Cited by 23

The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.

Insights into the Structures and Multimeric Status of APOBEC Proteins Involved in Viral Restriction and Other Cellular Functions

Chen, Xiaojiang S.·2021·Viruses

Abstract

Apolipoprotein B mRNA editing catalytic polypeptide-like (APOBEC) proteins belong to a family of deaminase proteins that can catalyze the deamination of cytosine to uracil on single-stranded DNA or/and RNA. APOBEC proteins are involved in diverse biological functions, including adaptive and innate immunity, which are critical for restricting viral infection and endogenous retroelements. Dysregulation of their functions can cause undesired genomic mutations and RNA modification, leading to various associated diseases, such as hyper-IgM syndrome and cancer. This review focuses on the structural and biochemical data on the multimerization status of individual APOBECs and the associated functional implications. Many APOBECs form various multimeric complexes, and multimerization is an important way to regulate functions for some of these proteins at several levels, such as deaminase activity, protein stability, subcellular localization, protein storage and activation, virion packaging, and antiviral activity. The multimerization of some APOBECs is more complicated than others, due to the associated complex RNA binding modes.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.3390/v13030497

Cites

2 of 2 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Show all 2 references

Research works printed but not linked: 204

  1. Prochnow, 2007, The APOBEC-2 crystal structure and functional implications for the deaminase AID, Nature, 445, 447, 10.1038/nature05492 · DOI
  2. Conticello, 2008, The AID/APOBEC family of nucleic acid mutators, Genome Biol., 9, 229, 10.1186/gb-2008-9-6-229 · DOI
  3. Olson, 2018, APOBEC Enzymes as Targets for Virus and Cancer Therapy, Cell Chem. Biol., 25, 36, 10.1016/j.chembiol.2017.10.007 · DOI · Paper page
  4. Muramatsu, 1999, Specific Expression of Activation-induced Cytidine Deaminase (AID), a Novel Member of the RNA-editing Deaminase Family in Germinal Center B Cells, J. Biol. Chem., 274, 18470, 10.1074/jbc.274.26.18470 · DOI
  5. Muto, 2000, Isolation, tissue distribution, and chromosomal localization of the human activation-induced cytidine deaminase (AID) gene, Genomics, 68, 85, 10.1006/geno.2000.6268 · DOI
  6. Cheng, 2019, Epstein-Barr virus BORF2 inhibits cellular APOBEC3B to preserve viral genome integrity, Nat. Microbiol., 4, 78, 10.1038/s41564-018-0284-6 · DOI
  7. Sheehy, 2002, Isolation of a human gene that inhibits HIV-1 infection and is suppressed by the viral Vif protein, Nat. Cell Biol., 418, 646
  8. Desimmie, 2014, Multiple APOBEC3 Restriction Factors for HIV-1 and One Vif to Rule Them All, J. Mol. Biol., 426, 1220, 10.1016/j.jmb.2013.10.033 · DOI
  9. Refsland, 2013, The APOBEC3 Family of Retroelement Restriction Factors, Curr.Top. Microbiol. Immunol., 371, 1
  10. Pollpeter, 2018, Deep sequencing of HIV-1 reverse transcripts reveals the multifaceted antiviral functions of APOBEC3G, Nat. Microbiol., 3, 220, 10.1038/s41564-017-0063-9 · DOI
  11. Xu, W.K., Byun, H., and Dudley, J.P. (2020). The Role of APOBECs in Viral Replication. Microorganisms, 8. · DOI
  12. Salter, 2019, Regulation of Antiviral Innate Immunity Through APOBEC Ribonucleoprotein Complexes, Subcell. Biochem., 93, 193, 10.1007/978-3-030-28151-9_6 · DOI
  13. Willems, 2015, APOBEC3 Interference during Replication of Viral Genomes, Viruses, 7, 2999, 10.3390/v7062757 · DOI
  14. Stavrou, 2015, APOBEC3 Proteins in Viral Immunity, J. Immunol., 195, 4565, 10.4049/jimmunol.1501504 · DOI
  15. Chen, 1987, Apolipoprotein B-48 is the product of a messenger RNA with an organ-specific in-frame stop codon, Science, 238, 363, 10.1126/science.3659919 · DOI
  16. Teng, 1993, Molecular cloning of an apolipoprotein B messenger RNA editing protein, Science, 260, 1816, 10.1126/science.8511591 · DOI · Paper page
  17. Liao, 1999, APOBEC-2, a Cardiac- and Skeletal Muscle-Specific Member of the Cytidine Deaminase Supergene Family, Biochem. Biophys. Res. Commun., 260, 398, 10.1006/bbrc.1999.0925 · DOI
  18. Etard, 2010, Lack of Apobec2-related proteins causes a dystrophic muscle phenotype in zebrafish embryos, J. Cell Biol., 189, 527, 10.1083/jcb.200912125 · DOI
  19. Ohtsubo, 2017, APOBEC2 negatively regulates myoblast differentiation in muscle regeneration, Int. J. Biochem. Cell Biol., 85, 91, 10.1016/j.biocel.2017.02.005 · DOI
  20. Sato, 2018, Apobec2 deficiency causes mitochondrial defects and mitophagy in skeletal muscle, FASEB J., 32, 1428, 10.1096/fj.201700493R · DOI
  21. Sato, 2010, Deficiency in APOBEC2 Leads to a Shift in Muscle Fiber Type, Diminished Body Mass, and Myopathy, J. Biol. Chem., 285, 7111, 10.1074/jbc.M109.052977 · DOI
  22. Marino, D., Perković, M., Hain, A., Vasudevan, A.A.J., Hofmann, H., Hanschmann, K.-M., Mühlebach, M.D., Schumann, G.G., König, R., and Cichutek, K. (2016). APOBEC4 Enhances the Replication of HIV-1. PLoS ONE, 11. · DOI
  23. Rogozin, 2005, APOBEC4, a New Member of the AID/APOBEC Family of Polynucleotide (Deoxy)Cytidine Deaminases Predicted by Computational Analysis, Cell Cycle, 4, 1281, 10.4161/cc.4.9.1994 · DOI
  24. Kankowski, 2018, A Novel RNA Editing Sensor Tool and a Specific Agonist Determine Neuronal Protein Expression of RNA-Edited Glycine Receptors and Identify a Genomic APOBEC1 Dimorphism as a New Genetic Risk Factor of Epilepsy, Front. Mol. Neurosci., 10, 439, 10.3389/fnmol.2017.00439 · DOI
  25. Burns, 2013, APOBEC3B is an enzymatic source of mutation in breast cancer, Nat. Cell Biol., 494, 366
  26. Venkatesan, 2018, Perspective: APOBEC mutagenesis in drug resistance and immune escape in HIV and cancer evolution, Ann. Oncol., 29, 563, 10.1093/annonc/mdy003 · DOI
  27. Chiu, 2006, High-molecular-mass APOBEC3G complexes restrict Alu retrotransposition, Proc. Natl. Acad. Sci. USA, 103, 15588, 10.1073/pnas.0604524103 · DOI
  28. Wedekind, 2006, Nanostructures of APOBEC3G Support a Hierarchical Assembly Model of High Molecular Mass Ribonucleoprotein Particles from Dimeric Subunits *, J. Biol. Chem., 281, 38122, 10.1074/jbc.C600253200 · DOI
  29. Niewiadomska, 2006, Differential Inhibition of Long Interspersed Element 1 by APOBEC3 Does Not Correlate with High-Molecular-Mass-Complex Formation or P-Body Association, J. Virol., 81, 9577, 10.1128/JVI.02800-06 · DOI
  30. Wichroski, M.J., Robb, G.B., and Rana, T.M. (2006). Human Retroviral Host Restriction Factors APOBEC3G and APOBEC3F Localize to mRNA Processing Bodies. PLoS Pathog., 2. · DOI
  31. Li, 2014, APOBEC3 Multimerization Correlates with HIV-1 Packaging and Restriction Activity in Living Cells, J. Mol. Biol., 426, 1296, 10.1016/j.jmb.2013.12.014 · DOI
  32. Kreisberg, 2006, Endogenous factors enhance HIV infection of tissue naive CD4 T cells by stimulating high molecular mass APOBEC3G complex formation, J. Exp. Med., 203, 865, 10.1084/jem.20051856 · DOI
  33. Burnett, 2007, APOBEC3G Multimers Are Recruited to the Plasma Membrane for Packaging into Human Immunodeficiency Virus Type 1 Virus-Like Particles in an RNA-Dependent Process Requiring the NC Basic Linker, J. Virol., 81, 5000, 10.1128/JVI.02237-06 · DOI
  34. Huthoff, H., Autore, F., Gallois-Montbrun, S., Fraternali, F., and Malim, M.H. (2009). RNA-Dependent Oligomerization of APOBEC3G Is Required for Restriction of HIV-1. PLoS Pathog., 5. · DOI
  35. Bohn, 2017, APOBEC3H structure reveals an unusual mechanism of interaction with duplex RNA, Nat. Commun., 8, 1021, 10.1038/s41467-017-01309-6 · DOI
  36. Matsuoka, 2018, Structural basis of chimpanzee APOBEC3H dimerization stabilized by double-stranded RNA, Nucleic Acids Res., 46, 10368, 10.1093/nar/gky676 · DOI
  37. Shaban, 2018, The Antiviral and Cancer Genomic DNA Deaminase APOBEC3H Is Regulated by a RNA-Mediated Dimerization Mechanism, SSRN Electron. J., 69, 75
  38. Ito, 2018, Understanding the Structure, Multimerization, Subcellular Localization and mC Selectivity of a Genomic Mutator and Anti-HIV Factor APOBEC3H, Sci. Rep., 8, 3763, 10.1038/s41598-018-21955-0 · DOI
  39. Conticello, 2004, Evolution of the AID/APOBEC Family of Polynucleotide (Deoxy)cytidine Deaminases, Mol. Biol. Evol., 22, 367, 10.1093/molbev/msi026 · DOI
  40. Bransteitter, 2006, First AID (Activation-induced Cytidine Deaminase) Is Needed to Produce High Affinity Isotype-switched Antibodies, J. Biol. Chem., 281, 16833, 10.1074/jbc.R600006200 · DOI
  41. Pham, 2003, Processive AID-catalysed cytosine deamination on single-stranded DNA simulates somatic hypermutation, Nat. Cell Biol., 424, 103
  42. Larijani, 2005, Methylation protects cytidines from AID-mediated deamination, Mol. Immunol., 42, 599, 10.1016/j.molimm.2004.09.007 · DOI
  43. Rogozin, 2006, The cytidine deaminase AID exhibits similar functional properties in yeast and mammals, Mol. Immunol., 43, 1481, 10.1016/j.molimm.2005.09.002 · DOI
  44. Honjo, 2005, AID to overcome the limitations of genomic information, Nat. Immunol., 6, 655, 10.1038/ni1218 · DOI
  45. Han, 2011, Overlapping activation-induced cytidine deaminase hotspot motifs in Ig class-switch recombination, Proc. Natl. Acad. Sci. USA, 108, 11584, 10.1073/pnas.1018726108 · DOI
  46. Yeap, 2015, Sequence-Intrinsic Mechanisms that Target AID Mutational Outcomes on Antibody Genes, Cell, 163, 1124, 10.1016/j.cell.2015.10.042 · DOI
  47. Yeap, 2019, Cis- and trans-factors affecting AID targeting and mutagenic outcomes in antibody diversification, Adv. Immunol., 141, 51, 10.1016/bs.ai.2019.01.002 · DOI
  48. Xu, 2012, Immunoglobulin class-switch DNA recombination: Induction, targeting and beyond, Nat. Rev. Immunol., 12, 517, 10.1038/nri3216 · DOI
  49. Revy, 2000, Activation-induced cytidine deaminase (AID) deficiency causes the autosomal recessive form of the Hy-per-IgM syndrome (HIGM2), Cell, 102, 565, 10.1016/S0092-8674(00)00079-9 · DOI
  50. Feng, 2020, AID in Antibody Diversification: There and Back Again, Trends Immunol., 41, 586, 10.1016/j.it.2020.04.009 · DOI
  51. Qiao, 2017, AID Recognizes Structured DNA for Class Switch Recombination, Mol. Cell, 67, 361, 10.1016/j.molcel.2017.06.034 · DOI
  52. Pham, 2016, Structural analysis of the activation-induced deoxycytidine deaminase required in immunoglobulin diversification, DNA Repair, 43, 48, 10.1016/j.dnarep.2016.05.029 · DOI
  53. Bransteitter, 2003, Activation-induced cytidine deaminase deaminates deoxycytidine on single-stranded DNA but requires the action of RNase, Proc. Natl. Acad. Sci. USA, 100, 4102, 10.1073/pnas.0730835100 · DOI
  54. Qian, 2014, B Cell Super-Enhancers and Regulatory Clusters Recruit AID Tumorigenic Activity, Cell, 159, 1524, 10.1016/j.cell.2014.11.013 · DOI
  55. Larijani, 2006, AID Associates with Single-Stranded DNA with High Affinity and a Long Complex Half-Life in a Sequence-Independent Manner, Mol. Cell. Biol., 27, 20, 10.1128/MCB.00824-06 · DOI
  56. Zheng, 2015, Non-coding RNA Generated following Lariat Debranching Mediates Targeting of AID to DNA, Cell, 161, 762, 10.1016/j.cell.2015.03.020 · DOI
  57. Chaudhuri, 2004, Class-switch recombination: Interplay of transcription, DNA deamination and DNA repair, Nat. Rev. Immunol., 4, 541, 10.1038/nri1395 · DOI
  58. Pavri, 2010, Activation-Induced Cytidine Deaminase Targets DNA at Sites of RNA Polymerase II Stalling by Interaction with Spt5, Cell, 143, 122, 10.1016/j.cell.2010.09.017 · DOI
  59. Xu, 2010, 14-3-3 adaptor proteins recruit AID to 5′-AGCT-3′-rich switch regions for class switch recombination, Nat. Struct. Mol. Biol., 17, 1124, 10.1038/nsmb.1884 · DOI
  60. Methot, 2018, A licensing step links AID to transcription elongation for mutagenesis in B cells, Nat. Commun., 9, 1248, 10.1038/s41467-018-03387-6 · DOI
  61. Powell, 1987, A novel form of tissue-specific RNA processing produces apolipoprotein-B48 in intestine, Cell, 50, 831, 10.1016/0092-8674(87)90510-1 · DOI
  62. Navaratnam, 1993, The p27 catalytic subunit of the apolipoprotein B mRNA editing enzyme is a cytidine deaminase, J. Biol. Chem., 268, 20709, 10.1016/S0021-9258(19)36836-X · DOI
  63. Blanc, 2010, Apobec-1 complementation factor modulates liver regeneration by post-transcriptional regulation of in-terleukin-6 mRNA stability, J. Biol. Chem., 285, 19184, 10.1074/jbc.M110.115147 · DOI
  64. Mehta, 2002, Identification of domains in apobec-1 complementation factor required for RNA binding and apolipoprotein-B mRNA editing, RNA, 8, 69, 10.1017/S1355838202015649 · DOI
  65. Lellek, 2000, Purification and Molecular Cloning of a Novel Essential Component of the Apolipoprotein B mRNA Editing Enzyme-Complex, J. Biol. Chem., 275, 19848, 10.1074/jbc.M001786200 · DOI · Paper page
  66. Chester, 2004, Optimization of apolipoprotein B mRNA editing by APOBEC1 apoenzyme and the role of its auxiliary factor, ACF, RNA, 10, 1399, 10.1261/rna.7490704 · DOI
  67. Fossat, 2014, C to U RNA editing mediated by APOBEC 1 requires RNA-binding protein RBM 47, EMBO Rep., 15, 903, 10.15252/embr.201438450 · DOI · Paper page
  68. Blanc, 2019, Apobec1 complementation factor (A1CF) and RBM47 interact in tissue-specific regulation of C to U RNA editing in mouse intestine and liver, RNA, 25, 70, 10.1261/rna.068395.118 · DOI · Paper page
  69. Fossat, 2016, Conditional restoration and inactivation ofRbm47reveal its tissue-context requirement for viability and growth, Genesis, 54, 115, 10.1002/dvg.22920 · DOI
  70. Snyder, 2017, APOBEC1 complementation factor (A1CF) is dispensable for C-to-U RNA editing in vivo, RNA, 23, 457, 10.1261/rna.058818.116 · DOI
  71. Wolfe, 2019, Comparison of RNA Editing Activity of APOBEC1-A1CF and APOBEC1-RBM47 Complexes Reconstituted in HEK293T Cells, J. Mol. Biol., 431, 1506, 10.1016/j.jmb.2019.02.025 · DOI · Paper page
  72. Rosenberg, 2011, Transcriptome-wide sequencing reveals numerous APOBEC1 mRNA-editing targets in transcript 3′ UTRs, Nat. Struct. Mol. Biol., 18, 230, 10.1038/nsmb.1975 · DOI · Paper page
  73. Blanc, 2014, Genome-wide identification and functional analysis of Apobec-1-mediated C-to-U RNA editing in mouse small intestine and liver, Genome Biol., 15, R79, 10.1186/gb-2014-15-6-r79 · DOI
  74. Smith, 1991, In vitro apolipoprotein B mRNA editing: Identification of a 27S editing complex, Proc. Natl. Acad. Sci. USA, 88, 1489, 10.1073/pnas.88.4.1489 · DOI
  75. Sowden, 2002, The editosome for cytidine to uridine mRNA editing has a native complexity of 27S: Identification of intracellular domains containing active and inactive editing factors, J. Cell Sci., 115, 1027, 10.1242/jcs.115.5.1027 · DOI
  76. Wolfe, 2020, The structure of APOBEC1 and insights into its RNA and DNA substrate selectivity, NAR Cancer, 2, 27, 10.1093/narcan/zcaa027 · DOI · Paper page
  77. Teng, 1999, Mutational analysis of apolipoprotein B mRNA editing enzyme (APOBEC1): Structure-function relationships of RNA editing and dimerization, J. Lipid Res., 40, 623, 10.1016/S0022-2275(20)32141-6 · DOI
  78. Lau, 1994, Dimeric structure of a human apolipoprotein B mRNA editing protein and cloning and chromosomal localization of its gene, Proc. Natl. Acad. Sci. USA, 91, 8522, 10.1073/pnas.91.18.8522 · DOI
  79. Chieca, M., Montini, M., Severi, F., Pecori, R., and Conticello, S.G. (2018). Dimerisation of APOBEC1 is dispensable for its RNA editing activity. bioRxiv. · DOI
  80. Vasudevan, 2013, Structural features of antiviral DNA cytidine deaminases, Biol. Chem., 394, 1357, 10.1515/hsz-2013-0165 · DOI
  81. Navaratnam, 1998, Escherichia coli cytidine deaminase provides a molecular model for ApoB RNA editing and a mechanism for RNA substrate recognition, J. Mol. Biol., 275, 695, 10.1006/jmbi.1997.1506 · DOI
  82. Chester, 2003, The apolipoprotein B mRNA editing complex performs a multifunctional cycle and suppresses nonsense-mediated decay, EMBO J., 22, 3971, 10.1093/emboj/cdg369 · DOI
  83. Banani, 2017, Biomolecular condensates: Organizers of cellular biochemistry, Nat. Rev. Mol. Cell Biol., 18, 285, 10.1038/nrm.2017.7 · DOI
  84. Feric, 2016, Coexisting Liquid Phases Underlie Nucleolar Subcompartments, Cell, 165, 1686, 10.1016/j.cell.2016.04.047 · DOI
  85. Hyman, 2014, Liquid-Liquid Phase Separation in Biology, Annu. Rev. Cell Dev. Biol., 30, 39, 10.1146/annurev-cellbio-100913-013325 · DOI · Paper page
  86. Shin, 2017, Liquid phase condensation in cell physiology and disease, Science, 357, eaaf4382, 10.1126/science.aaf4382 · DOI
  87. Ito, 2017, Family-Wide Comparative Analysis of Cytidine and Methylcytidine Deamination by Eleven Human APOBEC Pro-teins, J. Mol. Biol., 429, 1787, 10.1016/j.jmb.2017.04.021 · DOI
  88. Harris, 2002, RNA Editing Enzyme APOBEC1 and Some of Its Homologs Can Act as DNA Mutators, Mol. Cell, 10, 1247, 10.1016/S1097-2765(02)00742-6 · DOI
  89. Powell, 2014, Zinc-Binding Domain-Dependent, Deaminase-Independent Actions of Apolipoprotein B mRNA Editing Enzyme, Catalytic Polypeptide 2 (Apobec2) Mediate Its Effect on Zebrafish Retina Regeneration, J. Biol. Chem., 289, 28924, 10.1074/jbc.M114.603043 · DOI
  90. Vonica, 2011, APOBEC2, a selective inhibitor of TGFbeta signaling, regulates left-right axis specification during early embryogenesis, Dev. Biol., 350, 13, 10.1016/j.ydbio.2010.09.016 · DOI
  91. Krzysiak, 2012, APOBEC2 Is a Monomer in Solution: Implications for APOBEC3G Models, Biochemistry, 51, 2008, 10.1021/bi300021s · DOI
  92. Carpenter, 2012, Methylcytosine and Normal Cytosine Deamination by the Foreign DNA Restriction Enzyme APOBEC3A, J. Biol. Chem., 287, 34801, 10.1074/jbc.M112.385161 · DOI
  93. Gu, 2016, Biochemical Characterization of APOBEC3H Variants: Implications for Their HIV-1 Restriction Activity and mC Modification, J. Mol. Biol., 428, 4626, 10.1016/j.jmb.2016.08.012 · DOI
  94. Stenglein, 2010, APOBEC3 proteins mediate the clearance of foreign DNA from human cells, Nat. Struct. Mol. Biol., 17, 222, 10.1038/nsmb.1744 · DOI
  95. Narvaiza, I., Linfesty, D.C., Greener, B.N., Hakata, Y., Pintel, D.J., Logue, E., Landau, N.R., and Weitzman, M.D. (2009). Deaminase-Independent Inhibition of Parvoviruses by the APOBEC3A Cytidine Deaminase. PLoS Pathog., 5. · DOI
  96. Ahasan, 2015, APOBEC3A and 3C decrease human papillomavirus 16 pseudovirion infectivity, Biochem. Biophys. Res. Commun., 457, 295, 10.1016/j.bbrc.2014.12.103 · DOI
  97. Warren, 2014, APOBEC3A Functions as a Restriction Factor of Human Papillomavirus, J. Virol., 89, 688, 10.1128/JVI.02383-14 · DOI
  98. Wang, 2016, Role of the single deaminase domain APOBEC3A in virus restriction, retrotransposition, DNA damage and cancer, J. Gen. Virol., 97, 1, 10.1099/jgv.0.000320 · DOI
  99. McLaughlin, 2016, Conservation and Innovation of APOBEC3A Restriction Functions during Primate Evolution, Mol. Biol. Evol., 33, 1889, 10.1093/molbev/msw070 · DOI
  100. Richardson, 2014, APOBEC3A deaminates transiently exposed single-strand DNA during LINE-1 retrotransposition, Elife, 3, e02008, 10.7554/eLife.02008 · DOI
  101. Chen, 2006, APOBEC3A Is a Potent Inhibitor of Adeno-Associated Virus and Retrotransposons, Curr. Biol., 16, 480, 10.1016/j.cub.2006.01.031 · DOI
  102. Pham, 2013, A Biochemical Analysis Linking APOBEC3A to Disparate HIV-1 Restriction and Skin Cancer, J. Biol. Chem., 288, 29294, 10.1074/jbc.M113.504175 · DOI
  103. Filho, 2016, Impact of functional germline variants and a deletion polymorphism in APOBEC3A and APOBEC3B on breast cancer risk and survival in a Swedish study population, J. Cancer Res. Clin. Oncol., 142, 273, 10.1007/s00432-015-2038-7 · DOI
  104. Vural, 2018, Correlation of gene expression and associated mutation profiles of APOBEC3A, APOBEC3B, REV1, UNG, and FHIT with chemosensitivity of cancer cell lines to drug treatment, Hum. Genom., 12, 20, 10.1186/s40246-018-0150-x · DOI
  105. Sharma, 2015, APOBEC3A cytidine deaminase induces RNA editing in monocytes and macrophages, Nat. Commun., 6, 6881, 10.1038/ncomms7881 · DOI · Paper page
  106. Sharma, 2017, Stem-loop structure preference for site-specific RNA editing by APOBEC3A and APOBEC3G, PeerJ, 5, e4136, 10.7717/peerj.4136 · DOI
  107. Jalili, 2020, Quantification of ongoing APOBEC3A activity in tumor cells by monitoring RNA editing at hotspots, Nat. Commun., 11, 1, 10.1038/s41467-020-16802-8 · DOI
  108. Byeon, 2013, NMR structure of human restriction factor APOBEC3A reveals substrate binding and enzyme specificity, Nat. Commun., 4, 1890, 10.1038/ncomms2883 · DOI
  109. Bohn, 2015, The ssDNA Mutator APOBEC3A Is Regulated by Cooperative Dimerization, Structure, 23, 903, 10.1016/j.str.2015.03.016 · DOI
  110. Love, 2012, Biochemical Analysis of Hypermutation by the Deoxycytidine Deaminase APOBEC3A, J. Biol. Chem., 287, 30812, 10.1074/jbc.M112.393181 · DOI
  111. Adolph, 2017, Enzyme cycling contributes to efficient induction of genome mutagenesis by the cytidine deaminase APOBEC3B, Nucleic Acids Res., 45, 11925, 10.1093/nar/gkx832 · DOI
  112. Kouno, 2017, Crystal structure of APOBEC3A bound to single-stranded DNA reveals structural basis for cytidine deamination and specificity, Nat. Commun., 8, 15024, 10.1038/ncomms15024 · DOI
  113. Shi, 2017, Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B, Nat. Struct. Mol. Biol., 24, 131, 10.1038/nsmb.3344 · DOI
  114. Wittkopp, C.J., Adolph, M.B., Wu, L.I., Chelico, L., and Emerman, M. (2016). A Single Nucleotide Polymorphism in Human APOBEC3C Enhances Restriction of Lentiviruses. PLoS Pathog., 12. · DOI
  115. Yu, 2004, APOBEC3B and APOBEC3C Are Potent Inhibitors of Simian Immunodeficiency Virus Replication, J. Biol. Chem., 279, 53379, 10.1074/jbc.M408802200 · DOI
  116. Langlois, 2005, Mutational comparison of the single-domained APOBEC3C and double-domained APOBEC3F/G anti-retroviral cytidine deaminases provides insight into their DNA target site specificities, Nucleic Acids Res., 33, 1913, 10.1093/nar/gki343 · DOI
  117. Wang, 2008, Distinct viral determinants for the packaging of human cytidine deaminases APOBEC3G and APOBEC3C, Virology, 377, 71, 10.1016/j.virol.2008.04.012 · DOI
  118. Vasudevan, 2017, Enhancing the Catalytic Deamination Activity of APOBEC3C Is Insufficient to Inhibit Vif-Deficient HIV-1, J. Mol. Biol., 429, 1171, 10.1016/j.jmb.2017.03.015 · DOI
  119. Bourara, K., Liegler, T.J., and Grant, R.M. (2007). Target Cell APOBEC3C Can Induce Limited G-to-A Mutation in HIV-1. PLoS Pathog., 3. · DOI
  120. Kitamura, 2012, The APOBEC3C crystal structure and the interface for HIV-1 Vif binding, Nat. Struct. Mol. Biol., 19, 1005, 10.1038/nsmb.2378 · DOI
  121. Smith, 2010, Identification of Specific Determinants of Human APOBEC3F, APOBEC3C, and APOBEC3DE and African Green Monkey APOBEC3F That Interact with HIV-1 Vif, J. Virol., 84, 12599, 10.1128/JVI.01437-10 · DOI
  122. Muckenfuss, 2006, APOBEC3 Proteins Inhibit Human LINE-1 Retrotransposition, J. Biol. Chem., 281, 22161, 10.1074/jbc.M601716200 · DOI
  123. Baumert, 2007, Hepatitis B virus DNA is subject to extensive editing by the human deaminase APOBEC3C, Hepatology, 46, 682, 10.1002/hep.21733 · DOI
  124. Stauch, 2009, Model structure of APOBEC3C reveals a binding pocket modulating ribonucleic acid interaction required for encapsidation, Proc. Natl. Acad. Sci. USA, 106, 12079, 10.1073/pnas.0900979106 · DOI
  125. Schmidt, 2009, Species-specific Inhibition of APOBEC3C by the Prototype Foamy Virus Protein Bet, J. Biol. Chem., 284, 5819, 10.1074/jbc.M808853200 · DOI
  126. Horn, 2014, Human LINE-1 restriction by APOBEC3C is deaminase independent and mediated by an ORF1p interaction that affects LINE reverse transcriptase activity, Nucleic Acids Res., 42, 396, 10.1093/nar/gkt898 · DOI
  127. Aynaud, 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 · DOI
  128. Vartanian, 2008, Evidence for Editing of Human Papillomavirus DNA by APOBEC3 in Benign and Precancerous Lesions, Science, 320, 230, 10.1126/science.1153201 · DOI
  129. Henry, 2005, Extensive editing of both hepatitis B virus DNA strands by APOBEC3 cytidine deaminases in vitro and in vivo, Proc. Natl. Acad. Sci. USA, 102, 8321, 10.1073/pnas.0408223102 · DOI
  130. Adolph, 2017, Cytidine deaminase efficiency of the lentiviral viral restriction factor APOBEC3C correlates with dimerization, Nucleic Acids Res., 45, 3378, 10.1093/nar/gkx066 · DOI
  131. Duggal, 2013, Identification and antiviral activity of common polymorphisms in the APOBEC3 locus in human populations, Virology, 443, 329, 10.1016/j.virol.2013.05.016 · DOI
  132. McDonnell, 2020, APOBEC3C Tandem Domain Proteins Create Super Restriction Factors against HIV-1, mBio, 11, 134, 10.1128/mBio.00737-20 · DOI
  133. Vasudevan, 2020, Loop 1 of APOBEC3C Regulates its Antiviral Activity against HIV-1, J. Mol. Biol., 432, 6200, 10.1016/j.jmb.2020.10.014 · DOI
  134. OhAinle, 2008, Antiretroelement Activity of APOBEC3H was Lost Twice in Recent Human Evolution, Cell Host Microbe, 4, 249, 10.1016/j.chom.2008.07.005 · DOI
  135. OhAinle, 2006, Adaptive Evolution and Antiviral Activity of the Conserved Mammalian cytidine deaminase APOBEC3H, J. Virol., 80, 3853, 10.1128/JVI.80.8.3853-3862.2006 · DOI
  136. Wang, 2011, Analysis of Human APOBEC3H Haplotypes and Anti-Human Immunodeficiency Virus Type 1 Activity, J. Virol., 85, 3142, 10.1128/JVI.02049-10 · DOI
  137. Harari, 2008, Polymorphisms and Splice Variants Influence the Antiretroviral Activity of Human APOBEC3H, J. Virol., 83, 295, 10.1128/JVI.01665-08 · DOI
  138. Hultquist, 2011, Human and Rhesus APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H Demonstrate a Conserved Capacity To Restrict Vif-Deficient HIV-1, J. Virol., 85, 11220, 10.1128/JVI.05238-11 · DOI
  139. Ooms, 2013, HIV-1 Vif Adaptation to Human APOBEC3H Haplotypes, Cell Host Microbe, 14, 411, 10.1016/j.chom.2013.09.006 · DOI
  140. Refsland, E.W., Hultquist, J.F., Luengas, E.M., Ikeda, T., Shaban, N.M., Law, E.K., Brown, W.L., Reilly, C., Emerman, M., and Harris, R.S. (2014). Natural Polymorphisms in Human APOBEC3H and HIV-1 Vif Combine in Primary T Lymphocytes to Affect Viral G-to-A Mutation Levels and Infectivity. PLoS Genet., 10. · DOI
  141. Starrett, 2016, The DNA cytosine deaminase APOBEC3H haplotype I likely contributes to breast and lung cancer mutagenesis, Nat. Commun., 7, 12918, 10.1038/ncomms12918 · DOI
  142. Hix, 2020, Single-nucleotide polymorphism of the DNA cytosine deaminase APOBEC3H haplotype I leads to enzyme destabilization and correlates with lung cancer, NAR Cancer, 2, 134, 10.1093/narcan/zcaa023 · DOI
  143. Tan, 2008, Sole copy of Z2-type human cytidine deaminase APOBEC3H has inhibitory activity against retrotransposons and HIV-1, FASEB J., 23, 279, 10.1096/fj.07-088781 · DOI
  144. Mitra, 2015, Sequence and structural determinants of human APOBEC3H deaminase and anti-HIV-1 activities, Retrovirology, 12, 3, 10.1186/s12977-014-0130-8 · DOI
  145. Yang, 2020, Understanding the structural basis of HIV-1 restriction by the full length double-domain APOBEC3G, Nat. Commun., 11, 632, 10.1038/s41467-020-14377-y · DOI
  146. Bohn, 2019, Flexibility in Nucleic Acid Binding Is Central to APOBEC3H Antiviral Activity, J. Virol., 93, 137, 10.1128/JVI.01275-19 · DOI
  147. Xiao, 2016, Crystal structures of APOBEC3G N-domain alone and its complex with DNA, Nat. Commun., 7, 12193, 10.1038/ncomms12193 · DOI
  148. Harris, 2004, Retroviral restriction by APOBEC proteins, Nat. Rev. Immunol., 4, 868, 10.1038/nri1489 · DOI
  149. Cescon, 2016, DNA replication stress: A source of APOBEC3B expression in breast cancer, Genome Biol., 17, 202, 10.1186/s13059-016-1069-y · DOI
  150. Kumar, 2017, Elevated APOBEC3B expression drives a kataegic-like mutation signature and replication stress-related therapeutic vulnerabilities in p53-defective cells, Br. J. Cancer, 117, 113, 10.1038/bjc.2017.133 · DOI
  151. Kanu, 2016, DNA replication stress mediates APOBEC3 family mutagenesis in breast cancer, Genome Biol., 17, 185, 10.1186/s13059-016-1042-9 · DOI
  152. Burns, 2013, Evidence for APOBEC3B mutagenesis in multiple human cancers, Nat. Genet., 45, 977, 10.1038/ng.2701 · DOI
  153. Kuong, 2013, APOBEC3B mutagenesis in cancer, Nat. Genet., 45, 964, 10.1038/ng.2736 · DOI
  154. Taylor, 2013, DNA deaminases induce break-associated mutation showers with implication of APOBEC3B and 3A in breast cancer kataegis, eLife, 2, e00534, 10.7554/eLife.00534 · DOI
  155. Song, 2012, Signals in APOBEC3F N-terminal and C-terminal Deaminase Domains Each Contribute to Encapsidation in HIV-1 Virions and Are Both Required for HIV-1 Restriction, J. Biol. Chem., 287, 16965, 10.1074/jbc.M111.310839 · DOI
  156. Wang, 2007, 7SL RNA Mediates Virion Packaging of the Antiviral Cytidine Deaminase APOBEC3G, J. Virol., 81, 13112, 10.1128/JVI.00892-07 · DOI
  157. Apolonia, L., Schulz, R., Curk, T., Rocha, P., Swanson, C.M., Schaller, T., Ule, J., and Malim, M.H. (2015). Promiscuous RNA Binding Ensures Effective Encapsidation of APOBEC3 Proteins by HIV-1. PLoS Pathog., 11. · DOI
  158. York, A., Kutluay, S.B., Errando, M., and Bieniasz, P.D. (2016). The RNA Binding Specificity of Human APOBEC3 Proteins Resembles That of HIV-1 Nucleocapsid. PLoS Pathog., 12. · DOI
  159. Doehle, 2005, Human APOBEC3B is a potent inhibitor of HIV-1 infectivity and is resistant to HIV-1 Vif, Virology, 339, 281, 10.1016/j.virol.2005.06.005 · DOI
  160. Dang, 2006, Identification of APOBEC3DE as Another Antiretroviral Factor from the Human APOBEC Family, J. Virol., 80, 10522, 10.1128/JVI.01123-06 · DOI
  161. Xiao, 2017, Structural determinants of APOBEC3B non-catalytic domain for molecular assembly and catalytic regulation, Nucleic Acids Res., 45, 7494, 10.1093/nar/gkx362 · DOI
  162. Wang, 2007, Biochemical Differentiation of APOBEC3F and APOBEC3G Proteins Associated with HIV-1 Life Cycle, J. Biol. Chem., 282, 1585, 10.1074/jbc.M610150200 · DOI
  163. 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 · DOI
  164. Savoie, 2013, Binding of RNA by APOBEC3G controls deamination-independent restriction of retroviruses, Nucleic Acids Res., 41, 7438, 10.1093/nar/gkt527 · DOI
  165. Polevoda, 2017, DNA mutagenic activity and capacity for HIV-1 restriction of the cytidine deaminase APOBEC3G depend on whether DNA or RNA binds to tyrosine 315, J. Biol. Chem., 292, 8642, 10.1074/jbc.M116.767889 · DOI
  166. Holden, 2008, Crystal structure of the anti-viral APOBEC3G catalytic domain and functional implications, Nat. Cell Biol., 456, 121
  167. Polevoda, 2015, RNA binding to APOBEC3G induces the disassembly of functional deaminase complexes by displacing single-stranded DNA substrates, Nucleic Acids Res., 43, 9434, 10.1093/nar/gkv970 · DOI
  168. Maiti, 2018, Crystal structure of the catalytic domain of HIV-1 restriction factor APOBEC3G in complex with ssDNA, Nat. Commun., 9, 2460, 10.1038/s41467-018-04872-8 · DOI
  169. Maiti, 2020, Crystal Structure of a Soluble APOBEC3G Variant Suggests ssDNA to Bind in a Channel that Extends between the Two Domains, J. Mol. Biol., 432, 6042, 10.1016/j.jmb.2020.10.020 · DOI
  170. Iwatani, 2006, Biochemical Activities of Highly Purified, Catalytically Active Human APOBEC3G: Correlation with Antiviral Effect, J. Virol., 80, 5992, 10.1128/JVI.02680-05 · DOI
  171. Navarro, 2005, Complementary function of the two catalytic domains of APOBEC3G, Virology, 333, 374, 10.1016/j.virol.2005.01.011 · DOI
  172. Iwatani, 2007, Deaminase-independent inhibition of HIV-1 reverse transcription by APOBEC3G, Nucleic Acids Res., 35, 7096, 10.1093/nar/gkm750 · DOI
  173. Svarovskaia, 2004, Human apolipoprotein B mRNA-editing enzyme-catalytic polypeptide-like 3G (APOBEC3G) is incorporated into HIV-1 virions through interactions with viral and nonviral RNAs, J. Biol. Chem., 279, 35822, 10.1074/jbc.M405761200 · DOI
  174. Chelico, 2010, Structural Model for Deoxycytidine Deamination Mechanisms of the HIV-1 Inactivation Enzyme APOBEC3G, J. Biol. Chem., 285, 16195, 10.1074/jbc.M110.107987 · DOI
  175. Shi, 2015, Crystal Structure of the DNA Deaminase APOBEC3B Catalytic Domain, J. Biol. Chem., 290, 28120, 10.1074/jbc.M115.679951 · DOI
  176. Byeon, 2016, Nuclear Magnetic Resonance Structure of the APOBEC3B Catalytic Domain: Structural Basis for Substrate Binding and DNA Deaminase Activity, Biochemistry, 55, 2944, 10.1021/acs.biochem.6b00382 · DOI
  177. Bohn, 2013, Crystal Structure of the DNA Cytosine Deaminase APOBEC3F: The Catalytically Active and HIV-1 Vif-Binding Domain, Structure, 21, 1042, 10.1016/j.str.2013.04.010 · DOI
  178. Siu, 2013, Structural determinants of HIV-1 Vif susceptibility and DNA binding in APOBEC3F, Nat. Commun., 4, 2593, 10.1038/ncomms3593 · DOI
  179. Nakashima, 2015, Structural Insights into HIV-1 Vif-APOBEC3F Interaction, J. Virol., 90, 1034, 10.1128/JVI.02369-15 · DOI
  180. Shaban, 2016, 1.92 Angstrom Zinc-Free APOBEC3F Catalytic Domain Crystal Structure, J. Mol. Biol., 428, 2307, 10.1016/j.jmb.2016.04.026 · DOI
  181. Chen, 2008, Structure of the DNA deaminase domain of the HIV-1 restriction factor APOBEC3G, Nat. Cell Biol., 452, 116
  182. Furukawa, 2009, Structure, interaction and real-time monitoring of the enzymatic reaction of wild-type APOBEC3G, EMBO J., 28, 440, 10.1038/emboj.2008.290 · DOI
  183. Harjes, 2009, An Extended Structure of the APOBEC3G Catalytic Domain Suggests a Unique Holoenzyme Model, J. Mol. Biol., 389, 819, 10.1016/j.jmb.2009.04.031 · DOI
  184. Shandilya, 2010, Crystal Structure of the APOBEC3G Catalytic Domain Reveals Potential Oligomerization Interfaces, Structure, 18, 28, 10.1016/j.str.2009.10.016 · DOI
  185. Lu, 2015, Crystal Structure of DNA Cytidine Deaminase ABOBEC3G Catalytic Deamination Domain Suggests a Binding Mode of Full-length Enzyme to Single-stranded DNA, J. Biol. Chem., 290, 4010, 10.1074/jbc.M114.624262 · DOI
  186. Fang, 2018, Molecular Interactions of a DNA Modifying Enzyme APOBEC3F Catalytic Domain with a Single-Stranded DNA, J. Mol. Biol., 430, 87, 10.1016/j.jmb.2017.11.007 · DOI
  187. Ziegler, S.J., Liu, C., Landau, M., Buzovetsky, O., Desimmie, B.A., Zhao, Q., Sasaki, T., Burdick, R.C., Pathak, V.K., and Anderson, K.S. (2018). Insights into DNA substrate selection by APOBEC3G from structural, biochemical, and functional studies. PLoS ONE, 13. · DOI
  188. Cheng, 2018, Crystal Structure of Cytidine Deaminase Human APOBEC3F Chimeric Catalytic Domain in Complex with DNA, Chin. J. Chem., 36, 1241, 10.1002/cjoc.201800508 · DOI
  189. Hu, 2019, Structural basis of antagonism of human APOBEC3F by HIV-1 Vif, Nat. Struct. Mol. Biol., 26, 1176, 10.1038/s41594-019-0343-6 · DOI
  190. Kouno, 2015, Structure of the Vif-binding domain of the antiviral enzyme APOBEC3G, Nat. Struct. Mol. Biol., 22, 485, 10.1038/nsmb.3033 · DOI
  191. Salter, 2009, A Hydrodynamic Analysis of APOBEC3G Reveals a Monomer-Dimer-Tetramer Self-Association That Has Implications for Anti-HIV Function, Biochemistry, 48, 10685, 10.1021/bi901642c · DOI
  192. 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 · DOI
  193. Bulliard, 2009, Functional Analysis and Structural Modeling of Human APOBEC3G Reveal the Role of Evolutionarily Conserved Elements in the Inhibition of Human Immunodeficiency Virus Type 1 Infection and Alu Transposition, J. Virol., 83, 12611, 10.1128/JVI.01491-09 · DOI
  194. Morse, 2017, Dimerization regulates both deami-nase-dependent and deaminase-independent HIV-1 restriction by APOBEC3G, Nat. Commun., 8, 597, 10.1038/s41467-017-00501-y · DOI
  195. Gorle, 2017, Computational Model and Dynamics of Monomeric Full-Length APOBEC3G, ACS Central Sci., 3, 1180, 10.1021/acscentsci.7b00346 · DOI
  196. Soros, V.B., Yonemoto, W., and Greene, W.C. (2007). Newly Synthesized APOBEC3G Is Incorporated into HIV Virions, Inhibited by HIV RNA, and Subsequently Activated by RNase H. PLoS Pathog., 3. · DOI
  197. Zhang, 2010, Association of Potent Human Antiviral Cytidine Deaminases with 7SL RNA and Viral RNP in HIV-1 Virions, J. Virol., 84, 12903, 10.1128/JVI.01632-10 · DOI
  198. Newman, 2005, Antiviral Function of APOBEC3G Can Be Dissociated from Cytidine Deaminase Activity, Curr. Biol., 15, 166, 10.1016/j.cub.2004.12.068 · DOI
  199. Bishop, K.N., Verma, M., Kim, E.-Y., Wolinsky, S.M., and Malim, M.H. (2008). APOBEC3G Inhibits Elongation of HIV-1 Reverse Transcripts. PLoS Pathog., 4. · DOI
  200. Stenglein, 2008, Two Regions within the Amino-Terminal Half of APOBEC3G Cooperate To Determine Cytoplasmic Localization, J. Virol., 82, 9591, 10.1128/JVI.02471-07 · DOI

200 of 204 shown

Cited by

Sorted by citations

See all 23

Metadata

Authors
Chen, X. S.
Affiliations
Molecular and Computational Biology, Departments of Biological Sciences, Chemistry, University of Southern California, Los Angeles, CA 90089, USA
Venue
Viruses
Publisher
MDPI AG
Published
2021-03-17
Volume
13
Issue
3
Pages
497
ISSN
1999-4915
Cited by
23
References
2
Language
en

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review