Efficient Dicer processing of virus-derived double-stranded RNAs and its modulation by RIG-I-like receptor LGP2

Abstract

The interferon-regulated antiviral responses are essential for the induction of both innate and adaptive immunity in mammals. Production of virus-derived small-interfering RNAs (vsiRNAs) to restrict virus infection by RNA interference (RNAi) is a recently identified mammalian immune response to several RNA viruses, which cause important human diseases such as influenza and Zika virus. However, little is known about Dicer processing of viral double-stranded RNA replicative intermediates (dsRNA-vRIs) in mammalian somatic cells. Here we show that infected somatic cells produced more influenza vsiRNAs than cellular microRNAs when both were produced by human Dicer expressed de novo, indicating that dsRNA-vRIs are not poor Dicer substrates as previously proposed according to in vitro Dicer processing of synthetic long dsRNA. We report the first evidence both for canonical vsiRNA production during wild-type Nodamura virus infection and direct vsiRNA sequestration by its RNAi suppressor protein B2 in two strains of suckling mice. Moreover, Sindbis virus (SINV) accumulation in vivo was decreased by prior production of SINV-targeting vsiRNAs triggered by infection and increased by heterologous expression of B2 in cis from SINV genome, indicating an antiviral function for the induced RNAi response. These findings reveal that unlike artificial long dsRNA, dsRNA-vRIs made during authentic infection of mature somatic cells are efficiently processed by Dicer into vsiRNAs to direct antiviral RNAi. Interestingly, Dicer processing of dsRNA-vRIs into vsiRNAs was inhibited by LGP2 (laboratory of genetics and physiology 2), which was encoded by an interferon-stimulated gene (ISG) shown recently to inhibit Dicer processing of artificial long dsRNA in cell culture. Our work thus further suggests negative modulation of antiviral RNAi by a known ISG from the interferon response.

The Interaction of Influenza A NS1 and Cellular TRBP Protein Modulates the Function of RNA Interference Machinery

“…Dicer-mediated cleavage of viral dsRNAs into vsiRNAs leads to suppression of viral replication by knocking down viral genes. Our recent study indicates that NoV-derived siRNAs have antiviral function in vivo by constructing a recombinant SINV containing part of NoV genomic RNA 1 sequences ( Zhang et al, 2021 ). In addition, Zhou and colleagues designed peptides targeting the 3A protein of enterovirus A71 (EV-A71), which abrogate VSR function and promote vsiRNAs production ( Fang et al, 2021 ).…”

“…These IAV vsiRNAs have the characteristics of canonical viral siRNAs and are likely to have antiviral functions. Because both NoV and SINV can infect the muscle tissue of mice, we generated the SINV reporting system to detect the function of vsiRNAs from the NoV virus ( Zhang et al, 2021 ). Unfortunately, because IAV mainly replicates in lung tissues, the SINV reporting system is not suitable for testing the function of IAV vsiRNAs.…”

“…On the other hand, there is growing evidence that siRNA-based antiviral immunity plays an important role in mammals ( Li et al, 2013 ; Maillard et al, 2013 ; Li et al, 2016 ; Qiu et al, 2017 ; Han et al, 2020 ; Zeng et al, 2020 ). Recent studies including ours have shown several viruses, such as Nodamura virus (NoV), IAV, Sindbis virus (SINV), and ZIKV induce vsiRNA production in vitro or in vivo ( Li et al, 2013 ; Li et al, 2016 ; Zhang et al, 2020 ; Zhang et al, 2021 ). To counter the defense mechanism, many viruses encode viral suppressors of RNAi (VSRs), including NoV B2, IAV NS1, Ebolavirus (EBOV) VP35, and human enterovirus 71 (HEV71) 3A ( Fabozzi et al, 2011 ; Li et al, 2013 ; Li et al, 2016 ; Qiu et al, 2017 ).…”

Chicken-Derived Pattern Recognition Receptor chLGP2 Inhibits the Replication and Proliferation of Infectious Bronchitis Virus

“…For the Sendai virus, antiviral signals are restrained by LGP2 in a manner associated with the C-terminus of TRAF and affect its ubiquitin ligase activity ( Parisien et al, 2018 ). In addition, mammalian Dicer can cut virus-derived double-stranded RNA (dsRNA) efficiently in vivo , and the LGP2 regulates this process in vivo ( Zhang et al, 2021 ). Thus it maintains antiviral immune homeostasis through various immune-regulatory methods.…”

Mammalian antiviral systems directed by small RNA

“…Some IFN-stimulated genes (ISGs) encoded in mammalian genomes might function as endogenous RNAi suppressors, as IFN treatment represses small RNA processing by Dicer in noninfected cells [ 48 , 49 ]. At least one ISG, LGP2, has been shown to repress Dicer activity [ 49 – 51 ]. IFN stimulates hundreds of ISGs, and additional ISGs may also be involved in the suppression of RNAi.…”