NADPH-generating systems in bacteria and archaea

Frontiers in Microbiology

Volumn 6, Issue JUL, 2015, Pages

  Spaans, Sebastiaan K ^a   Weusthuis, Ruud A ^a   van der Oost, John ^a   Kengen, Servé W M ^a  

^a WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

Ferredoxin:NADP+ oxidoreductase; GAPN; Hydrogenase; Isocitrate dehydrogenase; Malic enzyme; NADPH regeneration; Pentose phosphate pathway; Transhydrogenase

Indexed keywords

GLUCOSE 6 PHOSPHATE DEHYDROGENASE; ISOCITRATE DEHYDROGENASE; MALATE DEHYDROGENASE (DECARBOXYLATING); NICOTINAMIDE ADENINE DINUCLEOTIDE (PHOSPHATE) TRANSHYDROGENASE; NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE; NICOTINAMIDE NUCLEOTIDE; NICOTINAMIDE RIBOSIDE; PHOSPHOGLUCONATE DEHYDROGENASE; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE;

APOPTOSIS; ARCHAEON; BACTERIUM; BIOTRANSFORMATION; CALCIUM HOMEOSTASIS; CARBON METABOLISM; CHLAMYDIA TRACHOMATIS; CORYNEBACTERIUM GLUTAMICUM; DEACETYLATION; DNA REPAIR; GAMMAPROTEOBACTERIA; GENE EXPRESSION; KLEBSIELLA PNEUMONIAE; METHANOCALDOCOCCUS JANNASCHII; MYCOBACTERIUM TUBERCULOSIS; NITROGEN FIXATION; NONHUMAN; OXIDATION REDUCTION POTENTIAL; REVIEW; SACCHAROMYCES CEREVISIAE; THERMODYNAMICS;

PROKARYOTA;

EID: 84938946682     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2015.00742     Document Type: Review

References (387)

1. Adachi, O., and Ameyama, M. (1981). d-Glucose dehydrogenase from Gluconobacter suboxydans: solubilization, purification and characterization. Agric. Biol. Chem. 45, 159-163.
2. Agledal, L., Niere, M., and Ziegler, M. (2010). The phosphate makes a difference: cellular functions of NADP. Redox Rep. 15, 2-10. doi: 10.1179/174329210X12650506623122
3. Ahmed, H., Ettema, T. J. G., Tjaden, B., Geerling, A. C. M., van der Oost, J., and Siebers, B. (2005). The semi-phosphorylative Entner-Doudoroff pathway in hyperthermophilic archaea: a re-evaluation. Biochem. J. 390, 529-540. doi: 10.1042/BJ20041711
4. Aliverti, A., Faber, R., Finnerty, C. M., Ferioli, C., Pandini, V., Negri, A., et al. (2001). Biochemical and crystallographic characterization of ferredoxin-NADP(+) reductase from nonphotosynthetic tissues. Biochemistry 40, 14501-14508. doi: 10.1021/bi011224c
5. Aliverti, A., Pandini, V., Pennati, A., de Rosa, M., and Zanetti, G. (2008). Structural and functional diversity of ferredoxin-NADP+ reductases. Arch. Biochem. Biophys. 474, 283-291. doi: 10.1016/j.abb.2008.02.014
6. Amador-Noguez, D., Brasg, I. A., Feng, X. J., Roquet, N., and Rabinowitz, J. D. (2011). Metabolome remodeling during the acidogenic-solventogenic transition in Clostridium acetobutylicum. Appl. Environ. Microbiol. 77, 7984-7997. doi: 10.1128/AEM.05374-11
7. Andersen, K. B., and von Meyenburg, K. (1977). Charges of nicotinamide adenine nucleotides and adenylate energy charge as regulatory parameters of the metabolism in Escherichia coli. J. Biol. Chem. 252, 4151-4156.
8. Angermayr, S. A., Paszota, M., and Hellingwerf, K. J. (2012). Engineering a cyanobacterial cell factory for production of lactic acid. Appl. Environ. Microbiol. 78, 7098-7106. doi: 10.1128/AEM.01587-12
9. Aoshima, M., and Igarashi, Y. (2008). Nondecarboxylating and decarboxylating isocitrate dehydrogenases: oxalosuccinate reductase as an ancestral form of isocitrate dehydrogenase. J. Bacteriol. 190, 2050-2055. doi: 10.1128/JB.01799-07
10. Aoshima, M., Ishii, M., and Igarashi, Y. (2004). A novel biotin protein required for reductive carboxylation of 2-oxoglutarate by isocitrate dehydrogenase in Hydrogenobacter thermophilus TK-6. Mol. Microbiol. 51, 791-798. doi: 10.1046/j.1365-2958.2003.03863.x
11. Arakaki, A. K., Ceccarelli, E. A., and Carrillo, N. (1997). Plant-type ferredoxin-NADP+ reductases: a basal structural framework and a multiplicity of functions. FASEB J. 11, 133-140.
12. Arnér, E. S. J., and Holmgren, A. (2000). Physiological functions of thioredoxin and thioredoxin reductase. Eur. J. Biochem. 267, 6102-6109. doi: 10.1046/j.1432-1327.2000.01701.x
13. Arutyunov, D., Schmalhausen, E., Orlov, V., Rahuel-Clermont, S., Nagradova, N., Branlant, G., et al. (2013). An unusual effect of NADP+ on the thermostability of the nonphosphorylating glyceraldehyde-3-phosphate dehydrogenase from Streptococcus mutans. Biochem. Cell Biol. 91, 295-302. doi: 10.1139/bcb-2012-0104
14. Asadollahi, M. A., Maury, J., Patil, K. R., Schalk, M., Clark, A., and Nielsen, J. (2009). Enhancing sesquiterpene production in Saccharomyces cerevisiae through in silico driven metabolic engineering. Metab. Eng. 11, 328-334. doi: 10.1016/j.ymben.2009.07.001
15. Bakke, P., Carney, N., Deloache, W., Gearing, M., Ingvorsen, K., Lotz, M., et al. (2009). Evaluation of three automated genome annotations for Halorhabdus utahensis. PLoS ONE 4:e6291. doi: 10.1371/journal.pone.0006291
16. Balconi, E., Pennati, A., Crobu, D., Pandini, V., Cerutti, R., Zanetti, G., et al. (2009). The ferredoxin-NADP+ reductase/ferredoxin electron transfer system of Plasmodium falciparum. FEBS J. 276, 3825-3836. doi: 10.1111/j.1742-4658.2009.07100.x
17. Banerjee, S., Nandyala, A., Podili, R., Katoch, V., and Hasnain, S. (2005). Comparison of Mycobacterium tuberculosis isocitrate dehydrogenases (ICD-1 and ICD-2) reveals differences in coenzyme affinity, oligomeric state, pH tolerance and phylogenetic affiliation. BMC Biochem. 6, 1-14. doi: 10.1186/1471-2091-6-20
18. Bark, K., Kampfer, P., Sponner, A., and Dott, W. (1993). Polyphosphate-dependent enzymes in some coryneform bacteria isolated from sewage sludge. FEMS Microbiol. Lett. 107, 133-138. doi: 10.1111/j.1574-6968.1993.tb06019.x
19. 13C metabolic flux analysis of pyruvate dehydrogenase complex-deficient, L-valine-producing Corynebacterium glutamicum. Appl. Environ. Microbiol. 77, 6644-6652. doi: 10.1128/AEM.00575-11
20. Bastian, S., Liu, X., Meyerowitz, J. T., Snow, C. D., Chen, M. M. Y., and Arnold, F. H. (2011). Engineered ketol-acid reductoisomerase and alcohol dehydrogenase enable anaerobic 2-methylpropan-1-ol production at theoretical yield in Escherichia coli. Metab. Eng. 13, 345-352. doi: 10.1016/j.ymben.2011.02.004
21. Becker, J., Klopprogge, C., Herold, A., Zelder, O., Bolten, C. J., and Wittmann, C. (2007). Metabolic flux engineering of l-lysine production in Corynebacterium glutamicum-over expression and modification of G6P dehydrogenase. J. Biotechnol. 132, 99-109. doi: 10.1016/j.jbiotec.2007.05.026
22. Becker, J., Klopprogge, C., Schroder, H., and Wittmann, C. (2009). Metabolic engineering of the tricarboxylic acid cycle for improved lysine production by Corynebacterium glutamicum. Appl. Environ. Microbiol. 75, 7866-7869. doi: 10.1128/AEM.01942-09
23. Becker, J., Klopprogge, C., Zelder, O., Heinzle, E., and Wittmann, C. (2005). 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. doi: 10.1128/AEM.71.12.8587-8596.2005
24. Begley, T. P., Kinsland, C., Mehl, R. A., Osterman, A., Dorrestein, P., and Gerald Litwack, T. B. (2001). The biosynthesis of nicotinamide adenine dinucleotides in bacteria. Vitam. Horm. 61, 103-119. doi: 10.1016/s0083-6729(01)61003-3
25. Beh, M., Strauss, G., Huber, R., Stetter, K.-O., and Fuchs, G. (1993). Enzymes of the reductive citric acid cycle in the autotrophic eubacterium Aquifex pyrophilus and in the archaebacterium Thermoproteus neutrophilus. Arch. Microbiol. 160, 306-311. doi: 10.1007/BF00292082
26. Bennett, B. D., Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., and Rabinowitz, J. D. (2009). Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat. Chem. Biol. 5, 593-599. doi: 10.1038/nchembio.186
27. Berk, H., and Thauer, R. K. (1997). Function of coenzyme F420-dependent NADP reductase in methanogenic archaea containing an NADP-dependent alcohol dehydrogenase. Arch. Microbiol. 168, 396-402. doi: 10.1007/s002030050514
28. Bi, J., Wang, H., and Xie, J. (2011). Comparative genomics of NAD(P) biosynthesis and novel antibiotic drug targets. J. Cell. Physiol. 226, 331-340. doi: 10.1002/jcp.22419
29. Bizouarn, T., Althage, M., Pedersen, A., Tigerström, A., Karlsson, J., Johansson, C., et al. (2002). The organization of the membrane domain and its interaction with the NADP(H)-binding site in proton-translocating transhydrogenase from E. coli. Biochim. Biophys. Acta Bioenerg. 1555, 122-127. doi: 10.1016/S0005-2728(02)00266-9
30. Bizouarn, T., Meuller, J., Axelsson, M., and Rydström, J. (2000). The transmembrane domain and the proton channel in proton-pumping transhydrogenases. Biochim. Biophys. Acta Bioenerg. 1459, 284-290. doi: 10.1016/S0005-2728(00)00163-8
31. Bock, A., King, P. W., Blokesch, M., and Posewitz, M. C. (2006). Maturation of hydrogenases. Adv. Microb. Physiol. 51, 1-71. doi: 10.1016/S0065-2911(06)51001-X
32. Bologna, F. P., Andreo, C. S., and Drincovich, M. F. (2007). Escherichia coli malic enzymes: two isoforms with substantial differences in kinetic properties, metabolic regulation, and structure. J. Bacteriol. 189, 5937-5946. doi: 10.1128/JB.00428-07
33. Bommareddy, R. R., Chen, Z., Rappert, S., and Zeng, A.-P. (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, 30-37. doi: 10.1016/j.ymben.2014.06.005
34. Boonstra, B., French, C. E., Wainwright, I., and Bruce, N. C. (1999). The udhA gene of Escherichia coli encodes a soluble pyridine nucleotide transhydrogenase. J. Bacteriol. 181, 1030-1034.
35. Boonstra, B., Rathbone, D. A., French, C. E., Walker, E. H., and Bruce, N. C. (2000). Cofactor regeneration by a soluble pyridine nucleotide transhydrogenase for biological production of hydromorphone. Appl. Environ. Microbiol. 66, 5161-5166. doi: 10.1128/AEM.66.12.5161-5166.2000
36. Boyd, D. A., Cvitkovitch, D. G., and Hamilton, I. R. (1995). Sequence, expression, and function of the gene for the nonphosphorylating, NADP-dependent glyceraldehyde-3-phosphate dehydrogenase of Streptococcus mutans. J. Bacteriol. 177, 2622-2627.
37. Bragg, P. D., Davies, P. L., and Hou, C. (1972). Function of energy-dependent transhydrogenase in Escherichia coli. Biochem. Biophys. Res. Commun. 47, 1248-1255. doi: 10.1016/0006-291X(72)90969-2
38. Brasen, C., Esser, D., Rauch, B., and Siebers, B. (2014). Carbohydrate metabolism in Archaea: current insights into unusual enzymes and pathways and their regulation. Microbiol. Mol. Biol. Rev. 78, 89-175. doi: 10.1128/MMBR.00041-13
39. Brown, D. I., and Griendling, K. K. (2009). Nox proteins in signal transduction. Free Radic. Biol. Med. 47, 1239-1253. doi: 10.1016/j.freeradbiomed.2009.07.023
40. Brunner, N. A., Brinkmann, H., Siebers, B., and Hensel, R. (1998). NAD+-dependent glyceraldehyde-3-phosphate dehydrogenase from Thermoproteus tenax. The first identified archaeal member of the aldehyde dehydrogenase superfamily is a glycolytic enzyme with unusual regulatory properties. J. Biol. Chem. 273, 6149-6156. doi: 10.1074/jbc.273.11.6149
41. Brunner, N. A., and Hensel, R. (2001). Nonphosphorylating glyceraldehyde-3-phosphate dehydrogenase from Thermoproteus tenax. Methods Enzymol. 331, 117-131. doi: 10.1016/S0076-6879(01)31051-0
42. Brunner, N. A., Siebers, B., and Hensel, R. (2001). Role of two different glyceraldehyde-3-phosphate dehydrogenases in controlling the reversible Embden-Meyerhof-Parnas pathway in Thermoproteus tenax: regulation on protein and transcript level. Extremophiles 5, 101-109. doi: 10.1007/s007920100181
43. Buckel, W., and Thauer, R. K. (2013). Energy conservation via electron bifurcating ferredoxin reduction and proton/Na(+) translocating ferredoxin oxidation. Biochim. Biophys. Acta 1827, 94-113. doi: 10.1016/j.bbabio.2012.07.002
44. Butler, J. R., and Mcguinness, E. T. (1982). Candida utilis NAD+ kinase: purification, properties and affinity gel studies. Int. J. Biochem. 14, 839-844. doi: 10.1016/0020-711X(82)90106-9
45. Butler, M. J., Bruheim, P., Jovetic, S., Marinelli, F., Postma, P. W., and Bibb, M. J. (2002). Engineering of primary carbon metabolism for improved antibiotic production in Streptomyces lividans. Appl. Environ. Microbiol. 68, 4731-4739. doi: 10.1128/AEM.68.10.4731-4739.2002
46. Bylund, J., Brown, K. L., Movitz, C., Dahlgren, C., and Karlsson, A. (2010). Intracellular generation of superoxide by the phagocyte NADPH oxidase: how, where, and what for?. Free Radic. Biol. Med. 49, 1834-1845. doi: 10.1016/j.freeradbiomed.2010.09.016
47. Canonaco, F., Hess, T. A., Heri, S., Wang, T., Szyperski, T., and Sauer, U. (2001). Metabolic flux response to phosphoglucose isomerase knock-out in Escherichia coli and impact of overexpression of the soluble transhydrogenase UdhA. FEMS Microbiol. Lett. 204, 247-252. doi: 10.1111/j.1574-6968.2001.tb10892.x
48. Cao, Z., Song, P., Xu, Q., Su, R., and Zhu, G. (2011). Overexpression and biochemical characterization of soluble pyridine nucleotide transhydrogenase from Escherichia coli. FEMS Microbiol. Lett. 320, 9-14. doi: 10.1111/j.1574-6968.2011.02287.x
49. Carrillo, N., and Ceccarelli, E. A. (2003). Open questions in ferredoxin-NADP+ reductase catalytic mechanism. Eur. J. Biochem. 270, 1900-1915. doi: 10.1046/j.1432-1033.2003.03566.x
50. Casalot, L., De Luca, G., Dermoun, Z., Rousset, M., and de Philip, P. (2002). Evidence for a fourth hydrogenase in Desulfovibrio fructosovorans. J. Bacteriol. 184, 853-856. doi: 10.1128/JB.184.3.853-856.2002
51. Ceccarelli, E. A., Arakaki, A. K., Cortez, N., and Carrillo, N. (2004). Functional plasticity and catalytic efficiency in plant and bacterial ferredoxin-NADP(H) reductases. Biochim. Biophys. Acta 1698, 155-165. doi: 10.1016/j.bbapap.2003.12.005
52. Celton, M., Goelzer, A., Camarasa, C., Fromion, V., and Dequin, S. (2012). A constraint-based model analysis of the metabolic consequences of increased NADPH oxidation in Saccharomyces cerevisiae. Metab. Eng. 14, 366-379. doi: 10.1016/j.ymben.2012.03.008
53. Centeno-Leija, S., Huerta-Beristain, G., Giles-Gomez, M., Bolivar, F., Gosset, G., and Martinez, A. (2014). Improving poly-3-hydroxybutyrate production in Escherichia coli by combining the increase in the NADPH pool and acetyl-CoA availability. Antonie Van Leeuwenhoek 105, 687-696. doi: 10.1007/s10482-014-0124-5
54. Centeno-Leija, S., Utrilla, J., Flores, N., Rodriguez, A., Gosset, G., and Martinez, A. (2013). Metabolic and transcriptional response of Escherichia coli with a NADP(+)-dependent glyceraldehyde 3-phosphate dehydrogenase from Streptococcus mutans. Antonie Van Leeuwenhoek 104, 913-924. doi: 10.1007/s10482-013-0010-6
55. Chang, D. Y., Hou, C., and Bragg, P. D. (1992). Anomalous effect of uncouplers on respiratory chain-linked transhydrogenation in Escherichia coli membranes: evidence for a localized proton pathway?. Arch. Biochem. Biophys. 293, 246-253. doi: 10.1016/0003-9861(92)90392-A
56. Chang, G.-G., and Tong, L. (2003). Structure and function of malic enzymes, a new class of oxidative decarboxylases. Biochemistry 42, 12721-12733. doi: 10.1021/bi035251+
57. Chemler, J. A., Fowler, Z. L., Mchugh, K. P., and Koffas, M. A. G. (2010). Improving NADPH availability for natural product biosynthesis in Escherichia coli by metabolic engineering. Metab. Eng. 12, 96-104. doi: 10.1016/j.ymben.2009.07.003
58. Chen, R., and Jeong, S. S. (2000). Functional prediction: identification of protein orthologs and paralogs. Protein Sci. 9, 2344-2353. doi: 10.1110/ps.9.12.2344
59. Chenault, H. K., Simon, E. S., and Whitesides, G. M. (1988). Cofactor regeneration for enzyme-catalysed synthesis. Biotechnol. Genet. Eng. Rev. 6, 221-270. doi: 10.1080/02648725.1988.10647849
60. Chenault, H. K., and Whitesides, G. M. (1987). Regeneration of nicotinamide cofactors for use in organic synthesis. Appl. Biochem. Biotechnol. 14, 147-197. doi: 10.1007/BF02798431
61. Chin, J. W., and Cirino, P. C. (2011). Improved NADPH supply for xylitol production by engineered Escherichia Coli with glycolytic mutations. Biotechnol. Prog. 27, 333-341. doi: 10.1002/btpr.559
62. Chin, J. W., Khankal, R., Monroe, C. A., Maranas, C. D., and Cirino, P. C. (2009). Analysis of NADPH supply during xylitol production by engineered Escherichia coli. Biotechnol. Bioeng. 102, 209-220. doi: 10.1002/bit.22060
63. Chini, E. N., and De Toledo, F. G. S. (2002). Nicotinic acid adenine dinucleotide phosphate: a new intracellular second messenger?. Am. J. Physiol. Cell Physiol. 282, C1191-C1198. doi: 10.1152/ajpcell.00475.2001
64. Choi, J.-C., Shin, H.-D., and Lee, Y.-H. (2003). Modulation of 3-hydroxyvalerate molar fraction in poly(3-hydroxybutyrate-3-hydroxyvalerate) using Ralstonia eutropha transformant co-amplifying phbC and NADPH generation-related zwf genes. Enzyme Microb. Technol. 32, 178-185. doi: 10.1016/S0141-0229(02)00274-0
65. Christiansen, T., Christensen, B., and Nielsen, J. (2002). Metabolic network analysis of Bacillus clausii on minimal and semirich medium using (13)C-labeled glucose. Metab. Eng. 4, 159-169. doi: 10.1006/mben.2001.0219
66. Churamani, D., Carrey, E. A., Dickinson, G. D., and Patel, S. (2004). Determination of cellular nicotinic acid-adenine dinucleotide phosphate (NAADP) levels. Biochem. J. 380, 449-454. doi: 10.1042/BJ20031754
67. Cohen, P. T., and Kaplan, N. O. (1970). Purification and properties of the pyridine nucleotide transhydrogenase from Pseudomonas aeruginosa. J. Biol. Chem. 245, 2825-2836.
68. Conway, T. (1992). The entner-doudoroff pathway: history, physiology and molecular biology. FEMS Microbiol. Rev. 9, 1-27. doi: 10.1111/j.1574-6968.1992.tb05822.x
69. Cotton, N. P., Lever, T. M., Nore, B. F., Jones, M. R., and Jackson, J. B. (1989). The coupling between protonmotive force and the NAD(P)+ transhydrogenase in chromatophores from photosynthetic bacteria. Eur. J. Biochem. 182, 593-603. doi: 10.1111/j.1432-1033.1989.tb14868.x
70. Cozzone, A. J. (1998). Regulation of acetate metabolism by protein phosphorylation in enteric bacteria. Annu. Rev. Microbiol. 52, 127-164. doi: 10.1146/annurev.micro.52.1.127
71. Crow, V. L., and Wittenberger, C. L. (1979). Separation and properties of NAD+-and NADP+-dependent glyceraldehyde-3-phosphate dehydrogenases from Streptococcus mutans. J. Biol. Chem. 254, 1134-1142.
72. Dauner, M., Storni, T., and Sauer, U. (2001). Bacillus subtilis metabolism and energetics in carbon-limited and excess-carbon chemostat culture. J. Bacteriol. 183, 7308-7317. doi: 10.1128/JB.183.24.7308-7317.2001
73. Davis, W. B. (1980). Identification of a nicotinamide adenine dinucleotide glycohydrolase and an associated inhibitor in isoniazid-susceptible and-resistant Mycobacterium phlei. Antimicrob. Agents Chemother. 17, 663-668. doi: 10.1128/AAC.17.4.663
74. Decorosi, F., Lori, L., Santopolo, L., Tatti, E., Giovannetti, L., and Viti, C. (2011). Characterization of a Cr(VI)-sensitive Pseudomonas corrugata 28 mutant impaired in a pyridine nucleotide transhydrogenase gene. Res. Microbiol. 162, 747-755. doi: 10.1016/j.resmic.2011.06.014
75. Driscoll, B. T., and Finan, T. M. (1997). Properties of NAD(+)-and NADP(+)-dependent malic enzymes of Rhizobium (Sinorhizobium) meliloti and differential expression of their genes in nitrogen-fixing bacteroids. Microbiology 143(Pt 2), 489-498. doi: 10.1099/00221287-143-2-489
76. Eguchi, T., Kuge, Y., Inoue, K., Yoshikawa, N., Mochida, K., and Uwajima, T. (1992). NADPH regeneration by glucose dehydrogenase from Gluconobacter scleroides for l-leucovorin synthesis. Biosci. Biotechnol. Biochem. 56, 701-703. doi: 10.1271/bbb.56.701
77. Eikmanns, B. J., Rittmann, D., and Sahm, H. (1995). Cloning, sequence analysis, expression, and inactivation of the Corynebacterium glutamicum icd gene encoding isocitrate dehydrogenase and biochemical characterization of the enzyme. J. Bacteriol. 177, 774-782.
78. English, C. M., Eckert, C., Brown, K., Seibert, M., and King, P. W. (2009). Recombinant and in vitro expression systems for hydrogenases: new frontiers in basic and applied studies for biological and synthetic H2 production. Dalton Trans. 9970-9978. doi: 10.1039/b913426n
79. Espariz, M., Repizo, G., Blancato, V., Mortera, P., Alarcon, S., and Magni, C. (2011). Identification of malic and soluble oxaloacetate decarboxylase enzymes in Enterococcus faecalis. FEBS J. 278, 2140-2151. doi: 10.1111/j.1742-4658.2011.08131.x
80. Esser, D., Kouril, T., Talfournier, F., Polkowska, J., Schrader, T., Bräsen, C., et al. (2013). Unraveling the function of paralogs of the aldehyde dehydrogenase super family from Sulfolobus solfataricus. Extremophiles 17, 205-216. doi: 10.1007/s00792-012-0507-3
81. Ettema, T. J. G., Ahmed, H., Geerling, A. C. M., Van Der Oost, J., and Siebers, B. (2008). The non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN) of Sulfolobus solfataricus: a key-enzyme of the semi-phosphorylative branch of the Entner-Doudoroff pathway. Extremophiles 12, 75-88. doi: 10.1007/s00792-007-0082-1
82. Everse, J., Griffin, J. B., and Kaplan, N. O. (1975). The pyridine nucleosidase from Bacillus subtilis. Kinetic properties and enzyme-inhibitor interactions. Arch. Biochem. Biophys. 169, 714-723. doi: 10.1016/0003-9861(75)90216-7
83. Ewen, K. M., Kleser, M., and Bernhardt, R. (2011). Adrenodoxin: the archetype of vertebrate-type [2Fe-2S] cluster ferredoxins. Biochim. Biophys. Acta Proteins Proteomics 1814, 111-125. doi: 10.1016/j.bbapap.2010.06.003
84. Fabris, M., Matthijs, M., Rombauts, S., Vyverman, W., Goossens, A., and Baart, G. J. E. (2012). The metabolic blueprint of Phaeodactylum tricornutum reveals a eukaryotic Entner-Doudoroff glycolytic pathway. Plant J. 70, 1004-1014. doi: 10.1111/j.1365-313X.2012.04941.x
85. Ferri, S., Kojima, K., and Sode, K. (2011). Review of glucose oxidases and glucose dehydrogenases: a bird's eye view of glucose sensing enzymes. J. Diabetes Sci. Technol. 5, 1068-1076. doi: 10.1177/193229681100500507
86. Fillinger, S., Boschi-Muller, S., Azza, S. D., Dervyn, E., Branlant, G., and Aymerich, S. (2000). Two Glyceraldehyde-3-phosphate dehydrogenases with opposite physiological roles in a nonphotosynthetic bacterium. J. Biol. Chem. 275, 14031-14037. doi: 10.1074/jbc.275.19.14031
87. Fischer, E., and Sauer, U. (2003). A novel metabolic cycle catalyzes glucose oxidation and anaplerosis in hungry Escherichia coli. J. Biol. Chem. 278, 46446-46451. doi: 10.1074/jbc.M307968200
88. Flamholz, A., Noor, E., Bar-Even, A., and Milo, R. (2012). eQuilibrator-the biochemical thermodynamics calculator. Nucleic Acids Res. 40, D770-D775. doi: 10.1093/nar/gkr874
89. Foreman, J., Demidchik, V., Bothwell, J. H. F., Mylona, P., Miedema, H., Torres, M. A., et al. (2003). Reactive oxygen species produced by NADPH oxidase regulate plant cell growth. Nature 422, 442-446. doi: 10.1038/nature01485
90. Forzi, L., and Sawers, R. G. (2007). Maturation of [NiFe]-hydrogenases in Escherichia coli. Biometals 20, 565-578. doi: 10.1007/s10534-006-9048-5
91. French, C. E., Boonstra, B., Bufton, K. A., and Bruce, N. C. (1997). Cloning, sequence, and properties of the soluble pyridine nucleotide transhydrogenase of Pseudomonas fluorescens. J. Bacteriol. 179, 2761-2765.
92. Frenkel, R. (1975). Regulation and physiological functions of malic enzymes. Curr. Top. Cell. Regul. 9, 157-181. doi: 10.1016/B978-0-12-152809-6.50012-3
93. Fuhrer, T., Fischer, E., and Sauer, U. (2005). Experimental identification and quantification of glucose metabolism in seven bacterial species. J. Bacteriol. 187, 1581-1590. doi: 10.1128/JB.187.5.1581-1590.2005
94. Fuhrer, T., and Sauer, U. (2009). Different biochemical mechanisms ensure network-wide balancing of reducing equivalents in microbial metabolism. J. Bacteriol. 191, 2112-2121. doi: 10.1128/JB.01523-08
95. Fukuda, C., Kawai, S., and Murata, K. (2007). NADP(H) Phosphatase activities of archaeal inositol monophosphatase and eubacterial 3'-Phosphoadenosine 5'-Phosphate phosphatase. Appl. Environ. Microbiol. 73, 5447-5452. doi: 10.1128/AEM.02703-06
96. Fukuda, W., Ismail, Y. S., Fukui, T., Atomi, H., and Imanaka, T. (2005). Characterization of an archaeal malic enzyme from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. Archaea 1, 293-301. doi: 10.1155/2005/250757
97. Garavaglia, S., Galizzi, A., and Rizzi, M. (2003). Allosteric regulation of Bacillus subtilis NAD kinase by quinolinic acid. J. Bacteriol. 185, 4844-4850. doi: 10.1128/JB.185.16.4844-4850.2003
98. Garrido-Pertierra, A., Martinez Marcos, C., Martin Fernandez, M., and Ruiz-Amil, M. (1983). Properties and function of malate enzyme from Pseudomonas putida. Biochimie 65, 629-635. doi: 10.1016/S0300-9084(84)80026-7
99. Gazzaniga, F., Stebbins, R., Chang, S. Z., Mcpeek, M. A., and Brenner, C. (2009). Microbial NAD metabolism: lessons from comparative genomics. Microbiol. Mol. Biol. Rev. 73, 529-541. doi: 10.1128/MMBR.00042-08
100. Gerdes, S. Y., Scholle, M. D., D'souza, M., Bernal, A., Baev, M. V., Farrell, M., et al. (2002). From genetic footprinting to antimicrobial drug targets: examples in cofactor biosynthetic pathways. J. Bacteriol. 184, 4555-4572. doi: 10.1128/JB.184.16.4555-4572.2002
101. Germer, F., Zebger, I., Saggu, M., Lendzian, F., Schulz, R., and Appel, J. (2009). Overexpression, isolation, and spectroscopic characterization of the bidirectional [NiFe] hydrogenase from Synechocystis sp. PCC 6803. J. Biol. Chem. 284, 36462-36472. doi: 10.1074/jbc.M109.028795
102. Ghosh, J., Anderson, P. J., Chandrasekaran, S., and Caparon, M. G. (2010). Characterization of Streptococcus pyogenes beta-NAD+ glycohydrolase: re-evaluation of enzymatic properties associated with pathogenesis. J. Biol. Chem. 285, 5683-5694. doi: 10.1074/jbc.M109.070300
103. Giro, M., Carrillo, N., and Krapp, A. R. (2006). Glucose-6-phosphate dehydrogenase and ferredoxin-NADP(H) reductase contribute to damage repair during the soxRS response of Escherichia coli. Microbiology 152, 1119-1128. doi: 10.1099/mic.0.28612-0
104. Goss, T., and Hanke, G. (2014). The end of the line: can ferredoxin and ferredoxin NADP(H) oxidoreductase determine the fate of photosynthetic electrons?. Curr. Protein Pept. Sci. 15, 385-393. doi: 10.2174/1389203715666140327113733
105. Gossmann, T. I., Ziegler, M., Puntervoll, P., De Figueiredo, L. F., Schuster, S., and Heiland, I. (2012). NAD+ biosynthesis and salvage-a phylogenetic perspective. FEBS J. 279, 3355-3363. doi: 10.1111/j.1742-4658.2012.08559.x
106. Gourdon, P., Baucher, M. F., Lindley, N. D., and Guyonvarch, A. (2000). Cloning of the malic enzyme gene from Corynebacterium glutamicum and role of the enzyme in lactate metabolism. Appl. Environ. Microbiol. 66, 2981-2987. doi: 10.1128/AEM.66.7.2981-2987.2000
107. Grose, J. H., Joss, L., Velick, S. F., and Roth, J. R. (2006). Evidence that feedback inhibition of NAD kinase controls responses to oxidative stress. Proc. Natl. Acad. Sci. U.S.A. 103, 7601-7606. doi: 10.1073/pnas.0602494103
108. Grzeszik, C., Lubbers, M., Reh, M., and Schlegel, H. G. (1997). Genes encoding the NAD-reducing hydrogenase of Rhodococcus opacus MR11. Microbiology 143(Pt 4), 1271-1286. doi: 10.1099/00221287-143-4-1271
109. Guo, Z.-P., Zhang, L., Ding, Z.-Y., Wang, Z.-X., and Shi, G.-Y. (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, 935-943. doi: 10.1007/s10295-010-0864-9
110. Hansen, E. J., and Juni, E. (1975). Isolation of mutants of Escherichia coli lacking NAD-and NADP-linked malic. Biochem. Biophys. Res. Commun. 65, 559-566. doi: 10.1016/S0006-291X(75)80183-5
111. Harold, F. M. (1986). The Vital Force: A Study of Bioenergetics. New York, NY: W. H. Freeman.
112. 13C-metabolic flux analysis. Biotechnol. Bioeng. 111, 575-585. doi: 10.1002/bit.25124
113. Hickman, J. W., Barber, R. D., Skaar, E. P., and Donohue, T. J. (2002). Link between the membrane-bound pyridine nucleotide transhydrogenase and glutathione-dependent processes in Rhodobacter sphaeroides. J. Bacteriol. 184, 400-409. doi: 10.1128/JB.184.2.400-409.2002
114. Hoek, J. B., and Rydstrom, J. (1988). Physiological roles of nicotinamide nucleotide transhydrogenase. Biochem. J. 254, 1-10.
115. Hojeberg, B., and Rydstrom, J. (1977). Ca2+-dependent allosteric regulation of nicotinamide nucleotide transhydrogenase from Pseudomonas aeruginosa. Eur. J. Biochem. 77, 235-241. doi: 10.1111/j.1432-1033.1977.tb11662.x
116. Hong, S. H., and Lee, S. Y. (2001). Metabolic flux analysis for succinic acid production by recombinant Escherichia coli with amplified malic enzyme activity. Biotechnol. Bioeng. 74, 89-95. doi: 10.1002/bit.1098
117. Hsieh, J.-Y., and Hung, H.-C. (2009). Engineering of the cofactor specificities and isoform-specific inhibition of malic enzyme. J. Biol. Chem. 284, 4536-4544. doi: 10.1074/jbc.M807008200
118. Hua, Q., Yang, C., Baba, T., Mori, H., and Shimizu, K. (2003). Responses of the central metabolism in Escherichia coli to phosphoglucose isomerase and glucose-6-phosphate dehydrogenase knockouts. J. Bacteriol. 185, 7053-7067. doi: 10.1128/JB.185.24.7053-7067.2003
119. Huang, H., Wang, S., Moll, J., and Thauer, R. K. (2012). Electron bifurcation involved in the energy metabolism of the acetogenic bacterium Moorella thermoacetica growing on glucose or H2 plus CO2. J. Bacteriol. 194, 3689-3699. doi: 10.1128/JB.00385-12
120. Huang, M., Wang, Y., Liu, J., and Mao, Z. (2011). Multiple strategies for metabolic engineering of Escherichia coli for efficient production of coenzyme. Chin. J. Chem. Eng. 19, 316-326. doi: 10.1016/S1004-9541(11)60171-7
121. Hügler, M., Menendez, C., Schägger, H., and Fuchs, G. (2002). Malonyl-coenzyme a reductase from Chloroflexus aurantiacus, a key enzyme of the 3-Hydroxypropionate cycle for autotrophic CO2 Fixation. J. Bacteriol. 184, 2404-2410. doi: 10.1128/JB.184.9.2404-2410.2002
122. Iddar, A., Valverde, F., Assobhei, O., Serrano, A., and Soukri, A. (2005). Widespread occurrence of non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase among gram-positive bacteria. Int. Microbiol. 8, 251-258.
123. Iddar, A., Valverde, F., Serrano, A., and Soukri, A. (2002). Expression, purification, and characterization of recombinant nonphosphorylating NADP-dependent glyceraldehyde-3-phosphate dehydrogenase from Clostridium acetobutylicum. Protein Expr. Purif. 25, 519-526. doi: 10.1016/S1046-5928(02)00032-3
124. Iddar, A., Valverde, F., Serrano, A., and Soukri, A. (2003). Purification of recombinant non-phosphorylating NADP-dependent glyceraldehyde-3-phosphate dehydrogenase from Streptococcus pyogenes expressed in E. coli. Mol. Cell. Biochem. 247, 195-203. doi: 10.1023/A:1024112027440
125. Ikeda, T., Nakamura, M., Arai, H., Ishii, M., and Igarashi, Y. (2009). Ferredoxin-NADP reductase from the thermophilic hydrogen-oxidizing bacterium, Hydrogenobacter thermophilus TK-6. FEMS Microbiol. Lett. 297, 124-130. doi: 10.1111/j.1574-6968.2009.01667.x
126. Imam, S., Noguera, D. R., and Donohue, T. J. (2013). Global insights into energetic and metabolic networks in Rhodobacter sphaeroides. BMC Syst. Biol. 7:89. doi: 10.1186/1752-0509-7-89
127. Inoue, H., Tamura, T., Ehara, N., Nishito, A., Nakayama, Y., Maekawa, M., et al. (2002). Biochemical and molecular characterization of the NAD(+)-dependent isocitrate dehydrogenase from the chemolithotroph Acidithiobacillus thiooxidans. FEMS Microbiol. Lett. 214, 127-132. doi: 10.1111/j.1574-6968.2002.tb11335.x
128. Ito, F., Chishiki, H., Fushinobu, S., and Wakagi, T. (2012). Comparative analysis of two glyceraldehyde-3-phosphate dehydrogenases from a thermoacidophilic archaeon, Sulfolobus tokodaii. FEBS Lett. 586, 3097-3103. doi: 10.1016/j.febslet.2012.07.059
129. Iwakura, M., Tokushige, M., Katsuki, H., and Muramatsu, S. (1978). Studies on regulatory functions of malic enzymes. V. Comparative studies of malic enzymes in bacteria. J. Biochem. 83, 1387-1394.
130. Jackson, B., Brocker, C., Thompson, D. C., Black, W., Vasiliou, K., Nebert, D. W., et al. (2011). Update on the aldehyde dehydrogenase gene (ALDH) superfamily. Hum. Genomics 5, 283-303. doi: 10.1186/1479-7364-5-4-283
131. Jackson, J. B. (2003). Proton translocation by transhydrogenase. FEBS Lett. 545, 18-24. doi: 10.1016/S0014-5793(03)00388-0
132. Jackson, J. B. (2012). A review of the binding-change mechanism for proton-translocating transhydrogenase. Biochim. Biophys. Acta 1817, 1839-1846. doi: 10.1016/j.bbabio.2012.04.006
133. Jackson, J. B., and Obiozo, U. M. (2009). "Proton-translocating transhydrogenase in photosynthetic bacteria," in The Purple Phototrophic Bacteria, eds C. N. Hunter, F. Daldal, M. Thurnauer, and J. T. Beatty (Dordrecht: Springer), 495-508.
134. Jackson, J. B., Quirk, P. G., Cotton, N. P., Venning, J. D., Gupta, S., Bizouarn, T., et al. (1998). Interdomain hydride transfer in proton-translocating transhydrogenase. Biochim. Biophys. Acta 1365, 79-86. doi: 10.1016/S0005-2728(98)00046-2
135. Jain, M. K., Datta, R., and Zeikus, J. G. (1989). "High-value organic acids fermentation-emerging processes and products," in Bioprocess Engineering: The First Generation, ed T. K. Ghose (Chichester: Ellis Horwood Ltd), 366-389.
136. Jan, J., Martinez, I., Wang, Y., Bennett, G. N., and San, K.-Y. (2013). Metabolic engineering and transhydrogenase effects on NADPH availability in Escherichia coli. Biotechnol. Prog. 29, 1124-1130. doi: 10.1002/btpr.1765
137. Jiang, L.-Y., Zhang, Y.-Y., Li, Z., and Liu, J.-Z. (2013). Metabolic engineering of Corynebacterium glutamicum for increasing the production of L-ornithine by increasing NADPH availability. J. Ind. Microbiol. Biotechnol. 40, 1143-1151. doi: 10.1007/s10295-013-1306-2
138. Jiao, Z., Baba, T., Mori, H., and Shimizu, K. (2003). Analysis of metabolic and physiological responses to gnd knockout in Escherichia coli by using C-13 tracer experiment and enzyme activity measurement. FEMS Microbiol. Lett. 220, 295-301. doi: 10.1016/S0378-1097(03)00133-2
139. Jonsbu, E., Christensen, B., and Nielsen, J. (2001). Changes of in vivo fluxes through central metabolic pathways during the production of nystatin by Streptomyces noursei in batch culture. Appl. Microbiol. Biotechnol. 56, 93-100. doi: 10.1007/s002530100613
140. Kabir, M. M., and Shimizu, K. (2003). Fermentation characteristics and protein expression patterns in a recombinant Escherichia coli mutant lacking phosphoglucose isomerase for poly(3-hydroxybutyrate) production. Appl. Microbiol. Biotechnol. 62, 244-255. doi: 10.1007/s00253-003-1257-z
141. Kabir, M. M., and Shimizu, K. (2004). Metabolic regulation analysis of icd-gene knockout Escherichia coli based on 2D electrophoresis with MALDI-TOF mass spectrometry and enzyme activity measurements. Appl. Microbiol. Biotechnol. 65, 84-96. doi: 10.1007/s00253-004-1627-1
142. Kabus, A., Georgi, T., Wendisch, V. F., and Bott, M. (2007). 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. doi: 10.1007/s00253-006-0804-9
143. Kanai, T., Ito, S., and Imanaka, T. (2003). Characterization of a cytosolic NiFe-hydrogenase from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. J. Bacteriol. 185, 1705-1711. doi: 10.1128/JB.185.5.1705-1711.2003
144. Kanai, T., Matsuoka, R., Beppu, H., Nakajima, A., Okada, Y., Atomi, H., et al. (2011). Distinct physiological roles of the three [NiFe]-hydrogenase orthologs in the hyperthermophilic archaeon Thermococcus kodakarensis. J. Bacteriol. 193, 3109-3116. doi: 10.1128/JB.01072-10
145. Kanao, T., Kawamura, M., Fukui, T., Atomi, H., and Imanaka, T. (2002). Characterization of isocitrate dehydrogenase from the green sulfur bacterium Chlorobium limicola. A carbon dioxide-fixing enzyme in the reductive tricarboxylic acid cycle. Eur. J. Biochem./FEBS 269, 1926-1931. doi: 10.1046/j.1432-1033.2002.02849.x
146. Kao, K. C., Tran, L. M., and Liao, J. C. (2005). A global regulatory role of gluconeogenic genes in Escherichia coli revealed by transcriptome network analysis. J. Biol. Chem. 280, 36079-36087. doi: 10.1074/jbc.M508202200
147. Karplus, P. A., and Faber, H. R. (2004). Structural aspects of plant ferredoxin: NADP(+) oxidoreductases. Photosyn. Res. 81, 303-315. doi: 10.1023/B:PRES.0000036884.57303.2e
148. Kataoka, M., Sri Rohani, L. P., Wada, M., Kita, K., Yanase, H., Urabe, I., et al. (1998). Escherichia coli transformant expressing the glucose dehydrogenase gene from Bacillus megaterium as a cofactor regenerator in a chiral alcohol production system. Biosci. Biotechnol. Biochem. 62, 167-169. doi: 10.1271/bbb.62.167
149. Kataoka, M., Yamamoto, K., Kawabata, H., Wada, M., Kita, K., Yanase, H., et al. (1999). Stereoselective reduction of ethyl 4-chloro-3-oxobutanoate by Escherichia coli transformant cells coexpressing the aldehyde reductase and glucose dehydrogenase genes. Appl. Microbiol. Biotechnol. 51, 486-490. doi: 10.1007/s002530051421
150. Kawai, S., Fukuda, C., Mukai, T., and Murata, K. (2005). MJ0917 in archaeon Methanococcus jannaschii is a novel NADP phosphatase/NAD kinase. J. Biol. Chem. 280, 39200-39207. doi: 10.1074/jbc.M506426200
151. Kawai, S., Mori, S., Mukai, T., Hashimoto, W., and Murata, K. (2001). Molecular characterization of Escherichia coli NAD kinase. Eur. J. Biochem. 268, 4359-4365. doi: 10.1046/j.1432-1327.2001.02358.x
152. Kawai, S., Mori, S., Mukai, T., and Murata, K. (2004). Cytosolic NADP phosphatases I and II from Arthrobacter sp. strain KM: implication in regulation of NAD+/NADP+ balance. J. Basic Microbiol. 44, 185-196. doi: 10.1002/jobm.200310362
153. Kawai, S., Mori, S., Mukai, T., Suzuki, S., Yamada, T., Hashimoto, W., et al. (2000). Inorganic Polyphosphate/ATP-NAD Kinase of Micrococcus flavus and Mycobacterium tuberculosis H37Rv. Biochem. Biophys. Res. Commun. 276, 57-63. doi: 10.1006/bbrc.2000.3433
154. Kawai, S., and Murata, K. (2008). Structure and function of NAD kinase and NADP phosphatase: key enzymes that regulate the intracellular balance of NAD(H) and NADP(H). Biosci. Biotechnol. Biochem. 72, 919-930. doi: 10.1271/bbb.70738
155. Kawai, S., Suzuki, H., Yamamoto, K., Inui, M., Yukawa, H., and Kumagai, H. (1996). Purification and characterization of a malic enzyme from the ruminal bacterium Streptococcus bovis ATCC 15352 and cloning and sequencing of its gene. Appl. Environ. Microbiol. 62, 2692-2700.
156. Kelly, G. J., and Gibbs, M. (1973). Nonreversible d-glyceraldehyde 3-phosphate dehydrogenase of plant tissues. Plant Physiol. 52, 111-118. doi: 10.1104/pp.52.2.111
157. Kim, Y. M., Cho, H.-S., Jung, G. Y., and Park, J. M. (2011). Engineering the pentose phosphate pathway to improve hydrogen yield in recombinant Escherichia coli. Biotechnol. Bioeng. 108, 2941-2946. doi: 10.1002/bit.23259
158. Kizaki, N., Yasohara, Y., Hasegawa, J., Wada, M., Kataoka, M., and Shimizu, S. (2001). Synthesis of optically pure ethyl (S)-4-chloro-3-hydroxybutanoate by Escherichia coli transformant cells coexpressing the carbonyl reductase and glucose dehydrogenase genes. Appl. Microbiol. Biotechnol. 55, 590-595. doi: 10.1007/s002530100599
159. Klasen, R., Bringer-Meyer, S., and Sahm, H. (1995). Biochemical characterization and sequence analysis of the gluconate:NADP 5-oxidoreductase gene from Gluconobacter oxydans. J. Bacteriol. 177, 2637-2643.
160. Kletzien, R. F., Harris, P. K., and Foellmi, L. A. (1994). Glucose-6-phosphate dehydrogenase: a "housekeeping" enzyme subject to tissue-specific regulation by hormones, nutrients, and oxidant stress. FASEB J. 8, 174-181.
161. Kobayashi, K., Ehrlich, S. D., Albertini, A., Amati, G., Andersen, K. K., Arnaud, M., et al. (2003). Essential Bacillus subtilis genes. Proc. Natl. Acad. Sci. U.S.A. 100, 4678-4683. doi: 10.1073/pnas.0730515100
162. Koh, H.-J., Lee, S.-M., Son, B.-G., Lee, S.-H., Ryoo, Z. Y., Chang, K.-T., et al. (2004). Cytosolic NADP+-dependent isocitrate dehydrogenase plays a key role in lipid metabolism. J. Biol. Chem. 279, 39968-39974. doi: 10.1074/jbc.M402260200
163. Koksharova, O., Schubert, M., Shestakov, S., and Cerff, R. (1998). Genetic and biochemical evidence for distinct key functions of two highly divergent GAPDH genes in catabolic and anabolic carbon flow of the cyanobacterium Synechocystis sp. PCC 6803. Plant Mol. Biol. 36, 183-194. doi: 10.1023/A:1005925732743
164. Komori, H., Seo, D., Sakurai, T., and Higuchi, Y. (2010). Crystal structure analysis of Bacillus subtilis ferredoxin-NADP(+) oxidoreductase and the structural basis for its substrate selectivity. Protein Sci. 19, 2279-2290. doi: 10.1002/pro.508
165. Kornberg, A. (1950). Enzymatic synthesis of triphosphopyridine nucleotide. J. Biol. Chem. 182, 805-813.
166. Kramer, D. M., and Evans, J. R. (2011). The importance of energy balance in improving photosynthetic productivity. Plant Physiol. 155, 70-78. doi: 10.1104/pp.110.166652
167. Krapp, A. R., Rodriguez, R. E., Poli, H. O., Paladini, D. H., Palatnik, J. F., and Carrillo, N. (2002). The flavoenzyme ferredoxin (flavodoxin)-NADP(H) reductase modulates NADP(H) homeostasis during the soxRS response of Escherichia coli. J. Bacteriol. 184, 1474-1480. doi: 10.1128/JB.184.5.1474-1480.2002
168. Kuo, C. C., Tsai, L. C., Chin, T. Y., Chang, G. G., and Chou, W. Y. (2000). Lysine residues 162 and 340 are involved in the catalysis and coenzyme binding of NADP(+)-dependent malic enzyme from pigeon. Biochem. Biophys. Res. Commun. 270, 821-825. doi: 10.1006/bbrc.2000.2502
169. Kurnasov, O., Goral, V., Colabroy, K., Gerdes, S., Anantha, S., Osterman, A., et al. (2003). NAD biosynthesis: identification of the tryptophan to quinolinate pathway in bacteria. Chem. Biol. 10, 1195-1204. doi: 10.1016/j.chembiol.2003.11.011
170. Labesse, G., Douguet, D., Assairi, L., and Gilles, A. M. (2002). Diacylglyceride kinases, sphingosine kinases and NAD kinases: distant relatives of 6-phosphofructokinases. Trends Biochem. Sci. 27, 273-275. doi: 10.1016/S0968-0004(02)02093-5
171. Lakshmi, T. M., and Helling, R. B. (1976). Selection for citrate synthase deficiency in icd mutants of Escherichia coli. J. Bacteriol. 127, 76-83.
172. Lamed, R., and Zeikus, J. G. (1981). Thermostable, ammonium-activated malic enzyme of Clostridium thermocellum. Biochim. Biophys. Acta 660, 251-255. doi: 10.1016/0005-2744(81)90167-4
173. Lampel, K. A., Uratani, B., Chaudhry, G. R., Ramaley, R. F., and Rudikoff, S. (1986). Characterization of the developmentally regulated Bacillus subtilis glucose dehydrogenase gene. J. Bacteriol. 166, 238-243.
174. Landete, J. M., Garcia-Haro, L., Blasco, A., Manzanares, P., Berbegal, C., Monedero, V., et al. (2010). Requirement of the Lactobacillus casei MaeKR two-component system for L-malic acid utilization via a malic enzyme pathway. Appl. Environ. Microbiol. 76, 84-95. doi: 10.1128/AEM.02145-09
175. Lauterbach, L., Lenz, O., and Vincent, K. A. (2013). H(2)-driven cofactor regeneration with NAD(P)(+)-reducing hydrogenases. FEBS J. 280, 3058-3068. doi: 10.1111/febs.12245
176. Lee, H. C. (1997). Mechanisms of calcium signaling by cyclic ADP-ribose and NAADP. Physiol. Rev. 77, 1133-1164.
177. Lee, H. C., Kim, J. S., Jang, W., and Kim, S. Y. (2009). Thymidine production by overexpressing NAD+ kinase in an Escherichia coli recombinant strain. Biotechnol. Lett. 31, 1929-1936. doi: 10.1007/s10529-009-0097-z
178. Lee, H. C., Kim, J. S., Jang, W., and Kim, S. Y. (2010). High NADPH/NADP+ ratio improves thymidine production by a metabolically engineered Escherichia coli strain. J. Biotechnol. 149, 24-32. doi: 10.1016/j.jbiotec.2010.06.011
179. Lee, J.-N., Shin, H.-D., and Lee, Y.-H. (2003). Metabolic engineering of pentose phosphate pathway in Ralstonia eutropha for enhanced biosynthesis of poly-β-hydroxybutyrate. Biotechnol. Prog. 19, 1444-1449. doi: 10.1021/bp034060v
180. Lee, W.-H., Chin, Y.-W., Han, N. S., Kim, M.-D., and Seo, J.-H. (2011). Enhanced production of GDP-L-fucose by overexpression of NADPH regenerator in recombinant Escherichia coli. Appl. Microbiol. Biotechnol. 91, 967-976. doi: 10.1007/s00253-011-3271-x
181. Lee, W.-H., Kim, J.-W., Park, E.-H., Han, N. S., Kim, M.-D., and Seo, J.-H. (2013a). Effects of NADH kinase on NADPH-dependent biotransformation processes in Escherichia coli. Appl. Microbiol. Biotechnol. 97, 1561-1569. doi: 10.1007/s00253-012-4431-3
182. Lee, W. H., Kim, M. D., Jin, Y. S., and Seo, J. H. (2013b). Engineering of NADPH regenerators in Escherichia coli for enhanced biotransformation. Appl. Microbiol. Biotechnol. 97, 2761-2772. doi: 10.1007/s00253-013-4750-z
183. Lee, W.-H., Park, J.-B., Park, K., Kim, M.-D., and Seo, J.-H. (2007a). Enhanced production of e-caprolactone by overexpression of NADPH-regenerating glucose 6-phosphate dehydrogenase in recombinant Escherichia coli harboring cyclohexanone monooxygenase gene. Appl. Microbiol. Biotechnol. 76, 329-338. doi: 10.1007/s00253-007-1016-7
184. Lee, Y., Yeom, J., Kang, Y.-S., Kim, J., Sung, J.-S., Jeon, C. O., et al. (2007b). Molecular characterization of fprB (ferredoxin-NADP+ reductase) in Pseudomonas putida KT2440. J. Microbiol. Biotechnol. 17, 1504-1512.
185. Lerondel, G., Doan, T., Zamboni, N., Sauer, U., and Aymerich, S. (2006). YtsJ has the major physiological role of the four paralogous malic enzyme isoforms in Bacillus subtilis. J. Bacteriol. 188, 4727-4736. doi: 10.1128/JB.00167-06
186. Lever, T. M., Palmer, T., Cunningham, I. J., Cotton, N. P., and Jackson, J. B. (1991). Purification and properties of the H(+)-nicotinamide nucleotide transhydrogenase from Rhodobacter capsulatus. Eur. J. Biochem. 197, 247-255. doi: 10.1111/j.1432-1033.1991.tb15905.x
187. Levy, H. R. (1979). Glucose-6-phosphate dehydrogenases. Adv. Enzymol. Relat. Areas Mol. Biol. 48, 97-192. doi: 10.1002/9780470122938.ch3
188. Lewis, T. A., Glassing, A., Harper, J., and Franklin, M. J. (2013). Role for ferredoxin:NAD(P)H oxidoreductase (FprA) in sulfate assimilation and siderophore biosynthesis in Pseudomonads. J. Bacteriol. 195, 3876-3887. doi: 10.1128/JB.00528-13
189. Li, Z.-J., Cai, L., Wu, Q., and Chen, G.-Q. (2009). Overexpression of NAD kinase in recombinant Escherichia coli harboring the phbCAB operon improves poly(3-hydroxybutyrate) production. Appl. Microbiol. Biotechnol. 83, 939-947. doi: 10.1007/s00253-009-1943-6
190. Lim, S.-J., Jung, Y.-M., Shin, H.-D., and Lee, Y.-H. (2002). Amplification of the NADPH-related genes zwf and gnd for the oddball biosynthesis of PHB in an E. coli transformant harboring a cloned phbCAB operon. J. Biosci. Bioeng. 93, 543-549. doi: 10.1016/S1389-1723(02)80235-3
191. Lindahl, R. (1992). Aldehyde dehydrogenases and their role in carcinogenesis. Crit. Rev. Biochem. Mol. Biol. 27, 283-335. doi: 10.3109/10409239209082565
192. Lindner, S. N., Niederholtmeyer, H., Schmitz, K., Schoberth, S. M., and Wendisch, V. F. (2010). Polyphosphate/ATP-dependent NAD kinase of Corynebacterium glutamicum: biochemical properties and impact of ppnK overexpression on lysine production. Appl. Microbiol. Biotechnol. 87, 583-593. doi: 10.1007/s00253-010-2481-y
193. Lipscomb, G. L., Stirrett, K., Schut, G. J., Yang, F., Jenney, F. E. Jr. Scott, R. A., et al. (2011). Natural competence in the hyperthermophilic archaeon Pyrococcus furiosus facilitates genetic manipulation: construction of markerless deletions of genes encoding the two cytoplasmic hydrogenases. Appl. Environ. Microbiol. 77, 2232-2238. doi: 10.1128/AEM.02624-10
194. Liu, W., and Wang, P. (2007). Cofactor regeneration for sustainable enzymatic biosynthesis. Biotechnol. Adv. 25, 369-384. doi: 10.1016/j.biotechadv.2007.03.002
195. Lloyd, A. J., and Weitzman, D. (1988). Purification and characterization of NAD-linked isocitrate dehydrogenase from Methylophilus methylotrophus. Biochem. Soc. Trans. 16, 871-872. doi: 10.1042/bst0160871
196. London, J., Meyer, E. Y., and Kulczyk, S. (1971). Comparative biochemical and immunological study of malic enzyme from two species of lactic acid bacteria: evolutionary implications. J. Bacteriol. 106, 126-137.
197. Lorentzen, E., Hensel, R., Knura, T., Ahmed, H., and Pohl, E. (2004). Structural Basis of allosteric regulation and substrate specificity of the non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase from Thermoproteus tenax. J. Mol. Biol. 341, 815-828. doi: 10.1016/j.jmb.2004.05.032
198. Lu, Y., and Mei, L. (2007). Co-expression of P450 BM3 and glucose dehydrogenase by recombinant Escherichia coli and its application in an NADPH-dependent indigo production system. J. Ind. Microbiol. Biotechnol. 34, 247-253. doi: 10.1007/s10295-006-0193-1
199. Lyon, E. J., Shima, S., Buurman, G., Chowdhuri, S., Batschauer, A., Steinbach, K., et al. (2004). UV-A/blue-light inactivation of the 'metal-free' hydrogenase (Hmd) from methanogenic archaea. Eur. J. Biochem. 271, 195-204. doi: 10.1046/j.1432-1033.2003.03920.x
200. Ma, K., and Adams, M. W. (2001a). Ferredoxin:NADP oxidoreductase from Pyrococcus furiosus. Meth. Enzymol. 334, 40-45. doi: 10.1016/S0076-6879(01)34456-7
201. Ma, K., and Adams, M. W. W. (2001b). "Hydrogenases I and II from Pyrococcus furiosus," in Methods in Enzymology, eds R. M. K. Michael and W. W. Adams (Academic Press), 208-216.
202. Ma, K., Weiss, R., and Adams, M. W. W. (2000). Characterization of hydrogenase II from the hyperthermophilic archaeon Pyrococcus furiosus and assessment of its role in sulfur reduction. J. Bacteriol. 182, 1864-1871. doi: 10.1128/JB.182.7.1864-1871.2000
203. Magni, G., Amici, A., Emanuelli, M., Orsomando, G., Raffaelli, N., and Ruggieri, S. (2004). Enzymology of NAD+ homeostasis in man. Cell. Mol. Life Sci. 61, 19-34. doi: 10.1007/s00018-003-3161-1
204. Magni, G., Amici, A., Emanuelli, M., Raffaelli, N., and Ruggieri, S. (1999). Enzymology of NAD+ synthesis. Adv. Enzymol. Relat. Areas Mol. Biol. 73, 135-182. doi: 10.1002/9780470123195.ch5
205. Magni, G., Orsomando, G., and Raffaelli, N. (2006). Structural and functional properties of NAD kinase, a key enzyme in NADP biosynthesis. Mini Rev. Med. Chem. 6, 739-746. doi: 10.2174/138955706777698688
206. Mailloux, R. J., Bériault, R., Lemire, J., Singh, R., Chénier, D. R., Hamel, R. D., et al. (2007). The tricarboxylic acid cycle, an ancient metabolic network with a novel twist. PLoS ONE 2:e690. doi: 10.1371/journal.pone.0000690
207. Malki, S., Saimmaime, I., De Luca, G., Rousset, M., Dermoun, Z., and Belaich, J. P. (1995). Characterization of an operon encoding an NADP-reducing hydrogenase in Desulfovibrio fructosovorans. J. Bacteriol. 177, 2628-2636.
208. Marchitti, S. A., Brocker, C., Stagos, D., and Vasiliou, V. (2008). Non-P450 aldehyde oxidizing enzymes: the aldehyde dehydrogenase superfamily. Exp. Opin. Drug Metab. Toxicol. 4, 697-720. doi: 10.1517/17425255.4.6.697
209. Martinez, I., Zhu, J., Lin, H., Bennett, G. N., and San, K.-Y. (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, 352-359. doi: 10.1016/j.ymben.2008.09.001
210. Martinez-Julvez, M., Medina, M., and Velazquez-Campoy, A. (2009). Binding thermodynamics of ferredoxin:NADP+ reductase: two different protein substrates and one energetics. Biophys. J. 96, 4966-4975. doi: 10.1016/j.bpj.2009.02.061
211. Marx, A., Eikmanns, B. J., Sahm, H., De Graaf, A. A., and Eggeling, L. (1999). Response of the central metabolism in Corynebacterium glutamicum to the use of an NADH-dependent glutamate dehydrogenase. Metab. Eng. 1, 35-48. doi: 10.1006/mben.1998.0106
212. Marx, A., Hans, S., Mockel, B., Bathe, B., De Graaf, A. A., Mccormack, A. C., et al. (2003). Metabolic phenotype of phosphoglucose isomerase mutants of Corynebacterium glutamicum. J. Biotechnol. 104, 185-197. doi: 10.1016/S0168-1656(03)00153-6
213. Mateos, M., and Serrano, A. (1992). Occurrence of phosphorylating and non-phosphorylating NADP+-dependent glyceraldehyde-3-phosphate dehydrogenases in photosynthetic organisms. Plant Sci. 84, 163-170. doi: 10.1016/0168-9452(92)90130-E
214. Mather, L. H., and Knight, M. (1972). A heat-stable nicotinamide-adenine dinucleotide glycohydrolase from Pseudomonas putida KB1. Partial purification and some properties of the enzyme and an inhibitory protein. Biochem. J. 129, 141-152.
215. Matsubara, K., Yokooji, Y., Atomi, H., and Imanaka, T. (2011). Biochemical and genetic characterization of the three metabolic routes in Thermococcus kodakarensis linking glyceraldehyde 3-phosphate and 3-phosphoglycerate. Mol. Microbiol. 81, 1300-1312. doi: 10.1111/j.1365-2958.2011.07762.x
216. Matsuda, F., Ishii, J., Kondo, T., Ida, K., Tezuka, H., and Kondo, A. (2013). Increased isobutanol production in Saccharomyces cerevisiae by eliminating competing pathways and resolving cofactor imbalance. Microb. Cell Fact. 12:119. doi: 10.1186/1475-2859-12-119
217. Matula, T. I., Mcdonald, I. J., and Martin, S. M. (1969). CO2 fixation by malic enzyme in a species of Micrococcus. Biochem. Biophys. Res. Commun. 34, 795-802. doi: 10.1016/0006-291X(69)90250-2
218. Mcdermott, T. R., and Kahn, M. L. (1992). Cloning and mutagenesis of the Rhizobium meliloti isocitrate dehydrogenase gene. J. Bacteriol. 174, 4790-4797.
219. Mcguinness, E. T., and Butler, J. R. (1985). NAD+ kinase-a review. Int. J. Biochem. 17, 1-11. doi: 10.1016/0020-711X(85)90079-5
220. Medina, M., and Gomez-Moreno, C. (2004). Interaction of Ferredoxin-NADP(+) Reductase with its substrates: optimal interaction for efficient electron transfer. Photosyn. Res. 79, 113-131. doi: 10.1023/B:PRES.0000015386.67746.2c
221. Mertens, R., Greiner, L., Van Den Ban, E. C. D., Haaker, H. B. C. M., and Liese, A. (2003). Practical applications of hydrogenase I from Pyrococcus furiosus for NADPH generation and regeneration. J. Mol. Catal. B 24-25, 39-52. doi: 10.1016/S1381-1177(03)00071-7
222. Meyer, F. M., and Stulke, J. (2013). Malate metabolism in Bacillus subtilis: distinct roles for three classes of malate-oxidizing enzymes. FEMS Microbiol. Lett. 339, 17-22. doi: 10.1111/1574-6968.12041
223. Middleditch, L. E., Atchison, R. W., and Chung, A. E. (1972). Pyridine nucleotide transhydrogenase from Azotobacter vinelandii. Some aspects of its structure. J. Biol. Chem. 247, 6802-6809.
224. Miller, W. L., and Auchus, R. J. (2011). The molecular biology, biochemistry, and physiology of human steroidogenesis and its disorders. Endocr. Rev. 32, 81-151. doi: 10.1210/er.2010-0013
225. Minard, K. I., and Mcalister-Henn, L. (2005). Sources of NADPH in yeast vary with carbon source. J. Biol. Chem. 280, 39890-39896. doi: 10.1074/jbc.M509461200
226. Moreira Dos Santos, M., Raghevendran, V., Kotter, P., Olsson, L., and Nielsen, J. (2004). Manipulation of malic enzyme in Saccharomyces cerevisiae for increasing NADPH production capacity aerobically in different cellular compartments. Metab. Eng. 6, 352-363. doi: 10.1016/j.ymben.2004.06.002
227. Mori, S., Kawai, S., Shi, F., Mikami, B., and Murata, K. (2005). Molecular conversion of NAD kinase to NADH kinase through single amino acid residue substitution. J. Biol. Chem. 280, 24104-24112. doi: 10.1074/jbc.M502518200
228. Morimoto, Y., Honda, K., Ye, X., Okano, K., and Ohtake, H. (2014). Directed evolution of thermotolerant malic enzyme for improved malate production. J. Biosci. Bioeng. 117, 147-152. doi: 10.1016/j.jbiosc.2013.07.005
229. Moritz, B., Striegel, K., De Graaf, A. A., and Sahm, H. (2000). Kinetic properties of the glucose-6-phosphate and 6-phosphogluconate dehydrogenases from Corynebacterium glutamicum and their application for predicting pentose phosphate pathway flux in vivo. Eur. J. Biochem. 267, 3442-3452. doi: 10.1046/j.1432-1327.2000.01354.x
230. Mulo, P. (2011). Chloroplast-targeted ferredoxin-NADP(+) oxidoreductase (FNR): structure, function and location. Biochim. Biophys. Acta 1807, 927-934. doi: 10.1016/j.bbabio.2010.10.001
231. Munekage, Y., Hashimoto, M., Miyake, C., Tomizawa, K.-I., Endo, T., Tasaka, M., et al. (2004). Cyclic electron flow around photosystem I is essential for photosynthesis. Nature 429, 579-582. doi: 10.1038/nature02598
232. Murakami, K., Iwata, S., Haneda, M., and Yoshino, M. (1997). Role of metal cations in the regulation of NADP-linked isocitrate dehydrogenase from porcine heart. Biometals 10, 169-174. doi: 10.1023/A:1018395510334
233. Muraki, N., Seo, D., Shiba, T., Sakurai, T., and Kurisu, G. (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, 403-414. doi: 10.1016/j.jmb.2010.06.024
234. Muro-Pastor, M. I., and Florencio, F. J. (1994). NADP (+)-isocitrate dehydrogenase from the Cyanobacterium Anabaena sp. strain PCC 7120: purification and characterization of the enzyme and cloning, sequencing, and disruption of the icd gene. J. Bacteriol. 176, 2718-2726.
235. Muro-Pastor, M. I., Reyes, J. C., and Florencio, F. J. (2005). Ammonium assimilation in cyanobacteria. Photosyn. Res. 83, 135-150. doi: 10.1007/s11120-004-2082-7
236. Musumeci, M. A., Ceccarelli, E. A., and Catalano-Dupuy, D. L. (2012). "The plant-type ferredoxin-NADP+ reductases," in Advances in Photosynthesis-Fundamental Aspects, ed D. M. Najafpour (Rijeka: InTech), 539-562. doi: 10.5772/28665
237. Nakamichi, Y., Yoshioka, A., Kawai, S., and Murata, K. (2013). Conferring the ability to utilize inorganic polyphosphate on ATP-specific NAD kinase. Sci. Rep. 3, 2632. doi: 10.1038/srep02632
238. Nakamura, M., Bhatnagar, A., and Sadoshima, J. (2012). Overview of pyridine nucleotides review series. Circ. Res. 111, 604-610. doi: 10.1161/CIRCRESAHA.111.247924
239. Netzer, R., Krause, M., Rittmann, D., Peters-Wendisch, P. G., Eggeling, L., Wendisch, V. F., et al. (2004). Roles of pyruvate kinase and malic enzyme in Corynebacterium glutamicum for growth on carbon sources requiring gluconeogenesis. Arch. Microbiol. 182, 354-363. doi: 10.1007/s00203-004-0710-4
240. Nicolas, C., Kiefer, P., Letisse, F., Kromer, J., Massou, S., Soucaille, P., et al. (2007). Response of the central metabolism of Escherichia coli to modified expression of the gene encoding the glucose-6-phosphate dehydrogenase. FEBS Lett. 581, 3771-3776. doi: 10.1016/j.febslet.2007.06.066
241. Noor, E., Bar-Even, A., Flamholz, A., Lubling, Y., Davidi, D., and Milo, R. (2012). An integrated open framework for thermodynamics of reactions that combines accuracy and coverage. Bioinformatics 28, 2037-2044. doi: 10.1093/bioinformatics/bts317
242. Noor, E., Haraldsdóttir, H. S., Milo, R., and Fleming, R. M. T. (2013). Consistent estimation of gibbs energy using component contributions. PLoS Comput. Biol. 9:e1003098. doi: 10.1371/journal.pcbi.1003098
243. Nordberg, J., and Arnér, E. S. J. (2001). Reactive oxygen species, antioxidants, and the mammalian thioredoxin system. Free Radic. Biol. Med. 31, 1287-1312. doi: 10.1016/S0891-5849(01)00724-9
244. Nouailler, M., Morelli, X., Bornet, O., Chetrit, B., Dermoun, Z., and Guerlesquin, F. (2006). Solution structure of HndAc: a thioredoxin-like domain involved in the NADP-reducing hydrogenase complex. Protein Sci. 15, 1369-1378.
245. Obanye, A. I. C., Hobbs, G., Gardner, D. C. J., and Oliver, S. G. (1996). Correlation between carbon flux through the pentose phosphate pathway and production of the antibiotic methylenomycin in Streptomyces coelicolor A3(2). Microbiology (Reading Engl). 142, 133-137. doi: 10.1099/13500872-142-1-133
246. Ochiai, A., Mori, S., Kawai, S., and Murata, K. (2004). Overexpression, purification, and characterization of ATP-NAD kinase of Sphingomonas sp. A1. Protein Expr. Purif. 36, 124-130. doi: 10.1016/j.pep.2004.03.012
247. Ogawa, T., Murakami, K., Mori, H., Ishii, N., Tomita, M., and Yoshin, M. (2007). Role of phosphoenolpyruvate in the NADP-isocitrate dehydrogenase and isocitrate lyase reaction in Escherichia coli. J. Bacteriol. 189, 1176-1178. doi: 10.1128/JB.01628-06
248. Oh, M.-K., Rohlin, L., Kao, K. C., and Liao, J. C. (2002). Global expression profiling of acetate-grown Escherichia coli. J. Biol. Chem. 277, 13175-13183. doi: 10.1074/jbc.M110809200
249. Olavarría, K., Valdés, D., and Cabrera, R. (2012). The cofactor preference of glucose-6-phosphate dehydrogenase from Escherichia coli-modeling the physiological production of reduced cofactors. FEBS J. 279, 2296-2309. doi: 10.1111/j.1742-4658.2012.08610.x
250. Onda, Y., Matsumura, T., Kimata-Ariga, Y., Sakakibara, H., Sugiyama, T., and Hase, T. (2000). Differential interaction of maize root ferredoxin:NADP(+) oxidoreductase with photosynthetic and non-photosynthetic ferredoxin isoproteins. Plant Physiol. 123, 1037-1045. doi: 10.1104/pp.123.3.1037
251. Outten, C. E., and Culotta, V. C. (2003). A novel NADH kinase is the mitochondrial source of NADPH in Saccharomyces cerevisiae. EMBO J. 22, 2015-2024. doi: 10.1093/emboj/cdg211
252. Owen, O. E., Kalhan, S. C., and Hanson, R. W. (2002). The key role of anaplerosis and cataplerosis for citric acid cycle function. J. Biol. Chem. 277, 30409-30412. doi: 10.1074/jbc.R200006200
253. Papagianni, M. (2012). Recent advances in engineering the central carbon metabolism of industrially important bacteria. Microb. Cell Fact. 11:50. doi: 10.1186/1475-2859-11-50
254. Park, H. J., Jung, J., Choi, H., Uhm, K.-N., and Kim, H. K. (2010). Enantioselective bioconversion using Escherichia coli cells expressing Saccharomyces cerevisiae reductase and Bacillus subtilis glucose dehydrogenase. J. Microbiol. Biotechnol. 20, 1300-1306. doi: 10.4014/jmb.1003.03025
255. Patel, S., Ramakrishnan, L., Rahman, T., Hamdoun, A., Marchant, J. S., Taylor, C. W., et al. (2011). The endo-lysosomal system as an NAADP-sensitive acidic Ca(2+) store: role for the two-pore channels. Cell Calcium 50, 157-167. doi: 10.1016/j.ceca.2011.03.011
256. Paul, L., Mishra, P., Blumenthal, R., and Matthews, R. (2007). Integration of regulatory signals through involvement of multiple global regulators: control of the Escherichia coli gltBDF operon by Lrp, IHF, Crp, and ArgR. BMC Microbiol. 7:2. doi: 10.1186/1471-2180-7-2
257. Pauly, H. E., and Pfleiderer, G. (1975). D-glucose dehydrogenase from Bacillus megaterium M 1286: purification, properties and structure. Hoppe-Seyler's Z. Physiol. Chem. 356, 1613-1623. doi: 10.1515/bchm2.1975.356.2.1613
258. Pedersen, A., Karlsson, G. B., and Rydstrom, J. (2008). Proton-translocating transhydrogenase: an update of unsolved and controversial issues. J. Bioenerg. Biomembr. 40, 463-473. doi: 10.1007/s10863-008-9170-x
259. Penyige, A., Deak, E., Kalmanczhelyi, A., and Barabas, G. (1996). Evidence of a role for NAD+-glycohydrolase and ADP-ribosyltransferase in growth and differentiation of Streptomyces griseus NRRL B-2682: inhibition by m-aminophenylboronic acid. Microbiology 142(Pt 8), 1937-1944. doi: 10.1099/13500872-142-8-1937
260. Peralta-Yahya, P. P., Zhang, F., Del Cardayre, S. B., and Keasling, J. D. (2012). Microbial engineering for the production of advanced Biofuels 488, 320-328. doi: 10.1038/nature11478
261. Peters, J. W., Schut, G. J., Boyd, E. S., Mulder, D. W., Shepard, E. M., Broderick, J. B., et al. (2015). [FeFe]-and [NiFe]-hydrogenase diversity, mechanism, and maturation. Biochim. Biophys. Acta Mol. Cell Res. 1853, 1350-1369. doi: 10.1016/j.bbamcr.2014.11.021
262. Petersen, S., De Graaf, A. A., Eggeling, L., Möllney, M., Wiechert, W., and Sahm, H. (2000). In vivo quantification of parallel and bidirectional fluxes in the anaplerosis of Corynebacterium glutamicum. J. Biol. Chem. 275, 35932-35941. doi: 10.1074/jbc.M908728199
263. Pollak, N., Dölle, C., and Ziegler, M. (2007). The power to reduce: pyridine nucleotides-small molecules with a multitude of functions. Biochem. J. 402, 205-218. doi: 10.1042/BJ20061638
264. Poncet-Montange, G., Assairi, L., Arold, S., Pochet, S., and Labesse, G. (2007). NAD kinases use substrate-assisted catalysis for specific recognition of NAD. J. Biol. Chem. 282, 33925-33934. doi: 10.1074/jbc.M701394200
265. Purwantini, E., and Daniels, L. (1996). Purification of a novel coenzyme F420-dependent glucose-6-phosphate dehydrogenase from Mycobacterium smegmatis. J. Bacteriol. 178, 2861-2866.
266. Purwantini, E., Gillis, T. P., and Daniels, L. (1997). Presence of F420-dependent glucose-6-phosphate dehydrogenase in Mycobacterium and Nocardia species, but absence from Streptomyces and Corynebacterium species and methanogenic Archaea. FEMS Microbiol. Lett. 146, 129-134. doi: 10.1111/j.1574-6968.1997.tb10182.x
267. Qi, H., Li, S., Zhao, S., Huang, D., Xia, M., and Wen, J. (2014). Model-driven redox pathway manipulation for improved isobutanol production in Bacillus subtilis complemented with experimental validation and metabolic profiling analysis. PLoS ONE 9:e93815. doi: 10.1371/journal.pone.0093815
268. Rahman, M. M. Q., Zhao, Q., Dou, W., Zhiming, R., and Xu, Z. (2012). Over-expression of NAD kinase in Corynebacterium crenatum and its impact on L-Arginine biosynthesis. Tropic. J. Pharm. Res. 11, 909-916. doi: 10.4314/tjpr.v11i6.6
269. Rathnasingh, C., Raj, S. M., Lee, Y., Catherine, C., Ashok, S., and Park, S. (2012). Production of 3-hydroxypropionic acid via malonyl-CoA pathway using recombinant Escherichia coli strains. J. Biotechnol. 157, 633-640. doi: 10.1016/j.jbiotec.2011.06.008
270. Razquin, P., Fillat, M. F., Schmitz, S., Stricker, O., Bohme, H., Gomez-Moreno, C., et al. (1996). Expression of ferredoxin-NADP+ reductase in heterocysts from Anabaena sp. Biochem. J. 316(Pt 1), 157-160.
271. Reddy, G. K., Lindner, S. N., and Wendisch, V. F. (2015). Metabolic Engineering an ATP-neutral EMP pathway in Corynebacterium glutamicum: adaptive point mutation in NADH dehydrogenase restores growth. Appl. Environ. Microbiol. 81, 1996-2005. doi: 10.1128/AEM.03116-14
272. Reidl, J., Schlor, S., Kraiss, A., Schmidt-Brauns, J., Kemmer, G., and Soleva, E. (2000). NADP and NAD utilization in Haemophilus influenzae. Mol. Microbiol. 35, 1573-1581. doi: 10.1046/j.1365-2958.2000.01829.x
273. Richhardt, J., Bringer, S., and Bott, M. (2013). Role of the pentose phosphate pathway and the Entner-Doudoroff pathway in glucose metabolism of Gluconobacter oxydans 621H. Appl. Microbiol. Biotechnol. 97, 4315-4323. doi: 10.1007/s00253-013-4707-2
274. Riedel, C., Rittmann, D., Dangel, P., Mockel, B., Petersen, S., Sahm, H., et al. (2001). Characterization of the phosphoenolpyruvate carboxykinase gene from Corynebacterium glutamicum and significance of the enzyme for growth and amino acid production. J. Mol. Microbiol. Biotechnol. 3, 573-583.
275. Poulsen, B. R., Nohr, J., Douthwaite, S., Hansen, L. V., Iversen, J. J. L., Visser, J., et al. (2005). Increased NADPH concentration obtained by metabolic engineering of the pentose phosphate pathway in Aspergillus niger. FEBS J. 272, 1313-1325. doi: 10.1111/j.1742-4658.2005.04554.x
276. Rydzak, T., Grigoryan, M., Cunningham, Z. J., Krokhin, O. V., Ezzati, P., Cicek, N., et al. (2014). Insights into electron flux through manipulation of fermentation conditions and assessment of protein expression profiles in Clostridium thermocellum. Appl. Microbiol. Biotechnol. 98, 6497-6510. doi: 10.1007/s00253-014-5798-0
277. Sahm, H., Eggeling, L., and De Graaf, A. A. (2000). Pathway analysis and metabolic engineering in Corynebacterium glutamicum. Biol. Chem. 381, 899-910. doi: 10.1515/BC.2000.111
278. Sakuraba, H., Kawakami, R., and Ohshima, T. (2005). First Archaeal Inorganic Polyphosphate/ATP-Dependent NAD Kinase, from Hyperthermophilic Archaeon Pyrococcus horikoshii: cloning, expression, and characterization. Appl. Environ. Microbiol. 71, 4352-4358. doi: 10.1128/AEM.71.8.4352-4358.2005
279. Sakuraba, H., Satomura, T., Kawakami, R., Yamamoto, S., Kawarabayasi, Y., Kikuchi, H., et al. (2002). L-Aspartate oxidase is present in the anaerobic hyperthermophilic archaeon Pyrococcus horikoshii OT-3: characteristics and role in the de novo biosynthesis of nicotinamide adenine dinucleotide proposed by genome sequencing. Extremophiles 6, 275-281. doi: 10.1007/s00792-001-0254-3
280. Saliola, M., Tramonti, A., Lanini, C., Cialfi, S., De Biase, D., and Falcone, C. (2012). Intracellular NADPH levels affect the oligomeric state of the glucose 6-phosphate dehydrogenase. Eukaryot. Cell 11, 1503-1511. doi: 10.1128/EC.00211-12
281. Sanchez, A. M., Andrews, J., Hussein, I., Bennett, G. N., and San, K.-Y. (2006). 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. doi: 10.1021/bp050375u
282. Sancho, J. (2006). Flavodoxins: sequence, folding, binding, function and beyond. Cell. Mol. Life Sci. 63, 855-864. doi: 10.1007/s00018-005-5514-4
283. Santangelo, T. J., Cubonova, L., and Reeve, J. N. (2011). Deletion of alternative pathways for reductant recycling in Thermococcus kodakarensis increases hydrogen production. Mol. Microbiol. 81, 897-911. doi: 10.1111/j.1365-2958.2011.07734.x
284. Sassetti, C. M., Boyd, D. H., and Rubin, E. J. (2003). Genes required for mycobacterial growth defined by high density mutagenesis. Mol. Microbiol. 48, 77-84. doi: 10.1046/j.1365-2958.2003.03425.x
285. Sato, T., and Atomi, H. (2011). Novel metabolic pathways in Archaea. Curr. Opin. Microbiol. 14, 307-314. doi: 10.1016/j.mib.2011.04.014
286. Sato, Y., Kameya, M., Fushinobu, S., Wakagi, T., Arai, H., Ishii, M., et al. (2012). A novel enzymatic system against oxidative stress in the thermophilic hydrogen-oxidizing bacterium Hydrogenobacter thermophilus. PLoS ONE 7:e34825. doi: 10.1371/journal.pone.0034825
287. Satoh, Y., Tajima, K., Tannai, H., and Munekata, M. (2003). Enzyme-catalyzed poly(3-hydroxybutyrate) synthesis from acetate with CoA recycling and NADPH regeneration in vitro. J. Biosci. Bioeng. 95, 335-341. doi: 10.1016/S1389-1723(03)80064-6
288. Sauer, U., Canonaco, F., Heri, S., Perrenoud, A., and Fischer, E. (2004). The soluble and membrane-bound transhydrogenases UdhA and PntAB have divergent functions in NADPH metabolism of Escherichia coli. J. Biol. Chem. 279, 6613-6619. doi: 10.1074/jbc.M311657200
289. Sauer, U., and Eikmanns, B. J. (2005). The PEP-pyruvate-oxaloacetate node as the switch point for carbon flux distribution in bacteria. FEMS Microbiol. Rev. 29, 765-794. doi: 10.1016/j.femsre.2004.11.002
290. Schäfer, T., and Schönheit, P. (1993). Gluconeogenesis from pyruvate in the hyperthermophilic archaeon Pyrococcus furiosus: involvement of reactions of the Embden-Meyerhof pathway. Arch. Microbiol. 159, 354-363. doi: 10.1007/BF00290918
291. Schmitz, O., Boison, G., Salzmann, H., Bothe, H., Schutz, K., Wang, S.-H., et al. (2002). HoxE-a subunit specific for the pentameric bidirectional hydrogenase complex (HoxEFUYH) of cyanobacteria. Biochim. Biophys. Acta 1554, 66-74. doi: 10.1016/S0005-2728(02)00214-1
292. Schut, G. J., Nixon, W. J., Lipscomb, G. L., Scott, R. A., and Adams, M. W. W. (2012). Mutational analyses of the enzymes involved in the metabolism of hydrogen by the hyperthermophilic archaeon Pyrococcus furiosus. Front. Microbiol. 3:163. doi: 10.3389/fmicb.2012.00163
293. Seeber, F., Aliverti, A., and Zanetti, G. (2005). The plant-type ferredoxin-NADP+ reductase/ferredoxin redox system as a possible drug target against apicomplexan human parasites. Curr. Pharm. Des. 11, 3159-3172. doi: 10.2174/1381612054864957
294. Seo, D., Kamino, K., Inoue, K., and Sakurai, H. (2004). Purification and characterization of ferredoxin-NADP+ reductase encoded by Bacillus subtilis yumC. Arch. Microbiol. 182, 80-89. doi: 10.1007/s00203-004-0701-5
295. Seo, D., and Sakurai, H. (2002). Purification and characterization of ferredoxin-NAD(P)(+) reductase from the green sulfur bacterium Chlorobium tepidum. Biochim. Biophys. Acta 1597, 123-132. doi: 10.1016/S0167-4838(02)00269-8
296. Shi, A., Zhu, X., Lu, J., Zhang, X., and Ma, Y. (2013). Activating transhydrogenase and NAD kinase in combination for improving isobutanol production. Metab. Eng. 16, 1-10. doi: 10.1016/j.ymben.2012.11.008
297. Shi, F., Huan, X., Wang, X., and Ning, J. (2012). Overexpression of NAD kinases improves the L-isoleucine biosynthesis in Corynebacterium glutamicum ssp. lactofermentum. Enzyme Microb. Technol. 51, 73-80. doi: 10.1016/j.enzmictec.2012.04.003
298. Shi, F., Li, Y., and Wang, X. (2009). Molecular properties, functions, and potential applications of NAD kinases. Acta Biochim. Biophys. Sin. (Shanghai). 41, 352-361. doi: 10.1093/abbs/gmp029
299. Shiba, H., Kawasumi, T., Igarashi, Y., Kodama, T., and Minoda, Y. (1985). The CO2 assimilation via the reductive tricarboxylic acid cycle in an obligately autotrophic, aerobic hydrogen-oxidizing bacterium, Hydrogenobacter thermophilus. Arch. Microbiol. 141, 198-203. doi: 10.1007/BF00408058
300. Shikanai, T. (2007). Cyclic electron transport around photosystem I: genetic approaches. Annu. Rev. Plant Biol. 58, 199-217. doi: 10.1146/annurev.arplant.58.091406.110525
301. Shima, S., and Thauer, R. K. (2007). A third type of hydrogenase catalyzing H2 activation. Chem. Rec. 7, 37-46. doi: 10.1002/tcr.20111
302. Shin, J.-A., Kwon, Y. D., Kwon, O.-H., Lee, H. S., and Kim, P. (2007). 5-Aminolevulinic acid biosynthesis in Escherichia coli coexpressing NADP-dependent malic enzyme and 5-aminolevulinate synthase. J. Microbiol. Biotechnol. 17, 1579-1584.
303. Shin, M., and Arnon, D. I. (1965). Enzymic mechanisms of pyridine nucleotide reduction in chloroplasts. J. Biol. Chem. 240, 1405-1411.
304. Siebers, B., and Schonheit, P. (2005). Unusual pathways and enzymes of central carbohydrate metabolism in Archaea. Curr. Opin. Microbiol. 8, 695-705. doi: 10.1016/j.mib.2005.10.014
305. Siedler, S., Bringer, S., and Bott, M. (2011). Increased NADPH availability in Escherichia coli: improvement of the product per glucose ratio in reductive whole-cell biotransformation. Appl. Microbiol. Biotechnol. 92, 929-937. doi: 10.1007/s00253-011-3374-4
306. Silva, P. J., Van Den Ban, E. C., Wassink, H., Haaker, H., De Castro, B., Robb, F. T., et al. (2000). Enzymes of hydrogen metabolism in Pyrococcus furiosus. Eur. J. Biochem. 267, 6541-6551. doi: 10.1046/j.1432-1327.2000.01745.x
307. Singh, R., Beriault, R., Middaugh, J., Hamel, R., Chenier, D., Appanna, V. D., et al. (2005). Aluminum-tolerant Pseudomonas fluorescens: ROS toxicity and enhanced NADPH production. Extremophiles 9, 367-373. doi: 10.1007/s00792-005-0450-7
308. Singh, R., Lemire, J., Mailloux, R. J., and Appanna, V. D. (2008). A novel strategy involved anti-oxidative defense: the conversion of NADH into NADPH by a metabolic network. PLoS ONE 3:e2682. doi: 10.1371/annotation/5fac086b-3806-4aa9-a5c5-2611b3355f8f
309. Singh, R., Mailloux, R. J., Puiseux-Dao, S., and Appanna, V. D. (2007). Oxidative stress evokes a metabolic adaptation that favors increased NADPH synthesis and decreased NADH production in Pseudomonas fluorescens. J. Bacteriol. 189, 6665-6675. doi: 10.1128/JB.00555-07
310. Smith, K. M., Cho, K.-M., and Liao, J. C. (2010). Engineering Corynebacterium glutamicum for isobutanol production. Appl. Microbiol. Biotechnol. 87, 1045-1055. doi: 10.1007/s00253-010-2522-6
311. Sophos, N. A., Pappa, A., Ziegler, T. L., and Vasiliou, V. (2001). Aldehyde dehydrogenase gene superfamily: the 2000 update. Chem. Biol. Interact. 130-132, 323-337. doi: 10.1016/S0009-2797(00)00275-1
312. Sophos, N. A., and Vasiliou, V. (2003). Aldehyde dehydrogenase gene superfamily: the 2002 update. Chem. Biol. Interact. 143-144, 5-22. doi: 10.1016/S0009-2797(02)00163-1
313. Steen, I. H., Lien, T., and Birkeland, N. K. (1997). Biochemical and phylogenetic characterization of isocitrate dehydrogenase from a hyperthermophilic archaeon, Archaeoglobus fulgidus. Arch. Microbiol. 168, 412-420. doi: 10.1007/s002030050516
314. Steen, I. H., Madern, D., Karlstrom, M., Lien, T., Ladenstein, R., and Birkeland, N. K. (2001). Comparison of isocitrate dehydrogenase from three hyperthermophiles reveals differences in thermostability, cofactor specificity, oligomeric state, and phylogenetic affiliation. J. Biol. Chem. 276, 43924-43931. doi: 10.1074/jbc.M105999200
315. Steuber, J., Krebs, W., Bott, M., and Dimroth, P. (1999). A Membrane-Bound NAD(P)(+)-Reducing hydrogenase provides reduced pyridine nucleotides during citrate fermentation by Klebsiella pneumoniae. J. Bacteriol. 181, 241-245.
316. Stokke, R., Madern, D., Fedoy, A.-E., Karlsen, S., Birkeland, N.-K., and Steen, I. H. (2007). Biochemical characterization of isocitrate dehydrogenase from Methylococcus capsulatus reveals a unique NAD+-dependent homotetrameric enzyme. Arch. Microbiol. 187, 361-370. doi: 10.1007/s00203-006-0200-y
317. Stols, L., and Donnelly, M. I. (1997). Production of succinic acid through overexpression of NAD(+)-dependent malic enzyme in an Escherichia coli mutant. Appl. Environ. Microbiol. 63, 2695-2701.
318. Stournaras, C., Maurer, P., and Kurz, G. (1983). 6-phospho-D-gluconate dehydrogenase from Pseudomonas fluorescens. Properties and subunit structure. Eur. J. Biochem. 130, 391-396. doi: 10.1111/j.1432-1033.1983.tb07165.x
319. Strand, M. K., Stuart, G. R., Longley, M. J., Graziewicz, M. A., Dominick, O. C., and Copeland, W. C. (2003). POS5 gene of Saccharomyces cerevisiae encodes a mitochondrial NADH kinase required for stability of mitochondrial DNA. Eukaryot. Cell 2, 809-820. doi: 10.1128/EC.2.4.809-820.2003
320. Summers, M. L., Wallis, J. G., Campbell, E. L., and Meeks, J. C. (1995). Genetic evidence of a major role for glucose-6-phosphate dehydrogenase in nitrogen fixation and dark growth of the cyanobacterium Nostoc sp. strain ATCC 29133. J. Bacteriol. 177, 6184-6194.
321. Sun, J., Hopkins, R. C., Jenney, F. E. Jr. Mcternan, P. M., and Adams, M. W. W. (2010). Heterologous expression and maturation of an NADP-Dependent [NiFe]-hydrogenase: a key enzyme in biofuel production. PLoS ONE 5:e10526. doi: 10.1371/journal.pone.0010526
322. Sung, J. Y., and Lee, Y. N. (2007). Isoforms of glucose 6-phosphate dehydrogenase in Deinococcus radiophilus. J. Microbiol. 45, 318-325.
323. Szaszák, M., Steven, P., Shima, K., Orzekowsky-Schröder, R., Hüttmann, G., König, I. R., et al. (2011). Fluorescence lifetime imaging unravels C. trachomatis metabolism and its crosstalk with the host cell. PLoS Pathog 7:e1002108. doi: 10.1371/journal.ppat.1002108
324. Szmant, H. H. (1989). Organic Building Blocks of the Chemical Industry. New York, NY: John Wiley & Sons.
325. Takeno, S., Murata, R., Kobayashi, R., Mitsuhashi, S., and Ikeda, M. (2010). Engineering of Corynebacterium glutamicum with an NADPH-generating glycolytic pathway for L-lysine production. Appl. Environ. Microbiol. 76, 7154-7160. doi: 10.1128/AEM.01464-10
326. Talfournier, F., Stines-Chaumeil, C., and Branlant, G. (2011). Methylmalonate-semialdehyde dehydrogenase from Bacillus subtilis: substrate specificity and coenzyme A binding. J. Biol. Chem. 286, 21971-21981. doi: 10.1074/jbc.M110.213280
327. Tang, K.-H., Yue, H., and Blankenship, R. E. (2010). Energy metabolism of Heliobacterium modesticaldum during phototrophic and chemotrophic growth. BMC Microbiol. 10:150. doi: 10.1186/1471-2180-10-150
328. Thanassi, J. A., Hartman-Neumann, S. L., Dougherty, T. J., Dougherty, B. A., and Pucci, M. J. (2002). Identification of 113 conserved essential genes using a high-throughput gene disruption system in Streptococcus pneumoniae. Nucleic Acids Res. 30, 3152-3162. doi: 10.1093/nar/gkf418
329. Thauer, R. K., Jungermann, K., and Decker, K. (1977). Energy conservation in chemotrophic anaerobic bacteria. Bacteriol. Rev. 41, 100-180.
330. Trchounian, A., and Gary Sawers, R. (2014). Novel insights into the bioenergetics of mixed-acid fermentation: can hydrogen and proton cycles combine to help maintain a proton motive force?. IUBMB Life 66, 1-7. doi: 10.1002/iub.1236
331. Trchounian, K., Poladyan, A., Vassilian, A., and Trchounian, A. (2012). Multiple and reversible hydrogenases for hydrogen production by Escherichia coli: dependence on fermentation substrate, pH and the F(0)F(1)-ATPase. Crit. Rev. Biochem. Mol. Biol. 47, 236-249. doi: 10.3109/10409238.2012.655375
332. Tseng, Y.-M., Harris, B. G., and Jacobson, M. K. (1979). Isolation and characterization of yeast nicotinamide adenine dinucleotide kinase. Biochim. Biophys. Acta 568, 205-214. doi: 10.1016/0005-2744(79)90287-0
333. Turner, W. L., Waller, J. C., and Snedden, W. A. (2005). Identification, molecular cloning and functional characterization of a novel NADH kinase from Arabidopsis thaliana (thale cress). Biochem. J. 385, 217-223. doi: 10.1042/BJ20040292
334. Uppada, V., Bhaduri, S., and Noronha, S. B. (2014). Cofactor regeneration-an important aspect of biocatalysis. Curr. Sci. 106, 946.
335. Van Der Donk, W. A., and Zhao, H. (2003). Recent developments in pyridine nucleotide regeneration. Curr. Opin. Biotechnol. 14, 421-426. doi: 10.1016/S0958-1669(03)00094-6
336. Van Haaster, D. J., Silva, P. J., Hagedoorn, P.-L., Jongejan, J. A., and Hagen, W. R. (2008). Reinvestigation of the steady-state kinetics and physiological function of the soluble NiFe-hydrogenase I of Pyrococcus furiosus. J. Bacteriol. 190, 1584-1587. doi: 10.1128/JB.01562-07
337. Vasiliou, V., Pappa, A., and Petersen, D. R. (2000). Role of aldehyde dehydrogenases in endogenous and xenobiotic metabolism. Chem. Biol. Interact. 129, 1-19. doi: 10.1016/S0009-2797(00)00211-8
338. Veech, R. L., Eggleston, L. V., and Krebs, H. A. (1969). The redox state of free nicotinamide-adenine dinucleotide phosphate in the cytoplasm of rat liver. Biochem. J. 115, 609-619.
339. Velayudhan, J., and Kelly, D. J. (2002). Analysis of gluconeogenic and anaplerotic enzymes in Campylobacter jejuni: an essential role for phosphoenolpyruvate carboxykinase. Microbiology 148, 685-694.
340. Vignais, P. M., and Billoud, B. (2007). Occurrence, classification, and biological function of hydrogenases: an overview. Chem. Rev. 107, 4206-4272. doi: 10.1021/cr050196r
341. Vignais, P. M., Billoud, B., and Meyer, J. (2001). Classification and phylogeny of hydrogenases. FEMS Microbiol. Rev. 25, 455-501. doi: 10.1111/j.1574-6976.2001.tb00587.x
342. Vignais, P. M., and Colbeau, A. (2004). Molecular biology of microbial hydrogenases. Curr. Issues Mol. Biol. 6, 159-188.
343. Voegele, R. T., Mitsch, M. J., and Finan, T. M. (1999). Characterization of two members of a novel malic enzyme class. Biochim. Biophys. Acta 1432, 275-285. doi: 10.1016/S0167-4838(99)00112-0
344. Voordouw, G., Hagen, W. R., Kruse-Wolters, K. M., Van Berkel-Arts, A., and Veeger, C. (1987). Purification and characterization of Desulfovibrio vulgaris (Hildenborough) hydrogenase expressed in Escherichia coli. Eur. J. Biochem. 162, 31-36. doi: 10.1111/j.1432-1033.1987.tb10537.x
345. Voordouw, G., van der Vies, S. M., and Themmen, A. P. (1983). Why are two different types of pyridine nucleotide transhydrogenase found in living organisms?. Eur. J. Biochem. 131, 527-533.
346. Voordouw, G., van der Vies, S., Scholten, J. W., and Veeger, C. (1980). Pyridine nucleotide transhydrogenase from Azotobacter vinelandii. Eur. J. Biochem. 107, 337-344. doi: 10.1111/j.1432-1033.1980.tb06034.x
347. Voordouw, G., Veeger, C., Van Breemen, J. F. L., and Van Bruggen, E. F. J. (1979). Structure of pyridine nucleotide transhydrogenase from Azotobacter vinelandii. Eur. J. Biochem. 98, 447-454. doi: 10.1111/j.1432-1033.1979.tb13205.x
348. Vu, C. Q., Lu, P. J., Ghen, C. S., and Jacobson, M. K. (1996). 2'-phospho-cyclic ADP-ribose, a calcium-mobilizing agent derived from NADP. J. Biol. Chem. 271, 4747-4754. doi: 10.1074/jbc.271.9.4747
349. Walsh, K., and Koshland, D. E. (1985). Branch point control by the phosphorylation state of isocitrate dehydrogenase. a quantitative examination of fluxes during a regulatory transition. J. Biol. Chem. 260, 8430-8437.
350. Wandrey, C. (2004). Biochemical reaction engineering for redox reactions. Chem. Rec. 4, 254-265. doi: 10.1002/tcr.20016
351. Wang, B., Wang, P., Zheng, E., Chen, X., Zhao, H., Song, P., et al. (2011a). Biochemical properties and physiological roles of NADP-dependent malic enzyme in Escherichia coli. J. Microbiol. 49, 797-802. doi: 10.1007/s12275-011-0487-5
352. Wang, P., Jin, M., Su, R., Song, P., Wang, M., and Zhu, G. (2011b). Enzymatic characterization of isocitrate dehydrogenase from an emerging zoonotic pathogen Streptococcus suis. Biochimie 93, 1470-1475. doi: 10.1016/j.biochi.2011.04.021
353. Wang, P., Jin, M., and Zhu, G. (2012). Biochemical and molecular characterization of NAD(+)-dependent isocitrate dehydrogenase from the ethanologenic bacterium Zymomonas mobilis. FEMS Microbiol. Lett. 327, 134-141. doi: 10.1111/j.1574-6968.2011.02467.x
354. Wang, P., Song, P., Jin, M., and Zhu, G. (2013a). Isocitrate dehydrogenase from Streptococcus mutans: biochemical properties and evaluation of a putative phosphorylation Site at Ser102. PLoS ONE 8:e58918. doi: 10.1371/journal.pone.0058918
355. Wang, S., Huang, H., Kahnt, J., Mueller, A. P., Kopke, M., and Thauer, R. K. (2013b). NADP-specific electron-bifurcating [FeFe]-hydrogenase in a functional complex with formate dehydrogenase in Clostridium autoethanogenum grown on CO. J. Bacteriol. 195, 4373-4386. doi: 10.1128/JB.00678-13
356. Wang, S., Huang, H., Moll, J., and Thauer, R. K. (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, 5115-5123. doi: 10.1128/JB.00612-10
357. Wang, Y., San, K.-Y., and Bennett, G. N. (2013c). Improvement of NADPH bioavailability in Escherichia coli by replacing NAD(+)-dependent glyceraldehyde-3-phosphate dehydrogenase GapA with NADP (+)-dependent GapB from Bacillus subtilis and addition of NAD kinase. J. Ind. Microbiol. Biotechnol. 40, 1449-1460. doi: 10.1007/s10295-013-1335-x
358. Wang, Y., San, K.-Y., and Bennett, G. N. (2013d). Improvement of NADPH bioavailability in Escherichia coli through the use of phosphofructokinase deficient strains. Appl. Microbiol. Biotechnol. 97, 6883-6893. doi: 10.1007/s00253-013-4859-0
359. Watanabe, S., Sasaki, D., Tominaga, T., and Miki, K. (2012). Structural basis of [NiFe] hydrogenase maturation by Hyp proteins. Biol. Chem. 393, 1089-1100. doi: 10.1515/hsz-2012-0197
360. Weckbecker, A., and Hummel, W. (2004). 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. doi: 10.1007/s10529-004-3746-2
361. Wells, M. A., Mercer, J., Mott, R. A., Pereira-Medrano, A. G., Burja, A. M., Radianingtyas, H., et al. (2011). Engineering a non-native hydrogen production pathway into Escherichia coli via a cyanobacterial [NiFe] hydrogenase. Metab. Eng. 13, 445-453. doi: 10.1016/j.ymben.2011.01.004
362. Whitehead, S. J., Iwaki, M., Cotton, N. P. J., Rich, P. R., and Jackson, J. B. (2009). Inhibition of proton-transfer steps in transhydrogenase by transition metal ions. Biochim. Biophys. Acta 1787, 1276-1288. doi: 10.1016/j.bbabio.2009.06.001
363. Whitehead, S. J., Rossington, K. E., Hafiz, A., Cotton, N. P. J., and Jackson, J. B. (2005). Zinc ions selectively inhibit steps associated with binding and release of NADP(H) during turnover of proton-translocating transhydrogenase. FEBS Lett. 579, 2863-2867. doi: 10.1016/j.febslet.2005.04.026
364. Wichmann, R., and Vasic-Racki, D. (2005). Cofactor regeneration at the lab scale. Adv. Biochem. Eng. Biotechnol. 92, 225-260. doi: 10.1007/b98911
365. Xu, Z., Jing, K., Liu, Y., and Cen, P. (2007). High-level expression of recombinant glucose dehydrogenase and its application in NADPH regeneration. J. Ind. Microbiol. Biotechnol. 34, 83-90. doi: 10.1007/s10295-006-0168-2
366. Yamauchi, Y., Hirasawa, T., Nishii, M., Furusawa, C., and Shimizu, H. (2014). Enhanced acetic acid and succinic acid production under microaerobic conditions by Corynebacterium glutamicum harboring Escherichia coli transhydrogenase gene pntAB. J. Gen. Appl. Microbiol. 60, 112-118. doi: 10.2323/jgam.60.112
367. Yamazaki, M., and Ichikawa, Y. (1990). Some properties of the apoenzyme of NADPH-adreno-ferredoxin reductase from bovine adrenocortical mitochondria. Int. J. Biochem. 22, 1147-1152. doi: 10.1016/0020-711X(90)90113-H
368. Yan, Z., Nam, Y.-W., Fushinobu, S., and Wakagi, T. (2014). Sulfolobus tokodaii ST2133 is characterized as a thioredoxin reductase-like ferredoxin:NADP+ oxidoreductase. Extremophiles 18, 99-110. doi: 10.1007/s00792-013-0601-1
369. Yang, Z., Zhang, H., Hung, H.-C., Kuo, C.-C., Tsai, L.-C., Yuan, H. S., et al. (2002). Structural studies of the pigeon cytosolic NADP(+)-dependent malic enzyme. Protein Sci. 11, 332-341. doi: 10.1110/ps.38002
370. Yeom, J., Jeon, C. O., Madsen, E. L., and Park, W. (2009). In vitro and in vivo interactions of ferredoxin-NADP+ reductases in Pseudomonas putida. J. Biochem. 145, 481-491. doi: 10.1093/jb/mvn185
371. Ying, W. (2008). NAD+/NADH and NADP+/NADPH in cellular functions and cell death: regulation and biological consequences. Antioxid. Redox Signal. 10, 179-206. doi: 10.1089/ars.2007.1672
372. Yokooji, Y., Sato, T., Fujiwara, S., Imanaka, T., and Atomi, H. (2013). Genetic examination of initial amino acid oxidation and glutamate catabolism in the hyperthermophilic archaeon Thermococcus kodakarensis. J. Bacteriol. 195, 1940-1948. doi: 10.1128/JB.01979-12
373. Yoon, J.-J., Hattori, T., and Shimada, M. (2003). Purification and characterization of NADP-linked isocitrate dehydrogenase from the copper-tolerant wood-rotting basidiomycete Fomitopsis palustris. Biosci. Biotechnol. Biochem. 67, 114-120. doi: 10.1271/bbb.67.114
374. Yun, H., Choi, H.-L., Fadnavis, N. W., and Kim, B.-G. (2005). Stereospecific synthesis of (R)-2-hydroxy carboxylic acids using recombinant E. coli BL21 overexpressing YiaE from Escherichia coli K12 and glucose dehydrogenase from Bacillus subtilis. Biotechnol. Prog. 21, 366-371. doi: 10.1021/bp049694w
375. Zalacain, M., Biswas, S., Ingraham, K. A., Ambrad, J., Bryant, A., Chalker, A. F., et al. (2003). A global approach to identify novel broad-spectrum antibacterial targets among proteins of unknown function. J. Mol. Microbiol. Biotechnol. 6, 109-126. doi: 10.1159/000076741
376. Zamboni, N., Fischer, E., Laudert, D., Aymerich, S., Hohmann, H.-P., and Sauer, U. (2004). The Bacillus subtilis yqjI gene encodes the NADP+-dependent 6-P-gluconate dehydrogenase in the pentose phosphate pathway. J. Bacteriol. 186, 4528-4534. doi: 10.1128/JB.186.14.4528-4534.2004
377. Zhang, J.-D., Li, A.-T., Yu, H.-L., Imanaka, T., and Xu, J.-H. (2011). Synthesis of optically pure S-sulfoxide by Escherichia coli transformant cells coexpressing the P450 monooxygenase and glucose dehydrogenase genes. J. Ind. Microbiol. Biotechnol. 38, 633-641. doi: 10.1007/s10295-010-0809-3
378. Zhang, J., and Xu, J. H. (2010). Biocatalysis, cofactor regeneration. Encyclopedia Ind. Biotechnol. 1-9. doi: 10.1002/9780470054581.eib073
379. Zhao, H., and Van Der Donk, W. A. (2003). Regeneration of cofactors for use in biocatalysis. Curr. Opin. Biotechnol. 14, 583-589. doi: 10.1016/j.copbio.2003.09.007
380. Zhao, H., Wang, P., Huang, E., Ge, Y., and Zhu, G. (2008). Physiologic roles of soluble pyridine nucleotide transhydrogenase in Escherichia coli as determined by homologous recombination. Ann. Microbiol. 58, 275-280. doi: 10.1007/BF03175329
381. Zhao, J., Baba, T., Mori, H., and Shimizu, K. (2004a). Effect of zwf gene knockout on the metabolism of Escherichia coli grown on glucose or acetate. Metab. Eng. 6, 164-174. doi: 10.1016/j.ymben.2004.02.004
382. 13C-labeling experiments and the measurement of enzyme activities. Appl. Microbiol. Biotechnol. 64, 91-98. doi: 10.1007/s00253-003-1458-5
383. Zhao, Z., Kuijvenhoven, K., Van Gulik, W. M., Heijnen, J. J., Van Winden, W. A., and Verheijen, P. J. T. (2011). Cytosolic NADPH balancing in Penicillium chrysogenum cultivated on mixtures of glucose and ethanol. Appl. Microbiol. Biotechnol. 89, 63-72. doi: 10.1007/s00253-010-2851-5
384. Zheng, H., Ohno, Y., Nakamori, T., and Suye, S.-I. (2009). Production of L-malic acid with fixation of HCO3(-) by malic enzyme-catalyzed reaction based on regeneration of coenzyme on electrode modified by layer-by-layer self-assembly method. J. Biosci. Bioeng. 107, 16-20. doi: 10.1016/j.jbiosc.2008.09.009
385. Zhou, J., Olson, D. G., Argyros, D. A., Deng, Y., Van Gulik, W. M., Van Dijken, J. P., et al. (2013). Atypical glycolysis in Clostridium thermocellum. Appl. Environ. Microbiol. 79, 3000-3008. doi: 10.1128/AEM.04037-12
386. Zhu, G., Golding, G. B., and Dean, A. M. (2005). The selective cause of an ancient adaptation. Science 307, 1279-1282. doi: 10.1126/science.1106974
387. Ziegler, M. (2000). New functions of a long-known molecule. Eur. J. Biochem. 267, 1550-1564. doi: 10.1046/j.1432-1327.2000.01187.x