ArticleMolecular biology and evolution2016
Large-Effect Beneficial Synonymous Mutations Mediate Rapid and Parallel Adaptation in a Bacterium.
Article in Molecular biology and evolution, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 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
40 citing papers in PubMed.
- Hurdles to horizontal gene transfer: species-specific effects of synonymous variation and plasmid copy number determine antibiotic resistance phenotype.Microbiology (Reading, England) · 2026Article
- Functional synonymous mutations and their evolutionary consequences.Nature reviews. Genetics · 2025Review
- Quantifying the intra- and inter-species community interactions in microbiomes by dynamic covariance mapping.Nature communications · 2025Article
- Fitness difference between two synonymous mutations of Phytophthora infestans ATP6 gene.BMC ecology and evolution · 2024Article
- Fitness benefits of a synonymous substitution in an ancient EF-Tu gene depend on the genetic background.Journal of bacteriology · 2024Article
- Molecular bases for strong phenotypic effects of single synonymous codon substitutions in the E. coli ccdB toxin gene.BMC genomics · 2023Article
- Genome Dynamics and Temperature Adaptation During Experimental Evolution of Obligate Intracellular Bacteria.Genome biology and evolution · 2023Article
- Most synonymous allelic variants in HIV tat are not silent.Genomics · 2023Article
- Article
- Conversion ofMicroorganisms · 2023Article
- Genome-wide sequencing identifies a thermal-tolerance related synonymous mutation in the mussel, Mytilisepta virgata.Communications biology · 2023Article
- The High Mutational Sensitivity of ccdA Antitoxin Is Linked to Codon Optimality.Molecular biology and evolution · 2022Article
- Article
- Genomics of Diversification of Pseudomonas aeruginosa in Cystic Fibrosis Lung-like Conditions.Genome biology and evolution · 2022Article
- Article
- Molecular signatures of Janthinobacterium lividum from Trinidad support high potential for crude oil metabolism.BMC microbiology · 2021Article
- ΦX174 Attenuation by Whole-Genome Codon Deoptimization.Genome biology and evolution · 2021Article
- Synonymous Site-to-Site Substitution Rate Variation Dramatically Inflates False Positive Rates of Selection Analyses: Ignore at Your Own Peril.Molecular biology and evolution · 2020Article
- Identifying the drivers of computationally detected correlated evolution among sites under antibiotic selection.Evolutionary applications · 2020Article
- Recent insights into the genotype-phenotype relationship from massively parallel genetic assays.Evolutionary applications · 2019Review
Corrections and comments
- Commented on by
Authors and funding
11 authors.
Funding
Abstract
Contrary to previous understanding, recent evidence indicates that synonymous codon changes may sometimes face strong selection. However, it remains difficult to generalize the nature, strength, and mechanism(s) of such selection. Previously, we showed that synonymous variants of a key enzyme-coding gene (fae) of Methylobacterium extorquens AM1 decreased enzyme production and reduced fitness dramatically. We now show that during laboratory evolution, these variants rapidly regained fitness via parallel yet variant-specific, highly beneficial point mutations in the N-terminal region of fae These mutations (including four synonymous mutations) had weak but consistently positive impacts on transcript levels, enzyme production, or enzyme activity. However, none of the proposed mechanisms (including internal ribosome pause sites or mRNA structure) predicted the fitness impact of evolved or additional, engineered point mutations. This study shows that synonymous mutations can be fixed through strong positive selection, but the mechanism for their benefit varies depending on the local sequence context.
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.