Whole-cell biocatalysis utilizes native or recombinant enzymes produced by cellular metabolism to perform synthetically interesting reactions. Besides hydrolases, oxidoreductases represent the most applied enzyme class in industry. Oxidoreductases are attributed a high future potential, especially for applications in the chemical and pharmaceutical industries, as they enable highly interesting chemistry (e.g., the selective oxyfunctionalization of unactivated C–H bonds). Redox reactions are characterized by electron transfer steps that often depend on redox cofactors as additional substrates. Their regeneration typically is accomplished via the metabolism of whole-cell catalysts. Traditionally, studies towards productive redox biocatalysis focused on the biocatalytic enzyme, its activity, selectivity, and specificity, and several successful examples of such processes are running commercially. However, redox cofactor regeneration by host metabolism was hardly considered for the optimization of biocatalytic rate, yield, and/or titer. This article reviews molecular mechanisms of oxidoreductases with synthetic potential and the host redox metabolism that fuels biocatalytic reactions with redox equivalents. The tools discussed in this review for investigating redox metabolism provide the basis for studies aiming at a deeper understanding of the interplay between synthetically active enzymes and metabolic networks. The ultimate goal of rational whole-cell biocatalyst engineering and use for fine chemical production is discussed. Antioxid. Redox Signal. 13, 349–394.
AfolabiPR, MohammedF, AmaratungaK, MajekodunmiO, DalesSL, GillR, ThompsonD, CooperJB, WoodSP, GoodwinPM, AnthonyC. Site-directed mutagenesis and X-ray crystallography of the PQQ-containing quinoprotein methanol dehydrogenase and its electron acceptor, cytochrome c(L)Biochemistry, 40:9799–9809. 2001.
5.
AlivisatosSG, UngarF, AbrahamG. Nonenzymatic interactions of reduced coenzyme I with inorganic phosphate and certain other anions. Nature, 203:973–975. 1964.
6.
AlperH, JinYS, MoxleyJF, StephanopoulosG. Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli. Metab Eng, 7:155–164. 2005.
7.
AlphandV, CarreaG, WohlgemuthR, FurstossR, WoodleyJM. Towards large-scale synthetic applications of Baeyer–Villiger monooxygenases. Trends Biotechnol, 21:318–323. 2003.
8.
AndersenKB, von MeyenburgK. Charges of nicotinamide adenine nucleotides and adenylate energy charge as regulatory parameters of the metabolism in Escherichia coli. J Biol Chem, 252:4151–4156. 1977.
9.
AndersenOA, StokkaAJ, FlatmarkT, HoughE. 2.0 angstrom resolution crystal structures of the ternary complexes of human phenylalanine hydroxylase catalytic domain with tetrahydrobiopterin and 3-(2-thienyl)-L-alanine or L-norleucine: Substrate specificity and molecular motions related to substrate binding. J Mol Biol, 333:747–757. 2003.
10.
AndreesenJR, FetznerS. The molybdenum-containing hydroxylases of nicotinate, isonicotinate, and nicotine. Met Ions Biol Syst, 39:405–430. 2002.
AustinRN, BuzziK, KimE, ZylstraGJ, GrovesJT. Xylene monooxygenase, a membrane-spanning nonheme di-iron enzyme that hydroxylates hydrocarbons via a substrate radical intermediate. J Biol Inorg Chem, 8:733–740. 2003.
16.
AustinRN, LuddyK, EricksonK, Pender–CudlipM, BertrandE, DengD, BuzdygonRS, van BeilenJB, GrovesJT. Cage escape competes with geminate recombination during alkane hydroxylation by the di-iron oxygenase AlkB. Angew Chem Int Ed, 47:5232–5234. 2008.
17.
BabelW, BrinkmannU, MullerRH. The auxiliary substrate concept. An approach for overcoming limits of microbial performances. Acta Biotechnol, 13:211–242. 1993.
18.
BaikMH, NewcombM, FriesnerRA, LippardSJ. Mechanistic studies on the hydroxylation of methane by methane monooxygenase. Chem Rev, 103:2385–2419. 2003.
19.
BaileyJE, SburlatiA, HatzimanikatisV, LeeK, RennerWA, TsaiPS. Inverse metabolic engineering: A strategy for directed genetic engineering of useful phenotypes. Biotechnol Bioeng, 79:568–579. 2002.
20.
BaileyLJ, MccoyJG, PhillipsGN, FoxBG. Structural consequences of effector protein complex formation in a di-iron hydroxylase. Proc Natl Acad Sci USA, 105:19194–19198. 2008.
21.
BakerPJ, BrittonKL, FisherM, EsclapezJ, PireC, BoneteMJ, FerrerJ, RiceDW. Active site dynamics in the zinc-dependent medium chain alcohol dehydrogenase superfamily. Proc Natl Acad Sci USA, 106:779–784. 2009.
22.
BaldwinCVF, WohlgemuthR, WoodleyJM. The first 200-L scale asymmetric Baeyer–Villiger oxidation using a whole-cell biocatalyst. Org Process Res Dev, 12:660–665. 2008.
23.
BartonL. Reverse electron flow. Structural and Functional Relationships in Prokaryotes. BartonL. New York: Springer, 2005; 447–448.
BeckerJ, KlopproggeC, ZelderO, HeinzleE, WittmannC. Amplified expression of fructose 1,6-bisphosphatase in Corynebacterium glutamicum increases in vivo flux through the pentose phosphate pathway and lysine production on different carbon sources. Appl Environ Microbiol, 71:8587–8596. 2005.
26.
BekkerM, de VriesS, Ter BeekA, HellingwerfKJ, de MattosMJT. Respiration of Escherichia coli can be fully uncoupled via the nonelectrogenic terminal cytochrome bd-II oxidase. J Bacteriol, 191:5510–5517. 2009.
27.
BermejoLL, WelkerNE, PapoutsakisET. Expression of Clostridium acetobutylicum ATCC 824 genes in Escherichia coli for acetone production and acetate detoxification. Appl Environ Microbiol, 64:1079–1085. 1998.
28.
BernhardtR. Cytochromes P450 as versatile biocatalysts. J Biotechnol, 124:128–145. 2006.
29.
BernofskyC, SwanM. An improved cycling assay for nicotinamide adenine dinucleotide. Anal Biochem, 53:452–458. 1973.
30.
Berrios–RiveraSJ, SanKY, BennettGN. The effect of NAPRTase overexpression on the total levels of NAD, the NADH/NAD+ ratio, and the distribution of metabolites in Escherichia coli. Metab Eng, 4:238–247. 2002.
31.
BjorklofK, ZickermannV, FinelM. Purification of the 45 kDa, membrane bound NADH dehydrogenase of Escherichia coli (NDH-2) and analysis of its interaction with ubiquinone analogues. FEBS Lett, 467:105–110. 2000.
32.
BlankLM, KoebmannBJ, MichelsenO, NielsenLK, JensenPR. Hemin reconstitutes proton extrusion in an H+-ATPase-negative mutant of Lactococcus lactis. J Bacteriol, 183:6707–6709. 2001.
33.
BlankLM, SauerU. TCA cycle activity in Saccharomyces cerevisiae is a function of the environmentally determined specific growth and glucose uptake rates. Microbiology, 150:1085–1093. 2004.
34.
BlankLM, KuepferL, SauerU. Large-scale 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast. Genome Biol, 6:R49. 2005.
35.
BlankLM, LehmbeckF, SauerU. Metabolic flux and network analysis in fourteen hemiascomycetous yeasts. FEMS Yeast Res, 5:545–558. 2005.
36.
BlankLM, McLaughlinRL, NielsenLK. Stable production of hyaluronic acid in Streptococcus zooepidemicus chemostats operated at high dilution rate. Biotechnol Bioeng, 90:685–693. 2005.
37.
BlankLM, EbertBE, BühlerB, SchmidA. Metabolic capacity estimation of Escherichia coli as a platform for redox biocatalysis: Constraint-based modeling and experimental verification. Biotechnol Bioeng, 100:1050–1065. 2008.
38.
BlankLM, IonidisG, EbertBE, BühlerB, SchmidA. Metabolic response of Pseudomonas putida during redox biocatalysis in the presence of a second octanol phase. FEBS J, 275:5173–5190. 2008.
39.
BlinovaK, CarrollS, BoseS, SmirnovAV, HarveyJJ, KnutsonJR, BalabanRS. Distribution of mitochondrial NADH fluorescence lifetimes: Steady-state kinetics of matrix NADH interactions. Biochemistry, 44:2585–2594. 2005.
40.
BoenderLG, de HulsterEA, van MarisAJ, Daran–LapujadePA, PronkJT. Quantitative physiology of Saccharomyces cerevisiae at near-zero specific growth rates. Appl Environ Microbiol, 75:5607–5614. 2009.
41.
BollingerJM, KrebsC. Stalking intermediates in oxygen activation by iron enzymes: Motivation and method. J Inorg Biochem, 100:586–605. 2006.
BolognaFP, AndreoCS, DrincovichMF. Escherichia coli malic enzymes: Two isoforms with substantial differences in kinetic properties, metabolic regulation, and structure. J Bacteriol, 189:5937–5946. 2007.
44.
BonariusHPJ, HatzimanikatisV, MeestersKPH, deGooijerCD, SchmidG, TramperJ. Metabolic flux analysis of hybridoma cells in different culture media using mass balances. Biotechnol Bioeng, 50:299–318. 1996.
45.
BonariusHPJ, SchmidG, TramperJ. Flux analysis of underdetermined metabolic networks: The quest for the missing constraints. Trends Biotech, 15:308–314. 1997.
46.
BoonstraB, FrenchCE, WainwrightI, BruceNC. The udhA gene of Escherichia coli encodes a soluble pyridine nucleotide transhydrogenase. J Bacteriol, 181:1030–1034. 1999.
47.
BossertID, WhitedG, GibsonDT, YoungLY. Anaerobic oxidation of p-cresol mediated by a partially purified methylhydroxylase from a denitrifying bacterium. J Bacteriol, 171:2956–2962. 1989.
48.
BoydDR, SharmaND, BowersNI, BranniganIN, GroocockMR, MaloneJE, McConvilleG, AllenCCR. Biocatalytic asymmetric dihydroxylation of conjugated mono- and poly-alkenes to yield enantiopure cyclic cis-diols. Adv Synth Catal, 347:1081–1089. 2005.
49.
BoydDR, BuggTDH. Arene cis-dihydrodiol formation: From biology to application. Org Biomol Chem, 4:181–192. 2006.
50.
BoylePM, SilverPA. Harnessing nature's toolbox: Regulatory elements for synthetic biology. J R Soc Interface, 6:S535–S546. 2009.
51.
BrazeauBJ, AustinRN, TarrC, GrovesJT, LipscombJD. Intermediate Q from soluble methane monooxygenase hydroxylates the mechanistic substrate probe norcarane: Evidence for a stepwise reaction. J Am Chem Soc, 123:11831–11837. 2001.
52.
BrazeauBJ, LipscombJD. Key amino acid residues in the regulation of soluble methane monooxygenase catalysis by component B. Biochemistry, 42:5618–5631. 2003.
53.
BrazeauBJ, JohnsonBJ, WilmotCM. Copper-containing amine oxidases. Biogenesis and catalysis; a structural perspective. Arch Biochem Biophys, 428:22–31. 2004.
54.
BroC, RegenbergB, NielsenJ. Genome-wide transcriptional response of a Saccharomyces cerevisiae strain with an altered redox metabolism. Biotechnol Bioeng, 85:269–276. 2004.
55.
BroC, RegenbergB, ForsterJ, NielsenJ. In silico aided metabolic engineering of Saccharomyces cerevisiae for improved bioethanol production. Metab Eng, 8:102–111. 2006.
56.
BrownCD, NeidigML, NeibergallMB, LipscombJD, SolomonEI. VTVH-MCD and DFT studies of thiolate bonding to {FeNO}7/{FeO2}8 complexes of isopenicillin N synthase: Substrate determination of oxidase versus oxygenase activity in nonheme Fe enzymes. J Am Chem Soc, 129:7427–7438. 2007.
57.
BruijnincxPCA, van KotenG, GebbinkRJMK. Mononuclear nonheme iron enzymes with the 2-His-1-carboxylate facial triad: Recent developments in enzymology and modeling studies. Chem Soc Rev, 37:2716–2744. 2008.
BühlerB, SchmidA, HauerB, WitholtB. Xylene monooxygenase catalyzes the multistep oxygenation of toluene and pseudocumene to corresponding alcohols, aldehydes, and acids in Escherichia coli JM101. J Biol Chem, 275:10085–10092. 2000.
60.
BühlerB, WitholtB, HauerB, SchmidA. Characterization and application of xylene monooxygenase for multistep biocatalysis. Appl Environ Microbiol, 68:560–568. 2002.
61.
BühlerB, BollhalderI, HauerB, WitholtB, SchmidA. Use of the two-liquid phase concept to exploit kinetically controlled multistep biocatalysis. Biotechnol Bioeng, 81:683–694. 2003.
62.
BühlerB, BollhalderI, HauerB, WitholtB, SchmidA. Chemical biotechnology for the specific oxyfunctionalization of hydrocarbons on a technical scale. Biotechnol Bioeng, 82:833–842. 2003.
63.
BühlerB, SchmidA. Process implementation aspects for biocatalytic hydrocarbon oxyfunctionalization. J Biotechnol, 113:183–210. 2004.
BühlerB, StraathofAJJ, WitholtB, SchmidA. Analysis of two-liquid-phase multistep biooxidation based on a process model: Indications for biological energy shortage. Org Process Res Dev, 10:628–643. 2006.
66.
BühlerB, StraathofAJJ, WitholtB, SchmidA. Analysis of two-liquid-phase multistep biooxidation based on a process model: Indications for biological energy shortage. Org Process Res Dev, 10:628–643. 2006.
67.
BühlerB, ParkJB, BlankLM, SchmidA. NADH availability limits asymmetric biocatalytic epoxidation in a growing recombinant Escherichia coli strain. Appl Environ Microbiol, 74:1436–1446. 2008.
68.
BühlerB, BlankLM, EbertBE, BuehlerK, SchmidA. Energy and cofactor issues in fermentation and oxyfunctionalization processes. The Metabolic Pathway Engineering Handbook: Tools and Applications. SmokeCD. Boca Raton, FL: CRC Press (Taylor & Francis Group), 2009; 21:1–32.
69.
BurgardAP, MaranasCD. Probing the performance limits of the Escherichia coli metabolic network subject to gene additions or deletions. Biotechnol Bioeng, 74:364–375. 2001.
70.
BurgardAP, PharkyaP, MaranasCD. OptKnock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol Bioeng, 84:647–657. 2003.
71.
BurtonSG. Oxidizing enzymes as biocatalysts. Trends Biotech, 21:543–549. 2003.
72.
CabanesJ, ChazarraS, Garcia–CarmonaF. Tyrosinase kinetics: A semi-quantitative model of the mechanism of oxidation of monohydric and dihydric phenolic substrates. Reply. J Theor Biol, 214:321–325. 2002.
73.
CarballeiraJD, QuezadaMA, HoyosP, SimeoY, HernaizMJ, AlcantaraAR, SinisterraJV. Microbial cells as catalysts for stereoselective redox reactions. Biotechnol Adv, 27:686–714. 2009.
74.
ChinJW, KhankalR, MonroeCA, MaranasCD, CirinoPC. Analysis of NADPH supply during xylitol production by engineered Escherichia coli. Biotechnol Bioeng, 102:209–220. 2009.
75.
CirinoPC, ArnoldFH. A self-sufficient peroxide-driven hydroxylation biocatalyst. Angew Chem Int Ed, 42:3299–3301. 2003.
76.
CliftonIJ, HsuehLC, BaldwinJE, HarlosK, SchofieldCJ. Structure of proline 3-hydroxylase. Evolution of the family of 2-oxoglutarate dependent oxygenases. Eur J Biochem, 268:6625–6636. 2001.
77.
CollinsAM, WoodleyJM, LiddellJM. Determination of reactor operation for the microbial hydroxylation of toluene in a 2-liquid phase process. J Ind Microbiol, 14:382–388. 1995.
78.
CoonMJ. Cytochrome P450: Nature's most versatile biological catalyst. Annu Rev Pharmacol, 45:1–25. 2005.
79.
CooneyCL, WangHY, WangDIC. Computer-aided material balancing for prediction of fermentation parameters. Biotechnol Bioeng, 19:55–67. 1977.
80.
CostasM, MehnMP, JensenMP, QueL. Dioxygen activation at mononuclear nonheme iron active sites: Enzymes, models, and intermediates. Chem Rev, 104:939–986. 2004.
81.
CovertMW, PalssonBO. Transcriptional regulation in constraints-based metabolic models of Escherichia coli. J Biol Chem, 277:28058–28064. 2002.
82.
CoxSJ, Shalel LevanonS, SanchezA, LinH, PeercyB, BennettGN, SanKY. Development of a metabolic network design and optimization framework incorporating implementation constraints: A succinate production case study. Metab Eng, 8:46–57. 2006.
83.
CozierGE, SallehRA, AnthonyC. Characterization of the membrane quinoprotein glucose dehydrogenase from Escherichia coli and characterization of a site-directed mutant in which histidine-262 has been changed to tyrosine. Biochem J, 340:639–647. 1999.
84.
CunaneLM, ChenZW, ShamalaN, MathewsFS, CroninCN, McIntireWS. Structures of the flavocytochrome p-cresol methylhydroxylase and its enzyme-substrate complex: Gated substrate entry and proton relays support the proposed catalytic mechanism. J Mol Biol, 295:357–374. 2000.
85.
CunaneLM, ChenZW, McIntireWS, MathewsFS. p-Cresol methylhydroxylase: Alteration of the structure of the flavoprotein subunit upon its binding to the cytochrome subunit. Biochemistry, 44:2963–2973. 2005.
86.
D'MelloR, HillS, PooleRK. The cytochrome bd quinol oxidase in Escherichia coli has an extremely high oxygen affinity and two oxygen-binding haems: Implications for regulation of activity in vivo by oxygen inhibition. Microbiology, 142:755–763. 1996.
87.
DaunerM, SondereggerM, HochuliM, SzyperskiT, WuthrichK, HohmannHP, SauerU, BaileyJE. Intracellular carbon fluxes in riboflavin-producing Bacillus subtilis during growth on two-carbon substrate mixtures. Appl Environ Microbiol, 68:1760–1771. 2002.
88.
DavidsonV. Electron transfer in quinoproteins. Arch Biochem Biophys, 428:32–40. 2004.
89.
DeckerA, SolomonEI. Dioxygen activation by copper, heme and nonheme iron enzymes: Comparison of electronic structures and reactivities. Curr Opin Chem Biol, 9:152–163. 2005.
90.
DembitskyVM. Oxidation, epoxidation and sulfoxidation reactions catalysed by haloperoxidases. Tetrahedron, 59:4701–4720. 2003.
91.
DolsM, ChraibiW, Remaud–SimeonM, LindleyND, MonsanPF. Growth and energetics of Leuconostoc mesenteroides NRRL B-1299 during metabolism of various sugars and their consequences for dextransucrase production. Appl Environ Microbiol, 63:2159–2165. 1997.
92.
DraganCA, BlankLM, BureikM. Increased TCA cycle activity and reduced oxygen consumption during cytochrome P450-dependent biotransformation in fission yeast. Yeast, 23:779–794. 2006.
DriscollBT, FinanTM. Properties of NAD(+)- and NADP(+)-dependent malic enzymes of Rhizobium (Sinorhizobium) meliloti and differential expression of their genes in nitrogen-fixing bacteroids. Microbiology, 143:489–498. 1997.
95.
DumasB, Brocard–MassonC, Assemat–LebrunK, AchstetterT. Hydrocortisone made in yeast: metabolic engineering turns a unicellular microorganism into a drug-synthesizing factory. Biotechnol J, 1:299–307. 2006.
96.
DunnMF, BiellmannJF, BranlantG. Roles of zinc ion and reduced coenzyme in horse liver alcohol dehydrogenase catalysis. Mechanism of aldehyde activation. Biochemistry, 14:3176–3182. 2002.
97.
EarhartCA, VettingMW, GosuR, Michaud–SoretI, QueL, OhlendorfDH. Structure of catechol 1,2-dioxygenase from Pseudomonas arvilla. Biochem Bioph Res Co, 338:198–205. 2005.
98.
EdwardsJS, IbarraRU, PalssonBO. In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nature Biotech, 19:125–130. 2001.
99.
EklundH, PlappBV, SamamaJP, BrandenCI. Binding of substrate in a ternary complex of horse liver alcohol dehydrogenase. J Biol Chem, 257:14349–14358. 1982.
100.
ElangoN, RadhakrishnanR, FrolandWA, WallarBJ, EarhartCA, LipscombJD, OhlendorfDH. Crystal structure of the hydroxylase component of methane monooxygenase from Methylosinus trichosporium OB3b. Protein Sci, 6:556–568. 1997.
101.
ElgrenTE, OrvilleAM, KellyKA, LipscombJD, OhlendorfDH, QueL. Crystal structure and resonance Raman studies of protocatechuate 3,4-dioxygenase complexed with 3,4-dihydroxyphenylacetate. Biochemistry, 36:11504–11513. 1997.
102.
EliasMD, NakamuraS, MigitaCT, MiyoshiH, ToyamaH, MatsushitaK, AdachiO, YamadaM. Occurrence of a bound ubiquinone and its function in Escherichia coli membrane-bound quinoprotein glucose dehydrogenase. J Biol Chem, 279:3078–3083. 2004.
103.
EmmerlingM, BaileyJE, SauerU. Glucose catabolism of Escherichia coli strains with increased activity and altered regulation of key glycolytic enzymes. Metab Eng, 1:117–127. 1999.
104.
ErnstM, KaupB, MullerM, Bringer–MeyerS, SahmH. Enantioselective reduction of carbonyl compounds by whole-cell biotransformation, combining a formate dehydrogenase and a (R)-specific alcohol dehydrogenase. Appl Microbiol Biotechnol, 66:629–634. 2005.
105.
EserBE, BarrEW, FrantornPA, SalehL, BollingerJM, KrebsC, FitzpatrickPF. Direct spectroscopic evidence for a high-spin Fe(IV) intermediate in tyrosine hydroxylase. J Am Chem Soc, 129:11334–11335. 2007.
106.
FellD. Understanding the Control of Metabolism. London: Portland, 1997; 301.
107.
FerraroDJ, GakharL, RamaswamyS. Rieske business: Structure–function of Rieske nonheme oxygenases. Biochem Bioph Res Co, 338:175–190. 2005.
108.
FischerE, SauerU. Metabolic flux profiling of Escherichia coli mutants in central carbon metabolism using GC-MS. Eur J Biochem, 270:880–891. 2003.
109.
FischerE, SauerU. A novel metabolic cycle catalyzes glucose oxidation and anaplerosis in hungry Escherichia coli. J Biol Chem, 278:46446–46451. 2003.
110.
FischerE, ZamboniN, SauerU. High-throughput metabolic flux analysis based on gas chromatography-mass spectrometry derived 13C constraints. Anal Biochem, 325:308–316. 2004.
111.
FitzpatrickPF. Mechanism of aromatic amino acid hydroxylation. Biochemistry, 42:14083–14091. 2003.
FrickO, WittmannC. Characterization of the metabolic shift between oxidative and fermentative growth in Saccharomyces cerevisiae by comparative C-13 flux analysis. Microb Cell Fact, 4:30. 2005.
114.
FuH, NewcombM, WongC-H. Pseudomonas oleovorans monooxygenase catalyzed asymmetric epoxidation of allyl alcohol derivatives and hydroxylation of a hypersensitive radical probe with the radical ring opening rate exceeding the oxygen rebound rate. J Am Chem Soc, 113:5878–5880. 1991.
115.
FuhrerT, FischerE, SauerU. Experimental identification and quantification of glucose metabolism in seven bacterial species. J Bacteriol, 187:1581–1590. 2005.
116.
FuhrerT, SauerU. Different biochemical mechanisms ensure network-wide balancing of reducing equivalents in microbial metabolism. J Bacteriol, 191:2112–2121. 2009.
117.
FurukawaH, WieserM, MoritaH, SugioT, NagasawaT. Purification and characterization of eugenol dehydrogenase from Pseudomonas fluorescens E118. Arch Microbiol, 171:37–43. 1998.
GladyshevVN, KhangulovSV, StadtmanTC. Properties of the selenium- and molybdenum-containing nicotinic acid hydroxylase from Clostridium barkeri. Biochemistry, 35:212–223. 1996.
120.
GlickmanMH, KlinmanJP. Lipoxygenase reaction mechanism: Demonstration that hydrogen abstraction from substrate precedes dioxygen binding during catalytic turnover. Biochemistry, 35:12882–12892. 1996.
121.
GoldbergK, EdeggerK, KroutilW, LieseA. Overcoming the thermodynamic limitation in asymmetric hydrogen transfer reactions catalyzed by whole cells. Biotechnol Bioeng, 95:192–198. 2006.
122.
GombertAK, Moreira dos SantosM, ChristensenB, NielsenJ. Network identification and flux quantification in the central metabolism of Saccharomyces cerevisiae under different conditions of glucose repression. J Bacteriol, 183:1441–1451. 2001.
123.
GorrenACF, MayerB. Nitric oxide synthase: A cytochrome P450 family foster child. Biochim Biophys Acta, 1770:432–445. 2007.
124.
GottschalkG, KnackmussHJ. Bacteria and the biodegradation of chemicals achieved naturally, by combination, or by construction. Angew Chem Int Ed, 32:1398–1408. 1993.
125.
GreenMT, DawsonJH, GrayHB. Oxoiron(IV) in chloroperoxidase compound II is basic: Implications for P450 chemistry. Science, 304:1653–1656. 2004.
126.
GreenMT. C-H bond activation in heme proteins: The role of thiolate ligation in cytochrome P450. Curr Opin Chem Biol, 13:84–88. 2009.
GuengerichFP. Cytochrome P450 oxidations in the generation of reactive electrophiles: Epoxidation and related reactions. Arch Biochem Biophys, 409:59–71. 2003.
129.
HakkiT, ZearoS, DraganCA, BureikM, BernhardtR. Coexpression of redox partners increases the hydrocortisone (cortisol) production efficiency in CYP11B1 expressing fission yeast Schizosaccharomyces pombe. J Biotechnol, 133:351–359. 2008.
130.
HalaouliS, AstherM, SigoillotJC, HamdiM, LomascoloA. Fungal tyrosinases: new prospects in molecular characteristics, bioengineering and biotechnological applications. J Appl Microbiol, 100:219–232. 2006.
131.
HarrisLM, BlankL, DesaiRP, WelkerNE, PapoutsakisET. Fermentation characterization and flux analysis of recombinant strains of Clostridium acetobutylicum with an inactivated solR gene. J Ind Microbiol Biot, 27:322–328. 2001.
132.
HausingerRP. Fe(II)/α-ketoglutarate-dependent hydroxylases and related enzymes. Crit Rev Biochem Mol, 39:21–68. 2004.
HerrmannU, MerfortM, JeudeM, Bringer–MeyerS, SahmH. Biotransformation of glucose to 5-keto-D-gluconic acid by recombinant Gluconobacter oxydans DSM 2343. Appl Microbiol Biotechnol, 64:86–90. 2004.
136.
HeuserF, SchroerK, LutzS, Bringer–MeyerS, SahmH. Enhancement of the NAD(P)(H) pool in Escherichia coli for biotransformation. Eng Life Sci, 7:343–353. 2007.
137.
HeylandJ, FuJ, BlankLM. Correlation between TCA cycle flux and glucose uptake rate during respiro-fermentative growth of Saccharomyces cerevisiae. Microbiology, 155:3827–3837. 2009.
138.
HibiM, YukitomoH, ItoM, MoriH. Improvement of NADPH-dependent bioconversion by transcriptome-based molecular breeding. Appl Environ Microbiol, 73:7657–7663. 2007.
139.
HilleR. Molybdenum enzymes containing the pyranopterin cofactor: An overview. Met Ions Biol Syst, 39:187–226. 2002.
140.
HimesRA, KarlinKD. Copper–dioxygen complex mediated C-H bond oxygenation: Relevance for particulate methane monooxygenase (pMMO)Curr Opin Chem Biol, 13:119–131. 2009.
141.
HoffmannF, RinasU. On-line estimation of the metabolic burden resulting from the synthesis of plasmid-encoded and heat-shock proteins by monitoring respiratory energy generation. Biotechnol Bioeng, 76:333–340. 2001.
142.
HofrichterM, UllrichR. Heme-thiolate haloperoxidases: Versatile biocatalysts with biotechnological and environmental significance. Appl Microbiol Biot, 71:276–288. 2006.
143.
HongSH. Systems approaches to succinic acid-producing microorganisms. Biotechnol Bioprocess Eng, 12:73–79. 2007.
144.
HopperDJ. Hydroxylation of p-cresol and its conversion to p-hydroxybenzaldehyde in Pseudomonas putida. Biochem Biophys Res Commun, 69:462–468. 1976.
145.
HopperDJ. Incorporation of [18O] water in the formation of p-hydroxybenzyl alcohol by the p-cresol methylhydroxylase from Pseudomonas putida. Biochem J, 175:345–347. 1978.
146.
HopperDJ, JonesMR, CauserMJ. Periplasmic location of p-cresol methylhydroxylase in Pseudomonas putida. FEBS Lett, 182:485–488. 1985.
147.
HsuHF, QueL, ShanklinJ. XAS studies of membrane bound alkane omega-hydroxylase: Evidence for a histidine-rich ligand environment in the nonheme di-iron site. J Inorg Biochem, 74:168–168. 1999.
148.
HummelW. Reduction of acetophenone to R(+)-phenylethanol by a new alcohol dehydrogenase from Lactobacillus kefir. Appl Microbiol Biotechnol, 34:15–19. 1990.
149.
HummelW. New alcohol dehydrogenases for the synthesis of chiral compounds. Berlin: Springer, 1997; 147–184.
150.
HurhB, YamaneT, NagasawaT. Purification and characterization of nicotinic acid dehydrogenase from Pseudomonas fluorescens Tn5. J Ferment Bioeng, 78:19–26. 1994.
151.
IdupulapatiNB, MainardiDS. Coordination and binding of ions in Ca2+- and Ba2+-containing methanol dehydrogenase and interactions with methanol. J Mol Struct-Theochem, 901:72–80. 2009.
152.
IversonTM, Luna–ChavezC, CecchiniG, ReesDC. Structure of the Escherichia coli fumarate reductase respiratory complex. Science, 284:1961–1966. 1999.
153.
JacksonJB, PeakeSJ, WhiteSA. Structure and mechanism of proton-translocating transhydrogenase. FEBS Lett, 464:1–8. 1999.
154.
JamshidiN, PalssonBO. Formulating genome-scale kinetic models in the post-genome era. Mol Syst Biol, 4:171. 2008.
155.
JankeD, FritscheW. Nature and significance of microbial cometabolism of xenobiotics. J Basic Microbiol, 25:603–619. 1985.
156.
JankowskiMD, HenryCS, BroadbeltLJ, HatzimanikatisV. Group contribution method for thermodynamic analysis of complex metabolic networks. Biophys J, 95:1487–1499. 2008.
157.
JohnsonHA, PelletierDA, SpormannAM. Isolation and characterization of anaerobic ethylbenzene dehydrogenase, a novel Mo-Fe-S enzyme. J Bacteriol, 183:4536–4542. 2001.
JörnvallH, PerssonM, JefferyM. Alcohol and polyol dehydrogenases are both divided into two protein types, and structural properties cross-relate the different enzyme activities within each type. Proc Natl Acad Sci USA, 78:4226–4230. 1981.
160.
JouhtenP, RintalaE, HuuskonenA, TamminenA, ToivariM, WiebeM, RuohonenL, PenttilaM, MaaheimoH. Oxygen dependence of metabolic fluxes and energy generation of Saccharomyces cerevisiae CEN.PK113-1A. BMC Systems Biol, 2:60. 2008.
KabusA, GeorgiT, WendischVF, BottM. Expression of the Escherichia coli pntAB genes encoding a membrane-bound transhydrogenase in Corynebacterium glutamicum improves L-lysine formation. Appl Microbiol Biotechnol, 75:47–53. 2007.
163.
KalnenieksU, GalininaN, StrazdinaI, KravaleZ, PickfordJL, RutkisR, PooleRK. NADH dehydrogenase deficiency results in low respiration rate and improved aerobic growth of Zymomonas mobilis. Microbiology, 154:989–994. 2008.
164.
KamerbeekNM, JanssenDB, van BerkelWJH, FraaijeMW. Baeyer-Villiger monooxygenases, an emerging family of flavin-dependent biocatalysts. Adv Synth Catal, 345:667–678. 2003.
165.
KantzA, ChinF, NallamothuN, NguyenT, GassnerGT. Mechanism of flavin transfer and oxygen activation by the two-component flavoenzyme styrene monooxygenase. Arch Biochem Biophys, 442:102–116. 2005.
166.
KasischkeKA, VishwasraoHD, FisherPJ, ZipfelWR, WebbWW. Neural activity triggers neuronal oxidative metabolism followed by astrocytic glycolysis. Science, 305:99–103. 2004.
167.
KatopodisAG, WimalasenaK, LeeJ, MayS. Mechanistic studies on nonheme iron monooxygenase catalysis: Epoxidation, aldehyde formation, and demethylation by the α-hydroxylation system of Pseudomonas oleovorans. J Am Chem Soc, 106:7928–7935. 1984.
168.
KatopodisAG, SmithHAJr., MayS. New oxyfunctionalization capabilities for ω-hydroxylases: Asymmetric aliphatic sulfoxidation and branched ether demethylation. J Am Chem Soc, 110:897–899. 1988.
KennedyCJ, BoylePM, WaksZ, SilverPA. Systems-level engineering of non-fermentative metabolism in yeast. Genetics, 183:385–397. 2009.
171.
KienerA. Enzymatic oxidation of methyl-groups on aromatic heterocycles; A versatile method for the preparation of heteroaromatic carboxylic acids. Angew Chem Int Edit, 31:774–775. 1992.
172.
KienerA. Biosynthesis of functionalized aromatic N-heterocycles. Chemtech, 25:31–35. 1995.
173.
KleifeldO, FrenkelA, MartinJM, SagiI. Active site electronic structure and dynamics during metalloenzyme catalysis. Nat Struct Biol, 10:98–103. 2003.
KoebmannB, BlankLM, SolemC, PetranovicD, NielsenLK, JensenPR. Increased biomass yield of Lactococcus lactis during energetically limited growth and respiratory conditions. Biotechnol Appl Biochem, 50:25–33. 2008.
177.
KoebmannBJ, NilssonD, KuipersOP, JensenPR. The membrane-bound H+-ATPase complex is essential for growth of Lactococcus lactis. J Bacteriol, 182:4738–4743. 2000.
178.
KoehntopKD, EmersonJP, QueL. The 2-His-1-carboxylate facial triad: A versatile platform for dioxygen activation by mononuclear nonheme iron(II) enzymes. J Biol Inorg Chem, 10:87–93. 2005.
179.
KoppDA, LippardSJ. Soluble methane monooxygenase: Activation of dioxygen and methane. Curr Opin Chem Biol, 6:568–576. 2002.
180.
KosjekB, StampferW, PogorevcM, GoesslerW, FaberK, KroutilW. Purification and characterization of a chemotolerant alcohol dehydrogenase applicable to coupled redox reactions. Biotechnol Bioeng, 86:55–62. 2004.
181.
KovalevaEG, LipscombJD. Crystal structures of Fe2+ dioxygenase superoxo, alkylperoxo, and bound product intermediates. Science, 316:453–457. 2007.
182.
KovalevaEG, NeibergallMB, ChakrabartyS, LipscombJD. Finding intermediates in the O2 activation pathways of nonheme iron oxygenases. Acc Chem Res, 40:475–483. 2007.
183.
KovalevaEG, LipscombJD. Versatility of biological nonheme Fe(II) centers in oxygen activation reactions. Nature Chem Biol, 4:186–193. 2008.
184.
KovalevaEG, LipscombJD. Intermediate in the O-O bond cleavage reaction of an extradiol dioxygenase. Biochemistry, 47:11168–11170. 2008.
185.
KraglU, VasicRackiD, WandreyC. Continuous production of L-tert-leucine in series of two enzyme membrane reactors. Modeling and computer simulation. Bioprocess Engineering, 14:291–297. 1996.
KulaMR, WichmannR, OdenU, WandreyC. Influence of substrate or product inhibition on the performance of enzyme reactors. Biochimie, 62:523–536. 1980.
188.
KulkarniAP. Lipoxygenase. A versatile biocatalyst for biotransformation of endobiotics and xenobiotics. Cell Mol Life Sci, 58:1805–1825. 2001.
189.
KummelA, PankeS, HeinemannM. Systematic assignment of thermodynamic constraints in metabolic network models. BMC Bioinformatics, 7:512. 2006.
190.
KweonO, KimSJ, BaekS, ChaeJC, AdjeiMD, BaekDH, KimYC, CernigliaCE. A new classification system for bacterial Rieske nonheme iron aromatic ring-hydroxylating oxygenases. BMC Biochem, 9:11. 2008.
191.
LadenBP, TangYZ, PorterTD. Cloning, heterologous expression, and enzymological characterization of human squalene monooxygenase. Arch Biochem Biophys, 374:381–388. 2000.
192.
LeakDJ, SheldonRA, WoodleyJM, AdlercreutzP. Biocatalysts for selective introduction of oxygen. Biocatal Biotransform, 27:1–26. 2009.
193.
LeeS-K, NesheimJC, LipscombJD. Transient intermediates of the methane monooxygenase catalytic cycle. J Biol Chem, 268:21569–21577. 1993.
194.
LeeS, PhalakornkuleC, DomachMM, GrossmannIE. Recursive MILP model for finding all the alternate optima in LP models for metabolic networks. Comput Chem Eng, 24:711–716. 2000.
195.
LeeSK, LipscombJD. Oxygen activation catalyzed by methane monooxygenase hydroxylase component: proton delivery during the O-O bond cleavage steps. Biochemistry, 38:4423–4432. 1999.
196.
LeeSY, HongSH, MoonSY. In silico metabolic pathway analysis and design: Succinic acid production by metabolically engineered Escherichia coli as an example. Genome Inform, 13:214–223. 2002.
197.
LeferinkNGH, HeutsDPHM, FraaijeMW, van BerkelWJH. The growing VAO flavoprotein family. Arch Biochem Biophys, 474:292–301. 2008.
198.
LeferinkNGH, FraaijeMW, JoostenHJ, SchaapPJ, MatteviA, van BerkelWJH. Identification of a gatekeeper residue that prevents dehydrogenases from acting as oxidases. J Biol Chem, 284:4392–4397. 2009.
199.
LenichA, GoodmanS. The purification and characterization of glutaryl-coenzyme A dehydrogenase from porcine and human liver. J Biol Chem, 261:4090–4096. 1986.
200.
LerondelG, DoanT, ZamboniN, SauerU, AymerichS. YtsJ has the major physiological role of the four paralogous malic enzyme isoforms in Bacillus subtilis. J Bacteriol, 188:4727–4736. 2006.
LiliusEM, MultanenVM, ToivonenV. Quantitative extraction and estimation of intracellular nicotinamide nucleotides of Escherichia coli. Anal Biochem, 99:22–27. 1979.
203.
LillyMD, WoodleyJM. A structured approach to design and operation of biotransformation processes. J Ind Microbiol, 17:24–29. 1996.
204.
LowryOH, PassonneauJV, RockMK. The stability of pyridine nucleotides. J Biol Chem, 236:2756–2759. 1961.
205.
LowryOH, PassonneauJV, SchulzDW, RockMK. The measurement of pyridine nucleotides by enzymatic cycling. J Biol Chem, 236:2746–2755. 1961.
206.
LuoB, GroenkeK, TakorsR, WandreyC, OldigesM. Simultaneous determination of multiple intracellular metabolites in glycolysis, pentose phosphate pathway and tricarboxylic acid cycle by liquid chromatography-mass spectrometry. J Chromatogr A, 1147:153–164. 2007.
207.
MahadevanR, SchillingCH. The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab Eng, 5:264–276. 2003.
208.
MailingerW, BaumeisterA, ReussM, RizziM. Rapid and highly automated determination of adenine and pyridine nucleotides in extracts of Saccharomyces cerevisiae using a micro robotic sample preparation-HPLC system. J Biotechnol, 63:155–166. 1998.
209.
MasseyV. Activation of molecular oxygen by flavins and flavoproteins. J Biol Chem, 269:22459–22462. 1994.
210.
MasseyV. The chemical and biological versatility of riboflavin. Biochem Soc Trans, 28:283–296. 2000.
211.
MathysRG, SchmidA, WitholtB. Integrated two-liquid phase bioconversion and product-recovery processes for the oxidation of alkanes: Process design and economic evaluation. Biotechnol Bioeng, 64:459–477. 1999.
212.
MatinA, GottschalJC. Influence of dilution rate on NAD(P) and NAD(P)H concentrations and ratios in a Pseudomonas sp. grown in continuous culture. J Gen Microbiol, 94:333–341. 1976.
MatteviA, FraaijeMW, MozzarelliA, OliviL, CodaA, van BerkelWJH. Crystal structures and inhibitor binding in the octameric flavoenzyme vanillyl-alcohol oxidase: The shape of the active-site cavity controls substrate specificity. Structure, 5:907–920. 1997.
215.
MayS, KatopodisAG. Oxygenation of alcohol and sulphide substrates by a prototypical non-haem iron monooxygenase: Catalysis and biotechnological potential. Enzyme Microb Technol, 8:17–21. 1986.
MerkxM, KoppDA, SazinskyMH, BlazykJL, MüllerJ, LippardSJ. Dioxygen activation and methane hydroxylation by soluble methane monooxygenase: A tale of two irons and three proteins. Angew Chem Int Ed, 40:2782–2807. 2001.
218.
MeullerJ, RydstromJ. The membrane topology of proton-pumping Escherichia coli transhydrogenase determined by cysteine labeling. J Biol Chem, 274:19072–19080. 1999.
219.
MeunierB, de VisserSP, ShaikS. Mechanism of oxidation reactions catalyzed by cytochrome P450 enzymes. Chem Rev, 104:3947–3980. 2004.
MiricaLM, KlinmanJP. The nature of O2 activation by the ethylene-forming enzyme 1-aminocyclopropane-1-carboxylic acid oxidase. Proc Natl Acad Sci USA, 105:1814–1819. 2008.
222.
MitchellKH, RoggeCE, GierahnT, FoxBG. Insight into the mechanism of aromatic hydroxylation by toluene 4-monooxygenase by use of specifically deuterated toluene and p-xylene. Proc Natl Acad Sci USA, 100:3784–3789. 2003.
223.
MoonenMJH, FraaijeMW, RietjensIMCM, LaaneC, van BerkelWJH. Flavoenzyme-catalyzed oxygenations and oxidations of phenolic compounds. Adv Synth Catal, 344:1023–1035. 2002.
224.
MunroAW, LeysDG, McLeanKJ, MarshallKR, OstTWB, DaffS, MilesCS, ChapmanSK, LysekDA, MoserCC, PageCC, DuttonPL. P450 BM3: The very model of a modern flavocytochrome. Trends Biochem Sci, 27:250–257. 2002.
225.
MunroAW, GirvanHM, McLeanKJ. Variations on a (t)heme. Novel mechanisms, redox partners and catalytic functions in the cytochrome P450 superfamily. Nat Prod Rep, 24:585–609. 2007.
226.
NagelM, AndreesenJR. Purification and characterization of the molybdoenzymes nicotinate dehydrogenase and 6-hydroxynicotinate dehydrogenase from Bacillus niacini. Arch Microbiol, 154:605–613. 1990.
227.
This reference has been deleted.
228.
NevesAR, RamosA, CostaH, vanSII, HugenholtzJ, KleerebezemM, de VosW, SantosH. Effect of different NADH oxidase levels on glucose metabolism by Lactococcus lactis: Kinetics of intracellular metabolite pools determined by in vivo nuclear magnetic resonance. Appl Environ Microbiol, 68:6332–6342. 2002.
229.
NevesAR, PoolWA, KokJ, KuipersOP, SantosH. Overview on sugar metabolism and its control in Lactococcus lactis. The input from in vivo NMR. FEMS Microbiol Rev, 29:531–554. 2005.
230.
NewcombM, HollenbergPF, CoonMJ. Multiple mechanisms and multiple oxidants in P450-catalyzed hydroxylations. Arch Biochem Biophys, 409:72–79. 2003.
231.
NewcombM, HalgrimsonJA, HornerJH, WasingerEC, ChenLX, SligarSG. X-ray absorption spectroscopic characterization of a cytochrome P450 compound II derivative. Proc Natl Acad Sci USA, 105:8179–8184. 2008.
232.
NielsenJH, VilladsenJ. Bioreaction Engineering Principles. New York: London Plenum Press, 1994; 456.
233.
NisselbaumJS, GreenS. A simple ultramicro method for determination of pyridine nucleotides in tissues. Anal Biochem, 27:212–217. 1969.
234.
NizamSA, ZhuJF, HoPY, ShimizuK. Effects of arcA and arcB genes knockout on the metabolism in Escherichia coli under aerobic condition. Biochem Eng J, 44:240–250. 2009.
235.
NoguchiY, NakaiY, ShimbaN, ToyosakiH, KawaharaY, SugimotoS, SuzukiE. The energetic conversion competence of Escherichia coli during aerobic respiration studied by 31P NMR using a circulating fermentation system. J Biochem, 136:509–515. 2004.
236.
OhIJ, KimDH, OhEK, LeeSY, LeeJ. Optimization and scale-up of succinic acid production by Mannheimia succiniciproducens LPK7. J Microbiol Biotechnol, 19:167–171. 2009.
OkamotoK, MatsumotoK, HilleR, EgerBT, PaiEF, NishinoT. The crystal structure of xanthine oxidoreductase during catalysis: Implications for reaction mechanism and enzyme inhibition. Proc Natl Acad Sci USA, 101:7931–7936. 2004.
239.
Ortiz de MontellanoPR, NishidaC, Rodriguez–CrespoI, GerberN. Nitric oxide synthase structure and electron transfer. Drug Metab Dispos, 26:1185–1189. 1998.
240.
OrvilleAM, LipscombJD. Cyanide and nitric oxide binding to reduced protocatechuate 3,4-dioxygenase: Insight into the basis for order-dependent ligand binding by intradiol catecholic dioxygenases. Biochemistry, 36:14044–14055. 1997.
241.
OttoK, HofstetterK, RothlisbergerM, WitholtB, SchmidA. Biochemical characterization of StyAB from Pseudomonas sp. strain VLB120 as a two-component flavin-diffusible monooxygenase. J Bacteriol, 186:5292–5302. 2004.
242.
OverkampKM, BakkerBM, SteensmaHY, van DijkenJP, PronkJT. Two mechanisms for oxidation of cytosolic NADPH by Kluyveromyces lactis mitochondria. Yeast, 19:813–824. 2002.
243.
PankeS, WitholtB, SchmidA, WubboltsMG. Towards a biocatalyst for (S)-styrene oxide production: characterization of the styrene degradation pathway of Pseudomonas sp. strain VLB120. Appl Environ Microbiol, 64:2032–2043. 1998.
244.
PankeS, WubboltsMG, SchmidA, WitholtB. Production of enantiopure styrene oxide by recombinant Escherichia coli synthesizing a two-component styrene monooxygenase. Biotechnol Bioeng, 69:91–100. 2000.
245.
PankeS, HeldM, WubboltsMG, WitholtB, SchmidA. Pilot-scale production of (S)-styrene oxide from styrene by recombinant Escherichia coli synthesizing styrene monooxygenase. Biotechnol Bioeng, 80:33–41. 2002.
246.
ParkJB, BühlerB, HabicherT, HauerB, PankeS, WitholtB, SchmidA. The efficiency of recombinant Escherichia coli as biocatalyst for stereospecific epoxidation. Biotechnol Bioeng, 95:501–512. 2006.
247.
ParkJB, ClarkDS. Deactivation mechanisms of chloroperoxidase during biotransformations. Biotechnol Bioeng, 93:1190–1195. 2006.
248.
PatelRN. Synthesis of chiral pharmaceutical intermediates by biocatalysis. Chem Rev, 252:659–701. 2008.
249.
PavonJA, FitzpatrickPF. Intrinsic isotope effects on benzylic hydroxylation by the aromatic amino acid hydroxylases: Evidence for hydrogen tunneling, coupled motion, and similar reactivities. J Am Chem Soc, 127:16414–16415. 2005.
250.
PavonJA, FitzpatrickPF. Insights into the catalytic mechanisms of phenylalanine and tryptophan hydroxylase from kinetic isotope effects on aromatic hydroxylation. Biochemistry, 45:11030–11037. 2006.
251.
PerrenoudA, SauerU. Impact of global transcriptional regulation by ArcA, ArcB, Cra, Crp, Cya, Fnr, and Mlc on glucose catabolism in Escherichia coli. J Bacteriol, 187:3171–3179. 2005.
252.
PetersFT, DraganCA, WildeDR, MeyerMR, ZappJ, BureikM, MaurerHH. Biotechnological synthesis of drug metabolites using human cytochrome P450 2D6 heterologously expressed in fission yeast exemplified for the designer drug metabolite 4'-hydroxymethyl-α-pyrrolidinobutyrophenone. Biochem Pharmacol, 74:511–520. 2007.
253.
PetersFT, DraganCA, KauffelsA, SchwaningerAE, ZappJ, BureikM, MaurerHH. Biotechnological synthesis of the designer drug metabolite 4'-hydroxymethyl-α-pyrrolidinohexanophenone in fission yeast heterologously expressing human cytochrome P450 2D6—A versatile alternative to multistep chemical synthesis. J Anal Toxicol, 33:190–197. 2009.
254.
PetersFT, DraganCA, SchwaningerAE, SauerC, ZappJ, BureikM, MaurerHH. Use of fission yeast heterologously expressing human cytochrome P450 2B6 in biotechnological synthesis of the designer drug metabolite N-(1-phenylcyclohexyl)-2-hydroxyethanamine. Forensic Sci Int, 184:69–73. 2009.
255.
PetersenS, de GraafAA, EggelingL, MollneyM, WiechertW, SahmH. In vivo quantification of parallel and bidirectional fluxes in the anaplerosis of Corynebacterium glutamicum. J Biol Chem, 275:35932–35941. 2000.
256.
PetersonJA, BasuD, CoonMJ. Enzymatic omega-oxidation. I. Electron carriers in fatty acid and hydrocarbon hydroxylation. J Biol Chem, 241:5162–5164. 1966.
257.
PooleRK, CookGM. Redundancy of aerobic respiratory chains in bacteria? Routes, reasons and regulation. Adv Microb Physiol, 43:165–224. 2000.
PrescottAG, LloydMD. The iron(II) and 2-oxoacid-dependent dioxygenases and their role in metabolism. Nat Prod Rep, 17:367–383. 2000.
260.
PriceND, ReedJL, PalssonBO. Genome-scale models of microbial cells: Evaluating the consequences of constraints. Nature Rev Microb, 2:886–897. 2004.
261.
PurperoV, MoranGR. The diverse and pervasive chemistries of the α-keto acid dependent enzymes. J Biol Inorg Chem, 12:587–601. 2007.
262.
QueL. One motif—Many different reactions. Nat Struct Biol, 7:182–184. 2000.
263.
RaberDJ, RodriguezW. Conformational properties of oxidation reduction cofactors. J Am Chem Soc, 107:4146–4147. 1985.
264.
RaoK, AlbroM, ZirrolliJ, van der VeldeD, JonesDN, FrermanF. Protonation of crotonyl-CoA dienolate by human glutaryl-CoA dehydrogenase occurs by solvent-derived protons. Biochemistry, 44:13932–13940. 2005.
ResnickSM, LeeK, GibsonDT. Diverse reactions catalyzed by naphthalene dioxygenase from Pseudomonas sp strain NCIB 9816. J Ind Microbiol Biot, 17:438–457. 1996.
267.
RichardsonDJ. Bacterial respiration: A flexible process for a changing environment. Microbiology, 146:551–571. 2000.
268.
RoachPL, CliftonIJ, HensgensCMH, ShibataN, SchofieldCJ, HajduJ, BaldwinJE. Structure of isopenicillin N synthase complexed with substrate and the mechanism of penicillin formation. Nature, 387:827–830. 1997.
269.
RoelsJA. Application of macroscopic principles to microbial metabolism. Biotechnol Bioeng, 22:2457–2514. 1980.
270.
RomanoAH, ConwayT. Evolution of carbohydrate metabolic pathways. Res Microbiol, 147:448–455. 1996.
271.
RosenzweigAC, FrederickCA, LippardSJ, NordlundP. Crystal structure of a bacterial non-haem iron hydroxylase that catalyses the biological oxidation of methane. Nature, 366:537–543. 1993.
272.
RosenzweigAC. The metal centres of particulate methane mono-oxygenase. Biochem Soc Trans, 36:1134–1137. 2008.
273.
Rover JuniorL, FernandesJC, de Oliveira NetoG, KubotaLT, KatekawaE, SerranoSH. Study of NADH stability using ultraviolet-visible spectrophotometric analysis and factorial design. Anal Biochem, 260:50–55. 1998.
274.
RuddatVC, WhitmanS, HolmanTR, BernasconiCF. Stopped-flow kinetic investigations of the activation of soybean lipoxygenase-1 and the influence of inhibitors on the allosteric site. Biochemistry, 42:4172–4178. 2003.
SanchezAM, AndrewsJ, HusseinI, BennettGN, SanKY. Effect of overexpression of a soluble pyridine nucleotide transhydrogenase (UdhA) on the production of poly(3-hydroxybutyrate) in Escherichia coli. Biotechnol Prog, 22:420–425. 2006.
278.
SauerU, HatzimanikatisV, HohmannHP, MannebergM, van LoonAP, BaileyJE. Physiology and metabolic fluxes of wild-type and riboflavin-producing Bacillus subtilis. Appl Environ Microbiol, 62:3687–3696. 1996.
279.
SauerU, BaileyJE. Estimation of P-to-O ratio in Bacillus subtilis and its influence on maximum riboflavin yield. Biotechnol Bioeng, 64:750–754. 1999.
280.
SauerU, LaskoDR, FiauxJ, HochuliM, GlaserR, SzyperskiT, WuthrichK, BaileyJE. Metabolic flux ratio analysis of genetic and environmental modulations of Escherichia coli central carbon metabolism. J Bacteriol, 181:6679–6688. 1999.
281.
SauerU, CanonacoF, HeriS, PerrenoudA, FischerE. The soluble and membrane-bound transhydrogenases UdhA and PntAB have divergent functions in NADPH metabolism of Escherichia coli. J Biol Chem, 279:6613–6619. 2004.
SavinellJM, PalssonBO. Network analysis of intermediary metabolism using linear optimization. I. Development of mathematical formalism. J Theor Biol, 154:421–454. 1992.
284.
SavinellJM, PalssonBO. Optimal selection of metabolic fluxes for in vivo measurement. II. Application to Escherichia coli and hybridoma cell metabolism. J Theor Biol, 155:215–242. 1992.
SchroerK, LuefPK, HartnerFS, GliederA, PscheidtB. Engineering the Pichia pastoris methanol oxidation pathway for improved NADH regeneration during whole-cell biotransformation. Metab Eng, 12:8–17. 2010.
291.
SchroerK, ZelicB, OldigesM, LutzS. Metabolomics for biotransformations: Intracellular redox cofactor analysis and enzyme kinetics offer insight into whole cell processes. Biotechnol Bioeng, 104:251–260. 2009.
292.
SchuetzR, KuepferL, SauerU. Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli. Mol Sys Biol, 3:119. 2007.
293.
SchüteH, FlossdorfJ, SahmH, KulaMR. Purification and properties of formaldehyde dehydrogenase and formate dehydrogenase from Candida boidinii. Eur J Biochem, 62:151–160. 1976.
294.
SchwartzJK, WeiPP, MitchellKH, FoxBG, SolomonEI. Geometric and electronic structure studies of the binuclear nonheme ferrous active site of toluene-4-monooxygenase: Parallels with methane monooxygenase and insight into the role of the effector proteins in O2 activation. J Am Chem Soc, 130:7098–7109. 2008.
295.
ShawNM, RobinsKT, KienerA. Lonza: 20 years of biotransformations. Adv Synth Catal, 345:425–435. 2003.
296.
ShengX, ZhangHM, HollenbergPF, NewcombM. Kinetic isotope effects in hydroxylation reactions effected by cytochrome P450 compounds I implicate multiple electrophilic oxidants for P450-catalyzed oxidations. Biochemistry, 48:1620–1627. 2009.
297.
ShibasakiT, HashimotoS, MoriH, OzakiA. Construction of a novel hydroxyproline-producing recombinant Escherichia coli by introducing a proline 4-hydroxylase gene. J Biosci Bioeng, 90:522–525. 2000.
298.
ShibasakiT, MoriH, OzakiA. Enzymatic production of trans-4-hydroxy-L-proline by regio- and stereospecific hydroxylation of L-proline. Biosci Biotechnol Biochem, 64:746–750. 2000.
299.
ShuL, NesheimJC, KauffmannK, MünckE, LipscombJD, QueLJr.An Fe2IVO2 diamond core structure for the key intermediate Q of methane monooxygenase. Science, 275:515–518. 1997.
300.
SlonczewskiJL, RosenBP, AlgerJR, MacnabRM. pH homeostasis in Escherichia coli: Measurement by 31P nuclear magnetic resonance of methylphosphonate and phosphate. Proc Natl Acad Sci USA, 78:6271–6275. 1981.
301.
SmithE, MorowitzHJ. Universality in intermediary metabolism. Proc Natl Acad Sci USA, 101:13168–13173. 2004.
302.
SmitsTH, BaladaSB, WitholtB, van BeilenJB. Functional analysis of alkane hydroxylases from gram-negative and gram-positive bacteria. J Bacteriol, 184:1733–1742. 2002.
StephanopoulosG, AristidouAA, NielsenJ. Metabolic Engineering: Principles and Methodologies. San Diego, CA: Academic Press, 1998; 725.
308.
SteuerR, JunkerBH. Computational models of metabolism: Stability and regulation in metabolic networks. Adv Chem Phys, 142:105–251. 2009.
309.
StewartJD. Cyclohexanone monooxygenase: A useful reagent for asymmetric Baeyer–Villiger reactions. Curr Org Chem, 2:195–216. 1998.
310.
StouthamerAH. The search for correlation between theoretical and experimental growth yields. International Review of Biochemistry: Microbial Biochemistry. QuayleJR. Baltimore: University Park Press, 1979; 1–47.
311.
StraathofAJ, PankeS, SchmidA. The production of fine chemicals by biotransformations. Curr Opin Biotechnol, 13:548–556. 2002.
SuskeWA, HeldM, SchmidA, FleischmannT, WubboltsMG, KohlerHP. Purification and characterization of 2-hydroxybiphenyl 3-monooxygenase, a novel NADH-dependent, FAD-containing aromatic hydroxylase from Pseudomonas azelaica HBP1. J Biol Chem, 272:24257–24265. 1997.
314.
SuzukiM, HayakawaT, ShawJP, RekikM, HarayamaS. Primary structure of xylene monooxygenase: Similarities to and differences from the alkane hydroxylation system. J Bacteriol, 173:1690–1695. 1991.
315.
SzczebaraFM, ChandelierC, VilleretC, MasurelA, BourotS, DuportC, BlanchardS, GroisillierA, TestetE, CostaglioliP, CauetG, DegryseE, BalbuenaD, WinterJ, AchstetterT, SpagnoliR, PomponD, DumasB. Total biosynthesis of hydrocortisone from a simple carbon source in yeast. Nat Biotechnol, 21:143–149. 2003.
316.
TangYJ, MartinHG, MyersS, RodriguezS, BaidooEEK, KeaslingJD. Advances in analysis of microbial metabolic fluxes via C-13 isotopic labeling. Mass Spectrom Rev, 28:362–375. 2009.
317.
TarrioN, BecerraM, CerdanME, SisoMIG. Reoxidation of cytosolic NADPH in Kluyveromyces lactis. FEMS Yeast Res, 6:371–380. 2006.
318.
TempestDW, NeijsselOM. Growth yield and energy distribution. Escherichia coli and Salmonella typhimurium cellular and molecular biology. NeidhardtFC, IngrahamJL. Washington, DC: American Society for Microbiology, 1987; 797–805.
319.
TishkovVI, PopovVO. Catalytic mechanism and application of formate dehydrogenase. Biochemistry, 69:1252–1268. 2004.
320.
TranQH, BongaertsJ, VladD, UndenG. Requirement for the proton-pumping NADH dehydrogenase I of Escherichia coli in respiration of NADH to fumarate and its bioenergetic implications. Eur J Biochem, 244:155–160. 1997.
321.
UllrichR, HofrichterM. Enzymatic hydroxylation of aromatic compounds. Cell Mol Life Sci, 64:271–293. 2007.
VaillancourtFH, BolinJT, EltisLD. The ins and outs of ring-cleaving dioxygenases. Crit Rev Biochem Mol, 41:241–267. 2006.
326.
ValderramaB, AyalaM, Vazquez–DuhaltR. Suicide inactivation of peroxidases and the challenge of engineering more robust enzymes. Chem Biol, 9:555–565. 2002.
327.
ValentineAM, StahlSS, LippardSJ. Mechanistic studies of the reaction of reduced methane monooxygenase hydroxylase with dioxygen and substrates. J Am Chem Soc, 121:3876–3887. 1999.
328.
van BeilenJB, KingmaJ, WitholtB. Substrate specificity of the alkane hydroxylase system of Pseudomonas oleovorans GPo1. Enzyme Microb Tech, 16:904–911. 1994.
329.
van BeilenJB, FunhoffEG. Expanding the alkane oxygenase toolbox: new enzymes and applications. Curr Opin Biotech, 16:308–314. 2005.
330.
van BeilenJB, SmitsTHM, RoosFF, BrunnerT, BaladaSB, RothlisbergerM, WitholtB. Identification of an amino acid position that determines the substrate range of integral membrane alkane hydroxylases. J Bacteriol, 187:85–91. 2005.
331.
van BerkelWJ, KamerbeekNM, FraaijeMW. Flavoprotein monooxygenases: A diverse class of oxidative biocatalysts. J Biotechnol, 124:670–689. 2006.
332.
van de VeldeF, van RantwijkF, SheldonRA. Improving the catalytic performance of peroxidases in organic synthesis. Trends Biotechnol, 19:73–80. 2001.
333.
van den HeuvelRHH, FraaijeMW, MatteviA, LaaneC, van BerkelWJH. Vanillyl-alcohol oxidase, a tasteful biocatalyst. J Mol Catal B-Enzym, 11:185–188. 2001.
334.
van den HeuvelRHH, LaaneC, van BerkelWJH. Exploring the biocatalytic potential of vanillyl-alcohol oxidase by site-directed mutagenesis. Adv Synth Catal, 343:515–520. 2001.
335.
van DeurzenMPJ, van RantwijkF, SheldonRA. Selective oxidations catalyzed by peroxidases. Tetrahedron, 53:13183–13220. 1997.
336.
van GulikWM, HeijnenJJ. A metabolic network stoichiometry analysis of microbial growth and product formation. Biotechnol Bioeng, 48:681–698. 1995.
337.
van MarisAJ, WinklerAA, PorroD, van DijkenJP, PronkJT. Homofermentative lactate production cannot sustain anaerobic growth of engineered Saccharomyces cerevisiae: Possible consequence of energy-dependent lactate export. Appl Environ Microbiol, 70:2898–2905. 2004.
338.
van RantwijkF, SheldonRA. Selective oxygen transfer catalysed by heme peroxidases: Synthetic and mechanistic aspects. Curr Opin Biotech, 11:554–564. 2000.
339.
VanderheijdenRTJM, RomeinB, HeijnenJJ, HellingaC, LuybenKCAM. Linear constraint relations in biochemical reaction systems. 2. Diagnosis and estimation of gross errors. Biotechnol Bioeng, 43:11–20. 1994.
340.
VarmaA, BoeschBW, PalssonBO. Biochemical production capabilities of Escherichia coli. Biotechnol Bioeng, 42:59–73. 1993.
341.
VeitA, PolenT, WendischVF. Global gene expression analysis of glucose overflow metabolism in Escherichia coli and reduction of aerobic acetate formation. Appl Microbiol Biotechnol, 74:406–421. 2007.
342.
VemuriGN, EitemanMA, AltmanE. Effects of growth mode and pyruvate carboxylase on succinic acid production by metabolically engineered strains of Escherichia coli. Appl Environ Microbiol, 68:1715–1727. 2002.
343.
VerhoR, RichardP, JonsonPH, SundqvistL, LondesboroughJ, PenttilaM. Identification of the first fungal NADP-GAPDH from Kluyveromyces lactis. Biochemistry, 41:13833–13838. 2002.
344.
VettingMW, WackettLP, QueL, LipscombJD, OhlendorfDH. Crystallographic comparison of manganese- and iron-dependent homoprotocatechuate 2,3-dioxygenases. J Bacteriol, 186:1945–1958. 2004.
345.
Vital–LopezFG, ArmaouA, NikolaevEV, MaranasCD. A computational procedure for optimal engineering interventions using kinetic models of metabolism. Biotech Progress, 22:1507–1517. 2006.
346.
WackettLP. Mechanism and applications of Rieske nonheme iron dioxygenases. Enzyme Microb Tech, 31:577–587. 2002.
347.
WallarBJ, LipscombJD. Dioxygen activation by enzymes containing binuclear nonheme iron clusters. Chem Rev, 96:2625–2658. 1996.
348.
WallarBJ, LipscombJD. Methane monooxygenase component B mutants alter the kinetics of steps throughout the catalytic cycle. Biochemistry, 40:2220–2233. 2001.
349.
WangHY, CooneyCL, WangDIC. On-line gas analysis for material balances and control. Biotechnol Bioeng Symp, 9:13–23. 1979.
350.
Webster's Encyclopedic Unabridged Dictionary of the English Language. New York: Gramercy Books, 1996; 2230.
351.
WeckbeckerA, HummelW. Improved synthesis of chiral alcohols with Escherichia coli cells co-expressing pyridine nucleotide transhydrogenase, NADP+-dependent alcohol dehydrogenase and NAD+-dependent formate dehydrogenase. Biotechnol Lett, 26:1739–1744. 2004.
352.
WermuthB, KaplanNO. Pyridine-nucleotide transhydrogenase from Pseudomonas aeruginosa. Purification by affinity chromatography and physicochemical properties. Arch Biochem Biophys, 176:136–143. 1976.
353.
WeryJ, Mendes da SilvaDI, de BontJA. A genetically modified solvent-tolerant bacterium for optimized production of a toxic fine chemical. Appl Microbiol Biotechnol, 54:180–185. 2000.
354.
WichmannR, WandreyC, BuckmannAF, KulaMR. Continuous enzymatic transformation in an enzyme membrane reactor with simultaneous NAD(H) regeneration. Biotechnol Bioeng, 23:2789–2802. 1981.
355.
WichmannR, Vasic–RackiD. Cofactor regeneration at the lab scale. Adv Biochem Eng Biotechnol, 92:225–260. 2005.
356.
WidmerF, KaplanNO. Pseudomonas aeruginosa transhydrogenase: Affinity of substrates for the regulatory site and possible hysteretic behavior. Biochem Biophys Res Commun, 76:1287–1292. 1977.
WilmotCM. Oxygen activation in a copper-containing amine oxidase. Biochem Soc Trans, 31:493–496. 2003.
359.
WimpennyJW, FirthA. Levels of nicotinamide adenine dinucleotide and reduced nicotinamide adenine dinucleotide in facultative bacteria and effect of oxygen. J Bacteriol, 11:24. 1972.
360.
WitayakranS, RagauskasAJ. Synthetic applications of laccase in green chemistry. Adv Synth Catal, 351:1187–1209. 2009.
361.
WittmannC, HeinzleE. Genealogy profiling through strain improvement by using metabolic network analysis: Metabolic flux genealogy of several generations of lysine-producing corynebacteria. Appl Environ Microbiol, 68:5843–5859. 2002.
362.
WoodleyJM. Microbial biocatalytic processes and their development. Adv Appl Microbiol, 60:1–15. 2006.
363.
WoodleyJM. Choice of biocatalyst form for scalable processes. Biochem Soc Trans, 34:301–303. 2006.
364.
WuJT, WuLH, KnightJA. Stability of NADPH: Effect of various factors on the kinetics of degradation. Clin Chem, 32:314–319. 1986.
365.
WubboltsMG, TerpstraP, van BeilenJB, KingmaJ, MeestersHA, WitholtB. Variation of cofactor levels in Escherichia coli. Sequence analysis and expression of the pncB gene encoding nicotinic acid phosphoribosyltransferase. J Biol Chem, 265:17665–17672. 1990.
366.
WubboltsMG, ReuvekampP, WitholtB. Tol plasmid-specified xylene oxygenase is a wide substrate range monooxygenase capable of olefin epoxidation. Enzyme Microb Tech, 16:608–615. 1994.
367.
XieW, XuA, YeungES. Determination of NAD(+) and NADH in a single cell under hydrogen peroxide stress by capillary electrophoresis. Anal Chem, 81:1280–1284. 2009.
368.
XuM, BhatS, SmithR, StephensG, SadhukhanJ. Multi-objective optimisation of metabolic productivity and thermodynamic performance. Comput Chem Eng, 33:1438–1450. 2009.
369.
YamadaK, HaraN, ShibataT, OsagoH, TsuchiyaM. The simultaneous measurement of nicotinamide adenine dinucleotide and related compounds by liquid chromatography/electrospray ionization tandem mass spectrometry. Anal Biochem, 352:282–285. 2006.
370.
YamaguchiM, HatefiY. Energy-transducing nicotinamide nucleotide transhydrogenase. Nucleotide-sequences of the genes and predicted amino-acid-sequences of the subunits of the enzyme from Rhodospirillum rubrum. J Bioenerg Biomembr, 26:435–445. 1994.
371.
YanF, MoonSJ, LiuP, ZhaoZ, LipscombJD, LiuA, LiuHW. Determination of the substrate binding mode to the active site iron of (S)-2-hydroxypropylphosphonic acid epoxidase using 17O-Enriched substrates and substrate analogues. Biochemistry, 46:12628–12638. 2007.
372.
YuQ, HeikalAA. Two-photon autofluorescence dynamics imaging reveals sensitivity of intracellular NADH concentration and conformation to cell physiology at the single-cell level. J Photochem Photobiol B, 95:46–57. 2009.
373.
YunCH, YimSK, KimDH, AhnT. Functional expression of human cytochrome P450 enzymes in Escherichia coli. Curr Drug Metabol, 7:411–429. 2006.
374.
ZamboniN, MounceyN, HohmannHP, SauerU. Reducing maintenance metabolism by metabolic engineering of respiration improves riboflavin production by Bacillus subtilis. Metab Eng, 5:49–55. 2003.
375.
ZamboniN, FischerE, LaudertD, AymerichS, HohmannHP, SauerU. The Bacillus subtilis yqjI gene encodes the NADP+-dependent 6-P-gluconate dehydrogenase in the pentose phosphate pathway. J Bacteriol, 186:4528–4534. 2004.
376.
ZhaoHM, van der DonkWA. Regeneration of cofactors for use in biocatalysis. Curr Opin Biotech, 14:583–589. 2003.
377.
ZhengY–J, XiaZ–X, ChenZ–W, MathewsF, BruiceT. Catalytic mechanism of quinoprotein methanol dehydrogenase: A theoretical and x-ray crystallographic investigation. Proc Natl Acad Sci USA, 98:432–434. 2001.
378.
ZieglerDM. An overview of the mechanism, substrate specificities, and structure of FMOs. Drug Metab Rev, 34:503–511. 2002.
