Viperin Reveals Its True Function

Abstract

Most cells respond to viral infections by activating innate immune pathways that lead to the induction of antiviral restriction factors. One such factor, viperin, was discovered almost two decades ago based on its induction during viral infection. Since then, viperin has been shown to possess activity against numerous viruses via multiple proposed mechanisms. Most recently, however, viperin was demonstrated to catalyze the conversion of cytidine triphosphate (CTP) to 3'-deoxy-3',4'-didehydro-CTP (ddhCTP), a previously unknown ribonucleotide. Incorporation of ddhCTP causes premature termination of RNA synthesis by the RNA-dependent RNA polymerase of some viruses. To date, production of ddhCTP by viperin represents the only activity of viperin that links its enzymatic activity directly to an antiviral mechanism in human cells. This review examines the multiple antiviral mechanisms and biological functions attributed to viperin.

Keywords: RNA-dependent RNA polymerase; RSAD2; chain terminator; interferon; radical SAM protein; viperin.

Figure 1

Molecular and biochemical properties of viperin. (a) Genetic organization of VIPERIN. The VIPERIN gene is located in the short arm of chromosome 2 and found adjacent to and inverted with respect to CMPK2. The gene lncRNA-CMPK2 is located adjacent to CMPK2 and acts as a negative regulator for CMPK2 levels. (b) Previously described domains of the viperin protein. The three predicted domains of viperin and their reported roles are shown. (c) Production of ddhCTP. The mitochondrial kinase CMPK2 catalyzes the phosphorylation of CDP to produce CTP, which can then be used as a substrate by viperin to produce ddhCTP. For a detailed mechanistic proposal for viperin catalysis, see Reference . (d) Crystal structure of mouse viperin in complex with SAH and its substrate CTP showing the RS and C-terminal domains are not isolable (6Q2P). Abbreviations: CDP, cytidine diphosphate; CIA, cytosolic iron-sulfur protein assembly; CTP, cytidine triphosphate; ddhCTP, 3′-deoxy-3′,4′-didehydro-cytidine triphosphate; DENV-2, dengue virus serotype-2; ER, endoplasmic reticulum; HCV, hepatitis C virus; LD, lipid droplet; RS, radical S-adenosyl-L-methionine; SAH, S-adenosylhomocysteine; SAM, S-adenosyl-L-methionine; ZIKV, Zika virus.

Figure 2

IFN-dependent and -independent pathways leading to induction of viperin upon viral infection. (a) Upon viral infection, sensing of viral nucleic acids by PRRs leads to the activation of downstream signaling factors that result in the induction of IFNs and, in some cases, viperin. The induction of IFN-β can occur to one of several mechanisms, including those dependent on endosomal TLRs and mitochondrial MAVS, that culminate in the activation of the transcription factors IRF3 and IRF7 that bind to the IFNB promoter and induce its expression. The direct induction of viperin can occur through peroxisomal MAVS and downstream activation of IRF1 or by IRF3. Viperin itself can increase IFNB induction by promoting TRAF6-dependent ubiquitination of IRAK1 and phosphorylation of IRF7. IFN-β is secreted and signals both in autocrine and paracrine manners upon binding to its receptor. Downstream activation of the Jak-STAT pathway results in the formation of the heterotrimeric complex ISGF3, which translocates to the nucleus and binds to the promoter of ISGs, including that of viperin, and other IFNs. The transcription factor PRDI-BF1 can act as a negative regulator by competing with ISGF3 for promoter binding. Additionally, IFN-γ secreted primarily by immune cells can activate IRF1 and directly induce viperin expression. (b) In binding of transcription factors to the VIPERIN promoter, the promoter contains two adjacent ISRE sites immediately upstream of the TSS for ISGF3 complex binding. The transcription factor IRF3 can directly bind to the ISREs and also to an upstream sequence. Activation of IRF1 by either IFN-γ signaling or peroxisomal MAVS can bind to two IRF-binding elements, IRF-E #2 and #3. A further upstream IRF-E sequence exists but does not appear to be involved in IRF1 binding. Abbreviations: AP-1, activator protein 1; IFN, interferon; IRAK1, interleukin-1 receptor-associated kinase 1; IRF, interferon regulatory factor; IRF-E, interferon regulatory factor element; ISGF3, interferon-stimulated gene factor 3; ISRE, interferon-stimulated response element; Jak-STAT, Janus kinase signal transducer and activator of transcription protein; MAVS, mitochondrial antiviral signaling; P, phosphorylated; PRDI-BF1, positive regulatory domain I binding factor 1; PRR, pattern recognition receptor; RLR, retinoic acid-inducible gene I (RIG-I)-like receptor; STAT, signal transducer and activator of transcription protein; TLR, Toll-like receptor; TRAF6, tumor necrosis factor receptor–associated factor 6; TSS, transcription start site.

Figure 3

Reported inhibitory mechanisms of viral infections by viperin. Viperin localizes on the cytosolic face of the ER and to LDs, both of which often serve as platforms for viral RCs. Viperin catalyzes the conversion of CTP, possibly produced by CMPK2, to ddhCTP, which serves as a chain terminator during flavivirus replication. Viperin can also promote viral protein degradation, bind to proteins from several different viruses, and interfere with Golgi-dependent trafficking of soluble proteins and promote the release of immature capsids through sequestration of the host factor GBF1. Viperin can inhibit cholesterol synthesis through binding to FPPS, resulting in disruption of lipid rafts at the plasma membrane used by some viruses during their egress. Abbreviations: CMPK2, cytidylate monophosphate kinase 2; CTP, cytidine triphosphate; ddhCTP, 3′-deoxy-3′,4′-didehydro-cytidine triphosphate; DENV, dengue virus; ER, endoplasmic reticulum; EV-A71, enterovirus A71; FPPS, farnesyl diphosphate synthase; GBF1, Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1; HCV, hepatitis C virus; HIV, human immunodeficiency virus; IAV, influenza A virus; JEV, Japanese encephalitis virus; LD, lipid droplet; RC, replication complex; TBEV, tick-borne encephalitis virus; WNV, West Nile virus; ZIKV, Zika virus.