ArticleProceedings of the National Academy of Sciences of the United States of America2012
Identification of two functionally redundant RNA elements in the coding sequence of poliovirus using computer-generated design.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Poliovirus 3Dpol polymerase region is essential for cleavage of poliovirus 3AB in vivo.PLoS pathogens · 2026Article
- Rapid development of attenuated IBV vaccine candidates through a versatile backbone applicable to variants.NPJ vaccines · 2025Article
- An efficientJournal of virology · 2024Article
- Multiple functions of the nonstructural protein 3D in picornavirus infection.Frontiers in immunology · 2024Review
- Article
- Development of safe and highly protective live-attenuated SARS-CoV-2 vaccine candidates by genome recoding.Cell reports · 2021Article
- Impact of Synonymous Genome Recoding on the HIV Life Cycle.Frontiers in microbiology · 2021Review
- New RNA Structural Elements Identified in the Coding Region of the Coxsackie B3 Virus Genome.Viruses · 2020Article
- Synonymous genome recoding: a tool to explore microbial biology and new therapeutic strategies.Nucleic acids research · 2019Review
- HIV-1 Protease Evolvability Is Affected by Synonymous Nucleotide Recoding.Journal of virology · 2018Article
- Emergency Services of Viral RNAs: Repair and Remodeling.Microbiology and molecular biology reviews : MMBR · 2018Review
- Limits of variation, specific infectivity, and genome packaging of massively recoded poliovirus genomes.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Picornaviral polymerase structure, function, and fidelity modulation.Virus research · 2017Review
- Poliovirus Polymerase Leu420 Facilitates RNA Recombination and Ribavirin Resistance.Journal of virology · 2016Article
- Article
- FRESCo: finding regions of excess synonymous constraint in diverse viruses.Genome biology · 2015Article
- Mapping overlapping functional elements embedded within the protein-coding regions of RNA viruses.Nucleic acids research · 2014Article
- Picornavirus morphogenesis.Microbiology and molecular biology reviews : MMBR · 2014Review
- Stability of the parainfluenza virus 5 genome revealed by deep sequencing of strains isolated from different hosts and following passage in cell culture.Journal of virology · 2014Article
- Non-diarrhoeal increased frequency of bowel movements (IFoBM-ND): enterovirus association with the symptoms in children.BMJ open gastroenterology · 2014Article
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Authors and funding
8 authors.
Funding
Abstract
Genomes of RNA viruses contain multiple functional RNA elements required for translation or RNA replication. We use unique approaches to identify functional RNA elements in the coding sequence of poliovirus (PV), a plus strand RNA virus. The general method is to recode large segments of the genome using synonymous codons, such that protein sequences, codon use, and codon pair bias are conserved but the nucleic acid sequence is changed. Such recoding does not affect the growth of PV unless it destroys the sequence/structure of a functional RNA element. Using genetic analyses and a method called "signal location search," we detected two unique functionally redundant RNA elements (α and β), each about 75 nt long and separated by 150 nt, in the 3'-terminal coding sequence of RNA polymerase, 3D(pol). The presence of wild type (WT) α or β was sufficient for the optimal growth of PV, but the alteration of both segments in the same virus yielded very low titers and tiny plaques. The nucleotide sequences and predicted RNA structures of α and β have no apparent resemblance to each other. In α, we narrowed down the functional domain to a 48-nt-long, highly conserved segment. The primary determinant of function in β is a stable and highly conserved hairpin. Reporter constructs showed that the α- and β-segments are required for RNA replication. Recoding offers a unique and effective method to search for unknown functional RNA elements in coding sequences of RNA viruses, particularly if the signals are redundant in function.
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