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Epstein–Barr virus BORF2 inhibits cellular APOBEC3B to preserve viral genome integrity

Nature Microbiology volume 4, pages 78–88 (2019)Cite this article

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Abstract

The apolipoprotein B messenger RNA editing enzyme, catalytic polypeptide-like (APOBEC) family of single-stranded DNA (ssDNA) cytosine deaminases provides innate immunity against virus and transposon replication1,2,3,4. A well-studied mechanism is APOBEC3G restriction of human immunodeficiency virus type 1, which is counteracted by a virus-encoded degradation mechanism1,2,3,4. Accordingly, most work has focused on retroviruses with obligate ssDNA replication intermediates and it is unclear whether large double-stranded DNA (dsDNA) viruses may be similarly susceptible to restriction. Here, we show that the large dsDNA herpesvirus Epstein–Barr virus (EBV), which is the causative agent of infectious mononucleosis and multiple cancers5, utilizes a two-pronged approach to counteract restriction by APOBEC3B. Proteomics studies and immunoprecipitation experiments showed that the ribonucleotide reductase large subunit of EBV, BORF26,7, binds APOBEC3B. Mutagenesis mapped the interaction to the APOBEC3B catalytic domain, and biochemical studies demonstrated that BORF2 stoichiometrically inhibits APOBEC3B DNA cytosine deaminase activity. BORF2 also caused a dramatic relocalization of nuclear APOBEC3B to perinuclear bodies. On lytic reactivation, BORF2-null viruses were susceptible to APOBEC3B-mediated deamination as evidenced by lower viral titres, lower infectivity and hypermutation. The Kaposi’s sarcoma-associated herpesvirus homologue, ORF61, also bound APOBEC3B and mediated relocalization. These data support a model where the genomic integrity of human γ-herpesviruses is maintained by active neutralization of the antiviral enzyme APOBEC3B.

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Fig. 1: EBV BORF2 interacts with cellular A3B.
Fig. 2: EBV BORF2 inhibits A3B catalytic activity specifically.
Fig. 3: BORF2 relocalizes A3B from the nuclear compartment to the endoplasmic reticulum.
Fig. 4: BORF2 functions to preserve EBV genome integrity from A3B.

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Data availability

The data that support the findings of this study are available on request from the corresponding authors.

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Acknowledgements

We thank B. Anderson for technical advice and RT–qPCR data; Y.-F. Chiu for sharing BAC EBV B95.8; H.-J. Delecluse for M81-transformed B cells; K. Hogquist and S. Dunmire for providing the Akata cells; T. Ikeda and C. Richards for cell culture assistance; M. Sanders and staff at the University of Minnesota Imaging Center for assistance with fluorescence microscopy and live cell imaging; A. Serebrenik for the gRNA construct targeting UNG2; G. Starrett for technical programming advice; and R. Khanna, S. Rice, S. Simon, and P. Southern for thoughtful comments. This work was supported by NCI R21-CA206309 (R.S.H.), the University of Minnesota (College of Biological Sciences, Academic Health Center, and Masonic Cancer Center to R.S.H.), and Canadian Institutes of Health Research grant 153014 (to L.F.). National Institutes of Health training grants provided salary support for A.Z.C. (F30 CA200432 and T32 GM008244) and M.C.J. (T32 CA009138). Salary support for J.L.M. was provided by a National Science Foundation Graduate Research Fellowship. J.Y.M. was funded by Secretaría Nacional de Educación Superior, Ciencia, Tecnología e Innovación. L.F. is a tier 1 Canada Research Chair in Molecular Virology. R.S.H. is the Margaret Harvey Schering Land Grant Chair for Cancer Research, a Distinguished University McKnight Professor, and an Investigator of the Howard Hughes Medical Institute.

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Author notes

  1. These authors contributed equally: Adam Z. Cheng, Jaime Yockteng-Melgar.

Authors and Affiliations

  1. Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA

    Adam Z. Cheng, Matthew C. Jarvis, Michael A. Carpenter, Jennifer L. McCann, Diako Ebrahimi, Nadine M. Shaban, William L. Brown & Reuben S. Harris

  2. Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA

    Adam Z. Cheng, Matthew C. Jarvis, Michael A. Carpenter, Jennifer L. McCann, Diako Ebrahimi, Nadine M. Shaban, William L. Brown & Reuben S. Harris

  3. Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA

    Adam Z. Cheng, Matthew C. Jarvis, Michael A. Carpenter, Jennifer L. McCann, Diako Ebrahimi, Nadine M. Shaban, William L. Brown & Reuben S. Harris

  4. Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA

    Adam Z. Cheng, Matthew C. Jarvis, Michael A. Carpenter, Jennifer L. McCann, Diako Ebrahimi, Nadine M. Shaban, William L. Brown & Reuben S. Harris

  5. Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada

    Jaime Yockteng-Melgar, Natasha Malik-Soni, Jack Greenblatt & Lori Frappier

  6. Ontario Institute for Cancer Research, MaRS Centre, Toronto, Ontario, Canada

    Ivan Borozan

  7. Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN, USA

    Michael A. Carpenter & Reuben S. Harris

  8. Donnelly Centre, University of Toronto, Toronto, Ontario, Canada

    Edyta Marcon & Jack Greenblatt

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Contributions

A.Z.C., J.Y.-M., L.F. and R.S.H. conceived and designed the studies. A.Z.C. and J.Y-M. performed the bulk of the experimental work. N.M.-S., E.M. and J.G. carried out the AP-MS analyses. M.C.J., M.A.C., J.L.M., N.M.Sh. and W.L.B. provided technical training and advice. J.L.M. helped validate the BORF2-A3B interaction and M.A.C. performed the UDG experiments. A.Z.C., I.B., M.C.J. and D.E. conducted the bioinformatics analyses. A.Z.C., J.Y.-M., L.F. and R.S.H. drafted the manuscript, and all authors contributed to revisions.

Corresponding authors

Correspondence to Lori Frappier or Reuben S. Harris.

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Competing interests

R.S.H. is a co-founder, shareholder, and consultant of ApoGen Biotechnologies Inc. The other authors declare no competing interests.

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Supplementary information

Supplementary Information

Supplementary Figures 1–14, Raw Images and Supplementary Video legends.

Reporting Summary

Supplementary Video 1

3D-reconstruction of z-stacks show A3B–BORF2 aggregates colocalizing within the endoplasmic reticulum.

Supplementary Video 2

z-series of reactivated AGS-EBV cells show BORF2 colocalization within the endoplasmic reticulum.

Supplementary Video 3

Effect of BORF2 induction on pre-existing A3B in U2OS cells.

Supplementary Video 4

Effect of BORF2 on A3B induction in U2OS cells.

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Cheng, A.Z., Yockteng-Melgar, J., Jarvis, M.C. et al. Epstein–Barr virus BORF2 inhibits cellular APOBEC3B to preserve viral genome integrity. Nat Microbiol 4, 78–88 (2019). https://doi.org/10.1038/s41564-018-0284-6

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