APOBEC3DE Antagonizes Hepatitis B Virus Restriction Factors APOBEC3F and APOBEC3G

Journal of Molecular Biology - Tập 428 - Trang 3514-3528 - 2016
Mohamed S. Bouzidi1, Vincent Caval1, Rodolphe Suspène1, Camille Hallez1, Pascal Pineau2, Simon Wain-Hobson1, Jean-Pierre Vartanian1
1Molecular Retrovirology Unit, Institut Pasteur, CNRS URA 3015, 28 rue du Dr. Roux, 75724 Paris CEDEX 15, France
2Nuclear Organization and Oncogenesis Unit, Institut Pasteur, INSERM U579, 28 rue du Dr. Roux, 75724 Paris CEDEX 15, France

Tài liệu tham khảo

Jarmuz, 2002, An anthropoid-specific locus of orphan C to U RNA-editing enzymes on chromosome 22, Genomics, 79, 285, 10.1006/geno.2002.6718 Conticello, 2005, Evolution of the AID/APOBEC family of polynucleotide (deoxy)cytidine deaminases, Mol. Biol. Evol., 22, 367, 10.1093/molbev/msi026 Harris, 2003, DNA deamination mediates innate immunity to retroviral infection, Cell, 113, 803, 10.1016/S0092-8674(03)00423-9 Lecossier, 2003, Hypermutation of HIV-1 DNA in the absence of the Vif protein, Science, 300, 1112, 10.1126/science.1083338 Mangeat, 2003, Broad antiretroviral defence by human APOBEC3G through lethal editing of nascent reverse transcripts, Nature, 424, 99, 10.1038/nature01709 Mariani, 2003, Species-specific exclusion of APOBEC3G from HIV-1 virions by Vif, Cell, 114, 21, 10.1016/S0092-8674(03)00515-4 Sheehy, 2002, Isolation of a human gene that inhibits HIV-1 infection and is suppressed by the viral Vif protein, Nature, 418, 646, 10.1038/nature00939 Lucifora, 2014, Specific and nonhepatotoxic degradation of nuclear hepatitis B virus cccDNA, Science, 343, 1221, 10.1126/science.1243462 Noguchi, 2005, G to A hypermutation of hepatitis B virus, Hepatology, 41, 626, 10.1002/hep.20580 Suspène, 2005, Extensive editing of both hepatitis B virus DNA strands by APOBEC3 cytidine deaminases in vitro and in vivo, Proc. Natl. Acad. Sci. U. S. A., 102, 8321, 10.1073/pnas.0408223102 Turelli, 2004, Inhibition of hepatitis B virus replication by APOBEC3G, Science, 303, 1829, 10.1126/science.1092066 Vartanian, 2010, Massive APOBEC3 editing of hepatitis B viral DNA in cirrhosis, PLoS Pathog., 6, 10.1371/journal.ppat.1000928 Suspène, 2011, Genetic editing of herpes simplex virus 1 and Epstein–Barr herpesvirus genomes by human APOBEC3 cytidine deaminases in culture and in vivo, J. Virol., 85, 7594, 10.1128/JVI.00290-11 Vartanian, 2008, Evidence for editing of human papillomavirus DNA by APOBEC3 in benign and precancerous lesions, Science, 320, 230, 10.1126/science.1153201 Wang, 2014, APOBEC3 deaminases induce hypermutation in human papillomavirus 16 DNA upon beta interferon stimulation, J. Virol., 88, 1308, 10.1128/JVI.03091-13 Warren, 2015, APOBEC3A functions as a restriction factor of human papillomavirus, J. Virol., 89, 688, 10.1128/JVI.02383-14 Bogerd, 2006, Cellular inhibitors of long interspersed element 1 and Alu retrotransposition, Proc. Natl. Acad. Sci. U. S. A., 103, 8780, 10.1073/pnas.0603313103 Chen, 2006, APOBEC3A is a potent inhibitor of adeno-associated virus and retrotransposons, Curr. Biol., 16, 480, 10.1016/j.cub.2006.01.031 Muckenfuss, 2006, APOBEC3 proteins inhibit human LINE-1 retrotransposition, J. Biol. Chem., 281, 22,161, 10.1074/jbc.M601716200 Suspène, 2004, APOBEC3G is a single-stranded DNA cytidine deaminase and functions independently of HIV reverse transcriptase, Nucleic Acids Res., 32, 2421, 10.1093/nar/gkh554 Aynaud, 2012, Human Tribbles 3 protects nuclear DNA from cytidine deamination by APOBEC3A, J. Biol. Chem., 287, 39,182, 10.1074/jbc.M112.372722 Bonvin, 2006, Interferon-inducible expression of APOBEC3 editing enzymes in human hepatocytes and inhibition of hepatitis B virus replication, Hepatology, 43, 1364, 10.1002/hep.21187 Koning, 2009, Defining APOBEC3 expression patterns in human tissues and hematopoietic cell subsets, J. Virol., 83, 9474, 10.1128/JVI.01089-09 Peng, 2006, Induction of APOBEC3 family proteins, a defensive maneuver underlying interferon-induced anti-HIV-1 activity, J. Exp. Med., 203, 41, 10.1084/jem.20051512 Stenglein, 2010, APOBEC3 proteins mediate the clearance of foreign DNA from human cells, Nat. Struct. Mol. Biol., 17, 222, 10.1038/nsmb.1744 Burns, 2013, APOBEC3B is an enzymatic source of mutation in breast cancer, Nature, 494, 366, 10.1038/nature11881 Caval, 2014, A prevalent cancer susceptibility APOBEC3A hybrid allele bearing APOBEC3B 3'UTR enhances chromosomal DNA damage, Nat. Commun., 5, 5129, 10.1038/ncomms6129 Mussil, 2013, Human APOBEC3A isoforms translocate to the nucleus and induce DNA double strand breaks leading to cell stress and death, PLoS ONE, 8, 10.1371/journal.pone.0073641 Shinohara, 2012, APOBEC3B can impair genomic stability by inducing base substitutions in genomic DNA in human cells, Sci. Rep., 2, 806, 10.1038/srep00806 Suspène, 2011, Somatic hypermutation of human mitochondrial and nuclear DNA by APOBEC3 cytidine deaminases, a pathway for DNA catabolism, Proc. Natl. Acad. Sci. U. S. A., 108, 4858, 10.1073/pnas.1009687108 Carpenter, 2012, Methylcytosine and normal cytosine deamination by the foreign DNA restriction enzyme APOBEC3A, J. Biol. Chem., 287, 34,801, 10.1074/jbc.M112.385161 Suspène, 2013, Efficient deamination of 5-methylcytidine and 5-substituted cytidine residues in DNA by human APOBEC3A cytidine deaminase, PLoS ONE, 8, 10.1371/journal.pone.0063461 Wijesinghe, 2012, Efficient deamination of 5-methylcytosines in DNA by human APOBEC3A, but not by AID or APOBEC3G, Nucleic Acids Res., 40, 9206, 10.1093/nar/gks685 Caval, 2014, Orthologous mammalian APOBEC3A cytidine deaminases hypermutate nuclear DNA, Mol. Biol. Evol., 31, 330, 10.1093/molbev/mst195 Landry, 2011, APOBEC3A can activate the DNA damage response and cause cell-cycle arrest, EMBO Rep., 12, 444, 10.1038/embor.2011.46 Bishop, 2004, Cytidine deamination of retroviral DNA by diverse APOBEC proteins, Curr. Biol., 14, 1392, 10.1016/j.cub.2004.06.057 Beale, 2004, Comparison of the differential context-dependence of DNA deamination by APOBEC enzymes: correlation with mutation spectra in vivo, J. Mol. Biol., 337, 585, 10.1016/j.jmb.2004.01.046 Hache, 2005, The retroviral hypermutation specificity of APOBEC3F and APOBEC3G is governed by the C-terminal DNA cytosine deaminase domain, J. Biol. Chem., 280, 10,920, 10.1074/jbc.M500382200 Newman, 2005, Antiviral function of APOBEC3G can be dissociated from cytidine deaminase activity, Curr. Biol., 15, 166, 10.1016/j.cub.2004.12.068 Henry, 2009, Genetic editing of HBV DNA by monodomain human APOBEC3 cytidine deaminases and the recombinant nature of APOBEC3G, PLoS ONE, 4, 10.1371/journal.pone.0004277 Bohn, 2015, The ssDNA Mutator APOBEC3A is regulated by cooperative dimerization, Structure, 23, 903, 10.1016/j.str.2015.03.016 Friew, 2009, Intracellular interactions between APOBEC3G, RNA, and HIV-1 Gag: APOBEC3G multimerization is dependent on its association with RNA, Retrovirology, 6, 56, 10.1186/1742-4690-6-56 Huthoff, 2009, RNA-dependent oligomerization of APOBEC3G is required for restriction of HIV-1, PLoS Pathog., 5, 10.1371/journal.ppat.1000330 Koyama, 2013, APOBEC3G oligomerization is associated with the inhibition of both Alu and LINE-1 retrotransposition, PLoS ONE, 8, 10.1371/journal.pone.0084228 Stauch, 2009, Model structure of APOBEC3C reveals a binding pocket modulating ribonucleic acid interaction required for encapsidation, Proc. Natl. Acad. Sci. U. S. A., 106, 12,079, 10.1073/pnas.0900979106 Wiegand, 2004, A second human antiretroviral factor, APOBEC3F, is suppressed by the HIV-1 and HIV-2 Vif proteins, EMBO J., 23, 2451, 10.1038/sj.emboj.7600246 Brar, 2008, Activation-induced deaminase, AID, is catalytically active as a monomer on single-stranded DNA, DNA Repair, 7, 77, 10.1016/j.dnarep.2007.08.002 Salter, 2009, A hydrodynamic analysis of APOBEC3G reveals a monomer-dimer-tetramer self-association that has implications for anti-HIV function, Biochemistry, 48, 10,685, 10.1021/bi901642c Chiu, 2006, High-molecular-mass APOBEC3G complexes restrict Alu retrotransposition, Proc. Natl. Acad. Sci. U. S. A., 103, 15,588, 10.1073/pnas.0604524103 McDougall, 2011, Deaminase activity on single-stranded DNA (ssDNA) occurs in vitro when APOBEC3G cytidine deaminase forms homotetramers and higher-order complexes, J. Biol. Chem., 286, 30,655, 10.1074/jbc.M111.269506 Wedekind, 2006, Nanostructures of APOBEC3G support a hierarchical assembly model of high molecular mass ribonucleoprotein particles from dimeric subunits, J. Biol. Chem., 281, 38,122, 10.1074/jbc.C600253200 Dang, 2011, Identification of a single amino acid required for APOBEC3 antiretroviral cytidine deaminase activity, J. Virol., 85, 5691, 10.1128/JVI.00243-11 Holmes, 2007, APOBEC3F can inhibit the accumulation of HIV-1 reverse transcription products in the absence of hypermutation. Comparisons with APOBEC3G, J. Biol. Chem., 282, 2587, 10.1074/jbc.M607298200 Nguyen, 2007, Deamination-independent inhibition of hepatitis B virus reverse transcription by APOBEC3G, J. Virol., 81, 4465, 10.1128/JVI.02510-06 Rosler, 2005, APOBEC-mediated interference with hepadnavirus production, Hepatology, 42, 301, 10.1002/hep.20801 LaRue, 2008, The artiodactyl APOBEC3 innate immune repertoire shows evidence for a multi-functional domain organization that existed in the ancestor of placental mammals, BMC Mol. Biol., 9, 104, 10.1186/1471-2199-9-104 Dang, 2006, Identification of APOBEC3DE as another antiretroviral factor from the human APOBEC family, J. Virol., 80, 10,522, 10.1128/JVI.01123-06 Peng, 2007, Myeloid differentiation and susceptibility to HIV-1 are linked to APOBEC3 expression, Blood, 110, 393, 10.1182/blood-2006-10-051763 Chaipan, 2013, APOBEC3G restricts HIV-1 to a greater extent than APOBEC3F and APOBEC3DE in human primary CD4+ T cells and macrophages, J. Virol., 87, 444, 10.1128/JVI.00676-12 Duggal, 2011, The breadth of antiviral activity of Apobec3DE in chimpanzees has been driven by positive selection, J. Virol., 85, 11,361, 10.1128/JVI.05046-11 Bennett, 2008, APOBEC3G subunits self-associate via the C-terminal deaminase domain, J. Biol. Chem., 283, 33,329, 10.1074/jbc.M803726200 Chelico, 2010, Structural model for deoxycytidine deamination mechanisms of the HIV-1 inactivation enzyme APOBEC3G, J. Biol. Chem., 285, 16,195, 10.1074/jbc.M110.107987 Shlyakhtenko, 2011, Atomic force microscopy studies provide direct evidence for dimerization of the HIV restriction factor APOBEC3G, J. Biol. Chem., 286, 3387, 10.1074/jbc.M110.195685 Suspène, 2005, Recovery of APOBEC3-edited human immunodeficiency virus G→A hypermutants by differential DNA denaturation PCR, J. Gen. Virol., 86, 125, 10.1099/vir.0.80426-0 Ara, 2014, Different mutagenic potential of HIV-1 restriction factors APOBEC3G and APOBEC3F is determined by distinct single-stranded DNA scanning mechanisms, PLoS Pathog., 10, 10.1371/journal.ppat.1004024 Stephens, 2012, The landscape of cancer genes and mutational processes in breast cancer, Nature, 486, 400, 10.1038/nature11017 Baumert, 2007, Hepatitis B virus DNA is subject to extensive editing by the human deaminase APOBEC3C, Hepatology, 46, 682, 10.1002/hep.21733 Hultquist, 2011, Human and rhesus APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H demonstrate a conserved capacity to restrict Vif-deficient HIV-1, J. Virol., 84, 11,220, 10.1128/JVI.05238-11 Sato, 2014, APOBEC3D and APOBEC3F potently promote HIV-1 diversification and evolution in humanized mouse model, PLoS Pathog., 10, 10.1371/journal.ppat.1004453 Schoggins, 2011, A diverse range of gene products are effectors of the type I interferon antiviral response, Nature, 472, 481, 10.1038/nature09907 Polson, 1996, RNA editing of hepatitis delta virus antigenome by dsRNA-adenosine deaminase, Nature, 380, 454, 10.1038/380454a0 Gagneux, 1999, Mitochondrial sequences show diverse evolutionary histories of African hominoids, Proc. Natl. Acad. Sci. U. S. A., 96, 5077, 10.1073/pnas.96.9.5077 Pineau, 2008, Chromosome instability in human hepatocellular carcinoma depends on p53 status and aflatoxin exposure, Mutat. Res., 653, 6, 10.1016/j.mrgentox.2008.01.012 Pineau, 1999, Identification of three distinct regions of allelic deletions on the short arm of chromosome 8 in hepatocellular carcinoma, Oncogene, 18, 3127, 10.1038/sj.onc.1202648 Marchio, 2000, Distinct chromosomal abnormality pattern in primary liver cancer of non-B, non-C patients, Oncogene, 19, 3733, 10.1038/sj.onc.1203713