Interferon-stimulated genes: a complex web of host defenses

Abstract

Interferon-stimulated gene (ISG) products take on a number of diverse roles. Collectively, they are highly effective at resisting and controlling pathogens. In this review, we begin by introducing interferon (IFN) and the JAK-STAT signaling pathway to highlight features that impact ISG production. Next, we describe ways in which ISGs both enhance innate pathogen-sensing capabilities and negatively regulate signaling through the JAK-STAT pathway. Several ISGs that directly inhibit virus infection are described with an emphasis on those that impact early and late stages of the virus life cycle. Finally, we describe ongoing efforts to identify and characterize antiviral ISGs, and we provide a forward-looking perspective on the ISG landscape.

Figure 1

The interferon (IFN)-signaling cascade. The three different classes of IFNs signal through distinct receptor complexes on the cell surface: type I IFNs act through IFN-α receptor 1 (IFNAR1) and 2 (IFNAR2) heterodimers; type III IFN through interleukin-10 receptor 2 (IL-10R2) and IFN-λ receptor 1 (IFNLR1) heterodimers; and type II IFN through dimers of heterodimers consisting of IFN-γ receptors 1 (IFNGR1) and 2 (IFNGR2). Binding of both type I and type III IFNs to their IFNAR1/2 or IL-10R2/IFNLR1 complexes, respectively, triggers phosphorylation of preassociated Janus kinase 1 (JAK1) and tyrosine kinase 2 (TYK2), which in turn phosphorylate the receptors at specific intracellular tyrosine residues. This leads to the recruitment and phosphorylation of signal transducers and activators of transcription 1 and 2 (STAT1 and 2). STAT1 and 2 associate to form a heterodimer, which in turn recruits the IFN-regulatory factor 9 (IRF9) to form the IFN-stimulated gene factor 3 (ISGF3). Binding of type II IFN dimers to the IFNGR1/2 complex leads to phosphorylation of preassociated JAK1 and JAK2 tyrosine kinases, and transphosphorylation of the receptor chains leads to recruitment and phosphorylation of STAT1. Phosphorylated STAT1 homodimers form the IFN-γ activation factor (GAF). Both ISGF3 and GAF translocate to the nucleus to induce genes regulated by IFN-stimulated response elements (ISRE) and gamma-activated sequence (GAS) promoter elements, respectively, resulting in expression of antiviral genes.

Figure 2

Cytosolic nucleic acid pattern recognition and activation of ISGs. Cytosolic pattern-recognition receptors (PRRs) recognize viral double-stranded (ds) or single-stranded (ss) DNA or RNA. AIM2-like receptors (ALRs), such as IFI16, DAI, or AIM2 itself, specialize in DNA detection, whereas RIG-I-like receptors (RLR)—RIG-I and MDA5—specialize in RNA detection. Cyclic GMP-AMP synthase acts as an additional DNA sensor. 2′-5′-oligoadenylate synthetase (OAS) senses foreign RNA and produces 2′-5′ adenylic acid, which activates latent RNase (RNaseL). Degradation products produced by RNaseL further stimulate RLRs. Protein kinase R (PKR) is an additional sensor for foreign RNA. PRR signals are transduced to transcription factor activity by stimulator of IFN genes (STING) and mitochondrial antiviral-signaling protein (MAVS) at the ER/mitochondrion-associated membrane. Activation of STING/MAVS leads to phosphorylation of interferon (IFN) response factors 3 or 7 (IRF3/7), or to phosphorylation and ubiquitin-mediated degradation of IκB. Phosphorylated dimers of IRF3/7 or NF-κB translocate to the nucleus, where they bind to and activate specific promoters, triggering expression of IFN as well as a subset of ISGs. These ISGs include IRFs and PRRs but also antiviral effectors such as viperin. IFN induces gene expression via the JAK-STAT pathway, resulting in expression of a large spectrum of ISGs that can be divided into antiviral effectors and negative or positive regulators of IFN signaling. A special case of positive regulators is IRF1, which upon expression directly translocates to the nucleus to enhance expression of a subset of ISGs.

Figure 3

Interferon (IFN) desensitization pathways. IFN signaling is negatively regulated by various mechanisms. (a) An immediate mechanism of IFN desensitization is endocytosis and turnover of IFN receptors, which rapidly reduces the level of JAK-STAT signaling within the cell. (b) Another early mechanism of IFN desensitization requires de novo synthesis of inhibitory proteins. IFN-stimulated suppressor of cytokine signaling (SOCS) proteins act as kinase inhibitors within the JAK-STAT phosphorylation cascade. Both SOCS1 and SOCS3 act as pseudosubstrates for receptor-associated JAKs. Protein inhibitors of activated STAT (PIAS) proteins bind to and inhibit phosphorylated STATs, thereby interrupting the signaling cascade. (c) The ubiquitin-specific peptidase 18 (USP18), expressed from an IFN-stimulated gene, leads to a more sustained shutdown of JAK-STAT signaling. USP18 binds to the intracellular side of the IFN-α receptor 2 (IFNAR2), resulting in conformational changes in the extracellular domains of IFNAR2, which keeps low-affinity IFNs such as IFN-α from binding, and hence from inducing, the JAK-STAT signaling cascade. In contrast, IFNs with higher receptor affinity, such as IFN-β, are still able to bind and initiate the signaling cascade. USP18 binding is specific to IFNAR2, and thus it does not interfere with type II or type III IFN signaling.

Figure 4

Targets for interferon (IFN)-stimulated proteins within viral life cycles. IFN-stimulated gene (ISG) products (stars) interfere with different stages of different viral life cycles. Cholesterol-25-hydroxylase (CH25H) affects viruses early, presumably at the host-membrane fusion event; at protein maturation of viral structural proteins by prenylation; and at protein maturation of viral replication enzymes. IFN-induced transmembrane (IFITM) protein members inhibit endocytic-fusion events of a broad spectrum of viruses. Tripartite motif protein 5 α (TRIM5 α) inhibits human immunodeficiency virus 1 (HIV-1) uncoating of the viral RNA. The myxoma resistance protein 1 (Mx1) inhibits a wide range of viruses by blocking endocytic traffic of incoming virus particles and uncoating of ribonucleocapsids. Some ISGs inhibit viruses by degrading viral RNA and/or blocking translation of viral mRNAs, such as 2′,5′-oligoadenylate synthetase (OAS) and latent ribonuclease L (RNase L), protein kinase R (PKR), Moloney leukemia virus 10 homolog (MOV10), and zinc-finger antiviral protein (ZAP). IFN-induced proteins with tetratricopeptide repeats (IFIT) inhibit protein translation and have been implicated in viral RNA degradation as well. TRIM22 inhibits viral transcription, replication, or trafficking of viral proteins to the plasma membrane. ISG15 can inhibit viral translation, replication, or egress. Viperin has been shown to inhibit viral replication or virus budding at the plasma membrane. Finally, tetherin traps otherwise mature virus particles on the plasma membrane and thus inhibits viral release, exerting its effect broadly on many enveloped viruses.

Figure 5

Canonical and noncanonical definition of interferon (IFN)-stimulated antiviral effectors. For years the canonical understanding of the IFN-mediated antiviral response has been that IFN triggers the transcription of IFN-stimulated genes (ISGs), which leads to changes in the cellular proteome and establishment of an antiviral state within cells. Recent studies suggest that the situation is likely more complex. (a) IFN treatment of cells promotes alternative transcriptional start site usage, and IFN-induced alternative mRNA splicing may give rise to transcript isoforms that encode for different protein products or transcripts with altered stability or translational efficiency (a1/a2). (b) In addition, IFN stimulation may alter the expression of microRNAs (miRNAs) or long noncoding RNAs (lncRNAs). LncRNAs may influence gene expression through interaction with chromatin remodeling complexes (b1) or may serve as a scaffold for the formation of RNA-protein complexes that confer antiviral activity (b2). IFN stimulation or pathogen recognition may promote translation of preexisting mRNAs. Finally, IFN stimulation influences the proteome directly by promoting proteins’ post-translational modification, altering protein stability, and increasing protein secretion.