ArticlePLoS computational biology2022
Global and gene-specific translational regulation in Escherichia coli across different conditions.
Article in PLoS computational biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 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
16 citing papers in PubMed, 25 citations in OpenAlex.
- Quorum-Sensing C12-HSL Drives Antibiotic Resistance Plasmid Transfer via Membrane Remodeling, Oxidative Stress, and RpoS-RMF Crosstalk.Microorganisms · 2025Article
- Transcriptome-Proteome Profiling inJournal of proteome research · 2025Article
- Ribosomal Hibernation Factor Links Quorum-Sensing to Acid Resistance in EHEC.Microorganisms · 2025Article
- Generative prediction of causal gene sets responsible for complex traits.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Case-Control Study of Factors Associated with Hemolytic Uremic Syndrome among Shiga Toxin-Producing Escherichia coli Patients, Ireland, 2017-2020.Emerging infectious diseases · 2025Article
- Integrative multi-omics analysis reveals the translational landscape of the plant-parasitic nematode Meloidogyne incognita.Communications biology · 2025Article
- The impact ofFrontiers in bioengineering and biotechnology · 2025Article
- Genome and transcriptomic analysis of the adaptation ofComputational and structural biotechnology journal · 2024Review
- Multi-omics approach for understanding the response ofHeliyon · 2024Article
- Physiology, fast and slow: bacterial response to variable resource stoichiometry and dilution rate.mSystems · 2024Article
- DDX21 functions as a potential novel oncopromoter in pancreatic ductal adenocarcinoma: a comprehensive analysis of the DExD box family.Discover oncology · 2024Article
- Investigating the Role of β-Disodium Glycerophosphate and Urea in Promoting Growth ofFoods (Basel, Switzerland) · 2024Article
- Mechanisms underlying the low-temperature adaptation of 17β-estradiol-degrading bacterial strainFrontiers in microbiology · 2024Article
- Translational efficiency in gas-fermenting bacteria: Adding a new layer of regulation to gene expression in acetogens.iScience · 2023Review
- Bioinformatic Analysis Reveals the Role of Translation Elongation Efficiency Optimisation in the Evolution ofBiology · 2023Article
- Recruitment of a Middling Promiscuous Enzyme Drives Adaptive Metabolic Evolution in Escherichia coli.Molecular biology and evolution · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 2 institutions in 3 countries.
Funding
Abstract
How well mRNA transcript levels represent protein abundances has been a controversial issue. Particularly across different environments, correlations between mRNA and protein exhibit remarkable variability from gene to gene. Translational regulation is likely to be one of the key factors contributing to mismatches between mRNA level and protein abundance in bacteria. Here, we quantified genome-wide transcriptome and relative translation efficiency (RTE) under 12 different conditions in Escherichia coli. By quantifying the mRNA-RTE correlation both across genes and across conditions, we uncovered a diversity of gene-specific translational regulations, cooperating with transcriptional regulations, in response to carbon (C), nitrogen (N), and phosphate (P) limitations. Intriguingly, we found that many genes regulating translation are themselves subject to translational regulation, suggesting possible feedbacks. Furthermore, a random forest model suggests that codon usage partially predicts a gene's cross-condition variability in translation efficiency; such cross-condition variability tends to be an inherent quality of a gene, independent of the specific nutrient limitations. These findings broaden the understanding of translational regulation under different environments and provide novel strategies for the control of translation in synthetic biology. In addition, our data offers a resource for future multi-omics studies.
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.