miR-122 does not impact recognition of the HCV genome by innate sensors of RNA but rather protects the 5′ end from the cellular pyrophosphatases, DOM3Z and DUSP11

Abstract

Hepatitis C virus (HCV) recruits two molecules of the liver-specific microRNA-122 (miR-122) to the 5′ end of its genome. This interaction promotes viral RNA accumulation, but the precise mechanism(s) remain incompletely understood. Previous studies suggest that miR-122 is able to protect the HCV genome from 5′ exonucleases (Xrn1/2), but this protection is not sufficient to account for the effect of miR-122 on HCV RNA accumulation. Thus, we investigated whether miR-122 was also able to protect the viral genome from innate sensors of RNA or cellular pyrophosphatases. We found that miR-122 does not play a protective role against recognition by PKR, RIG-I-like receptors, or IFITs 1 and 5. However, we found that knockdown of both the cellular pyrophosphatases, DOM3Z and DUSP11, was able to rescue viral RNA accumulation of subgenomic replicons in the absence of miR-122. Nevertheless, pyrophosphatase knockdown increased but did not restore viral RNA accumulation of full-length HCV RNA in miR-122 knockout cells, suggesting that miR-122 likely plays an additional role(s) in the HCV life cycle, beyond 5′ end protection. Overall, our results support a model in which miR-122 stabilizes the HCV genome by shielding its 5′ terminus from cellular pyrophosphatase activity and subsequent turnover by exonucleases (Xrn1/2).

Location specific small RNA annealing to the HCV 5’ UTR promotes Hepatitis C Virus replication by favoring IRES formation and stimulating virus translation

“…For example: si19(21–37) is 19 nucleotides long with 17 nucleotides (21-matching the HCV 5’ UTR (Figure 6A). Similarly, si19(23–37), si19(25–37), si19(27–37), si19(27–37), si19(29–37) and si19(31–37) have between 15 and 7 matching nucleotides. si19(21–37), si19(23–37) promoted HCV replication as efficiently as si19-37 and the others did not promote at all (Figure 6B).…”

“…Similarly, si19(23–37), si19(25–37), si19(27–37), si19(27–37), si19(29–37) and si19(31–37) have between 15 and 7 matching nucleotides. si19(21–37), si19(23–37) promoted HCV replication as efficiently as si19-37 and the others did not promote at all (Figure 6B). From the 3’ end we generated siRNAs with sequence matches of 16, si19(19–35), 14, si19(19–33), and 12, si19(19–31) matches (Figure 6A) and only si19(19–35) promoted HCV replication (Figure 6C).…”

“…HCV replication is undetectable in the absence of miR-122 and the mechanism behind miR-122’s stimulatory effect is not fully understood. miR-122 stabilizes the viral RNA by protecting it from degradation by host exonuclease Xrn1, and phosphatases Dom3Z and DUSP11 (21–23). However, simultaneous knock-down of these three enzymes cannot completely rescue HCV replication in the absence of miR-122, suggesting that other roles exist (23).…”

“…miR-122 stabilizes the viral RNA by protecting it from degradation by host exonuclease Xrn1, and phosphatases Dom3Z and DUSP11 (21–23). However, simultaneous knock-down of these three enzymes cannot completely rescue HCV replication in the absence of miR-122, suggesting that other roles exist (23). miR-122 also promotes HCV translation and recent reports hypothesize that miR-122 modifies the HCV genome to induce the canonical 5’UTR IRES structure (Figure 1B and C) (12, 13, 24).…”

Hepatitis C Virus Regulates its Replication by Maturing miR-122 Through Akt-Dependent Phosphorylation of KSRP

“…The 5'-UTR contains the internal ribosome entry site (IRES) that mediates cap-independent translation of viral proteins (Friebe, Lohmann, Krieger, & Bartenschlager, 2001;Honda, Beard, Ping, & Lemon, 1999). miR-122 binding to the 5'-UTR triggers AGO2 recruitment, thereby protecting the HCV RNA molecules from 5'-RNA decay (Amador-Canizares, Bernier, Wilson, & Sagan, 2018;Sedano & Sarnow, 2014;Shimakami et al, 2012). Finally, the Poly(RC)-binding protein 2 (PCBP2) is displaced from the viral RNA by miR-122, resulting in increased replication and decreased translation .…”