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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Journal ArticleDOI
Advances in the dynamic control of metabolic pathways in Saccharomyces cerevisiae
TL;DR: In this article , the successful utilization of transcription factor (TF)-based biosensors within the dynamic regulatory network of Saccharomyces cerevisiae has been discussed, and the potential of omics tools for the discovery of novel responsive promoters was explored.
Posted ContentDOI
The landscape of toxic intermediates in the metabolic networks of pathogenic fungi reveals targets for antifungal drugs
J. Ewald,P. M. Jansen,Sascha Brunke,D. Hiller,Christian H. Luther,Humberto González-Díaz,Humberto González-Díaz,Marcus Dittrich,Andre Fleissner,Bernhard Hube,Bernhard Hube,Stefan Schuster,Christoph Kaleta +12 more
TL;DR: In this paper, the authors explore the landscape of toxic intermediates in the metabolic networks of fungal pathogens and provide a web-service, FunTox-Networks, which is able to extract toxic pathway intermediates and their controlling enzymes.
Book ChapterDOI
Microbial biosensors for discovery and engineering of enzymes and metabolism
TL;DR: This chapter aims to give an overview of current methods and applications regarding the utilization of biosensors for both discovery and engineering approaches.
Posted ContentDOI
Towards universal synthetic heterotrophy using a metabolic coordinator
Sean F. Sullivan,Anuj Shetty,Tharun Bharadwaj,Naveen B. Krishna,Vikas Trivedi,Venkatesh Endalur Gopinarayanan,Todd C. Chappell,Daniel M. Sellers,Pravin Kumar R.,Nikhil U. Nair +9 more
TL;DR: Gal3pS25144.1 as mentioned in this paper is a variant of Gal3pMC that exhibits robust GAL regulon activation in the presence of structurally diverse substrates and recapitulates the dynamics of the native system.
Journal ArticleDOI
Towards universal synthetic heterotrophy using a metabolic coordinator
TL;DR: Gal3pSyn4.1 as mentioned in this paper is a variant of Gal3pMC that exhibits robust GAL regulon activation in the presence of structurally diverse substrates and recapitulates the dynamics of the native system.
References
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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.
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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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