Identification and comparative analysis of hepatitis C virus–host cell protein interactions

Abstract

Hepatitis C virus (HCV) alters the global behavior of the host cell to create an environment conducive to its own replication, but much remains unknown about how HCV proteins elicit these changes. Thus, a better understanding of the interface between the virus and host cell is required. Here we report the results of a large-scale yeast two-hybrid screen to identify protein-protein interactions between HCV genotype 2a (strain JFH1) and cellular factors. Our study identified 112 unique interactions between 7 HCV and 94 human proteins, over 40% of which have been linked to HCV infection by other studies. These interactions develop a more complete picture of HCV infection, providing insight into HCV manipulation of pathways, such as lipid and cholesterol metabolism, that were previously linked to HCV infection and implicating novel targets within microtubule-organizing centers, the complement system and cell cycle regulatory machinery. In an effort to understand the relationship between HCV and related viruses, we compared the HCV 2a interactome to those of other HCV genotypes and to the related dengue virus. Greater overlap was observed between HCV and dengue virus targets than between HCV genotypes, demonstrating the value of parallel screening approaches when comparing virus-host cell interactomes. Using siRNAs to inhibit expression of cellular proteins, we found that five of the ten shared targets tested (CUL7, PCM1, RILPL2, RNASET2, and TCF7L2) were required for replication of both HCV and dengue virus. These shared interactions provide insight into common features of the viral life cycles of the family Flaviviridae.

A Combined Proteomics/Genomics Approach Links Hepatitis C Virus Infection with Nonsense-Mediated mRNA Decay

“…Systematic approaches have identified host proteins key to HCV infection, including RNAi screens (Li et al, 2009; Suratanee et al, 2010; Tai et al, 2009) and a two-hybrid method (de Chassey et al, 2008; Dolan et al, 2013). A systematic affinity tag purification/mass spectrometry (AP-MS) approach was first used to construct a comprehensive host-pathogen protein-protein interaction (PPI) map for HIV-1 (Jager et al, 2011).…”

Elucidation of host–pathogen protein–protein interactions to uncover mechanisms of host cell rewiring

“…Although this method generates direct binary interaction datasets at high throughput, the need for exhaustive screens hampers its feasibility, and its technical challenges such as the non-physiological expression system provokes high rates of false negatives [15]. Nonetheless, many studies in the field of infectious diseases have successfully employed Y2H screens to investigate (near) genome-wide virus-host interactions [16–23], to compare homologous viral proteins from various strains [24,25], or to systematically map bacterial effector proteins – host interactions [26–31] (see supplementary table 1). In the context of Mycobacterium tuberculosis infections, a Y2H screen along with functional validations, enabled the discovery of a molecular mechanism by which an effector protein, named EsxH, targets the Endosomal Sorting Complexes Required for Transport (ESCRT) necessary for endosomal membrane trafficking, thereby impairing the phagosomal maturation and fusion with the lysosomes [28].…”

Protein-protein interactions of human viruses

“…During the last decade numerous protein interactions between human viruses and their host cells have been mapped and more thoroughly investigated. Most of these efforts focused on relatively few viruses, such as Hepatitis C virus [6][7][8][9], Human Immunodeficiency Virus [10,11], Influenza A virus [12], herpesviruses [13] such as Epstein-Barr Virus [14,15], as well as Dengue [16] and a few others [17]. As a consequence of many high-throughput screens, databases of PPIs have been filled with tens of thousands of virus-human interactions.…”