ArticleACS synthetic biology2017
Deconvolution of Gene Expression Noise into Spatial Dynamics of Transcription Factor-Promoter Interplay.
Article in ACS synthetic biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 47 citations in OpenAlex.
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- A Network Approach to Genetic Circuit Designs.ACS synthetic biology · 2022Article
- Standardization of regulatory nodes for engineering heterologous gene expression: a feasibility study.Microbial biotechnology · 2022Article
- Combinatorial pathway balancing provides biosynthetic access to 2-fluoro-Chem catalysis · 2021Article
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- Subcellular Architecture of themBio · 2021Article
- Contextual dependencies expand the re-usability of genetic inverters.Nature communications · 2021Article
- Review
- Modelling co-translational dimerization for programmable nonlinearity in synthetic biology.Journal of the Royal Society, Interface · 2020Article
- Exploring the synthetic biology potential of bacteriophages for engineering non-model bacteria.Nature communications · 2020Review
- Synthetic control of plasmid replication enables target- and self-curing of vectors and expedites genome engineering ofMetabolic engineering communications · 2020Article
- Physical decoupling of XylS/Pm regulatory elements and conditional proteolysis enable precise control of gene expression in Pseudomonas putida.Microbial biotechnology · 2020Article
- Pathways to cellular supremacy in biocomputing.Nature communications · 2019Review
- Communicating Structure and Function in Synthetic Biology Diagrams.ACS synthetic biology · 2019Article
- Dynamical Task Switching in Cellular Computers.Life (Basel, Switzerland) · 2019Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Gene expression noise is not only the mere consequence of stochasticity, but also a signal that reflects the upstream physical dynamics of the cognate molecular machinery. Soil bacteria facing recalcitrant pollutants exploit noise of catabolic promoters to deploy beneficial phenotypes such as metabolic bet-hedging and/or division of biochemical labor. Although the role of upstream promoter-regulator interplay in the origin of this noise is little understood, its specifications are probably ciphered in flow cytometry data patterns. We studied Pm promoter activity of the environmental bacterium Pseudomonas putida and its cognate regulator XylS by following expression of Pm-gfp fusions in single cells. Using mathematical modeling and computational simulations, we determined the kinetic properties of the system and used them as a baseline code to interpret promoter activity in terms of upstream regulator dynamics. Transcriptional noise was predicted to depend on the intracellular physical distance between regulator source (where XylS is produced) and the target promoter. Experiments with engineered bacteria in which this distance is minimized or enlarged confirmed the predicted effects of source/target proximity on noise patterns. This approach allowed deconvolution of cytometry data into mechanistic information on gene expression flow. It also provided a basis for selecting programmable noise levels in synthetic regulatory circuits.
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Registered trials
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