Comparative Profiling of Ubiquitin Proteasome System Interplay with Influenza A Virus PB2 Polymerase Protein Recapitulating Virus Evolution in Humans Elise Biquand, a Juline Poirson, b * Marwah Karim, a Marion Declercq, a Nicolas Malausse, a Patricia Cassonnet, a Cyril Barbezange, a * Marie-Laure Straub, b Louis Jones, a Sandie Munier, a Nadia Naffakh, a Sylvie van der Werf, a Yves Jacob, a Murielle Masson, b Caroline Demeret a Molecular Genetics of RNA Viruses, CNRS UMR 3569, Université Paris Diderot, Sorbonne Paris Cité, Institut Pasteur, Paris, France a ; Ecole Supérieure de Biotechnologie Strasbourg, UMR-7242, CNRS, Université de Strasbourg, Illkirch, France b ABSTRACT The optimized exploitation of cell resources is one cornerstone of a suc- cessful infection. Differential mapping of host-pathogen protein-protein interactions (PPIs) on the basis of comparative interactomics of multiple strains is an effective strategy to highlight correlations between host proteome hijacking and biological or pathogenic traits. Here, we developed an interactomic pipeline to deliver high- confidence comparative maps of PPIs between a given pathogen and the human ubiquitin proteasome system (UPS). This subarray of the human proteome repre- sents a range of essential cellular functions and promiscuous targets for many vi- ruses. The screening pipeline was applied to the influenza A virus (IAV) PB2 polymer- ase proteins of five strains representing different levels of virulence in humans. An extensive PB2-UPS interplay has been detected that recapitulates the evolution of IAVs in humans. Functional validation with several IAV strains, including the seasonal H1N1 pdm09 and H3N2 viruses, confirmed the biological relevance of most identified UPS factors and revealed strain-independent and strain-specific effects of UPS factor invalidation on IAV infection. This strategy is applicable to proteins from any other virus or pathogen, providing a valuable resource with which to explore the UPS- pathogen interplay and its relationship with pathogenicity. IMPORTANCE Influenza A viruses (IAVs) are responsible for mild-to-severe seasonal respiratory illness of public health concern worldwide, and the risk of avian strain outbreaks in humans is a constant threat. Elucidating the requisites of IAV adapta- tion to humans is thus of prime importance. In this study, we explored how PB2 replication proteins of IAV strains with different levels of virulence in humans hijack a major protein modification pathway of the human host cell, the ubiquitin protea- some system (UPS). We found that the PB2 protein engages in an extended inter- play with the UPS that evolved along with the virus’s adaptation to humans. This suggests that UPS hijacking underlies the efficient infection of humans and can be used as an indicator for evaluation of the potential of avian IAVs to infect humans. Several UPS factors were found to be necessary for infection with circulating IAV strains, pointing to potential targets for therapeutic approaches. KEYWORDS comparative interactomics, influenza viruses, ubiquitination, virus-host interactions Received 25 July 2017 Accepted 2 November 2017 Published 22 November 2017 Citation Biquand E, Poirson J, Karim M, Declercq M, Malausse N, Cassonnet P, Barbezange C, Straub M-L, Jones L, Munier S, Naffakh N, van der Werf S, Jacob Y, Masson M, Demeret C. 2017. Comparative profiling of ubiquitin proteasome system interplay with influenza A virus PB2 polymerase protein recapitulating virus evolution in humans. mSphere 2:e00330-17. https://doi.org/10.1128/ mSphere.00330-17. Editor Martin Schwemmle, University Medical Center Freiburg Copyright © 2017 Biquand et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Caroline Demeret, caroline.demeret@pasteur.fr. * Present address: Juline Poirson, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada; Cyril Barbezange, National Influenza Center, Scientific Institute of Public Health, Brussels, Belgium. E.B. and J.P. contributed equally to this work. M.M. and C.D. are co-supervising scientists. RESEARCH ARTICLE Host-Microbe Biology crossm November/December 2017 Volume 2 Issue 6 e00330-17 msphere.asm.org 1 on June 17, 2020 by guest http://msphere.asm.org/ Downloaded from