Journal ArticleDOI
Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA.
TLDR
Combined effect of the genetic interventions was found to be synergistic based on a developed analysis method that correlates genetic modification to cell phenotype, specifically the identified knockout targets and overexpression targets can cooperatively force carbon flux towards malonyl-CoA.About:
This article is published in Metabolic Engineering.The article was published on 2011-09-01. It has received 304 citations till now.read more
Citations
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Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods
TL;DR: This work describes a phylogeny of COBRA methods that has rapidly evolved from the few early methods, such as flux balance analysis and elementary flux mode analysis, into a repertoire of more than 100 methods, including antibiotic discovery, metabolic engineering and modelling of microbial community behaviour.
Journal ArticleDOI
Improving fatty acids production by engineering dynamic pathway regulation and metabolic control
TL;DR: A genetically encoded metabolic switch that enables dynamic regulation of fatty acids (FA) biosynthesis in Escherichia coli was reported, able to dynamically compensate the critical enzymes involved in the supply and consumption of malonyl-CoA and efficiently redirect carbon flux toward FA biosynthesis.
Journal ArticleDOI
Modular optimization of multi-gene pathways for fatty acids production in E. coli
Peng Xu,Qin Gu,Wenya Wang,Wenya Wang,Lynn Wong,Adam G.W. Bower,Cynthia H. Collins,Mattheos A. G. Koffas +7 more
TL;DR: A modular engineering approach was systematically removed metabolic pathway bottlenecks and led to significant titre improvements in a multi-gene fatty acid metabolic pathway to demonstrate a generalized approach to engineering cell factories for valuable metabolites production.
Journal ArticleDOI
Genome‐scale engineering for systems and synthetic biology
TL;DR: Current technologies and methodologies for genome‐scale engineering are reviewed, the prospects for extending efficient genome modification to new hosts are discussed, and the implications of continued advances toward the development of flexibly programmable chasses, novel biochemistries, and safer organismal and ecological engineering are explored.
Journal ArticleDOI
ATP drives direct photosynthetic production of 1-butanol in cyanobacteria
Ethan I. Lan,James C. Liao +1 more
TL;DR: It is shown that artificially engineered ATP consumption through a pathway modification can drive this reaction forward and enables for the first time the direct photosynthetic production of 1-butanol from cyanobacteria Synechococcus elongatus PCC 7942.
References
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One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products
TL;DR: A simple and highly efficient method to disrupt chromosomal genes in Escherichia coli in which PCR primers provide the homology to the targeted gene(s), which should be widely useful, especially in genome analysis of E. coli and other bacteria.
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Flavonoid Biosynthesis. A Colorful Model for Genetics, Biochemistry, Cell Biology, and Biotechnology
TL;DR: The role of flavonoids as the major red, blue, and purple pigments in plants has gained these secondary products a great deal of attention over the years.
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Natural Products in Drug Discovery and Development
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A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information.
Adam M. Feist,Christopher S. Henry,Jennifer L. Reed,Markus Krummenacker,Andrew R. Joyce,Peter D. Karp,Linda J. Broadbelt,Vassily Hatzimanikatis,Bernhard O. Palsson +8 more
TL;DR: An updated genome‐scale reconstruction of the metabolic network in Escherichia coli K‐12 MG1655 with increased scope and computational capability is presented, expected to broaden the spectrum of both basic biology and applied systems biology studies of E. coli metabolism.
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Analysis of optimality in natural and perturbed metabolic networks
TL;DR: The method of minimization of metabolic adjustment (MOMA), whereby the hypothesis that knockout metabolic fluxes undergo a minimal redistribution with respect to the flux configuration of the wild type is tested, is tested and found to be useful in understanding the evolutionary optimization of metabolism.