1
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Kundnani DL, Yang T, Gombolay AL, Mukherjee K, Newnam G, Meers C, Verma I, Chhatlani K, Mehta ZH, Mouawad C, Storici F. Distinct features of ribonucleotides within genomic DNA in Aicardi-Goutières syndrome ortholog mutants of Saccharomyces cerevisiae. iScience 2024; 27:110012. [PMID: 38868188 PMCID: PMC11166700 DOI: 10.1016/j.isci.2024.110012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 03/15/2024] [Accepted: 05/14/2024] [Indexed: 06/14/2024] Open
Abstract
Ribonucleoside monophosphates (rNMPs) are abundantly found within genomic DNA of cells. The embedded rNMPs alter DNA properties and impact genome stability. Mutations in ribonuclease (RNase) H2, a key enzyme for rNMP removal, are associated with the Aicardi-Goutières syndrome (AGS), a severe neurological disorder. Here, we engineered orthologs of the human RNASEH2A-G37S and RNASEH2C-R69W AGS mutations in yeast Saccharomyces cerevisiae: rnh201-G42S and rnh203-K46W. Using the ribose-seq technique and the Ribose-Map bioinformatics toolkit, we unveiled rNMP abundance, composition, hotspots, and sequence context in these AGS-ortholog mutants. We found a high rNMP presence in the nuclear genome of rnh201-G42S-mutant cells, and an elevated rCMP content in both mutants, reflecting preferential cleavage of RNase H2 at rGMP. We discovered unique rNMP patterns in each mutant, showing differential activity of the AGS mutants on the leading or lagging replication strands. This study guides future research on rNMP characteristics in human genomes with AGS mutations.
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Affiliation(s)
- Deepali L. Kundnani
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Taehwan Yang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Alli L. Gombolay
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Bacterial Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Kuntal Mukherjee
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Gary Newnam
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Chance Meers
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Ishika Verma
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Kirti Chhatlani
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Zeel H. Mehta
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Celine Mouawad
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Francesca Storici
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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2
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Xu P, Yang T, Kundnani DL, Sun M, Marsili S, Gombolay A, Jeon Y, Newnam G, Balachander S, Bazzani V, Baccarani U, Park V, Tao S, Lori A, Schinazi R, Kim B, Pursell Z, Tell G, Vascotto C, Storici F. Light-strand bias and enriched zones of embedded ribonucleotides are associated with DNA replication and transcription in the human-mitochondrial genome. Nucleic Acids Res 2024; 52:1207-1225. [PMID: 38117983 PMCID: PMC10853789 DOI: 10.1093/nar/gkad1204] [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: 04/28/2023] [Revised: 11/30/2023] [Accepted: 12/05/2023] [Indexed: 12/22/2023] Open
Abstract
Abundant ribonucleoside-triphosphate (rNTP) incorporation into DNA by DNA polymerases in the form of ribonucleoside monophosphates (rNMPs) is a widespread phenomenon in nature, resulting in DNA-structural change and genome instability. The rNMP distribution, characteristics, hotspots and association with DNA metabolic processes in human mitochondrial DNA (hmtDNA) remain mostly unknown. Here, we utilize the ribose-seq technique to capture embedded rNMPs in hmtDNA of six different cell types. In most cell types, the rNMPs are preferentially embedded on the light strand of hmtDNA with a strong bias towards rCMPs; while in the liver-tissue cells, the rNMPs are predominately found on the heavy strand. We uncover common rNMP hotspots and conserved rNMP-enriched zones across the entire hmtDNA, including in the control region, which links the rNMP presence to the frequent hmtDNA replication-failure events. We show a strong correlation between coding-sequence size and rNMP-embedment frequency per nucleotide on the non-template, light strand in all cell types, supporting the presence of transient RNA-DNA hybrids preceding light-strand replication. Moreover, we detect rNMP-embedment patterns that are only partly conserved across the different cell types and are distinct from those found in yeast mtDNA. The study opens new research directions to understand the biology of hmtDNA and genomic rNMPs.
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Affiliation(s)
- Penghao Xu
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332, GA, USA
| | - Taehwan Yang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332, GA, USA
| | - Deepali L Kundnani
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332, GA, USA
| | - Mo Sun
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332, GA, USA
| | - Stefania Marsili
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332, GA, USA
| | - Alli L Gombolay
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332, GA, USA
| | - Youngkyu Jeon
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332, GA, USA
| | - Gary Newnam
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332, GA, USA
| | - Sathya Balachander
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332, GA, USA
| | - Veronica Bazzani
- Department of Medicine, University of Udine, Udine 33100, Italy
- IMol Polish Academy of Sciences, Warsaw 02-247, Poland
| | - Umberto Baccarani
- Department of Medicine, University of Udine, Udine 33100, Italy
- General Surgery Clinic and Liver Transplant Center, University-Hospital of Udine, Udine 33100, Italy
| | - Vivian S Park
- Department of Biochemistry and Molecular Biology, Tulane Cancer Center, Tulane University of Medicine, New Orleans, LA 70118, USA
| | - Sijia Tao
- Center for ViroScience and Cure, Department of Pediatrics, Laboratory of Biochemical Pharmacology, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta 30322, GA, USA
| | - Adriana Lori
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta 30329, GA, USA
- Department of Population Science, American Cancer Society, Kennesaw 30144, GA, USA
| | - Raymond F Schinazi
- Center for ViroScience and Cure, Department of Pediatrics, Laboratory of Biochemical Pharmacology, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta 30322, GA, USA
| | - Baek Kim
- Center for ViroScience and Cure, Department of Pediatrics, Laboratory of Biochemical Pharmacology, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta 30322, GA, USA
| | - Zachary F Pursell
- Department of Biochemistry and Molecular Biology, Tulane Cancer Center, Tulane University of Medicine, New Orleans, LA 70118, USA
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, Udine 33100, Italy
| | - Carlo Vascotto
- Department of Medicine, University of Udine, Udine 33100, Italy
- IMol Polish Academy of Sciences, Warsaw 02-247, Poland
| | - Francesca Storici
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332, GA, USA
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3
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Kundnani DL, Yang T, Gombolay AL, Mukherjee K, Newnam G, Meers C, Mehta ZH, Mouawad C, Storici F. Distinct features of ribonucleotides within genomic DNA in Aicardi-Goutières syndrome (AGS)-ortholog mutants of Saccharomyces cerevisiae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.02.560505. [PMID: 37873120 PMCID: PMC10592897 DOI: 10.1101/2023.10.02.560505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Ribonucleoside monophosphates (rNMPs) are abundantly found within genomic DNA of cells. The embedded rNMPs alter DNA properties and impact genome stability. Mutations in ribonuclease (RNase) H2, a key enzyme for rNMP removal, are associated with the Aicardi-Goutières syndrome (AGS), a severe neurological disorder. Here, we engineered two AGS-ortholog mutations in Saccharomyces cerevisiae: rnh201-G42S and rnh203-K46W. Using the ribose-seq technique and the Ribose-Map bioinformatics toolkit, we unveiled rNMP abundance, composition, hotspots, and sequence context in these yeast AGS-ortholog mutants. We found higher rNMP incorporation in the nuclear genome of rnh201-G42S than in wild-type and rnh203-K46W-mutant cells, and an elevated rCMP content in both mutants. Moreover, we uncovered unique rNMP patterns in each mutant, highlighting a differential activity of the AGS mutants towards rNMPs embedded on the leading or on the lagging strand of DNA replication. This study guides future research on rNMP characteristics in human genomic samples carrying AGS mutations.
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Affiliation(s)
- Deepali L Kundnani
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Taehwan Yang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Alli L Gombolay
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Bacterial Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Kuntal Mukherjee
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Gary Newnam
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Chance Meers
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Zeel H Mehta
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Celine Mouawad
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Francesca Storici
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
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4
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Xu D, Luo L, Huang Y, Lu M, Tang L, Diao Y, Kapranov P. Dynamic Patterns of Mammalian Mitochondrial DNA Replication Uncovered Using SSiNGLe-5'ES. Int J Mol Sci 2023; 24:ijms24119711. [PMID: 37298662 DOI: 10.3390/ijms24119711] [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: 04/17/2023] [Revised: 05/30/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023] Open
Abstract
The proper replication of mitochondrial DNA is key to the maintenance of this crucial organelle. Multiple studies aimed at understanding the mechanisms of replication of the mitochondrial genome have been conducted in the past several decades; however, while highly informative, they were conducted using relatively low-sensitivity techniques. Here, we established a high-throughput approach based on next-generation sequencing to identify replication start sites with nucleotide-level resolution and applied it to the genome of mitochondria from different human and mouse cell types. We found complex and highly reproducible patterns of mitochondrial initiation sites, both previously annotated and newly discovered in this work, that showed differences among different cell types and species. These results suggest that the patterns of the replication initiation sites are dynamic and might reflect, in some yet unknown ways, the complexities of mitochondrial and cellular physiology. Overall, this work suggests that much remains unknown about the details of mitochondrial DNA replication in different biological states, and the method established here opens up a new avenue in the study of the replication of mitochondrial and potentially other genomes.
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Affiliation(s)
- Dongyang Xu
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China
| | - Lingcong Luo
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China
| | - Yu Huang
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China
| | - Meng Lu
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China
| | - Lu Tang
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China
| | - Yong Diao
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China
| | - Philipp Kapranov
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
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5
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Determination of the Ribonucleotide Content of mtDNA Using Alkaline Gels. Methods Mol Biol 2023; 2615:293-314. [PMID: 36807800 DOI: 10.1007/978-1-0716-2922-2_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Impaired mitochondrial DNA (mtDNA) maintenance, due to, e.g., defects in the replication machinery or an insufficient dNTP supply, underlies a number of mitochondrial disorders. The normal process of mtDNA replication leads to the incorporation of multiple single ribonucleotides (rNMPs) per mtDNA molecule. Given that embedded rNMPs alter the stability and properties of the DNA, they may have consequences for mtDNA maintenance and thereby for mitochondrial disease. They also serve as a readout of the intramitochondrial NTP/dNTP ratios. In this chapter, we describe a method for the determination of mtDNA rNMP content using alkaline gel electrophoresis and Southern blotting. This procedure is suited for the analysis of mtDNA in total genomic DNA preparations as well as in purified form. Moreover, it can be performed using equipment found in most biomedical laboratories, allows the simultaneous analysis of 10-20 samples depending on the gel system employed, and can be modified for the analysis of other mtDNA modifications.
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6
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Mitochondrial DNA Repair in Neurodegenerative Diseases and Ageing. Int J Mol Sci 2022; 23:ijms231911391. [PMID: 36232693 PMCID: PMC9569545 DOI: 10.3390/ijms231911391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 11/17/2022] Open
Abstract
Mitochondria are the only organelles, along with the nucleus, that have their own DNA. Mitochondrial DNA (mtDNA) is a double-stranded circular molecule of ~16.5 kbp that can exist in multiple copies within the organelle. Both strands are translated and encode for 22 tRNAs, 2 rRNAs, and 13 proteins. mtDNA molecules are anchored to the inner mitochondrial membrane and, in association with proteins, form a structure called nucleoid, which exerts a structural and protective function. Indeed, mitochondria have evolved mechanisms necessary to protect their DNA from chemical and physical lesions such as DNA repair pathways similar to those present in the nucleus. However, there are mitochondria-specific mechanisms such as rapid mtDNA turnover, fission, fusion, and mitophagy. Nevertheless, mtDNA mutations may be abundant in somatic tissue due mainly to the proximity of the mtDNA to the oxidative phosphorylation (OXPHOS) system and, consequently, to the reactive oxygen species (ROS) formed during ATP production. In this review, we summarise the most common types of mtDNA lesions and mitochondria repair mechanisms. The second part of the review focuses on the physiological role of mtDNA damage in ageing and the effect of mtDNA mutations in neurodegenerative disorders such as Alzheimer’s and Parkinson’s disease. Considering the central role of mitochondria in maintaining cellular homeostasis, the analysis of mitochondrial function is a central point for developing personalised medicine.
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7
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Qiu Y, Huang Y, Chen M, Yang Y, Li X, Zhang W. Mitochondrial DNA in NLRP3 inflammasome activation. Int Immunopharmacol 2022; 108:108719. [DOI: 10.1016/j.intimp.2022.108719] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 02/26/2022] [Accepted: 03/17/2022] [Indexed: 12/20/2022]
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8
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Fan Z, Yang JY, Guo Y, Liu YX, Zhong XY. Altered levels of circulating mitochondrial DNA in elderly people with sarcopenia: Association with mitochondrial impairment. Exp Gerontol 2022; 163:111802. [DOI: 10.1016/j.exger.2022.111802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 03/25/2022] [Accepted: 04/04/2022] [Indexed: 01/07/2023]
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9
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Shintaku J, Pernice WM, Eyaid W, Gc JB, Brown ZP, Juanola-Falgarona M, Torres-Torronteras J, Sommerville EW, Hellebrekers DM, Blakely EL, Donaldson A, van de Laar IM, Leu CS, Marti R, Frank J, Tanji K, Koolen DA, Rodenburg RJ, Chinnery PF, Smeets HJM, Gorman GS, Bonnen PE, Taylor RW, Hirano M. RRM1 variants cause a mitochondrial DNA maintenance disorder via impaired de novo nucleotide synthesis. J Clin Invest 2022; 132:145660. [PMID: 35617047 PMCID: PMC9246377 DOI: 10.1172/jci145660] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 05/19/2022] [Indexed: 11/17/2022] Open
Abstract
Mitochondrial DNA (mtDNA) depletion/deletions syndromes (MDDS) encompass a clinically and etiologically heterogenous group of mitochondrial disorders due to impaired mtDNA maintenance. Among the most frequent causes of MDDS are defects in nucleoside/nucleotide metabolism, which is critical for synthesis and homeostasis of the deoxynucleoside triphosphate (dNTP) substrates of mtDNA replication. A central enzyme for generating dNTPs is ribonucleotide reductase, a critical mediator of de novo nucleotide synthesis composed of catalytic RRM1 subunits in complex with RRM2 or p53R2. Here, we report five probands from four families who presented with ptosis and ophthalmoplegia, plus other manifestations and multiple mtDNA deletions in muscle. We identified three RRM1 loss-of-function variants, including a dominant catalytic site variant (NP_001024.1: p.N427K) and two homozygous recessive variants at p.R381, which has evolutionarily conserved interactions with the specificity site. Atomistic molecular dynamics simulations indicate mechanisms by which RRM1 variants affect protein structure. Cultured primary skin fibroblasts of probands manifested mtDNA depletion under cycling conditions, indicating impaired de novo nucleotide synthesis. Fibroblasts also exhibited aberrant nucleoside diphosphate and dNTP pools and mtDNA ribonucleotide incorporation. Our data reveal primary RRM1 deficiency and, by extension, impaired de novo nucleotide synthesis are causes of MDDS.
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Affiliation(s)
- Jonathan Shintaku
- Department of Neurology, Columbia University Irving Medical Center, New York, United States of America
| | - Wolfgang M Pernice
- Department of Neurology, Columbia University Irving Medical Center, New York, United States of America
| | - Wafaa Eyaid
- Department of Pediatrics, King Saud bin Abdulaziz University for Health Science, Riyadh, Saudi Arabia
| | - Jeevan B Gc
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, United States of America
| | - Zuben P Brown
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, United States of America
| | - Marti Juanola-Falgarona
- Department of Neurology, Columbia University Irving Medical Center, New York, United States of America
| | | | - Ewen W Sommerville
- Wellcome Trust Centre for Mitochondrial Research, Newcastle University, Newcastle, United Kingdom
| | - Debby Mei Hellebrekers
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | - Emma L Blakely
- Wellcome Trust Centre for Mitochondrial Research, Newcastle University, Newcastle, United Kingdom
| | - Alan Donaldson
- Clinical Genetics Department, University of Bristol, Bristol, United Kingdom
| | - Ingrid Mbh van de Laar
- Department of Clinical Genetics, Erasmus Medical Center Rotterdam, Rotterdam, Netherlands
| | - Cheng-Shiun Leu
- Biostatistics, Columbia University, New York, United States of America
| | - Ramon Marti
- Laboratori de patologia neuromuscular i mitocondrial, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Joachim Frank
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, United States of America
| | - Kurenai Tanji
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, United States of America
| | - David A Koolen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Richard J Rodenburg
- Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Patrick F Chinnery
- Cambridge Biomedical Campus, University of Cambridge, Cambridge, United Kingdom
| | - H J M Smeets
- University of Maastricht, Maastricht, Netherlands
| | - Gráinne S Gorman
- Wellcome Trust Centre for Mitochondrial Research, Newcastle University, Newcastle, United Kingdom
| | - Penelope E Bonnen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States of America
| | | | - Michio Hirano
- Department of Neurology, Columbia University Irving Medical Center, New York, United States of America
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10
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Abstract
Significance: The small, multicopy mitochondrial genome (mitochondrial DNA [mtDNA]) is essential for efficient energy production, as alterations in its coding information or a decrease in its copy number disrupt mitochondrial ATP synthesis. However, the mitochondrial replication machinery encounters numerous challenges that may limit its ability to duplicate this important genome and that jeopardize mtDNA stability, including various lesions in the DNA template, topological stress, and an insufficient nucleotide supply. Recent Advances: An ever-growing array of DNA repair or maintenance factors are being reported to localize to the mitochondria. We review current knowledge regarding the mitochondrial factors that may contribute to the tolerance or repair of various types of changes in the mitochondrial genome, such as base damage, incorporated ribonucleotides, and strand breaks. We also discuss the newly discovered link between mtDNA instability and activation of the innate immune response. Critical Issues: By which mechanisms do mitochondria respond to challenges that threaten mtDNA maintenance? What types of mtDNA damage are repaired, and when are the affected molecules degraded instead? And, finally, which forms of mtDNA instability trigger an immune response, and how? Future Directions: Further work is required to understand the contribution of the DNA repair and damage-tolerance factors present in the mitochondrial compartment, as well as the balance between mtDNA repair and degradation. Finally, efforts to understand the events underlying mtDNA release into the cytosol are warranted. Pursuing these and many related avenues can improve our understanding of what goes wrong in mitochondrial disease. Antioxid. Redox Signal. 36, 885-905.
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Affiliation(s)
- Gustavo Carvalho
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Bruno Marçal Repolês
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Isabela Mendes
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Paulina H Wanrooij
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
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11
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Wu Q, Tsai HI, Zhu H, Wang D. The Entanglement between Mitochondrial DNA and Tumor Metastasis. Cancers (Basel) 2022; 14:cancers14081862. [PMID: 35454769 PMCID: PMC9028275 DOI: 10.3390/cancers14081862] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Mitochondrial dysfunction is one of the main features of cancer cells. As genetic material in mitochondria, mitochondrial DNA (mtDNA) variations and dysregulation of mitochondria-encoded genes have been shown to correlate with survival outcomes in cancer patients. Cancer metastasis is often a major cause of treatment failure, which is a multi-step cascade process. With the development of gene sequencing and in vivo modeling technology, the role of mtDNA in cancer metastasis has been continuously explored. Our review systematically provides a summary of the multiple roles of mtDNA in cancer metastasis and presents the broad prospects for mtDNA in cancer prediction and therapy. Abstract Mitochondrial DNA, the genetic material in mitochondria, encodes essential oxidative phosphorylation proteins and plays an important role in mitochondrial respiration and energy transfer. With the development of genome sequencing and the emergence of novel in vivo modeling techniques, the role of mtDNA in cancer biology is gaining more attention. Abnormalities of mtDNA result in not only mitochondrial dysfunction of the the cancer cells and malignant behaviors, but regulation of the tumor microenvironment, which becomes more aggressive. Here, we review the recent progress in the regulation of cancer metastasis using mtDNA and the underlying mechanisms, which may identify opportunities for finding novel cancer prediction and therapeutic targets.
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Affiliation(s)
- Qiwei Wu
- Department of Medical Imaging, The Affiliated Hospital of Jiangsu University, Zhenjiang 212001, China;
| | - Hsiang-i Tsai
- Laboratory of Radiology, The Affiliated Hospital of Jiangsu University, Zhenjiang 212001, China;
| | - Haitao Zhu
- Department of Medical Imaging, The Affiliated Hospital of Jiangsu University, Zhenjiang 212001, China;
- Laboratory of Radiology, The Affiliated Hospital of Jiangsu University, Zhenjiang 212001, China;
- Correspondence: (H.Z.); (D.W.); Tel.: +86-138-6139-0259 (D.W.)
| | - Dongqing Wang
- Department of Medical Imaging, The Affiliated Hospital of Jiangsu University, Zhenjiang 212001, China;
- Correspondence: (H.Z.); (D.W.); Tel.: +86-138-6139-0259 (D.W.)
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12
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Williams JS, Kunkel TA. Ribonucleotide Incorporation by Eukaryotic B-family Replicases and Its Implications for Genome Stability. Annu Rev Biochem 2022; 91:133-155. [PMID: 35287470 DOI: 10.1146/annurev-biochem-032620-110354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Our current view of how DNA-based genomes are efficiently and accurately replicated continues to evolve as new details emerge on the presence of ribonucleotides in DNA. Ribonucleotides are incorporated during eukaryotic DNA replication at rates that make them the most common noncanonical nucleotide placed into the nuclear genome, they are efficiently repaired, and their removal impacts genome integrity. This review focuses on three aspects of this subject: the incorporation of ribonucleotides into the eukaryotic nuclear genome during replication by B-family DNA replicases, how these ribonucleotides are removed, and the consequences of their presence or removal for genome stability and disease. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Jessica S Williams
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA;
| | - Thomas A Kunkel
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA;
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13
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Zhang H, Li Y, Li Z, Lam CWK, Zhu P, Wang C, Zhou H, Zhang W. MTBSTFA derivatization-LC-MS/MS approach for the quantitative analysis of endogenous nucleotides in human colorectal carcinoma cells. J Pharm Anal 2022; 12:77-86. [PMID: 35573880 PMCID: PMC9073140 DOI: 10.1016/j.jpha.2021.01.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 10/28/2020] [Accepted: 01/14/2021] [Indexed: 11/28/2022] Open
Abstract
Endogenous ribonucleotides (RNs) and deoxyribonucleotides (dRNs) are important metabolites related to the pathogenesis of many diseases. In light of their physiological and pathological significances, a novel and sensitive pre-column derivatization method with N-(t-butyldimethylsilyl)-N-methyltrifluoroacetamide (MTBSTFA) was developed to determine RNs and dRNs in human cells using high-performance liquid chromatography tandem mass spectrometry (HPLC-MS/MS). A one-step extraction of cells with 85% methanol followed by a simple derivatization reaction within 5 min at room temperature contributed to shortened analysis time. The derivatives of 22 nucleoside mono-, di- and triphosphates were retained on the typical C18 column and eluted by ammonium acetate and acetonitrile in 9 min. Under these optimal conditions, good linearity was achieved in the tested calibration ranges. The lower limit of quantitation (LLOQ) was determined to be 0.1-0.4 μM for the tested RNs and 0.001-0.1 μM for dRNs. In addition, the precision (CV) was <15% and the RSD of stability was lower than 10.4%. Furthermore, this method was applied to quantify the endogenous nucleotides in human colorectal carcinoma cell lines HCT 116 exposed to 10-hydroxycamptothecin. In conclusion, our method has proven to be simple, rapid, sensitive, and reliable. It may be used for specific expanded studies on intracellular pharmacology in vitro.
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Affiliation(s)
| | | | - Zheng Li
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, China
| | - Christopher Wai-Kei Lam
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, China
| | - Peng Zhu
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, China
| | - Caiyun Wang
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, China
| | - Hua Zhou
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, China
| | - Wei Zhang
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, China
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14
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Singh M, Posse V, Peter B, Falkenberg M, Gustafsson C. Ribonucleotides embedded in template DNA impair mitochondrial RNA polymerase progression. Nucleic Acids Res 2022; 50:989-999. [PMID: 35018464 PMCID: PMC8789056 DOI: 10.1093/nar/gkab1251] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 11/30/2021] [Accepted: 12/07/2021] [Indexed: 11/12/2022] Open
Abstract
Human mitochondria lack ribonucleotide excision repair pathways, causing misincorporated ribonucleotides (rNMPs) to remain embedded in the mitochondrial genome. Previous studies have demonstrated that human mitochondrial DNA polymerase γ can bypass a single rNMP, but that longer stretches of rNMPs present an obstacle to mitochondrial DNA replication. Whether embedded rNMPs also affect mitochondrial transcription has not been addressed. Here we demonstrate that mitochondrial RNA polymerase elongation activity is affected by a single, embedded rNMP in the template strand. The effect is aggravated at stretches with two or more consecutive rNMPs in a row and cannot be overcome by addition of the mitochondrial transcription elongation factor TEFM. Our findings lead us to suggest that impaired transcription may be of functional relevance in genetic disorders associated with imbalanced nucleotide pools and higher levels of embedded rNMPs.
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Affiliation(s)
- Meenakshi Singh
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, SE-405 30, Sweden
| | - Viktor Posse
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, SE-405 30, Sweden
| | - Bradley Peter
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, SE-405 30, Sweden
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, SE-405 30, Sweden
| | - Claes M Gustafsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, SE-405 30, Sweden
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15
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Ciesielska EJ, Kim S, Bisimwa HGM, Grier C, Rahman MM, Young CKJ, Young MJ, Oliveira MT, Ciesielski GL. Remdesivir triphosphate blocks DNA synthesis and increases exonucleolysis by the replicative mitochondrial DNA polymerase, Pol γ. Mitochondrion 2021; 61:147-158. [PMID: 34619353 PMCID: PMC8595818 DOI: 10.1016/j.mito.2021.09.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/16/2021] [Accepted: 09/22/2021] [Indexed: 01/18/2023]
Abstract
The COVID-19 pandemic prompted the FDA to authorize a new nucleoside analogue, remdesivir, for emergency use in affected individuals. We examined the effects of its active metabolite, remdesivir triphosphate (RTP), on the activity of the replicative mitochondrial DNA polymerase, Pol γ. We found that while RTP is not incorporated by Pol γ into a nascent DNA strand, it remains associated with the enzyme impeding its synthetic activity and stimulating exonucleolysis. In spite of that, we found no evidence for deleterious effects of remdesivir treatment on the integrity of the mitochondrial genome in human cells in culture.
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Affiliation(s)
- Elena J Ciesielska
- Department of Chemistry, Auburn University at Montgomery, Montgomery, AL 36117, United States
| | - Shalom Kim
- Department of Chemistry, Auburn University at Montgomery, Montgomery, AL 36117, United States
| | | | - Cody Grier
- Department of Chemistry, Auburn University at Montgomery, Montgomery, AL 36117, United States
| | - Md Mostafijur Rahman
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, United States
| | - Carolyn K J Young
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, United States
| | - Matthew J Young
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, United States
| | - Marcos T Oliveira
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista "Júlio de Mesquita Filho", Jaboticabal, SP, Brazil
| | - Grzegorz L Ciesielski
- Department of Chemistry, Auburn University at Montgomery, Montgomery, AL 36117, United States.
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16
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Inatomi T, Matsuda S, Ishiuchi T, Do Y, Nakayama M, Abe S, Kasho K, Wanrooij S, Nakada K, Ichiyanagi K, Sasaki H, Yasukawa T, Kang D. TFB2M and POLRMT are essential for mammalian mitochondrial DNA replication. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1869:119167. [PMID: 34744028 DOI: 10.1016/j.bbamcr.2021.119167] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 10/13/2021] [Accepted: 10/13/2021] [Indexed: 12/24/2022]
Abstract
Two classes of replication intermediates have been observed from mitochondrial DNA (mtDNA) in many mammalian tissue and cells with two-dimensional agarose gel electrophoresis. One is assigned to leading-strand synthesis in the absence of synchronous lagging-strand synthesis (strand-asynchronous replication), and the other has properties of coupled leading- and lagging-strand synthesis (strand-coupled replication). While strand-asynchronous replication is primed by long noncoding RNA synthesized from a defined transcription initiation site, little is known about the commencement of strand-coupled replication. To investigate it, we attempted to abolish strand-asynchronous replication in cultured human cybrid cells by knocking out the components of the transcription initiation complexes, mitochondrial transcription factor B2 (TFB2M/mtTFB2) and mitochondrial RNA polymerase (POLRMT/mtRNAP). Unexpectedly, removal of either protein resulted in complete mtDNA loss, demonstrating for the first time that TFB2M and POLRMT are indispensable for the maintenance of human mtDNA. Moreover, a lack of TFB2M could not be compensated for by mitochondrial transcription factor B1 (TFB1M/mtTFB1). These findings indicate that TFB2M and POLRMT are crucial for the priming of not only strand-asynchronous but also strand-coupled replication, providing deeper insights into the molecular basis of mtDNA replication initiation.
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Affiliation(s)
- Teppei Inatomi
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
| | - Shigeru Matsuda
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan; Department of Modomics Biology and Medicine, Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryocho, Aoba-ku, Sendai-shi, Miyagi 980-8575, Japan
| | - Takashi Ishiuchi
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
| | - Yura Do
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
| | - Masunari Nakayama
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
| | - Shusaku Abe
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
| | - Kazutoshi Kasho
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Sjoerd Wanrooij
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Kazuto Nakada
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba-shi, Ibaraki 305-8572, Japan
| | - Kenji Ichiyanagi
- Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya-shi, Aichi 464-8601, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
| | - Takehiro Yasukawa
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan; Department of Pathology and Oncology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan.
| | - Dongchon Kang
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
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17
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Straube H, Niehaus M, Zwittian S, Witte CP, Herde M. Enhanced nucleotide analysis enables the quantification of deoxynucleotides in plants and algae revealing connections between nucleoside and deoxynucleoside metabolism. THE PLANT CELL 2021; 33:270-289. [PMID: 33793855 PMCID: PMC8136904 DOI: 10.1093/plcell/koaa028] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 11/12/2020] [Indexed: 05/02/2023]
Abstract
Detecting and quantifying low-abundance (deoxy)ribonucleotides and (deoxy)ribonucleosides in plants remains difficult; this is a major roadblock for the investigation of plant nucleotide (NT) metabolism. Here, we present a method that overcomes this limitation, allowing the detection of all deoxy- and ribonucleotides as well as the corresponding nucleosides from the same plant sample. The method is characterized by high sensitivity and robustness enabling the reproducible detection and absolute quantification of these metabolites even if they are of low abundance. Employing the new method, we analyzed Arabidopsis thaliana null mutants of CYTIDINE DEAMINASE, GUANOSINE DEAMINASE, and NUCLEOSIDE HYDROLASE 1, demonstrating that the deoxyribonucleotide (dNT) metabolism is intricately interwoven with the catabolism of ribonucleosides (rNs). In addition, we discovered a function of rN catabolic enzymes in the degradation of deoxyribonucleosides in vivo. We also determined the concentrations of dNTs in several mono- and dicotyledonous plants, a bryophyte, and three algae, revealing a correlation of GC to AT dNT ratios with genomic GC contents. This suggests a link between the genome and the metabolome previously discussed but not experimentally addressed. Together, these findings demonstrate the potential of this new method to provide insight into plant NT metabolism.
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Affiliation(s)
- Henryk Straube
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
| | - Markus Niehaus
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
| | - Sarah Zwittian
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
| | - Claus-Peter Witte
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
| | - Marco Herde
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
- Author for correspondence:
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18
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Malfatti MC, Antoniali G, Codrich M, Burra S, Mangiapane G, Dalla E, Tell G. New perspectives in cancer biology from a study of canonical and non-canonical functions of base excision repair proteins with a focus on early steps. Mutagenesis 2021; 35:129-149. [PMID: 31858150 DOI: 10.1093/mutage/gez051] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 12/05/2019] [Indexed: 12/15/2022] Open
Abstract
Alterations of DNA repair enzymes and consequential triggering of aberrant DNA damage response (DDR) pathways are thought to play a pivotal role in genomic instabilities associated with cancer development, and are further thought to be important predictive biomarkers for therapy using the synthetic lethality paradigm. However, novel unpredicted perspectives are emerging from the identification of several non-canonical roles of DNA repair enzymes, particularly in gene expression regulation, by different molecular mechanisms, such as (i) non-coding RNA regulation of tumour suppressors, (ii) epigenetic and transcriptional regulation of genes involved in genotoxic responses and (iii) paracrine effects of secreted DNA repair enzymes triggering the cell senescence phenotype. The base excision repair (BER) pathway, canonically involved in the repair of non-distorting DNA lesions generated by oxidative stress, ionising radiation, alkylation damage and spontaneous or enzymatic deamination of nucleotide bases, represents a paradigm for the multifaceted roles of complex DDR in human cells. This review will focus on what is known about the canonical and non-canonical functions of BER enzymes related to cancer development, highlighting novel opportunities to understand the biology of cancer and representing future perspectives for designing new anticancer strategies. We will specifically focus on APE1 as an example of a pleiotropic and multifunctional BER protein.
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Affiliation(s)
- Matilde Clarissa Malfatti
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Giulia Antoniali
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Marta Codrich
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Silvia Burra
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Giovanna Mangiapane
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Emiliano Dalla
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
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19
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Zhou ZX, Williams JS, Lujan SA, Kunkel TA. Ribonucleotide incorporation into DNA during DNA replication and its consequences. Crit Rev Biochem Mol Biol 2021; 56:109-124. [PMID: 33461360 DOI: 10.1080/10409238.2020.1869175] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Ribonucleotides are the most abundant non-canonical nucleotides in the genome. Their vast presence and influence over genome biology is becoming increasingly appreciated. Here we review the recent progress made in understanding their genomic presence, incorporation characteristics and usefulness as biomarkers for polymerase enzymology. We also discuss ribonucleotide processing, the genetic consequences of unrepaired ribonucleotides in DNA and evidence supporting the significance of their transient presence in the nuclear genome.
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Affiliation(s)
- Zhi-Xiong Zhou
- Genome Integrity & Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Durham, NC, USA
| | - Jessica S Williams
- Genome Integrity & Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Durham, NC, USA
| | - Scott A Lujan
- Genome Integrity & Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Durham, NC, USA
| | - Thomas A Kunkel
- Genome Integrity & Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Durham, NC, USA
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20
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El-Sayed WMM, Gombolay AL, Xu P, Yang T, Jeon Y, Balachander S, Newnam G, Tao S, Bowen NE, Brůna T, Borodovsky M, Schinazi RF, Kim B, Chen Y, Storici F. Disproportionate presence of adenosine in mitochondrial and chloroplast DNA of Chlamydomonas reinhardtii. iScience 2020; 24:102005. [PMID: 33490913 PMCID: PMC7809514 DOI: 10.1016/j.isci.2020.102005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/29/2020] [Accepted: 12/23/2020] [Indexed: 11/02/2022] Open
Abstract
Ribonucleoside monophosphates (rNMPs) represent the most common non-standard nucleotides found in the genome of cells. The distribution of rNMPs in DNA has been studied only in limited genomes. Using the ribose-seq protocol and the Ribose-Map bioinformatics toolkit, we reveal the distribution of rNMPs incorporated into the whole genome of a photosynthetic unicellular green alga, Chlamydomonas reinhardtii. We discovered a disproportionate incorporation of adenosine in the mitochondrial and chloroplast DNA, in contrast to the nuclear DNA, relative to the corresponding nucleotide content of these C. reinhardtii organelle genomes. Our results demonstrate that the rNMP content in the DNA of the algal organelles reflects an elevated ATP level present in the algal cells. We reveal specific biases and patterns in rNMP distributions in the algal mitochondrial, chloroplast, and nuclear DNA. Moreover, we identified the C. reinhardtii orthologous genes for all three subunits of the RNase H2 enzyme using GeneMark-EP + gene finder.
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Affiliation(s)
- Waleed M M El-Sayed
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.,School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.,Marine Microbiology Department, National Institute of Oceanography and Fisheries, Red Sea, 84517, Egypt
| | - Alli L Gombolay
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Penghao Xu
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Taehwan Yang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Youngkyu Jeon
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Sathya Balachander
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Gary Newnam
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Sijia Tao
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA 30309, USA
| | - Nicole E Bowen
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA 30309, USA
| | - Tomáš Brůna
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Mark Borodovsky
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.,Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.,School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Raymond F Schinazi
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA 30309, USA
| | - Baek Kim
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA 30309, USA
| | - Yongsheng Chen
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Francesca Storici
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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21
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Giuditta A, Grassi Zucconi G, Sadile A. Brain metabolic DNA: recent evidence for a mitochondrial connection. Rev Neurosci 2020; 32:/j/revneuro.ahead-of-print/revneuro-2020-0050/revneuro-2020-0050.xml. [PMID: 32866135 DOI: 10.1515/revneuro-2020-0050] [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: 05/30/2020] [Accepted: 07/18/2020] [Indexed: 02/24/2024]
Abstract
This review highlights recent data concerning the synthesis of brain metabolic DNA (BMD) by cytoplasmic reverse transcription and the prompt acquisition of the double-stranded configuration that allows its partial transfer to nuclei. BMD prevails in the mitochondrial fraction and is present in presynaptic regions and astroglial processes where it undergoes a turnover lasting a few weeks. Additional data demonstrate that BMD sequences are modified by learning, thus indicating that the modified synaptic activity allowing proper brain responses is encoded in learning BMD. In addition, several converging observations regarding the origin of BMD strongly suggest that BMD is reverse transcribed by mitochondrial telomerase.
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Affiliation(s)
- Antonio Giuditta
- Accademia di Scienze Fisiche e Matematiche, Via Mezzocannone 8, Naples, I-80134,Italy
| | | | - Adolfo Sadile
- Department of Experimental Medicine, L. Vanvitelli Medical School, University Campania, Via S. Andrea delle dame 7, Naples, I-80138,Italy
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22
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Fu Y, Tigano M, Sfeir A. Safeguarding mitochondrial genomes in higher eukaryotes. Nat Struct Mol Biol 2020; 27:687-695. [PMID: 32764737 DOI: 10.1038/s41594-020-0474-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 07/02/2020] [Indexed: 12/20/2022]
Abstract
Mitochondria respond to DNA damage and preserve their own genetic material in a manner distinct from that of the nucleus but that requires organized mito-nuclear communication. Failure to resolve mtDNA breaks leads to mitochondrial dysfunction and affects host cells and tissues. Here, we review the pathways that safeguard mitochondrial genomes and examine the insights gained from studies of cellular and tissue-wide responses to mtDNA damage and mito-nuclear genome incompatibility.
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Affiliation(s)
- Yi Fu
- Skirball Institute of Biomolecular Medicine, Cell Biology Department, NYU Grossman School of Medicine, New York, NY, USA
| | - Marco Tigano
- Skirball Institute of Biomolecular Medicine, Cell Biology Department, NYU Grossman School of Medicine, New York, NY, USA
| | - Agnel Sfeir
- Skirball Institute of Biomolecular Medicine, Cell Biology Department, NYU Grossman School of Medicine, New York, NY, USA.
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23
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24
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Zhao L, Sumberaz P. Mitochondrial DNA Damage: Prevalence, Biological Consequence, and Emerging Pathways. Chem Res Toxicol 2020; 33:2491-2502. [PMID: 32486637 DOI: 10.1021/acs.chemrestox.0c00083] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mitochondria have a plethora of functions within a eukaryotic cell, ranging from energy production, cell signaling, and protein cofactor synthesis to various aspects of metabolism. Mitochondrial dysfunction is known to cause over 200 named disorders and has been implicated in many human diseases and aging. Mitochondria have their own genetic material, mitochondrial DNA (mtDNA), which encodes 13 protein subunits in the oxidative phosphorylation system and a full set of transfer and rRNAs. Although more than 99% of the proteins in mitochondria are nuclear DNA (nDNA)-encoded, the integrity of mtDNA is critical for mitochondrial functions, as evidenced by mitochondrial diseases sourced from mtDNA mutations and depletions and the vital role of fragmented mtDNA molecules in cell signaling pathways. Previous research has shown that mtDNA is an important target of genotoxic assaults by a variety of chemical and physical factors. This Perspective discusses the prevalence of mtDNA damage by comparing the abundance of lesions in mDNA and nDNA and summarizes current knowledge on the biological pathways to cope with mtDNA damage, including mtDNA repair, mtDNA degradation, and mitochondrial fission and fusion. Also, emerging roles of mtDNA damage in mutagenesis and immune responses are reviewed.
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Affiliation(s)
- Linlin Zhao
- Department of Chemistry and Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, California 92521, United States
| | - Philip Sumberaz
- Department of Chemistry and Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, California 92521, United States
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25
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Elimination of rNMPs from mitochondrial DNA has no effect on its stability. Proc Natl Acad Sci U S A 2020; 117:14306-14313. [PMID: 32513727 PMCID: PMC7322039 DOI: 10.1073/pnas.1916851117] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Mammalian mitochondria contain their own genome (mtDNA) that encodes key subunits of the machinery that produces the majority of the cell’s energy. mtDNA integrity is crucial for normal energy production, and its loss due to deletions or point mutations can lead to various human disorders and might contribute to aging. We asked whether ribonucleotides—the building blocks of RNA and an established threat to nuclear genome stability—contribute to the loss of mtDNA integrity observed during aging. We show that the persistent presence of ribonucleotides in mtDNA over the course of the mouse life span has no major impact on mtDNA stability. This indicates that the physiological level of ribonucleotides does not pose a serious threat to mtDNA quality. Ribonucleotides (rNMPs) incorporated in the nuclear genome are a well-established threat to genome stability and can result in DNA strand breaks when not removed in a timely manner. However, the presence of a certain level of rNMPs is tolerated in mitochondrial DNA (mtDNA) although aberrant mtDNA rNMP content has been identified in disease models. We investigated the effect of incorporated rNMPs on mtDNA stability over the mouse life span and found that the mtDNA rNMP content increased during early life. The rNMP content of mtDNA varied greatly across different tissues and was defined by the rNTP/dNTP ratio of the tissue. Accordingly, mtDNA rNMPs were nearly absent in SAMHD1−/− mice that have increased dNTP pools. The near absence of rNMPs did not, however, appreciably affect mtDNA copy number or the levels of mtDNA molecules with deletions or strand breaks in aged animals near the end of their life span. The physiological rNMP load therefore does not contribute to the progressive loss of mtDNA quality that occurs as mice age.
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26
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Ribonucleotide incorporation in yeast genomic DNA shows preference for cytosine and guanosine preceded by deoxyadenosine. Nat Commun 2020; 11:2447. [PMID: 32415081 PMCID: PMC7229183 DOI: 10.1038/s41467-020-16152-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 04/14/2020] [Indexed: 12/14/2022] Open
Abstract
Despite the abundance of ribonucleoside monophosphates (rNMPs) in DNA, sites of rNMP incorporation remain poorly characterized. Here, by using ribose-seq and Ribose-Map techniques, we built and analyzed high-throughput sequencing libraries of rNMPs derived from mitochondrial and nuclear DNA of budding and fission yeast. We reveal both common and unique features of rNMP sites among yeast species and strains, and between wild type and different ribonuclease H-mutant genotypes. We demonstrate that the rNMPs are not randomly incorporated in DNA. We highlight signatures and patterns of rNMPs, including sites within trinucleotide-repeat tracts. Our results uncover that the deoxyribonucleotide immediately upstream of the rNMPs has a strong influence on rNMP distribution, suggesting a mechanism of rNMP accommodation by DNA polymerases as a driving force of rNMP incorporation. Consistently, we find deoxyadenosine upstream from the most abundant genomic rCMPs and rGMPs. This study establishes a framework to better understand mechanisms of rNMP incorporation in DNA. Ribonucleoside monophosphates are incorporated by DNA polymerases into double-stranded DNA. Here, the authors use ribose-seq and Ribose-Map techniques to reveal that signatures and patterns of ribonucleotide incorporation in yeast mitochondrial and nuclear DNA show preference for cytosine and guanosine preceded by deoxyadenosine.
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27
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Ghodke PP, Guengerich FP. Impact of 1, N 6-ethenoadenosine, a damaged ribonucleotide in DNA, on translesion synthesis and repair. J Biol Chem 2020; 295:6092-6107. [PMID: 32213600 DOI: 10.1074/jbc.ra120.012829] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/23/2020] [Indexed: 01/02/2023] Open
Abstract
Incorporation of ribonucleotides into DNA can severely diminish genome integrity. However, how ribonucleotides instigate DNA damage is poorly understood. In DNA, they can promote replication stress and genomic instability and have been implicated in several diseases. We report here the impact of the ribonucleotide rATP and of its naturally occurring damaged analog 1,N 6-ethenoadenosine (1,N 6-ϵrA) on translesion synthesis (TLS), mediated by human DNA polymerase η (hpol η), and on RNase H2-mediated incision. Mass spectral analysis revealed that 1,N 6-ϵrA in DNA generates extensive frameshifts during TLS, which can lead to genomic instability. Moreover, steady-state kinetic analysis of the TLS process indicated that deoxypurines (i.e. dATP and dGTP) are inserted predominantly opposite 1,N 6-ϵrA. We also show that hpol η acts as a reverse transcriptase in the presence of damaged ribonucleotide 1,N 6-ϵrA but has poor RNA primer extension activities. Steady-state kinetic analysis of reverse transcription and RNA primer extension showed that hpol η favors the addition of dATP and dGTP opposite 1,N 6-ϵrA. We also found that RNase H2 recognizes 1,N 6-ϵrA but has limited incision activity across from this lesion, which can lead to the persistence of this detrimental DNA adduct. We conclude that the damaged and unrepaired ribonucleotide 1,N 6-ϵrA in DNA exhibits mutagenic potential and can also alter the reading frame in an mRNA transcript because 1,N 6-ϵrA is incompletely incised by RNase H2.
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Affiliation(s)
- Pratibha P Ghodke
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37323-0146
| | - F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37323-0146.
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28
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Ebrahimi KH, Howie D, Rowbotham JS, McCullagh J, Armstrong FA, James WS. Viperin, through its radical-SAM activity, depletes cellular nucleotide pools and interferes with mitochondrial metabolism to inhibit viral replication. FEBS Lett 2020; 594:1624-1630. [PMID: 32061099 DOI: 10.1002/1873-3468.13761] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 01/29/2020] [Accepted: 01/31/2020] [Indexed: 12/11/2022]
Abstract
Viperin (RSAD2) is an antiviral radical S-adenosylmethionine (SAM) enzyme highly expressed in different cell types upon viral infection. Recently, it has been reported that the radical-SAM activity of viperin transforms cytidine triphosphate (CTP) to its analogue 3'-deoxy-3',4'-didehydro-CTP (ddhCTP). Based on biochemical studies and cell biological experiments, it was concluded that ddhCTP and its nucleoside form ddhC do not affect the cellular concentration of nucleotide triphosphates and that ddhCTP acts as replication chain terminator. However, our re-evaluation of the reported data and new results indicate that ddhCTP is not an effective viral chain terminator but depletes cellular nucleotide pools and interferes with mitochondrial activity to inhibit viral replication. Our analysis is consistent with a unifying view of the antiviral and radical-SAM activities of viperin.
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Affiliation(s)
| | - Duncan Howie
- Sir William Dunn School of Pathology, University of Oxford, UK
| | | | | | | | - William S James
- Sir William Dunn School of Pathology, University of Oxford, UK
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29
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Nava GM, Grasso L, Sertic S, Pellicioli A, Muzi Falconi M, Lazzaro F. One, No One, and One Hundred Thousand: The Many Forms of Ribonucleotides in DNA. Int J Mol Sci 2020; 21:E1706. [PMID: 32131532 PMCID: PMC7084774 DOI: 10.3390/ijms21051706] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 02/26/2020] [Accepted: 02/28/2020] [Indexed: 12/14/2022] Open
Abstract
In the last decade, it has become evident that RNA is frequently found in DNA. It is now well established that single embedded ribonucleoside monophosphates (rNMPs) are primarily introduced by DNA polymerases and that longer stretches of RNA can anneal to DNA, generating RNA:DNA hybrids. Among them, the most studied are R-loops, peculiar three-stranded nucleic acid structures formed upon the re-hybridization of a transcript to its template DNA. In addition, polyribonucleotide chains are synthesized to allow DNA replication priming, double-strand breaks repair, and may as well result from the direct incorporation of consecutive rNMPs by DNA polymerases. The bright side of RNA into DNA is that it contributes to regulating different physiological functions. The dark side, however, is that persistent RNA compromises genome integrity and genome stability. For these reasons, the characterization of all these structures has been under growing investigation. In this review, we discussed the origin of single and multiple ribonucleotides in the genome and in the DNA of organelles, focusing on situations where the aberrant processing of RNA:DNA hybrids may result in multiple rNMPs embedded in DNA. We concluded by providing an overview of the currently available strategies to study the presence of single and multiple ribonucleotides in DNA in vivo.
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Affiliation(s)
| | | | | | | | - Marco Muzi Falconi
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, 20133 Milano, Italy; (G.M.N.); (L.G.); (S.S.); (A.P.)
| | - Federico Lazzaro
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, 20133 Milano, Italy; (G.M.N.); (L.G.); (S.S.); (A.P.)
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30
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Sommerville EW, Dalla Rosa I, Rosenberg MM, Bruni F, Thompson K, Rocha M, Blakely EL, He L, Falkous G, Schaefer AM, Yu‐Wai‐Man P, Chinnery PF, Hedstrom L, Spinazzola A, Taylor RW, Gorman GS. Identification of a novel heterozygous guanosine monophosphate reductase (GMPR) variant in a patient with a late-onset disorder of mitochondrial DNA maintenance. Clin Genet 2020; 97:276-286. [PMID: 31600844 PMCID: PMC7004030 DOI: 10.1111/cge.13652] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/18/2019] [Accepted: 09/27/2019] [Indexed: 12/18/2022]
Abstract
Autosomal dominant progressive external ophthalmoplegia (adPEO) is a late-onset, Mendelian mitochondrial disorder characterised by paresis of the extraocular muscles, ptosis, and skeletal-muscle restricted multiple mitochondrial DNA (mtDNA) deletions. Although dominantly inherited, pathogenic variants in POLG, TWNK and RRM2B are among the most common genetic defects of adPEO, identification of novel candidate genes and the underlying pathomechanisms remains challenging. We report the clinical, genetic and molecular investigations of a patient who presented in the seventh decade of life with PEO. Oxidative histochemistry revealed cytochrome c oxidase-deficient fibres and occasional ragged red fibres showing subsarcolemmal mitochondrial accumulation in skeletal muscle, while molecular studies identified the presence of multiple mtDNA deletions. Negative candidate screening of known nuclear genes associated with PEO prompted diagnostic exome sequencing, leading to the prioritisation of a novel heterozygous c.547G>C variant in GMPR (NM_006877.3) encoding guanosine monophosphate reductase, a cytosolic enzyme required for maintaining the cellular balance of adenine and guanine nucleotides. We show that the novel c.547G>C variant causes aberrant splicing, decreased GMPR protein levels in patient skeletal muscle, proliferating and quiescent cells, and is associated with subtle changes in nucleotide homeostasis protein levels and evidence of disturbed mtDNA maintenance in skeletal muscle. Despite confirmation of GMPR deficiency, demonstrating marked defects of mtDNA replication or nucleotide homeostasis in patient cells proved challenging. Our study proposes that GMPR is the 19th locus for PEO and highlights the complexities of uncovering disease mechanisms in late-onset PEO phenotypes.
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Affiliation(s)
- Ewen W. Sommerville
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Ilaria Dalla Rosa
- Department of Clinical and Movement Neurosciences, UCL Queens Square Institute of Neurology, Royal Free CampusUniversity College LondonLondonUK
| | | | - Francesco Bruni
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of Bari “ldo Moro”BariItaly
| | - Kyle Thompson
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Mariana Rocha
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Emma L. Blakely
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Langping He
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Gavin Falkous
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Andrew M. Schaefer
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Patrick Yu‐Wai‐Man
- NIHR Biomedical Research Centre at Moorfields Eye Hospital and UCL Institute of OphthalmologyLondonUK
- MRC Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
- Cambridge Centre for Brain Repair, Department of Clinical NeurosciencesUniversity of CambridgeCambridgeUK
| | - Patrick F. Chinnery
- Department of Clinical Neuroscience & Medical Research Council Mitochondrial Biology UnitSchool of Clinical Medicine, University of CambridgeCambridgeUK
| | - Lizbeth Hedstrom
- Department of BiologyBrandeis UniversityWalthamMA
- Department of ChemistryBrandeis University, 415 South St.WalthamMA
| | - Antonella Spinazzola
- Department of Clinical and Movement Neurosciences, UCL Queens Square Institute of Neurology, Royal Free CampusUniversity College LondonLondonUK
- MRC Centre for Neuromuscular DiseasesUCL Institute of Neurology and National Hospital for Neurology and NeurosurgeryLondonUK
| | - Robert W. Taylor
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Gráinne S. Gorman
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
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31
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Abstract
DNA replication in human mitochondria has been studied for several decades; however, its mechanism still remains unclear. During the last 15 years, many new experimental data on the mitochondrial replication have appeared, although extremely contradictory. Two asynchronous (strand displacement and RITOLS) and one synchronous (strand-coupled) replication models have been proposed. In the asynchronous models, replication from the origin in the H-chain starts earlier, so that the replication of the two chains ends at different times. The synchronous model is more traditional and implies two replication forks with leading and lagging strands initiated at the same origin. For each of the three models, both confirming and contradicting experimental data exist. Most likely, there is no single model of mitochondrial replication. It is possible that the unique mitochondrial replication machinery that has originated as a results of endosymbiosis has an unexpected variety of replication strategies to maintain the mitochondrial genome. An unusual combination of enzymes of different origin (phage, bacterial, eukaryotic) and unique features of the mitochondrial genome (existance of heavy and light chains, insertions of ribonucleotides, a variety of origins) can allow replication through different mechanisms. In human mitochondria, asynchronous replication seems to dominate; however, synchronous replication is also possible under certain conditions. In the human heart mitochondria, circular mitochondrial DNA (mtDNA) molecules can rearrange in a network of rapidly replicating linear genomes, thereby suggesting possible existence of a wide range of replication mechanisms in the mitochondria. The review describes the main stages of mtDNA replication and enzymes involved in this process, as well as discusses the prospects of mitochondrial replication studies.
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Affiliation(s)
- L A Zinovkina
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119234, Russia.
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32
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Mitochondria in the signaling pathways that control longevity and health span. Ageing Res Rev 2019; 54:100940. [PMID: 31415807 PMCID: PMC7479635 DOI: 10.1016/j.arr.2019.100940] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 07/09/2019] [Accepted: 08/06/2019] [Indexed: 12/26/2022]
Abstract
Genetic and pharmacological intervention studies have identified evolutionarily conserved and functionally interconnected networks of cellular energy homeostasis, nutrient-sensing, and genome damage response signaling pathways, as prominent regulators of longevity and health span in various species. Mitochondria are the primary sites of ATP production and are key players in several other important cellular processes. Mitochondrial dysfunction diminishes tissue and organ functional performance and is a commonly considered feature of the aging process. Here we review the evidence that through reciprocal and multilevel functional interactions, mitochondria are implicated in the lifespan modulation function of these pathways, which altogether constitute a highly dynamic and complex system that controls the aging process. An important characteristic of these pathways is their extensive crosstalk and apparent malleability to modification by non-invasive pharmacological, dietary, and lifestyle interventions, with promising effects on lifespan and health span in animal models and potentially also in humans.
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33
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Wheeler JH, Young CKJ, Young MJ. Analysis of Human Mitochondrial DNA Content by Southern Blotting and Nonradioactive Probe Hybridization. CURRENT PROTOCOLS IN TOXICOLOGY 2019; 80:e75. [PMID: 30982231 PMCID: PMC6581606 DOI: 10.1002/cptx.75] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A single cell can contain several thousand copies of the mitochondrial DNA genome or mtDNA. Tools for assessing mtDNA content are necessary for clinical and toxicological research, as mtDNA depletion is linked to genetic disease and drug toxicity. For instance, mtDNA depletion syndromes are typically fatal childhood disorders that are characterized by severe declines in mtDNA content in affected tissues. Mitochondrial toxicity and mtDNA depletion have also been reported in human immunodeficiency virus-infected patients treated with certain nucleoside reverse transcriptase inhibitors. Further, cell culture studies have demonstrated that exposure to oxidative stress stimulates mtDNA degradation. Here we outline a Southern blot and nonradioactive digoxigenin-labeled probe hybridization method to estimate mtDNA content in human genomic DNA samples. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Joel H. Wheeler
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, Illinois 62901
| | - Carolyn K. J. Young
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, Illinois 62901
| | - Matthew J. Young
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, Illinois 62901
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34
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Wanrooij PH, Chabes A. Ribonucleotides in mitochondrial DNA. FEBS Lett 2019; 593:1554-1565. [PMID: 31093968 DOI: 10.1002/1873-3468.13440] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/09/2019] [Accepted: 05/09/2019] [Indexed: 01/05/2023]
Abstract
The incorporation of ribonucleotides (rNMPs) into DNA during genome replication has gained substantial attention in recent years and has been shown to be a significant source of genomic instability. Studies in yeast and mammals have shown that the two genomes, the nuclear DNA (nDNA) and the mitochondrial DNA (mtDNA), differ with regard to their rNMP content. This is largely due to differences in rNMP repair - whereas rNMPs are efficiently removed from the nuclear genome, mitochondria lack robust mechanisms for removal of single rNMPs incorporated during DNA replication. In this minireview, we describe the processes that determine the frequency of rNMPs in the mitochondrial genome and summarise recent findings regarding the effect of incorporated rNMPs on mtDNA stability and function.
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Affiliation(s)
- Paulina H Wanrooij
- Department of Medical Biochemistry and Biophysics, Umeå University, Sweden
| | - Andrei Chabes
- Department of Medical Biochemistry and Biophysics, Umeå University, Sweden.,Laboratory for Molecular Infection Medicine Sweden, Umeå University, Sweden
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35
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Sassa A, Yasui M, Honma M. Current perspectives on mechanisms of ribonucleotide incorporation and processing in mammalian DNA. Genes Environ 2019; 41:3. [PMID: 30700998 PMCID: PMC6346524 DOI: 10.1186/s41021-019-0118-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 01/08/2019] [Indexed: 01/09/2023] Open
Abstract
Ribonucleotides, which are RNA precursors, are often incorporated into DNA during replication. Although embedded ribonucleotides in the genome are efficiently removed by canonical ribonucleotide excision repair (RER), inactivation of RER causes genomic ribonucleotide accumulation, leading to various abnormalities in cells. Mutation of genes encoding factors involved in RER is associated with the neuroinflammatory autoimmune disorder Aicardi–Goutières syndrome. Over the last decade, the biological impact of ribonucleotides in the genome has attracted much attention. In the present review, we particularly focus on recent studies that have elucidated possible mechanisms of ribonucleotide incorporation and repair and their significance in mammals.
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Affiliation(s)
- Akira Sassa
- 1Department of Biology, Graduate School of Science, Chiba University, Chiba, 263-8522 Japan
| | - Manabu Yasui
- 2Division of Genetics and Mutagenesis, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki 210-9501 Japan
| | - Masamitsu Honma
- 2Division of Genetics and Mutagenesis, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki 210-9501 Japan
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36
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Posse V, Al-Behadili A, Uhler JP, Clausen AR, Reyes A, Zeviani M, Falkenberg M, Gustafsson CM. RNase H1 directs origin-specific initiation of DNA replication in human mitochondria. PLoS Genet 2019; 15:e1007781. [PMID: 30605451 PMCID: PMC6317783 DOI: 10.1371/journal.pgen.1007781] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 10/23/2018] [Indexed: 11/21/2022] Open
Abstract
Human mitochondrial DNA (mtDNA) replication is first initiated at the origin of H-strand replication. The initiation depends on RNA primers generated by transcription from an upstream promoter (LSP). Here we reconstitute this process in vitro using purified transcription and replication factors. The majority of all transcription events from LSP are prematurely terminated after ~120 nucleotides, forming stable R-loops. These nascent R-loops cannot directly prime mtDNA synthesis, but must first be processed by RNase H1 to generate 3′-ends that can be used by DNA polymerase γ to initiate DNA synthesis. Our findings are consistent with recent studies of a knockout mouse model, which demonstrated that RNase H1 is required for R-loop processing and mtDNA maintenance in vivo. Both R-loop formation and DNA replication initiation are stimulated by the mitochondrial single-stranded DNA binding protein. In an RNase H1 deficient patient cell line, the precise initiation of mtDNA replication is lost and DNA synthesis is initiated from multiple sites throughout the mitochondrial control region. In combination with previously published in vivo data, the findings presented here suggest a model, in which R-loop processing by RNase H1 directs origin-specific initiation of DNA replication in human mitochondria. Human mitochondria contain a double-stranded DNA genome that codes for key components of the oxidative phosphorylation system. The mitochondrial DNA (mtDNA) is replicated by a replication machinery distinct from that operating in the nucleus and mutations affecting individual replication factors have been associated with an array of rare, human diseases. In the present work, we demonstrate that RNase H1 directs origin-specific initiation of DNA replication in human mitochondria and that disease-causing mutations may impair this process. A unique feature of mtDNA replication is that primers required for initiation of leading-strand DNA replication are produced by the mitochondrial transcription machinery. A substantial fraction of all transcription events is prematurely terminated about 120 nucleotides downstream of the promoter and the RNA remains firmly associated with the genome, forming R-loops. Interestingly, the free 3′-end of these R-loops cannot directly prime initiation of DNA synthesis, but must first be processed by RNase H1. The process is stimulated by the mitochondrial single-stranded DNA binding protein and faithfully reconstitutes replication events mapped in vivo. In combination with mapping of replication events in fibroblasts derived from patients with mutations in RNASEH1, our findings point to a possible model for replication initiation in human mitochondria similar to that previously described in the E. coli plasmid, ColE1.
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Affiliation(s)
- Viktor Posse
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Ali Al-Behadili
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Jay P Uhler
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Anders R Clausen
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Aurelio Reyes
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Massimo Zeviani
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Claes M Gustafsson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
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37
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Röthlisberger P, Levi-Acobas F, Sarac I, Ricoux R, Mahy JP, Herdewijn P, Marlière P, Hollenstein M. Incorporation of a minimal nucleotide into DNA. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.10.036] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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38
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Al-Behadili A, Uhler JP, Berglund AK, Peter B, Doimo M, Reyes A, Wanrooij S, Zeviani M, Falkenberg M. A two-nuclease pathway involving RNase H1 is required for primer removal at human mitochondrial OriL. Nucleic Acids Res 2018; 46:9471-9483. [PMID: 30102370 PMCID: PMC6182146 DOI: 10.1093/nar/gky708] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 06/21/2018] [Accepted: 07/24/2018] [Indexed: 11/12/2022] Open
Abstract
The role of Ribonuclease H1 (RNase H1) during primer removal and ligation at the mitochondrial origin of light-strand DNA synthesis (OriL) is a key, yet poorly understood, step in mitochondrial DNA maintenance. Here, we reconstitute the replication cycle of L-strand synthesis in vitro using recombinant mitochondrial proteins and model OriL substrates. The process begins with initiation of DNA replication at OriL and ends with primer removal and ligation. We find that RNase H1 partially removes the primer, leaving behind the last one to three ribonucleotides. These 5'-end ribonucleotides disturb ligation, a conclusion which is supported by analysis of RNase H1-deficient patient cells. A second nuclease is therefore required to remove the last ribonucleotides and we demonstrate that Flap endonuclease 1 (FEN1) can execute this function in vitro. Removal of RNA primers at OriL thus depends on a two-nuclease model, which in addition to RNase H1 requires FEN1 or a FEN1-like activity. These findings define the role of RNase H1 at OriL and help to explain the pathogenic consequences of disease causing mutations in RNase H1.
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Affiliation(s)
- Ali Al-Behadili
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, Sweden
| | - Jay P Uhler
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, Sweden
| | - Anna-Karin Berglund
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, Sweden
| | - Bradley Peter
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, Sweden
| | - Mara Doimo
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden
| | - Aurelio Reyes
- MRC-Mitochondrial Biology Unit, University of Cambridge, MRC Building, Hills Road, Cambridge CB2 0XY, UK
| | - Sjoerd Wanrooij
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden
| | - Massimo Zeviani
- MRC-Mitochondrial Biology Unit, University of Cambridge, MRC Building, Hills Road, Cambridge CB2 0XY, UK
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, Sweden
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39
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Pohjoismäki JLO, Forslund JME, Goffart S, Torregrosa-Muñumer R, Wanrooij S. Known Unknowns of Mammalian Mitochondrial DNA Maintenance. Bioessays 2018; 40:e1800102. [DOI: 10.1002/bies.201800102] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 06/18/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Jaakko L. O. Pohjoismäki
- Department of Environmental and Biological Sciences, University of Eastern Finland; 80101 Joensuu Finland
| | | | - Steffi Goffart
- Department of Environmental and Biological Sciences, University of Eastern Finland; 80101 Joensuu Finland
| | - Rubén Torregrosa-Muñumer
- Department of Environmental and Biological Sciences, University of Eastern Finland; 80101 Joensuu Finland
| | - Sjoerd Wanrooij
- Department of Medical Biochemistry and Biophysics, Umeå University; 90187 Umeå Sweden
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40
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Randrianjatovo-Gbalou I, Rosario S, Sismeiro O, Varet H, Legendre R, Coppée JY, Huteau V, Pochet S, Delarue M. Enzymatic synthesis of random sequences of RNA and RNA analogues by DNA polymerase theta mutants for the generation of aptamer libraries. Nucleic Acids Res 2018; 46:6271-6284. [PMID: 29788485 PMCID: PMC6158600 DOI: 10.1093/nar/gky413] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/12/2018] [Accepted: 05/04/2018] [Indexed: 12/17/2022] Open
Abstract
Nucleic acid aptamers, especially RNA, exhibit valuable advantages compared to protein therapeutics in terms of size, affinity and specificity. However, the synthesis of libraries of large random RNAs is still difficult and expensive. The engineering of polymerases able to directly generate these libraries has the potential to replace the chemical synthesis approach. Here, we start with a DNA polymerase that already displays a significant template-free nucleotidyltransferase activity, human DNA polymerase theta, and we mutate it based on the knowledge of its three-dimensional structure as well as previous mutational studies on members of the same polA family. One mutant exhibited a high tolerance towards ribonucleotides (NTPs) and displayed an efficient ribonucleotidyltransferase activity that resulted in the assembly of long RNA polymers. HPLC analysis and RNA sequencing of the products were used to quantify the incorporation of the four NTPs as a function of initial NTP concentrations and established the randomness of each generated nucleic acid sequence. The same mutant revealed a propensity to accept other modified nucleotides and to extend them in long fragments. Hence, this mutant can deliver random natural and modified RNA polymers libraries ready to use for SELEX, with custom lengths and balanced or unbalanced ratios.
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Affiliation(s)
- Irina Randrianjatovo-Gbalou
- Unit of Structural Dynamics of Biological Macromolecules, CNRS UMR 3528, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Sandrine Rosario
- Unit of Structural Dynamics of Biological Macromolecules, CNRS UMR 3528, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Odile Sismeiro
- Transcriptome and EpiGenome platform, BioMics, Center of Innovation and Technological Research, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Hugo Varet
- Transcriptome and EpiGenome platform, BioMics, Center of Innovation and Technological Research, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
- Hub informatique et Biostatistique, Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI, USR 3756 IP-CNRS), Institut Pasteur, 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Rachel Legendre
- Transcriptome and EpiGenome platform, BioMics, Center of Innovation and Technological Research, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
- Hub informatique et Biostatistique, Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI, USR 3756 IP-CNRS), Institut Pasteur, 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Jean-Yves Coppée
- Transcriptome and EpiGenome platform, BioMics, Center of Innovation and Technological Research, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Valérie Huteau
- Unité de Chimie et Biocatalyse, CNRS UMR 3523, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Sylvie Pochet
- Unité de Chimie et Biocatalyse, CNRS UMR 3523, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Marc Delarue
- Unit of Structural Dynamics of Biological Macromolecules, CNRS UMR 3528, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France
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41
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Accurate estimation of 5-methylcytosine in mammalian mitochondrial DNA. Sci Rep 2018; 8:5801. [PMID: 29643477 PMCID: PMC5895755 DOI: 10.1038/s41598-018-24251-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 03/28/2018] [Indexed: 02/06/2023] Open
Abstract
Whilst 5-methylcytosine (5mC) is a major epigenetic mark in the nuclear DNA in mammals, whether or not mitochondrial DNA (mtDNA) receives 5mC modification remains controversial. Herein, we exhaustively analysed mouse mtDNA using three methods that are based upon different principles for detecting 5mC. Next-generation bisulfite sequencing did not give any significant signatures of methylation in mtDNAs of liver, brain and embryonic stem cells (ESCs). Also, treatment with methylated cytosine-sensitive endonuclease McrBC resulted in no substantial decrease of mtDNA band intensities in Southern hybridisation. Furthermore, mass spectrometric nucleoside analyses of highly purified liver mtDNA preparations did not detect 5-methyldeoxycytidine at the levels found in the nuclear DNA but at a range of only 0.3-0.5% of deoxycytidine. Taken together, we propose that 5mC is not present at any specific region(s) of mtDNA and that levels of the methylated cytosine are fairly low, provided the modification occurs. It is thus unlikely that 5mC plays a universal role in mtDNA gene expression or mitochondrial metabolism.
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42
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The presence of rNTPs decreases the speed of mitochondrial DNA replication. PLoS Genet 2018; 14:e1007315. [PMID: 29601571 PMCID: PMC5895052 DOI: 10.1371/journal.pgen.1007315] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 04/11/2018] [Accepted: 03/19/2018] [Indexed: 11/19/2022] Open
Abstract
Ribonucleotides (rNMPs) are frequently incorporated during replication or repair by DNA polymerases and failure to remove them leads to instability of nuclear DNA (nDNA). Conversely, rNMPs appear to be relatively well-tolerated in mitochondrial DNA (mtDNA), although the mechanisms behind the tolerance remain unclear. We here show that the human mitochondrial DNA polymerase gamma (Pol γ) bypasses single rNMPs with an unprecedentedly high fidelity and efficiency. In addition, Pol γ exhibits a strikingly low frequency of rNMP incorporation, a property, which we find is independent of its exonuclease activity. However, the physiological levels of free rNTPs partially inhibit DNA synthesis by Pol γ and render the polymerase more sensitive to imbalanced dNTP pools. The characteristics of Pol γ reported here could have implications for forms of mtDNA depletion syndrome (MDS) that are associated with imbalanced cellular dNTP pools. Our results show that at the rNTP/dNTP ratios that are expected to prevail in such disease states, Pol γ enters a polymerase/exonuclease idling mode that leads to mtDNA replication stalling. This could ultimately lead to mtDNA depletion and, consequently, to mitochondrial disease phenotypes such as those observed in MDS.
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43
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Moss CF, Dalla Rosa I, Hunt LE, Yasukawa T, Young R, Jones AWE, Reddy K, Desai R, Virtue S, Elgar G, Voshol P, Taylor MS, Holt IJ, Reijns MAM, Spinazzola A. Aberrant ribonucleotide incorporation and multiple deletions in mitochondrial DNA of the murine MPV17 disease model. Nucleic Acids Res 2018; 45:12808-12815. [PMID: 29106596 PMCID: PMC5728394 DOI: 10.1093/nar/gkx1009] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 10/17/2017] [Indexed: 12/24/2022] Open
Abstract
All DNA polymerases misincorporate ribonucleotides despite their preference for deoxyribonucleotides, and analysis of cultured cells indicates that mammalian mitochondrial DNA (mtDNA) tolerates such replication errors. However, it is not clear to what extent misincorporation occurs in tissues, or whether this plays a role in human disease. Here, we show that mtDNA of solid tissues contains many more embedded ribonucleotides than that of cultured cells, consistent with the high ratio of ribonucleotide to deoxynucleotide triphosphates in tissues, and that riboadenosines account for three-quarters of them. The pattern of embedded ribonucleotides changes in a mouse model of Mpv17 deficiency, which displays a marked increase in rGMPs in mtDNA. However, while the mitochondrial dGTP is low in the Mpv17−/− liver, the brain shows no change in the overall dGTP pool, leading us to suggest that Mpv17 determines the local concentration or quality of dGTP. Embedded rGMPs are expected to distort the mtDNA and impede its replication, and elevated rGMP incorporation is associated with early-onset mtDNA depletion in liver and late-onset multiple deletions in brain of Mpv17−/− mice. These findings suggest aberrant ribonucleotide incorporation is a primary mtDNA abnormality that can result in pathology.
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Affiliation(s)
| | - Ilaria Dalla Rosa
- MRC Laboratory, Mill Hill, London NW7 1AA, UK.,Department of Clinical Neurosciences, Institute of Neurology, Royal Free Campus, University College London NW3 2PF, UK
| | - Lilian E Hunt
- Advanced Sequencing Facility, Francis Crick Institute, London NW1 1AT, UK
| | | | - Robert Young
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Aleck W E Jones
- MRC Laboratory, Mill Hill, London NW7 1AA, UK.,Department of Clinical Neurosciences, Institute of Neurology, Royal Free Campus, University College London NW3 2PF, UK
| | - Kaalak Reddy
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Radha Desai
- MRC Laboratory, Mill Hill, London NW7 1AA, UK
| | - Sam Virtue
- MRC Metabolic Diseases Unit, Wellcome Trust-MRC Institute of Metabolic Science, Cambridge CB2 0QQ, UK
| | - Greg Elgar
- Advanced Sequencing Facility, Francis Crick Institute, London NW1 1AT, UK
| | - Peter Voshol
- MRC Metabolic Diseases Unit, Wellcome Trust-MRC Institute of Metabolic Science, Cambridge CB2 0QQ, UK
| | - Martin S Taylor
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Ian J Holt
- MRC Laboratory, Mill Hill, London NW7 1AA, UK.,Department of Clinical Neurosciences, Institute of Neurology, Royal Free Campus, University College London NW3 2PF, UK.,Biodonostia Health Research Institute, 20014 San Sebastián, Spain and IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Martin A M Reijns
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Antonella Spinazzola
- MRC Laboratory, Mill Hill, London NW7 1AA, UK.,Department of Clinical Neurosciences, Institute of Neurology, Royal Free Campus, University College London NW3 2PF, UK.,MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology and National Hospital for Neurology and Neurosurgery, Queen Square, London WC1N 3BG, UK
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44
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Young MJ. Off-Target Effects of Drugs that Disrupt Human Mitochondrial DNA Maintenance. Front Mol Biosci 2017; 4:74. [PMID: 29214156 PMCID: PMC5702650 DOI: 10.3389/fmolb.2017.00074] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 10/31/2017] [Indexed: 12/17/2022] Open
Abstract
Nucleoside reverse transcriptase inhibitors (NRTIs) were the first drugs used to treat human immunodeficiency virus (HIV) the cause of acquired immunodeficiency syndrome. Development of severe mitochondrial toxicity has been well documented in patients infected with HIV and administered NRTIs. In vitro biochemical experiments have demonstrated that the replicative mitochondrial DNA (mtDNA) polymerase gamma, Polg, is a sensitive target for inhibition by metabolically active forms of NRTIs, nucleotide reverse transcriptase inhibitors (NtRTIs). Once incorporated into newly synthesized daughter strands NtRTIs block further DNA polymerization reactions. Human cell culture and animal studies have demonstrated that cell lines and mice exposed to NRTIs display mtDNA depletion. Further complicating NRTI off-target effects on mtDNA maintenance, two additional DNA polymerases, Pol beta and PrimPol, were recently reported to localize to mitochondria as well as the nucleus. Similar to Polg, in vitro work has demonstrated both Pol beta and PrimPol incorporate NtRTIs into nascent DNA. Cell culture and biochemical experiments have also demonstrated that antiviral ribonucleoside drugs developed to treat hepatitis C infection act as off-target substrates for POLRMT, the mitochondrial RNA polymerase and primase. Accompanying the above-mentioned topics, this review examines: (1) mtDNA maintenance in human health and disease, (2) reports of DNA polymerases theta and zeta (Rev3) localizing to mitochondria, and (3) additional drugs with off-target effects on mitochondrial function. Lastly, mtDNA damage may induce cell death; therefore, the possibility of utilizing compounds that disrupt mtDNA maintenance to kill cancer cells is discussed.
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Affiliation(s)
- Matthew J Young
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL, United States
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45
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Kreisel K, Engqvist MKM, Clausen AR. Simultaneous Mapping and Quantitation of Ribonucleotides in Human Mitochondrial DNA. J Vis Exp 2017. [PMID: 29286447 PMCID: PMC5755389 DOI: 10.3791/56551] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Established approaches to estimate the number of ribonucleotides present in a genome are limited to the quantitation of incorporated ribonucleotides using short synthetic DNA fragments or plasmids as templates and then extrapolating the results to the whole genome. Alternatively, the number of ribonucleotides present in a genome may be estimated using alkaline gels or Southern blots. More recent in vivo approaches employ Next-generation sequencing allowing genome-wide mapping of ribonucleotides, providing the position and identity of embedded ribonucleotides. However, they do not allow quantitation of the number of ribonucleotides which are incorporated into a genome. Here we describe how to simultaneously map and quantitate the number of ribonucleotides which are incorporated into human mitochondrial DNA in vivo by Next-generation sequencing. We use highly intact DNA and introduce sequence specific double strand breaks by digesting it with an endonuclease, subsequently hydrolyzing incorporated ribonucleotides with alkali. The generated ends are ligated with adapters and these ends are sequenced on a Next-generation sequencing machine. The absolute number of ribonucleotides can be calculated as the number of reads outside the recognition site per average number of reads at the recognition site for the sequence specific endonuclease. This protocol may also be utilized to map and quantitate free nicks in DNA and allows adaption to map other DNA lesions that can be processed to 5´-OH ends or 5´-phosphate ends. Furthermore, this method can be applied to any organism, given that a suitable reference genome is available. This protocol therefore provides an important tool to study DNA replication, 5´-end processing, DNA damage, and DNA repair.
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Affiliation(s)
- Katrin Kreisel
- Department for Medical Biochemistry and Cell Biology, University of Gothenburg
| | - Martin K M Engqvist
- Department for Medical Biochemistry and Cell Biology, University of Gothenburg; Department of Biology and Biological Engineering, Chalmers University of Technology
| | - Anders R Clausen
- Department for Medical Biochemistry and Cell Biology, University of Gothenburg;
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46
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Ribonucleotides incorporated by the yeast mitochondrial DNA polymerase are not repaired. Proc Natl Acad Sci U S A 2017; 114:12466-12471. [PMID: 29109257 DOI: 10.1073/pnas.1713085114] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Incorporation of ribonucleotides into DNA during genome replication is a significant source of genomic instability. The frequency of ribonucleotides in DNA is determined by deoxyribonucleoside triphosphate/ribonucleoside triphosphate (dNTP/rNTP) ratios, by the ability of DNA polymerases to discriminate against ribonucleotides, and by the capacity of repair mechanisms to remove incorporated ribonucleotides. To simultaneously compare how the nuclear and mitochondrial genomes incorporate and remove ribonucleotides, we challenged these processes by changing the balance of cellular dNTPs. Using a collection of yeast strains with altered dNTP pools, we discovered an inverse relationship between the concentration of individual dNTPs and the amount of the corresponding ribonucleotides incorporated in mitochondrial DNA, while in nuclear DNA the ribonucleotide pattern was only altered in the absence of ribonucleotide excision repair. Our analysis uncovers major differences in ribonucleotide repair between the two genomes and provides concrete evidence that yeast mitochondria lack mechanisms for removal of ribonucleotides incorporated by the mtDNA polymerase. Furthermore, as cytosolic dNTP pool imbalances were transmitted equally well into the nucleus and the mitochondria, our results support a view of the cytosolic and mitochondrial dNTP pools in frequent exchange.
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