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Viral immune modulators perturb the human molecular network by common and unique strategies

Abstract

Viruses must enter host cells to replicate, assemble and propagate. Because of the restricted size of their genomes, viruses have had to evolve efficient ways of exploiting host cell processes to promote their own life cycles and also to escape host immune defence mechanisms1,2. Many viral open reading frames (viORFs) with immune-modulating functions essential for productive viral growth have been identified across a range of viral classes3,4. However, there has been no comprehensive study to identify the host factors with which these viORFs interact for a global perspective of viral perturbation strategies5,6,7,8,9,10,11. Here we show that different viral perturbation patterns of the host molecular defence network can be deduced from a mass-spectrometry-based host-factor survey in a defined human cellular system by using 70 innate immune-modulating viORFs from 30 viral species. The 579 host proteins targeted by the viORFs mapped to an unexpectedly large number of signalling pathways and cellular processes, suggesting yet unknown mechanisms of antiviral immunity. We further experimentally verified the targets heterogeneous nuclear ribonucleoprotein U, phosphatidylinositol-3-OH kinase, the WNK (with-no-lysine) kinase family and USP19 (ubiquitin-specific peptidase 19) as vulnerable nodes in the host cellular defence system. Evaluation of the impact of viral immune modulators on the host molecular network revealed perturbation strategies used by individual viruses and by viral classes. Our data are also valuable for the design of broad and specific antiviral therapies.

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Figure 1: Host factor survey set-up and general properties of the data set.
Figure 2: Network of identified targets and network perturbation induced by viORFs.
Figure 3: Functional validation of USP19, hnRNP-U and WNK kinases as viral targets.
Figure 4: Similarities of viORF actions.

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ArrayExpress

Data deposits

The protein interactions from this publication have been submitted to the IMEx consortium (http://imex.sf.net) through IntAct (identifier IM-17331). Mass spectrometry data are available at http://inhibitomev1.sf.net; microarray data were deposited in ArrayExpress (accession number E-MTAB-1148).

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Acknowledgements

We thank C. Basler, A. Bergthaler, K.-K. Conzelmann, A. Garcia-Sastre, M. Hardy, W. Kaiser, E. Mühlberger, R. Randall, B. Roizman, N. Ruggli, B. Sherry and T. Wolf for providing viral ORF cDNAs; P. Jordan for providing WNK expression constructs; S. Nakagawa for Flag-hnRNP-U; M. Sophie-Hiet for GFP-NS5A; M. Zayas for the pFK-Jc1-NS5A-HA expression plasmid; E. Rudashevskaya, A. Stukalov, F. Breitwieser and M. Trippler for support; H. Pickersgill and T. Brummelkamp for critically reading the manuscript; C. Baumann for discussions; and M. Vidal for discussions and for sharing unpublished information. The work was funded by the Austrian Academy of Sciences, an i-FIVE European Research Council grant to G.S.-F., a European Molecular Biology Organization long-term fellowship to A.P. (ATLF 463-2008), Science Foundation Ireland grant 07/IN1/B934 to O.M. and A.G.B., Deutsche Forschungsgemeinschaft grants We 2616/5-2 and SFB 593/B13 to F.W., Ko1579/5-1 to G.K., and FOR1202, TP1 to R.B., and the German Ministry for Education and Research (Suszeptibilität bei Infektionen: HCV; TP1, 01KI 0786) to R.B. J.C. is funded by the Austrian Ministry of Science and Research (GEN-AU/BIN).

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A.P., G.A., O.M., R.S., M.H., M.B., A.S., C.A.E., A.G., A.C.M., A.F., C.H., S.G., F.W. and G.K. performed experiments. A.P. and G.S.-F. conceived the study. A.P., G.A., R.B., A.G.B. and G.S.-F. designed experiments. K.K., A.C.M., K.L.B. and J.C. performed mass spectrometry and bioinformatic data analysis. T.B., K.L., S.G., G.K., F.W., R.B. and A.G.B. provided critical material. All authors contributed to the discussion of results and participated in manuscript preparation. A.P., K.K., J.C. and G.S.-F. wrote the manuscript.

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Correspondence to Giulio Superti-Furga.

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Pichlmair, A., Kandasamy, K., Alvisi, G. et al. Viral immune modulators perturb the human molecular network by common and unique strategies. Nature 487, 486–490 (2012). https://doi.org/10.1038/nature11289

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