1
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He Q, Liu C, Liu Q, Wang L, Song L. CgADAR1 involved in regulating the synthesis of interferon-like protein in Crassostrea gigas. FISH & SHELLFISH IMMUNOLOGY 2024; 150:109620. [PMID: 38740229 DOI: 10.1016/j.fsi.2024.109620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/24/2024] [Accepted: 05/10/2024] [Indexed: 05/16/2024]
Abstract
Adenosine deaminases acting on RNA 1 (ADAR1) is a dsRNA adenosine (A)-to-inosine (I) editing enzyme that regulates the innate immune response against virus invasion. In the present study, a novel CgADAR1 was identified from the oyster Crassostrea gigas. The open reading frame (ORF) of CgADAR1 was of 3444 bp encoding a peptide of 1147 amino acid residues with two Zα domains, one dsRNA binding motif (DSRM) and one RNA adenosine deaminase domain (ADEAMc). The mRNA transcripts of CgADAR1 were detected in all the examined tissues, with higher expression levels in mantle and gill, which were 7.11-fold and 4.90-fold (p < 0.05) of that in labial palp, respectively. The mRNA transcripts of CgADAR1 in haemocytes were significantly induced at 24 h and 36 h after Poly (A: U) stimulation, which were 6.03-fold (p < 0.01) and 1.37-fold (p < 0.001) of that in control group, respectively. At 48 h after Poly (A:U) stimulation, the mRNA expression of CgRIG-Ⅰ, CgIRF8 and CgIFNLP significantly increased, which were 4.36-fold (p < 0.001), 1.82-fold (p < 0.05) and 1.92-fold (p < 0.05) of that in control group. After CgADAR1 expression was inhibited by RNA interference (RNAi), the mRNA expression levels of CgMDA5, CgRIG-Ⅰ, CgTBK1, CgIRF8 and CgIFNLP were significantly increased, which were 11.88-fold, 11.51-fold, 2.22-fold, 2.85-fold and 2.52-fold of that in control group (p < 0.001), and the phosphorylation level of CgTBK1 was also significantly increased. These results suggested that CgADAR1 played a regulation role in the early stages of viral infection by inhibiting the synthesis of interferon-like protein.
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Affiliation(s)
- Qianqian He
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Chang Liu
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China.
| | - Qian Liu
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Lingling Wang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Southern Laboratory of Ocean Science and Engineering, Guangdong, Zhuhai, 519000, China
| | - Linsheng Song
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Southern Laboratory of Ocean Science and Engineering, Guangdong, Zhuhai, 519000, China.
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2
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Roy A, Ghosh A. Epigenetic Restriction Factors (eRFs) in Virus Infection. Viruses 2024; 16:183. [PMID: 38399958 PMCID: PMC10892949 DOI: 10.3390/v16020183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
The ongoing arms race between viruses and their hosts is constantly evolving. One of the ways in which cells defend themselves against invading viruses is by using restriction factors (RFs), which are cell-intrinsic antiviral mechanisms that block viral replication and transcription. Recent research has identified a specific group of RFs that belong to the cellular epigenetic machinery and are able to restrict the gene expression of certain viruses. These RFs can be referred to as epigenetic restriction factors or eRFs. In this review, eRFs have been classified into two categories. The first category includes eRFs that target viral chromatin. So far, the identified eRFs in this category include the PML-NBs, the KRAB/KAP1 complex, IFI16, and the HUSH complex. The second category includes eRFs that target viral RNA or, more specifically, the viral epitranscriptome. These epitranscriptomic eRFs have been further classified into two types: those that edit RNA bases-adenosine deaminase acting on RNA (ADAR) and pseudouridine synthases (PUS), and those that covalently modify viral RNA-the N6-methyladenosine (m6A) writers, readers, and erasers. We delve into the molecular machinery of eRFs, their role in limiting various viruses, and the mechanisms by which viruses have evolved to counteract them. We also examine the crosstalk between different eRFs, including the common effectors that connect them. Finally, we explore the potential for new discoveries in the realm of epigenetic networks that restrict viral gene expression, as well as the future research directions in this area.
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Affiliation(s)
- Arunava Roy
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA;
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3
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Singh K, Mehta D, Dumka S, Chauhan AS, Kumar S. Quasispecies Nature of RNA Viruses: Lessons from the Past. Vaccines (Basel) 2023; 11:vaccines11020308. [PMID: 36851186 PMCID: PMC9963406 DOI: 10.3390/vaccines11020308] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/22/2023] [Accepted: 01/23/2023] [Indexed: 01/31/2023] Open
Abstract
Viral quasispecies are distinct but closely related mutants formed by the disparity in viral genomes due to recombination, mutations, competition, and selection pressure. Theoretical derivation for the origin of a quasispecies is owed to the error-prone replication by polymerase and mutants of RNA replicators. Here, we briefly addressed the theoretical and mathematical origin of quasispecies and their dynamics. The impact of quasispecies for major salient human pathogens is reviewed. In the current global scenario, rapid changes in geographical landscapes favor the origin and selection of mutants. It comes as no surprise that a cauldron of mutants poses a significant risk to public health, capable of causing pandemics. Mutation rates in RNA viruses are magnitudes higher than in DNA organisms, explaining their enhanced virulence and evolvability. RNA viruses cause the most devastating pandemics; for example, members of the Orthomyxoviridae family caused the great influenza pandemic (1918 flu or Spanish flu), the SARS (severe acute respiratory syndrome) and MERS (Middle East respiratory syndrome) outbreak, and the human immunodeficiency viruses (HIV), lentiviruses of the Retroviridae family, caused worldwide devastation. Rapidly evolving RNA virus populations are a daunting challenge for the designing of effective control measures like vaccines. Developing awareness of the evolutionary dispositions of RNA viral mutant spectra and what influences their adaptation and virulence will help curtail outbreaks of past and future pathogens.
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4
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Chen P, Zhu J, Yu J, Liu R, Lao M, Yu L, Gao F, Jiang Y, Liu C, Tong W, Liu H, Tong G, Zhou Y. Porcine epidemic diarrhea virus strain FJzz1 infection induces type I/III IFNs production through RLRs and TLRs-mediated signaling. Front Immunol 2022; 13:984448. [PMID: 35958569 PMCID: PMC9357978 DOI: 10.3389/fimmu.2022.984448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 07/06/2022] [Indexed: 11/13/2022] Open
Abstract
Interferons (IFNs) including type I/III IFNs are the major components of the host innate immune response against porcine epidemic diarrhea virus (PEDV) infection, and several viral proteins have been identified to antagonize type I/III IFNs productions through diverse strategies. However, the modulation of PEDV infection upon the activation of the host’s innate immune response has not been fully characterized. In this study, we observed that various IFN-stimulated genes (ISGs) were upregulated significantly in a time- and dose-dependent manner in LLC-PK1 cells infected with the PEDV G2 strain FJzz1. The transcriptions of IRF9 and STAT1 were increased markedly in the late stage of FJzz1 infection and the promotion of the phosphorylation and nuclear translocation of STAT1, implicating the activation of the JAK-STAT signaling pathway during FJzz1 infection. In addition, abundant type I/III IFNs were produced after FJzz1 infection. However, type I/III IFNs and ISGs decreased greatly in FJzz1-infected LLC-PK1 cells following the silencing of the RIG-I-like receptors (RLRs), including RIG-I and MDA5, and the Toll-like receptors (TLRs) adaptors, MyD88 and TRIF. Altogether, FJzz1 infection induces the production of type-I/III IFNs in LLC-PK1 cells, in which RLRs and TLRs signaling pathways are involved, followed by the activation of the JAK-STAT signaling cascade, triggering the production of numerous ISGs to exert antiviral effects of innate immunity.
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Affiliation(s)
- Pengfei Chen
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Institute of Animal Husbandry and Veterinary, Shanghai Academy of Agricultural Science, Shanghai, China
| | - Junrui Zhu
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Jiarong Yu
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Ruilin Liu
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Mengqin Lao
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Lingxue Yu
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Fei Gao
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yifeng Jiang
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Changlong Liu
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Wu Tong
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Huili Liu
- Institute of Animal Husbandry and Veterinary, Shanghai Academy of Agricultural Science, Shanghai, China
| | - Guangzhi Tong
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- *Correspondence: Guangzhi Tong, ; Yanjun Zhou,
| | - Yanjun Zhou
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- *Correspondence: Guangzhi Tong, ; Yanjun Zhou,
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5
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Piontkivska H, Wales-McGrath B, Miyamoto M, Wayne ML. ADAR Editing in Viruses: An Evolutionary Force to Reckon with. Genome Biol Evol 2021; 13:evab240. [PMID: 34694399 PMCID: PMC8586724 DOI: 10.1093/gbe/evab240] [Citation(s) in RCA: 4] [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] [Accepted: 10/21/2021] [Indexed: 02/06/2023] Open
Abstract
Adenosine Deaminases that Act on RNA (ADARs) are RNA editing enzymes that play a dynamic and nuanced role in regulating transcriptome and proteome diversity. This editing can be highly selective, affecting a specific site within a transcript, or nonselective, resulting in hyperediting. ADAR editing is important for regulating neural functions and autoimmunity, and has a key role in the innate immune response to viral infections, where editing can have a range of pro- or antiviral effects and can contribute to viral evolution. Here we examine the role of ADAR editing across a broad range of viral groups. We propose that the effect of ADAR editing on viral replication, whether pro- or antiviral, is better viewed as an axis rather than a binary, and that the specific position of a given virus on this axis is highly dependent on virus- and host-specific factors, and can change over the course of infection. However, more research needs to be devoted to understanding these dynamic factors and how they affect virus-ADAR interactions and viral evolution. Another area that warrants significant attention is the effect of virus-ADAR interactions on host-ADAR interactions, particularly in light of the crucial role of ADAR in regulating neural functions. Answering these questions will be essential to developing our understanding of the relationship between ADAR editing and viral infection. In turn, this will further our understanding of the effects of viruses such as SARS-CoV-2, as well as many others, and thereby influence our approach to treating these deadly diseases.
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Affiliation(s)
- Helen Piontkivska
- Department of Biological Sciences, Kent State University, Ohio, USA
- School of Biomedical Sciences, Kent State University, Ohio, USA
- Brain Health Research Institute, Kent State University, Ohio, USA
| | | | - Michael Miyamoto
- Department of Biology, University of Florida, Gainesville, Florida, USA
| | - Marta L Wayne
- Department of Biology, University of Florida, Gainesville, Florida, USA
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6
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Abstract
C6 deamination of adenosine (A) to inosine (I) in double-stranded RNA (dsRNA) is catalyzed by a family of enzymes known as ADARs (adenosine deaminases acting on RNA) encoded by three genes in mammals. Alternative promoters and splicing produce two ADAR1 proteins, an interferon-inducible cytoplasmic p150 and a constitutively expressed p110 that like ADAR2 is a nuclear enzyme. ADAR3 lacks deaminase activity. A-to-I editing occurs with both viral and cellular RNAs. Deamination activity is dependent on dsRNA substrate structure and regulatory RNA-binding proteins and ranges from highly site selective with hepatitis D RNA and glutamate receptor precursor messenger RNA (pre-mRNA) to hyperediting of measles virus and polyomavirus transcripts and cellular inverted Alu elements. Because I base-pairs as guanosine instead of A, editing can alter mRNA decoding, pre-mRNA splicing, and microRNA silencing. Editing also alters dsRNA structure, thereby suppressing innate immune responses including interferon production and action. Expected final online publication date for the Annual Review of Virology, Volume 8 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Christian K Pfaller
- Division of Veterinary Medicine, Paul-Ehrlich-Institute, Langen 63225, Germany
| | - Cyril X George
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California 93106, USA;
| | - Charles E Samuel
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California 93106, USA;
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7
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Asthana V, Stern BS, Tang Y, Bugga P, Li A, Ferguson A, Asthana A, Bao G, Drezek RA. Development of a Novel Class of Self-Assembling dsRNA Cancer Therapeutics: A Proof-of-Concept Investigation. MOLECULAR THERAPY-ONCOLYTICS 2020; 18:419-431. [PMID: 32913891 PMCID: PMC7452102 DOI: 10.1016/j.omto.2020.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 07/28/2020] [Indexed: 10/26/2022]
Abstract
Cancer has proven to be an extremely difficult challenge to treat. Several fundamental issues currently underlie cancer treatment, including differentiating self from nonself, functional coupling of the recognition and therapeutic components of various therapies, and the propensity of cancerous cells to develop resistance to common treatment modalities via evolutionary pressure. Given these limitations, there is an increasing need to develop an all-encompassing therapeutic that can uniquely target malignant cells, decouple recognition from treatment, and overcome evolutionarily driven cancer resistance. We describe herein a new class of programmable self-assembling double-stranded RNA (dsRNA)-based cancer therapeutics that uniquely targets aberrant genetic sequences and in a functionally decoupled manner, undergoes oncogenic RNA-activated displacement (ORAD), initiating a therapeutic cascade that induces apoptosis and immune activation. As a proof of concept, we show that RNA strands targeting the EWS/Fli1 fusion gene in Ewing sarcoma cells that are end blocked with phosphorothioate bonds and additionally sealed with a 2'-deoxyuridine (2'-U)-modified DNA protector can be used to induce specific and potent killing of cells containing the target oncogenic sequence but not wild type.
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Affiliation(s)
| | - Brett S Stern
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Yuqi Tang
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Pallavi Bugga
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Ang Li
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Adam Ferguson
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Anantratn Asthana
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Gang Bao
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Rebekah A Drezek
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
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8
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Vogel OA, Han J, Liang CY, Manicassamy S, Perez JT, Manicassamy B. The p150 Isoform of ADAR1 Blocks Sustained RLR signaling and Apoptosis during Influenza Virus Infection. PLoS Pathog 2020; 16:e1008842. [PMID: 32898178 PMCID: PMC7500621 DOI: 10.1371/journal.ppat.1008842] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 09/18/2020] [Accepted: 07/28/2020] [Indexed: 12/24/2022] Open
Abstract
Signaling through retinoic acid inducible gene I (RIG-I) like receptors (RLRs) is tightly regulated, with activation occurring upon sensing of viral nucleic acids, and suppression mediated by negative regulators. Under homeostatic conditions aberrant activation of melanoma differentiation-associated protein-5 (MDA5) is prevented through editing of endogenous dsRNA by RNA editing enzyme Adenosine Deaminase Acting on RNA (ADAR1). In addition, ADAR1 is postulated to play pro-viral and antiviral roles during viral infections that are dependent or independent of RNA editing activity. Here, we investigated the importance of ADAR1 isoforms in modulating influenza A virus (IAV) replication and revealed the opposing roles for ADAR1 isoforms, with the nuclear p110 isoform restricting versus the cytoplasmic p150 isoform promoting IAV replication. Importantly, we demonstrate that p150 is critical for preventing sustained RIG-I signaling, as p150 deficient cells showed increased IFN-β expression and apoptosis during IAV infection, independent of RNA editing activity. Taken together, the p150 isoform of ADAR1 is important for preventing sustained RIG-I induced IFN-β expression and apoptosis during viral infection.
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Affiliation(s)
- Olivia A. Vogel
- Department of Microbiology, University of Chicago, Chicago, Illinois, United States of America
| | - Julianna Han
- Department of Microbiology, University of Chicago, Chicago, Illinois, United States of America
| | - Chieh-Yu Liang
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, United States of America
| | - Santhakumar Manicassamy
- Cancer Immunology, Inflammation, and Tolerance Program, GRU Cancer Center, Augusta University, Augusta, Georgia
| | - Jasmine T. Perez
- Department of Microbiology, University of Chicago, Chicago, Illinois, United States of America
| | - Balaji Manicassamy
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, United States of America
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9
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Christofi T, Zaravinos A. RNA editing in the forefront of epitranscriptomics and human health. J Transl Med 2019; 17:319. [PMID: 31547885 PMCID: PMC6757416 DOI: 10.1186/s12967-019-2071-4] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 09/17/2019] [Indexed: 12/21/2022] Open
Abstract
Post-transcriptional modifications have been recently expanded with the addition of RNA editing, which is predominantly mediated by adenosine and cytidine deaminases acting on DNA and RNA. Here, we review the full spectrum of physiological processes in which these modifiers are implicated, among different organisms. Adenosine to inosine (A-to-I) editors, members of the ADAR and ADAT protein families are important regulators of alternative splicing and transcriptional control. On the other hand, cytidine to uridine (C-to-U) editors, members of the AID/APOBEC family, are heavily implicated in innate and adaptive immunity with important roles in antibody diversification and antiviral response. Physiologically, these enzymes are present in the nucleus and/or the cytoplasm, where they modify various RNA molecules, including miRNAs, tRNAs apart from mRNAs, whereas DNA editing is also possible by some of them. The expansion of next generation sequencing technologies provided a wealth of data regarding such modifications. RNA editing has been implicated in various disorders including cancer, and neurological diseases of the brain or the central nervous system. It is also related to cancer heterogeneity and the onset of carcinogenesis. Response to treatment can also be affected by the RNA editing status where drug efficacy is significantly compromised. Studying RNA editing events can pave the way to the identification of new disease biomarkers, and provide a more personalised therapy to various diseases.
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Affiliation(s)
- Theodoulakis Christofi
- Department of Life Sciences, School of Sciences, European University Cyprus, 2404, Nicosia, Cyprus
| | - Apostolos Zaravinos
- Department of Life Sciences, School of Sciences, European University Cyprus, 2404, Nicosia, Cyprus. .,Centre for Risk and Decision Sciences (CERIDES), 2404, Nicosia, Cyprus.
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10
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Mussil B, Suspène R, Caval V, Durandy A, Wain-Hobson S, Vartanian JP. Genotoxic stress increases cytoplasmic mitochondrial DNA editing by human APOBEC3 mutator enzymes at a single cell level. Sci Rep 2019; 9:3109. [PMID: 30816165 PMCID: PMC6395610 DOI: 10.1038/s41598-019-39245-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 11/23/2018] [Indexed: 01/23/2023] Open
Abstract
Human cells are stressed by numerous mechanisms that can lead to leakage of mitochondrial DNA (mtDNA) to the cytoplasm and ultimately apoptosis. This agonist DNA constitutes a danger to the cell and is counteracted by cytoplasmic DNases and APOBEC3 cytidine deamination of DNA. To investigate APOBEC3 editing of leaked mtDNA to the cytoplasm, we performed a PCR analysis of APOBEC3 edited cytoplasmic mtDNA (cymtDNA) at the single cell level for primary CD4+ T cells and the established P2 EBV blast cell line. Up to 17% of primary CD4+ T cells showed signs of APOBEC3 edited cymtDNA with ~50% of all mtDNA sequences showing signs of APOBEC3 editing - between 1500-5000 molecules. Although the P2 cell line showed a much lower frequency of stressed cells, the number of edited mtDNA molecules in such cells was of the same order. Addition of the genotoxic molecules, etoposide or actinomycin D increased the number of cells showing APOBEC3 edited cymtDNA to around 40%. These findings reveal a very dynamic image of the mitochondrial network, which changes considerably under stress. APOBEC3 deaminases are involved in the catabolism of mitochondrial DNA to circumvent chronic immune stimulation triggered by released mitochondrial DNA from damaged cells.
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Affiliation(s)
- Bianka Mussil
- Molecular Retrovirology Unit, Institut Pasteur, CNRS, UMR 3569, 28 rue du Dr. Roux, F-75724, Paris cedex 15, France
- Unit of Infection Models, German Primate Centre, Kellnerweg 4, D-37077, Goettingen, Germany
| | - Rodolphe Suspène
- Molecular Retrovirology Unit, Institut Pasteur, CNRS, UMR 3569, 28 rue du Dr. Roux, F-75724, Paris cedex 15, France
| | - Vincent Caval
- Molecular Retrovirology Unit, Institut Pasteur, CNRS, UMR 3569, 28 rue du Dr. Roux, F-75724, Paris cedex 15, France
| | - Anne Durandy
- INSERM UMR 1163, The Human Lymphohematopoiesis Laboratory, Institut Imagine, 24 boulevard du Montparnasse, F-75015, Paris, France
| | - Simon Wain-Hobson
- Molecular Retrovirology Unit, Institut Pasteur, CNRS, UMR 3569, 28 rue du Dr. Roux, F-75724, Paris cedex 15, France
| | - Jean-Pierre Vartanian
- Molecular Retrovirology Unit, Institut Pasteur, CNRS, UMR 3569, 28 rue du Dr. Roux, F-75724, Paris cedex 15, France.
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11
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Dolan PT, Whitfield ZJ, Andino R. Mechanisms and Concepts in RNA Virus Population Dynamics and Evolution. Annu Rev Virol 2018; 5:69-92. [PMID: 30048219 DOI: 10.1146/annurev-virology-101416-041718] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
RNA viruses are unique in their evolutionary capacity, exhibiting high mutation rates and frequent recombination. They rapidly adapt to environmental changes, such as shifts in immune pressure or pharmacological challenge. The evolution of RNA viruses has been brought into new focus with the recent developments of genetic and experimental tools to explore and manipulate the evolutionary dynamics of viral populations. These studies have uncovered new mechanisms that enable viruses to overcome evolutionary challenges in the environment and have emphasized the intimate relationship of viral populations with evolution. Here, we review some of the emerging viral and host mechanisms that underlie the evolution of RNA viruses. We also discuss new studies that demonstrate that the relationship between evolutionary dynamics and virus biology spans many spatial and temporal scales, affecting transmission dynamics within and between hosts as well as pathogenesis.
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Affiliation(s)
- Patrick T Dolan
- Department of Biology, Stanford University, Stanford, California 94305, USA.,Department of Microbiology and Immunology, University of California, San Francisco, California 94143, USA;
| | - Zachary J Whitfield
- Department of Microbiology and Immunology, University of California, San Francisco, California 94143, USA;
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, California 94143, USA;
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12
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Mauger F, How-Kit A, Tost J. COLD-PCR Technologies in the Area of Personalized Medicine: Methodology and Applications. Mol Diagn Ther 2018; 21:269-283. [PMID: 28101802 DOI: 10.1007/s40291-016-0254-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Somatic mutations bear great promise for use as biomarkers for personalized medicine, but are often present only in low abundance in biological material and are therefore difficult to detect. Many assays for mutation analysis in cancer-related genes (hotspots) have been developed to improve diagnosis, prognosis, prediction of drug resistance, and monitoring of the response to treatment. Two major approaches have been developed: mutation-specific amplification methods and methods that enrich and detect mutations without prior knowledge on the exact location and identity of the mutation. CO-amplification at Lower Denaturation temperature Polymerase Chain Reaction (COLD-PCR) methods such as full-, fast-, ice- (improved and complete enrichment), enhanced-ice, and temperature-tolerant COLD-PCR make use of a critical temperature in the polymerase chain reaction to selectively denature wild-type-mutant heteroduplexes, allowing the enrichment of rare mutations. Mutations can subsequently be identified using a variety of laboratory technologies such as high-resolution melting, digital polymerase chain reaction, pyrosequencing, Sanger sequencing, or next-generation sequencing. COLD-PCR methods are sensitive, specific, and accurate if appropriately optimized and have a short time to results. A large variety of clinical samples (tumor DNA, circulating cell-free DNA, circulating cell-free fetal DNA, and circulating tumor cells) have been studied using COLD-PCR in many different applications including the detection of genetic changes in cancer and infectious diseases, non-invasive prenatal diagnosis, detection of microorganisms, or DNA methylation analysis. In this review, we describe in detail the different COLD-PCR approaches, highlighting their specificities, advantages, and inconveniences and demonstrating their use in different fields of biological and biomedical research.
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Affiliation(s)
- Florence Mauger
- Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-Institut de Génomique, Batiment G2, 2 rue Gaston Crémieux, 91000, Evry, France
| | - Alexandre How-Kit
- Laboratory for Genomics, Fondation Jean Dausset-CEPH, 75010, Paris, France
| | - Jörg Tost
- Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-Institut de Génomique, Batiment G2, 2 rue Gaston Crémieux, 91000, Evry, France.
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13
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Sanjuán R, Domingo-Calap P. Mechanisms of viral mutation. Cell Mol Life Sci 2016; 73:4433-4448. [PMID: 27392606 PMCID: PMC5075021 DOI: 10.1007/s00018-016-2299-6] [Citation(s) in RCA: 488] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 06/20/2016] [Accepted: 06/22/2016] [Indexed: 02/08/2023]
Abstract
The remarkable capacity of some viruses to adapt to new hosts and environments is highly dependent on their ability to generate de novo diversity in a short period of time. Rates of spontaneous mutation vary amply among viruses. RNA viruses mutate faster than DNA viruses, single-stranded viruses mutate faster than double-strand virus, and genome size appears to correlate negatively with mutation rate. Viral mutation rates are modulated at different levels, including polymerase fidelity, sequence context, template secondary structure, cellular microenvironment, replication mechanisms, proofreading, and access to post-replicative repair. Additionally, massive numbers of mutations can be introduced by some virus-encoded diversity-generating elements, as well as by host-encoded cytidine/adenine deaminases. Our current knowledge of viral mutation rates indicates that viral genetic diversity is determined by multiple virus- and host-dependent processes, and that viral mutation rates can evolve in response to specific selective pressures.
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Affiliation(s)
- Rafael Sanjuán
- Department of Genetics and Institute for Integrative Systems Biology (I2SysBio), Universitat de València, C/Catedrático José Beltrán 2, 46980, Paterna, Valencia, Spain.
| | - Pilar Domingo-Calap
- Laboratoire d'ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx Transplantex, Centre de Recherche d'Immunologie et d'Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Fédération Hospitalo-Universitaire OMICARE, Centre de Recherche d'Immunologie et d'Hématologie, Strasbourg, France
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14
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Tang YD, Zhang X, Na L, Wang XF, Fu LH, Zhu CH, Wang X, Zhou JH. Double-stranded-RNA-specific adenosine deaminase 1 (ADAR1) is proposed to contribute to the adaptation of equine infectious anemia virus from horses to donkeys. Arch Virol 2016; 161:2667-72. [PMID: 27383210 DOI: 10.1007/s00705-016-2951-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 06/25/2016] [Indexed: 12/14/2022]
Abstract
Equine infectious anemia virus (EIAV) is a member of the genus Lentivirus of the family Retroviridae. Horses are the most susceptible equids to EIAV infection and are therefore the primary hosts of this virus. In contrast, infected donkeys do not develop clinically active equine infectious anemia (EIA). This phenomenon is similar to what has been observed with HIV-1, which fails to induce AIDS in non-human primates. Interestingly, Shen et al. developed a donkey-tropic pathogenic virus strain (EIAVDV117, DV117) by serially passaging a horse-tropic pathogenic strain, EIAVLN40 (LN40), in donkeys. LN40, which was generated by passaging a field isolate in horses, displayed enhanced virulence in horses but caused no clinical symptoms in donkeys. Infection with DV117 induced acute EIA in nearly 100 % of donkeys. Genomic analysis of DV117 revealed a significantly higher frequency of A-to-G substitutions when compared to LN40. Furthermore, detailed analysis of dinucleotide editing showed that A-to-G mutations had a preference for 5'TpA and 5'ApA. These results strongly implicated the activity of the adenosine deaminase, ADAR1, in this type of mutation. Further investigation demonstrated that overexpression of donkey ADAR1 increased A-to-G mutations within the genome of EIAV. Together with our previous finding that multiple mutations in multiple genes are generated in DV117 during its adaptation from horses to donkeys, the present study suggests that ADAR1-induced A-to-G mutations occur during virus adaption to related new hosts contributing to the alteration of EIAV host tropism.
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Affiliation(s)
- Yan-Dong Tang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, China
| | - Xiang Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, China
| | - Lei Na
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, China
| | - Xue-Feng Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, China
| | - Li-Hua Fu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, China
| | - Chun-Hui Zhu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, China.,Reproductive Medicine Center, Subei People's Hospital of Jiangsu Province (Clinic Medical College of Yang Zhou University), Yangzhou, 225001, China
| | - Xiaojun Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, China.
| | - Jian-Hua Zhou
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, China. .,Harbin Pharmaceutical Group Biovaccine Company, Harbin, 150069, China.
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15
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Cuevas JM, Combe M, Torres-Puente M, Garijo R, Guix S, Buesa J, Rodríguez-Díaz J, Sanjuán R. Human norovirus hyper-mutation revealed by ultra-deep sequencing. INFECTION GENETICS AND EVOLUTION 2016; 41:233-239. [PMID: 27094861 PMCID: PMC7172324 DOI: 10.1016/j.meegid.2016.04.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 04/11/2016] [Accepted: 04/15/2016] [Indexed: 02/02/2023]
Abstract
Human noroviruses (NoVs) are a major cause of gastroenteritis worldwide. It is thought that, similar to other RNA viruses, high mutation rates allow NoVs to evolve fast and to undergo rapid immune escape at the population level. However, the rate and spectrum of spontaneous mutations of human NoVs have not been quantified previously. Here, we analyzed the intra-patient diversity of the NoV capsid by carrying out RT-PCR and ultra-deep sequencing with 100,000-fold coverage of 16 stool samples from symptomatic patients. This revealed the presence of low-frequency sequences carrying large numbers of U-to-C or A-to-G base transitions, suggesting a role for hyper-mutation in NoV diversity. To more directly test for hyper-mutation, we performed transfection assays in which the production of mutations was restricted to a single cell infection cycle. This confirmed the presence of sequences with multiple U-to-C/A-to-G transitions, and suggested that hyper-mutation contributed a large fraction of the total NoV spontaneous mutation rate. The type of changes produced and their sequence context are compatible with ADAR-mediated editing of the viral RNA. Norovirus U-to-C hyper-mutants are present in patient samples. Analysis of hyper-mutants in cell culture suggests ADAR-mediated RNA edition. Hyper-mutation may contribute to norovirus diversity and evolution.
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Affiliation(s)
- José M Cuevas
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, Valencia, Spain
| | - Marine Combe
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, Valencia, Spain
| | - Manoli Torres-Puente
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana, Valencia, Spain
| | - Raquel Garijo
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, Valencia, Spain
| | - Susana Guix
- Departament de Microbiologia, Universitat de Barcelona, Barcelona, Spain
| | - Javier Buesa
- Departament de Microbiologia, Universitat de València, Valencia, Spain
| | | | - Rafael Sanjuán
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, Valencia, Spain; Departament de Genètica, Universitat de València, Valencia, Spain.
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16
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Cuevas JM, Geller R, Garijo R, López-Aldeguer J, Sanjuán R. Extremely High Mutation Rate of HIV-1 In Vivo. PLoS Biol 2015; 13:e1002251. [PMID: 26375597 PMCID: PMC4574155 DOI: 10.1371/journal.pbio.1002251] [Citation(s) in RCA: 233] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 08/10/2015] [Indexed: 11/18/2022] Open
Abstract
Rates of spontaneous mutation critically determine the genetic diversity and evolution of RNA viruses. Although these rates have been characterized in vitro and in cell culture models, they have seldom been determined in vivo for human viruses. Here, we use the intrapatient frequency of premature stop codons to quantify the HIV-1 genome-wide rate of spontaneous mutation in DNA sequences from peripheral blood mononuclear cells. This reveals an extremely high mutation rate of (4.1 ± 1.7) × 10−3 per base per cell, the highest reported for any biological entity. Sequencing of plasma-derived sequences yielded a mutation frequency 44 times lower, indicating that a large fraction of viral genomes are lethally mutated and fail to reach plasma. We show that the HIV-1 reverse transcriptase contributes only 2% of mutations, whereas 98% result from editing by host cytidine deaminases of the A3 family. Hypermutated viral sequences are less abundant in patients showing rapid disease progression compared to normal progressors, highlighting the antiviral role of A3 proteins. However, the amount of A3-mediated editing varies broadly, and we find that low-edited sequences are more abundant among rapid progressors, suggesting that suboptimal A3 activity might enhance HIV-1 genetic diversity and pathogenesis. The rate of spontaneous mutation of the HIV-1 genome within its human host is exceptionally high, is mostly driven by host cytidine deaminases, and probably plays a role in disease progression. The high levels of genetic diversity of the HIV-1 virus grant it the ability to escape the immune system, to rapidly evolve drug resistance, and to circumvent vaccination strategies. However, our knowledge of HIV-1 mutation rates has been largely restricted to in vitro and cell culture studies because of the inherent complexity of measuring these rates in vivo. Here, by analyzing the frequency of premature stop codons, we show that the HIV-1 mutation rate in vivo is two orders of magnitude higher than that predicted by in vitro studies, making it the highest reported mutation rate for any biological system. A large component of this rate is from host cellular cytidine deaminases, which induce mutations in the viral DNA as a defense mechanism. While the HIV-1 genome is hypermutated in blood cells, only a very small fraction of these mutations reach the plasma, indicating that many viruses are defective as a result of the extremely high mutation load. In addition, we find that the HIV-1 mutation rate tends to be higher in patients showing normal disease progression than in those undergoing rapid progression, emphasizing the negative impact on viral fitness of hypermutation by host cytidine deaminases. However, we also observe subpopulations of weakly-mutated viral genomes whose sequence diversity may influence viral pathogenesis. Our work highlights the fine balance for HIV-1 between enough mutation to evade host responses and too much mutation that can inactivate the virus.
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Affiliation(s)
- José M. Cuevas
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Valencia, Spain
| | - Ron Geller
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Valencia, Spain
| | - Raquel Garijo
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Valencia, Spain
| | - José López-Aldeguer
- Hospital Universitario La Fe, Valencia, Spain
- CoRIS and HIV Biobank, Spanish AIDS Research Network, Spain
| | - Rafael Sanjuán
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Valencia, Spain
- Departament de Genètica, Universitat de València, Valencia, Spain
- * E-mail:
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17
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Castellanos-Rizaldos E, Richardson K, Lin R, Wu G, Makrigiorgos MG. Single-tube, highly parallel mutation enrichment in cancer gene panels by use of temperature-tolerant COLD-PCR. Clin Chem 2015; 61:267-77. [PMID: 25297854 PMCID: PMC4281501 DOI: 10.1373/clinchem.2014.228361] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
BACKGROUND Multiplexed detection of low-level mutations presents a technical challenge for many technologies, including cancer gene panels used for targeted-resequencing. Analysis of mutations below approximately 2%-5% abundance in tumors with heterogeneity, samples with stromal contamination, or biofluids is problematic owing to increased noise from sequencing errors. Technologies that reduce noise via deep sequencing unavoidably reduce throughput and increase cost. Here we provide proof of principle that coamplification at lower denaturation temperature (COLD)-PCR technology enables multiplex low-level mutation detection in cancer gene panels while retaining throughput. METHODS We have developed a multiplex temperature-tolerant COLD-PCR (fast-TT-COLD-PCR) approach that uses cancer gene panels developed for massively parallel sequencing. After multiplex preamplification from genomic DNA, we attach tails to all amplicons and perform fast-TT-COLD-PCR. This approach gradually increases denaturation temperatures in a step-wise fashion, such that all possible denaturation temperatures are encompassed. By introducing modified nucleotides, fast-COLD-PCR is adapted to enrich for melting temperature (Tm)-increasing mutations over all amplicons, in a single tube. Therefore, in separate reactions, both Tm-decreasing and Tm-increasing mutations are enriched. RESULTS Using custom-made and commercial gene panels containing 8, 50, 190, or 16 000 amplicons, we demonstrate that fast-TT-COLD-PCR enriches mutations on all examined targets simultaneously. Incorporation of deoxyinosine triphosphate (dITP)/2,6-diaminopurine triphosphate (dDTP) in place of deoxyguanosine triphosphate (dGTP)/deoxyadenosine triphosphate (dATP) enables enrichment of Tm-increasing mutations. Serial dilution experiments demonstrate a limit of detection of approximately 0.01%-0.1% mutation abundance by use of Ion-Torrent and 0.1%-0.3% by use of Sanger sequencing. CONCLUSIONS Fast-TT-COLD-PCR improves the limit of detection of cancer gene panels by enabling mutation enrichment in multiplex, single-tube reactions. This novel adaptation of COLD-PCR converts subclonal mutations to clonal, thereby facilitating detection and subsequent mutation sequencing.
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Affiliation(s)
| | | | - Rui Lin
- Transgenomic Inc., Omaha, NE
| | | | - Mike G Makrigiorgos
- Division of DNA Repair and Genome Stability and Division of Medical Physics and Biophysics, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA;
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18
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Liu Y, Ma T, Liu J, Zhao X, Cheng Z, Guo H, Xu R, Wang S. Circulating type 1 vaccine-derived poliovirus may evolve under the pressure of adenosine deaminases acting on RNA. J Matern Fetal Neonatal Med 2014; 28:2096-9. [PMID: 25330844 DOI: 10.3109/14767058.2014.979147] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Poliovirus, the causative agent of poliomyelitis, is a human enterovirus and member of the Picornaviridae family. An effective live-attenuated poliovirus vaccine strain (Sabin 1) has been developed and has protected humans from polio. However, a few cases of vaccine virulence reversion have been documented in several countries. For instance, circulating type 1 vaccine-derived poliovirus is a highly pathogenic poliovirus that evolved from an avirulent strain, but the mechanism by which vaccine strains undergo reversion remains unclear. In this study, vaccine strains exhibited A to G/U to C and G to A/C to U hypermutations in the reversed evolution of Sabin 1. Furthermore, the mutation ratios of U to C and C to U were higher than those of other mutation types. Dinucleotide editing context was then analyzed. Results showed that A to G and U to C mutations exhibited preferences similar to adenosine deaminases acting on RNA (ADAR). Hence, ADARs may participate in poliovirus vaccine evolution.
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Affiliation(s)
- Yanhan Liu
- a College of Veterinary Medicine, Research Center for Animal Disease Control Engineering Shandong Province , Shandong Agricultural University , Tai`an , China
| | - Tengfei Ma
- a College of Veterinary Medicine, Research Center for Animal Disease Control Engineering Shandong Province , Shandong Agricultural University , Tai`an , China
| | - Jianzhu Liu
- a College of Veterinary Medicine, Research Center for Animal Disease Control Engineering Shandong Province , Shandong Agricultural University , Tai`an , China
| | - Xiaona Zhao
- a College of Veterinary Medicine, Research Center for Animal Disease Control Engineering Shandong Province , Shandong Agricultural University , Tai`an , China
| | - Ziqiang Cheng
- a College of Veterinary Medicine, Research Center for Animal Disease Control Engineering Shandong Province , Shandong Agricultural University , Tai`an , China
| | - Huijun Guo
- a College of Veterinary Medicine, Research Center for Animal Disease Control Engineering Shandong Province , Shandong Agricultural University , Tai`an , China
| | - Ruixue Xu
- a College of Veterinary Medicine, Research Center for Animal Disease Control Engineering Shandong Province , Shandong Agricultural University , Tai`an , China
| | - Shujing Wang
- a College of Veterinary Medicine, Research Center for Animal Disease Control Engineering Shandong Province , Shandong Agricultural University , Tai`an , China
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19
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Cachat A, Alais S, Chevalier SA, Journo C, Fusil F, Dutartre H, Boniface A, Ko NL, Gessain A, Cosset FL, Suspène R, Vartanian JP, Mahieux R. ADAR1 enhances HTLV-1 and HTLV-2 replication through inhibition of PKR activity. Retrovirology 2014; 11:93. [PMID: 25389016 PMCID: PMC4245799 DOI: 10.1186/s12977-014-0093-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 10/16/2014] [Indexed: 11/25/2022] Open
Abstract
Background The role of innate immunity in general and of type I interferon
(IFN-I) in particular in HTLV-1 pathogenesis is still a matter of debate.
ADAR1-p150 is an Interferon Stimulated Gene (ISG) induced by IFN-I that can edit
viral RNAs. We therefore investigated whether it could play the role of an
anti-HTLV factor. Results We demonstrate here that ADAR1 is also expressed in the absence of
IFN stimulation in activated primary T-lymphocytes that are the natural target of
this virus and in HTLV-1 or HTLV-2 chronically infected T-cells. ADAR1 expression
is also increased in primary lymphocytes obtained from HTLV-1 infected
individuals. We show that ADAR1 enhances HTLV-1 and HTLV-2 infection in
T-lymphocytes and that this proviral effect is independent from its editing
activity. ADAR1 expression suppresses IFN-α inhibitory effect on HTLV-1 and HTLV-2
and acts through the repression of PKR phosphorylation. Discussion This study demonstrates that two interferon stimulated genes, i.e.
PKR and ADAR1 have opposite effects on HTLV replication in
vivo. The balanced expression of those proteins could determine the
fate of the viral cycle in the course of infection. Electronic supplementary material The online version of this article (doi:10.1186/s12977-014-0093-9) contains supplementary material, which is available to authorized
users.
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Affiliation(s)
- Anne Cachat
- Equipe Oncogenèse Rétrovirale, Lyon, Cedex 07, France. .,Equipe labellisée "Ligue Nationale Contre le Cancer", Lyon, Cedex 07, France. .,Centre international de recherche en infectiologie, INSERM U1111 - CNRS UMR5308, Lyon, Cedex 07, France. .,Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364, Lyon, Cedex 07, France. .,Université Lyon 1, LabEx ECOFECT - Eco-evolutionary dynamics of infectious diseases, 69364, Lyon, Cedex 07, France.
| | - Sandrine Alais
- Equipe Oncogenèse Rétrovirale, Lyon, Cedex 07, France. .,Equipe labellisée "Ligue Nationale Contre le Cancer", Lyon, Cedex 07, France. .,Centre international de recherche en infectiologie, INSERM U1111 - CNRS UMR5308, Lyon, Cedex 07, France. .,Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364, Lyon, Cedex 07, France. .,Université Lyon 1, LabEx ECOFECT - Eco-evolutionary dynamics of infectious diseases, 69364, Lyon, Cedex 07, France.
| | - Sébastien Alain Chevalier
- Equipe Oncogenèse Rétrovirale, Lyon, Cedex 07, France. .,Equipe labellisée "Ligue Nationale Contre le Cancer", Lyon, Cedex 07, France. .,Centre international de recherche en infectiologie, INSERM U1111 - CNRS UMR5308, Lyon, Cedex 07, France. .,Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364, Lyon, Cedex 07, France. .,Université Lyon 1, LabEx ECOFECT - Eco-evolutionary dynamics of infectious diseases, 69364, Lyon, Cedex 07, France.
| | - Chloé Journo
- Equipe Oncogenèse Rétrovirale, Lyon, Cedex 07, France. .,Equipe labellisée "Ligue Nationale Contre le Cancer", Lyon, Cedex 07, France. .,Centre international de recherche en infectiologie, INSERM U1111 - CNRS UMR5308, Lyon, Cedex 07, France. .,Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364, Lyon, Cedex 07, France. .,Université Lyon 1, LabEx ECOFECT - Eco-evolutionary dynamics of infectious diseases, 69364, Lyon, Cedex 07, France.
| | - Floriane Fusil
- Centre international de recherche en infectiologie, INSERM U1111 - CNRS UMR5308, Lyon, Cedex 07, France. .,Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364, Lyon, Cedex 07, France. .,Université Lyon 1, LabEx ECOFECT - Eco-evolutionary dynamics of infectious diseases, 69364, Lyon, Cedex 07, France. .,Equipe virus enveloppés, Lyon, Cedex 07, France.
| | - Hélène Dutartre
- Equipe Oncogenèse Rétrovirale, Lyon, Cedex 07, France. .,Equipe labellisée "Ligue Nationale Contre le Cancer", Lyon, Cedex 07, France. .,Centre international de recherche en infectiologie, INSERM U1111 - CNRS UMR5308, Lyon, Cedex 07, France. .,Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364, Lyon, Cedex 07, France. .,Université Lyon 1, LabEx ECOFECT - Eco-evolutionary dynamics of infectious diseases, 69364, Lyon, Cedex 07, France.
| | - Adrien Boniface
- Equipe Oncogenèse Rétrovirale, Lyon, Cedex 07, France. .,Equipe labellisée "Ligue Nationale Contre le Cancer", Lyon, Cedex 07, France. .,Centre international de recherche en infectiologie, INSERM U1111 - CNRS UMR5308, Lyon, Cedex 07, France. .,Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364, Lyon, Cedex 07, France. .,Université Lyon 1, LabEx ECOFECT - Eco-evolutionary dynamics of infectious diseases, 69364, Lyon, Cedex 07, France. .,Biology Department, Master Biosciences, Lyon, Cedex 07, France.
| | - Nga Ling Ko
- Unité d'épidémiologie et physiopathoglogie des virus oncogènes, Institut Pasteur, Paris, 75015, France.
| | - Antoine Gessain
- Unité d'épidémiologie et physiopathoglogie des virus oncogènes, Institut Pasteur, Paris, 75015, France.
| | - François-Loïc Cosset
- Centre international de recherche en infectiologie, INSERM U1111 - CNRS UMR5308, Lyon, Cedex 07, France. .,Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364, Lyon, Cedex 07, France. .,Université Lyon 1, LabEx ECOFECT - Eco-evolutionary dynamics of infectious diseases, 69364, Lyon, Cedex 07, France. .,Equipe virus enveloppés, Lyon, Cedex 07, France.
| | - Rodolphe Suspène
- Unité de rétrovirologie moléculaire, Institut Pasteur, Paris, 75015, France.
| | | | - Renaud Mahieux
- Equipe Oncogenèse Rétrovirale, Lyon, Cedex 07, France. .,Equipe labellisée "Ligue Nationale Contre le Cancer", Lyon, Cedex 07, France. .,Centre international de recherche en infectiologie, INSERM U1111 - CNRS UMR5308, Lyon, Cedex 07, France. .,Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364, Lyon, Cedex 07, France. .,Université Lyon 1, LabEx ECOFECT - Eco-evolutionary dynamics of infectious diseases, 69364, Lyon, Cedex 07, France.
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Otani S, Ayata M, Takeuchi K, Takeda M, Shintaku H, Ogura H. Biased hypermutation occurred frequently in a gene inserted into the IC323 recombinant measles virus during its persistence in the brains of nude mice. Virology 2014; 462-463:91-7. [PMID: 24967743 DOI: 10.1016/j.virol.2014.05.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 03/03/2014] [Accepted: 05/19/2014] [Indexed: 01/01/2023]
Abstract
Measles virus (MV) is the causative agent of measles and its neurological complications, subacute sclerosing panencephalitis (SSPE) and measles inclusion body encephalitis (MIBE). Biased hypermutation in the M gene is a characteristic feature of SSPE and MIBE. To determine whether the M gene is the preferred target of hypermutation, an additional transcriptional unit containing a humanized Renilla reniformis green fluorescent protein (hrGFP) gene was introduced into the IC323 MV genome, and nude mice were inoculated intracerebrally with the virus. Biased hypermutation occurred in the M gene and also in the hrGFP gene when it was inserted between the leader and the N gene, but not between the H and L gene. These results indicate that biased hypermutation is usually found in a gene whose function is not essential for viral proliferation in the brain and that the location of a gene in the MV genome can affect its mutational frequency.
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Affiliation(s)
- Sanae Otani
- Department of Virology and Graduate School of Medicine, Osaka City University, 1-4-3 Asahimachi, Abeno-ku, Osaka 545-8585, Japan; Department of Pediatrics, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Minoru Ayata
- Department of Virology and Graduate School of Medicine, Osaka City University, 1-4-3 Asahimachi, Abeno-ku, Osaka 545-8585, Japan.
| | - Kaoru Takeuchi
- Laboratory of Environmental Microbiology, Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Makoto Takeda
- Department of Virology 3, National Institute of Infectious Diseases, Tokyo, Japan
| | - Haruo Shintaku
- Department of Pediatrics, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Hisashi Ogura
- Department of Virology and Graduate School of Medicine, Osaka City University, 1-4-3 Asahimachi, Abeno-ku, Osaka 545-8585, Japan
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21
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MicroRNA editing facilitates immune elimination of HCMV infected cells. PLoS Pathog 2014; 10:e1003963. [PMID: 24586166 PMCID: PMC3937316 DOI: 10.1371/journal.ppat.1003963] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 01/16/2014] [Indexed: 01/05/2023] Open
Abstract
The human cytomegalovirus (HCMV) is extremely prevalent in the human population. Infection by HCMV is life threatening in immune compromised individuals and in immune competent individuals it can cause severe birth defects, developmental retardation and is even associated with tumor development. While numerous mechanisms were developed by HCMV to interfere with immune cell activity, much less is known about cellular mechanisms that operate in response to HCMV infection. Here we demonstrate that in response to HCMV infection, the expression of the short form of the RNA editing enzyme ADAR1 (ADAR1-p110) is induced. We identified the specific promoter region responsible for this induction and we show that ADAR1-p110 can edit miR-376a. Accordingly, we demonstrate that the levels of the edited-miR-376a (miR-376a(e)) increase during HCMV infection. Importantly, we show that miR-376a(e) downregulates the immune modulating molecule HLA-E and that this consequently renders HCMV infected cells susceptible to elimination by NK cells.
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Ko NL, Birlouez E, Wain-Hobson S, Mahieux R, Vartanian JP. Hyperediting of human T-cell leukemia virus type 2 and simian T-cell leukemia virus type 3 by the dsRNA adenosine deaminase ADAR-1. J Gen Virol 2012; 93:2646-2651. [PMID: 22993189 DOI: 10.1099/vir.0.045146-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
RNA editing mediated by adenosine deaminases acting on RNA (ADARs) converts adenosine (A) to inosine (I) residues in dsRNA templates. While ADAR-1-mediated editing was essentially described for RNA viruses, the present work addresses the issue for two δ-retroviruses, human T-cell leukemia virus type 2 and simian T-cell leukemia virus type 3 (HTLV-2 and STLV-3). We examined whether ADAR-1 could edit HTLV-2 and STLV-3 virus genomes in cell culture and in vivo. Using a highly sensitive PCR-based method, referred to as 3DI-PCR, we showed that ADAR-1 could hypermutate adenosine residues in HTLV-2. STLV-3 hypermutation was obtained without using 3DI-PCR, suggesting a higher mutation frequency for this virus. Detailed analysis of the dinucleotide editing context showed preferences for 5' ArA and 5' UrA. In conclusion, the present observations demonstrate that ADAR-1 massively edits HTLV-2 and STLV-3 retroviruses in vitro, but probably remains a rare phenomenon in vivo.
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Affiliation(s)
- Nga Ling Ko
- Epidemiology and Physiopathology of Oncogenic Viruses, Institut Pasteur, CNRS URA 3015, 28 rue du Dr Roux, 75724 Paris cedex 15, France
| | - Emmanuel Birlouez
- Molecular Retrovirology Unit, Institut Pasteur, CNRS URA 3015, 28 rue du Dr Roux, 75724 Paris cedex 15, France
| | - Simon Wain-Hobson
- Molecular Retrovirology Unit, Institut Pasteur, CNRS URA 3015, 28 rue du Dr Roux, 75724 Paris cedex 15, France
| | - Renaud Mahieux
- Retroviral Oncogenesis, U758 Human virology, ENS Lyon, UMS3444/US8 Biosciences Gerland-Lyon Sud, 46 allée d'Italie, 69007 Lyon, France.,Epidemiology and Physiopathology of Oncogenic Viruses, Institut Pasteur, CNRS URA 3015, 28 rue du Dr Roux, 75724 Paris cedex 15, France
| | - Jean-Pierre Vartanian
- Molecular Retrovirology Unit, Institut Pasteur, CNRS URA 3015, 28 rue du Dr Roux, 75724 Paris cedex 15, France
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Abstract
Double-stranded RNA (dsRNA) functions both as a substrate of ADARs and also as a molecular trigger of innate immune responses. ADARs, adenosine deaminases that act on RNA, catalyze the deamination of adenosine (A) to produce inosine (I) in dsRNA. ADARs thereby can destablize RNA structures, because the generated I:U mismatch pairs are less stable than A:U base pairs. Additionally, I is read as G instead of A by ribosomes during translation and by viral RNA-dependent RNA polymerases during RNA replication. Members of several virus families have the capacity to produce dsRNA during viral genome transcription and replication. Sequence changes (A-G, and U-C) characteristic of A-I editing can occur during virus growth and persistence. Foreign viral dsRNA also mediates both the induction and the action of interferons. In this chapter our current understanding of the role and significance of ADARs in the context of innate immunity, and as determinants of the outcome of viral infection, will be considered.
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Affiliation(s)
- Charles E Samuel
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, USA.
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Enhancement of replication of RNA viruses by ADAR1 via RNA editing and inhibition of RNA-activated protein kinase. J Virol 2011; 85:8460-6. [PMID: 21490091 DOI: 10.1128/jvi.00240-11] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Adenosine deaminase acting on RNA 1 (ADAR1) is a double-stranded RNA binding protein and RNA-editing enzyme that modifies cellular and viral RNAs, including coding and noncoding RNAs. This interferon (IFN)-induced protein was expected to have an antiviral role, but recent studies have demonstrated that it promotes the replication of many RNA viruses. The data from these experiments show that ADAR1 directly enhances replication of hepatitis delta virus, human immunodeficiency virus type 1, vesicular stomatitis virus, and measles virus. The proviral activity of ADAR1 occurs through two mechanisms: RNA editing and inhibition of RNA-activated protein kinase (PKR). While these pathways have been found independently, the two mechanisms can act in concert to increase viral replication and contribute to viral pathogenesis. This novel type of proviral regulation by an IFN-induced protein, combined with some antiviral effects of hyperediting, sheds new light on the importance of ADAR1 during viral infection and transforms our overall understanding of the innate immune response.
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Kawai K, Kodera H, Majima T. Photocatalytic formation of I-I bonds using DNA which enables detection of single nucleotide polymorphisms. J Am Chem Soc 2011; 132:14216-20. [PMID: 20860356 DOI: 10.1021/ja105850d] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
By decreasing the HOMO energy gap between the base-pairs to increase the charge conductivity of DNA, the positive charge photochemically generated in DNA can be made to migrate along the π-way of DNA over long distances to form a long-lived charge-separated state. By fine-tuning the kinetics of the charge-transfer reactions, we designed a functionalized DNA system in which absorbed photon energy is converted into chemical energy to form I-I covalent bonds, where more than 100 I(2) molecules were produced per functionalized DNA. Utilizing the fact that charge-transfer kinetics through DNA is sensitive to the presence of a single mismatch that causes the perturbation of the π-stacks, single nucleotide polymorphisms (SNPs) in genomic sequences were detected by measuring the photon energy conversion efficiency in DNA by a conventional starch iodine method.
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Affiliation(s)
- Kiyohiko Kawai
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan.
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Samuel CE. Adenosine deaminases acting on RNA (ADARs) are both antiviral and proviral. Virology 2011; 411:180-93. [PMID: 21211811 DOI: 10.1016/j.virol.2010.12.004] [Citation(s) in RCA: 235] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Accepted: 12/04/2010] [Indexed: 12/18/2022]
Abstract
A-to-I RNA editing, the deamination of adenosine (A) to inosine (I) that occurs in regions of RNA with double-stranded character, is catalyzed by a family of Adenosine Deaminases Acting on RNA (ADARs). In mammals there are three ADAR genes. Two encode proteins that possess demonstrated deaminase activity: ADAR1, which is interferon-inducible, and ADAR2 which is constitutively expressed. ADAR3, by contrast, has not yet been shown to be an active enzyme. The specificity of the ADAR1 and ADAR2 deaminases ranges from highly site-selective to non-selective, dependent on the duplex structure of the substrate RNA. A-to-I editing is a form of nucleotide substitution editing, because I is decoded as guanosine (G) instead of A by ribosomes during translation and by polymerases during RNA-dependent RNA replication. Additionally, A-to-I editing can alter RNA structure stability as I:U mismatches are less stable than A:U base pairs. Both viral and cellular RNAs are edited by ADARs. A-to-I editing is of broad physiologic significance. Among the outcomes of A-to-I editing are biochemical changes that affect how viruses interact with their hosts, changes that can lead to either enhanced or reduced virus growth and persistence depending upon the specific virus.
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Affiliation(s)
- Charles E Samuel
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, USA.
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27
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Bioinformatic Approaches for Identification of A-to-I Editing Sites. Curr Top Microbiol Immunol 2011; 353:145-62. [DOI: 10.1007/82_2011_147] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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28
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Double-stranded RNA adenosine deaminase ADAR-1-induced hypermutated genomes among inactivated seasonal influenza and live attenuated measles virus vaccines. J Virol 2010; 85:2458-62. [PMID: 21159878 DOI: 10.1128/jvi.02138-10] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We sought to examine ADAR-1 editing of measles and influenza virus genomes derived from inactivated seasonal influenza and live attenuated measles virus vaccines grown on chicken cells as the culture substrate. Using highly sensitive 3DI-PCR (R. Suspène et al., Nucleic Acids Res. 36:e72, 2008), it was possible to show that ADAR-1 could hyperdeaminate adenosine residues in both measles virus and influenza virus A genomes. Detailed analysis of the dinucleotide editing context showed preferences for 5'ArA and 5'UrA, which is typical of editing in mammalian cells. The hyperedited mutant frequency, including genomes and antigenomes, was a log greater for influenza virus compared to measles virus, suggesting a greater sensitivity to restriction by ADAR-1.
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Perales C, Lorenzo-Redondo R, López-Galíndez C, Martínez MA, Domingo E. Mutant spectra in virus behavior. Future Virol 2010. [DOI: 10.2217/fvl.10.61] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
RNA viruses replicate as complex mutant spectra, also termed ‘mutant clouds’, known as viral quasispecies. While this is a widely observed viral population structure, it is less known that a number of biologically relevant features of this important group of viral pathogens depend on (or are strongly influenced by) the complexity and composition of mutant spectra. Among them, fitness increase or decrease depending on intrapopulation complementation or interference, selection triggered by memory genomes, pathogenic potential of viruses, disease evolution and the response to antiviral treatments. Quasispecies represent the recognition of complex behavior in viruses, and it is an oversimplification to equate such a population structure with the classic polymorphism of population biology. Darwinian principles acting on genome collectivities that replicate with high error rates provide a unique population structure prone to flexible and largely unpredictable behavior.
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Affiliation(s)
- Celia Perales
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), C/ Nicolás Cabrera, 1 Universidad Autónoma de Madrid, Cantoblanco, Madrid 28049, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
| | - Ramón Lorenzo-Redondo
- Centro Nacional de Microbiología (CNM), Instituto de Salud Carlos III, Majadahonda, Madrid 28220, Spain
| | - Cecilio López-Galíndez
- Centro Nacional de Microbiología (CNM), Instituto de Salud Carlos III, Majadahonda, Madrid 28220, Spain
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30
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G-C Content Independent Long-Range Charge Transfer Through DNA. ELECTRONIC AND MAGNETIC PROPERTIES OF CHIRAL MOLECULES AND SUPRAMOLECULAR ARCHITECTURES 2010; 298:129-42. [DOI: 10.1007/128_2010_90] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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31
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Kawai K, Kodera H, Majima T. Long-Range Charge Transfer through DNA by Replacing Adenine with Diaminopurine. J Am Chem Soc 2009; 132:627-30. [DOI: 10.1021/ja907409z] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Kiyohiko Kawai
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Haruka Kodera
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Tetsuro Majima
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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32
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Petit V, Vartanian JP, Wain-Hobson S. Powerful mutators lurking in the genome. Philos Trans R Soc Lond B Biol Sci 2009; 364:705-15. [PMID: 19042181 PMCID: PMC2660927 DOI: 10.1098/rstb.2008.0272] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The human genome encodes numerous enzymes capable of deaminating polynucleotides. While they are capable of exquisite specificity, occasionally they result in hypermutation where up to 90 per cent of cytidine or adenosine residues may be edited. As such, they constitute a formidable anti-viral barrier, for no virus can survive such a high mutation rate. As the APOBEC3 group of cytidine deaminases edit single-stranded viral DNA, the crucial question is can they hyperedit chromosomal DNA? Everything points to a positive answer. Nonetheless, hypermutants per se have not yet been described, probably being countered by highly efficient mismatch repair. For the APOBEC3 genes, not only is their physiological function unknown, but also their role in the induction of cancer remains to be determined. Yet given the pace of research, all this is certain to change in the next few years.
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Affiliation(s)
| | | | - Simon Wain-Hobson
- Molecular Retrovirology Unit, CNRS URA 3015, Institut Pasteur28 rue du Docteur Roux, 75724 Paris cedex 15, France
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