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Viral Mutations00:36

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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...
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RNA viruses are categorized into positive-strand, negative-strand, or double-stranded groups based on their genomic structure and replication mechanisms. This classification dictates how they exploit host cellular machinery for protein synthesis and replication. Some RNA viruses also utilize reverse transcription as part of their life cycle, further diversifying their replication strategies.Positive-Strand RNA VirusesPositive-strand RNA viruses have genomes that function directly as messenger...
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siRNA - Small Interfering RNAs02:30

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Small interfering RNAs, or siRNAs, are short regulatory RNA molecules that can silence genes post-transcriptionally, as well as the transcriptional level in some cases. siRNAs are important for protecting cells against viral infections and silencing transposable genetic elements.
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RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
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Reverse Genetics to Engineer Positive-Sense RNA Virus Variants
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Mutations in virus-derived small RNAs.

Deepti Nigam1, Katherine LaTourrette1, Hernan Garcia-Ruiz2

  • 1Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska-Lincoln, Nebraska, United States of America.

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Antiviral gene silencing imposes selection on RNA virus populations, leading to mutations in virus-derived small interfering RNAs (siRNAs). Both viral and cellular RNA-dependent RNA polymerases contribute to these mutations.

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Area of Science:

  • Plant virology
  • Molecular biology
  • RNA silencing

Background:

  • RNA viruses exist as diverse populations of genome variants.
  • Plants defend against RNA viruses using gene silencing, producing 21-24 nucleotide small interfering RNAs (siRNAs) from viral RNA.
  • Understanding mutations in virus-derived siRNAs is crucial for comprehending virus evolution and host-pathogen interactions.

Purpose of the Study:

  • To investigate the mutation profiles of virus-derived siRNAs in three Potyviridae viruses: Turnip mosaic virus (TuMV), Papaya ringspot virus (PRSV), and Wheat streak mosaic virus (WSMV).
  • To determine the role of antiviral gene silencing and viral/cellular RNA-dependent RNA polymerases in generating mutations within virus-derived siRNAs.

Main Methods:

  • Analysis of mutation profiles in virus-derived siRNAs from infected Arabidopsis thaliana plants (mechanically inoculated and systemically infected tissues).
  • Genetic manipulation to remove plant gene silencing and viral silencing suppression.
  • Examination of mutations in siRNAs derived from a PRSV coat protein transgene in non-replicating conditions.

Main Results:

  • Mutation profiles in TuMV-infected Arabidopsis thaliana were consistent with selection pressures from local and systemic viral movement.
  • Antiviral gene silencing was shown to impose selection on viral populations.
  • Cellular RNA-dependent RNA polymerases contribute to mutations in virus-derived siRNAs, even in the absence of viral replication.

Conclusions:

  • Antiviral gene silencing acts as a selective pressure on viral genomes.
  • Two primary sources contribute to mutations in virus-derived siRNAs: viral RNA-dependent RNA polymerases during replication and cellular RNA-dependent RNA polymerases during gene silencing amplification.