A Viral Noncoding RNA Generated bycis-Element-Mediated Protection against 5′→3′ RNA Decay Represses both Cap-Independent and Cap-Dependent Translation

Abstract

Positive-strand RNA viruses use diverse mechanisms to regulate viral and host gene expression for ensuring their efficient proliferation or persistence in the host. We found that a small viral noncoding RNA (0.4 kb), named SR1f, accumulated in Red clover necrotic mosaic virus (RCNMV)-infected plants and protoplasts and was packaged into virions. The genome of RCNMV consists of two positive-strand RNAs, RNA1 and RNA2. SR1f was generated from the 3 untranslated region (UTR) of RNA1, which contains RNA elements essential for both cap-independent translation and negative-strand RNA synthesis. A 58-nucleotide sequence in the 3 UTR of RNA1 (Seq1f58) was necessary and sufficient for the generation of SR1f. SR1f was neither a subgenomic RNA nor a defective RNA replicon but a stable degradation product generated by Seq1f58-mediated protection against 533 decay. SR1f efficiently suppressed both cap-independent and cap-dependent translation both in vitro and in vivo. SR1f trans inhibited negative-strand RNA synthesis of RCNMV genomic RNAs via repression of replicase protein production but not via competition of replicase proteins in vitro. RCNMV seems to use cellular enzymes to generate SR1f that might play a regulatory role in RCNMV infection. Our results also suggest that Seq1f58 is an RNA element that protects the 3-side RNA sequences against 533 decay in plant cells as reported for the poly(G) tract and stable stem-loop structure in Saccharomyces cerevisiae. Many lines of recent evidence indicate that noncodingRNAs including microRNAs and small interfering RNAs play an important role in the control of gene expression in diverse cellular processes and in defense responses against molecular parasites such as viruses and transposons. Viruses also use many different types of RNAs in trans for regulating the expression of their own genomes or host genomes temporally and spatially to ensure efficient virus proliferation and/or latency in host cells. These RNAs include subgenomic RNAs (sgRNAs), viral genomic RNA itself, and many types of noncoding viral RNAs.For example, the adenovirus virus-associated RNAs (VA RNAs) (23) are small noncoding RNA transcripts. They inhibit the activation of RNA-induced protein kinase and thereby interfere with the activation of the interferon-induced cellular antiviral defense systems (38). VA RNAs also interfere with RNA interference pathways by acting as substrates for Dicer and suppressing the activity of Dicer probably involved in cellular antiviral mechanisms (2, 55). Epstein-Barr virus-encoded RNAs (EBERs) (56) inhibit RNA-induced protein kinase as VA RNAs (38). They also are known to encode microRNAs, which are thought to work for persistent infection (28). On the other hand, recently, EBERs have been reported to be recognized by RIG-I, a cytosolic protein with a DexD/H box RNA helicase domain that recognizes viral RNA in mammalian cells, and to activate signaling to induce type I interferon (35). Thus, associations of viral small RNAs with virus infection are complicated.sgRNAs also fun...

Computational analysis of functional long noncoding RNAs reveals lack of peptide-coding capacity and parallels with 3′ UTRs

“…Furthermore, these studies have revealed the presence of remarkable similarities between the lncRNAs and 39 UTRs of protein-coding RNAs. Interestingly, recent global transcriptome analyses suggest that many 39 UTRs give rise to independent lncRNA transcripts, and there is at least one example of a viral lncRNA that is generated from a 39 UTR after the rest of the original proteincoding message has been degraded (Iwakawa et al 2008;Mercer et al 2011). These findings, together with the results discussed above, suggest that the different classes of cellular RNA regulatory sequences share features that may contribute to their RNA-mediated mode of regulation.…”

Poly(A)-Binding Protein Facilitates Translation of an Uncapped/Nonpolyadenylated Viral RNA by Binding to the 3′ Untranslated Region

“…EtBr-stained 18S/26S rRNAs were used as loading controls for Northern blotting. SR1f is a stable degradation product derived from the 3= UTR of RNA1 (28). gation in order to assess the formation of the 80S and 48S initiation complexes.…”

A noncoding RNA produced by arthropod-borne flaviviruses inhibits the cellular exoribonuclease XRN1 and alters host mRNA stability

“…These include the large stem-loop structures present in the ambisense RNA segments of arenaviruses (Pinschewer et al 2005) and pseudoknot/double hairpin structures of coronaviruses (Stammler et al 2011). Several positive-sense plant viruses also generate some apparent subgenomic stable decay products that may arise by a mechanism similar to the flavivirus sfRNA (Iwakawa et al 2008;Peltier et al 2012). We are currently assessing if these viruses may interact with XRN1 through mechanisms related to those we describe here for Dengue and West Nile viruses.…”