Viral noncoding RNAs: more surprises

Abstract

Eukaryotic cells produce several classes of long and small noncoding RNA (ncRNA). Many DNA and RNA viruses synthesize their own ncRNAs. Like their host counterparts, viral ncRNAs associate with proteins that are essential for their stability, function, or both. Diverse biological roles--including the regulation of viral replication, viral persistence, host immune evasion, and cellular transformation--have been ascribed to viral ncRNAs. In this review, we focus on the multitude of functions played by ncRNAs produced by animal viruses. We also discuss their biogenesis and mechanisms of action.

Keywords: gene regulation; lncRNA; miRNA; ribonucleoprotein; sisRNA; virus.

Figure 1.

(A) VA RNA_I and RNA_II. The PKR-binding site on VA RNA_I is indicated. (B) Epstein-Barr virus (EBV)-encoded RNA 1 (EBER1) and EBER2. Both RNAs are highly conserved among related viruses (conserved nucleotides are shown in red). Known interaction sites of binding proteins are indicated. L22 binds three stem–loops of EBER1, while La binds the polyU tract at the 3′ end of both EBERs. The exact binding sites of AU-rich element-binding factor 1 (AUF1) and nucleolin have not been determined. Paired box protein 5 (PAX5) likely binds EBER2 indirectly. The EBER2 nucleotides highlighted in blue engage in RNA–RNA interactions with the terminal repeat (TR) transcript. (C) Recruitment mechanism of the EBER2–PAX5 complex to the TR regions of the EBV genome (Lee et al. 2015). EBER2 and PAX5 interact indirectly through an unknown bridging factor (denoted as X). Base-pairing of EBER2 with nascent TR transcripts acts to recruit and/or stabilize PAX5 binding to TR DNA. The variable number of TRs (≤20) in the EBV genome is indicated by TR_n.

Figure 2.

Nucleotide sequences and predicted secondary structures of HSURs 1–7 and hvs-pre-miR-HSURs 2, 4, and 5. Predicted base-pairing interactions between HSURs 1, 2, or 5 and host miR-142-3p and miR-16 as well as the experimentally determined interaction between HSUR 1 and miR-27 are shown with the miRNA seed sequences colored red. Arrowheads indicate the 3′ ends of the mature HSURs in the HSUR–pre-miRNA chimeras. Mature HVS miRNAs are shaded gray. The Sm-binding site and 3′ box sequences are boxed.

Figure 3.

Viral miRNA biogenesis pathways. (A) The canonical pathway. pri-miRNAs are typically transcribed by RNA Pol II, 5′-capped, and 3′-polyadenylated. The Microprocessor complex (Drosha and DGCR8) cleaves pri-miRNAs to release pre-miRNA hairpins, which are exported by Exportin-5 and processed by Dicer into mature miRNA duplexes in the cytoplasm. One miRNA strand is preferentially selected by AGO to form RISCs. (B) Drosha-independent miRNA biogenesis in animal viruses. MHV68 pri-miRNAs are tRNA–pre-miRNA chimeras that are processed by RNaseZ at the 5′ end of the first pre-miRNA hairpin. The enzyme that separates the two pre-miRNAs is unknown. HVS pri-miRNAs are snRNA–pre-miRNA chimeras that are processed by Integrator to release the pre-miRNA. The 3′ end formation mechanism for HVS pre-miRNAs remains elusive. Bovine leukemia virus (BLV) and some SFV miRNAs are derived from pre-miRNAs that are directly transcribed by RNA Pol III as endogenous shRNAs. All viral pre-miRNAs pictured are exported by XPO5 and processed by Dicer.

Figure 4.

(A) KSHV PAN RNA contains two key stabilization elements: the ORF57/MTA recognition element for ORF57/MTA binding at the 5′ end and a stabilization element known as the ENE near the 3′ end. (B) The ENE clamps the polyA tail of PAN RNA. (C) The X-ray structure revealed that the oligoA (purple) binds both sides of the U-rich internal loop within a stem–loop structure of the PAN RNA (green) to form an RNA triple helix (Protein Data Bank [PDB] 3P22) (Mitton-Fry et al. 2010). (D) Watson-Crick and Hoogsten H bonds stabilize the triple-helical structure and prevent access of deadenylases to the polyA tail of PAN RNA.

Figure 5.

Cartoon of the primary transcript encoding the EBNAs. The W repeat region (encoding EBNA-LP) is indicated with gray boxes representing the W1 and W2 coding exons. The short intron generating ebv-sisRNA-1 is in red, and the long intron is in black (with the large hairpin [HP] in orange). The boxed region zooms in on ∼1.5 W repeats and is annotated as above. Dotted black lines point to cartoon structures of the large 586-nt hairpin and the sequence/secondary structure of ebv-sisRNA-1.

Figure 6.

Schematic representation of the secondary structure of sfRNA from WNV. The elements shown were all experimentally verified in DENV and some in WNV (Chapman et al. 2014b). (SL) Stem–loop; (DB) dumbbell. Pseudoknot (pk) interactions are indicated by blue lines. Adapted from Macrae (2014), with permission from Elsevier. (Not to scale.)