Extended Data Fig. 1: ER protein depletion in virus infection.

a, Phylogenetic analysis of metazoan ATL proteins collected from a subset of publicly available metazoan predicted proteomes. ATL sequences were aligned with MUSCLE and manually trimmed into a 494-site alignment. Phylogenies were reconstructed, and node support values were calculated using MrBayes for posterior probability and RAxML for maximum likelihood and presented as inset (MrBayes/RAxML). The MrBayes tree topology is shown. Scale bar: number of estimated substitutions per site. For genomes used see Supplementary Table 7 b-h, A549 cells were transduced with constructs encoding for shRNAs (b-e, and g-h) or transfected with siRNA (f) targeting indicated mRNA transcripts, or a non-targeting (NT) shRNA or siRNA. b-d, 96 h post transduction, mRNA levels, protein levels and cell viability were evaluated. b, ATLs mRNA transcript levels were evaluated by RT-qPCR and values corrected using HPRT. Graphs show average percent change compared to NT shRNA for 3 independent experiments. c, ATL protein levels evaluated by western blot. Graph shows average protein levels compared to NT shRNA treated cells from 3 experimental replicates. d, Graph shows mean cell viability as percent survival compared to NT shRNA treated cells. e, 48 h after transduction cells were infected with DV (MOI=1) for 48 h. DV titre were determined by PFU assay. Graph show average fold change in PFU/mL (titre). * and ** - p values lower than 0.05 or 0.01, respectively, determined using one-way ANOVA with a Dunnett’s multiple comparison analysis. RTN, reticulon; LNP, lunapark. f, 96 h post transduction, cells were lysed for RNA analysis. Graph shows average percent change vs. NTshRNA for 3 independent experiments g-h, 48 h after transduction cells were infected with DV or RVFV (MOI=1) for 48 h. DV titre were evaluated using a PFU assay and RVFV replication was determined by luciferase assay. Graphs show average fold change in PFU/mL (titre) or average fold change in RLU/mL (replication) relative to NT shRNA expressing cells for three independent experiments. For all graphs, error bars show SEM and N= ≥ 3 biological replicates.