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
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Journal ArticleDOI
Photosynthetic conversion of CO2 to farnesyl diphosphate-derived phytochemicals (amorpha-4,11-diene and squalene) by engineered cyanobacteria.
Sun Young Choi,Sun Young Choi,Hyun Jeong Lee,Jaeyeon Choi,Ji-Ye Kim,Ji-Ye Kim,Sang Jun Sim,Youngsoon Um,Yunje Kim,Taek Soon Lee,Taek Soon Lee,Jay D. Keasling,Han Min Woo +12 more
TL;DR: This is the first demonstration of photosynthetic production of amorpha-4,11-diene from CO2 in cyanobacteria and production of squalene in S. elongatus PCC 7942, and the optimized modular OverMEP strain (SeHL33) with either co-expression of ADS or SQS demonstrated the highest production levels, which could expand the list of farnesyl diphosphate-derived isoprenoids fromCO2 as bio-s
Journal ArticleDOI
Microbial Platform for Terpenoid Production: Escherichia coli and Yeast.
Chonglong Wang,Mudanguli Liwei,Ji-Bin Park,Seong-Hee Jeong,Gongyuan Wei,Yujun Wang,Seon-Won Kim +6 more
TL;DR: This review summarizes recent progresses in engineering of industrial model strains, E. coli and yeasts, for terpenoids production and concludes that both strains are expected to present the great potential as a platform of terpenoid synthesis.
Journal ArticleDOI
Design and engineering of intracellular-metabolite-sensing/regulation gene circuits in Saccharomyces cerevisiae
TL;DR: A new strategy for design, construction, and fine‐tuning of intracellular‐metabolite‐sensing/regulation gene circuits by repurposing bacterial transcription factors and eukaryotic promoters is reported, which should be generally applicable and highly useful for evolutionary engineering of proteins, pathways, and genomes in S. cerevisiae.
Journal ArticleDOI
Orthogonal monoterpenoid biosynthesis in yeast constructed on an isomeric substrate.
Codruta Ignea,Morten H. Raadam,Mohammed Saddik Motawia,Antonios M. Makris,Claudia E. Vickers,Claudia E. Vickers,Sotirios C. Kampranis +6 more
TL;DR: An orthogonal monoterpenoid pathway is established by selecting the cis isomer of GPP as an alternative precursor and achieve high titer monoterpene production to highlight the introduction of synthetic metabolism as an effective strategy for high-value compound production.
Journal ArticleDOI
Control Theory for Synthetic Biology: Recent Advances in System Characterization, Control Design, and Controller Implementation for Synthetic Biology
TL;DR: Synthetic biology as a field might best be characterized as a learn-by-building approach, in which scientists attempt to engineer molecular pathways that do not exist in nature, in doing so, they test the limits of both natural and engineered organisms.
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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