Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

The interferon-inducible isoform of NCOA7 inhibits endosome-mediated viral entry

An Author Correction to this article was published on 22 January 2019

This article has been updated

Abstract

Interferons (IFNs) mediate cellular defence against viral pathogens by upregulation of IFN-stimulated genes whose products interact with viral components or alter cellular physiology to suppress viral replication1,2,3. Among the IFN-stimulated genes that can inhibit influenza A virus (IAV)4 are the myxovirus resistance 1 GTPase5 and IFN-induced transmembrane protein 3 (refs 6,7). Here, we use ectopic expression and gene knockout to demonstrate that the IFN-inducible 219-amino acid short isoform of human nuclear receptor coactivator 7 (NCOA7) is an inhibitor of IAV as well as other viruses that enter the cell by endocytosis, including hepatitis C virus. NCOA7 interacts with the vacuolar H+-ATPase (V-ATPase) and its expression promotes cytoplasmic vesicle acidification, lysosomal protease activity and the degradation of endocytosed antigen. Step-wise dissection of the IAV entry pathway demonstrates that NCOA7 inhibits fusion of the viral and endosomal membranes and subsequent nuclear translocation of viral ribonucleoproteins. Therefore, NCOA7 provides a mechanism for immune regulation of endolysosomal physiology that not only suppresses viral entry into the cytosol from this compartment but may also regulate other V-ATPase-associated cellular processes, such as physiological adjustments to nutritional status, or the maturation and function of antigen-presenting cells.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Fig. 1: NCOA7 inhibits infection by viruses entering through the endocytic pathway.
Fig. 2: NCOA7 function inhibits IAV membrane fusion.
Fig. 3: NCOA7 interacts with V-ATPase and promotes cytoplasmic vesicle acidification and lysosomal protease activation.

Data availability

The datasets generated and/or analysed during the current study are available from the corresponding authors on reasonable request.

Change history

  • 22 January 2019

    In the version of Supplementary Fig. 5a originally published with this Letter, the authors mistakenly duplicated images of LAMP1 staining in place of CD63 staining; this has now been amended to the correct version shown below.

References

  1. Doyle, T., Goujon, C. & Malim, M. H. HIV-1 and interferons: who’s interfering with whom? Nat. Rev. Microbiol. 13, 403–413 (2015).

    CAS  Article  Google Scholar 

  2. McNab, F., Mayer-Barber, K., Sher, A., Wack, A. & O’Garra, A. Type I interferons in infectious disease. Nat. Rev. Immunol. 15, 87–103 (2015).

    CAS  Article  Google Scholar 

  3. Randall, R. E. & Goodbourn, S. Interferons and viruses: an interplay between induction, signalling, antiviral responses and virus countermeasures. J. Gen. Virol. 89, 1–47 (2008).

    CAS  Article  Google Scholar 

  4. Iwasaki, A. & Pillai, P. S. Innate immunity to influenza virus infection. Nat. Rev. Immunol. 14, 315–328 (2014).

    CAS  Article  Google Scholar 

  5. Haller, O. & Kochs, G. Human MxA protein: an interferon-induced dynamin-like GTPase with broad antiviral activity. J. Interferon Cytokine Res. 31, 79–87 (2011).

    CAS  Article  Google Scholar 

  6. Brass, A. L. et al. The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus. Cell 139, 1243–1254 (2009).

    Article  Google Scholar 

  7. Everitt, A. R. et al. IFITM3 restricts the morbidity and mortality associated with influenza. Nature 484, 519–523 (2012).

    CAS  Article  Google Scholar 

  8. Goujon, C. & Malim, M. H. Characterization of the alpha interferon-induced postentry block to HIV-1 infection in primary human macrophages and T cells. J. Virol. 84, 9254–9266 (2010).

    CAS  Article  Google Scholar 

  9. Goujon, C. et al. Human MX2 is an interferon-induced post-entry inhibitor of HIV-1 infection. Nature 502, 559–562 (2013).

    CAS  Article  Google Scholar 

  10. Yu, L. et al. Induction of a unique isoform of the NCOA7 oxidation resistance gene by interferon β-1b. J. Interferon Cytokine Res. 35, 186–199 (2015).

    CAS  Article  Google Scholar 

  11. Naldini, L. et al. In vivo gene delivery and stable transduction of nondividing cells by a lentiviral vector. Science 272, 263–267 (1996).

    CAS  Article  Google Scholar 

  12. Herold, N. et al. HIV-1 entry in SupT1-R5, CEM-ss, and primary CD4+ T cells occurs at the plasma membrane and does not require endocytosis. J. Virol. 88, 13956–13970 (2014).

    Article  Google Scholar 

  13. Mercer, J., Schelhaas, M. & Helenius, A. Virus entry by endocytosis. Annu. Rev. Biochem. 79, 803–833 (2010).

    CAS  Article  Google Scholar 

  14. Banerjee, I., Yamauchi, Y., Helenius, A. & Horvath, P. High-content analysis of sequential events during the early phase of influenza A virus infection. PLoS ONE 8, e68450 (2013).

    CAS  Article  Google Scholar 

  15. Banerjee, I. et al. Influenza A virus uses the aggresome processing machinery for host cell entry. Science 346, 473–477 (2014).

    CAS  Article  Google Scholar 

  16. Webster, R. G., Brown, L. E. & Jackson, D. C. Changes in the antigenicity of the hemagglutinin molecule of H3 influenza virus at acidic pH. Virology 126, 587–599 (1983).

    CAS  Article  Google Scholar 

  17. Shelton, H., Roberts, K. L., Molesti, E., Temperton, N. & Barclay, W. S. Mutations in haemagglutinin that affect receptor binding and pH stability increase replication of a PR8 influenza virus with H5 HA in the upper respiratory tract of ferrets and may contribute to transmissibility. J. Gen. Virol. 94, 1220–1229 (2013).

    CAS  Article  Google Scholar 

  18. Russier, M. et al. Molecular requirements for a pandemic influenza virus: an acid-stable hemagglutinin protein. Proc. Natl Acad. Sci. USA 113, 1636–1641 (2016).

    CAS  Article  Google Scholar 

  19. Shao, W., Halachmi, S. & Brown, M. ERAP140, a conserved tissue-specific nuclear receptor coactivator. Mol. Cell. Biol. 22, 3358–3372 (2002).

    CAS  Article  Google Scholar 

  20. Durand, M. et al. The OXR domain defines a conserved family of eukaryotic oxidation resistance proteins. BMC Cell. Biol. 8, 13 (2007).

    Article  Google Scholar 

  21. Merkulova, M. et al. Mapping the H+ (V)-ATPase interactome: identification of proteins involved in trafficking, folding, assembly and phosphorylation. Sci. Rep. 5, 14827 (2015).

    CAS  Article  Google Scholar 

  22. Huttlin, E. L. et al. The BioPlex network: a systematic exploration of the human interactome. Cell 162, 425–440 (2015).

    CAS  Article  Google Scholar 

  23. Merkulova, M. et al. Targeted deletion of the Ncoa7 gene results in incomplete distal renal tubular acidosis in mice. Am. J. Physiol. Renal Physiol. 315, F173–F185 (2018).

    CAS  Article  Google Scholar 

  24. Trombetta, E. S., Ebersold, M., Garrett, W., Pypaert, M. & Mellman, I. Activation of lysosomal function during dendritic cell maturation. Science 299, 1400–1403 (2003).

    CAS  Article  Google Scholar 

  25. Cotter, K., Stransky, L., McGuire, C. & Forgac, M. Recent insights into the structure, regulation, and function of the V-ATPases. Trends Biochem. Sci. 40, 611–622 (2015).

    CAS  Article  Google Scholar 

  26. Bright, N. A., Davis, L. J. & Luzio, J. P. Endolysosomes are the principal intracellular sites of acid hydrolase activity. Curr. Biol. 26, 2233–2245 (2016).

    CAS  Article  Google Scholar 

  27. Wang, Z., Berkey, C. D. & Watnick, P. I. The Drosophila protein mustard tailors the innate immune response activated by the immune deficiency pathway. J. Immunol. 188, 3993–4000 (2012).

    CAS  Article  Google Scholar 

  28. Colacurcio, D. J. & Nixon, R. A. Disorders of lysosomal acidification—the emerging role of v-ATPase in aging and neurodegenerative disease. Ageing Res. Rev. 32, 75–88 (2016).

    CAS  Article  Google Scholar 

  29. Sennoune, S. R. & Martinez-Zaguilan, R. Vacuolar H+-ATPase signaling pathway in cancer. Curr. Protein Pept. Sci. 13, 152–163 (2012).

    CAS  Article  Google Scholar 

  30. Cavrois, M., De Noronha, C. & Greene, W. C. A sensitive and specific enzyme-based assay detecting HIV-1 virion fusion in primary T lymphocytes. Nat. Biotechnol. 20, 1151–1154 (2002).

    CAS  Article  Google Scholar 

  31. Mangeot, P. E. et al. High levels of transduction of human dendritic cells with optimized SIV vectors. Mol. Ther. 5, 283–290 (2002).

    CAS  Article  Google Scholar 

  32. Saenz, D. T., Teo, W., Olsen, J. C. & Poeschla, E. M. Restriction of feline immunodeficiency virus by Ref1, Lv1, and primate TRIM5α proteins. J. Virol. 79, 15175–15188 (2005).

    CAS  Article  Google Scholar 

  33. O’Rourke, J. P., Newbound, G. C., Kohn, D. B., Olsen, J. C. & Bunnell, B. A. Comparison of gene transfer efficiencies and gene expression levels achieved with equine infectious anemia virus- and human immunodeficiency virus type 1-derived lentivirus vectors. J. Virol. 76, 1510–1515 (2002).

    Article  Google Scholar 

  34. Jarrosson-Wuilleme, L. et al. Transduction of nondividing human macrophages with gammaretrovirus-derived vectors. J. Virol. 80, 1152–1159 (2006).

    CAS  Article  Google Scholar 

  35. Sandrin, V. et al. Lentiviral vectors pseudotyped with a modified RD114 envelope glycoprotein show increased stability in sera and augmented transduction of primary lymphocytes and CD34+ cells derived from human and nonhuman primates. Blood 100, 823–832 (2002).

    CAS  Article  Google Scholar 

  36. Wickersham, I. R., Finke, S., Conzelmann, K. K. & Callaway, E. M. Retrograde neuronal tracing with a deletion-mutant rabies virus. Nat. Methods 4, 47–49 (2007).

    CAS  Article  Google Scholar 

  37. Tran, V., Moser, L. A., Poole, D. S. & Mehle, A. Highly sensitive real-time in vivo imaging of an influenza reporter virus reveals dynamics of replication and spread. J. Virol. 87, 13321–13329 (2013).

    CAS  Article  Google Scholar 

  38. Walters, K. A. et al. Genomic analysis reveals a potential role for cell cycle perturbation in HCV-mediated apoptosis of cultured hepatocytes. PLoS Pathog. 5, e1000269 (2009).

    Article  Google Scholar 

  39. Sanjana, N. E., Shalem, O. & Zhang, F. Improved vectors and genome-wide libraries for CRISPR screening. Nat. Methods 11, 783–784 (2014).

    CAS  Article  Google Scholar 

  40. Blight, K. J., McKeating, J. A. & Rice, C. M. Highly permissive cell lines for subgenomic and genomic hepatitis C virus RNA replication. J. Virol. 76, 13001–13014 (2002).

    CAS  Article  Google Scholar 

  41. Mangeot, P. E. et al. Protein transfer into human cells by VSV-G-induced nanovesicles. Mol. Ther. 19, 1656–1666 (2011).

    CAS  Article  Google Scholar 

  42. Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).

    CAS  Article  Google Scholar 

  43. Lindenbach, B. D. et al. Complete replication of hepatitis C virus in cell culture. Science 309, 623–626 (2005).

    CAS  Article  Google Scholar 

  44. Catanese, M. T. et al. Different requirements for scavenger receptor class B type I in hepatitis C virus cell-free versus cell-to-cell transmission. J. Virol. 87, 8282–8293 (2013).

    CAS  Article  Google Scholar 

  45. Sakai, T. et al. Dual wavelength imaging allows analysis of membrane fusion of influenza virus inside cells. J. Virol. 80, 2013–2018 (2006).

    CAS  Article  Google Scholar 

Download references

Acknowledgements

We thank W. Barclay, F. Blanchet, M. Bonazzi, L. Espert, M. Huttunen, J. Long, E. Martinez, J. Mercer, D. Muriaux, P. Rocha, R. Schulz and Y. Yamauchi for generous provision of reagents and helpful discussions. We are grateful to A. Vaughan for instruction in IAV amplification, P. J. Chana (Biomedical Research Centre (BRC) Flow Core) for training and advice on imaging flow cytometry, I. Ali (King’s College London Nikon Imaging Centre) for advice with confocal microscopy and image acquisition, I. Parham for help with the time-lapse microscopy, and M. Boyer and B. Monterroso (‘MRI’ imaging and flow cytometry facility) for cell sorting and advice with flow cytometry and confocal microscopy, respectively. This work was supported by the UK Medical Research Council (G1000196 to M.H.M.), the Wellcome Trust (106223/Z/14/Z to M.H.M.), the NIH (DA033773), a Wellcome Trust Research Training Fellowship and National Institute for Health Research BRC King’s Prize Fellowship (to T.D.), the Institut National de la Santé et de la Recherche Médicale (to C.G.), the European Research Council under the European Union’s Horizon 2020 research and innovation programme (grant agreement number 759226 to C.G.), the ATIP-Avenir Program (to C.G.), institutional funds from the Centre National de la Recherche Scientifique and Montpellier University (to C.G.), France Recherche Nord & Sud Sida/HIV et Hépatites (to O.M.), a PhD studentship from the Ministry of Higher Education and Research (to B.B.), King’s College London departmental start-up funds (to M.-T.C.), and the Department of Health via a National Institute for Health Research BRC award to Guy’s and St. Thomas’ NHS Foundation Trust in partnership with King’s College London and King’s College Hospital NHS Foundation Trust. We acknowledge the imaging facility MRI, a member of the national infrastructure France-BioImaging supported by the French National Research Agency (ANR-10-INBS-04).

Author information

Authors and Affiliations

Authors

Contributions

T.D., O.M., M.-T.C., C.G. and M.H.M. conceived and designed the experiments. T.D., O.M., B.B., D.P., M.L., M.T., L.A. and C.G. performed the experiments. All authors analysed the data. T.D., C.G. and M.H.M. wrote the manuscript with input from all authors.

Corresponding authors

Correspondence to Caroline Goujon or Michael H. Malim.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Supplementary Information

Supplementary Figures 1–6

Reporting Summary

Supplementary Movie 1

NCOA7 inhibits IAV infection. 293T cells constitutively expressing CD8 or NCOA7 were plated in 48-well plates and transfected with a GFP reporter construct responsive to the IAV RNA polymerase. Cells were infected with A/Eng/195/2009 and visualized by time-lapse microscopy. Productive infection is reflected by GFP expression; time post infection is indicated. The experiment was repeated independently three times with similar results.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Doyle, T., Moncorgé, O., Bonaventure, B. et al. The interferon-inducible isoform of NCOA7 inhibits endosome-mediated viral entry. Nat Microbiol 3, 1369–1376 (2018). https://doi.org/10.1038/s41564-018-0273-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41564-018-0273-9

Further reading

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing