ArticleBMC biotechnology2007
Construction and model-based analysis of a promoter library for E. coli: an indispensable tool for metabolic engineering.
Article in BMC biotechnology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers.
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Who cites it
71 citing papers in PubMed.
- Protection AgainstVaccines · 2026Article
- Engineering an AlkS-PalkB Transcription Factor-Based Biosensor With Improved Sensitivity to Isobutanol and Other Short-Chain Alcohols.Microbial biotechnology · 2025Article
- Deep Generative Model-Driven Design of Microbial Synthetic Promoters.Journal of microbiology and biotechnology · 2025Review
- Biological Switches: Past and Future Milestones of Transcription Factor-Based Biosensors.ACS synthetic biology · 2025Review
- Exploring the Promoter Generation and Prediction ofInternational journal of molecular sciences · 2024Article
- Enhancing metabolic efficiency via novel constitutive promoters to produce protocatechuic acid in Escherichia coli.Applied microbiology and biotechnology · 2024Article
- CAPE: a deep learning framework with Chaos-Attention net for Promoter Evolution.Briefings in bioinformatics · 2024Article
- Biosensor-assisted CRISPRi high-throughput screening to identify genetic targets inSynthetic and systems biotechnology · 2024Article
- Towards a rational approach to promoter engineering: understanding the complexity of transcription initiation in prokaryotes.FEMS microbiology reviews · 2024Review
- Fine-Tuning Gene Expression in Bacteria by Synthetic Promoters.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Standardization of Fluorescent Reporter Assays in Synthetic Biology across the Visible Light Spectrum.ACS synthetic biology · 2023Article
- MoBioS: Modular Platform Technology for High-Throughput Construction and Characterization of Tunable Transcriptional Biological Sensors.Biosensors · 2023Article
- Dynamic feedback regulation for efficient membrane protein production using a small RNA-based genetic circuit in Escherichia coli.Microbial cell factories · 2022Article
- Biosensor-driven, model-based optimization of the orthogonally expressed naringenin biosynthesis pathway.Microbial cell factories · 2022Article
- A Brief Journey into the History of and Future Sources and Uses of Fatty Acids.Frontiers in nutrition · 2021Review
- Removing the Bottleneck: Introducing cMatch - A Lightweight Tool for Construct-Matching in Synthetic Biology.Frontiers in bioengineering and biotechnology · 2021Article
- Impact of the Expression System on Recombinant Protein Production inFrontiers in microbiology · 2021Article
- Predictive design of sigma factor-specific promoters.Nature communications · 2020Article
- Article
- Promoter Architecture and Promoter Engineering inMetabolites · 2020Review
11 more citing papers are in PubMed but not listed here.
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5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundNowadays, the focus in metabolic engineering research is shifting from massive overexpression and inactivation of genes towards the model-based fine tuning of gene expression. In this context, the construction of a library of synthetic promoters of Escherichia coli as a useful tool for fine tuning gene expression is discussed here.
resultsA degenerated oligonucleotide sequence that encodes consensus sequences for E. coli promoters separated by spacers of random sequences has been designed and synthesized. This 57 bp long sequence contains 24 conserved, 13 semi-conserved (W, R and D) and 20 random nucleotides. This mixture of DNA fragments was cloned into a promoter probing vector (pVIK165). The ligation mixtures were transformed into competent E. coli MA8 and the resulting clones were screened for GFP activity by measuring the relative fluorescence units; some clones produced high fluorescence intensity, others weak fluorescence intensity. The clones cover a range of promoter activities from 21.79 RFU/OD600 ml to 7606.83 RFU/OD600 ml. 57 promoters were sequenced and used for promoter analysis. The present results conclusively show that the postulates, which link promoter strength to anomalies in the -10 box and/or -35 box, and to the length of the spacer, are not generally valid. However, by applying Partial Least Squares regression, a model describing the promoter strength was built and validated.
conclusionFor Escherichia coli, the promoter strength can not been linked to anomalies in the -10 box and/or -35 box, and to the length of the spacer. Also a probabilistic approach to relate the promoter sequence to its strength has some drawbacks. However, by applying Partial Least Squares regression, a good correlation was found between promoter sequence and promoter strength. This PLS model can be a useful tool to rationally design a suitable promoter in order to fine tune gene expression.
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