Roles of host and viral microRNAs in human cytomegalovirus biology

Abstract

Human cytomegalovirus (HCMV) has a relatively large and complex genome, a protracted lytic replication cycle, and employs a strategy of replicational latency as part of its lifelong persistence in the infected host. An important form of gene regulation in plants and animals revolves around a type of small RNA known as microRNA (miRNA). miRNAs can serve as major regulators of key developmental pathways, as well as provide subtle forms of regulatory control. The human genome encodes over 900 miRNAs, and miRNAs are also encoded by some viruses, including HCMV, which encodes at least 14 miRNAs. Some of the HCMV miRNAs are known to target both viral and cellular genes, including important immunomodulators. In addition to expressing their own miRNAs, infections with some viruses, including HCMV, can result in changes in the expression of cellular miRNAs that benefit virus replication. In this review, we summarize the connections between miRNAs and HCMV biology. We describe the nature of miRNA genes, miRNA biogenesis and modes of action, methods for studying miRNAs, HCMV-encoded miRNAs, effects of HCMV infection on cellular miRNA expression, roles of miRNAs in HCMV biology, and possible HCMV-related diagnostic and therapeutic applications of miRNAs.

Fig. 1

miRNA biogenesis: nuclear events. The major features of miRNA biogenesis are similar, regardless of whether the miRNA is encoded on the host or virus genome. Pri-miRNAs that arise from intergenic or intronic transcripts can harbor single or multiple hairpins that are each excised by Drosha/DGCR8. Hairpins arising from miRtrons are excised in the spliceosome via splice signals located near the base of the stem-loop structure. After editing (indicated as red bases), hairpins are exported by exportin 5/RanGTP through nuclear pores to the cytoplasm for subsequent processing (Fig. 2). RNA segments corresponding to mature miRNAs are indicated in red and blue.

Fig. 2

miRNA biogenesis and activity: cytoplasmic events. RNA segments corresponding to mature miRNAs are indicated in red and blue. As indicated, the major path of miRNA activity involves imperfect miRNA/mRNA hybrids and results in translational suppression.

Fig. 3

Predicted interaction between a miRNA (miR-100) and one of its predicted targets (Raptor mRNA). Possible Watson-Crick basepairing is indicated by vertical bars and the perfectly basepaired seed sequence at miRNA positions 2 through 8 is italicized.

Fig. 4

Genomic locations and environments of HCMV-encoded miRNAs. HCMV genomic architecture and open reading frames representative of clinical strains are illustrated across the top of the diagram (Davison et al., 2003). Loci encoding miRNAs are indicated with small red boxes and by letters. Each of the lettered regions is expanded below (all at the same scale). In the expanded diagrams, locations of miRNA hairpins are indicated by pennants that consist of a staff that marks the location of the 5′ end of the stem-loop structure, a blue triangle representing the 5′ stem, a red line representing the loop, and a green triangle representing the 3′ stem. Other than the location of the staff, the pennants are not drawn to scale; at scale, the stem-loop structures would be shorter than the blue triangles. For miRNAs that do not span protein coding regions, only the sequence of the stem-loop region is shown (5′ stem in blue, loop in red, and 3′ stem in green; sequence segments at the 5′ and 3′ ends of the stem-loop sequences that may extend beyond the known miRNA sequences are not shown). For miRNAs that span protein coding regions, the protein coding sequence and the protein sequence are also shown. Stem-loop arms that are processed to mature miRNAs are indicated with the miRNA name. miR-UL31-1 (locus B) may be expressed as a miRtron, so the intron/exon boundaries are shown. All sequences are from HCMV strain AD169 (Accession number NC_001347), except for miR-148D-1, which is from the HCMV strain Merlin sequence (Accession number NC_006273).

Fig. 5

HCMV management of the PI3K/AKT/mTOR pathway. The schematic illustrates some of the major inputs and regulatory control points along the PI3K/AKT/mTOR pathway, including points where HCMV is known to exert influence (indicated in blue) (Alwine, 2008; Buchkovich et al., 2008). The two mTOR-containing complexes, mTORC1 and mTORC2 are indicated in red. As described in the text, levels of mTOR, Rictor, and Raptor may be regulated in part by miRNAs that are downregulated after HCMV infection (Wang et al., 2008). Dashed lines and objects indicate the loss of inhibitory subunits, which is required as part of activation of mTORC1 and eIF4E.