Journal ArticleDOI
Engineering dynamic pathway regulation using stress-response promoters
Robert H. Dahl,Fuzhong Zhang,Jorge Alonso-Gutierrez,Jorge Alonso-Gutierrez,Edward E. K. Baidoo,Edward E. K. Baidoo,Tanveer S. Batth,Tanveer S. Batth,Alyssa M. Redding-Johanson,Alyssa M. Redding-Johanson,Christopher J. Petzold,Christopher J. Petzold,Aindrila Mukhopadhyay,Aindrila Mukhopadhyay,Taek Soon Lee,Taek Soon Lee,Paul D. Adams,Paul D. Adams,Paul D. Adams,Jay D. Keasling +19 more
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TLDR
This paper applied whole-genome transcript arrays to identify promoters that respond to the accumulation of toxic intermediates, and then used these promoters to control accumulation of the intermediate and improve the final titers of a desired product.Abstract:
Heterologous pathways used in metabolic engineering may produce intermediates toxic to the cell. Dynamic control of pathway enzymes could prevent the accumulation of these metabolites, but such a strategy requires sensors, which are largely unknown, that can detect and respond to the metabolite. Here we applied whole-genome transcript arrays to identify promoters that respond to the accumulation of toxic intermediates, and then used these promoters to control accumulation of the intermediate and improve the final titers of a desired product. We apply this approach to regulate farnesyl pyrophosphate (FPP) production in the isoprenoid biosynthetic pathway in Escherichia coli. This strategy improved production of amorphadiene, the final product, by twofold over that from inducible or constitutive promoters, eliminated the need for expensive inducers, reduced acetate accumulation and improved growth. We extended this approach to another toxic intermediate to demonstrate the broad utility of identifying novel sensor-regulator systems for dynamic regulation.read more
Citations
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Book ChapterDOI
Synthetic Regulatory Tools to Engineer Microbial Cell Factories for Chemical Production
TL;DR: The synthetic regulatory tools along with the design strategies and applications in the context of metabolic engineering are reviewed.
Journal ArticleDOI
Mitigating Host Burden of Genetic Circuits by Engineering Autonegatively Regulated Parts and Improving Functional Prediction.
Ying Guan,Xinmao Chen,Bin Shao,Xingyue Ji,Yanhui Xiang,Guoqiang Jiang,Lina Xu,Zhanglin Lin,Q. Ouyang,Chunbo Lou +9 more
TL;DR: It is demonstrated that growth burden and circuit dysregulation occurred in a concentration-dependent manner for specific transcription factors in E.coli, and direct negative feedback modules were able to control the concentration of CymR*/CymR, mitigate growth burden, and restore circuit functions.
Dissertation
Controlling Enzyme Expression Dynamics to Improve Production from Engineered Biosynthetic Pathways
Book ChapterDOI
Systems and synthetic metabolic engineering for production of biochemicals
TL;DR: The bioproduction of high value biochemicals using the microbial cell factories developed by systems and synthetic metabolic engineering strategies, including modular engineering, spatial organization engineering, dynamic regulation, transcriptomics, metabonomics and so on have been summarized.
Book ChapterDOI
Construction of Microbial Cell Factories by Systems and Synthetic Biotechnology
TL;DR: The applications of modular metabolic engineering and dynamic regulation for the further optimization and regulation of metabolic network were discussed and the role of system biology such as omics technology, genomics-based metabolic model, and genome-scale engineering tools were highlighted.
References
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Journal ArticleDOI
Production of the antimalarial drug precursor artemisinic acid in engineered yeast
Dae-Kyun Ro,Eric M. Paradise,Mario Ouellet,Karl Fisher,Karyn L. Newman,John M. Ndungu,Ho Kimberly,Eachus Rachel,Timothy S. Ham,James Kirby,Michelle C. Y. Chang,Sydnor T. Withers,Yoichiro Shiba,Richmond Sarpong,Jay D. Keasling +14 more
TL;DR: The engineering of Saccharomyces cerevisiae to produce high titres (up to 100 mg l-1) of artemisinic acid using an engineered mevalonate pathway, amorphadiene synthase, and a novel cytochrome P450 monooxygenase from A. annua that performs a three-step oxidation of amorpha-4,11-diene to art Artemisinic acid.
Journal ArticleDOI
Genesis: cluster analysis of microarray data
TL;DR: Genesis integrates various tools for microarray data analysis such as filters, normalization and visualization tools, distance measures as well as common clustering algorithms including hierarchical clustering, self-organizing maps, k-means, principal component analysis, and support vector machines.
Journal ArticleDOI
Engineering a mevalonate pathway in Escherichia coli for production of terpenoids
TL;DR: The strains developed in this study can serve as platform hosts for the production of any terpenoid compound for which a terpene synthase gene is available, and are the universal precursors to all isoprenoids.
Journal ArticleDOI
Automated design of synthetic ribosome binding sites to control protein expression
TL;DR: A predictive method for designing synthetic ribosome binding sites is developed, enabling a rational control over the protein expression level, and is demonstrated by rationally optimizing protein expression to connect a genetic sensor to a synthetic circuit.
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