SARS-CoV-2-encoded small RNAs are able to repress the host expression of SERINC5 to facilitate viral replication

Abstract

Serine incorporator protein 5 (SERINC5) is a key innate immunity factor that operates in the cell to restrict the infectivity of certain viruses. Different viruses have developed strategies to antagonize SERINC5 function but, how SERINC5 is controlled during viral infection is poorly understood. Here, we report that SERINC5 levels are reduced in COVID-19 patients during the infection by SARS-CoV-2 and, since no viral protein capable of repressing the expression of SERINC5 has been identified, we hypothesized that SARS-CoV-2 non-coding small viral RNAs (svRNAs) could be responsible for this repression. Two newly identified svRNAs with predicted binding sites in the 3′-untranslated region (3’-UTR) of the SERINC5 gene were characterized and we found that the expression of both svRNAs during the infection was not dependent on the miRNA pathway proteins Dicer and Argonaute-2. By using svRNAs mimic oligonucleotides, we demonstrated that both viral svRNAs can bind the 3’UTR of SERINC5 mRNA, reducing SERINC5 expression in vitro. Moreover, we found that an anti-svRNA treatment to Vero E6 cells before SARS-CoV-2 infection recovered the levels of SERINC5 and reduced the levels of N and S viral proteins. Finally, we showed that SERINC5 positively controls the levels of Mitochondrial Antiviral Signalling (MAVS) protein in Vero E6. These results highlight the therapeutic potential of targeting svRNAs based on their action on key proteins of the innate immune response during SARS-CoV-2 viral infection.

The Antiviral Factor SERINC5 Impairs the Expression of Non-Self-DNA

“…First, the virus uses ORF7a to prevent SERINC5 incorporation into nascent particles [ 19 ]. Second, SARS-CoV-2 generates small viral RNAs (svRNAs)—which work in an analogous manner to miRNAs—to decrease SERINC5 expression [ 46 ]. Hence, the lack of impact of SERINC5 on SARS-CoV-2 RNA and proteins may be due to these countermeasures.…”

“…In our study, we did not see such effect on SARS-CoV-2. Even when SARS-CoV-2 is equipped to counteract SERINC5 [ 19 , 46 ], we would expect a defect in replication since SERINC5 was already present in our cells prior to the infection and the subsequent synthesis of ORF7a and svRNAs—the SERINC5 antagonists in SARS-CoV-2. Thus, there must be a more specific mechanism causing the silencing of non-self-DNA, although MDA5 signaling might have an additive effect.…”

The emerging roles of MARCH8 in viral infections: A double-edged Sword

“…Notably, a recent work indicated the host SERINC5 targeted SARS-CoV-2 S glycoprotein and inhibited viral replication. In this case, SARS-CoV-2 employed its ORF-7 [ 70 ] and encoded small RNAs [ 71 ] to counteract SERINC5-imposed restriction, similar to HIV-1 Nef and MLV glycoGag [ 40 , 72 , 73 ], which should provide some hints to dissect the possible SARS-CoV-2-MARCH8 combating mechanism. MDMs are believed to be the initial targets of EBOV early-stage infection.…”

SARS-CoV-2 and innate immunity: the good, the bad, and the “goldilocks”

“…In addition to IFITMs that exert their antiviral function at membranous structures, SERINC5 is a cellular multipass transmembrane protein that is involved in lipid transport and biosynthesis and is most well known for its inhibition of human immunodeficiency virus (HIV) infection and for being a target of the HIV antagonist protein Nef [ 86 – 89 ]. SERINC5 is incorporated into budding virions and prevents viral entry by blocking virus‒cell fusion; SARS-CoV-2 ORF7a has been demonstrated to block the incorporation of SERINC5 in budding SARS-CoV-2 virions, thus antagonizing the antiviral action of SERINC5 [ 86 , 87 ].…”