Related Experiment Video
Updated: May 15, 2026
10:34
Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
Published on: December 9, 2022
Altering SARS coronavirus frameshift efficiency affects genomic and subgenomic RNA production
Ewan P Plant1, Amy C Sims, Ralph S Baric
1Laboratory of Emerging Pathogens, Division of Transfusion-Transmitted Diseases, Food and Drug Administration, Bethesda, Maryland 20892, USA. Ewan.Plant@fda.hhs.gov
Viruses
|January 22, 2013
Summary
Synonymous codon changes in coronaviruses alter RNA production by affecting programmed ribosomal frameshifting efficiency. This suggests RNA sequence, not protein sequence, critically impacts viral replication and optimal virus yield.
Area of Science:
- Virology
- Molecular Biology
- Genetics
Background:
- Coronaviruses exhibit variations in genomic and subgenomic RNA production linked to mutations in the programmed ribosomal frameshift signal.
- Previous studies could not definitively attribute these variations to genomic sequence, protein sequence, or frameshifting frequency.
Purpose of the Study:
- To investigate the impact of synonymous codon changes on coronavirus RNA production.
- To determine whether protein sequence or RNA sequence/frameshifting efficiency is the primary driver of altered RNA ratios.
Main Methods:
- Engineered coronaviruses with synonymous codon changes within the programmed ribosomal frameshift signal.
- Quantified genomic and subgenomic RNA ratios.
- Assessed frameshifting efficiency and viral titers (TCID50).
Main Results:
- Synonymous codon changes led to altered genomic and subgenomic RNA ratios.
- These changes were attributed to modifications in the frameshift signal structure and efficiency, not the resulting protein sequence.
- Minor variations in frameshifting efficiency caused significant changes in genomic RNA production and viral titer (TCID50).
Conclusions:
- The RNA sequence, specifically through its influence on frameshifting efficiency, is the primary determinant of altered genomic and subgenomic RNA production in coronaviruses.
- A minimum frameshifting frequency threshold is crucial for optimal virus production.
- Either the RNA sequence itself or the resulting viral protein ratios from varying frameshifting levels influence viral replication.
Related Concept Videos
02:28Leaky Scanning
During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA. Marilyn Kozak discovered that the sequence RCCAUGG (where R stands for...
01:30Point and Frameshift Mutations
Point mutations are genetic alterations involving the change of a single nucleotide base pair in DNA. Depending on how the alteration affects protein synthesis, they can lead to various consequences.Point mutations fall into the following types:Silent mutations occur when a nucleotide change does not alter the amino acid sequence due to the redundancy of the genetic code. For instance, changing ACC to ACA still encodes threonine, leaving the protein function unaffected. This occurs because...
02:05Gene Evolution - Fast or Slow?
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
In contrast, regions which code...
02:23RNA Editing
RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
01:29Translational Regulation
Translational regulation in prokaryotes ensures efficient protein synthesis by controlling ribosome access to mRNA. This regulation is mediated by secondary RNA structures, including translational riboswitches, RNA thermometers, and small RNAs (sRNAs), which respond to intracellular and environmental signals to modulate gene expression.Translational RiboswitchesRiboswitches in the leader region of mRNAs can regulate translation by altering the accessibility of the Shine-Dalgarno (SD) sequence,...
00:36Viral Mutations
A mutation is a change in the sequence of bases of DNA or RNA in a genome. Some mutations occur during replication of the genome due to errors made by the polymerase enzymes that replicate DNA or RNA. Unlike DNA polymerase, RNA polymerase is prone to errors because it is not capable of “proofreading” its work. Viruses with RNA-based genomes, like HIV, therefore accrue mutations faster than viruses with DNA-based genomes. Because mutation and recombination provide the raw material for adaptive...