Critical Nodes of Virus–Host Interaction Revealed Through an Integrated Network Analysis

Korbinian Bösl; Aleksandr Ianevski; Thoa T. Than; Petter I. Andersen; Suvi Kuivanen; Mona Teppor; Eva Zusinaite; Uga Dumpis; Astra Vitkauskiene; Rebecca J. Cox; Hannimari Kallio-Kokko; Anders Bergqvist; Tanel Tenson; Valentyn Oksenych; Magnar Bjørås; Marit W. Anthonsen; David Shum; Mari Kaarbø; Olli Vapalahti; Marc P. Windisch; Giulio Superti-Furga; Berend Snijder; Denis Kainov; Richard K. Kandasamy

Given that the viral proteins were interacting with a large number of host proteins, we analysed the sub-cellular location of the host proteins. We performed gene-set enrichment analysis of sub-cellular localization information provided by UniProt database. We binned the localization into 11 compartments and estimated the percent of host proteins in a given compartment as compared to the total number of host proteins targeted by a given virus. We found that the viral targets were distributed across multiple subcellular compartments with cytoplasm being the most common (Fig. S4A ). The hvPPI includes two different strains of IAV-PR8 (H1N1) and Udorn (H3N2). The subcellular localization analysis showed that both strains were enriched for nuclear proteins. Nonstructural protein 1 (NS1) from both the strains had the highest number of nuclear targets but their targets were very different (Fig. 4A ). NS1 of Udorn was enriched for a large number of histones as compared to NS1 of PR8 that had large number of heterogeneous nuclear ribonucleoproteins (hnRNPs), such as HNRNPU -a known restriction factor for many viruses. This corroborates with the observation that NS1 protein has short linear histone mimicry motifs that can suppress the host antiviral response (Marazzi et al. 2012) . In our analysis, we found that it is NS1 of Udorn that has a histone mimicry motif "ARSK" (Fig. S4B) . Similarly, HPV11 and HPV18 E5 proteins interact more often with host proteins located in the endoplasmic reticulum (ER). We found both common and specific subsets of ER proteins targeted by the E5 protein (Fig. 4B ). HPV18 E5 protein ER targets were enriched for phospholipid biosynthesis as well as GPI anchor related proteins, such as phosphatidylinositol glycan anchor biosynthesis class S/T/U (PIGS, PIGT and PIGU), glycosylphosphatidylinositol anchor attachment 1 (GPAA1) and phosphatidylserine synthase 2 (PTDSS2). HPV11 E5 protein ER targets were enriched for ER-associated ubiquitin-dependent protein catabolism involving host proteins such as ER degradation enhancing alpha-mannosidase-like protein 3 (EDEM3) and ER lipid raft associated 1 (ERLIN1). ER targets common to HPV18 and HPV11 E5 protein were enriched for unfolded protein response, N-linked glycosylation and protein folding involving host proteins such as SRP receptor alpha/beta subunit (SRPRA/SRPRB) and catalytic subunits of the oligosaccharyltransferase complex (STT3A and STT3B). Two independent CRISPR/Cas9 screening studies identified multiple ER associated components including STT3A and STT3B as host factors for DENV, Zika virus (ZIKV) and Japanese encephalitis virus (JEV) , Marceau et al. 2016 . The non-canonical function of STT3A and STT3B is required for DENV replication and that NS1 protein of DENV interacts with these proteins (Marceau et al. 2016 ). Our orthogonal approach can lead to the identification of critical host factors, and similar functions of ER components, such as STT3A and STT3B, are used by HPV11 and HPV18 as well. Thus targeting the non-canonical function of STT3A and STT3B could be a broad antiviral strategy. Overall, the enrichment analysis clearly shows that there is commonality and specificity in the subcellular targets of the viral proteins and that detailed interrogation of these targets can give vital clues into the viral evasion mechanisms. preprint author/funder. All rights reserved. No reuse allowed without permission.