Investigation of Novel RNA Elements in the 3'UTR of Tobacco Necrosis Virus-D.

RNA elements in the untranslated regions of plus-strand RNA viruses can control a variety of viral processes including translation, replication, packaging, and subgenomic mRNA production. The 3' untranslated region (3'UTR) of Tobacco necrosis virus strain D (TNV-D; genus , family ) contains several well studied regulatory RNA elements. Here, we explore a previously unexamined region of the viral 3'UTR, the sequence located upstream of the 3'-cap independent translation enhancer (3'CITE).

Biologically-supported structural model for a viral satellite RNA.

Satellite RNAs (satRNAs) are a class of small parasitic RNA replicon that associate with different viruses, including plus-strand RNA viruses. Because satRNAs do not encode a polymerase or capsid subunit, they rely on a companion virus to provide these proteins for their RNA replication and packaging. SatRNAs recruit these and other required factors via their RNA sequences and structures.

Global organization of a positive-strand RNA virus genome.

The genomes of plus-strand RNA viruses contain many regulatory sequences and structures that direct different viral processes. The traditional view of these RNA elements are as local structures present in non-coding regions. However, this view is changing due to the discovery of regulatory elements in coding regions and functional long-range intra-genomic base pairing interactions.

Multifaceted regulation of translational readthrough by RNA replication elements in a tombusvirus.

Translational readthrough of stop codons by ribosomes is a recoding event used by a variety of viruses, including plus-strand RNA tombusviruses. Translation of the viral RNA-dependent RNA polymerase (RdRp) in tombusviruses is mediated using this strategy and we have investigated this process using a variety of in vitro and in vivo approaches. Our results indicate that readthrough generating the RdRp requires a novel long-range RNA-RNA interaction, spanning a distance of ∼3.

Subgenomic mRNA transcription in tobacco necrosis virus.

Tobacco necrosis virus-D (TNV-D), a positive-strand RNA Necrovirus in the family Tombusviridae, transcribes two subgenomic (sg) mRNAs during infections. We have investigated the strategy used by TNV-D in this process and uncovered evidence that it employs a premature termination (PT) mechanism for the transcription of its sg mRNAs. Structural and mutational analysis of the TNV-D genome identified local RNA structures upstream from transcriptional initiation sites that functioned in the plus-strand as attenuation structures and mediated the production of sg mRNA-sized minus-strands.

Tombusvirus recruitment of host translational machinery via the 3' UTR.

RNA viruses recruit the host translational machinery by different mechanisms that depend partly on the structure of their genomes. In this regard, the plus-strand RNA genomes of several different pathogenic plant viruses do not contain traditional translation-stimulating elements, i.e.

Evidence for a premature termination mechanism of subgenomic mRNA transcription in a carmovirus.

The transcriptional mechanism utilized by turnip crinkle carmovirus to synthesize subgenomic (sg) mRNAs was investigated by analyzing viral RNAs and their associated regulatory RNA elements. In vivo analyses revealed the following: (i) that minus-strand sg RNAs are detectable in infections, (ii) that minus-strand sg RNA accumulation can be partially uncoupled from that of their plus-strand sg mRNA counterparts, and (iii) that an RNA secondary structure located upstream of the sg mRNA start site mediates transcription by functioning in the plus strand of the viral genome. Collectively, these observations are consistent with this carmovirus using a premature termination mechanism for sg mRNA transcription.

A discontinuous RNA platform mediates RNA virus replication: building an integrated model for RNA-based regulation of viral processes.

Plus-strand RNA viruses contain RNA elements within their genomes that mediate a variety of fundamental viral processes. The traditional view of these elements is that of local RNA structures. This perspective, however, is changing due to increasing discoveries of functional viral RNA elements that are formed by long-range RNA-RNA interactions, often spanning thousands of nucleotides.

Uncoupling RNA virus replication from transcription via the polymerase: functional and evolutionary insights.

Many eukaryotic positive-strand RNA viruses transcribe subgenomic (sg) mRNAs that are virus-derived messages that template the translation of a subset of viral proteins. Currently, the premature termination (PT) mechanism of sg mRNA transcription, a process thought to operate in a variety of viruses, is best understood in tombusviruses. The viral RNA elements involved in regulating this mechanism have been well characterized in several systems; however, no corresponding protein factors have been identified yet.

A second functional RNA domain in the 5' UTR of the Tomato bushy stunt virus genome: intra- and interdomain interactions mediate viral RNA replication.

The 5' untranslated regions (UTRs) of (+)-strand RNA viruses play a variety of roles in the reproductive cycles of these infectious agents. Tomato bushy stunt virus (TBSV) belongs to this class of RNA virus and is the prototype member of the genus Tombusvirus. Previous studies have demonstrated that a T-shaped domain (TSD) forms in the 5' half of the TBSV 5' UTR and that it plays a central role in viral RNA replication.