ArticleNucleic acids research2015
A predictive biophysical model of translational coupling to coordinate and control protein expression in bacterial operons.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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51 citing papers in PubMed, 105 citations in OpenAlex.
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- Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications.Chemical reviews · 2026Review
- Autonomous biogenesis of all thirty proteins of the Escherichia coli translation machinery.Nature communications · 2025Article
- Boosting Gene Translation by a Short ORF Encoding for a "Nonsense" Peptide Positioned Immediately Upstream.ACS synthetic biology · 2025Article
- Translational coupling of neighboring genes in prokaryotes.Journal of bacteriology · 2025Review
- Codon usage modulates the relationship between the burden and yield of protein overexpression.Journal of biological engineering · 2025Article
- The knowledge driven DBTL cycle provides mechanistic insights while optimising dopamine production in Escherichia coli.Microbial cell factories · 2025Article
- Untranslated region engineering strategies for gene overexpression, fine-tuning, and dynamic regulation.Journal of microbiology (Seoul, Korea) · 2025Review
- Synthetic translational coupling element for multiplexed signal processing and cellular control.Nucleic acids research · 2024Article
- Design of a self-regulating mRNA gene circuit.Scientific reports · 2024Article
- Guide RNA structure design enables combinatorial CRISPRa programs for biosynthetic profiling.Nature communications · 2024Article
- CRISPR-Cas tools for simultaneous transcription & translation control in bacteria.Nucleic acids research · 2024Article
- Biosynthesis of C4-C8 3-Hydroxycarboxylic Acids from Glucose through the Inverted Fatty Acid β-Oxidation by Metabolically EngineeredBiomolecules · 2024Article
- Initiation at AUGUG and GUGUG sequences can lead to translation of overlapping reading frames in E. coli.Nucleic acids research · 2023Article
- Unidirectional gene pairs in archaea and bacteria require overlaps or very short intergenic distances for translational coupling via termination-reinitiation and often encode subunits of heteromeric complexes.Frontiers in microbiology · 2023Article
- Modelling ribosome kinetics and translational control on dynamic mRNA.PLoS computational biology · 2023Article
- High quality genome annotation and expression visualisation of a mupirocin-producing bacterium.PloS one · 2022Article
- The diversity of Shine-Dalgarno sequences sheds light on the evolution of translation initiation.RNA biology · 2021Review
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Natural and engineered genetic systems require the coordinated expression of proteins. In bacteria, translational coupling provides a genetically encoded mechanism to control expression level ratios within multi-cistronic operons. We have developed a sequence-to-function biophysical model of translational coupling to predict expression level ratios in natural operons and to design synthetic operons with desired expression level ratios. To quantitatively measure ribosome re-initiation rates, we designed and characterized 22 bi-cistronic operon variants with systematically modified intergenic distances and upstream translation rates. We then derived a thermodynamic free energy model to calculate de novo initiation rates as a result of ribosome-assisted unfolding of intergenic RNA structures. The complete biophysical model has only five free parameters, but was able to accurately predict downstream translation rates for 120 synthetic bi-cistronic and tri-cistronic operons with rationally designed intergenic regions and systematically increased upstream translation rates. The biophysical model also accurately predicted the translation rates of the nine protein atp operon, compared to ribosome profiling measurements. Altogether, the biophysical model quantitatively predicts how translational coupling controls protein expression levels in synthetic and natural bacterial operons, providing a deeper understanding of an important post-transcriptional regulatory mechanism and offering the ability to rationally engineer operons with desired behaviors.
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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.