.
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Affiliation(s)
- Oluwaseun B. Ogunbona
- Department of Physiology, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
- Department of Pathology & Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA, United States
| | - Steven M. Claypool
- Department of Physiology, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
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13
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Cogliati S, Lorenzi I, Rigoni G, Caicci F, Soriano ME. Regulation of Mitochondrial Electron Transport Chain Assembly. J Mol Biol 2018; 430:4849-4873. [DOI: 10.1016/j.jmb.2018.09.016] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/20/2018] [Accepted: 09/25/2018] [Indexed: 12/26/2022]
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14
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Zhang X, Wang H, Coulter JA, Yang R. Octaarginine-modified gold nanoparticles enhance the radiosensitivity of human colorectal cancer cell line LS180 to megavoltage radiation. Int J Nanomedicine 2018; 13:3541-3552. [PMID: 29950834 PMCID: PMC6016276 DOI: 10.2147/ijn.s161157] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Background This study investigated the effectiveness and underpinning mechanisms of radiosensitization using octaarginine (R8)-modified gold nanoparticle–poly(ethylene glycol) (GNP-PEG-R8) in colorectal cancer cell line LS180 to megavoltage radiotherapy in vitro. Method In-house synthesized GNP-PEG was characterized by transmission electron microscopy, dynamic light scattering, ultraviolet–visible spectrophotometry, and X-ray photoelectron spectroscopy. Inductively coupled plasma mass spectroscopy was used to quantify internalization. Direct cytotoxicity was established using the Cell Counting Kit-8, while radiosensitivity was determined using the gold standard in vitro clonogenic assay. Cell-cycle distribution, apoptosis, reactive oxygen species (ROS), and mitochondrial membrane potential (MMP) were analyzed by flow cytometry, further exploring the key mechanisms driving GNP-PEG-R8 radiosensitization. Results The core GNP diameter was 6.3±1.1 nm (mean±SD). Following functionalization, the hydrodynamic diameter increased to 19.7±2.8 nm and 27.8±1.8 nm for GNP-PEG and GNP-PEG-R8, with respective surface plasmon resonance peaks of 515 nm and 525 nm. Furthermore, incorporation of the R8 significantly increased nanoparticle internalization compared to GNP-PEG (p<0.001) over a 1 h treatment period. Functionalized GNPs confer little cytotoxicity below 400 nM. In clonogenic assays, radiation combined with GNP-PEG-R8 induced a significant reduction in colony formation compared with radiation alone, generating a sensitizer enhancement ratio of 1.59. Furthermore, GNP-PEG-R8 plus radiation predominantly induced cell-cycle arrest in the G2/M phase, increasing G2/M stalling by an additional 10% over GNP-PEG, markedly promoting apoptosis (p<0.001). Finally, ROS levels and alterations in MMP were investigated, indicating a highly significant (p<0.001) change in both parameters following the combined treatment of GNP-PEG-R8 and radiation over radiation alone. Conclusion R8-modified GNPs were efficiently internalized by LS180 cells, exhibiting minimal cytotoxicity. This yielded significant radiosensitization in response to megavoltage radiation. GNP-PEG-R8 may enhance radiosensitivity by arresting cell cycle and inducing apoptosis, with elevated ROS identified as the likely initiator.
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Affiliation(s)
- Xuyang Zhang
- Department of Radiation Oncology, Peking University Third Hospital, Beijing, China
| | - Hao Wang
- Department of Radiation Oncology, Peking University Third Hospital, Beijing, China
| | | | - Ruijie Yang
- Department of Radiation Oncology, Peking University Third Hospital, Beijing, China
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15
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Ogunbona OB, Baile MG, Claypool SM. Cardiomyopathy-associated mutation in the ADP/ATP carrier reveals translation-dependent regulation of cytochrome c oxidase activity. Mol Biol Cell 2018; 29:1449-1464. [PMID: 29688796 PMCID: PMC6014099 DOI: 10.1091/mbc.e17-12-0700] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 03/16/2018] [Accepted: 04/18/2018] [Indexed: 01/07/2023] Open
Abstract
How the absence of the major mitochondrial ADP/ATP carrier in yeast, Aac2p, results in a specific defect in cytochrome c oxidase (COX; complex IV) activity is a long-standing mystery. Aac2p physically associates with respiratory supercomplexes, which include complex IV, raising the possibility that its activity is dependent on its association with Aac2p. Here, we have leveraged a transport-dead pathogenic AAC2 point mutant to determine the basis for the reduced COX activity in the absence of Aac2p. The steady-state levels of complex IV subunits encoded by the mitochondrial genome are significantly reduced in the absence of Aac2p function, whether its association with respiratory supercomplexes is preserved or not. This diminution in COX amounts is not caused by a reduction in the mitochondrial genome copy number or the steady-state level of its transcripts, and does not reflect a defect in complex IV assembly. Instead, the absence of Aac2p activity, genetically or pharmacologically, results in an aberrant pattern of mitochondrial translation. Interestingly, compared with the complete absence of Aac2p, the complex IV-related defects are greater in mitochondria expressing the transport-inactive Aac2p mutant. Our results highlight a critical role for Aac2p transport in mitochondrial translation whose disturbance uniquely impacts cytochrome c oxidase.
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Affiliation(s)
- Oluwaseun B. Ogunbona
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2185
| | | | - Steven M. Claypool
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2185
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16
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17
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Callegari S, Dennerlein S. Sensing the Stress: A Role for the UPR mt and UPR am in the Quality Control of Mitochondria. Front Cell Dev Biol 2018; 6:31. [PMID: 29644217 PMCID: PMC5882792 DOI: 10.3389/fcell.2018.00031] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 03/12/2018] [Indexed: 01/01/2023] Open
Abstract
Mitochondria exist as compartmentalized units, surrounded by a selectively permeable double membrane. Within is contained the mitochondrial genome and protein synthesis machinery, required for the synthesis of OXPHOS components and ultimately, ATP production. Despite their physical barrier, mitochondria are tightly integrated into the cellular environment. A constant flow of information must be maintained to and from the mitochondria and the nucleus, to ensure mitochondria are amenable to cell metabolic requirements and also to feedback on their functional state. This review highlights the pathways by which mitochondrial stress is signaled to the nucleus, with a particular focus on the mitochondrial unfolded protein response (UPRmt) and the unfolded protein response activated by the mistargeting of proteins (UPRam). Although these pathways were originally discovered to alleviate proteotoxic stress from the accumulation of mitochondrial-targeted proteins that are misfolded or unimported, we review recent findings indicating that the UPRmt can also sense defects in mitochondrial translation. We further discuss the regulation of OXPHOS assembly and speculate on a possible role for mitochondrial stress pathways in sensing OXPHOS biogenesis.
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Affiliation(s)
- Sylvie Callegari
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Sven Dennerlein
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
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18
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Lin PI, Tai YT, Chan WP, Lin YL, Liao MH, Chen RM. Estrogen/ERα signaling axis participates in osteoblast maturation via upregulating chromosomal and mitochondrial complex gene expressions. Oncotarget 2017; 9:1169-1186. [PMID: 29416685 PMCID: PMC5787428 DOI: 10.18632/oncotarget.23453] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 12/09/2017] [Indexed: 01/08/2023] Open
Abstract
Estrogen deficiency usually leads to bone loss and osteoporosis in postmenopausal women. Osteoblasts play crucial roles in bone formation. However, osteoblast functions are influenced by mitochondrial bioenergetic conditions. In this study, we investigated the roles of the estrogen and estrogen receptor alpha (ERα) axis in mitochondrial energy metabolism and subsequent osteoblast mineralization. Exposure of rat calvarial osteoblasts to estradiol caused substantial improvements in alkaline phosphatase activities and cell calcification. In parallel, treatment of human osteoblast-like U2OS cells, derived from a female osteosarcoma patient, with estradiol specifically augmented ERα levels. Sequentially, estradiol stimulated translocation of ERα to nuclei in human osteoblasts and induced expressions of genomic respiratory chain complex NDUFA10, UQCRC1, cytochrome c oxidase (COX)8A, COX6A2, COX8C, COX6C, COX6B2, COX412, and ATP12A genes. Concurrently, estradiol stimulated translocation of ERα to mitochondria from the cytoplasm. A bioinformatic search found the existence of four estrogen response elements in the 5’-promoter region of the mitochondrial cox i gene. Interestingly, estradiol induced COX I mRNA and protein expressions in human osteoblasts or rat calvarial osteoblasts. Knocking-down ERα translation concurrently downregulated estradiol-induced COX I mRNA expression. Consequently, exposure to estradiol led to successive increases in the mitochondrial membrane potential, the mitochondrial enzyme activity, and cellular adenosine triphosphate levels. Taken together, this study showed the roles of the estradiol/ERα signaling axis in improving osteoblast maturation through upregulating the mitochondrial bioenergetic system due to induction of definite chromosomal and mitochondrial complex gene expressions. Our results provide novel insights elucidating the roles of the estrogen/ERα alliance in regulating bone formation.
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Affiliation(s)
- Pei-I Lin
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Yu-Ting Tai
- Cell Physiology and Molecular Image Research Center and Department of Anesthesiology, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Wing P Chan
- Department of Radiology, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Yi-Ling Lin
- Cell Physiology and Molecular Image Research Center and Department of Anesthesiology, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Mei-Hsiu Liao
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Cell Physiology and Molecular Image Research Center and Department of Anesthesiology, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Ruei-Ming Chen
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Cell Physiology and Molecular Image Research Center and Department of Anesthesiology, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan.,Anesthesiology and Health Policy Research Center, Taipei Medical University Hospital, Taipei, Taiwan
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19
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Plasticity of Mitochondrial Translation. Trends Cell Biol 2017; 27:712-721. [DOI: 10.1016/j.tcb.2017.05.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 05/15/2017] [Accepted: 05/16/2017] [Indexed: 11/21/2022]
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20
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Couvillion MT, Churchman LS. Mitochondrial Ribosome (Mitoribosome) Profiling for Monitoring Mitochondrial Translation In Vivo. ACTA ACUST UNITED AC 2017; 119:4.28.1-4.28.25. [PMID: 28678443 DOI: 10.1002/cpmb.41] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Translation in the mitochondria is regulated by mechanisms distinct from those acting in the cytosol and in bacteria, yet precise methods for investigating it have lagged behind. This unit describes an approach, mitochondrial ribosome (mitoribosome) profiling, to quantitatively monitor mitochondrial translation with high temporal and spatial resolution in Saccharomyces cerevisiae. Mitoribosomes are immunoprecipitated from whole-cell lysate and the protected mRNA fragments are isolated. These fragments are then converted to sequencing libraries or analyzed by northern blot hybridization to reveal the distribution of mitoribosomes across the mitochondrial transcriptome. As information about RNA abundance is required to resolve translational from RNA effects, we also present an RNA sequencing approach that can be performed in parallel. Accurately capturing the biologically relevant distribution of mitoribosome positions depends on several critical parameters that are discussed. Application of mitoribosome profiling can reveal mechanisms of mitochondrial translational control that were not previously possible to uncover. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Mary T Couvillion
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
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21
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Cao X, Qin Y. Mitochondrial translation factors reflect coordination between organelles and cytoplasmic translation via mTOR signaling: Implication in disease. Free Radic Biol Med 2016; 100:231-237. [PMID: 27101739 DOI: 10.1016/j.freeradbiomed.2016.04.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 04/11/2016] [Accepted: 04/13/2016] [Indexed: 12/24/2022]
Abstract
Mitochondria are semi-autonomous organelle possessing their own translation machinery to biosynthesize mitochondrial DNA (mtDNA)-encoded polypeptides, which are the core subunits of oxidative phosphorylation (OXPHOS) complexes. Mitochondrial translation elongation factor 4 (mtEF4) is a key quality control factor in mitochondrial translation (mt-translation) that regulates mitochondrial tRNA translocation and modulates cellular responses by influencing cytoplasmic translation (ct-translation). In addition to mtEF4, mt-translational activators, mitochondrial microRNAs (mitomiRs), and MITRAC have been reported recently as crucial mt-translation regulators. Here, we focus on the novel ways how these factors regulate mt-translation, discuss the main cellular response of mammalian target of rapamycin (mTOR) signalling upon mt-translation defects, and summarize the related human diseases.
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Affiliation(s)
- Xintao Cao
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Qin
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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22
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Couvillion MT, Soto IC, Shipkovenska G, Churchman LS. Synchronized mitochondrial and cytosolic translation programs. Nature 2016; 533:499-503. [PMID: 27225121 PMCID: PMC4964289 DOI: 10.1038/nature18015] [Citation(s) in RCA: 233] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 04/18/2016] [Indexed: 01/21/2023]
Abstract
Oxidative phosphorylation (OXPHOS) is fundamental for life. OXPHOS complexes pose a unique challenge for the cell, because their subunits are encoded on two different genomes, the nuclear genome and the mitochondrial genome. Genomic approaches designed to study nuclear/cytosolic and bacterial gene expression have not been broadly applied to the mitochondrial system; thus the co-regulation of OXPHOS genes remains largely unexplored. Here we globally monitored mitochondrial and nuclear gene expression processes in Saccharomyces cerevisiae during mitochondrial biogenesis, when OXPHOS complexes are synthesized. Nuclear- and mitochondrial-encoded OXPHOS transcript levels do not increase concordantly. Instead, we observe that mitochondrial and cytosolic translation are rapidly and dynamically regulated in a strikingly synchronous fashion. Furthermore, the coordinated translation programs are controlled unidirectionally through the intricate and dynamic control of cytosolic translation. Thus the nuclear genome carefully directs the coordination of mitochondrial and cytosolic translation to orchestrate the timely synthesis of each OXPHOS complex, representing an unappreciated regulatory layer shaping the mitochondrial proteome. Our whole-cell genomic profiling approach establishes a foundation for global gene regulatory studies of mitochondrial biology.
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Affiliation(s)
- Mary T Couvillion
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Iliana C Soto
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Gergana Shipkovenska
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - L Stirling Churchman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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23
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Kuzmenko A, Derbikova K, Salvatori R, Tankov S, Atkinson GC, Tenson T, Ott M, Kamenski P, Hauryliuk V. Aim-less translation: loss of Saccharomyces cerevisiae mitochondrial translation initiation factor mIF3/Aim23 leads to unbalanced protein synthesis. Sci Rep 2016; 6:18749. [PMID: 26728900 PMCID: PMC4700529 DOI: 10.1038/srep18749] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 11/09/2015] [Indexed: 12/22/2022] Open
Abstract
The mitochondrial genome almost exclusively encodes a handful of transmembrane constituents of the oxidative phosphorylation (OXPHOS) system. Coordinated expression of these genes ensures the correct stoichiometry of the system’s components. Translation initiation in mitochondria is assisted by two general initiation factors mIF2 and mIF3, orthologues of which in bacteria are indispensible for protein synthesis and viability. mIF3 was thought to be absent in Saccharomyces cerevisiae until we recently identified mitochondrial protein Aim23 as the missing orthologue. Here we show that, surprisingly, loss of mIF3/Aim23 in S. cerevisiae does not indiscriminately abrogate mitochondrial translation but rather causes an imbalance in protein production: the rate of synthesis of the Atp9 subunit of F1F0 ATP synthase (complex V) is increased, while expression of Cox1, Cox2 and Cox3 subunits of cytochrome c oxidase (complex IV) is repressed. Our results provide one more example of deviation of mitochondrial translation from its bacterial origins.
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Affiliation(s)
- Anton Kuzmenko
- University of Tartu, Institute of Technology, Nooruse 1, 50411 Tartu, Estonia.,Molecular Biology Department, Faculty of Biology, M.V. Lomonosov Moscow State University, 1/12 Leninskie Gory, 119991 Moscow, Russia
| | - Ksenia Derbikova
- Molecular Biology Department, Faculty of Biology, M.V. Lomonosov Moscow State University, 1/12 Leninskie Gory, 119991 Moscow, Russia
| | - Roger Salvatori
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Stoyan Tankov
- University of Tartu, Institute of Technology, Nooruse 1, 50411 Tartu, Estonia
| | - Gemma C Atkinson
- University of Tartu, Institute of Technology, Nooruse 1, 50411 Tartu, Estonia.,Department of Molecular Biology, Umeå University, Building 6K, 6L University Hospital Area, SE-901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Building 6K and 6L, University Hospital Area, SE-901 87 Umeå, Sweden
| | - Tanel Tenson
- University of Tartu, Institute of Technology, Nooruse 1, 50411 Tartu, Estonia
| | - Martin Ott
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Piotr Kamenski
- Molecular Biology Department, Faculty of Biology, M.V. Lomonosov Moscow State University, 1/12 Leninskie Gory, 119991 Moscow, Russia
| | - Vasili Hauryliuk
- University of Tartu, Institute of Technology, Nooruse 1, 50411 Tartu, Estonia.,Department of Molecular Biology, Umeå University, Building 6K, 6L University Hospital Area, SE-901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Building 6K and 6L, University Hospital Area, SE-901 87 Umeå, Sweden
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24
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Kehrein K, Schilling R, Möller-Hergt BV, Wurm CA, Jakobs S, Lamkemeyer T, Langer T, Ott M. Organization of Mitochondrial Gene Expression in Two Distinct Ribosome-Containing Assemblies. Cell Rep 2015; 10:843-853. [PMID: 25683707 DOI: 10.1016/j.celrep.2015.01.012] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 11/17/2014] [Accepted: 12/31/2014] [Indexed: 12/27/2022] Open
Abstract
Mitochondria contain their own genetic system that provides subunits of the complexes driving oxidative phosphorylation. A quarter of the mitochondrial proteome participates in gene expression, but how all these factors are orchestrated and spatially organized is currently unknown. Here, we established a method to purify and analyze native and intact complexes of mitochondrial ribosomes. Quantitative mass spectrometry revealed extensive interactions of ribosomes with factors involved in all the steps of posttranscriptional gene expression. These interactions result in large expressosome-like assemblies that we termed mitochondrial organization of gene expression (MIOREX) complexes. Superresolution microscopy revealed that most MIOREX complexes are evenly distributed throughout the mitochondrial network, whereas a subset is present as nucleoid-MIOREX complexes that unite the whole spectrum of organellar gene expression. Our work therefore provides a conceptual framework for the spatial organization of mitochondrial protein synthesis that likely developed to facilitate gene expression in the organelle.
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Affiliation(s)
- Kirsten Kehrein
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
| | - Ramon Schilling
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
| | - Braulio Vargas Möller-Hergt
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
| | - Christian A Wurm
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, 37070 Göttingen, Germany
| | - Stefan Jakobs
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, 37070 Göttingen, Germany; Department of Neurology, University of Göttingen Medical School, 37073 Göttingen, Germany; Center Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), 37073 Göttingen, Germany
| | - Tobias Lamkemeyer
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Thomas Langer
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany; Institute for Genetics, University of Cologne, 50931 Cologne, Germany; Center for Molecular Medicine (CMMC), University of Cologne, 50931 Cologne, Germany; Max-Planck-Institute for Biology of Aging, 50931 Cologne, Germany
| | - Martin Ott
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden.
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25
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Lytovchenko O, Naumenko N, Oeljeklaus S, Schmidt B, von der Malsburg K, Deckers M, Warscheid B, van der Laan M, Rehling P. The INA complex facilitates assembly of the peripheral stalk of the mitochondrial F1Fo-ATP synthase. EMBO J 2014; 33:1624-38. [PMID: 24942160 DOI: 10.15252/embj.201488076] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Mitochondrial F1Fo-ATP synthase generates the bulk of cellular ATP. This molecular machine assembles from nuclear- and mitochondria-encoded subunits. Whereas chaperones for formation of the matrix-exposed hexameric F1-ATPase core domain have been identified, insight into how the nuclear-encoded F1-domain assembles with the membrane-embedded Fo-region is lacking. Here we identified the INA complex (INAC) in the inner membrane of mitochondria as an assembly factor involved in this process. Ina22 and Ina17 are INAC constituents that physically associate with the F1-module and peripheral stalk, but not with the assembled F1Fo-ATP synthase. Our analyses show that loss of Ina22 and Ina17 specifically impairs formation of the peripheral stalk that connects the catalytic F1-module to the membrane embedded Fo-domain. We conclude that INAC represents a matrix-exposed inner membrane protein complex that facilitates peripheral stalk assembly and thus promotes a key step in the biogenesis of mitochondrial F1Fo-ATP synthase.
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Affiliation(s)
- Oleksandr Lytovchenko
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Nataliia Naumenko
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Silke Oeljeklaus
- Department of Biochemistry and Functional Proteomics, Faculty for Biology, University of Freiburg, Freiburg, Germany BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Bernhard Schmidt
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Karina von der Malsburg
- Institute for Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, Freiburg, Germany
| | - Markus Deckers
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Bettina Warscheid
- Department of Biochemistry and Functional Proteomics, Faculty for Biology, University of Freiburg, Freiburg, Germany BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Martin van der Laan
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany Institute for Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, Freiburg, Germany
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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26
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Jitkova Y, Gronda M, Hurren R, Wang X, Goard CA, Jhas B, Schimmer AD. A novel formulation of tigecycline has enhanced stability and sustained antibacterial and antileukemic activity. PLoS One 2014; 9:e95281. [PMID: 24871339 PMCID: PMC4037176 DOI: 10.1371/journal.pone.0095281] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 03/25/2014] [Indexed: 01/23/2023] Open
Abstract
Tigecycline is a broad-spectrum, first-in-class glycylcycline antibiotic currently used to treat complicated skin and intra-abdominal infections, as well as community-acquired pneumonia. In addition, we have demonstrated that tigecycline also has in vitro and in vivo activity against acute myeloid leukemia (AML) due to its ability to inhibit mitochondrial translation. Tigecycline is relatively unstable after reconstitution, and this instability may limit the use of the drug in ambulatory infusions for the treatment of infection and may prevent the development of optimal dosing schedules for the treatment of AML. This study sought to identify a formulation that improved the stability of the drug after reconstitution and maintained its antimicrobial and antileukemic activity. A panel of chemical additives was tested to identify excipients that enhanced the stability of tigecycline in solution at room temperature for up to one week. We identified a novel formulation containing the oxygen-reducing agents ascorbic acid (3 mg/mL) and pyruvate (60 mg/mL), in saline solution, pH 7.0, in which tigecycline (1 mg/mL) remained intact when protected from light for at least 7 days. This formulation also preserved the drug's antibacterial and antileukemic activity in vitro. Moreover, the novel formulation retained tigecycline's antileukemic activity in vivo. Thus, we identified and characterized a novel formulation for tigecycline that preserves its stability and efficacy after reconstitution.
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Affiliation(s)
- Yulia Jitkova
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Marcela Gronda
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Rose Hurren
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Xiaoming Wang
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Carolyn A. Goard
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Bozhena Jhas
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Aaron D. Schimmer
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- * E-mail:
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27
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De Silva D, Fontanesi F, Barrientos A. The DEAD box protein Mrh4 functions in the assembly of the mitochondrial large ribosomal subunit. Cell Metab 2013; 18:712-25. [PMID: 24206665 PMCID: PMC3857544 DOI: 10.1016/j.cmet.2013.10.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 09/04/2013] [Accepted: 10/08/2013] [Indexed: 12/24/2022]
Abstract
Proteins in a cell are universally synthesized by ribosomes. Mitochondria contain their own ribosomes, which specialize in the synthesis of a handful of proteins required for oxidative phosphorylation. The pathway of mitoribosomal biogenesis and factors involved are poorly characterized. An example is the DEAD box proteins, widely known to participate in the biogenesis of bacterial and cytoplasmic eukaryotic ribosomes as either RNA helicases or RNA chaperones, whose mitochondrial counterparts remain completely unknown. Here, we have identified the Saccharomyces cerevisiae mitochondrial DEAD box protein Mrh4 as essential for large mitoribosome subunit biogenesis. Mrh4 interacts with the 21S rRNA, mitoribosome subassemblies, and fully assembled mitoribosomes. In the absence of Mrh4, the 21S rRNA is matured and forms part of a large on-pathway assembly intermediate missing proteins Mrpl16 and Mrpl39. We conclude that Mrh4 plays an essential role during the late stages of mitoribosome assembly by promoting remodeling of the 21S rRNA-protein interactions.
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Affiliation(s)
- Dasmanthie De Silva
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL-33136 (USA)
| | - Flavia Fontanesi
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL-33136 (USA)
| | - Antoni Barrientos
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL-33136 (USA)
- Department of Neurology University of Miami Miller School of Medicine, Miami, FL-33136 (USA)
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Goard CA, Schimmer AD. Mitochondrial matrix proteases as novel therapeutic targets in malignancy. Oncogene 2013; 33:2690-9. [PMID: 23770858 DOI: 10.1038/onc.2013.228] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 04/23/2013] [Accepted: 04/30/2013] [Indexed: 12/30/2022]
Abstract
Although mitochondrial function is often altered in cancer, it remains essential for tumor viability. Tight control of protein homeostasis is required for the maintenance of mitochondrial function, and the mitochondrial matrix houses several coordinated protein quality control systems. These include three evolutionarily conserved proteases of the AAA+ superfamily-the Lon, ClpXP and m-AAA proteases. In humans, these proteases are proposed to degrade, process and chaperone the assembly of mitochondrial proteins in the matrix and inner membrane involved in oxidative phosphorylation, mitochondrial protein synthesis, mitochondrial network dynamics and nucleoid function. In addition, these proteases are upregulated by a variety of mitochondrial stressors, including oxidative stress, unfolded protein stress and imbalances in respiratory complex assembly. Given that tumor cells must survive and proliferate under dynamic cellular stress conditions, dysregulation of mitochondrial protein quality control systems may provide a selective advantage. The association of mitochondrial matrix AAA+ proteases with cancer and their potential for therapeutic modulation therefore warrant further consideration. Although our current knowledge of the endogenous human substrates of these proteases is limited, we highlight functional insights gained from cultured human cells, protease-deficient mouse models and other eukaryotic model organisms. We also review the consequences of disrupting mitochondrial matrix AAA+ proteases through genetic and pharmacological approaches, along with implications of these studies on the potential of these proteases as anticancer therapeutic targets.
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Affiliation(s)
- C A Goard
- Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada
| | - A D Schimmer
- Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada
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