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Updated: Jul 30, 2026
Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency
Published on: June 16, 2011
The versatility of paramyxovirus RNA polymerase stuttering
S Hausmann1, D Garcin, C Delenda
1Department of Genetics and Microbiology, University of Geneva School of Medicine, CH1211 Geneva, Switzerland.
Abstract:
Paramyxoviruses cotranscriptionally edit their P gene mRNAs by expanding the number of Gs of a conserved AnGn run. Different viruses insert different distributions of guanylates, e.g., Sendai virus inserts a single G, whereas parainfluenza virus type 3 inserts one to six Gs. The sequences conserved at the editing site, as well as the experimental evidence, suggest that the insertions occur by a stuttering process, i.e., by pseudotemplated transcription. The number of times the polymerase "stutters" at the editing site before continuing strictly templated elongation is directed by a cis-acting sequence found upstream of the insertions. We have examined the stuttering process during natural virus infections by constructing recombinant Sendai viruses with mutations in their cis-acting sequences. We found that the template stutter site is precisely determined (C1052) and that a relatively short region (approximately 6 nucleotides) just upstream of the AnGn run can modulate the overall frequency of mRNA editing as well as the distribution of the nucleotide insertions. The positions more proximal to the 5' AnGn run are the most important in this respect. We also provide evidence that the stability of the mRNA/template hybrid plays a determining role in the overall frequency and range of mRNA editing. When the template U run is extended all the way to the stutter site, adenylates rather than guanylates are added at the editing site and their distribution begins to resemble the polyadenylation associated with mRNA 3' end formation by the viral polymerase. Our data suggest how paramyxovirus mRNA editing and polyadenylation are related mechanistically and how editing sites may have evolved from poly(A)-termination sites or vice versa.
Insights
Paramyxoviruses edit P gene mRNAs through a stuttering transcription process at a specific site. Upstream sequences and mRNA-template hybrid stability control the frequency and distribution of nucleotide insertions during viral RNA editing.
Area of Science:
- Molecular Virology
- RNA Biology
- Gene Expression
Background:
- Paramyxoviruses are known to edit their P gene mRNAs via cotranscriptional insertion of guanylates into a conserved AnGn run.
- The extent of guanylate insertion varies among different paramyxoviruses, suggesting regulatory mechanisms control this process.
- Previous studies proposed a pseudotemplated transcription (stuttering) mechanism for these insertions, directed by cis-acting sequences.
Purpose of the Study:
- To investigate the molecular mechanisms governing paramyxovirus mRNA editing during natural infections.
- To identify the specific cis-acting sequences and RNA structural elements that regulate the frequency and distribution of nucleotide insertions.
- To explore the relationship between mRNA editing and polyadenylation in paramyxoviruses.
Main Methods:
- Construction and analysis of recombinant Sendai viruses with mutations in cis-acting sequences upstream of the editing site.
- Precise mapping of the stutter site and identification of key nucleotides modulating editing frequency.
- Investigation of mRNA/template hybrid stability's role in editing outcomes.
Main Results:
- The stutter site for RNA editing was precisely determined to be at C1052.
- A short upstream region (approx. 6 nucleotides) significantly modulates mRNA editing frequency and insertion distribution, with proximal sites being most influential.
- Increased mRNA/template hybrid stability correlates with altered editing frequency and range; extending the template U run to the stutter site results in adenylate insertion, mimicking polyadenylation.
Conclusions:
- Paramyxovirus mRNA editing is a precisely regulated process influenced by specific cis-acting sequences and RNA-template hybrid stability.
- The findings reveal a mechanistic link between mRNA editing and polyadenylation, suggesting a common evolutionary origin.
- This study elucidates the intricate control of nucleotide insertion during viral RNA synthesis and its implications for viral gene expression.
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