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APOBEC3 proteins mediate the clearance of foreign DNA from human cells

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Abstract

Bacteria evolved restriction endonucleases to prevent interspecies DNA transmission and bacteriophage infection. Here we show that human cells possess an analogous mechanism. APOBEC3A is induced by interferon following DNA detection, and it deaminates foreign double-stranded DNA cytidines to uridines. These atypical DNA nucleosides are converted by the uracil DNA glycosylase UNG2 to abasic lesions, which lead to foreign DNA degradation. This mechanism is evident in cell lines and primary monocytes, where up to 97% of cytidines in foreign DNA are deaminated. In contrast, cellular genomic DNA appears unaffected. Several other APOBEC3s also restrict foreign gene transfer. Related proteins exist in all vertebrates, indicating that foreign DNA restriction may be a conserved innate immune defense mechanism. The efficiency and fidelity of genetic engineering, gene therapy, and DNA vaccination are likely to be influenced by this anti-DNA defense system.

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Figure 1: APOBEC3A is expressed in monocytes and macrophages and is induced by interferon and CpG DNA.
Figure 2: Foreign DNA restriction by APOBEC3A.
Figure 3: APOBEC3A deaminates transfected plasmid DNA and generates lesions for uracil DNA glycosylase.
Figure 4: APOBEC3A mutates foreign DNA in primary human cells.
Figure 5: Foreign DNA restriction by multiple human APOBEC3 proteins.
Figure 6: Lack of detectable genomic DNA mutation in cells that restrict foreign DNA.
Figure 7: A model for foreign DNA restriction.

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Acknowledgements

We thank J. Albin, J. Hultquist, D. Kaufman, L. Lackey and D. Trono for thoughtful feedback, P. Hackett and S. McIvor (University of Minnesota) for SB reagents, H. Bull (University of Saskatchewan) for help with antibody production, B. Thielen and J. Lingappa (Univ. of Washington) for sharing in vitro DNA deaminase assay protocols, M. Cornwell and J. Valesano for technical assistance, B. Cullen (Duke University), R. Tsien (University of California, San Diego), and J. DiNoia (Institut de recherches cliniques de Montréal) for plasmid constructs and J. Hanten (3M) for reagents and helpful discussions in the early stages of these studies. M.D.S. was supported in part by a 3M Graduate Fellowship and a Cancer Biology Training Grant (CA009138). M.B.B. was supported in part by the Children's Cancer Research Fund, Minneapolis, Minnesota, USA. This work was supported by grants from the US National Institutes of Health, GM090437 and AI064046.

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M.D.S. worked together with R.S.H. on all aspects of these studies and did most of the experiments; M.B.B. and M.L. established the TK mutation assay and the in vitro DNA deamination assays, respectively; J.L. performed the virus infectivity experiments.

Corresponding author

Correspondence to Reuben S Harris.

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Supplementary Figures 1–7, Supplementary Tables 1–4 and Supplementary Methods (PDF 1439 kb)

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Stenglein, M., Burns, M., Li, M. et al. APOBEC3 proteins mediate the clearance of foreign DNA from human cells. Nat Struct Mol Biol 17, 222–229 (2010). https://doi.org/10.1038/nsmb.1744

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