Synthesis of subgenomic RNAs by positive-strand RNA viruses.

  title={Synthesis of subgenomic RNAs by positive-strand RNA viruses.},
  author={W. Allen Miller and Gennadiy Koev},
  volume={273 1},
f b w t ( t g s p t n p Many RNA viruses encode more than one gene on a single genomic RNA. Yet only the first gene, or open reading frame (ORF), on a normal eukaryotic mRNA is translated. Thus, downstream genes on viral genomes are expressed either via novel translational events or, more commonly, by deployment of subgenomic mRNAs (sgRNAs). Subgenomic RNAs of positive-strand viruses have the same 39 ends as genomic RNA, but have deleions at the 59 ends to bring the 59 end of the RNA in… 

Figures from this paper

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

It is shown that tombusvirus genome replication can be effectively uncoupled from sg mRNA transcription in vivo by C‐terminal modifications in its RNA‐dependent RNA polymerase (RdRp), and the results suggest a simple evolutionary scheme by which the virus could gain or enhance its transcriptional activity.

Continuous and Discontinuous RNA Synthesis in Coronaviruses.

Coronaviruses encode proofreading machinery, unique in the RNA virus world, to ensure the maintenance of their large genome size.

Higher-Order RNA Structural Requirements and Small-Molecule Induction of Tombusvirus Subgenomic mRNA Transcription

These findings provide important new insights into the premature termination mechanism and present a novel approach to regulate the transcriptional process, defining the minimum overall thermodynamic stability required for an operational higher-order RNA attenuation structure.

Synthesis in Vitro of Rabbit Hemorrhagic Disease Virus Subgenomic RNA by Internal Initiation on (–)Sense Genomic RNA

This study reports the first description of a subgenomic promoter in a member of the Caliciviridae, and investigates in vitro the sgRNA synthesis mechanism using recombinant R HDV RNA-dependent RNA polymerase produced in baculovirus-infected insect cells and synthetic RHDV (–)RNAs of different lengths containing regions located upstream of the subgenomics start site.

Characterization of barley yellow dwarf virus subgenomic RNAs

It is found that a small stem-loop containing the conserved hexanucleotide sequence GUGAAG at its 5’ end supports basal levels of sgRNA2 synthesis, and that both the primary and secondary structures are required for synthesis of subgenomic RNA2.

Arterivirus Nsp1 Modulates the Accumulation of Minus-Strand Templates to Control the Relative Abundance of Viral mRNAs

This first report on protein-mediated, mRNA-specific control of nidovirus RNA synthesis reveals the existence of an integral control mechanism to fine-tune replication, sg mRNA synthesis, and virus production, and establishes a major role for nsp1 in coordinating the arterivirus replicative cycle.

A complex network of RNA–RNA interactions controls subgenomic mRNA transcription in a tombusvirus

The results establish specific roles for the different RNA components of a multipartite RNA‐based control system, support a premature termination mechanism for tombusvirus sg mRNA transcription and reveal a close mechanistic relationship between sg RNA transcription, viral RNA replication and RNA recombination.

trans Regulation of Cap-Independent Translation by a Viral Subgenomic RNA

It is concluded that sgRNA2 is a riboregulator that switches off translation of replication genes from gRNA while permitting translation of structural genes from sg RNA1, a new role for a viral subgenomic RNA, and a new mechanism for RNA-mediated regulation of translation.



Synthesis of brome mosaic virus subgenomic RNA in vitro by internal initiation on (−)-sense genomic RNA

Evidence is provided that subgenomic RNA arises by internal initiation on the (−)-strand of genomic RNA, and it is believed that this also represents the first in vitro demonstration of a replicase from a eukaryotic (+)-stranded RNA virus capable of initiating synthesis of (+)-sense RNA.

Subgenomic mRNA regulation by a distal RNA element in a (+)-strand RNA virus.

It is proposed that the upstream sequence represents a cis-acting RNA element which facilitates sg mRNA accumulation by promoting efficient synthesis of sg RNA2 via a long-distance RNA-RNA interaction.

A Positive-Strand RNA Virus with Three Very Different Subgenomic RNA Promoters

It is shown that neither sgRNA2 nor sg RNA3 is required for BYDV RNA replication, which implies a complex system for promoter recognition and regulation of subgenomic RNA synthesis.

RNA-mediated trans-activation of transcription from a viral RNA.

A model is proposed in which direct binding of RNA-2 to RNA-1 trans-activates sgRNA synthesis, which is unusual among RNA viruses, which typically rely on protein regulators.

Coronavirus transcription: subgenomic mouse hepatitis virus replicative intermediates function in RNA synthesis

Findings in 17CL1 mouse cells that had been infected with the A59 strain of mouse hepatitis virus strongly suggest that coronaviruses utilize a novel replication strategy that employs the synthesis of subgenome negative strands to produce subgenomic mRNAs.

Characterization and engineering of sequences controlling in vivo synthesis of brome mosaic virus subgenomic RNA

Subgenomic RNA production at normal levels required sequences extending to at least -74 but not beyond -95, and loss of an (rA)18 tract immediately upstream of the -20 to +16 "core promoter" particularly inhibited subgenomicRNA synthesis.

Sequence-specific recognition of a subgenomic RNA promoter by a viral RNA polymerase.

It is shown that the RdRp of the plant-infected BMV is capable of accurately, albeit inefficiently, initiating RNA synthesis from the subgenomic promoter of the animal-infecting Semliki Forest virus.

In vivo DNA expression of functional brome mosaic virus RNA replicons in Saccharomyces cerevisiae

DNA plasmids from which BMV RNA3 and RNA3 derivatives can be transcribed in vivo from the galactose-inducible yeast GAL1 promoter are constructed and terminated by a self-cleaving ribozyme at or near their natural 3' ends.

Subgenomic RNAs mediate expression of cistrons located internally on the genomic RNA of tobacco necrosis virus strain A

It is shown that the region upstream of the coat protein promotes internal initiation of translation in vitro, however, this region is functionally inactive in vivo, suggesting that TNV-A genomic RNA is not important for coat protein synthesis in plants.