They were then used as viral baits against human cDNA libraries. Viral ORFs coding for NS3 and NS5 proteins were isolated from distinct human pathogens belonging to major flavivirus evolutionary lineages: Saracatinib order (i) aedes-borne pathogen: DENV; (ii) culex-borne pathogens: WNV (including the Kunjin Australian variant
(KUNV)) and JEV; (iii) tick-borne pathogens: Tick-borne encephalitis (TBEV) and Alkhurma (ALKV) viruses. Protein sequence comparison study revealed that the functional enzymatic domains of NS3 are highly conserved amongst these viruses (Additional file 2). At least three independent screenings against human cDNA libraries were performed for each viral bait. Eighty-five percent of the identified cellular targets of each bait were then tested pairwise against all the viral proteins baits including the original bait using an array-based Y2H strategy which confirmed 90% of the interactions identified in the initial screens. Furthermore, the bait panel versus selected targets strategy used in the array cross experiment enabled us to identify 69 additional, novel virus-host Idasanutlin cost interactions not detected in the first screen. Repetition and confirmation of our Y2H experiment by the array strategy allowed us to be very stringent in obtaining a high quality set of 108 human proteins that interacted with one
or more of the viral protein baits (Additional file 3). In one of our previously published studies using the same Y2H screening settings, the the validation rate obtained by co-affinity purification reached 85% [12]. We conducted GST-pull down assays to further validate our Y2H data (Additional file 4). An extensive literature curation allowed us to finally complete our set of data by 16 previously published interactions, 15 of which not identified by our screen (Additional file 3). Analysis of the
flavivirus-human protein-protein interaction network Based on our high-throughput Y2H screen and literature search, we created the flavivirus NS3 and NS5 proteins interaction network composed of 186 interactions involving 120 distinct human proteins, 108 from our screen and 13 from the literature (Table 1, Figure 1, additional files 3 and 5). We emphasize that among the 186 interactions, 171 were obtained from our Y2H screen and only 16 from previously published work. Despite the conserved amino acid patterns within the different viral ORFs that we used as viral baits, only one third of the cellular targeted proteins identified in our study interacted with two or more flaviviruses (Table 2). Moreover, only five cellular proteins (CAMTA2, CEP250, SSB, ENO1, and FAM184A) were found to interact with both NS3 and NS5 proteins (Figure 1, additional file 5).