ArticleScientific reports2019
Quantitative modeling of transcription and translation of an all-E. coli cell-free system.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- A Data-Centric Diagnostic Framework for Experimental Design and Mechanistic Modeling: Application to mRNA Production.Industrial & engineering chemistry research · 2026Article
- Nucleotide-Level Chemical Reaction Network Modeling Enables Quantitative Prediction of Reconstituted Cell-Free Expression Systems.ACS synthetic biology · 2026Article
- Systematic Evaluation of Different Ribonucleoprotein Complexes as Posttranscriptional Biosensors in Cell-Free TX-TL Systems.ACS synthetic biology · 2026Article
- Absolute quantification of fluorescent protein fusions by mass spectrometry.Protein science : a publication of the Protein Society · 2026Article
- Bacterial chromosome conformation and cell-free gene expression in synthetic 2D compartments.Nature communications · 2025Article
- Reconstituting alternative life using the test-bed of cell-free systems.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- Cell-Free Gene Expression: Methods and Applications.Chemical reviews · 2025Review
- Autonomous ribosome biogenesis in vitro.Nature communications · 2025Article
- Modular Golden Gate Assembly of Linear DNA Templates for Cell-Free Prototyping.Methods in molecular biology (Clifton, N.J.) · 2025Article
- A mathematical model of cell-free transcription-translation with plasmid crosstalk.Synthetic biology (Oxford, England) · 2025Article
- Challenges in observing transcription-translation for bottom-up synthetic biology.QRB discovery · 2025Review
- Review
- Leveraging Active Learning to Establish Efficient In Vitro Transcription and Translation from Bacterial Chromosomal DNA.ACS omega · 2024Article
- A genetic circuit on a single DNA molecule as an autonomous dissipative nanodevice.Nature communications · 2024Article
- Detection of viral RNAs at ambient temperature via reporter proteins produced through the target-splinted ligation of DNA probes.Nature biomedical engineering · 2023Article
- Engineering activatable promoters for scalable and multi-input CRISPRa/i circuits.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- The Long Road to a Synthetic Self-Replicating Central Dogma.Biochemistry · 2023Review
- Bacteriophage-based techniques for elucidating the function of zebrafish gut microbiota.Applied microbiology and biotechnology · 2023Review
- Article
- Rapid Single-Pot Assembly of Modular Chromatin Proteins for Epigenetic Engineering.Methods in molecular biology (Clifton, N.J.) · 2023Article
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Authors and funding
2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Cell-free transcription-translation (TXTL) is expanding as a polyvalent experimental platform to engineer biological systems outside living organisms. As the number of TXTL applications and users is rapidly growing, some aspects of this technology could be better characterized to provide a broader description of its basic working mechanisms. In particular, developing simple quantitative biophysical models that grasp the different regimes of in vitro gene expression, using relevant kinetic constants and concentrations of molecular components, remains insufficiently examined. In this work, we present an ODE (Ordinary Differential Equation)-based model of the expression of a reporter gene in an all E. coli TXTL that we apply to a set of regulatory elements spanning several orders of magnitude in strengths, far beyond the T7 standard system used in most of the TXTL platforms. Several key biochemical constants are experimentally determined through fluorescence assays. The robustness of the model is tested against the experimental parameters, and limitations of TXTL resources are described. We establish quantitative references between the performance of E. coli and synthetic promoters and ribosome binding sites. The model and the data should be useful for the TXTL community interested either in gene network engineering or in biomanufacturing beyond the conventional platforms relying on phage transcription.
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