Interferon inhibits a model RNA virus via a limited set of inducible effector genes

Abstract

Interferons control viral infection by inducing the expression of antiviral effector proteins encoded by interferon-stimulated genes (ISGs). The field has mostly focused on identifying individual antiviral ISG effectors and defining their mechanisms of action. However, fundamental gaps in knowledge about the interferon response remain. For example, it is not known how many ISGs are required to protect cells from a particular virus, though it is theorized that numerous ISGs act in concert to achieve viral inhibition. Here, we used CRISPR-based loss-of-function screens to identify a markedly limited set of ISGs that confer interferon-mediated suppression of a model alphavirus, Venezuelan equine encephalitis virus (VEEV). We show via combinatorial gene targeting that three antiviral effectors, ZAP, IFIT3, and IFIT1, together constitute the majority of interferon-mediated restriction of VEEV, while accounting for less than 0.5% of the interferon-induced transcriptome. Together, our data suggests a refined model of the antiviral interferon response in which a small subset of 'dominant' ISGs may confer the bulk of the inhibition of a given virus.

Endogenous ZAP affects Zika virus RNA interactome

“…The sensitivity of Zika virus was previously tested to ectopically overexpressed ZAP against the background of endogenous ZAP [48]. Overexpression screening is a powerful approach, but overexpressing individual genes may also miss antiviral effectors that work in multiprotein complexes [53]. Indeed, it is known that ZAP can augment other antiviral systems [14].…”

Endogenous ZAP is associated with altered Zika virus infection phenotype

“…Nonetheless, two important innate immune genes-IFIT1 and ISG15-were upregulated in transfected or infected ZAP-WT cells in both studies, suggesting their ZAP-mediated augmentation in the absence of the type I IFN system. Potential type I IFN-independent and -dependent interactions between ZAP and IFIT1 are of interest because ZAP and IFIT1 together have recently been identified to constitute the majority of IFN-mediated restriction of alphavirus, specifically Venezuelan equine encephalitis virus [26].…”

“…Overexpression screening is a powerful approach, but overexpressing individual genes may also miss antiviral effectors that work in multiprotein complexes [26]. Here, we compared Zika virus infection and characterized global cellular gene expression in uninfected and Zika-infected wildtype and ZAP knockout VERO cells.…”