Numerous human APOBEC3 cytidine deaminases have proven to be, inter alia, host cell restriction factors for retroviruses and hepadnaviruses. Although they can bind to genomic RNA and become encapsidated, they are only catalytically active on single-stranded DNA. As there are many cellular deoxyribonucleases (DNases), we hypothesized that a parallel could be struck between APOBEC3 and DNases. For human hepatitis B virus (HBV), we show that DNase I can considerably reduce the virion genome copy number from a variety of transfected or infected cells. DNASE1 is overexpressed and encapsidated in HBV particles in vitro in hypoxic environments and in vivo in cirrhotic patient livers as well as in the serum of infected patients. The use of CoCl2 and dimethyloxalylglycine, mimetic agents used to induce hypoxia by inhibiting prolyl hydroxylase enzymes that stabilize hypoxia-inducible factor (HIF)-1α, showed that the formation of HIF-1α/HIF-1β heterodimers results in the induction of DNASE1. Indeed, transfection with HIF-1α and HIF-1β expression constructs upregulated DNASE1. These findings suggest that human DNase I can impact HBV replication through the catabolism of the DNA genome within the capsid. The activity of DNases in general may explain in part the high frequency of empty or ‘light’ hepatitis B virions observed in vivo.
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Malim, M. H. & Bieniasz, P. D. HIV restriction factors and mechanisms of evasion. Cold Spring Harb. Perspect. Med. 2, a006940 (2012).
Simon, V., Bloch, N. & Landau, N. R. Intrinsic host restrictions to HIV-1 and mechanisms of viral escape. Nat. Immunol. 16, 546–553 (2015).
Bishop, K. N. et al. Cytidine deamination of retroviral DNA by diverse APOBEC proteins. Curr. Biol. 14, 1392–1396 (2004).
Kirchhoff, F. Immune evasion and counteraction of restriction factors by HIV-1 and other primate lentiviruses. Cell Host Microbe 8, 55–67 (2010).
Hatziioannou, T., Perez-Caballero, D., Yang, A., Cowan, S. & Bieniasz, P. D. Retrovirus resistance factors Ref1 and Lv1 are species-specific variants of TRIM5α. Proc. Natl Acad. Sci. USA 101, 10774–10779 (2004).
Laguette, N. et al. Samhd1 is the dendritic- and myeloid-cell-specific HIV-1 restriction factor counteracted by Vpx. Nature 474, 654–657 (2011).
Neil, S. J., Zang, T. & Bieniasz, P. D. Tetherin inhibits retrovirus release and is antagonized by HIV-1 Vpu. Nature 451, 425–430 (2008).
Rosa, A. et al. HIV-1 Nef promotes infection by excluding SERINC5 from virion incorporation. Nature 526, 212–217 (2015).
Stremlau, M. et al. The cytoplasmic body component TRIM5α restricts HIV-1 infection in Old World monkeys. Nature 427, 848–853 (2004).
Usami, Y., Wu, Y. & Gottlinger, H. G. SERINC3 and SERINC5 restrict HIV-1 infectivity and are counteracted by Nef. Nature 526, 218–223 (2015).
Suspène, R. et al. Extensive editing of both hepatitis B virus DNA strands by APOBEC3 cytidine deaminases in vitro and in vivo. Proc. Natl Acad. Sci. USA 102, 8321–8326 (2005).
Ko, C., Lee, S., Windisch, M. P. & Ryu, W. S. DDX3 DEAD-box RNA helicase is a host factor that restricts hepatitis B virus replication at the transcriptional level. J. Virol. 88, 13689–13698 (2014).
Chelico, L., Pham, P., Calabrese, P. & Goodman, M. F. APOBEC3G DNA deaminase acts processively 3′→5′ on single-stranded DNA. Nat. Struct. Mol. Biol. 13, 392–399 (2006).
Peitsch, M. C. et al. Characterization of the endogenous deoxyribonuclease involved in nuclear DNA degradation during apoptosis (programmed cell death). EMBO J. 12, 371–377 (1993).
Kimura-Kataoka, K. et al. Identification of the functional alleles of the nonsynonymous single-nucleotide polymorphisms potentially implicated in systemic lupus erythematosus in the human deoxyribonuclease I gene. DNA Cell Biol. 33, 492–502 (2014).
Oliveri, M. et al. DNase I mediates internucleosomal DNA degradation in human cells undergoing drug-induced apoptosis. Eur. J. Immunol. 31, 743–751 (2001).
Amoura, Z. et al. Circulating plasma levels of nucleosomes in patients with systemic lupus erythematosus: correlation with serum antinucleosome antibody titers and absence of clear association with disease activity. Arthritis Rheum. 40, 2217–2225 (1997).
Alberti, A., Diana, S., Scullard, G. H., Eddleston, W. F. & Williams, R. Full and empty Dane particles in chronic hepatitis B virus infection: relation to hepatitis B e antigen and presence of liver damage. Gastroenterology 75, 869–874 (1978).
Kaplan, P. M., Ford, E. C., Purcell, R. H. & Gerin, J. L. Demonstration of subpopulations of Dane particles. J. Virol. 17, 885–893 (1976).
Luckenbaugh, L., Kitrinos, K. M., Delaney, W. E. T. & Hu, J. Genome-free hepatitis B virion levels in patient sera as a potential marker to monitor response to antiviral therapy. J. Viral Hepat. 22, 561–570 (2015).
Ning, X. et al. Secretion of genome-free hepatitis B virus—single strand blocking model for virion morphogenesis of para-retrovirus. PLoS Pathog. 7, e1002255 (2011).
Gerin, J. L., Ford, E. C. & Purcell, R. H. Biochemical characterization of Australia antigen. Evidence for defective particles of hepatitis B virus. Am. J. Pathol. 81, 651–668 (1975).
Sakamoto, Y. et al. Full and empty particles of hepatitis B virus in hepatocytes from patients with HBsAg-positive chronic active hepatitis. Lab. Invest. 48, 678–682 (1983).
Wang, G. L., Jiang, B. H., Rue, E. A. & Semenza, G. L. Hypoxia-inducible factor 1 is a basic-helix-loop-helix-PAS heterodimer regulated by cellular O2 tension. Proc. Natl Acad. Sci. USA 92, 5510–5514 (1995).
Fu, X. S., Choi, E., Bubley, G. J. & Balk, S. P. Identification of hypoxia-inducible factor-1α (HIF-1α) polymorphism as a mutation in prostate cancer that prevents normoxia-induced degradation. Prostate 63, 215–221 (2005).
Zhang, C. et al. Hypoxia induces the breast cancer stem cell phenotype by HIF-dependent and ALKBH5-mediated m6A-demethylation of NANOG mRNA. Proc. Natl Acad. Sci. USA 113, 2047–2056 (2016).
Zhang, H. et al. HIF-1α activates hypoxia-induced PFKFB4 expression in human bladder cancer cells. Biochem. Biophys. Res. Commun. 476, 146–152 (2016).
Zhu, B. et al. DNase I aggravates islet β-cell apoptosis in type 2 diabetes. Mol. Med. Rep. 13, 4577–4584 (2016).
Kominato, Y. et al. Hypoxia induces upregulation of the deoxyribonuclease I gene in the human pancreatic cancer cell line QGP-1. Biochim. Biophys. Acta 1770, 1567–1575 (2007).
Liaw, Y. F. & Chu, C. M. Hepatitis B virus infection. Lancet 373, 582–592 (2009).
Parsiegla, G., Noguere, C., Santell, L., Lazarus, R. A. & Bourne, Y. The structure of human DNase I bound to magnesium and phosphate ions points to a catalytic mechanism common to members of the DNase I-like superfamily. Biochemistry 51, 10250–10258 (2012).
Stenglein, M. D., Burns, M. B., Li, M., Lengyel, J. & Harris, R. S. APOBEC3 proteins mediate the clearance of foreign DNA from human cells. Nat. Struct. Mol. Biol. 17, 222–229 (2010).
Ladner, S. K. et al. Inducible expression of human hepatitis B virus (HBV) in stably transfected hepatoblastoma cells: a novel system for screening potential inhibitors of HBV replication. Antimicrob. Agents Chemother. 41, 1715–1720 (1997).
Suspène, R., Henry, M., Guillot, S., Wain-Hobson, S. & Vartanian, J. P. Recovery of APOBEC3-edited human immunodeficiency virus G->A hypermutants by differential DNA denaturation PCR. J. Gen. Virol. 86, 125–129 (2005).
Vartanian, J. P. et al. Massive APOBEC3 editing of hepatitis B viral DNA in cirrhosis. PLoS Pathog. 6, e1000928 (2010).
Bayard, F. et al. T-cell responses to hepatitis B splice-generated protein of hepatitis B virus and inflammatory cytokines/chemokines in chronic hepatitis B patients. ANRS study: HB EP 02 HBSP-FIBRO. J. Viral Hepat. 19, 872–880 (2012).
Couillin, I. et al. Specific vaccine therapy in chronic hepatitis B: induction of T cell proliferative responses specific for envelope antigens. J. Infect. Dis. 180, 15–26 (1999).
Ke, Q. & Costa, M. Hypoxia-inducible factor-1 (HIF-1). Mol. Pharmacol. 70, 1469–1480 (2006).
Semenza, G. L. Involvement of oxygen-sensing pathways in physiologic and pathologic erythropoiesis. Blood 114, 2015–2019 (2009).
Sonna, L. A., Cullivan, M. L., Sheldon, H. K., Pratt, R. E. & Lilly, C. M. Effect of hypoxia on gene expression by human hepatocytes (HepG2). Physiol. Genomics 12, 195–207 (2003).
Henry, M. et al. Genetic editing of HBV DNA by monodomain human APOBEC3 cytidine deaminases and the recombinant nature of APOBEC3G. PLoS ONE 4, e4277 (2009).
Sasaki, Y., Miyoshi, D. & Sugimoto, N. Regulation of DNA nucleases by molecular crowding. Nucleic Acids Res. 35, 4086–4093 (2007).
Gibson, W. Structure and formation of the cytomegalovirus virion. Curr. Top. Microbiol. Immunol. 325, 187–204 (2008).
Tandon, R. & Mocarski, E. S. Viral and host control of cytomegalovirus maturation. Trends Microbiol. 20, 392–401 (2012).
Suspène, R. et al. Somatic hypermutation of human mitochondrial and nuclear DNA by APOBEC3 cytidine deaminases, a pathway for DNA catabolism. Proc. Natl Acad. Sci. USA 108, 4858–4863 (2011).
Aynaud, M. M. et al. Human Tribbles 3 protects nuclear DNA from cytidine deamination by APOBEC3A. J. Biol. Chem. 287, 39182–39192 (2012).
Zahn, A. & Allain, J. P. Hepatitis C virus and hepatitis B virus bind to heparin: purification of largely IgG-free virions from infected plasma by heparin chromatography. J. Gen. Virol. 86, 677–685 (2005).
Bouzidi, M. S. et al. APOBEC3DE antagonizes hepatitis B virus restriction factors APOBEC3F and APOBEC3G. J. Mol. Biol. 428, 3514–3528 (2016).
De Castro Martin, I. F. et al. Influenza virus genome reaches the plasma membrane via a modified endoplasmic reticulum and Rab11-dependent vesicles. Nat. Commun. 8, 1396 (2017).
Slot, J. W., Geuze, H. J., Gigengack, S., Lienhard, G. E. & James, D. E. Immuno-localization of the insulin regulatable glucose transporter in brown adipose tissue of the rat. J. Cell Biol. 113, 123–135 (1991).
Lanzhou Institute of Biological Products Co., Ltd. is a subsidiary company of China National Biotec Group Company Limited. This work was supported by grants from the Institut Pasteur and Centre National de la Recherche Scientifique. C.H. and M.S.B. were supported by the Allocation de Recherche du Ministère de la Recherche and Ligue contre le Cancer, respectively. X.L. was supported by a stipend from the Lanzhou Institute of Biological Products Co., Ltd, subsidiary company of China National Biotec Group Company Limited and by a stipend from the Pasteur-Paris University International PhD program. V.L. was supported by the Fondation pour la Recherche Medicale (project no. ING20160435328). C.D. was supported by an EMBO Long Term Fellowship (EMBO ALTF 1428–2016). The study of patients was sponsored by the French National Agency for research on AIDS and hepatitis (ANRS). This work has been published within the framework of IdEx Université de Strasbourg and has received funding from the French State via the French National Research Agency (ANR) as part of the program ‘Investissements d’avenir’ to R.G. This work was supported by an ATIP-AVENIR starting grant to R.G. We would like to thank S. Urban for providing HepG2-NTCP cells; P. Pineau and A. Marchio for the cirrhotic liver samples; M.-L. Michel and S. Pol for serum samples; C. Neuveut, P. Moreau, P. Maillard and B. Quioc for HBV infection; Y. Jacob for the HIF-1α and HIF-1β plasmids; J. Krijnse-Locker and C. Schmitt for electron microscopy immunolabelling and V. Caval, N. Frampton and J. McKeating for helpful discussions.
The authors declare no competing interests.
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Supplementary Figures 1–7, Supplementary Tables 1 and 2, Raw Image Figures and Raw Image.
Three-dimensional time-lapse of the crop presented in Supplementary Figure 5.
Three-dimensional isosurface time-lapse of the of the crop presented in Supplementary Figure 5.
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Hallez, C., Li, X., Suspène, R. et al. Hypoxia-induced human deoxyribonuclease I is a cellular restriction factor of hepatitis B virus. Nat Microbiol 4, 1196–1207 (2019). https://doi.org/10.1038/s41564-019-0405-x
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