Cofactor engineering for advancing chemical biotechnology

Bera, 2011, A genetic overhaul of Saccharomyces cerevisiae 424A(LNH-ST) to improve xylose fermentation, J Ind Microbiol Biotechnol, 38, 617, 10.1007/s10295-010-0806-6 Guo, 2011, Minimization of glycerol synthesis in industrial ethanol yeast without influencing its fermentation performance, Metab Eng, 13, 49, 10.1016/j.ymben.2010.11.003 Guo, 2011, Improving ethanol productivity by modification of glycolytic redox factor generation in glycerol-3-phosphate dehydrogenase mutants of an industrial ethanol yeast, J Ind Microbiol Biotechnol, 38, 935, 10.1007/s10295-010-0864-9 Hector, 2011, Saccharomyces cerevisiae engineered for xylose metabolism requires gluconeogenesis and the oxidative branch of the pentose phosphate pathway for aerobic xylose assimilation, Yeast, 28, 645, 10.1002/yea.1893 Kim, 2012, Effects of deletion of glycerol-3-phosphate dehydrogenase and glutamate dehydrogenase genes on glycerol and ethanol metabolism in recombinant Saccharomyces cerevisiae, Bioprocess Biosyst Eng, 35, 49, 10.1007/s00449-011-0590-3 Tamakawa, 2011, Ethanol production from xylose by a recombinant Candida utilis strain expressing protein-engineered xylose reductase and xylitol dehydrogenase, Biosci Biotechnol Biochem, 75, 1994, 10.1271/bbb.110426 Zhang, 2012, Decreased xylitol formation during xylose fermentation in Saccharomyces cerevisiae due to overexpression of water-forming NADH oxidase, Appl Environ Microbiol, 78, 1081, 10.1128/AEM.06635-11 Shen, 2011, Driving forces enable high-titer anaerobic 1-butanol synthesis in Escherichia coli, Appl Environ Microbiol, 77, 2905, 10.1128/AEM.03034-10 Bell, 2010, Protein recognition in ferredoxin-P450 electron transfer in the class I CYP199A2 system from Rhodopseudomonas palustris, J Biol Inorg Chem, 15, 315, 10.1007/s00775-009-0604-7 Kim, 2009, Tricistronic overexpression of cytochrome P450cam, putidaredoxin, and putidaredoxin reductase provides a useful cell-based catalytic system, Biotechnol Lett, 31, 1427, 10.1007/s10529-009-0016-3 Pham, 2013, Engineering of recombinant E. coli cells co-expressing P450pyrTM monooxygenase and glucose dehydrogenase for highly regio- and stereoselective hydroxylation of alicycles with cofactor recycling, Biotechnol Bioeng, 110, 363, 10.1002/bit.24632 Wang, 2012, Nanotube-supported bioproduction of 4-hydroxy-2-butanone via in situ cofactor regeneration, Appl Microbiol Biotechnol, 94, 1233, 10.1007/s00253-011-3699-z Xiao, 2010, A novel whole-cell biocatalyst with NAD+ regeneration for production of chiral chemicals, PLoS One, 5, e8860, 10.1371/journal.pone.0008860 Celton, 2012, A constraint-based model analysis of the metabolic consequences of increased NADPH oxidation in Saccharomyces cerevisiae, Metab Eng, 14, 366, 10.1016/j.ymben.2012.03.008 Celton, 2012, A comparative transcriptomic, fluxomic and metabolomic analysis of the response of Saccharomyces cerevisiae to increases in NADPH oxidation, BMC Genomics, 13, 317, 10.1186/1471-2164-13-317 Ghosh, 2011, Genome-scale consequences of cofactor balancing in engineered pentose utilization pathways in Saccharomyces cerevisiae, PLoS One, 6, e27316, 10.1371/journal.pone.0027316 Trinh, 2012, Elucidating and reprogramming Escherichia coli metabolisms for obligate anaerobic n-butanol and isobutanol production, Appl Microbiol Biotechnol, 95, 1083, 10.1007/s00253-012-4197-7 Agapakis, 2010, Modular electron transfer circuits for synthetic biology: insulation of an engineered biohydrogen pathway, Bioeng Bugs, 1, 413, 10.4161/bbug.1.6.12462 Bastian, 2011, Engineered ketol-acid reductoisomerase and alcohol dehydrogenase enable anaerobic 2-methylpropan-1-ol production at theoretical yield in Escherichia coli, Metab Eng, 13, 345, 10.1016/j.ymben.2011.02.004 Hoelsch, 2013, Engineering of formate dehydrogenase: synergistic effect of mutations affecting cofactor specificity and chemical stability, Appl Microbiol Biotechnol, 97, 2473, 10.1007/s00253-012-4142-9 Liu, 2012, Structure-guided engineering of Lactococcus lactis alcohol dehydrogenase LlAdhA for improved conversion of isobutyraldehyde to isobutanol, J Biotechnol, 164, 188, 10.1016/j.jbiotec.2012.08.008 Ma, 2010, Relaxing the coenzyme specificity of 1, 3-propanediol oxidoreductase from Klebsiella pneumoniae by rational design, J Biotechnol, 146, 173, 10.1016/j.jbiotec.2010.02.005 Paladini, 2009, Induced fit and equilibrium dynamics for high catalytic efficiency in ferredoxin-NADP(H) reductases, Biochemistry, 48, 5760, 10.1021/bi9004232 Lovley, 2012, Electromicrobiology, Annu Rev Microbiol, 66, 391, 10.1146/annurev-micro-092611-150104 Lan, 2012, Microbial synthesis of n-butanol, isobutanol, and other higher alcohols from diverse resources, Bioresour Technol Sieber, 2012, Genomic insights into syntrophy: the paradigm for anaerobic metabolic cooperation, Annu Rev Microbiol, 66, 429, 10.1146/annurev-micro-090110-102844 Cai, 2013, Analysis of redox responses during TNT transformation by Clostridium acetobutylicum ATCC 824 and mutants exhibiting altered metabolism, Appl Microbiol Biotechnol, 10.1007/s00253-012-4253-3 Choi, 2012, Butyrate production enhancement by Clostridium tyrobutyricum using electron mediators and a cathodic electron donor, Biotechnol Bioeng, 109, 2494, 10.1002/bit.24520 Li, 2012, Effect of ribose, xylose, aspartic acid, glutamine and nicotinic acid on ethyl (S)-4-chloro-3-hydroxybutanoate synthesis by recombinant Escherichia coli, Bioresour Technol, 118, 572, 10.1016/j.biortech.2012.02.102 Baroni, 2012, A single tyrosine hydroxyl group almost entirely controls the NADPH specificity of Plasmodium falciparum ferredoxin-NADP+ reductase, Biochemistry, 51, 3819, 10.1021/bi300078p Komori, 2010, Crystal structure analysis of Bacillus subtilis ferredoxin-NADP(+) oxidoreductase and the structural basis for its substrate selectivity, Protein Sci, 19, 2279, 10.1002/pro.508 Muraki, 2010, Asymmetric dimeric structure of ferredoxin-NAD(P)+ oxidoreductase from the green sulfur bacterium Chlorobaculum tepidum: implications for binding ferredoxin and NADP+, J Mol Biol, 401, 403, 10.1016/j.jmb.2010.06.024 Poehlein, 2012, An ancient pathway combining carbon dioxide fixation with the generation and utilization of a sodium ion gradient for ATP synthesis, PLoS One, 7, e33439, 10.1371/journal.pone.0033439 Schut, 2009, The iron-hydrogenase of Thermotoga maritima utilizes ferredoxin and NADH synergistically: a new perspective on anaerobic hydrogen production, J Bacteriol, 191, 4451, 10.1128/JB.01582-08 Buckel, 2013, Energy conservation via electron bifurcating ferredoxin reduction and proton/Na(+) translocating ferredoxin oxidation, Biochim Biophys Acta, 1827, 94, 10.1016/j.bbabio.2012.07.002 Wang, 2010, NADP+ reduction with reduced ferredoxin and NADP+ reduction with NADH are coupled via an electron-bifurcating enzyme complex in Clostridium kluyveri, J Bacteriol, 192, 5115, 10.1128/JB.00612-10 Delebecque, 2011, Organization of intracellular reactions with rationally designed RNA assemblies, Science, 333, 470, 10.1126/science.1206938 Gao, 2012, Characterization of H2O-forming NADH oxidase from Streptococcus pyogenes and its application in l-rare sugar production, Bioorg Med Chem Lett, 22, 1931, 10.1016/j.bmcl.2012.01.049 Guo, 2012, Fine tuning of the lactate and diacetyl production through promoter engineering in Lactococcus lactis, PLoS One, 7, e36296, 10.1371/journal.pone.0036296 Pain, 2010, Mitochondrial NADH kinase, Pos5p, is required for efficient iron-sulfur cluster biogenesis in Saccharomyces cerevisiae, J Biol Chem, 285, 39409, 10.1074/jbc.M110.178947 Shi, 2011, Role of mitochondrial NADH kinase and NADPH supply in the respiratory chain activity of Saccharomyces cerevisiae, Acta Biochim Biophys Sin, 43, 989, 10.1093/abbs/gmr092 Hou, 2009, Impact of overexpressing NADH kinase on glucose and xylose metabolism in recombinant xylose-utilizing Saccharomyces cerevisiae, Appl Microbiol Biotechnol, 82, 909, 10.1007/s00253-009-1900-4 Hou, 2009, Metabolic impact of redox cofactor perturbations in Saccharomyces cerevisiae, Metab Eng, 11, 253, 10.1016/j.ymben.2009.05.001 Lee, 2013, Effects of NADH kinase on NADPH-dependent biotransformation processes in Escherichia coli, Appl Microbiol Biotechnol, 97, 1561, 10.1007/s00253-012-4431-3 Lindner, 2010, Polyphosphate/ATP-dependent NAD kinase of Corynebacterium glutamicum: biochemical properties and impact of ppnK overexpression on lysine production, Appl Microbiol Biotechnol, 87, 583, 10.1007/s00253-010-2481-y Takeno, 2010, Engineering of Corynebacterium glutamicum with an NADPH-generating glycolytic pathway for l-lysine production, Appl Environ Microbiol, 76, 7154, 10.1128/AEM.01464-10 Chin, 2011, Improved NADPH supply for xylitol production by engineered Escherichia coli with glycolytic mutations, Biotechnol Prog, 27, 333, 10.1002/btpr.559 Kim, 2011, Engineering the pentose phosphate pathway to improve hydrogen yield in recombinant Escherichia coli, Biotechnol Bioeng, 108, 2941, 10.1002/bit.23259 Siedler, 2012, Engineering yield and rate of reductive biotransformation in Escherichia coli by partial cyclization of the pentose phosphate pathway and PTS-independent glucose transport, Appl Microbiol Biotechnol, 93, 1459, 10.1007/s00253-011-3626-3 Siedler, 2011, Increased NADPH availability in Escherichia coli: improvement of the product per glucose ratio in reductive whole-cell biotransformation, Appl Microbiol Biotechnol, 92, 929, 10.1007/s00253-011-3374-4 Chin, 2011, Improved NADPH supply for xylitol production by engineered Escherichia coli with glycolytic mutations, Biotechnol Progr, 27, 333, 10.1002/btpr.559 Wang, 2013, Improvement of NADPH Bioavailability in Escherichia coli through the use of phosphofructokinase deficient strains, Appl Microbiol Biotechnol, 97, 6883, 10.1007/s00253-013-4859-0 Akinterinwa, 2011, Anaerobic obligatory xylitol production in Escherichia coli strains devoid of native fermentation pathways, Appl Environ Microbiol, 77, 706, 10.1128/AEM.01890-10 Rathnasingh, 2012, Production of 3-hydroxypropionic acid via malonyl-CoA pathway using recombinant Escherichia coli strains, J Biotechnol, 157, 633, 10.1016/j.jbiotec.2011.06.008 Blombach, 2011, Corynebacterium glutamicum tailored for efficient isobutanol production, Appl Environ Microbiol, 77, 3300, 10.1128/AEM.02972-10 Bartek, 2011, Comparative 13C metabolic flux analysis of pyruvate dehydrogenase complex-deficient, l-valine-producing Corynebacterium glutamicum, Appl Environ Microbiol, 77, 6644, 10.1128/AEM.00575-11 Ma, 2010, Relaxing the coenzyme specificity of 1,3-propanediol oxidoreductase from Klebsiella pneumoniae by rational design, J Biotechnol, 146, 173, 10.1016/j.jbiotec.2010.02.005 Lan, 2012, ATP drives direct photosynthetic production of 1-butanol in cyanobacteria, Proc Natl Acad Sci U S A, 109, 6018, 10.1073/pnas.1200074109 Lee, 2010, High NADPH/NADP+ ratio improves thymidine production by a metabolically engineered Escherichia coli strain, J Biotechnol, 149, 24, 10.1016/j.jbiotec.2010.06.011 Saha, 2011, Biotechnological production of mannitol and its applications, Appl Microbiol Biotechnol, 89, 879, 10.1007/s00253-010-2979-3 Lo Piccolo, 2011, Involvement of an alkane hydroxylase system of Gordonia sp. strain SoCg in degradation of solid n-alkanes, Appl Environ Microbiol, 77, 1204, 10.1128/AEM.02180-10 Wang, 2011, Biohydrogenation from biomass sugar mediated by in vitro synthetic enzymatic pathways, Chem Biol, 18, 372, 10.1016/j.chembiol.2010.12.019 Jan J, Martinez I, Wang Y, Bennett GN, San K-Y: The title and authors are Metabolic Engineering and Transhydrogenase Effects on NADPH Availability in Escherichia coli. unpublished data.