1
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Kim S, Tan S, Ku J, Widowati TA, Ku D, Lee K, You K, Kim Y. RNA 5-methylcytosine marks mitochondrial double-stranded RNAs for degradation and cytosolic release. Mol Cell 2024; 84:2935-2948.e7. [PMID: 39019044 PMCID: PMC11316625 DOI: 10.1016/j.molcel.2024.06.023] [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: 11/01/2023] [Revised: 05/20/2024] [Accepted: 06/21/2024] [Indexed: 07/19/2024]
Abstract
Mitochondria are essential regulators of innate immunity. They generate long mitochondrial double-stranded RNAs (mt-dsRNAs) and release them into the cytosol to trigger an immune response under pathological stress conditions. Yet the regulation of these self-immunogenic RNAs remains largely unknown. Here, we employ CRISPR screening on mitochondrial RNA (mtRNA)-binding proteins and identify NOP2/Sun RNA methyltransferase 4 (NSUN4) as a key regulator of mt-dsRNA expression in human cells. We find that NSUN4 induces 5-methylcytosine (m5C) modification on mtRNAs, especially on the termini of light-strand long noncoding RNAs. These m5C-modified RNAs are recognized by complement C1q-binding protein (C1QBP), which recruits polyribonucleotide nucleotidyltransferase to facilitate RNA turnover. Suppression of NSUN4 or C1QBP results in increased mt-dsRNA expression, while C1QBP deficiency also leads to increased cytosolic mt-dsRNAs and subsequent immune activation. Collectively, our study unveils the mechanism underlying the selective degradation of light-strand mtRNAs and establishes a molecular mark for mtRNA decay and cytosolic release.
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Affiliation(s)
- Sujin Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Stephanie Tan
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Jayoung Ku
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Tria Asri Widowati
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Doyeong Ku
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Keonyong Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Kwontae You
- Xaira Therapeutics, Foster City, CA 94404, USA
| | - Yoosik Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Graduate School of Engineering Biology, KAIST, Daejeon 34141, Republic of Korea; KAIST Institute for BioCentury, KAIST, Daejeon 34141, Republic of Korea; KAIST Institute for Health Science and Technology (KIHST), KAIST, Daejeon 34141, Republic of Korea.
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2
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Moran JC, Brivanlou A, Brischigliaro M, Fontanesi F, Rouskin S, Barrientos A. The human mitochondrial mRNA structurome reveals mechanisms of gene expression. Science 2024; 385:eadm9238. [PMID: 39024447 DOI: 10.1126/science.adm9238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 05/24/2024] [Indexed: 07/20/2024]
Abstract
The human mitochondrial genome encodes crucial oxidative phosphorylation system proteins, pivotal for aerobic energy transduction. They are translated from nine monocistronic and two bicistronic transcripts whose native structures remain unexplored, posing a gap in understanding mitochondrial gene expression. In this work, we devised the mitochondrial dimethyl sulfate mutational profiling with sequencing (mitoDMS-MaPseq) method and applied detection of RNA folding ensembles using expectation-maximization (DREEM) clustering to unravel the native mitochondrial messenger RNA (mt-mRNA) structurome in wild-type (WT) and leucine-rich pentatricopeptide repeat-containing protein (LRPPRC)-deficient cells. Our findings elucidate LRPPRC's role as a holdase contributing to maintaining mt-mRNA folding and efficient translation. mt-mRNA structural insights in WT mitochondria, coupled with metabolic labeling, unveil potential mRNA-programmed translational pausing and a distinct programmed ribosomal frameshifting mechanism. Our data define a critical layer of mitochondrial gene expression regulation. These mt-mRNA folding maps provide a reference for studying mt-mRNA structures in diverse physiological and pathological contexts.
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Affiliation(s)
- J Conor Moran
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, 1600 NW 10th Avenue, Miami, FL 33136, USA
- University of Miami Medical Scientist Training Program, University of Miami Miller School of Medicine, 1600 NW 10th Avenue, Miami, FL 33136, USA
| | - Amir Brivanlou
- Department of Microbiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Michele Brischigliaro
- Department of Neurology, University of Miami Miller School of Medicine, 1600 NW 10th Avenue, Miami, FL 33136, USA
| | - Flavia Fontanesi
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, 1600 NW 10th Avenue, Miami, FL 33136, USA
| | - Silvi Rouskin
- Department of Microbiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Antoni Barrientos
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, 1600 NW 10th Avenue, Miami, FL 33136, USA
- Department of Neurology, University of Miami Miller School of Medicine, 1600 NW 10th Avenue, Miami, FL 33136, USA
- The Miami Veterans Affairs (VA) Medical System, 1201 NW 16th Street, Miami, FL 33125, USA
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3
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Kumar J, Kowluru RA. Mitochondrial DNA transcription and mitochondrial genome-encoded long noncoding RNA in diabetic retinopathy. Mitochondrion 2024; 78:101925. [PMID: 38944370 DOI: 10.1016/j.mito.2024.101925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 06/13/2024] [Accepted: 06/26/2024] [Indexed: 07/01/2024]
Abstract
In diabetic retinopathy, mitochondrial DNA (mtDNA) is damaged and mtDNA-encoded genes and long noncoding RNA cytochrome B (LncCytB) are downregulated. LncRNAs lack an open reading frame, but they can regulate gene expression by associating with DNA/RNA/protein. Double stranded mtDNA has promoters on both heavy (HSP) and light (LSP) strands with binding sites for mitochondrial transcription factor A (TFAM) between them. The aim was to investigate the role of LncCytB in mtDNA transcription in diabetic retinopathy. Using human retinal endothelial cells incubated in high glucose, the effect of regulation of LncCytB on TFAM binding at mtDNA promoters was investigated by Chromatin immunoprecipitation, and binding of LncCytB at TFAM by RNA immunoprecipitation and RNA fluorescence in situ hybridization. High glucose decreased TFAM binding at both HSP and LSP, and binding of LncCytB at TFAM. While LncCytB overexpression ameliorated decrease in TFAM binding and transcription of genes encoded by both H- and L- strands, LncCytB-siRNA further downregulated them. Maintenance of mitochondrial homeostasis by overexpressing mitochondrial superoxide dismutase or Sirtuin-1 protected diabetes-induced decrease in TFAM binding at mtDNA and LncCytB binding at TFAM, and mtDNA transcription. Similar results were obtained from mouse retinal microvessels from streptozotocin-induced diabetic mice. Thus, LncCytB facilitates recruitment of TFAM at HSP and LSP, and its downregulation in diabetes compromises the binding, resulting in the downregulation of polypeptides encoded by mtDNA. Regulation of LncCytB, in addition to protecting mitochondrial genomic stability, should also help in maintaining the transcription of mtDNA encoded genes and electron transport chain integrity in diabetic retinopathy.
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Affiliation(s)
- Jay Kumar
- Ophthalmology, Visual and Anatomical Sciences, Wayne State University, 4717 St. Antoine, Detroit, MI 48201, USA
| | - Renu A Kowluru
- Ophthalmology, Visual and Anatomical Sciences, Wayne State University, 4717 St. Antoine, Detroit, MI 48201, USA.
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4
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Brischigliaro M, Sierra-Magro A, Ahn A, Barrientos A. Mitochondrial ribosome biogenesis and redox sensing. FEBS Open Bio 2024. [PMID: 38849194 DOI: 10.1002/2211-5463.13844] [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: 03/29/2024] [Revised: 05/06/2024] [Accepted: 05/29/2024] [Indexed: 06/09/2024] Open
Abstract
Mitoribosome biogenesis is a complex process involving RNA elements encoded in the mitochondrial genome and mitoribosomal proteins typically encoded in the nuclear genome. This process is orchestrated by extra-ribosomal proteins, nucleus-encoded assembly factors, which play roles across all assembly stages to coordinate ribosomal RNA processing and maturation with the sequential association of ribosomal proteins. Both biochemical studies and recent cryo-EM structures of mammalian mitoribosomes have provided insights into their assembly process. In this article, we will briefly outline the current understanding of mammalian mitoribosome biogenesis pathways and the factors involved. Special attention is devoted to the recent identification of iron-sulfur clusters as structural components of the mitoribosome and a small subunit assembly factor, the existence of redox-sensitive cysteines in mitoribosome proteins and assembly factors, and the role they may play as redox sensor units to regulate mitochondrial translation under stress.
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Affiliation(s)
| | - Ana Sierra-Magro
- Department of Neurology, University of Miami Miller School of Medicine, FL, USA
| | - Ahram Ahn
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, FL, USA
| | - Antoni Barrientos
- Department of Neurology, University of Miami Miller School of Medicine, FL, USA
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, FL, USA
- Bruce W. Carter Department of Veterans Affairs VA Medical Center, Miami, FL, USA
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5
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Santonoceto G, Jurkiewicz A, Szczesny RJ. RNA degradation in human mitochondria: the journey is not finished. Hum Mol Genet 2024; 33:R26-R33. [PMID: 38779774 DOI: 10.1093/hmg/ddae043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/03/2024] [Accepted: 03/05/2024] [Indexed: 05/25/2024] Open
Abstract
Mitochondria are vital organelles present in almost all eukaryotic cells. Although most of the mitochondrial proteins are nuclear-encoded, mitochondria contain their own genome, whose proper expression is necessary for mitochondrial function. Transcription of the human mitochondrial genome results in the synthesis of long polycistronic transcripts that are subsequently processed by endonucleases to release individual RNA molecules, including precursors of sense protein-encoding mRNA (mt-mRNA) and a vast amount of antisense noncoding RNAs. Because of mitochondrial DNA (mtDNA) organization, the regulation of individual gene expression at the transcriptional level is limited. Although transcription of most protein-coding mitochondrial genes occurs with the same frequency, steady-state levels of mature transcripts are different. Therefore, post-transcriptional processes are important for regulating mt-mRNA levels. The mitochondrial degradosome is a complex composed of the RNA helicase SUV3 (also known as SUPV3L1) and polynucleotide phosphorylase (PNPase, PNPT1). It is the best-characterized RNA-degrading machinery in human mitochondria, which is primarily responsible for the decay of mitochondrial antisense RNA. The mechanism of mitochondrial sense RNA decay is less understood. This review aims to provide a general picture of mitochondrial genome expression, with a particular focus on mitochondrial RNA (mtRNA) degradation.
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Affiliation(s)
- Giulia Santonoceto
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, Warsaw 02-106, Poland
| | - Aneta Jurkiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, Warsaw 02-106, Poland
| | - Roman J Szczesny
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, Warsaw 02-106, Poland
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Vučković A, Freyer C, Wredenberg A, Hillen HS. The molecular machinery for maturation of primary mtDNA transcripts. Hum Mol Genet 2024; 33:R19-R25. [PMID: 38779769 PMCID: PMC11112384 DOI: 10.1093/hmg/ddae023] [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: 01/31/2024] [Revised: 01/31/2024] [Accepted: 02/08/2024] [Indexed: 05/25/2024] Open
Abstract
Human mitochondria harbour a circular, polyploid genome (mtDNA) encoding 11 messenger RNAs (mRNAs), two ribosomal RNAs (rRNAs) and 22 transfer RNAs (tRNAs). Mitochondrial transcription produces long, polycistronic transcripts that span almost the entire length of the genome, and hence contain all three types of RNAs. The primary transcripts then undergo a number of processing and maturation steps, which constitute key regulatory points of mitochondrial gene expression. The first step of mitochondrial RNA processing consists of the separation of primary transcripts into individual, functional RNA molecules and can occur by two distinct pathways. Both are carried out by dedicated molecular machineries that substantially differ from RNA processing enzymes found elsewhere. As a result, the underlying molecular mechanisms remain poorly understood. Over the last years, genetic, biochemical and structural studies have identified key players involved in both RNA processing pathways and provided the first insights into the underlying mechanisms. Here, we review our current understanding of RNA processing in mammalian mitochondria and provide an outlook on open questions in the field.
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MESH Headings
- Humans
- DNA, Mitochondrial/genetics
- RNA Processing, Post-Transcriptional
- Mitochondria/genetics
- Mitochondria/metabolism
- RNA, Mitochondrial/genetics
- RNA, Mitochondrial/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Animals
- Transcription, Genetic
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
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Affiliation(s)
- Ana Vučković
- Department of Cellular Biochemistry, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
- Research Group Structure and Function of Molecular Machines, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Christoph Freyer
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Anna Steckséns gata 47, 171 64 Solna, Sweden
| | - Anna Wredenberg
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Anna Steckséns gata 47, 171 64 Solna, Sweden
| | - Hauke S Hillen
- Department of Cellular Biochemistry, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
- Research Group Structure and Function of Molecular Machines, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, Robert-Koch-Straße 40, 37073 Göttingen, Germany
- Research Group Structure and Function of Molecular Machines, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Justus-von-Liebig-Weg 11, Goettingen 37077, Germany
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7
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Giarmarco M, Seto J, Brock D, Brockerhoff S. Spatial detection of mitochondrial DNA and RNA in tissues. Front Cell Dev Biol 2024; 12:1346778. [PMID: 38808224 PMCID: PMC11130414 DOI: 10.3389/fcell.2024.1346778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 04/12/2024] [Indexed: 05/30/2024] Open
Abstract
Background Mitochondrial health has gained attention in a number of diseases, both as an indicator of disease state and as a potential therapeutic target. The quality and amount of mitochondrial DNA (mtDNA) and RNA (mtRNA) can be important indicators of mitochondrial and cell health, but are difficult to measure in complex tissues. Methods mtDNA and mtRNA in zebrafish retina samples were fluorescently labeled using RNAscope™ in situ hybridization, then mitochondria were stained using immunohistochemistry. Pretreatment with RNase was used for validation. Confocal images were collected and analyzed, and relative amounts of mtDNA and mtRNA were reported. Findings regarding mtDNA were confirmed using qPCR. Results Signals from probes detecting mtDNA and mtRNA were localized to mitochondria, and were differentially sensitive to RNase. This labeling strategy allows for quantification of relative mtDNA and mtRNA levels in individual cells. As a demonstration of the method in a complex tissue, single photoreceptors in zebrafish retina were analyzed for mtDNA and mtRNA content. An increase in mtRNA but not mtDNA coincides with proliferation of mitochondria at night in cones. A similar trend was measured in rods. Discussion Mitochondrial gene expression is an important component of cell adaptations to disease, stress, or aging. This method enables the study of mtDNA and mtRNA in single cells of an intact, complex tissue. The protocol presented here uses commercially-available tools, and is adaptable to a range of species and tissue types.
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Affiliation(s)
- Michelle Giarmarco
- Department of Ophthalmology, University of Washington, Seattle, WA, United States
| | - Jordan Seto
- Department of Ophthalmology, University of Washington, Seattle, WA, United States
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Daniel Brock
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Susan Brockerhoff
- Department of Ophthalmology, University of Washington, Seattle, WA, United States
- Department of Biochemistry, University of Washington, Seattle, WA, United States
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Liu D, Zhou X, He Y, Zhao J. The Roles of CircRNAs in Mitochondria. J Cancer 2024; 15:2759-2769. [PMID: 38577612 PMCID: PMC10988319 DOI: 10.7150/jca.92111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 03/02/2024] [Indexed: 04/06/2024] Open
Abstract
Mitochondria participate in varieties of cellular events. It is widely accepted that human mitochondrial genome encodes 13 proteins, 2 rRNAs, and 22 tRNAs. Gene variation derived from human nuclear genome cannot completely explain mitochondrial diseases. The advent of high-throughput sequencing coupled with novel bioinformatic analyses decode the complexity of mitochondria-derived transcripts. Recently, circular RNAs (circRNAs) from both human mitochondrial genome and nuclear genome have been found to be located at mitochondria. Studies about the roles and molecular mechanisms underlying trafficking of the nucleus encoded circRNAs to mitochondria and mitochondria encoded circRNAs to the nucleus or cytoplasm in mammals are only beginning to emerge. These circRNAs have been associated with a variety of diseases, especially cancers. Here, we discuss the emerging field of mitochondria-located circRNAs by reviewing their identification, expression patterns, regulatory roles, and functional mechanisms. Mitochondria-located circRNAs have regulatory roles in cellular physiology and pathology. We also highlight future perspectives and challenges in studying mitochondria-located circRNAs, as well as their potential biomedical applications.
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Affiliation(s)
- Donghong Liu
- Department of Special Medical Care, Third Affiliated Hospital of Naval Medical University, Shanghai, 200438, China
| | - Xinyu Zhou
- Department of Epidemiology, Naval Medical University, Shanghai, 200433, China
| | - Yida He
- Department of Epidemiology, Naval Medical University, Shanghai, 200433, China
| | - Jun Zhao
- Department of Special Medical Care, Third Affiliated Hospital of Naval Medical University, Shanghai, 200438, China
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Lin Y, Dong ZH, Ye TY, Yang JM, Xie M, Luo JC, Gao J, Guo AY. Optimization of FFPE preparation and identification of gene attributes associated with RNA degradation. NAR Genom Bioinform 2024; 6:lqae008. [PMID: 38298182 PMCID: PMC10830353 DOI: 10.1093/nargab/lqae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/30/2023] [Accepted: 01/16/2024] [Indexed: 02/02/2024] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues are widely available specimens for clinical studies. However, RNA degradation in FFPE tissues often restricts their utility. In this study, we determined optimal FFPE preparation conditions, including tissue ischemia at 4°C (<48 h) or 25°C for a short time (0.5 h), 48-h fixation at 25°C and sampling from FFPE scrolls instead of sections. Notably, we observed an increase in intronic reads and a significant change in gene rank based on expression level in the FFPE as opposed to fresh-frozen (FF) samples. Additionally, we found that more reads were mapped to genes associated with chemical stimulus in FFPE samples. Furthermore, we demonstrated that more degraded genes in FFPE samples were enriched in genes with short transcripts and high free energy. Besides, we found 40 housekeeping genes exhibited stable expression in FF and FFPE samples across various tissues. Moreover, our study showed that FFPE samples yielded comparable results to FF samples in dimensionality reduction and pathway analyses between case and control samples. Our study established the optimal conditions for FFPE preparation and identified gene attributes associated with degradation, which would provide useful clues for the utility of FFPE tissues in clinical practice and research.
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Affiliation(s)
- Yu Lin
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- Department of thoracic surgery, West China Biomedical Big Data Center, West China Hospital, Med-X Center for Informatics, Sichuan University, Chengdu 610041, China
| | - Zhou-Huan Dong
- The First Medical Center, Chinese People’s Liberation Army (PLA) General Hospital, Beijing 100853, China
| | - Ting-Yue Ye
- Nanjing Vazyme Biotech Co., Ltd., Nanjing 210000, China
| | - Jing-Min Yang
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Mei Xie
- Department of Respiratory and Critical Care, Chinese People’s Liberation Army (PLA) General Hospital, Beijing 100853, China
| | | | - Jie Gao
- The First Medical Center, Chinese People’s Liberation Army (PLA) General Hospital, Beijing 100853, China
| | - An-Yuan Guo
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- Department of thoracic surgery, West China Biomedical Big Data Center, West China Hospital, Med-X Center for Informatics, Sichuan University, Chengdu 610041, China
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10
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Lv M, Zhou W, Hao Y, Li F, Zhang H, Yao X, Shi Y, Zhang L. Structural insights into the specific recognition of mitochondrial ribosome-binding factor hsRBFA and 12 S rRNA by methyltransferase METTL15. Cell Discov 2024; 10:11. [PMID: 38291322 PMCID: PMC10828496 DOI: 10.1038/s41421-023-00634-z] [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: 05/08/2023] [Accepted: 12/02/2023] [Indexed: 02/01/2024] Open
Abstract
Mitochondrial rRNA modifications are essential for mitoribosome assembly and its proper function. The m4C methyltransferase METTL15 maintains mitochondrial homeostasis by catalyzing m4C839 located in 12 S rRNA helix 44 (h44). This modification is essential to fine-tuning the ribosomal decoding center and increasing decoding fidelity according to studies of a conserved site in Escherichia coli. Here, we reported a series of crystal structures of human METTL15-hsRBFA-h44-SAM analog, METTL15-hsRBFA-SAM, METTL15-SAM and apo METTL15. The structures presented specific interactions of METTL15 with different substrates and revealed that hsRBFA recruits METTL15 to mitochondrial small subunit for further modification instead of 12 S rRNA. Finally, we found that METTL15 deficiency caused increased reactive oxygen species, decreased membrane potential and altered cellular metabolic state. Knocking down METTL15 caused an elevated lactate secretion and increased levels of histone H4K12-lactylation and H3K9-lactylation. METTL15 might be a suitable model to study the regulation between mitochondrial metabolism and histone lactylation.
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Affiliation(s)
- Mengqi Lv
- Hefei National Research Center for Cross Disciplinary Science, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, Hefei, Anhui, China.
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
| | - Wanwan Zhou
- Hefei National Research Center for Cross Disciplinary Science, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, Hefei, Anhui, China
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Yijie Hao
- Hefei National Research Center for Cross Disciplinary Science, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, Hefei, Anhui, China
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Fudong Li
- Hefei National Research Center for Cross Disciplinary Science, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, Hefei, Anhui, China
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Huafeng Zhang
- Hefei National Research Center for Cross Disciplinary Science, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, Hefei, Anhui, China
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Xuebiao Yao
- Hefei National Research Center for Cross Disciplinary Science, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, Hefei, Anhui, China
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Yunyu Shi
- Hefei National Research Center for Cross Disciplinary Science, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, Hefei, Anhui, China
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Liang Zhang
- Hefei National Research Center for Cross Disciplinary Science, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, Hefei, Anhui, China.
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
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11
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Bruni F. Human mtDNA-Encoded Long ncRNAs: Knotty Molecules and Complex Functions. Int J Mol Sci 2024; 25:1502. [PMID: 38338781 PMCID: PMC10855489 DOI: 10.3390/ijms25031502] [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: 12/20/2023] [Revised: 01/18/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Until a few decades ago, most of our knowledge of RNA transcription products was focused on protein-coding sequences, which were later determined to make up the smallest portion of the mammalian genome. Since 2002, we have learnt a great deal about the intriguing world of non-coding RNAs (ncRNAs), mainly due to the rapid development of bioinformatic tools and next-generation sequencing (NGS) platforms. Moreover, interest in non-human ncRNAs and their functions has increased as a result of these technologies and the accessibility of complete genome sequences of species ranging from Archaea to primates. Despite not producing proteins, ncRNAs constitute a vast family of RNA molecules that serve a number of regulatory roles and are essential for cellular physiology and pathology. This review focuses on a subgroup of human ncRNAs, namely mtDNA-encoded long non-coding RNAs (mt-lncRNAs), which are transcribed from the mitochondrial genome and whose disparate localisations and functions are linked as much to mitochondrial metabolism as to cellular physiology and pathology.
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Affiliation(s)
- Francesco Bruni
- Department of Biosciences, Biotechnologies and Environment, University of Bari Aldo Moro, 70125 Bari, Italy
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12
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Głodowicz P, Kuczyński K, Val R, Dietrich A, Rolle K. Mitochondrial transport of catalytic RNAs and targeting of the organellar transcriptome in human cells. J Mol Cell Biol 2024; 15:mjad051. [PMID: 37591617 PMCID: PMC11148835 DOI: 10.1093/jmcb/mjad051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 08/03/2023] [Accepted: 08/07/2023] [Indexed: 08/19/2023] Open
Abstract
Mutations in the small genome present in mitochondria often result in severe pathologies. Different genetic strategies have been explored, aiming to rescue such mutations. A number of these strategies were based on the capacity of human mitochondria to import RNAs from the cytosol and designed to repress the replication of the mutated genomes or to provide the organelles with wild-type versions of mutant transcripts. However, the mutant RNAs present in mitochondria turned out to be an obstacle to therapy and little attention has been devoted so far to their elimination. Here, we present the development of a strategy to knockdown mitochondrial RNAs in human cells using the transfer RNA-like structure of Brome mosaic virus or Tobacco mosaic virus as a shuttle to drive trans-cleaving ribozymes into the organelles in human cell lines. We obtained a specific knockdown of the targeted mitochondrial ATP6 mRNA, followed by a deep drop in ATP6 protein and a functional impairment of the oxidative phosphorylation chain. Our strategy provides a powerful approach to eliminate mutant organellar transcripts and to analyse the control and communication of the human organellar genetic system.
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Affiliation(s)
- Paweł Głodowicz
- Department of Molecular Neurooncology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, ul. Z. Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Konrad Kuczyński
- Department of Molecular Neurooncology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, ul. Z. Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Romain Val
- Institute of Plant Molecular Biology, French National Center for Scientific Research (CNRS) and University of Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
| | - André Dietrich
- Institute of Plant Molecular Biology, French National Center for Scientific Research (CNRS) and University of Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
| | - Katarzyna Rolle
- Department of Molecular Neurooncology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, ul. Z. Noskowskiego 12/14, 61-704 Poznan, Poland
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Conor Moran J, Brivanlou A, Brischigliaro M, Fontanesi F, Rouskin S, Barrientos A. The human mitochondrial mRNA structurome reveals mechanisms of gene expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.31.564750. [PMID: 37961485 PMCID: PMC10635011 DOI: 10.1101/2023.10.31.564750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The mammalian mitochondrial genome encodes thirteen oxidative phosphorylation system proteins, crucial in aerobic energy transduction. These proteins are translated from 9 monocistronic and 2 bicistronic transcripts, whose native structures remain unexplored, leaving fundamental molecular determinants of mitochondrial gene expression unknown. To address this gap, we developed a mitoDMS-MaPseq approach and used DREEM clustering to resolve the native human mitochondrial mt-mRNA structurome. We gained insights into mt-mRNA biology and translation regulatory mechanisms, including a unique programmed ribosomal frameshifting for the ATP8/ATP6 transcript. Furthermore, absence of the mt-mRNA maintenance factor LRPPRC led to a mitochondrial transcriptome structured differently, with specific mRNA regions exhibiting increased or decreased structuredness. This highlights the role of LRPPRC in maintaining mRNA folding to promote mt-mRNA stabilization and efficient translation. In conclusion, our mt-mRNA folding maps reveal novel mitochondrial gene expression mechanisms, serving as a detailed reference and tool for studying them in different physiological and pathological contexts.
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Potter A, Cabrera-Orefice A, Spelbrink JN. Let's make it clear: systematic exploration of mitochondrial DNA- and RNA-protein complexes by complexome profiling. Nucleic Acids Res 2023; 51:10619-10641. [PMID: 37615582 PMCID: PMC10602928 DOI: 10.1093/nar/gkad697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 07/18/2023] [Accepted: 08/11/2023] [Indexed: 08/25/2023] Open
Abstract
Complexome profiling (CP) is a powerful tool for systematic investigation of protein interactors that has been primarily applied to study the composition and dynamics of mitochondrial protein complexes. Here, we further optimized this method to extend its application to survey mitochondrial DNA- and RNA-interacting protein complexes. We established that high-resolution clear native gel electrophoresis (hrCNE) is a better alternative to preserve DNA- and RNA-protein interactions that are otherwise disrupted when samples are separated by the widely used blue native gel electrophoresis (BNE). In combination with enzymatic digestion of DNA, our CP approach improved the identification of a wide range of protein interactors of the mitochondrial gene expression system without compromising the detection of other multiprotein complexes. The utility of this approach was particularly demonstrated by analysing the complexome changes in human mitochondria with impaired gene expression after transient, chemically induced mitochondrial DNA depletion. Effects of RNase on mitochondrial protein complexes were also evaluated and discussed. Overall, our adaptations significantly improved the identification of mitochondrial DNA- and RNA-protein interactions by CP, thereby unlocking the comprehensive analysis of a near-complete mitochondrial complexome in a single experiment.
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Affiliation(s)
- Alisa Potter
- Department of Pediatrics, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alfredo Cabrera-Orefice
- Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Functional Proteomics, Institute for Cardiovascular Physiology, Goethe University, Frankfurt am Main, Germany
| | - Johannes N Spelbrink
- Department of Pediatrics, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Center, Nijmegen, The Netherlands
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Loguercio Polosa P, Capriglia F, Bruni F. Molecular Investigation of Mitochondrial RNA19 Role in the Pathogenesis of MELAS Disease. Life (Basel) 2023; 13:1863. [PMID: 37763267 PMCID: PMC10532844 DOI: 10.3390/life13091863] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/16/2023] [Accepted: 08/31/2023] [Indexed: 09/29/2023] Open
Abstract
In mammalian mitochondria, the processing of primary RNA transcripts involves a coordinated series of cleavage and modification events, leading to the formation of processing intermediates and mature mt-RNAs. RNA19 is an unusually stable unprocessed precursor, physiologically polyadenylated, which includes the 16S mt-rRNA, the mt-tRNALeuUUR and the mt-ND1 mRNA. These peculiarities, together with the alteration of its steady-state levels in cellular models with defects in mitochondrial function, make RNA19 a potentially important molecule for the physiological regulation of mitochondrial molecular processes as well as for the pathogenesis of mitochondrial diseases. In this work, we quantitatively and qualitatively examined RNA19 in MELAS trans-mitochondrial cybrids carrying the mtDNA 3243A>G transition and displaying a profound mitochondrial translation defect. Through a combination of isokinetic sucrose gradient and RT-qPCR experiments, we found that RNA19 accumulated and co-sedimented with the mitoribosomal large subunit (mt-LSU) in mutant cells. Intriguingly, exogenous expression of the isolated LARS2 C-terminal domain (Cterm), which was shown to rescue defective translation in MELAS cybrids, decreased the levels of mt-LSU-associated RNA19 by relegating it to the pool of free unbound RNAs. Overall, the data reported here support a regulatory role for RNA19 in mitochondrial physiopathological processes, designating this RNA precursor as a possible molecular target in view of therapeutic strategy development.
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Affiliation(s)
| | | | - Francesco Bruni
- Department of Biosciences, Biotechnologies and Environment, University of Bari ‘Aldo Moro’, 70125 Bari, Italy; (P.L.P.); (F.C.)
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Ramasubramanian A, Ramani P, Kannan B, Arumugam P. High expression of novel biomarker TBRG4 promotes the progression and invasion of oral squamous cell carcinoma. J Oral Pathol Med 2023; 52:738-745. [PMID: 37537882 DOI: 10.1111/jop.13470] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 06/29/2023] [Accepted: 07/19/2023] [Indexed: 08/05/2023]
Abstract
BACKGROUND Transforming growth factor β regulator 4 (TBRG4) is a potential prognostic indicator in various cancers, especially squamous cell carcinomas, and is associated with disease amelioration and poor outcomes. The study aimed to assess the expression pattern of TBRG4 in patients with operable oral squamous cell carcinoma (OSCC) to understand its role in tumour progression using indicators of disease outcome like tumour stage, grade, nodal metastasis, and pattern of invasion. METHODS TBRG4 expression was assessed by analyzing 51 cancer and adjacent non-cancerous tissues of OSCC patients using quantitative real-time PCR, and Western blot. TBRG4 expression was also analysed in The Cancer Genome Atlas Head-Neck Squamous Cell Carcinoma (TCGA-HNSC) dataset using the UALCAN tool (http://ualcan.path.uab.edu/). The relationship between TBRG4 expression and the patient's prognosis was analysed using Kaplan-Meier plotter. RESULTS Both mRNA and protein levels of TBRG4 were significantly increased in OSCC tissues. The TBGR4 expression was significantly associated with advanced stages (III and IV) and the worst pattern of invasion (WPOI-4 and 5). High TBRG4 expression was also significantly associated with reduced overall survival (p = 0.011). In addition, the analysis of TBRG4 gene expression and clinical data from TCGA, identified that TBRG4 was highly expressed in HPV negative OSCC patients and positively correlated with worst overall survival. CONCLUSION The present study suggests that the high expression of TBRG4 might serve as a novel prognostic biomarker for HPV-negative OSCC, which can be validated by future additional investigations in larger cohorts along with functional studies.
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Affiliation(s)
- Abilasha Ramasubramanian
- Department of Oral Pathology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, India
| | - Pratibha Ramani
- Department of Oral Pathology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, India
| | - Balachander Kannan
- Centre for Cellular and Molecular Research, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, India
| | - Paramasivam Arumugam
- Centre for Cellular and Molecular Research, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, India
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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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Sun CL, Van Gilst M, Crowder CM. Hypoxia-induced mitochondrial stress granules. Cell Death Dis 2023; 14:448. [PMID: 37468471 PMCID: PMC10356818 DOI: 10.1038/s41419-023-05988-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 07/10/2023] [Accepted: 07/12/2023] [Indexed: 07/21/2023]
Abstract
Perturbations of mitochondrial proteostasis have been associated with aging, neurodegenerative diseases, and recently with hypoxic injury. While examining hypoxia-induced mitochondrial protein aggregation in C. elegans, we found that sublethal hypoxia, sodium azide, or heat shock-induced abundant ethidium bromide staining mitochondrial granules that preceded evidence of protein aggregation. Genetic manipulations that reduce cellular and organismal hypoxic death block the formation of these mitochondrial stress granules (mitoSG). Knockdown of mitochondrial nucleoid proteins also blocked the formation of mitoSG by a mechanism distinct from the mitochondrial unfolded protein response. Lack of the major mitochondrial matrix protease LONP-1 resulted in the constitutive formation of mitoSG without external stress. Ethidium bromide-staining RNA-containing mitochondrial granules were also observed in rat cardiomyocytes treated with sodium azide, a hypoxia mimetic. Mitochondrial stress granules are an early mitochondrial pathology controlled by LONP and the nucleoid, preceding hypoxia-induced protein aggregation.
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Affiliation(s)
- Chun-Ling Sun
- Department of Anesthesiology and Pain Medicine, University of Washington School of Medicine, Seattle, Washington, 98109, USA
- Mitochondrial and Metabolism Center, University of Washington School of Medicine, Seattle, Washington, 98109, USA
| | - Marc Van Gilst
- Department of Anesthesiology and Pain Medicine, University of Washington School of Medicine, Seattle, Washington, 98109, USA
- Mitochondrial and Metabolism Center, University of Washington School of Medicine, Seattle, Washington, 98109, USA
| | - C Michael Crowder
- Department of Anesthesiology and Pain Medicine, University of Washington School of Medicine, Seattle, Washington, 98109, USA.
- Mitochondrial and Metabolism Center, University of Washington School of Medicine, Seattle, Washington, 98109, USA.
- Department of Genome Science, University of Washington School of Medicine, Seattle, Washington, 98109, USA.
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19
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Liu M, Ji W, Zhao X, Liu X, Hu JF, Cui J. Therapeutic potential of engineering the mitochondrial genome. Biochim Biophys Acta Mol Basis Dis 2023:166804. [PMID: 37429560 DOI: 10.1016/j.bbadis.2023.166804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/29/2023] [Accepted: 07/05/2023] [Indexed: 07/12/2023]
Abstract
Mitochondrial diseases are a group of clinical disorders caused by mutations in the genes encoded by either the nuclear or the mitochondrial genome involved in mitochondrial oxidative phosphorylation. Disorders become evident when mitochondrial dysfunction reaches a cell-specific threshold. Similarly, the severity of disorders is related to the degree of gene mutation. Clinical treatments for mitochondrial diseases mainly rely on symptomatic management. Theoretically, replacing or repairing dysfunctional mitochondria to acquire and preserve normal physiological functions should be effective. Significant advances have been made in gene therapies, including mitochondrial replacement therapy, mitochondrial genome manipulation, nuclease programming, mitochondrial DNA editing, and mitochondrial RNA interference. In this paper, we review the recent progress in these technologies by focusing on advancements that overcome limitations.
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Affiliation(s)
- Mengmeng Liu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin 130061, China
| | - Wei Ji
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin 130061, China
| | - Xin Zhao
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin 130061, China
| | - Xiaoliang Liu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin 130061, China
| | - Ji-Fan Hu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin 130061, China; Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA.
| | - Jiuwei Cui
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin 130061, China.
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20
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Chen PL. SUV3 Helicase and Mitochondrial Homeostasis. Int J Mol Sci 2023; 24:9233. [PMID: 37298184 PMCID: PMC10253155 DOI: 10.3390/ijms24119233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/21/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023] Open
Abstract
SUV3 is a nuclear-encoded helicase that is highly conserved and localizes to the mitochondrial matrix. In yeast, loss of SUV3 function leads to the accumulation of group 1 intron transcripts, ultimately resulting in the loss of mitochondrial DNA, causing a petite phenotype. However, the mechanism leading to the loss of mitochondrial DNA remains unknown. SUV3 is essential for survival in higher eukaryotes, and its knockout in mice results in early embryonic lethality. Heterozygous mice exhibit a range of phenotypes, including premature aging and an increased cancer incidence. Furthermore, cells derived from SUV3 heterozygotes or knockdown cultural cells show a reduction in mtDNA. Transient downregulation of SUV3 leads to the formation of R-loops and the accumulation of double-stranded RNA in mitochondria. This review aims to provide an overview of the current knowledge regarding the SUV3-containing complex and discuss its potential mechanism for tumor suppression activity.
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Affiliation(s)
- Phang-Lang Chen
- Department of Biological Chemistry, University of California, Irvine, CA 92697, USA
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21
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Kienzle L, Bettinazzi S, Choquette T, Brunet M, Khorami HH, Jacques JF, Moreau M, Roucou X, Landry CR, Angers A, Breton S. A small protein coded within the mitochondrial canonical gene nd4 regulates mitochondrial bioenergetics. BMC Biol 2023; 21:111. [PMID: 37198654 DOI: 10.1186/s12915-023-01609-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 05/03/2023] [Indexed: 05/19/2023] Open
Abstract
BACKGROUND Mitochondria have a central role in cellular functions, aging, and in certain diseases. They possess their own genome, a vestige of their bacterial ancestor. Over the course of evolution, most of the genes of the ancestor have been lost or transferred to the nucleus. In humans, the mtDNA is a very small circular molecule with a functional repertoire limited to only 37 genes. Its extremely compact nature with genes arranged one after the other and separated by short non-coding regions suggests that there is little room for evolutionary novelties. This is radically different from bacterial genomes, which are also circular but much larger, and in which we can find genes inside other genes. These sequences, different from the reference coding sequences, are called alternatives open reading frames or altORFs, and they are involved in key biological functions. However, whether altORFs exist in mitochondrial protein-coding genes or elsewhere in the human mitogenome has not been fully addressed. RESULTS We found a downstream alternative ATG initiation codon in the + 3 reading frame of the human mitochondrial nd4 gene. This newly characterized altORF encodes a 99-amino-acid-long polypeptide, MTALTND4, which is conserved in primates. Our custom antibody, but not the pre-immune serum, was able to immunoprecipitate MTALTND4 from HeLa cell lysates, confirming the existence of an endogenous MTALTND4 peptide. The protein is localized in mitochondria and cytoplasm and is also found in the plasma, and it impacts cell and mitochondrial physiology. CONCLUSIONS Many human mitochondrial translated ORFs might have so far gone unnoticed. By ignoring mtaltORFs, we have underestimated the coding potential of the mitogenome. Alternative mitochondrial peptides such as MTALTND4 may offer a new framework for the investigation of mitochondrial functions and diseases.
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Affiliation(s)
- Laura Kienzle
- Département de sciences biologiques, Université de Montréal, Montréal, Canada
| | - Stefano Bettinazzi
- Département de sciences biologiques, Université de Montréal, Montréal, Canada
| | - Thierry Choquette
- Département de sciences biologiques, Université de Montréal, Montréal, Canada
| | - Marie Brunet
- Service de génétique médicale, Département de pédiatrie, Université de Sherbrooke, Sherbrooke, Canada
- Centre de recherche du Centre hospitalier universitaire de Sherbrooke (CRCHUS), Sherbrooke, Canada
| | | | - Jean-François Jacques
- Département de biochimie et génomique fonctionnelle, Université de Sherbrooke, Sherbrooke, Canada
| | - Mathilde Moreau
- Département de biochimie et génomique fonctionnelle, Université de Sherbrooke, Sherbrooke, Canada
| | - Xavier Roucou
- Centre de recherche du Centre hospitalier universitaire de Sherbrooke (CRCHUS), Sherbrooke, Canada
- Département de biochimie et génomique fonctionnelle, Université de Sherbrooke, Sherbrooke, Canada
| | - Christian R Landry
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, Canada
- Institut de biologie intégrative et des systèmes, Université Laval, Québec, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec, Canada
- Centre de recherche sur les données massives, Université Laval, Québec, Canada
- Département de biologie, Faculté des sciences et de génie, Université Laval, Québec, Canada
| | - Annie Angers
- Département de sciences biologiques, Université de Montréal, Montréal, Canada
| | - Sophie Breton
- Département de sciences biologiques, Université de Montréal, Montréal, Canada.
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Wang BZ, Zhou YC, Lin YW, Chen XC, Yu ZY, Xu YH, Tan JH, Huang ZS, Chen SB. Fluorescent Quinolinium Derivative as Novel Mitochondria Probe and Function Modulator by Targeting Mitochondrial RNA. Molecules 2023; 28:molecules28062690. [PMID: 36985661 PMCID: PMC10053327 DOI: 10.3390/molecules28062690] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/10/2023] [Accepted: 03/15/2023] [Indexed: 03/19/2023] Open
Abstract
Mitochondria have a crucial role in regulating energy metabolism and their dysfunction has been linked to tumorigenesis. Cancer diagnosis and intervention have a great interest in the development of new agents that target biomolecules within mitochondria. However, monitoring and modulating mitochondria RNA (mtRNA), an essential component in mitochondria, in cells is challenging due to limited functional research and the absence of targeting agents. In this study, we designed and synthesized a fluorescent quinolinium derivative, QUCO-1, which actively lit up with mtRNA in both normal and cancer cells in vitro. Additionally, we evaluated the function of QUCO-1 as an mtRNA ligand and found that it effectively induced severe mitochondrial dysfunction and OXPHOS inhibition in RKO colorectal cancer cells. Treatment with QUCO-1 resulted in apoptosis, cell cycle blockage at the G2/M phase, and the effective inhibition of cell proliferation. Our findings suggest that QUCO-1 has great potential as a promising probe and therapeutic agent for mtRNA, with the potential for treating colorectal cancer.
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23
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Delivery Systems for Mitochondrial Gene Therapy: A Review. Pharmaceutics 2023; 15:pharmaceutics15020572. [PMID: 36839894 PMCID: PMC9964608 DOI: 10.3390/pharmaceutics15020572] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/26/2023] [Accepted: 02/05/2023] [Indexed: 02/11/2023] Open
Abstract
Mitochondria are membrane-bound cellular organelles of high relevance responsible for the chemical energy production used in most of the biochemical reactions of cells. Mitochondria have their own genome, the mitochondrial DNA (mtDNA). Inherited solely from the mother, this genome is quite susceptible to mutations, mainly due to the absence of an effective repair system. Mutations in mtDNA are associated with endocrine, metabolic, neurodegenerative diseases, and even cancer. Currently, therapeutic approaches are based on the administration of a set of drugs to alleviate the symptoms of patients suffering from mitochondrial pathologies. Mitochondrial gene therapy emerges as a promising strategy as it deeply focuses on the cause of mitochondrial disorder. The development of suitable mtDNA-based delivery systems to target and transfect mammalian mitochondria represents an exciting field of research, leading to progress in the challenging task of restoring mitochondria's normal function. This review gathers relevant knowledge on the composition, targeting performance, or release profile of such nanosystems, offering researchers valuable conceptual approaches to follow in their quest for the most suitable vectors to turn mitochondrial gene therapy clinically feasible. Future studies should consider the optimization of mitochondrial genes' encapsulation, targeting ability, and transfection to mitochondria. Expectedly, this effort will bring bright results, contributing to important hallmarks in mitochondrial gene therapy.
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Rehman A, Kumari R, Kamthan A, Tiwari R, Srivastava RK, van der Westhuizen FH, Mishra PK. Cell-free circulating mitochondrial DNA: An emerging biomarker for airborne particulate matter associated with cardiovascular diseases. Free Radic Biol Med 2023; 195:103-120. [PMID: 36584454 DOI: 10.1016/j.freeradbiomed.2022.12.083] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/16/2022] [Accepted: 12/20/2022] [Indexed: 12/29/2022]
Abstract
The association of airborne particulate matter exposure with the deteriorating function of the cardiovascular system is fundamentally driven by the impairment of mitochondrial-nuclear crosstalk orchestrated by aberrant redox signaling. The loss of delicate balance in retrograde communication from mitochondria to the nucleus often culminates in the methylation of the newly synthesized strand of mitochondrial DNA (mtDNA) through DNA methyl transferases. In highly metabolic active tissues such as the heart, mtDNA's methylation state alteration impacts mitochondrial bioenergetics. It affects transcriptional regulatory processes involved in biogenesis, fission, and fusion, often accompanied by the integrated stress response. Previous studies have demonstrated a paradoxical role of mtDNA methylation in cardiovascular pathologies linked to air pollution. A pronounced alteration in mtDNA methylation contributes to systemic inflammation, an etiological determinant for several co-morbidities, including vascular endothelial dysfunction and myocardial injury. In the current article, we evaluate the state of evidence and examine the considerable promise of using cell-free circulating methylated mtDNA as a predictive biomarker to reduce the more significant burden of ambient air pollution on cardiovascular diseases.
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Affiliation(s)
- Afreen Rehman
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India.
| | - Roshani Kumari
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India.
| | - Arunika Kamthan
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India.
| | - Rajnarayan Tiwari
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India.
| | | | | | - Pradyumna Kumar Mishra
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India.
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25
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Kuwasako K, Suzuki S, Nameki N, Takizawa M, Takahashi M, Tsuda K, Nagata T, Watanabe S, Tanaka A, Kobayashi N, Kigawa T, Güntert P, Shirouzu M, Yokoyama S, Muto Y. 1H, 13C, and 15N resonance assignments and solution structures of the KH domain of human ribosome binding factor A, mtRbfA, involved in mitochondrial ribosome biogenesis. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:297-303. [PMID: 35666428 DOI: 10.1007/s12104-022-10094-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
Ribosome biogenesis is a complicated, multistage process coordinated by ribosome assembly factors. Ribosome binding factor A (RbfA) is a bacterial one, which possesses a single structural type-II KH domain. By this domain, RbfA binds to a 16S rRNA precursor in small ribosomal subunits to promote its 5'-end processing. The human RbfA homolog, mtRbfA, binds to 12S rRNAs in the mitoribosomal small subunits and promotes its critical maturation process, the dimethylation of two highly conserved consecutive adenines, which differs from that of RbfA. However, the structural basis of the mtRbfA-mediated maturation process is poorly understood. Herein, we report the 1H, 15N, and 13C resonance assignments of the KH domain of mtRbfA and its solution structure. The mtRbfA domain adopts essentially the same α1-β1-β2-α2(kinked)-β3 topology as the type-II KH domain. Comparison with the RbfA counterpart showed structural differences in specific regions that function as a putative RNA-binding site. Particularly, the α2 helix of mtRbfA forms a single helix with a moderate kink at the Ser-Ala-Ala sequence, whereas the corresponding α2 helix of RbfA is interrupted by a distinct kink at the Ala-x-Gly sequence, characteristic of bacterial RbfA proteins, to adopt an α2-kink-α3 conformation. Additionally, the region linking α1 and β1 differs considerably in the sequence and structure between RbfA and mtRbfA. These findings suggest some variations of the RNA-binding mode between them and provide a structural basis for mtRbfA function in mitoribosome biogenesis.
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Affiliation(s)
- Kanako Kuwasako
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Sakura Suzuki
- RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - Nobukazu Nameki
- Division of Molecular Science, Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu-shi, Gunma, 376-8515, Japan
| | - Masayuki Takizawa
- Faculty of Pharmacy and Research Institute of Pharmaceutical Sciences, Musashino University, Tokyo, 202-8585, Japan
| | - Mari Takahashi
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Kengo Tsuda
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Takashi Nagata
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- Institute of Advanced Energy and Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Satoru Watanabe
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN Yokohama NMR Facility, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Akiko Tanaka
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Naohiro Kobayashi
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN Yokohama NMR Facility, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Takanori Kigawa
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Peter Güntert
- Tatsuo Miyazawa Memorial Program, RIKEN Genomic Sciences Center, Yokohama, 230-0045, Japan
- Institute of Biophysical Chemistry, Goethe-University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
- Department of Chemistry, Tokyo Metropolitan University, 1-1 Minami-Ohsawa, Hachioji, Tokyo, 192-0397, Japan
| | - Mikako Shirouzu
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Shigeyuki Yokoyama
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.
- RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan.
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.
- RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.
- RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan.
| | - Yutaka Muto
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.
- RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan.
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.
- Faculty of Pharmacy and Research Institute of Pharmaceutical Sciences, Musashino University, Tokyo, 202-8585, Japan.
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26
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Tan BG, Mutti CD, Shi Y, Xie X, Zhu X, Silva-Pinheiro P, Menger KE, Díaz-Maldonado H, Wei W, Nicholls TJ, Chinnery PF, Minczuk M, Falkenberg M, Gustafsson CM. The human mitochondrial genome contains a second light strand promoter. Mol Cell 2022; 82:3646-3660.e9. [PMID: 36044900 DOI: 10.1016/j.molcel.2022.08.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/21/2022] [Accepted: 08/07/2022] [Indexed: 11/30/2022]
Abstract
The human mitochondrial genome must be replicated and expressed in a timely manner to maintain energy metabolism and supply cells with adequate levels of adenosine triphosphate. Central to this process is the idea that replication primers and gene products both arise via transcription from a single light strand promoter (LSP) such that primer formation can influence gene expression, with no consensus as to how this is regulated. Here, we report the discovery of a second light strand promoter (LSP2) in humans, with features characteristic of a bona fide mitochondrial promoter. We propose that the position of LSP2 on the mitochondrial genome allows replication and gene expression to be orchestrated from two distinct sites, which expands our long-held understanding of mitochondrial gene expression in humans.
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Affiliation(s)
- Benedict G Tan
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg 405 30, Sweden
| | - Christian D Mutti
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Yonghong Shi
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg 405 30, Sweden
| | - Xie Xie
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg 405 30, Sweden
| | - Xuefeng Zhu
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg 405 30, Sweden
| | - Pedro Silva-Pinheiro
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Katja E Menger
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Héctor Díaz-Maldonado
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg 405 30, Sweden
| | - Wei Wei
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK; Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Thomas J Nicholls
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Patrick F Chinnery
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK; Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Michal Minczuk
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK.
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg 405 30, Sweden.
| | - Claes M Gustafsson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg 405 30, Sweden.
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27
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Falchi FA, Pizzoccheri R, Briani F. Activity and Function in Human Cells of the Evolutionary Conserved Exonuclease Polynucleotide Phosphorylase. Int J Mol Sci 2022; 23:ijms23031652. [PMID: 35163574 PMCID: PMC8836086 DOI: 10.3390/ijms23031652] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 01/28/2022] [Accepted: 01/28/2022] [Indexed: 02/04/2023] Open
Abstract
Polynucleotide phosphorylase (PNPase) is a phosphorolytic RNA exonuclease highly conserved throughout evolution. Human PNPase (hPNPase) is located in mitochondria and is essential for mitochondrial function and homeostasis. Not surprisingly, mutations in the PNPT1 gene, encoding hPNPase, cause serious diseases. hPNPase has been implicated in a plethora of processes taking place in different cell compartments and involving other proteins, some of which physically interact with hPNPase. This paper reviews hPNPase RNA binding and catalytic activity in relation with the protein structure and in comparison, with the activity of bacterial PNPases. The functions ascribed to hPNPase in different cell compartments are discussed, highlighting the gaps that still need to be filled to understand the physiological role of this ancient protein in human cells.
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