Metabolic modeling and response surface analysis of an Escherichia coli strain engineered for shikimic acid production

[1]  Jean-Charles Portais,et al.  Plasmid‐encoded biosynthetic genes alleviate metabolic disadvantages while increasing glucose conversion to shikimate in an engineered Escherichia coli strain , 2017, Biotechnology and bioengineering.

[2]  M. Inui,et al.  Metabolic engineering of Corynebacterium glutamicum for shikimate overproduction by growth-arrested cell reaction. , 2016, Metabolic engineering.

[3]  Francisco Bolívar,et al.  Shikimic Acid Production in Escherichia coli: From Classical Metabolic Engineering Strategies to Omics Applied to Improve Its Production , 2015, Front. Bioeng. Biotechnol..

[4]  Edward J. O'Brien,et al.  Computing the functional proteome: recent progress and future prospects for genome-scale models. , 2015, Current opinion in biotechnology.

[5]  M. R. Long,et al.  Computational methods in metabolic engineering for strain design. , 2015, Current opinion in biotechnology.

[6]  R. Burnap Systems and Photosystems: Cellular Limits of Autotrophic Productivity in Cyanobacteria , 2014, Front. Bioeng. Biotechnol..

[7]  C. Maranas,et al.  Recent advances in the reconstruction of metabolic models and integration of omics data. , 2014, Current opinion in biotechnology.

[8]  Marjan De Mey,et al.  Multivariate modular metabolic engineering for pathway and strain optimization. , 2014, Current opinion in biotechnology.

[9]  Francisco Bolivar,et al.  Engineering Escherichia coli to overproduce aromatic amino acids and derived compounds , 2014, Microbial Cell Factories.

[10]  Wei Shen,et al.  Metabolic engineering of Escherichia coli for improving shikimate synthesis from glucose. , 2014, Bioresource technology.

[11]  Stephen S. Fong,et al.  Computational approaches to metabolic engineering utilizing systems biology and synthetic biology , 2014, Computational and structural biotechnology journal.

[12]  Francisco Bolívar,et al.  Current perspectives on applications of shikimic and aminoshikimic acids in pharmaceutical chemistry , 2014 .

[13]  Daniel Machado,et al.  Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism , 2014, PLoS Comput. Biol..

[14]  Jian-Zhong Liu,et al.  Production of shikimic acid from Escherichia coli through chemically inducible chromosomal evolution and cofactor metabolic engineering , 2014, Microbial Cell Factories.

[15]  Ying Li,et al.  Isolation of a novel alkaline-stable lipase from a metagenomic library and its specific application for milkfat flavor production , 2014, Microbial Cell Factories.

[16]  Francisco Bolivar,et al.  Constitutive expression of selected genes from the pentose phosphate and aromatic pathways increases the shikimic acid yield in high-glucose batch cultures of an Escherichia coli strain lacking PTS and pykF , 2013, Microbial Cell Factories.

[17]  H. Orozco,et al.  Genetic manipulation of longevity-related genes as a tool to regulate yeast life span and metabolite production during winemaking , 2013, Microbial Cell Factories.

[18]  Amalia Estévez,et al.  A short overview on the medicinal chemistry of (-)-shikimic acid. , 2012, Mini reviews in medicinal chemistry.

[19]  Saptarshi Ghosh,et al.  Production of shikimic acid. , 2012, Biotechnology advances.

[20]  Christian Baumgartner,et al.  MUMAL: Multivariate analysis in shotgun proteomics using machine learning techniques , 2012, BMC Genomics.

[21]  Paula Jouhten,et al.  Metabolic modelling in the development of cell factories by synthetic biology , 2012, Computational and structural biotechnology journal.

[22]  F. Bolivar,et al.  Genetic changes during a laboratory adaptive evolution process that allowed fast growth in glucose to an Escherichia coli strain lacking the major glucose transport system , 2012, BMC Genomics.

[23]  Sang Yup Lee,et al.  Recent advances in reconstruction and applications of genome-scale metabolic models. , 2012, Current opinion in biotechnology.

[24]  Doraiswami Ramkrishna,et al.  Dynamic models of metabolism: Review of the cybernetic approach , 2012 .

[25]  Doraiswami Ramkrishna,et al.  Prediction of dynamic behavior of mutant strains from limited wild-type data. , 2012, Metabolic engineering.

[26]  Lore Cloots,et al.  Network-based functional modeling of genomics, transcriptomics and metabolism in bacteria. , 2011, Current opinion in microbiology.

[27]  L. Qin,et al.  Illicium verum: a review on its botany, traditional use, chemistry and pharmacology. , 2011, Journal of ethnopharmacology.

[28]  José L. Iborra,et al.  Metabolic adaptation of Escherichia coli to long-term exposure to salt stress , 2010 .

[29]  Guillermo Gosset,et al.  Production of aromatic compounds in bacteria. , 2009, Current opinion in biotechnology.

[30]  J. Liao,et al.  Ensemble Modeling for Aromatic Production in Escherichia coli , 2009, PloS one.

[31]  K. N. Ganeshaiah,et al.  Prospecting for alternate sources of shikimic acid, a precursor of Tamiflu, a bird-flu drug , 2009 .

[32]  D. Ramkrishna,et al.  Reduction of a set of elementary modes using yield analysis , 2009, Biotechnology and bioengineering.

[33]  Dong-Yup Lee,et al.  Exploring the effects of carbon sources on the metabolic capacity for shikimic acid production in Escherichia coli using in silico metabolic predictions. , 2008, Journal of microbiology and biotechnology.

[34]  Jörg Stelling,et al.  Large-scale computation of elementary flux modes with bit pattern trees , 2008, Bioinform..

[35]  Francisco Bolívar,et al.  Acetate Metabolism in Escherichia coli Strains Lacking Phosphoenolpyruvate: Carbohydrate Phosphotransferase System; Evidence of Carbon Recycling Strategies and Futile Cycles , 2008, Journal of Molecular Microbiology and Biotechnology.

[36]  Francisco Bolívar,et al.  Utility of an Escherichia coli strain engineered in the substrate uptake system for improved culture performance at high glucose and cell concentrations: An alternative to fed‐batch cultures , 2008, Biotechnology and bioengineering.

[37]  F. Bolivar,et al.  Coutilization of glucose and glycerol enhances the production of aromatic compounds in an Escherichia coli strain lacking the phosphoenolpyruvate: carbohydrate phosphotransferase system , 2008, Microbial cell factories.

[38]  U. Sauer,et al.  Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli , 2007, Molecular systems biology.

[39]  M. S. Gelfand,et al.  Use of the flux model of amino acid metabolism of Escherichia coli , 2006, Biochemistry (Moscow).

[40]  Alfredo Martínez,et al.  Role of Pyruvate Oxidase in Escherichia coli Strains Lacking the Phosphoenolpyruvate:Carbohydrate Phosphotransferase System , 2005, Journal of Molecular Microbiology and Biotechnology.

[41]  Francisco Bolívar,et al.  Adaptation for fast growth on glucose by differential expression of central carbon metabolism and gal regulon genes in an Escherichia coli strain lacking the phosphoenolpyruvate:carbohydrate phosphotransferase system. , 2005, Metabolic engineering.

[42]  J. Nielsen,et al.  Integration of gene expression data into genome-scale metabolic models. , 2004, Metabolic engineering.

[43]  J. Stelling Mathematical models in microbial systems biology. , 2004, Current opinion in microbiology.

[44]  F. Bolivar,et al.  Metabolic engineering and protein directed evolution increase the yield of L‐phenylalanine synthesized from glucose in Escherichia coli , 2004, Biotechnology and bioengineering.

[45]  M. Araúzo-Bravo,et al.  Effect of a pyruvate kinase (pykF-gene) knockout mutation on the control of gene expression and metabolic fluxes in Escherichia coli. , 2004, FEMS microbiology letters.

[46]  Susan Jones In Brief , 2004, Nature Reviews Microbiology.

[47]  Kiran Raosaheb Patil,et al.  Use of genome-scale microbial models for metabolic engineering. , 2004, Current opinion in biotechnology.

[48]  Kazuyuki Shimizu,et al.  Gene expression patterns for metabolic pathway in pgi knockout Escherichia coli with and without phb genes based on RT-PCR. , 2003, Journal of biotechnology.

[49]  Roel Bovenberg,et al.  Metabolic engineering for microbial production of shikimic acid. , 2003, Metabolic engineering.

[50]  Jason A. Papin,et al.  Genome-scale microbial in silico models: the constraints-based approach. , 2003, Trends in biotechnology.

[51]  A. D. de Graaf,et al.  Analysis of carbon metabolism in Escherichia coli strains with an inactive phosphotransferase system by (13)C labeling and NMR spectroscopy. , 2002, Metabolic Engineering.

[52]  Abhijit Anand Namjoshi,et al.  Multiplicity and stability of steady states in continuous bioreactors: dissection of cybernetic models , 2001 .

[53]  M. Wubbolts,et al.  Metabolic engineering for microbial production of aromatic amino acids and derived compounds. , 2001, Metabolic engineering.

[54]  B O Palsson,et al.  Metabolic modeling of microbial strains in silico. , 2001, Trends in biochemical sciences.

[55]  B. Wanner,et al.  One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[56]  Doraiswami Ramkrishna,et al.  The non-linear analysis of cybernetic models. Guidelines for model formulation , 1999 .

[57]  J. Liao,et al.  Pathway engineering for production of aromatics in Escherichia coli: Confirmation of stoichiometric analysis by independent modulation of AroG, TktA, and Pps activities , 1995, Biotechnology and bioengineering.

[58]  G W Luli,et al.  Comparison of growth, acetate production, and acetate inhibition of Escherichia coli strains in batch and fed-batch fermentations , 1990, Applied and environmental microbiology.

[59]  G. T. Tsao,et al.  Investigation of bacterial growth on mixed substrates: Experimental evaluation of cybernetic models , 1986, Biotechnology and bioengineering.

[60]  Kazuyuki Shimizu,et al.  A New Insight into the Main Metabolic Regulation of Escherichia coli Based on Systems Biology Approach , 2013 .

[61]  Po Ting Chen,et al.  Genomic engineering of Escherichia coli for production of intermediate metabolites in the aromatic pathway , 2011 .

[62]  Kaspar Valgepea,et al.  Specific growth rate dependent transcriptome profiling of Escherichia coli K12 MG1655 in accelerostat cultures. , 2010, Journal of biotechnology.

[63]  Ralph Von Daeniken,et al.  Phosphoenolpyruvate Availability and the Biosynthesis of Shikimic Acid , 2003, Biotechnology progress.

[64]  J. W. Frost,et al.  Modulation of Phosphoenolpyruvate Synthase Expression Increases Shikimate Pathway Product Yields in E. coli , 2002, Biotechnology progress.