ArticleNucleic acids research2019
De novo design of programmable inducible promoters.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- CRISPR-enhanced microalgae biosynthesis: a promising approach for future functional feed ingredients.Journal of animal science and biotechnology · 2026Review
- Extending dynamic and operational range of the biosensor responding to l-carnitine by directed evolution.Synthetic and systems biotechnology · 2025Article
- The Tetracycline-Inducible/CRISPR-Cas9 System is an Efficient Tool for Studying Gene Function in Phytophthora sojae.Molecular plant pathology · 2025Article
- Modeling and designing enhancers by introducing and harnessing transcription factor binding units.Nature communications · 2025Article
- Biological Switches: Past and Future Milestones of Transcription Factor-Based Biosensors.ACS synthetic biology · 2025Review
- The rise and future of CRISPR-based approaches for high-throughput genomics.FEMS microbiology reviews · 2024Review
- Delaying production with prokaryotic inducible expression systems.Microbial cell factories · 2024Review
- Utilizing 5' UTR Engineering Enables Fine-Tuning of Multiple Genes within Operons to Balance Metabolic Flux inBiology · 2024Article
- A coarse-grained bacterial cell model for resource-aware analysis and design of synthetic gene circuits.Nature communications · 2024Article
- Synthetic Homoserine Lactone Sensors for Gram-PositiveACS synthetic biology · 2024Article
- Deep Learning-Assisted Design of Novel Promoters inAdvanced genetics (Hoboken, N.J.) · 2023Article
- Applications of artificial intelligence and machine learning in dynamic pathway engineering.Biochemical Society transactions · 2023Review
- Deep flanking sequence engineering for efficient promoter design using DeepSEED.Nature communications · 2023Article
- Cell factory engineering: Challenges and opportunities for synthetic biology applications.Biotechnology and bioengineering · 2023Review
- A lentiviral vector for the production of T cells with an inducible transgene and a constitutively expressed tumour-targeting receptor.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
- Characterizing and utilizing oxygen-dependent promoters for efficient dynamic metabolic engineering.Metabolic engineering · 2023Article
- De novo design of the global transcriptional factor Cra-regulated promoters enables highly sensitive glycolysis flux biosensor for dynamic metabolic control.Microbial biotechnology · 2023Article
- Multilayered safety framework for living diagnostics in the colon.Frontiers in systems biology · 2023Article
- Engineering an AI-based forward-reverse platform for the design of cross-ribosome binding sites of a transcription factor biosensor.Computational and structural biotechnology journal · 2023Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Ligand-responsive allosteric transcription factors (aTF) play a vital role in genetic circuits and high-throughput screening because they transduce biochemical signals into gene expression changes. Programmable control of gene expression from aTF-regulated promoter is important because different downstream effector genes function optimally at different expression levels. However, tuning gene expression of native promoters is difficult due to complex layers of homeostatic regulation encoded within them. We engineered synthetic promoters de novo by embedding operator sites with varying affinities and radically reshaped binding preferences within a minimal, constitutive Escherichia coli promoter. Multiplexed cell-based screening of promoters for three TetR-like aTFs generated with this approach gave rich diversity of gene expression levels, dynamic ranges and ligand sensitivities and were 50- to 100-fold more active over their respective native promoters. Machine learning on our dataset revealed that relative position of the core motif and bases flanking the core motif play an important role in modulating induction response. Our generalized approach yields customizable and programmable aTF-regulated promoters for engineering cellular pathways and enables the discovery of new small molecule biosensors.
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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.