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Rosani U, Bai CM, Maso L, Shapiro M, Abbadi M, Domeneghetti S, Wang CM, Cendron L, MacCarthy T, Venier P. A-to-I editing of Malacoherpesviridae RNAs supports the antiviral role of ADAR1 in mollusks. BMC Evol Biol 2019; 19:149. [PMID: 31337330 PMCID: PMC6651903 DOI: 10.1186/s12862-019-1472-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 07/04/2019] [Indexed: 02/06/2023] Open
Abstract
Background Adenosine deaminase enzymes of the ADAR family are conserved in metazoans. They convert adenine into inosine in dsRNAs and thus alter both structural properties and the coding potential of their substrates. Acting on exogenous dsRNAs, ADAR1 exerts a pro- or anti-viral role in vertebrates and Drosophila. Results We traced 4 ADAR homologs in 14 lophotrochozoan genomes and we classified them into ADAD, ADAR1 or ADAR2, based on phylogenetic and structural analyses of the enzymatic domain. Using RNA-seq and quantitative real time PCR we demonstrated the upregulation of one ADAR1 homolog in the bivalve Crassostrea gigas and in the gastropod Haliotis diversicolor supertexta during Ostreid herpesvirus-1 or Haliotid herpesvirus-1 infection. Accordingly, we demonstrated an extensive ADAR-mediated editing of viral RNAs. Single nucleotide variation (SNV) profiles obtained by pairing RNA- and DNA-seq data from the viral infected individuals resulted to be mostly compatible with ADAR-mediated A-to-I editing (up to 97%). SNVs occurred at low frequency in genomic hotspots, denoted by the overlapping of viral genes encoded on opposite DNA strands. The SNV sites and their upstream neighbor nucleotide indicated the targeting of selected adenosines. The analysis of viral sequences suggested that, under the pressure of the ADAR editing, the two Malacoherpesviridae genomes have evolved to reduce the number of deamination targets. Conclusions We report, for the first time, evidence of an extensive editing of Malacoherpesviridae RNAs attributable to host ADAR1 enzymes. The analysis of base neighbor preferences, structural features and expression profiles of molluscan ADAR1 supports the conservation of the enzyme function among metazoans and further suggested that ADAR1 exerts an antiviral role in mollusks. Electronic supplementary material The online version of this article (10.1186/s12862-019-1472-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Umberto Rosani
- Department of Biology, University of Padova, 32121, Padova, Italy. .,Helmholtz Centre for Polar and Marine Research, Alfred Wegener Institute (AWI), Wadden Sea Station, 25992, List auf Sylt, Germany.
| | - Chang-Ming Bai
- Chinese Academy of Fishery Sciences, Yellow Sea Fisheries Research Institute, Qingdao, China
| | - Lorenzo Maso
- Department of Biology, University of Padova, 32121, Padova, Italy
| | - Maxwell Shapiro
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
| | - Miriam Abbadi
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020, Legnaro, Italy
| | | | - Chong-Ming Wang
- Chinese Academy of Fishery Sciences, Yellow Sea Fisheries Research Institute, Qingdao, China
| | - Laura Cendron
- Department of Biology, University of Padova, 32121, Padova, Italy
| | - Thomas MacCarthy
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
| | - Paola Venier
- Department of Biology, University of Padova, 32121, Padova, Italy.
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2
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Fedeles BI, Essigmann JM. Impact of DNA lesion repair, replication and formation on the mutational spectra of environmental carcinogens: Aflatoxin B 1 as a case study. DNA Repair (Amst) 2018; 71:12-22. [PMID: 30309820 DOI: 10.1016/j.dnarep.2018.08.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In a multicellular organism, somatic mutations represent a permanent record of the past chemical and biochemical perturbations experienced by a cell in its local microenvironment. Akin to a perpetual recording device, with every replication, genomic DNA accumulates mutations in patterns that reflect: i) the sequence context-dependent formation of DNA damage, due to environmental or endogenous reactive species, including spontaneous processes; ii) the activity of DNA repair pathways, which, depending on the type of lesion, can erase, ignore or exacerbate the mutagenic consequences of that DNA damage; and iii) the choice of replication machinery that synthesizes the nascent genomic copy. These three factors result in a richly contoured sequence context-dependent mutational spectrum that, from appearances, is distinct for most individual forms of DNA damage. Such a mutagenic legacy, if appropriately decoded, can reveal the local history of genome-altering events such as chemical or pathogen exposures, metabolic stress, and inflammation, which in turn can provide an indication of the underlying causes and mechanisms of genetic disease. Modern tools have positioned us to develop a deep mechanistic understanding of the cellular factors and pathways that modulate a mutational process and, in turn, provide opportunities for better diagnostic and prognostic biomarkers, better exposure risk assessment and even actionable therapeutic targets. The goal of this Perspective is to present a bottom-up, lesion-centric framework of mutagenesis that integrates the contributions of lesion replication, lesion repair and lesion formation to explain the complex mutational spectra that emerge in the genome following exposure to mutagens. The mutational spectra of the well-studied hepatocarcinogen aflatoxin B1 are showcased here as specific examples, but the implications are meant to be generalizable.
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Affiliation(s)
- Bogdan I Fedeles
- Departments of Biological Engineering, Chemistry and The Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - John M Essigmann
- Departments of Biological Engineering, Chemistry and The Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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3
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Gansmo LB, Romundstad P, Hveem K, Vatten L, Nik-Zainal S, Lønning PE, Knappskog S. APOBEC3A/B deletion polymorphism and cancer risk. Carcinogenesis 2018; 39:118-124. [PMID: 29140415 PMCID: PMC5862322 DOI: 10.1093/carcin/bgx131] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Activity of the apolipoprotein B mRNA editing enzyme, catalytic-polypeptide-like (APOBEC) enzymes has been linked to specific mutational processes in human cancer genomes. A germline APOBEC3A/B deletion polymorphism is associated with APOBEC-dependent mutational signatures, and the deletion allele has been reported to confer an elevated risk of some cancers in Asian populations, while the results in European populations, so far, have been conflicting. We genotyped the APOBEC3A/B deletion polymorphism in a large population-based sample consisting of 11 106 Caucasian (Norwegian) individuals, including 7279 incident cancer cases (1769 breast, 1360 lung, 1585 colon, and 2565 prostate cancer) and a control group of 3827 matched individuals without cancer (1918 females and 1909 males) from the same population. Overall, the APOBEC3A/B deletion polymorphism was not associated with risk of any of the four cancer types. However, in subgroup analyses stratified by age, we found that the deletion allele was associated with increased risk for lung cancer among individuals <50 years of age (OR 2.17, CI 1.19-3.97), and that the association was gradually reduced with increasing age (P = 0.01). A similar but weaker pattern was observed for prostate cancer. In support of these findings, the APOBEC3A/B deletion was associated with young age at diagnosis among the cancer cases for both cancer forms (lung cancer: P = 0.02; dominant model and prostate cancer: P = 0.03; recessive model). No such associations were observed for breast or colon cancer.
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Affiliation(s)
- Liv B Gansmo
- Section of Oncology, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Paal Romundstad
- Department of Public Health, Faculty of Medicine, Trondheim, Norway
| | - Kristian Hveem
- Department of Public Health, Faculty of Medicine, K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Lars Vatten
- Department of Public Health, Faculty of Medicine, Trondheim, Norway
| | - Serena Nik-Zainal
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
- Department of Medical Genetics, Addenbrooke’s Hospital National Health Service (NHS) Trust, Cambridge, UK
| | - Per Eystein Lønning
- Section of Oncology, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Stian Knappskog
- Section of Oncology, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
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4
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Romanov GA, Sukhoverov VS, Vanyushin BF. Epigenetic mutagenesis as program of age-related protein dysfunction and aging. Russ J Dev Biol 2015. [DOI: 10.1134/s106236041502006x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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5
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Knisbacher BA, Levanon EY. DNA and RNA editing of retrotransposons accelerate mammalian genome evolution. Ann N Y Acad Sci 2015; 1341:115-25. [PMID: 25722083 DOI: 10.1111/nyas.12713] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Genome evolution is commonly viewed as a gradual process that is driven by random mutations that accumulate over time. However, DNA- and RNA-editing enzymes have been identified that can accelerate evolution by actively modifying the genomically encoded information. The apolipoprotein B mRNA editing enzymes, catalytic polypeptide-like (APOBECs) are potent restriction factors that can inhibit retroelements by cytosine-to-uridine editing of retroelement DNA after reverse transcription. In some cases, a retroelement may successfully integrate into the genome despite being hypermutated. Such events introduce unique sequences into the genome and are thus a source of genomic innovation. adenosine deaminases that act on RNA (ADARs) catalyze adenosine-to-inosine editing in double-stranded RNA, commonly formed by oppositely oriented retroelements. The RNA editing confers plasticity to the transcriptome by generating many transcript variants from a single genomic locus. If the editing produces a beneficial variant, the genome may maintain the locus that produces the RNA-edited transcript for its novel function. Here, we discuss how these two powerful editing mechanisms, which both target inserted retroelements, facilitate expedited genome evolution.
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Affiliation(s)
- Binyamin A Knisbacher
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
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6
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Nik-Zainal S, Wedge DC, Alexandrov LB, Petljak M, Butler AP, Bolli N, Davies HR, Knappskog S, Martin S, Papaemmanuil E, Ramakrishna M, Shlien A, Simonic I, Xue Y, Tyler-Smith C, Campbell PJ, Stratton MR. Association of a germline copy number polymorphism of APOBEC3A and APOBEC3B with burden of putative APOBEC-dependent mutations in breast cancer. Nat Genet 2014; 46:487-91. [PMID: 24728294 PMCID: PMC4137149 DOI: 10.1038/ng.2955] [Citation(s) in RCA: 210] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 03/06/2014] [Indexed: 12/13/2022]
Abstract
The somatic mutations in a cancer genome are the aggregate outcome of one or more mutational processes operative through the lifetime of the individual with cancer. Each mutational process leaves a characteristic mutational signature determined by the mechanisms of DNA damage and repair that constitute it. A role was recently proposed for the APOBEC family of cytidine deaminases in generating particular genome-wide mutational signatures and a signature of localized hypermutation called kataegis. A germline copy number polymorphism involving APOBEC3A and APOBEC3B, which effectively deletes APOBEC3B, has been associated with modestly increased risk of breast cancer. Here we show that breast cancers in carriers of the deletion show more mutations of the putative APOBEC-dependent genome-wide signatures than cancers in non-carriers. The results suggest that the APOBEC3A-APOBEC3B germline deletion allele confers cancer susceptibility through increased activity of APOBEC-dependent mutational processes, although the mechanism by which this increase in activity occurs remains unknown.
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Affiliation(s)
- Serena Nik-Zainal
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
- Department of Medical Genetics, Box 134, Addenbrooke’s Hospital NHS Trust, Hills Road, Cambridge CB2 0QQ
| | - David C. Wedge
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Ludmil B. Alexandrov
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Mia Petljak
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Adam P. Butler
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Niccolo Bolli
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
- Department of Haematology, University of Cambridge, Cambridge CB2 2XY, UK
| | - Helen R. Davies
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Stian Knappskog
- Section of Oncology, Department of Clinical Science, University of Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Sancha Martin
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Elli Papaemmanuil
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Manasa Ramakrishna
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Adam Shlien
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
- Department of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Ingrid Simonic
- Regional Genetics Laboratories, Box 143, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0QQ
| | - Yali Xue
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Chris Tyler-Smith
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
| | - Peter J. Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
- Department of Haematology, University of Cambridge, Cambridge CB2 2XY, UK
| | - Michael R. Stratton
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
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7
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Mussil B, Suspène R, Aynaud MM, Gauvrit A, Vartanian JP, Wain-Hobson S. Human APOBEC3A isoforms translocate to the nucleus and induce DNA double strand breaks leading to cell stress and death. PLoS One 2013; 8:e73641. [PMID: 23977391 PMCID: PMC3748023 DOI: 10.1371/journal.pone.0073641] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 07/21/2013] [Indexed: 01/14/2023] Open
Abstract
Human APOBEC3 enzymes deaminate single stranded DNA. At least five can deaminate mitochondrial DNA in the cytoplasm, while three can deaminate viral DNA in the nucleus. However, only one, APOBEC3A, can hypermutate genomic DNA. We analysed the distribution and function of the two APOBEC3A isoforms p1 and p2 in transfected cell lines. Both can translocate to the nucleus and hypermutate CMYC DNA and induce DNA double strand breaks as visualized by the detection of ©H2AX or Chk2. APOBEC3A induced G1 phase cell cycle arrest and triggered several members of the intrinsic apoptosis pathway. Activation of purified human CD4+ T lymphocytes with PHA, IL2 and interferon α resulted in C->T hypermutation of genomic DNA and double stranded breaks suggesting a role for APOBEC3A in pro-inflammatory conditions. As chronic inflammation underlies many diseases including numerous cancers, it is possible that APOBEC3A induction may generate many of the lesions typical of a cancer genome.
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Affiliation(s)
- Bianka Mussil
- Molecular Retrovirology Unit, Institut Pasteur, Paris, France
| | | | | | - Anne Gauvrit
- Molecular Retrovirology Unit, Institut Pasteur, Paris, France
| | | | - Simon Wain-Hobson
- Molecular Retrovirology Unit, Institut Pasteur, Paris, France
- * E-mail:
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8
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Ali S, Karki N, Bhattacharya C, Zhu R, MacDuff DA, Stenglein MD, Schumacher AJ, Demorest ZL, Harris RS, Matin A, Aggarwal S. APOBEC3 inhibits DEAD-END function to regulate microRNA activity. BMC Mol Biol 2013; 14:16. [PMID: 23890083 PMCID: PMC3729616 DOI: 10.1186/1471-2199-14-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 07/09/2013] [Indexed: 12/21/2022] Open
Abstract
The RNA binding protein DEAD-END (DND1) is one of the few proteins known to regulate microRNA (miRNA) activity at the level of miRNA-mRNA interaction. DND1 blocks miRNA interaction with the 3′-untranslated region (3′-UTR) of specific mRNAs and restores protein expression. Previously, we showed that the DNA cytosine deaminase, APOBEC3 (apolipoprotein B mRNA-editing enzyme, catalytic polypeptide like 3), interacts with DND1. APOBEC3 has been primarily studied for its role in restricting and inactivating retroviruses and retroelements. In this report, we examine the significance of DND1-APOBEC3 interaction. We found that while human DND1 inhibits miRNA-mediated inhibition of P27, human APOBEC3G is able to counteract this repression and restore miRNA activity. APOBEC3G, by itself, does not affect the 3′-UTR of P27. We found that APOBEC3G also blocks DND1 function to restore miR-372 and miR-206 inhibition through the 3′-UTRs of LATS2 and CX43, respectively. In corollary experiments, we tested whether DND1 affects the viral restriction function or mutator activity of APOBEC3. We found that DND1 does not affect APOBEC3 inhibition of infectivity of exogenous retrovirus HIV (ΔVif) or retrotransposition of MusD. In addition, examination of Ter/Ter;Apobec3−/− mice, lead us to conclude that DND1 does not regulate the mutator activity of APOBEC3 in germ cells. In summary, our results show that APOBEC3 is able to modulate DND1 function to regulate miRNA mediated translational regulation in cells but DND1 does not affect known APOBEC3 function.
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Affiliation(s)
- Sara Ali
- Department of Genetics, University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA
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9
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Panyukov VV, Ozoline ON. Promoters of Escherichia coli versus promoter islands: function and structure comparison. PLoS One 2013; 8:e62601. [PMID: 23717391 PMCID: PMC3661553 DOI: 10.1371/journal.pone.0062601] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 03/23/2013] [Indexed: 12/21/2022] Open
Abstract
Expression of bacterial genes takes place under the control of RNA polymerase with exchangeable σ-subunits and multiple transcription factors. A typical promoter region contains one or several overlapping promoters. In the latter case promoters have the same or different σ-specificity and are often subjected to different regulatory stimuli. Genes, transcribed from multiple promoters, have on average higher expression levels. However, recently in the genome of Escherichia coli we found 78 regions with an extremely large number of potential transcription start points (promoter islands, PIs). It was shown that all PIs interact with RNA polymerase in vivo and are able to form transcriptionally competent open complexes both in vitro and in vivo but their transcriptional activity measured by oligonucleotide microarrays was very low, if any. Here we confirmed transcriptional defectiveness of PIs by analyzing the 5'-end specific RNA-seq data, but showed their ability to produce short oligos (9-14 bases). This combination of functional properties indicated a deliberate suppression of transcriptional activity within PIs. According to our data this suppression may be due to a specific conformation of the DNA double helix, which provides an ideal platform for interaction with both RNA polymerase and the histone-like nucleoid protein H-NS. The genomic DNA of E.coli contains therefore several dozen sites optimized by evolution for staying in a heterochromatin-like state. Since almost all promoter islands are associated with horizontally acquired genes, we offer them as specific components of bacterial evolution involved in acquisition of foreign genetic material by turning off the expression of toxic or useless aliens or by providing optimal promoter for beneficial genes. The putative molecular mechanism underlying the appearance of promoter islands within recipient genomes is discussed.
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Affiliation(s)
- Valeriy V. Panyukov
- Department of Bioinformatics, Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
| | - Olga N. Ozoline
- Department of Functional Genomics and Cellular Stress, Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
- Department of Cell Biology, Pushchino State Institute of Natural Sciences, Pushchino, Moscow Region, Russian Federation
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10
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Münk C, Willemsen A, Bravo IG. An ancient history of gene duplications, fusions and losses in the evolution of APOBEC3 mutators in mammals. BMC Evol Biol 2012; 12:71. [PMID: 22640020 PMCID: PMC3495650 DOI: 10.1186/1471-2148-12-71] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Accepted: 05/01/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The APOBEC3 (A3) genes play a key role in innate antiviral defense in mammals by introducing directed mutations in the DNA. The human genome encodes for seven A3 genes, with multiple splice alternatives. Different A3 proteins display different substrate specificity, but the very basic question on how discerning self from non-self still remains unresolved. Further, the expression of A3 activity/ies shapes the way both viral and host genomes evolve. RESULTS We present here a detailed temporal analysis of the origin and expansion of the A3 repertoire in mammals. Our data support an evolutionary scenario where the genome of the mammalian ancestor encoded for at least one ancestral A3 gene, and where the genome of the ancestor of placental mammals (and possibly of the ancestor of all mammals) already encoded for an A3Z1-A3Z2-A3Z3 arrangement. Duplication events of the A3 genes have occurred independently in different lineages: humans, cats and horses. In all of them, gene duplication has resulted in changes in enzyme activity and/or substrate specificity, in a paradigmatic example of convergent adaptive evolution at the genomic level. Finally, our results show that evolutionary rates for the three A3Z1, A3Z2 and A3Z3 motifs have significantly decreased in the last 100 Mya. The analysis constitutes a textbook example of the evolution of a gene locus by duplication and sub/neofunctionalization in the context of virus-host arms race. CONCLUSIONS Our results provide a time framework for identifying ancestral and derived genomic arrangements in the APOBEC loci, and to date the expansion of this gene family for different lineages through time, as a response to changes in viral/retroviral/retrotransposon pressure.
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Affiliation(s)
- Carsten Münk
- Clinic for Gastroenterology, Hepatology and Infectiology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Anouk Willemsen
- Genomics and Health, Centre for Public Health Research (CSISP), Valencia, Spain
| | - Ignacio G Bravo
- Genomics and Health, Centre for Public Health Research (CSISP), Valencia, Spain
- Infections and Cancer, Catalan Institute of Oncology (ICO) | Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain
- Infections and Cancer, Catalan Institute of Oncology (ICO), Avda. Gran Via, 199-203, L’Hospitalet de Llobregat, Barcelona, 08908, Spain
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Narvaiza I, Landry S, Weitzman MD. APOBEC3 proteins and genomic stability: the high cost of a good defense. Cell Cycle 2012; 11:33-8. [PMID: 22157092 PMCID: PMC3272230 DOI: 10.4161/cc.11.1.18706] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Revised: 11/07/2011] [Accepted: 11/08/2011] [Indexed: 01/07/2023] Open
Abstract
The human APOBEC3 family of cytidine deaminases constitutes a cellular intrinsic defense mechanism that is effective against a range of viruses and retro-elements. While it is well established that these enzymes are powerful mutators of viral DNA, the possibility that their activity could threaten the integrity of the host genome has only recently begun to be investigated. Here, we discuss the implications of new evidence suggesting that APOBEC3 proteins can mediate the deamination of cellular DNA. The maintenance of genomic integrity in the face of this potential off-target activity must require high fidelity DNA repair and strict regulation of APOBEC3 gene expression and enzyme activity. Conversely, the ability of specific members of the APOBEC3 family to activate DNA damage signaling pathways might also reflect another way that these proteins contribute to the host immune response.
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Affiliation(s)
- Iñigo Narvaiza
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, USA
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12
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Large-scale DNA editing of retrotransposons accelerates mammalian genome evolution. Nat Commun 2011; 2:519. [PMID: 22044998 DOI: 10.1038/ncomms1525] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Accepted: 10/03/2011] [Indexed: 11/08/2022] Open
Abstract
Retrotransposons had an important role in genome evolution, including the formation of new genes and promoters and the rewiring of gene networks. However, it is unclear how such a repertoire of functions emerged from a relatively limited number of source sequences. Here we show that DNA editing, an antiviral mechanism, accelerated the evolution of mammalian genomes by large-scale modification of their retrotransposon sequences. We find numerous pairs of retrotransposons containing long clusters of G-to-A mutations that cannot be attributed to random mutagenesis. These clusters, which we find across different mammalian genomes and retrotransposon families, are the hallmark of APOBEC3 activity, a potent antiretroviral protein family with cytidine deamination function. As DNA editing simultaneously generates a large number of mutations, each affected element begins its evolutionary trajectory from a unique starting point, thereby increasing the probability of developing a novel function. Our findings thus suggest a potential mechanism for retrotransposon domestication.
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13
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Thielen BK, McNevin JP, McElrath MJ, Hunt BVS, Klein KC, Lingappa JR. Innate immune signaling induces high levels of TC-specific deaminase activity in primary monocyte-derived cells through expression of APOBEC3A isoforms. J Biol Chem 2010; 285:27753-66. [PMID: 20615867 PMCID: PMC2934643 DOI: 10.1074/jbc.m110.102822] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Revised: 07/05/2010] [Indexed: 01/06/2023] Open
Abstract
In HIV-1-infected individuals, G-to-A hypermutation is found in HIV-1 DNA isolated from peripheral blood mononuclear cells (PBMCs). These mutations are thought to result from editing by one or more host enzymes in the APOBEC3 (A3) family of cytidine deaminases, which act on CC (APOBEC3G) and TC (other A3 proteins) dinucleotide motifs in DNA (edited cytidine underlined). Although many A3 proteins display high levels of deaminase activity in model systems, only low levels of A3 deaminase activity have been found in primary cells examined to date. In contrast, here we report high levels of deaminase activity at TC motifs when whole PBMCs or isolated primary monocyte-derived cells were treated with interferon-alpha (IFNalpha) or IFNalpha-inducing toll-like receptor ligands. Induction of TC-specific deaminase activity required new transcription and translation and correlated with the appearance of two APOBEC3A (A3A) isoforms. Knockdown of A3A in monocytes with siRNA abolished TC-specific deaminase activity, confirming that A3A isoforms are responsible for all TC-specific deaminase activity observed. Both A3A isoforms appear to be enzymatically active; moreover, our mutational studies raise the possibility that the smaller isoform results from internal translational initiation. In contrast to the high levels of TC-specific activity observed in IFNalpha-treated monocytes, CC-specific activity remained low in PBMCs, suggesting that A3G deaminase activity is relatively inhibited, unlike that of A3A. Together, these findings suggest that deaminase activity of A3A isoforms in monocytes and macrophages may play an important role in host defense against viruses.
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Affiliation(s)
- Beth K. Thielen
- From the Department of Global Health, University of Washington, Seattle, Washington 98102
| | - John P. McNevin
- the Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, and
| | - M. Juliana McElrath
- the Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, and
- the Department of Medicine, University of Washington, Seattle, Washington 98195
| | | | - Kevin C. Klein
- From the Department of Global Health, University of Washington, Seattle, Washington 98102
| | - Jaisri R. Lingappa
- From the Department of Global Health, University of Washington, Seattle, Washington 98102
- the Department of Medicine, University of Washington, Seattle, Washington 98195
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The 30th anniversary of quasispecies. Meeting on 'Quasispecies: past, present and future'. EMBO Rep 2009; 10:444-8. [PMID: 19343047 DOI: 10.1038/embor.2009.61] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2009] [Accepted: 03/04/2009] [Indexed: 12/23/2022] Open
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