ArticleNucleic acids research2016
Discharging tRNAs: a tug of war between translation and detoxification in Escherichia coli.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers, 1 of them a synthesis that pooled it.
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, 1 synthesis or guideline pooled it, 57 citations in OpenAlex.
- Synonymous but Not Silent: The Codon Usage Code for Gene Expression and Protein Folding.Annual review of biochemistry · 2021Pooled it
- Automated prototyping of genetic codes.Nature · 2026Article
- Comprehensive post-transcriptional modification profiles in individual Staphylococcus aureus tRNA species.Nucleic acids research · 2026Article
- DEAD-box ATPase-marked condensates coordinate compartmentalized translation and antibiotic persistence.Science advances · 2026Article
- Nanopore sequencing of intact aminoacylated tRNAs.Nature communications · 2025Article
- An empirical model of aminoacylation kinetics for E. coli class I and II aminoacyl tRNA synthetases.PLoS computational biology · 2025Article
- The landscape of Arabidopsis tRNA aminoacylation.The Plant journal : for cell and molecular biology · 2024Article
- Nucleotidyltransferase toxin MenT extends aminoacyl acceptor ends of serine tRNAs to control Mycobacterium tuberculosis growth.Nature communications · 2024Article
- How DoesACS synthetic biology · 2024Article
- Bacterial nucleoid is a riddle wrapped in a mystery inside an enigma.Journal of bacteriology · 2024Review
- Whole-cell modeling of E. coli confirms that in vitro tRNA aminoacylation measurements are insufficient to support cell growth and predicts a positive feedback mechanism regulating arginine biosynthesis.Nucleic acids research · 2023Article
- Article
- Oxidative stress strongly restricts the effect of codon choice on the efficiency of protein synthesis inFrontiers in microbiology · 2022Article
- Estimation of peptide elongation times from ribosome profiling spectra.Nucleic acids research · 2021Article
- Full-length ribosome density prediction by a multi-input and multi-output model.PLoS computational biology · 2021Article
- Directed Evolution of theInternational journal of molecular sciences · 2021Article
- Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin inFrontiers in microbiology · 2021Article
- Codon Resolution Analysis of Ribosome Profiling Data.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Biochemistry of fluoroprolines: the prospect of making fluorine a bioelement.Beilstein journal of organic chemistry · 2021Review
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Translation is a central cellular process and is optimized for speed and fidelity. The speed of translation of a single codon depends on the concentration of aminoacyl-tRNAs. Here, we used microarray-based approaches to analyze the charging levels of tRNAs in Escherichia coli growing at different growth rates. Strikingly, we observed a non-uniform aminoacylation of tRNAs in complex media. In contrast, in minimal medium, the level of aminoacyl-tRNAs is more uniform and rises to approximately 60%. Particularly, the charging level of tRNA(Ser), tRNA(Cys), tRNA(Thr) and tRNA(His) is below 50% in complex medium and their aminoacylation levels mirror the degree that amino acids inhibit growth when individually added to minimal medium. Serine is among the most toxic amino acids for bacteria and tRNAs(Ser) exhibit the lowest charging levels, below 10%, at high growth rate although intracellular serine concentration is plentiful. As a result some serine codons are among the most slowly translated codons. A large fraction of the serine is most likely degraded by L-serine-deaminase, which competes with the seryl-tRNA-synthetase that charges the tRNAs(Ser) These results indicate that the level of aminoacylation in complex media might be a competition between charging for translation and degradation of amino acids that inhibit growth.
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.