Systems metabolic engineering strategies for the production of amino acids

Lee, 2015, Systems strategies for developing industrial microbial strains, Nat Biotech, 33, 1061, 10.1038/nbt.3365 Lee, 2011, Systems metabolic engineering for chemicals and materials, Trends Biotechnol, 29, 370, 10.1016/j.tibtech.2011.04.001 Chubukov, 2016, Synthetic and systems biology for microbial production of commodity chemicals, Npj Syst Biol Appl, 2, 16009, 10.1038/npjsba.2016.9 Soyer, 2013, Evolutionary systems biology: what it is and why it matters, BioEssays, 35, 696, 10.1002/bies.201300029 Bassalo, 2016, Directed evolution and synthetic biology applications to microbial systems, Curr Opin Biotech, 39, 126, 10.1016/j.copbio.2016.03.016 Eggeling, 2015, A giant market and a powerful metabolism: l-lysine provided by Corynebacterium glutamicum, Appl Microbiol Biot, 99, 3387, 10.1007/s00253-015-6508-2 Lee, 2012, Systems metabolic engineering of microorganisms for natural and non-natural chemicals, Nat Chem Biol, 8, 536, 10.1038/nchembio.970 Lindner, 2011, Phosphotransferase system-independent glucose utilization in Corynebacterium glutamicum by inositol permeases and glucokinases, Appl Environ Microb, 77, 3571, 10.1128/AEM.02713-10 Chen, 1997, Comparative studies of Escherichia coli strains using different glucose uptake systems: metabolism and energetics, Biotechnol Bioeng, 56, 583, 10.1002/(SICI)1097-0290(19971205)56:5<583::AID-BIT12>3.0.CO;2-D Tatarko, 2001, Disruption of a global regulatory gene to enhance central carbon flux into phenylalanine biosynthesis in Escherichia coli, Curr Microbiol, 43, 26, 10.1007/s002840010255 Engels, 2007, The DeoR-type regulator SugR represses expression of ptsG in Corynebacterium glutamicum, J Bacteriol, 189, 2955, 10.1128/JB.01596-06 Krause, 2010, Increased glucose utilization in Corynebacterium glutamicum by use of maltose, and its application for the improvement of l-valine productivity, Appl Environ Microb, 76, 370, 10.1128/AEM.01553-09 Henrich, 2013, Maltose uptake by the novel ABC transport system MusEFGK2I causes increased expression of ptsG in Corynebacterium glutamicum, J Bacteriol, 195, 2573, 10.1128/JB.01629-12 Aristidou, 2000, Metabolic engineering applications to renewable resource utilization, Curr Opin Biotech, 11, 187, 10.1016/S0958-1669(00)00085-9 Jarmander, 2014, Simultaneous uptake of lignocellulose-based monosaccharides by Escherichia coli, Biotechnol Bioeng, 111, 1108, 10.1002/bit.25182 Kawaguchi, 2006, Engineering of a xylose metabolic pathway in Corynebacterium glutamicum, Appl Environ Microb, 72, 3418, 10.1128/AEM.72.5.3418-3428.2006 Meiswinkel, 2013, Accelerated pentose utilization by Corynebacterium glutamicum for accelerated production of lysine, glutamate, ornithine and putrescine, Microb Biotechnol, 6, 131, 10.1111/1751-7915.12001 Kang, 2014, Synthetic biology platform of CoryneBrick vectors for gene expression in Corynebacterium glutamicum and its application to xylose utilization, Appl Microbiol Biot, 98, 5991, 10.1007/s00253-014-5714-7 Jo, 2017, Modular pathway engineering of Corynebacterium glutamicum to improve xylose utilization and succinate production, J Biotechnol, 10.1016/j.jbiotec.2017.01.015 Qin, 2015, Metabolic engineering of Corynebacterium glutamicum strain ATCC13032 to produce l-methionine, Biotechnol Appl Biochem, 62, 563, 10.1002/bab.1290 Hasegawa, 2013, Engineering of Corynebacterium glutamicum for high-yield l-valine production under oxygen deprivation conditions, Appl Environ Microb, 79, 1250, 10.1128/AEM.02806-12 Zhu, 2015, l-Serine overproduction with minimization of by-product synthesis by engineered Corynebacterium glutamicum, Appl Microbiol Biot, 99, 1665, 10.1007/s00253-014-6243-0 Dong, 2016, Attenuating l-lysine production by deletion of ddh and lysE and their effect on l-threonine and l-isoleucine production in Corynebacterium glutamicum, Enzyme Microb Tech, 93–94, 70, 10.1016/j.enzmictec.2016.07.013 Vogt, 2015, The contest for precursors: channelling l-isoleucine synthesis in Corynebacterium glutamicum without byproduct formation, Appl Microbiol Biot, 99, 791, 10.1007/s00253-014-6109-5 Guo, 2015, Analysis of acetohydroxyacid synthase variants from branched-chain amino acids-producing strains and their effects on the synthesis of branched-chain amino acids in Corynebacterium glutamicum, Protein Expres Purif, 109, 106, 10.1016/j.pep.2015.02.006 Chen, 2014, Deregulation of feedback inhibition of phosphoenolpyruvate carboxylase for improved lysine production in Corynebacterium glutamicum, Appl Environ Microb, 80, 1388, 10.1128/AEM.03535-13 Vogt, 2014, Pushing product formation to its limit: metabolic engineering of Corynebacterium glutamicum for L-leucine overproduction, Metab Eng, 22, 40, 10.1016/j.ymben.2013.12.001 Kalinowski, 2003, The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of l-aspartate-derived amino acids and vitamins, J Biotechnol, 104, 5, 10.1016/S0168-1656(03)00154-8 Simic, 2001, L-Threonine export: use of peptides to identify a new translocator from Corynebacterium glutamicum, J Biotechnol, 183, 5317 Lubitz, 2016, Roles of export genes cgmA and lysE for the production of l-arginine and l-citrulline by Corynebacterium glutamicum, Appl Microbiol Biot, 100, 8465, 10.1007/s00253-016-7695-1 Yin, 2013, Increasing l-isoleucine production in Corynebacterium glutamicum by overexpressing global regulator Lrp and two-component export system BrnFE, J Appl Microbiol, 114, 1369, 10.1111/jam.12141 Chen, 2015, Metabolic engineering of Corynebacterium glutamicum ATCC13869 for l-valine production, Metab Eng, 29, 66, 10.1016/j.ymben.2015.03.004 Xie, 2012, Effect of transport proteins on l-isoleucine production with the l-isoleucine-producing strain Corynebacterium glutamicum YILW, J Ind Microbiol Biot, 39, 1549, 10.1007/s10295-012-1155-4 Huang, 2017, Cofactor recycling for co-production of 1,3-propanediol and glutamate by metabolically engineered Corynebacterium glutamicum, Sci Rep, 7, 42246, 10.1038/srep42246 Li, 2016, Metabolic engineering of Corynebacterium glutamicum for methionine production by removing feedback inhibition and increasing NADPH level, Ant Leeuw, 109, 1185, 10.1007/s10482-016-0719-0 Xu, 2016, Enhanced succinic acid production in Corynebacterium glutamicum with increasing the available NADH supply and glucose consumption rate by decreasing H+-ATPase activity, Biotechnol Lett, 38, 1181, 10.1007/s10529-016-2093-4 Wang, 2016, Elucidation of the regulatory role of the fructose operon reveals a novel target for enhancing the NADPH supply in Corynebacterium glutamicum, Metab Eng, 38, 344, 10.1016/j.ymben.2016.08.004 Bommareddy, 2014, A de novo NADPH generation pathway for improving lysine production of Corynebacterium glutamicum by rational design of the coenzyme specificity of glyceraldehyde 3-phosphate dehydrogenase, Metab Eng, 25, 30, 10.1016/j.ymben.2014.06.005 Park, 2007, Metabolic engineering of Escherichia coli for the production of L-valine based on transcriptome analysis and in silico gene knockout simulation, P Natl Acad Sci, 104, 7797, 10.1073/pnas.0702609104 Lee, 2007, Systems metabolic engineering of Escherichia coli for L-threonine production, Mol Syst Biol, 3, 2025, 10.1038/msb4100196 Krömer, 2004, In-depth profiling of lysine-producing Corynebacterium glutamicum by combined analysis of the transcriptome, metabolome, and fluxome, J Bacteriol, 186, 1769, 10.1128/JB.186.6.1769-1784.2004 Buchinger, 2009, A combination of metabolome and transcriptome analyses reveals new targets of the Corynebacterium glutamicum nitrogen regulator AmtR, J Biotechnol, 140, 68, 10.1016/j.jbiotec.2008.10.009 Ohnishi, 2002, A novel methodology employing Corynebacterium glutamicum genome information to generate a new L-lysine-producing mutant, Appl Microbiol Biot, 58, 217, 10.1007/s00253-001-0883-6 Toya, 2013, Flux analysis and metabolomics for systematic metabolic engineering of microorganisms, Biotechnol Adv, 31, 818, 10.1016/j.biotechadv.2013.05.002 Park, 2009, Constraints-based genome-scale metabolic simulation for systems metabolic engineering, Biotechnol Adv, 27, 979, 10.1016/j.biotechadv.2009.05.019 Nguyen, 2015, Fermentative production of the diamine putrescine: system metabolic engineering of Corynebacterium glutamicum, Metabolites, 5, 211, 10.3390/metabo5020211 Shlomi, 2005, Regulatory on/off minimization of metabolic flux changes after genetic perturbations, P Natl Acad Sci, 102, 7695, 10.1073/pnas.0406346102 Kim, 2008, Metabolic flux analysis and metabolic engineering of microorganisms, Mol Biosyst, 4, 113, 10.1039/B712395G Zhang, 2011, Biosensors and their applications in microbial metabolic engineering, Trends Microbiol, 19, 323, 10.1016/j.tim.2011.05.003 Binder, 2013, Recombineering in Corynebacterium glutamicum combined with optical nanosensors: a general strategy for fast producer strain generation, Nucleic Acids Res, 41, 6360, 10.1093/nar/gkt312 Liu, 2015, Applications and advances of metabolite biosensors for metabolic engineering, Metab Eng, 31, 35, 10.1016/j.ymben.2015.06.008 Williams, 2016, Synthetic evolution of metabolic productivity using biosensors, Trends Biotechnol, 34, 371, 10.1016/j.tibtech.2016.02.002 Mahr, 2015, Biosensor-driven adaptive laboratory evolution of l-valine production in Corynebacterium glutamicum, Metab Eng, 32, 184, 10.1016/j.ymben.2015.09.017 Binder, 2012, A high-throughput approach to identify genomic variants of bacterial metabolite producers at the single-cell level, Genome Biol, 13, R40, 10.1186/gb-2012-13-5-r40 Eggeling, 2015, Novel screening methods—biosensors, Curr Opin Biotech, 35, 30, 10.1016/j.copbio.2014.12.021 Mustafi, 2012, The development and application of a single-cell biosensor for the detection of l -methionine and branched-chain amino acids, Metab Eng, 14, 449, 10.1016/j.ymben.2012.02.002 Becker J, Gießelmann G, Hoffmann, SL, Wittmann C. Corynebacterium glutamicum for sustainable bioproduction: from metabolic physiology to systems metabolic engineering. Springer Berlin Heidelberg: Berlin, Heidelberg. 1–47. Nakamura, 2007, Mutations of the Corynebacterium glutamicum NCgl1221 gene, encoding a mechanosensitive channel homolog, induce l-glutamic acid production, Appl Environ Microb, 73, 4491, 10.1128/AEM.02446-06 Asakura, 2007, Altered metabolic flux due to deletion of odhA causes L-glutamate overproduction in Corynebacterium glutamicum, Appl Environ Microbiol, 73, 1308, 10.1128/AEM.01867-06 Radmacher, 2005, Ethambutol, a cell wall inhibitor of Mycobacterium tuberculosis, elicits L-glutamate efflux of Corynebacterium glutamicum, Microbiology, 151, 1359, 10.1099/mic.0.27804-0 Hoischen, 1990, Membrane alteration is necessary but not sufficient for effective glutamate secretion in Corynebacterium glutamicum, J Bacteriol, 172, 3409, 10.1128/jb.172.6.3409-3416.1990 Bokas, 2007, Cell envelope fluidity modification for an effective glutamate excretion in Corynebacterium glutamicum 2262, Appl Microbiol Biot, 76, 773, 10.1007/s00253-007-1046-1 Becker, 2013, Glutamate efflux mediated by Corynebacterium glutamicum MscCG, Escherichia coli MscS, and their derivatives, BBA-Biomembranes, 1828, 1230, 10.1016/j.bbamem.2013.01.001 Bayan, 2003, Mycomembrane and S-layer: two important structures of Corynebacterium glutamicum cell envelope with promising biotechnology applications, J Biotechnol, 104, 55, 10.1016/S0168-1656(03)00163-9 Wada, 2016, Effects of phosphoenolpyruvate carboxylase desensitization on glutamic acid production in Corynebacterium glutamicum ATCC 13032, J Biosci Bioeng, 121, 172, 10.1016/j.jbiosc.2015.06.008 Shirai, 2007, Study on roles of anaplerotic pathways in glutamate overproduction of Corynebacterium glutamicum by metabolic flux analysis, Microb Cell Fact, 6, 19, 10.1186/1475-2859-6-19 Guo, 2013, Enhancing the supply of oxaloacetate for l-glutamate production by pyc overexpression in different Corynebacterium glutamicum, Biotechnol Lett, 35, 943, 10.1007/s10529-013-1241-3 Delaunay, 1999, Importance of phosphoenolpyruvate carboxylase of Corynebacterium glutamicum during the temperature triggered glutamic acid fermentation, Metab Eng, 1, 334, 10.1006/mben.1999.0131 Becker, 2011, From zero to hero—design-based systems metabolic engineering of Corynebacterium glutamicum for L-lysine production, Metab Eng, 13, 159, 10.1016/j.ymben.2011.01.003 Ning, 2016, Pathway construction and metabolic engineering for fermentative production of ectoine in Escherichia coli, Metab Eng, 36, 10, 10.1016/j.ymben.2016.02.013 Zhang, 2016, Production of α-ketobutyrate using engineered Escherichia coli via temperature shift, Biotechnol Bioeng, 113, 2054, 10.1002/bit.25959 Chen, 2017, Rational design and metabolic analysis of Escherichia coli for effective production of L-tryptophan at high concentration, Appl Microbiol Biot, 101, 559, 10.1007/s00253-016-7772-5