Related Experiment Video
Updated: Sep 18, 2025
09:25
Rapid, Seamless Generation of Recombinant Poxviruses using Host Range and Visual Selection
Published on: May 24, 2020
5.4K
Mechanism of Forced-Copy-Choice RNA Recombination by Enteroviral RNA-Dependent RNA Polymerases
Jamie J Arnold1,2, Alexandre Martinez1, Abha Jain2
1Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.
ACS Bio & Med Chem Au
|June 25, 2025
Summary
Poliovirus RNA-dependent RNA polymerase (RdRp) uses a "plus-one" intermediate to perform forced-copy-choice recombination, potentially repairing viral genomes. This process favors certain nucleotides and can involve multiple template switches.
Area of Science:
- Virology
- Molecular Biology
- Biochemistry
Background:
- Forced-copy-choice recombination occurs at template ends, unlike internal copy-choice recombination.
- This mechanism may facilitate the assembly of full-length viral genomes from fragments generated during host antiviral responses.
- Previous studies showed poliovirus RNA-dependent RNA polymerase (RdRp) template switching *in vitro*.
Purpose of the Study:
- To investigate the mechanism of poliovirus RdRp-catalyzed forced-copy-choice RNA recombination.
- To elucidate the role of the 3'-end of donor templates and intermediate formation in template switching.
- To explore the potential repair function of this recombination mechanism in viral genome assembly.
Main Methods:
- Development of a primed-template system to study poliovirus RdRp-mediated recombination.
- Analysis of the effect of nucleotide addition to the 3'-end of double-stranded RNA products (plus-one intermediate).
- Evaluation of template switching efficiency with varying base pairing and the use of synthetic intermediates.
Main Results:
- Poliovirus RdRp forms a 'plus-one' intermediate by adding a single nontemplated nucleotide, favoring CMP.
- A single base pair between the intermediate and acceptor template is sufficient for switching, which can occur without RdRp dissociation.
- Up to five consecutive template switches were observed, suggesting a repair function; UMP addition is disfavored, potentially preventing nonsense mutations.
Conclusions:
- Poliovirus RdRp-catalyzed forced-copy-choice recombination involves a rate-limiting plus-one intermediate formation.
- This recombination mechanism likely contributes to viral genome repair and assembly, with specific nucleotide preferences.
- A structure-based hypothesis for the poliovirus RdRp-plus-one intermediate complex is proposed.
Related Concept Videos
00:57Viral Recombination
23.8K
Cells are sometimes infected by more than one virus at once. When two viruses disassemble to expose their genomes for replication in the same cell, similar regions of their genomes can pair together and exchange sequences in a process called recombination. Alternatively, viruses with segmented genomes can swap segments in a process called reassortment.
23.8K
01:10Retrovirus Life Cycles
47.0K
Retroviruses have a single-stranded RNA genome that undergoes a special form of replication. Once the retrovirus has entered the host cell, an enzyme called reverse transcriptase synthesizes double-stranded DNA from the retroviral RNA genome. This DNA copy of the genome is then integrated into the host’s genome inside the nucleus via an enzyme called integrase. Consequently, the retroviral genome is transcribed into RNA whenever the host’s genome is transcribed, allowing the...
47.0K
00:36Viral Mutations
33.1K
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...
33.1K
01:29Viruses with RNA Genomes
146
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...
146
02:33Retroviruses
12.7K
Retroviruses and retrotransposons both insert copies of their genetic elements into the genome of the host cell. Thus, the viral genes are passed on when the host genome is replicated or translated. A typical retroviral DNA sequence contains 3-4 genes that encode the different proteins required for its structural assembly and function as a molecular parasite. This DNA is transcribed into a single mRNA, which is very similar in structure to conventional mRNAs, i.e., it is capped at the 5’...
12.7K
02:53Conservative Site-specific Recombination and Phase Variation
6.1K
Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
The recognition sites for Cre recombinase called LoxP...
6.1K