Cell Host & Microbe

crAss-phage MCP HMM-profiles and Microviridae HMM-profiles

Data presented with sequence in the manuscript

Human cytomegalovirus (HCMV) is an important pathogen with multiple immune evasion strategies, including virally facilitated degradation of host antiviral restriction factors. Here, we describe a multiplexed approach to discover proteins with innate immune function on the basis of active degradation by the proteasome or lysosome during early phase HCMV infection. Using three orthogonal proteomic/transcriptomic screens to quantify protein degradation, with high confidence we identified 35 proteins enriched in antiviral restriction factors. A final screen employed a comprehensive panel of viral mutants to predict viral genes that target >250 human proteins. This approach revealed Helicase-like Transcription Factor (HLTF), a DNA helicase important in DNA repair, potently inhibits early viral gene expression but is rapidly degraded during infection. The functionally unknown HCMV protein UL145 facilitates HLTF degradation by recruiting the Cullin4 E3 ligase complex. Our approach and data will enable further identifications of innate pathways targeted by HCMV and other viruses. See https://www.cell.com/cell-host-microbe/fulltext/S1931-3128(18)30381-0 for full publication.

As shown in Fig. 3h, the C7a/t virus contained two C variants: HA-C (~12.5 kDa) and C7 (~10.5 kDa) proteins with an estimated molecular ratio of 1:30, whereas the WT ZIKV had only full-length C protein (~11.4 kDa). As expected, both C7a/t and WT viruses contained mature M and E proteins. As controls, culture medium from replicon-transfected cells contained only NS1 protein, with no detectable structural proteins (C, M, or E). The data suggest that C7a/t ZIKV contains both HA-C and C7 proteins. Western blot analysis of C7a/t virus. Supernatants from replicon RNA-transfected BHK-HA-C cells (day 4 p.t.), WT RNA-transfected Vero cells (day 4 p.t.), and C7a RNA-transfected BHK-HA-C cells (day 4 p.t.) were analyzed for viral proteins (HA-C, C, M, E, and NS1) using Western blotting.

Virulence-relevant KOs Database allows the prediction of bacterial virulence factor genes from 16S-based metagenomics using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) algorithm. After normalisation for 16S rDNA copy number and total species count, KEGG Orthologs (KO) abundances can be estimated using PICRUSt pre-computed files and virulence-specific genes parsed using VFDB_KO_unique file.

Dataset of the immune effector function induced by 168 Ebola virus glycoprotein-specific monoclonal antibodies.

These are the raw DNA sequencing files and corresponding metadata for the 16S rRNA sequencing analyzed in Jacobson et al. 2018

Supplemental movie files and legends