ArticleNucleic acids research2020
Improving the prediction accuracy of protein abundance in Escherichia coli using mRNA accessibility.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 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
12 citing papers in PubMed.
- Gradient-based optimization for mRNA sequence design.Bioinformatics (Oxford, England) · 2026Article
- Article
- Transfer learning for cross-context prediction of protein expression from 5'UTR sequence.Nucleic acids research · 2024Article
- PARROT: Prediction of enzyme abundances using protein-constrained metabolic models.PLoS computational biology · 2023Article
- Ultradeep characterisation of translational sequence determinants refutes rare-codon hypothesis and unveils quadruplet base pairing of initiator tRNA and transcript.Nucleic acids research · 2023Article
- DeepRaccess: high-speed RNA accessibility prediction using deep learning.Frontiers in bioinformatics · 2023Article
- QRNAstruct: a method for extracting secondary structural features of RNA via regression with biological activity.Nucleic acids research · 2022Article
- Analysis of 11,430 recombinant protein production experiments reveals that protein yield is tunable by synonymous codon changes of translation initiation sites.PLoS computational biology · 2021Article
- TISIGNER.com: web services for improving recombinant protein production.Nucleic acids research · 2021Article
- Universal Constraints on Protein Evolution in the Long-Term Evolution Experiment with Escherichia coli.Genome biology and evolution · 2021Article
- Ligand-dependent tRNA processing by a rationally designed RNase P riboswitch.Nucleic acids research · 2021Article
- Learning the Regulatory Code of Gene Expression.Frontiers in molecular biosciences · 2021Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA secondary structure around translation initiation sites strongly affects the abundance of expressed proteins in Escherichia coli. However, detailed secondary structural features governing protein abundance remain elusive. Recent advances in high-throughput DNA synthesis and experimental systems enable us to obtain large amounts of data. Here, we evaluated six types of structural features using two large-scale datasets. We found that accessibility, which is the probability that a given region around the start codon has no base-paired nucleotides, showed the highest correlation with protein abundance in both datasets. Accessibility showed a significantly higher correlation (Spearman's ρ = 0.709) than the widely used minimum free energy (0.554) in one of the datasets. Interestingly, accessibility showed the highest correlation only when it was calculated by a log-linear model, indicating that the RNA structural model and how to utilize it are important. Furthermore, by combining the accessibility and activity of the Shine-Dalgarno sequence, we devised a method for predicting protein abundance more accurately than existing methods. We inferred that the log-linear model has a broader probabilistic distribution than the widely used Turner energy model, which contributed to more accurate quantification of ribosome accessibility to translation initiation sites.
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.