Hepatitis C Virus Frameshift/Alternate Reading Frame Protein Suppresses Interferon Responses Mediated by Pattern Recognition Receptor Retinoic-Acid-Inducible Gene-I

Abstract

Hepatitis C virus (HCV) actively evades host interferon (IFN) responses but the mechanisms of how it does so are not completely understood. In this study, we present evidence for an HCV factor that contributes to the suppression of retinoic-acid-inducible gene-I (RIG-I)-mediated IFN induction. Expression of frameshift/alternate reading frame protein (F/ARFP) from HCV -2/+1 frame in Huh7 hepatoma cells suppressed type I IFN responses stimulated by HCV RNA pathogen-associated molecular pattern (PAMP) and poly(IC). The suppression occurred independently of other HCV factors; and activation of interferon stimulated genes, TNFα, IFN-λ1, and IFN-λ2/3 was likewise suppressed by HCV F/ARFP. Point mutations in the full-length HCV sequence (JFH1 genotype 2a strain) were made to introduce premature termination codons in the -2/+1 reading frame coding for F/ARFP while preserving the original reading frame, which enhanced IFNα and IFNβ induction by HCV. The potentiation of IFN response by the F/ARFP mutations was diminished in Huh7.5 cells, which already have a defective RIG-I, and by decreasing RIG-I expression in Huh7 cells. Furthermore, adding F/ARFP back via trans-complementation suppressed IFN induction in the F/ARFP mutant. The F/ARFP mutants, on the other hand, were not resistant to exogenous IFNα. Finally, HCV-infected human liver samples showed significant F/ARFP antibody reactivity, compared to HCV-uninfected control livers. Therefore, HCV F/ARFP likely cooperates with other viral factors to suppress type I and III IFN induction occurring through the RIG-I signaling pathway. This study identifies a novel mechanism of pattern recognition receptor modulation by HCV and suggests a biological function of the HCV alternate reading frame in the modulation of host innate immunity.

Hepatitis C Virus Translation Regulation

“…Two more described functions indicate how expression of the ARF/core+1 protein could provide evident advantages for HCV replication in the body. Overexpression of the ARF/core+1 protein suppresses the expression of interferon-stimulated genes (ISGs), including the pattern recognition receptor retinoic-acid-inducible gene-I (RIG-I) [244]. This indicates that the ARF/core+1 protein contributes to establishing long-term HCV replication in the liver.…”

Asymmetric evolution in viral overlapping genes is a source of selective protein adaptation

“…Several other de novo proteins under asymmetric evolution are known to play a role in viral pathogenicity. Eight de novo proteins (ARFP, VP5, L*, X, VF1, PB1-F2, P6, and NSs) act as suppressor or antagonist of the interferon response by the host (Park et al, 2016;Lauksund et al, 2015;Sorgeelos et al, 2013;Wensman et al, 2013;McFadden et al, 2011;Varga et al, 2011;García-Rosado et al, 2008;Jääskeläinen et al, 2007). Four de novo proteins (p19, p69, AC4, and movement protein) act as suppressor of RNA silencing (Silhavy et al, 2002;Chen et al, 2004;Chellappan et al, 2005;Yaegashi et al, 2008).…”

Small Proteins Encoded by Unannotated ORFs are Rising Stars of the Proteome, Confirming Shortcomings in Genome Annotations and Current Vision of an mRNA

“…Such alternative reading frame proteins can be detected in patients developing specific antibodies . One of these proteins, the alternate F protein seems to modulate the immune system . West Nile Virus also generates alternative reading frame proteins .…”