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Proteotype profiling unmasks a viral signalling network essential for poxvirus assembly and transcriptional competence

Nature Microbiology volume 3, pages 588–599 (2018)Cite this article

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Abstract

To orchestrate context-dependent signalling programmes, poxviruses encode two dual-specificity enzymes, the F10 kinase and the H1 phosphatase. These signalling mediators are essential for poxvirus production, yet their substrate profiles and systems-level functions remain enigmatic. Using a phosphoproteomic screen of cells infected with wild-type, F10 and H1 mutant vaccinia viruses, we systematically defined the viral signalling network controlled by these enzymes. Quantitative cross-comparison revealed 33 F10 and/or H1 phosphosites within 17 viral proteins. Using this proteotype dataset to inform genotype–phenotype relationships, we found that H1-deficient virions harbour a hidden hypercleavage phenotype driven by reversible phosphorylation of the virus protease I7 (S134). Quantitative phosphoproteomic profiling further revealed that the phosphorylation-dependent activity of the viral early transcription factor, A7 (Y367), underlies the transcription-deficient phenotype of H1 mutant virions. Together, these results highlight the utility of combining quantitative proteotype screens with mutant viruses to uncover proteotype–phenotype–genotype relationships that are masked by classical genetic studies.

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Fig. 1: Proteotype-based decoding of the viral signalling network.
Fig. 2: F10-dependent phosphorylation of I7 modulates cleavage of viral structural proteins.
Fig. 3: Phosphorylation of I7 S134 is temporally regulated during virus assembly.
Fig. 4: H1 regulates virion-associated I7 proteolytic activity.
Fig. 5: Tyrosine phosphorylation of viral early transcription factor A7 controls virion transcription but not assembly.
Fig. 6: Intact mature virions are formed in the absence of A7 Tyr phosphorylation exemplifying phosphodynamic regulation of poxvirus assembly by F10 and H1.

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Acknowledgements

We would like to thank P. Traktman, R. Condit, B. Moss and P. H. Verardi for generously donating VACV mutants for this study. We greatly acknowledge A. Frei, S. Götze and A. Leitner for maintenance of the mass spectrometers. We are grateful to all members of the Mercer and Wollscheid laboratories for critical comments and suggestions throughout this project. This work was supported by the Swiss National Science Foundation (31003A_160259 to B.W.) and the InfectX project from the Swiss Initiative in Systems Biology SystemsX.ch (to B.W.), the MRC Programme Grant (MC_UU12018/7) (J.M.), the European Research Council (649101 UbiProPox) (J.M.) and the Swiss National Foundation Ambizione (PZ00P3_131988) (J.M.).

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  1. These authors contributed equally: Karel Novy and Samuel Kilcher.

Authors and Affiliations

  1. Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland

    Karel Novy, Ulrich Omasits, Alessio Maiolica & Bernd Wollscheid

  2. Biomedical Proteomics Platform, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland

    Karel Novy, Ulrich Omasits & Bernd Wollscheid

  3. Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland

    Karel Novy, Ulrich Omasits & Bernd Wollscheid

  4. MRC-Laboratory for Molecular Cell Biology, University College London, London, UK

    Samuel Kilcher, Corina Beerli, Caroline K. Martin, Ian White & Jason Mercer

  5. Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Basel, Switzerland

    Christopher Karl Ernst Bleck

  6. Biognosys AG, Schlieren, Switzerland

    Jakob Vowinckel

  7. Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland

    Mohammedyaseen Syedbasha

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Contributions

K.N., S.K., J.M. and B.W. designed the project and wrote the manuscript. K.N. performed the proteomic experiments. K.N., U.O. and J.V. analysed the proteomics data and U.O. performed the phosphorylation site relocalization analysis. M.S. produced the viruses. S.K., C.B. and C.K.M. designed and performed the biochemical validations. S.K, C.K.E.B. and I.W. performed the EM analysis. A.M. contributed ideas and gave assistance for the phosphoproteomic workflows. All authors discussed the results and implications of the findings and provided comments on the manuscript at all stages.

Corresponding authors

Correspondence to Jason Mercer or Bernd Wollscheid.

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Competing interests

J.V. is an employee of Biognosys AG and helped with the Spectronaut DIA analysis in the revised version of the manuscript. K.N. joined Biognosys AG during the revision process of the manuscript upon finishing his PhD at ETH Zurich.

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Supplementary Information

Supplementary Figures 1–8, Supplementary Reference.

Reporting Summary

Supplementary Table 1

Label-free quantification phosphoproteome data of HeLa cells infected with VACV WT, H1 and F10, and uninfected cells.

Supplementary Table 2

Label-free quantification of MV WT versus H1 proteomes.

Supplementary Table 3

Label-free quantification phosphoproteome data of MV WT versus H1.

Supplementary Table 4

Label-free quantification data of MV WT versus H1 phosphotyrosine enrichment.

Supplementary Table 5

Primers used in this study.

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Novy, K., Kilcher, S., Omasits, U. et al. Proteotype profiling unmasks a viral signalling network essential for poxvirus assembly and transcriptional competence. Nat Microbiol 3, 588–599 (2018). https://doi.org/10.1038/s41564-018-0142-6

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