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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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2
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How RNases Shape Mitochondrial Transcriptomes. Int J Mol Sci 2022; 23:ijms23116141. [PMID: 35682820 PMCID: PMC9181182 DOI: 10.3390/ijms23116141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 11/17/2022] Open
Abstract
Mitochondria are the power houses of eukaryote cells. These endosymbiotic organelles of prokaryote origin are considered as semi-autonomous since they have retained a genome and fully functional gene expression mechanisms. These pathways are particularly interesting because they combine features inherited from the bacterial ancestor of mitochondria with characteristics that appeared during eukaryote evolution. RNA biology is thus particularly diverse in mitochondria. It involves an unexpectedly vast array of factors, some of which being universal to all mitochondria and others being specific from specific eukaryote clades. Among them, ribonucleases are particularly prominent. They play pivotal functions such as the maturation of transcript ends, RNA degradation and surveillance functions that are required to attain the pool of mature RNAs required to synthesize essential mitochondrial proteins such as respiratory chain proteins. Beyond these functions, mitochondrial ribonucleases are also involved in the maintenance and replication of mitochondrial DNA, and even possibly in the biogenesis of mitochondrial ribosomes. The diversity of mitochondrial RNases is reviewed here, showing for instance how in some cases a bacterial-type enzyme was kept in some eukaryotes, while in other clades, eukaryote specific enzymes were recruited for the same function.
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3
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Tian H, Hu Z, Wang C. The Therapeutic Potential of tRNA-derived Small RNAs in Neurodegenerative Disorders. Aging Dis 2022; 13:389-401. [PMID: 35371602 PMCID: PMC8947841 DOI: 10.14336/ad.2021.0903] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 09/02/2021] [Indexed: 11/01/2022] Open
Abstract
Gene expressions and functions at various levels, namely post-transcriptional, transcriptional, and epigenetic, can be regulated by transfer RNA (tRNA)-derived small RNAs (tsRNAs), which are as well-established as tRNA fragments or tRFs. This regulation occurs when tsRNAs are created through the special endonuclease-mediated cleavage of mature or precursor tRNAs. However, tsRNAs are newly discovered entities, and molecular functions associated with tsRNAs are still not clearly understood. There is increasingly robust evidence suggesting that specific tsRNAs perform fundamental tasks in the pathogenesis of neurodevelopmental, neurodegenerative, and neurobehavioral disorders. Indeed, the patterns of tsRNA expression are uncertain and could be altered in patients suffering from Parkinson's disease, pontocerebellar hypoplasia, amyotrophic lateral sclerosis, Alzheimer's disease, and other neurodegenerative disorders. In the present article, a review is conducted of recent domestic and international progress in research on the potential cellular and molecular mechanisms of tsRNA biogenesis. We also describe endogenous tsRNAs during neuronal development and neurodegenerative disorders, thereby providing theoretical support and guidance for further revealing the therapeutic potential of tsRNAs in neurodegenerative disorders.
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Affiliation(s)
- Haihua Tian
- 1Ningbo Key Laboratory of Behavioral Neuroscience, Ningbo University School of Medicine, Ningbo, Zhejiang, China.,2Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China.,3Department of Physiology and Pharmacology, Ningbo University School of Medicine, Ningbo, Zhejiang, China.,4Department of Laboratory Medicine, Ningbo Kangning Hospital, Ningbo, Zhejiang, China
| | - Zhenyu Hu
- 5Department of Child Psychiatry, Ningbo Kanning Hospital, Ningbo, Zhejiang, China
| | - Chuang Wang
- 1Ningbo Key Laboratory of Behavioral Neuroscience, Ningbo University School of Medicine, Ningbo, Zhejiang, China.,2Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China.,3Department of Physiology and Pharmacology, Ningbo University School of Medicine, Ningbo, Zhejiang, China
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4
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Migunova E, Theophilopoulos J, Mercadante M, Men J, Zhou C, Dubrovsky EB. ELAC2/RNaseZ-linked cardiac hypertrophy in Drosophila melanogaster. Dis Model Mech 2021; 14:271965. [PMID: 34338278 PMCID: PMC8419712 DOI: 10.1242/dmm.048931] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 07/20/2021] [Indexed: 12/16/2022] Open
Abstract
A severe form of infantile cardiomyopathy (CM) has been linked to mutations in ELAC2, a highly conserved human gene. It encodes Zinc phosphodiesterase ELAC protein 2 (ELAC2), which plays an essential role in the production of mature tRNAs. To establish a causal connection between ELAC2 variants and CM, here we used the Drosophila melanogaster model organism, which carries the ELAC2 homolog RNaseZ. Even though RNaseZ and ELAC2 have diverged in some of their biological functions, our study demonstrates the use of the fly model to study the mechanism of ELAC2-related pathology. We established transgenic lines harboring RNaseZ with CM-linked mutations in the background of endogenous RNaseZ knockout. Importantly, we found that the phenotype of these flies is consistent with the pathological features in human patients. Specifically, expression of CM-linked variants in flies caused heart hypertrophy and led to reduction in cardiac contractility associated with a rare form of CM. This study provides first experimental evidence for the pathogenicity of CM-causing mutations in the ELAC2 protein, and the foundation to improve our understanding and diagnosis of this rare infantile disease. This article has an associated First Person interview with the first author of the paper. Summary: A newly established Drosophila model recapitulates key features of human heart pathology linked to mutations in ELAC2, thus providing experimental evidence of the pathogenicity of ELAC2 variants.
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Affiliation(s)
- Ekaterina Migunova
- Department of Biological Sciences, Fordham University, Bronx, NY 10458, USA
| | | | - Marisa Mercadante
- Department of Biological Sciences, Fordham University, Bronx, NY 10458, USA
| | - Jing Men
- Department of Biomedical Engineering, Washington University in St Louis, St Louis, MO 63105, USA.,Department of Electrical and Computer Engineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Chao Zhou
- Department of Biomedical Engineering, Washington University in St Louis, St Louis, MO 63105, USA
| | - Edward B Dubrovsky
- Department of Biological Sciences, Fordham University, Bronx, NY 10458, USA.,Center for Cancer, Genetic diseases, and Gene Regulation, Department of Biological Sciences, Fordham University, Bronx, NY 10458, USA
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5
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Pajak A, Laine I, Clemente P, El-Fissi N, Schober FA, Maffezzini C, Calvo-Garrido J, Wibom R, Filograna R, Dhir A, Wedell A, Freyer C, Wredenberg A. Defects of mitochondrial RNA turnover lead to the accumulation of double-stranded RNA in vivo. PLoS Genet 2019; 15:e1008240. [PMID: 31365523 PMCID: PMC6668790 DOI: 10.1371/journal.pgen.1008240] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 06/11/2019] [Indexed: 12/02/2022] Open
Abstract
The RNA helicase SUV3 and the polynucleotide phosphorylase PNPase are involved in the degradation of mitochondrial mRNAs but their roles in vivo are not fully understood. Additionally, upstream processes, such as transcript maturation, have been linked to some of these factors, suggesting either dual roles or tightly interconnected mechanisms of mitochondrial RNA metabolism. To get a better understanding of the turn-over of mitochondrial RNAs in vivo, we manipulated the mitochondrial mRNA degrading complex in Drosophila melanogaster models and studied the molecular consequences. Additionally, we investigated if and how these factors interact with the mitochondrial poly(A) polymerase, MTPAP, as well as with the mitochondrial mRNA stabilising factor, LRPPRC. Our results demonstrate a tight interdependency of mitochondrial mRNA stability, polyadenylation and the removal of antisense RNA. Furthermore, disruption of degradation, as well as polyadenylation, leads to the accumulation of double-stranded RNAs, and their escape out into the cytoplasm is associated with an altered immune-response in flies. Together our results suggest a highly organised and inter-dependable regulation of mitochondrial RNA metabolism with far reaching consequences on cellular physiology. Although a number of factors have been implemented in the turnover of mitochondrial (mt) DNA-derived transcripts, their exact functions and interplay with one another is not entirely clear. Several of these factors have been proposed to co-ordinately regulate both transcript maturation, as well as degradation, but the order of events during mitochondrial RNA turnover is less well understood. Using a range of different genetically modified Drosophila melanogaster models, we studied the involvement of the RNA helicase SUV3, the polynucleotide phosphorylase PNPase, the leucine-rich pentatricopeptide repeat motif-containing protein LRPPRC, and the mitochondrial RNA poly(A) polymerase MTPAP, in stabilisation, polyadenylation, and degradation of mitochondrial transcripts. Our results show a tight collaborative activity of these factors in vivo and reveal a clear hierarchical order of events leading to mitochondrial mRNA maturation. Furthermore, we demonstrate that the loss of SUV3, PNPase, or MTPAP leads to the accumulation of mitochondrial-derived antisense RNA in the cytoplasm of cells, which is associated with an altered immune-response in flies.
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Affiliation(s)
- Aleksandra Pajak
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Isabelle Laine
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Paula Clemente
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Najla El-Fissi
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Florian A. Schober
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Camilla Maffezzini
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Javier Calvo-Garrido
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Rolf Wibom
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Roberta Filograna
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Ashish Dhir
- Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Anna Wedell
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Christoph Freyer
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
- * E-mail: (CF); (AW)
| | - Anna Wredenberg
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
- * E-mail: (CF); (AW)
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6
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Shang J, Yang Y, Wu L, Zou M, Huang Y. The S. pombe mitochondrial transcriptome. RNA (NEW YORK, N.Y.) 2018; 24:1241-1254. [PMID: 29954949 PMCID: PMC6097661 DOI: 10.1261/rna.064477.117] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 06/26/2018] [Indexed: 05/22/2023]
Abstract
Mitochondrial gene expression is largely controlled through post-transcriptional processes including mitochondrial RNA (mt-RNA) processing, modification, decay, and quality control. Defective mitochondrial gene expression results in mitochondrial oxidative phosphorylation (OXPHOS) deficiency and has been implicated in human disease. To fully understand mitochondrial transcription and RNA processing, we performed RNA-seq analyses of mt-RNAs from the fission yeast Schizosaccharomyces pombe RNA-seq analyses show that the abundance of mt-RNAs vary greatly. Analysis of data also reveals mt-RNA processing sites including an unusual RNA cleavage event by mitochondrial tRNA (mt-tRNA) 5'-end processing enzyme RNase P. Additionally, this analysis reveals previously unknown mitochondrial transcripts including the rnpB-derived fragment, mitochondrial small RNAs (mitosRNAs) such as mt-tRNA-derived fragments (mt-tRFs) and mt-tRNA halves, and mt-tRNAs marked with 3'-CCACCA/CCACC in S. pombe Finally, RNA-seq reveals that inactivation of trz2 encoding S. pombe mitochondrial tRNA 3'-end processing enzyme globally impairs mt-tRNA 3'-end processing, inhibits mt-mRNA 5'-end processing, and causes accumulation of unprocessed transcripts, demonstrating the feasibility of using RNA-seq to examine the protein known or predicted to be involved in mt-RNA processing in S. pombe Our work uncovers the complexity of a fungal mitochondrial transcriptome and provides a framework for future studies of mitochondrial gene expression using S. pombe as a model system.
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Affiliation(s)
- Jinjie Shang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Yanmei Yang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Lin Wu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Mengting Zou
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Ying Huang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
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7
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Liu J, Huang L, Wang Y, Huang Y. Characterization of cis-elements in the promoter of trz2 encoding Schizosaccharomyces pombe mitochondrial tRNA 3′-end processing enzyme. Microbiology (Reading) 2017; 163:75-85. [DOI: 10.1099/mic.0.000398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Affiliation(s)
- Jinyu Liu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, School of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, PR China
| | - Linting Huang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, School of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, PR China
| | - Yirong Wang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, School of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, PR China
| | - Ying Huang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, School of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, PR China
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8
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Sen A, Karasik A, Shanmuganathan A, Mirkovic E, Koutmos M, Cox RT. Loss of the mitochondrial protein-only ribonuclease P complex causes aberrant tRNA processing and lethality in Drosophila. Nucleic Acids Res 2016; 44:6409-22. [PMID: 27131785 PMCID: PMC5291253 DOI: 10.1093/nar/gkw338] [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: 02/26/2016] [Accepted: 04/14/2016] [Indexed: 12/26/2022] Open
Abstract
Proteins encoded by mitochondrial DNA are translated using mitochondrially encoded tRNAs and rRNAs. As with nuclear encoded tRNAs, mitochondrial tRNAs must be processed to become fully functional. The mitochondrial form of ribonuclease P (mt:RNase P) is responsible for 5′-end maturation and is comprised of three proteins; mitochondrial RNase P protein (MRPP) 1 and 2 together with proteinaceous RNase P (PRORP). However, its mechanism and impact on development is not yet known. Using homology searches, we have identified the three proteins composing Drosophila mt:RNase P: Mulder (PRORP), Scully (MRPP2) and Roswell (MRPP1). Here, we show that each protein is essential and localizes with mitochondria. Furthermore, reducing levels of each causes mitochondrial deficits, which appear to be due at least in part to defective mitochondrial tRNA processing. Overexpressing two members of the complex, Mulder and Roswell, is also lethal, and in the case of Mulder, causes abnormal mitochondrial morphology. These data are the first evidence that defective mt:RNase P causes mitochondrial dysfunction, lethality and aberrant mitochondrial tRNA processing in vivo, underscoring its physiological importance. This in vivo mt:RNase P model will advance our understanding of how loss of mitochondrial tRNA processing causes tissue failure, an important aspect of human mitochondrial disease.
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Affiliation(s)
- Aditya Sen
- Department of Biochemistry and Molecular Biology, Uniformed Services University, Bethesda, MD, 20814, USA
| | - Agnes Karasik
- Department of Biochemistry and Molecular Biology, Uniformed Services University, Bethesda, MD, 20814, USA
| | | | | | - Markos Koutmos
- Department of Biochemistry and Molecular Biology, Uniformed Services University, Bethesda, MD, 20814, USA
| | - Rachel T Cox
- Department of Biochemistry and Molecular Biology, Uniformed Services University, Bethesda, MD, 20814, USA
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