ArticleBiophysical journal2015
Synonymous mutations reduce genome compactness in icosahedral ssRNA viruses.
Article in Biophysical journal, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 47 citations in OpenAlex.
- Periodic genome sequences facilitate packaging in a single-stranded DNA virus.Journal of virology · 2026Article
- Structure of Stacked Aggregates of Semiflexible Rings Under Spherical Confinement: A Computational Study.Polymers · 2026Article
- The mutational landscape of SARS-CoV-2 provides new insight into viral evolution and fitness.Nature communications · 2025Article
- Measuring intramolecular connectivity in long RNA molecules using two-dimensional DNA patch-probe arrays.Nucleic acids research · 2025Article
- Genetic diversity of murine norovirus associated with ethanol sensitivity.Applied microbiology and biotechnology · 2025Article
- Molecular Dynamics Characterization of the Free and Encapsidated RNA2 of CCMV with the oxRNA Model.Macromolecular rapid communications · 2024Article
- Context-dependent structure formation of hairpin motifs in bacteriophage MS2 genomic RNA.Biophysical journal · 2024Article
- Molecular transition of SARS-CoV-2 from critical patients during the first year of the COVID-19 pandemic in Mexico City.Frontiers in cellular and infection microbiology · 2023Article
- Structural Studies Reveal that Endosomal Cations Promote Formation of Infectious Coxsackievirus A9 A-Particles, Facilitating RNA and VP4 Release.Journal of virology · 2022Article
- Ecological and evolutionary dynamics of multi-strain RNA viruses.Nature ecology & evolution · 2022Review
- Global SNP analysis of 11,183 SARS-CoV-2 strains reveals high genetic diversity.Transboundary and emerging diseases · 2021Article
- Novel Fusari- and Toti-like Viruses, with Probable Different Origins, in the Plant Pathogenic OomyceteViruses · 2021Article
- Relationships between RNA topology and nucleocapsid structure in a model icosahedral virus.Biophysical journal · 2021Article
- RNA-Mediated Virus Assembly: Mechanisms and Consequences for Viral Evolution and Therapy.Annual review of biophysics · 2019Review
- Large-Scale Synonymous Substitutions in Cucumber Mosaic Virus RNA 3 Facilitate Amino Acid Mutations in the Coat Protein.Journal of virology · 2018Article
- A modelling paradigm for RNA virus assembly.Current opinion in virology · 2018Review
- The Evolution of Molecular Compatibility between Bacteriophage ΦX174 and its Host.Scientific reports · 2018Article
- Compactness of viral genomes: effect of disperse and localized random mutations.Journal of physics. Condensed matter : an Institute of Physics journal · 2018Article
- Varieties of charge distributions in coat proteins of ssRNA+ viruses.Journal of physics. Condensed matter : an Institute of Physics journal · 2018Article
- Recent advances in coarse-grained modeling of virus assembly.Current opinion in virology · 2016Review
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Authors and funding
4 authors at 3 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent studies have shown that single-stranded (ss) viral RNAs fold into more compact structures than random RNA sequences with similar chemical composition and identical length. Based on this comparison, it has been suggested that wild-type viral RNA may have evolved to be atypically compact so as to aid its encapsidation and assist the viral assembly process. To further explore the compactness selection hypothesis, we systematically compare the predicted sizes of >100 wild-type viral sequences with those of their mutants, which are evolved in silico and subject to a number of known evolutionary constraints. In particular, we enforce mutation synonynimity, preserve the codon-bias, and leave untranslated regions intact. It is found that progressive accumulation of these restricted mutations still suffices to completely erase the characteristic compactness imprint of the viral RNA genomes, making them in this respect physically indistinguishable from randomly shuffled RNAs. This shows that maintaining the physical compactness of the genome is indeed a primary factor among ssRNA viruses' evolutionary constraints, contributing also to the evidence that synonymous mutations in viral ssRNA genomes are not strictly neutral.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.