Murine cytomegalovirus encodes a miR-27 inhibitor disguised as a target

Abstract

Individual microRNAs (miRNAs) are rapidly down-regulated during conditions of cellular activation and infection, but factors mediating miRNA turnover are poorly understood. Infection of mouse cells with murine cytomegalovirus (MCMV) induces the rapid down-regulation of an antiviral cellular miRNA, miR-27. Here, we identify a transcript produced by MCMV that binds to miR-27 and mediates its degradation. UV-crosslinking and high-throughput sequencing [CRAC (UV-crosslinking and analysis of cDNA)] identified MCMV RNA segments associated with the miRNA-binding protein Argonaute 2 (Ago2). A cluster of hits mapped to a predicted miR-27-binding site in the 3′UTR of the previously uncharacterized ORF, m169. The expression kinetics of the m169 transcript correlated with degradation of miR-27 during infection, and m169 expression inhibited miR-27 functional activity in a reporter assay. siRNA knockdown of m169 demonstrated its requirement for miR-27 degradation following infection and did not affect other host miRNAs. Substitution of the miR-27-binding site in m169 to create complementarity to a different cellular miRNA, miR-24, resulted in down-regulation of only miR-24 following infection. The m169 transcript is cytoplasmic, capped, polyadenylated, and interacts with miRNA-27 through seed pairing: characteristic features of the normal messenger RNA (mRNA) targets of miRNAs. This virus-host interaction reveals a mode of miRNA regulation in which a mRNA directs the degradation of a miRNA. We speculate that RNA-mediated miRNA degradation could be a more general viral strategy for manipulating host cells.V iruses devote a large portion of their genomes to strategies for manipulating host cells and evading antiviral defense mechanisms. Numerous host miRNA-binding sites have been predicted in different viral genomes, but the validity and functional relevance of most predictions remain unclear. The best studied miRNA-virus interactions demonstrate that RNA viruses can use cellular miRNAs to regulate their life cycles; for example, the interaction between hepatitis C virus and miR-122 enhances viral replication (1), whereas the interaction between HIV-1 and miR-29 mediates its localization to P bodies (2). Direct interactions between host miRNAs and viral genes can also suppress viral gene expression and replication (3-6) (reviewed in Ref. 7). However, the factors driving the evolution of these interactions remain somewhat controversial, because they may relate to viral mechanisms for persistence and latency rather than host defense (8, 9). At the same time, the expression levels of specific miRNAs can indirectly influence infections; miRNAs are key components of the innate immune response (10, 11) and exert antiviral properties by modulating host cofactors and pathways required by viruses (12-15). We previously showed that miR-27 limits the replication capacity of murine cytomegalovirus (MCMV) but is rapidly degraded during the lytic infection (16). Actinomycin D treatment upon infection prevents miR-27 down-regulation, suggest...

The mammalian microRNA response to bacterial infections

“…similar to what has been described for Herpesvirus and cytomegalovirus. [27][28][29] However, it should be noted that the ability of bacterial pathogens to actively deliver RNAs into host cells has not been demonstrated yet.…”

“…25 and 26), although a mechanism by which viral RNAs mediate the direct degradation of host miRNAs has been recently unveiled. [27][28][29] Several studies have explored the impact of apicomplexan parasites, many of which cause serious diseases in humans, on host microRNA expression during infection. Interestingly, modulation of host microRNA profiles was observed upon infection with several parasites, including Cryptosporidium parvum, 30,31 Plasmodium chabaudii, 32 Toxoplasma gondii 33 and Eimeria papillata.…”

CLIP: viewing the RNA world from an RNA-protein interactome perspective

“…This exciting discovery revealed "an important RNA that had flown under the radar" [129]. Another exemplary study was conducted by Libri et al [130] using CRAC. They demonstrated that an OFR of murine cytomegalovirus (MCMV), m169, acted as a miRNA sponge and mediated the degradation of miR-27 in host cells.…”

RNA-mediated degradation of microRNAs: A widespread viral strategy?

“…Furthermore comparison of these RNAs reveals little in common: HSUR-1 is a small nuclear RNA (snRNA) of 143 nt whereas m169 is a »1.7 kb spliced mRNA transcript that localizes predominantly to the cytoplasm. 19 Tailing and trimming of miRNAs: inside or outside of RISC?…”

“…We and others subsequently identified an MCMV transcript that directly associates with mature miR-27 and mediates its degradation. 19,20 The miR-27 binding site is within the 3 0 UTR of the m169 gene and mutation of this binding site results in virus attenuation following in vivo infection. 20 Also in 2010, a distantly related herpesvirus from squirrel monkeys, Herpesvirus saimiri (HVS), was shown to produce a small non-coding RNA, termed HSUR-1, which binds to the same cellular miRNA, and also mediates its degradation; 21 this is thought to be involved in activation and potentially transformation of T-cells.…”