ArticleNucleic acids research2013
Conservation of mRNA secondary structures may filter out mutations in Escherichia coli evolution.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
13 citing papers in PubMed, 25 citations in OpenAlex.
- Quantifying the Evolution of SNPs That Affect RNA Secondary Structure in Arabidopsis thaliana Genes.Molecular biology and evolution · 2025Article
- "Outlaw" mutations in quasispecies of SARS-CoV-2 inhibit replication.Emerging microbes & infections · 2024Article
- Rock, scissors, paper: How RNA structure informs function.The Plant cell · 2023Article
- Mechanisms governing codon usage bias and the implications for protein expression in the chloroplast of Chlamydomonas reinhardtii.The Plant journal : for cell and molecular biology · 2022Review
- Structural landscape of the complete genomes of dengue virus serotypes and other viral hemorrhagic fevers.BMC genomics · 2021Article
- MutaRNA: analysis and visualization of mutation-induced changes in RNA structure.Nucleic acids research · 2020Article
- A pan-cancer analysis of synonymous mutations.Nature communications · 2019Article
- Conformational Dynamics of the RNA G-Quadruplex and its Effect on Translation Efficiency.Molecules (Basel, Switzerland) · 2019Article
- A Method for RNA Structure Prediction Shows Evidence for Structure in lncRNAs.Frontiers in molecular biosciences · 2018Article
- Large-Effect Beneficial Synonymous Mutations Mediate Rapid and Parallel Adaptation in a Bacterium.Molecular biology and evolution · 2016Article
- Compensating the Fitness Costs of Synonymous Mutations.Molecular biology and evolution · 2016Article
- Population transcriptomics uncovers the regulation of gene expression variation in adaptation to changing environment.Scientific reports · 2016Article
- The impact of RNA structure on coding sequence evolution in both bacteria and eukaryotes.BMC evolutionary biology · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent reports indicate that mutations in viral genomes tend to preserve RNA secondary structure, and those mutations that disrupt secondary structural elements may reduce gene expression levels, thereby serving as a functional knockout. In this article, we explore the conservation of secondary structures of mRNA coding regions, a previously unknown factor in bacterial evolution, by comparing the structural consequences of mutations in essential and nonessential Escherichia coli genes accumulated over 40 000 generations in the course of the 'long-term evolution experiment'. We monitored the extent to which mutations influence minimum free energy (MFE) values, assuming that a substantial change in MFE is indicative of structural perturbation. Our principal finding is that purifying selection tends to eliminate those mutations in essential genes that lead to greater changes of MFE values and, therefore, may be more disruptive for the corresponding mRNA secondary structures. This effect implies that synonymous mutations disrupting mRNA secondary structures may directly affect the fitness of the organism. These results demonstrate that the need to maintain intact mRNA structures imposes additional evolutionary constraints on bacterial genomes, which go beyond preservation of structure and function of the encoded proteins.
Indexed as
Identifiers
What OpenQuestion holds
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.