Mini ways to stop a virus: microRNAs and HIV-1 replication

Abstract

Cellular restriction of HIV-1 replication has traditionally been thought of as protein mediated: APOBEC3G hypermutates HIV-1 genomic RNA, but is counteracted by Vif; Tetherin inhibits the release of budding virions but is counteracted by Vpu. In recent years, new evidence suggesting that miRNAs and other components of the miRNA pathway act as HIV-1 restriction factors has come to light, along with the identification of strategies that HIV-1 employs to surmount these host obstacles. In this article, we summarize and discuss the literature to date regarding the complex relationship between HIV-1 and miRNA-mediated inhibition.

Figure 1. Mechanisms of cellular miRNA-mediated inhibition of HIV-1 replication

Transcription of miRNA coding regions generates primary miRNAs (pri-miRNAs), which form stem–loop structures due to imperfect complementarity. Pre-miRNA is generated when the Drosha-DGCR8 complex cleaves at the hairpin stem of the pri-miRNA. The pre-miRNA is exported to the cytoplasm and cleaved near the terminal loop by Dicer, in complex with TRBP and one of the Argonaute proteins. The miRNA:miRNA* duplex is then loaded onto Ago, where it is unwound, followed by preferential incorporation of the guide strand and release and degradation of the miRNA* strand. The miRISC also includes, among many other proteins, Dicer and the GW182 proteins, which are necessary for gene repression. Recognition of target mRNA is mediated by sequence complementarity, which is typically imperfect, with the miRNA; binding sites are typically found in the 3′UTR. miR-198 and miR-17/92 target Cyclin T1 mRNA and PCAF mRNA, respectively, for translational inhibition, which results in decreased viral transcription, as both Cyclin T1 and PCAF are co-factors of the viral transactivation protein Tat. Nascent viral transcripts form a stem–loop structure (TAR RNA) that is bound by Tat, which then recruits Cyclin T1 and Cdk9 (the P-TEFb complex). These are necessary for the processivity of Pol II during transcriptional elongation, while PCAF is a histone acetyltransferase that acetylates Tat, increasing its transactivation activity. Cellular miRNAs, such as miR-28, miR-29a-c, miR-125b, miR-150, miR-223 and miR-382 can also target HIV-1 RNA directly, via sites mostly located in the 3′UTR, which leads to decreased viral gene expression. Furthermore, miR-29a has been shown to enhance viral RNA association with P-bodies, cytoplasmic foci with high concentrations of proteins involved in translational repression and mRNA decapping, deadenylation and degradation. Sequestration of transcripts targeted by miRNAs in P-bodies presumably results in translational repression or mRNA degradation, as disruption of P-bodies increases viral production. RISC proteins Ago and GW182 also localize to P-bodies, where they associate with the Dcp1–Dcp2 mRNA decapping complex, the Ccr4–Not1 deadenylation complex, Rck, a decapping activator, APOBEC3G and 3F (A3G, A3F), the HIV-1 restriction factors and MOV10, a putative RNA helicase that is also incorporated into HIV-1 virions and inhibits infectivity. Ago2: Argonaute-2; DGCR8: DiGeorge syndrome critical region gene 8; pri-miRNAs: Primary miRNA; pre-miRNA: Precursor miRNA; TRBP: TAR RNA-binding protein; RISC: RNA-induced silencing complex.