The Interactomes of Influenza Virus NS1 and NS2 Proteins Identify New Host Factors and Provide Insights for ADAR1 Playing a Supportive Role in Virus Replication

Benoît De Chassey,Philippe-Emmanuel Mangeot,Laurène Meyniel-Schicklin,Alessia Ruggieri,Anne Aublin-Gex,Lionel Tafforeau,Thibault Chantier,Fabrine Pradezynski,Patrice André,Nathalie Davoust,Ralf Bartenschlager,Claire Ciancia,Laure Perrin-Cocon,Vincent Lotteau,Sumit K Chanda

doi:10.1371/journal.ppat.1003440

Abstract

Influenza A NS1 and NS2 proteins are encoded by the RNA segment 8 of the viral genome. NS1 is a multifunctional protein and a virulence factor while NS2 is involved in nuclear export of viral ribonucleoprotein complexes. A yeast two-hybrid screening strategy was used to identify host factors supporting NS1 and NS2 functions. More than 560 interactions between 79 cellular proteins and NS1 and NS2 proteins from 9 different influenza virus strains have been identified. These interacting proteins are potentially involved in each step of the infectious process and their contribution to viral replication was tested by RNA interference. Validation of the relevance of these host cell proteins for the viral replication cycle revealed that 7 of the 79 NS1 and/or NS2-interacting proteins positively or negatively controlled virus replication. One of the main factors targeted by NS1 of all virus strains was double-stranded RNA binding domain protein family. In particular, adenosine deaminase acting on RNA 1 (ADAR1) appeared as a pro-viral host factor whose expression is necessary for optimal viral protein synthesis and replication. Surprisingly, ADAR1 also appeared as a pro-viral host factor for dengue virus replication and directly interacted with the viral NS3 protein. ADAR1 editing activity was enhanced by both viruses through dengue virus NS3 and influenza virus NS1 proteins, suggesting a similar virus-host co-evolution.

Highlights

Influenza A viruses are the causative agents of seasonal and pandemic infections and are responsible for the death of at least half a million people worldwide each year
As most biological processes are sustained by protein-protein interactions, the identification of interactions between viral and host proteins can provide a global overview about the cellular functions engaged during viral replication
These interacting host cell proteins are potentially involved in many steps of the virus life cycle and 7 can directly control the viral replication

Summary

Introduction

Influenza A viruses are the causative agents of seasonal and pandemic infections and are responsible for the death of at least half a million people worldwide each year. The genome of influenza A viruses is composed of eight negative-sense singlestranded RNAs encoding 13 proteins. NS1 and NS2 are derived from alternatively spliced RNAs that are transcribed from the eighth RNA segment. The segments are encapsidated by binding to nucleoproteins (NP) and the polymerase complex (PA, PB1 and PB2) forming the viral ribonucleoproteins (vRNPs). The viral particle contains eight vRNPs, the surface glycoproteins haemagglutinin (HA) and neuraminidase (NA), the matrix proteins (M1 and M2) and the NS2 protein. Some strains express the proapoptotic PB1-F2 protein and two additional virulence factors, PB1-N40 and PA-X, have been recently identified [1,2,3]

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Conclusion