ESCHERICHIA COLI REDOX MUTANTS AS MICROBIAL CELL FACTORIES FOR THE SYNTHESIS OF REDUCED BIOCHEMICALS

Verlinden, 2007, Bacterial synthesis of biodegradable polyhydroxyalkanoates, J Appl Microbiol, 102, 1437, 10.1111/j.1365-2672.2007.03335.x Gomez, 2012, Making green polymers even greener: towards sustainable production of polyhydroxyalkanoates from agroindustrial by-products, 41 Clomburg, 2010, Biofuel production in Escherichia coli: the role of metabolic engineering and synthetic biology, Appl Microbiol Biotechnol, 86, 419, 10.1007/s00253-010-2446-1 Geddes, 2011, Advances in ethanol production, Curr Opin Biotechnol, 22, 312, 10.1016/j.copbio.2011.04.012 Biebl, 1999, Microbial production of 1,3-propanediol, Appl Microbiol Biotechnol, 52, 289, 10.1007/s002530051523 Kaur, 2012, Advances in biotechnological production of 1,3-propanediol, Biochem Eng J, 64, 106, 10.1016/j.bej.2012.03.002 Thakker, 2012, Succinate production in Escherichia coli, Biotechnol J, 7, 213, 10.1002/biot.201100061 Okano, 2010, Biotechnological production of enantiomeric pure lactic acid from renewable resources: recent achievements, perspectives, and limits, Appl Microbiol Biotechnol, 85, 413, 10.1007/s00253-009-2280-5 Vickers, 2012, Examining the feasibility of bulk commodity production in Escherichia coli, Biotechnol Lett, 34, 585, 10.1007/s10529-011-0821-3 Gottschalk, 1986 Guest, 1989, Structure, expression, and protein engineering of the pyruvate dehydrogenase complex of Escherichia coli, Ann N Y Acad Sci, 573, 76, 10.1111/j.1749-6632.1989.tb14988.x Mattevi, 1992, Atomic structure of the cubic core of the pyruvate dehydrogenase multienzyme complex, Science, 255, 1544, 10.1126/science.1549782 Patschkowski, 2000, Mechanisms for sensing and responding to oxygen deprivation, 61 Unden, 1997, Alternative respiratory pathways of Escherichia coli: energetics and transcriptional regulation in response to electron acceptors, Biochim Biophys Acta, 1320, 217, 10.1016/S0005-2728(97)00034-0 Gunsalus, 1992, Control of electron flow in Escherichia coli: coordinated transcription of respiratory pathway genes, J Bacteriol, 174, 7069, 10.1128/jb.174.22.7069-7074.1992 Cavicchioli, 1996, Role of the periplasmic domain of the Escherichia coli NarX sensor-transmitter protein in nitrate-dependent signal transduction and gene regulation, Mol Microbiol, 21, 901, 10.1046/j.1365-2958.1996.491422.x Iuchi, 1996, Cellular and molecular physiology of Escherichia coli in the adaptation to aerobic environments, J Biochem, 120, 1055, 10.1093/oxfordjournals.jbchem.a021519 Becker, 1997, Regulatory O2 tensions for the synthesis of fermentation products in Escherichia coli and relation to aerobic respiration, Arch Microbiol, 168, 290, 10.1007/s002030050501 Clark, 1989, The fermentation pathways of Escherichia coli, FEMS Microbiol Rev, 5, 223 Böck, 1996, Fermentation, vol. 1, 262 de Graef, 1999, The steady-state internal redox state (NADH/NAD) reflects the external redox state and is correlated with catabolic adaptation in Escherichia coli, J Bacteriol, 181, 2351, 10.1128/JB.181.8.2351-2357.1999 Murarka, 2010, Metabolic analysis of wild-type Escherichia coli and a pyruvate dehydrogenase complex (PDHC)-deficient derivative reveals the role of PDHC in the fermentative metabolism of glucose, J Biol Chem, 285, 31548, 10.1074/jbc.M110.121095 Sawers, 1988, Anaerobic regulation of pyruvate formate-lyase from Escherichia coli K-12, J Bacteriol, 170, 5330, 10.1128/jb.170.11.5330-5336.1988 Sawers, 1989, Transcription initiation at multiple promoters of the pfl gene by Eσ70-dependent transcription in vitro and heterologous expression in Pseudomonas putida in vivo, J Bacteriol, 171, 4930, 10.1128/jb.171.9.4930-4937.1989 Sawers, 1992, Anaerobic induction of pyruvate formate-lyase gene expression is mediated by the ArcA and FNR proteins, J Bacteriol, 174, 3474, 10.1128/jb.174.11.3474-3478.1992 Sawers, 1993, Specific transcriptional requirements for positive regulation of the anaerobically inducible pfl operon by ArcA and FNR, Mol Microbiol, 10, 737, 10.1111/j.1365-2958.1993.tb00944.x Sirko, 1993, Integration host factor is required for anaerobic pyruvate induction of pfl operon expression in Escherichia coli, J Bacteriol, 175, 5769, 10.1128/jb.175.18.5769-5777.1993 Kaiser, 1995, Nitrate repression of the Escherichia coli pfl operon is mediated by the dual sensors NarQ and NarX and the dual regulators NarL and NarP, J Bacteriol, 177, 3647, 10.1128/jb.177.13.3647-3655.1995 Wagner, 1992, The free radical in pyruvate formate-lyase is located on glycine-734, Proc Natl Acad Sci USA, 89, 996, 10.1073/pnas.89.3.996 Alexeeva, 2000, Effects of limited aeration and of the ArcAB system on intermediary pyruvate catabolism in Escherichia coli, J Bacteriol, 182, 4934, 10.1128/JB.182.17.4934-4940.2000 Shalel-Levanon, 2005, Effect of ArcA and FNR on the expression of genes related to the oxygen regulation and the glycolysis pathway in Escherichia coli under microaerobic growth conditions, Biotechnol Bioeng, 92, 147, 10.1002/bit.20583 Birkmann, 1987, Factors affecting transcriptional regulation of the formate-hydrogen-lyase pathway of Escherichia coli, Arch Microbiol, 148, 44, 10.1007/BF00429646 Rossmann, 1991, Mechanism of regulation of the formate-hydrogen lyase pathway by oxygen, nitrate, and pH: definition of the formate regulon, Mol Microbiol, 5, 2807, 10.1111/j.1365-2958.1991.tb01989.x Suppmann, 1994, Isolation and characterization of hypophosphite-resistant mutants of Escherichia coli: identification of the FocA protein, encoded by the pfl operon, as a putative formate transporter, Mol Microbiol, 11, 965, 10.1111/j.1365-2958.1994.tb00375.x Dittrich, 2005, Characterization of the acetate-producing pathways in Escherichia coli, Biotechnol Prog, 21, 1062, 10.1021/bp050073s Garvie, 1980, Bacterial lactate dehydrogenases, Microbiol Rev, 44, 106, 10.1128/MMBR.44.1.106-139.1980 Ashworth, 1966, The anaplerotic fixation of carbon dioxide by Escherichia coli, Proc R Soc Lond B Biol Sci, 165, 179, 10.1098/rspb.1966.0063 Cronan, 1996, Tricarboxylic acid cycle and glyoxylate bypass, vol. 1, 206 Dellomonaco, 2010, Engineered respiro-fermentative metabolism for the production of biofuels and biochemicals from fatty acid-rich feedstocks, Appl Environ Microbiol, 76, 5067, 10.1128/AEM.00046-10 Kim, 2010, Simultaneous consumption of pentose and hexose sugars: an optimal microbial phenotype for efficient fermentation of lignocellulosic biomass, Appl Microbiol Biotechnol, 88, 1077, 10.1007/s00253-010-2839-1 Dellomonaco, 2011, Engineered reversal of the β-oxidation cycle for the synthesis of fuels and chemicals, Nature, 476, 355, 10.1038/nature10333 Jang, 2012, Bio-based production of C2-C6 platform chemicals, Biotechnol Bioeng, 109, 2437, 10.1002/bit.24599 Lee, 2012, Systems metabolic engineering of microorganisms for natural and non-natural chemicals, Nat Chem Biol, 8, 536, 10.1038/nchembio.970 Keseler, 2011, EcoCyc: a comprehensive database of Escherichia coli biology, Nucleic Acids Res, 39, D583, 10.1093/nar/gkq1143 Martínez-Antonio, 2003, Identifying global regulators in transcriptional regulatory networks in bacteria, Curr Opin Microbiol, 6, 482, 10.1016/j.mib.2003.09.002 Unden, 1995, O2-sensing and O2-dependent gene regulation in facultatively anaerobic bacteria, Arch Microbiol, 164, 81 Green, 2004, Bacterial redox sensors, Nat Rev Microbiol, 2, 954, 10.1038/nrmicro1022 Kiley, 1998, Oxygen sensing by the global regulator, FNR: the role of the iron-sulfur cluster, FEMS Microbiol Rev, 22, 341, 10.1111/j.1574-6976.1998.tb00375.x Unden, 2002, Control of FNR function of Escherichia coli by O2 and reducing conditions, J Mol Microbiol Biotechnol, 4, 263 Iuchi, 1988, arcA (dye), a global regulatory gene in Escherichia coli mediating repression of enzymes in aerobic pathways, Proc Natl Acad Sci USA, 85, 1888, 10.1073/pnas.85.6.1888 Lynch, 1996, Responses to molecular oxygen, vol. 1, 1526 Alexeeva, 2003, Requirement of ArcA for redox regulation in Escherichia coli under microaerobic but not anaerobic or aerobic conditions, J Bacteriol, 185, 204, 10.1128/JB.185.1.204-209.2003 Shalel-Levanon, 2005, Effect of oxygen on the Escherichia coli ArcA and FNR regulation systems and metabolic responses, Biotechnol Bioeng, 89, 556, 10.1002/bit.20381 Salmon, 2005, Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcA, J Biol Chem, 280, 15084, 10.1074/jbc.M414030200 Avison, 2001, Escherichia coli CreBC is a global regulator of gene expression that responds to growth in minimal media, J Biol Chem, 276, 26955, 10.1074/jbc.M011186200 Wiechert, 2001, 13C metabolic flux analysis, Metab Eng, 3, 195, 10.1006/mben.2001.0187 Sauer, 2004, High-throughput phenomics: experimental methods for mapping fluxomes, Curr Opin Biotechnol, 15, 58, 10.1016/j.copbio.2003.11.001 Shimizu, 2004, Metabolic flux analysis based on 13C-labeling experiments and integration of the information with gene and protein expression patterns, Adv Biochem Eng Biotechnol, 91, 1 Zamboni, 2009, Novel biological insights through metabolomics and 13C-flux analysis, Curr Opin Microbiol, 12, 553, 10.1016/j.mib.2009.08.003 Perrenoud, 2005, Impact of global transcriptional regulation by ArcA, ArcB, Cra, Crp, Cya, Fnr, and Mlc on glucose catabolism in Escherichia coli, J Bacteriol, 187, 3171, 10.1128/JB.187.9.3171-3179.2005 Zhu, 2006, Effect of the global redox sensing/regulation networks on Escherichia coli and metabolic flux distribution based on C-13 labeling experiments, Metab Eng, 8, 619, 10.1016/j.ymben.2006.07.002 Nikel, 2009, Metabolic flux analysis of Escherichia coli creB and arcA mutants reveals shared control of carbon catabolism under microaerobic growth conditions, J Bacteriol, 191, 5538, 10.1128/JB.00174-09 Yamamoto, 2005, Functional characterization in vitro of all two-component signal transduction systems from Escherichia coli, J Biol Chem, 280, 1448, 10.1074/jbc.M410104200 Groban, 2009, Kinetic buffering of cross talk between bacterial two-component sensors, J Mol Biol, 390, 380, 10.1016/j.jmb.2009.05.007 Rolfe, 2011, Transcript profiling and inference of Escherichia coli K-12 ArcA activity across the range of physiologically relevant oxygen concentrations, J Biol Chem, 286, 10147, 10.1074/jbc.M110.211144 Anderson, 1990, Occurrence, metabolism, metabolic role, and industrial uses of bacterial polyhydroxyalkanoates, Microbiol Rev, 54, 450, 10.1128/MMBR.54.4.450-472.1990 Steinbüchel, 1995, Diversity of bacterial polyhydroxyalkanoic acids, FEMS Microbiol Lett, 128, 219, 10.1016/0378-1097(95)00125-O Keshavarz, 2010, Polyhydroxyalkanoates: bioplastics with a green agenda, Curr Opin Microbiol, 13, 321, 10.1016/j.mib.2010.02.006 Harding, 2007, Environmental analysis of plastic production processes: comparing petroleum-based polypropylene and polyethylene with biologically based poly-β-hydroxybutyric acid using life cycle analysis, J Biotechnol, 130, 57, 10.1016/j.jbiotec.2007.02.012 Pettinari, 2001, Poly(3-hydroxybutyrate) synthesis genes in Azotobacter sp. strain FA8, Appl Environ Microbiol, 67, 5331, 10.1128/AEM.67.11.5331-5334.2001 Nikel, 2006, Poly(3-hydroxybutyrate) synthesis by recombinant Escherichia coli arcA mutants in microaerobiosis, Appl Environ Microbiol, 72, 2614, 10.1128/AEM.72.4.2614-2620.2006 Nikel, 2008, Escherichia coli arcA mutants: metabolic profile characterization of microaerobic cultures using glycerol as a carbon source, J Mol Microbiol Biotechnol, 15, 48, 10.1159/000111992 Nikel, 2010, Redox driven metabolic tuning: carbon source and aeration affect synthesis of poly(3-hydroxybutyrate) in Escherichia coli, Bioeng Bugs, 1, 291, 10.4161/bbug.1.4.12103 Dobson, 2012, Microbial utilization of crude glycerol for the production of value-added products, J Ind Microbiol Biotechnol, 39, 217, 10.1007/s10295-011-1038-0 Pettinari, 2012, Glycerol as a substrate for bioprocesses in different O2 availability conditions, 139 Nikel, 2008, Poly(3-hydroxybutyrate) synthesis from glycerol by a recombinant Escherichia coli arcA mutant in fed-batch microaerobic cultures, Appl Microbiol Biotechnol, 77, 1337, 10.1007/s00253-007-1255-7 Nikel, 2010, Ethanol synthesis from glycerol by Escherichia coli redox mutants expressing adhE from Leuconostoc mesenteroides, J Appl Microbiol, 109, 492, 10.1111/j.1365-2672.2010.04668.x Nikel, 2010, Metabolic selective pressure stabilizes plasmids carrying biosynthetic genes for reduced biochemicals in Escherichia coli redox mutants, Appl Microbiol Biotechnol, 88, 563, 10.1007/s00253-010-2774-1 Theodorou, 2012, Involvement of the AtoSCDAEB regulon in the high molecular weight poly-(R)-3-hydroxybutyrate biosynthesis in phaCAB+ Escherichia coli, Metab Eng, 14, 354, 10.1016/j.ymben.2012.03.010 Pettinari, 1998, trans activation of the Escherichia coli ato structural genes by a regulatory protein from Bacillus megaterium: potential use in polyhydroxyalkanoate production, Appl Microbiol Biotechnol, 49, 737, 10.1007/s002530051240 Wei, 2009, Effect of anaerobic promoters on the microaerobic production of polyhydroxybutyrate (PHB) in recombinant Escherichia coli, Appl Microbiol Biotechnol, 82, 703, 10.1007/s00253-008-1816-4 Wang, 2012, Enhanced co-production of hydrogen and poly-(R)-3-hydroxybutyrate by recombinant PHB producing E. coli over-expressing hydrogenase 3 and acetyl-CoA synthetase, Metab Eng, 14, 496, 10.1016/j.ymben.2012.07.003 Zeng, 2002, Bulk chemicals from biotechnology: the case of 1,3-propanediol production and the new trends, Adv Biochem Eng Biotechnol, 74, 239 Maervoet, 2011, Enhancing the microbial conversion of glycerol to 1,3-propanediol using metabolic engineering, Org Process Res Dev, 15, 189, 10.1021/op1001929 Freund, 1881, Über die Bildung und Darstellung von Trimethylenalkohol aus Glycerin, Monatsheft Für Chimie, 2, 636, 10.1007/BF01516545 Nakamura, 2003, Metabolic engineering for the microbial production of 1,3-propanediol, Curr Opin Biotechnol, 14, 454, 10.1016/j.copbio.2003.08.005 Saxena, 2009, Microbial production of 1,3-propanediol: recent developments and emerging opportunities, Biotechnol Adv, 27, 895, 10.1016/j.biotechadv.2009.07.003 Altaras, 1999, Metabolic engineering of a 1,2-propanediol pathway in Escherichia coli, Appl Environ Microbiol, 65, 1180, 10.1128/AEM.65.3.1180-1185.1999 Zhang, 2009, Introduction of an NADH regeneration system into Klebsiella oxytoca leads to an enhanced oxidative and reductive metabolism of glycerol, Metab Eng, 11, 101, 10.1016/j.ymben.2008.11.001 Tang, 2009, Microbial conversion of glycerol to 1,3-propanediol by an engineered strain of Escherichia coli, Appl Environ Microbiol, 75, 1628, 10.1128/AEM.02376-08 Pettinari, 2008, ArcA redox mutants as a source of reduced bioproducts, J Mol Microbiol Biotechnol, 15, 41, 10.1159/000111991 Cervin MA, Soucaille P, Valle F (2010) Process for the biological production of 1,3-propanediol with high yield. USA Patent US7745184. Jana, 2005, Strategies for efficient production of heterologous proteins in Escherichia coli, Appl Microbiol Biotechnol, 67, 289, 10.1007/s00253-004-1814-0 Waegeman, 2011, Increasing recombinant protein production in Escherichia coli through metabolic and genetic engineering, J Ind Microbiol Biotechnol, 38, 1891, 10.1007/s10295-011-1034-4 Sevastsyanovich, 2010, Sense and nonsense from a systems biology approach to microbial recombinant protein production, Biotechnol Appl Biochem, 55, 9, 10.1042/BA20090174 Gonçalves, 2012, Rational engineering of Escherichia coli strains for plasmid biopharmaceutical manufacturing, Biotechnol J, 7, 251, 10.1002/biot.201100062 Luli, 1990, Comparison of growth, acetate production, and acetate inhibition of Escherichia coli strains in batch and fed-batch fermentations, Appl Environ Microbiol, 56, 1004, 10.1128/AEM.56.4.1004-1011.1990 El-Mansi, 2004, Flux to acetate and lactate excretions in industrial fermentations: physiological and biochemical implications, J Ind Microbiol Biotechnol, 31, 295, 10.1007/s10295-004-0149-2 Andersen, 1980, Are growth rates of Escherichia coli in batch cultures limited by respiration?, J Bacteriol, 144, 114, 10.1128/JB.144.1.114-123.1980 De Mey, 2007, Minimizing acetate formation in E. coli fermentations, J Ind Microbiol Biotechnol, 34, 689, 10.1007/s10295-007-0244-2 Vemuri, 2006, Increased recombinant protein production in Escherichia coli strains with overexpressed water-forming NADH oxidase and a deleted ArcA regulatory protein, Biotechnol Bioeng, 94, 538, 10.1002/bit.20853 Vemuri, 2006, Overflow metabolism in Escherichia coli during steady-state growth: transcriptional regulation and effect of the redox ratio, Appl Environ Microbiol, 72, 3653, 10.1128/AEM.72.5.3653-3661.2006 Waegeman, 2011, Effect of iclR and arcA knockouts on biomass formation and metabolic fluxes in Escherichia coli K12 and its implications on understanding the metabolism of Escherichia coli BL21 (DE3), BMC Microbiol, 11, 70, 10.1186/1471-2180-11-70 Waegeman, 2011, Effect of iclR and arcA deletions on physiology and metabolic fluxes in Escherichia coli BL21 (DE3), Biotechnol Lett, 34, 329, 10.1007/s10529-011-0774-6 Bidart, 2012, Manipulation of the anoxic metabolism in Escherichia coli by ArcB deletion variants in the ArcBA two-component system, Appl Environ Microbiol, 78, 8784, 10.1128/AEM.02558-12 Zhou, 2010, Doubling the catabolic reducing power (NADH) output of Escherichia coli fermentation for production of reduced products, Biotechnol Prog, 26, 45 Martínez, 2008, Replacing Escherichia coli NAD-dependent glyceraldehyde 3-phosphate dehydrogenase (GAPDH) with a NADP-dependent enzyme from Clostridium acetobutylicum facilitates NADPH dependent pathways, Metab Eng, 10, 352, 10.1016/j.ymben.2008.09.001 Zhu, 2011, Manipulating respiratory levels in Escherichia coli for aerobic formation of reduced chemical products, Metab Eng, 13, 704, 10.1016/j.ymben.2011.09.006 Herrgård, 2012, Analyzing the genomic variation of microbial cell factories in the era of “New Biotechnology”, Comput Struct Biotechnol J, 3, e201210012, 10.5936/csbj.201210012 Jouhten, 2012, Metabolic modelling in the development of cell factories by synthetic biology, Comput Struct Biotechnol J, 3, e201210009, 10.5936/csbj.201210009