ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2018
Genome scale analysis of Escherichia coli with a comprehensive prokaryotic sequence-based biophysical model of translation initiation and elongation.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed, 27 citations in OpenAlex.
- Structure of the 30S translation initiation complex coupled to paused RNA polymerase and its potential for riboregulation.Nature communications · 2025Article
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- Decoding stoichiometric protein synthesis inBiophysical reports · 2023Article
- spotter: a single-nucleotide resolution stochastic simulation model of supercoiling-mediated transcription and translation in prokaryotes.Nucleic acids research · 2023Article
- Stochastic dynamics and ribosome-RNAP interactions in transcription-translation coupling.Biophysical journal · 2023Article
- Global and gene-specific translational regulation in Escherichia coli across different conditions.PLoS computational biology · 2022Article
- Synergistic Regulation of Transcription and Translation in Escherichia coli Revealed by Codirectional Increases in mRNA Concentration and Translation Efficiency.Microbiology spectrum · 2022Article
- Functional characterization of HigBA toxin-antitoxin system in an Arctic bacterium, Bosea sp. PAMC 26642.Journal of microbiology (Seoul, Korea) · 2022Article
- Prokaryotic rRNA-mRNA interactions are involved in all translation steps and shape bacterial transcripts.RNA biology · 2021Article
- Dynamics of transcription-translation coordination tune bacterial indole signaling.Nature chemical biology · 2020Article
- Coupled Transcription-Translation in Prokaryotes: An Old Couple With New Surprises.Frontiers in microbiology · 2020Review
- Networks of ribosome flow models for modeling and analyzing intracellular traffic.Scientific reports · 2019Article
- Genome-Scale Analysis of Perturbations in Translation Elongation Based on a Computational Model.Scientific reports · 2018Article
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2 authors at 1 institution in 1 country.
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Abstract
Translation initiation in prokaryotes is affected by the mRNA folding and interaction of the ribosome binding site with the ribosomal RNA. The elongation rate is affected, among other factors, by the local biophysical properties of the coding regions, the decoding rates of different codons, and the interactions among ribosomes. Currently, there is no comprehensive biophysical model of translation that enables the prediction of mRNA translation dynamics based only on the transcript sequence and while considering all of these fundamental aspects of translation. In this study, we provide, for the first time, a computational simulative biophysical model of both translation initiation and elongation with all aspects mentioned above. We demonstrate our model performance and advantages focusing on Escherichia coli genes. We further show that the model enables prediction of translation rate, protein levels, and ribosome densities. In addition, our model enables quantifying the effect of silent mutations on translation rate in different parts of the transcript, the relative effect of mutations on translation initiation and elongation, and the effect of mutations on ribosome traffic jams. Thus, unlike previous models, the proposed one provides comprehensive information, facilitating future research in disciplines such as molecular evolution, synthetic biology, and functional genomics. A toolkit to estimate translation dynamics of transcripts is available at: https://www.cs.tau.ac.il/∼tamirtul/transim.
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