The flexible feedstock concept in Industrial Biotechnology: Metabolic engineering of Escherichia coli, Corynebacterium glutamicum, Pseudomonas, Bacillus and yeast strains for access to alternative carbon sources

Journal of Biotechnology

Volumn 234, Issue , 2016, Pages 139-157

  Wendisch, Volker F ^a   Brito, Luciana Fernandes ^a   Gil Lopez, Marina ^a   Hennig, Guido ^a   Pfeifenschneider, Johannes ^a   Sgobba, Elvira ^a   Veldmann, Kareen H ^a  

^a BIELEFELD UNIVERSITY   (Germany)

Author keywords

Bacillus; Bio based value added chemicals; Biofuels; Biorefinery; C. glutamicum; CO2; E. coli; Flexible feedstock concept; Hydrolysates; Lignocellulosics; Metabolic engineering; Methanol; Pseudomonas; Second generation feedstocks; Strain development; Yeast

Indexed keywords

BACILLI; BACTERIA; BACTERIOLOGY; BIOCONVERSION; BIOFUELS; BIOTECHNOLOGY; CARBON DIOXIDE; ENZYMATIC HYDROLYSIS; ESCHERICHIA COLI; FEEDSTOCKS; GLUCOSE; METABOLISM; METHANOL; ORGANIC CHEMICALS; REFINING; STRAIN; YEAST;

BIOREFINERIES; C. GLUTAMICUM; E. COLI; FLEXIBLE FEEDSTOCK CONCEPT; HYDROLYSATES; LIGNO-CELLULOSICS; PSEUDOMONAS; SECOND GENERATION; STRAIN DEVELOPMENT; VALUE-ADDED CHEMICALS;

METABOLIC ENGINEERING;

2,4 DINITROTOLUENE; ACETIC ACID; ACETOIN; ALCOHOL; ALGINIC ACID; AMINO ACID; AMINOSUGAR; ARABINOSE; AROMATIC COMPOUND; BIOFUEL; CARBOXYLIC ACID; CELLULOSE; CHITIN; CHITOSAN; CYANOPHYCIN; DICARBOXYLIC ACID; FORMIC ACID; GALACTOSE; GLUCAN; GLYCEROL; LACTOSE; METHANOL; MONOSACCHARIDE; ORGANOPHOSPHATE; POLYMER; PROTEIN HYDROLYSATE; STARCH; URONIC ACID; XYLAN; XYLOSE; CARBON;

ANIMAL FOOD; BACILLUS; BACILLUS SUBTILIS; BIOTECHNOLOGICAL PRODUCTION; CARBON SOURCE; CORYNEBACTERIUM GLUTAMICUM; ESCHERICHIA COLI; FERMENTATION; FUNGAL BIOMASS; FUNGAL STRAIN; HYDROLYSIS; METABOLIC ENGINEERING; MICROBIAL BIOMASS; NONHUMAN; PRIORITY JOURNAL; PSEUDOMONAS; REVIEW; SACCHAROMYCES CEREVISIAE; BIOMASS; BIOTECHNOLOGY; CHEMISTRY; GENETICS; METABOLISM; MICROBIOLOGY; PROCEDURES; YEAST;

BACILLUS; BIOFUELS; BIOMASS; BIOTECHNOLOGY; CARBON; CORYNEBACTERIUM GLUTAMICUM; ESCHERICHIA COLI; METABOLIC ENGINEERING; PSEUDOMONAS; YEASTS;

EID: 84982783997     PISSN: 01681656     EISSN: 18734863     Source Type: Journal    
DOI: 10.1016/j.jbiotec.2016.07.022     Document Type: Review

References (204)

1. Abbott, D.W., Boraston, A.B., Structural biology of pectin degradation by Enterobacteriaceae. Microbiol. Mol. Biol. Rev. 72:2 (2008), 301–316.
2. Adachi, N., Takahashi, C., Ono-Murota, N., Yamaguchi, R., Tanaka, T., Kondo, A., Direct L-lysine production from cellobiose by Corynebacterium glutamicum displaying β-glucosidase on its cell surface. Appl. Microbiol. Biotechnol. 97:16 (2013), 7165–7172, 10.1007/s00253-013-5009-4.
3. Álvarez-Añorve, L.I., Calcagno, M.L., Plumbridge, J., Why does Escherichia coli grow more slowly on glucosamine than on N-acetylglucosamine? Effects of enzyme levels and allosteric activation of GlcN6P deaminase (NagB) on growth rates. J. Bacteriol. 187:9 (2005), 2974–2982, 10.1128/JB.187.9.2974-2982.2005.
4. Anthony, C., The Biochemistry of Methylotrophs, vol. 75, 1983, Academic, London, 10.1016/0300-9629(83)90116-0.
5. 2 in Escherichia coli. Cell 166:1 (2016), 115–125, 10.1016/j.cell.2016.05.064.
6. Anusree, M., Wendisch, V.F., Nampoothiri, K.M., Co-expression of endoglucanase and β-glucosidase in Corynebacterium glutamicum DM1729 towards direct lysine fermentation from cellulose. Bioresour. Technol., 2016, 10.1016/j.biortech.2016.03.019.
7. 2 as a chemical feedstock: opportunities and challenges. Dalton Trans. 28 (2007), 2975–2992, 10.1039/b700658f.
8. Arruda, A., Reis, V.C.B., Batista, V.D.F., Daher, B.S., Piva, L.C., De Marco, J.L., de Moraes, L.M.P., Torres, F.A.G., A constitutive expression system for Pichia pastoris based on the PGK1 promoter. Biotechnol. Lett. 38:3 (2016), 509–517, 10.1007/s10529-015-2002-2.
9. Badur, A.H., Jagtap, S.S., Yalamanchili, G., Lee, J.-K., Zhao, H., Rao, C.V., Alginate lyases from alginate-degrading Vibrio splendidus 12B01 are endolytic. Appl. Environ. Microbiol. 81:5 (2015), 1865–1873, 10.1128/AEM.03460-14.
10. Bar-Even, A., Noor, E., Milo, R., A survey of carbon fixation pathways through a quantitative lens. J. Exp. Bot. 63:6 (2012), 2325–2342, 10.1093/jxb/err417.
11. Barrett, E., Stanton, C., Zelder, O., Fitzgerald, G., Ross, R.P., Al, B.E.T., Heterologous expression of lactose- and galactose-utilizing pathways from lactic acid bacteria in Corynebacterium glutamicum for production of lysine in whey. Appl. Environ. Microbiol. 70:5 (2004), 2861–2866, 10.1128/AEM.70.5.2861-2866.2004.
12. Bayer, E.A., Chanzy, H., Lamed, R., Shoham, Y., Cellulose, cellulases and cellulosomes. Curr. Opin. Struct. Biol. 8:5 (1998), 548–557, 10.1016/S0959-440X(98)80143-7.
13. Beceiro-González, E., Concha-Graña, E., Guimaraes, A., Gonçalves, C., Muniategui-Lorenzo, S., Alpendurada, M.F., Optimisation and validation of a solid-phase microextraction method for simultaneous determination of different types of pesticides in water by gas chromatography–mass spectrometry. J. Chromatogr. A 1141:2 (2007), 165–173, 10.1016/j.chroma.2006.12.042.
14. Beer, L.L., Boyd, E.S., Peters, J.W., Posewitz, M.C., Engineering algae for biohydrogen and biofuel production. Curr. Opin. Biotechnol. 20:3 (2009), 264–271, 10.1016/j.copbio.2009.06.002.
15. Bhatia, S.K., Shim, Y.H., Jeon, J.M., Brigham, C.J., Kim, Y.H., Kim, H.J., Seo, H.M., Lee, J.H., Kim, J.H., Yi, D.H., Lee, Y.K., Yang, Y.H., Starch based polyhydroxybutyrate production in engineered Escherichia coli. Bioprocess Biosyst. Eng. 38:8 (2015), 1479–1484, 10.1007/s00449-015-1390-y.
16. Blombach, B., Seibold, G.M., Carbohydrate metabolism in Corynebacterium glutamicum and applications for the metabolic engineering of L-lysine production strains. Appl. Microbiol. Biotechnol. 86:5 (2010), 1313–1322, 10.1007/s00253-010-2537-z.
17. Bonacci, W., Teng, P.K., Afonso, B., Niederholtmeyer, H., Grob, P., Silver, P.A., Savage, D.F., Modularity of a carbon-fixing protein organelle. Proc. Natl. Acad. Sci. 109:2 (2012), 478–483, 10.1073/pnas.1108557109.
18. Brabetz, W., Liebl, W., Schleifer, K.-H.H., Studies on the utilization of lactose by Corynebacterium glutamicum, bearing the lactose operon of Escherichia coli. Arch. Microbiol. 155:6 (1991), 607–612, 10.1007/BF00245357.
19. Brautaset, T., Jakobsen, E.M., Josefsen, K.D., Flickinger, M.C., Ellingsen, T.E., Jakobsen, O.M., Ellingsen, T.E., Bacillus methanolicus: a candidate for industrial production of amino acids from methanol at 50 °C. Appl. Microbiol. Biotechnol. 74:1 (2007), 22–34, 10.1007/s00253-006-0757-z.
20. Buchanan, B.B., Arnon, D.I., A reverse Krebs cycle in photosynthesis: consensus at last. Photosynth. Res. 24:1 (1990), 47–53, 10.1007/BF00032643.
21. Chen, J.-K., Shen, C.-R., Liu, C.-L., N-Acetylglucosamine: production and applications. Mar. Drugs 8:9 (2010), 2493–2516, 10.3390/md8092493.
22. Cheng, K.-K., Lee, B.-S., Masuda, T., Ito, T., Ikeda, K., Hirayama, A., Deng, L., Dong, J., Shimizu, K., Soga, T., Tomita, M., Palsson, B.O., Robert, M., Global metabolic network reorganization by adaptive mutations allows fast growth of Escherichia coli on glycerol. Nat. Commun., 2014, 5, 10.1038/ncomms4233.
23. Choo, S., Um, Y., Ok, S., Min, H., Engineering of Corynebacterium glutamicum to utilize methyl acetate, a potential feedstock derived by carbonylation of methanol with CO. J. Biotechnol. 224:79 (2016), 47–50, 10.1016/j.jbiotec.2016.03.011.
24. Conway, T., The Entner-Doudoroff pathway: history, physiology and molecular biology. FEMS Microbiol. Rev. 9:1 (1992), 1–27, 10.1111/j.1574-6968.1992.tb05822.x.
25. De La Peña Mattozzi, M., Tehara, S.K., Hong, T., Keasling, J.D., Mineralization of paraoxon and its use as a sole C and P source by a rationally designed catabolic pathway in Pseudomonas putida. Appl. Environ. Microbiol. 72:10 (2006), 6699–6706, 10.1128/AEM.00907-06.
26. DeFrank, J.J., Organophosphorus cholinesterase inhibitors: detoxification by microbial enzymes. Applications of Enzyme Biotechnology, 1991, Springer, Boston, MA, US, 165–180, 10.1007/978-1-4757-9235-5_13.
27. Den Haan, R., Van Zyl, W.H., Enhanced xylan degradation and utilisation by Pichia stipitis overproducing fungal xylanolytic enzymes. Enzyme Microb. Technol. 33:5 (2003), 620–628, 10.1016/S0141-0229(03)00183-2.
28. Desai, T.A., Rao, C.V., Regulation of arabinose and xylose metabolism in Escherichia coli. Appl. Environ. Microbiol. 76:5 (2010), 1524–1532, 10.1128/AEM.01970-09.
29. Dobrowolski, A., Mituła, P., Rymowicz, W., Mirończuk, A.M., Efficient conversion of crude glycerol from various industrial wastes into single cell oil by yeast Yarrowia lipolytica. Bioresour. Technol. 207 (2016), 237–243, 10.1016/j.biortech.2016.02.039.
30. Domingues, L., Guimarães, P.M.R., Oliveira, C., Metabolic engineering of Saccharomyces cerevisiae for lactose/whey fermentation. Bioeng. Bugs 1:3 (2010), 164–171, 10.4161/bbug.1.3.10619.
31. Ducat, D., Silver, P., 2013. Improving carbon fixation pathways. 16, 337–344. doi:10.1016/j.cbpa.2012.05.002.
32. Enquist-Newman, M., Faust, A.M., Bravo, D.D., Santos, C.N., Raisner, R.M., Hanel, A., Sarvabhowman, P., Le, C., Regitsky, D.D., Cooper, S.R., Peereboom, L., Clark, A., Martinez, Y., Goldsmith, J., Cho, M.Y., Donohoue, P.D., Luo, L., Lamberson, B., Tamrakar, P., Kim, E.J., Villari, J.L., Gill, A., Tripathi, S.A., Karamchedu, P., Paredes, C.J., Rajgarhia, V., Kotlar, H.K., Bailey, R.B., Miller, D.J., Ohler, N.L., Swimmer, C., Yoshikuni, Y., Efficient ethanol production from brown macroalgae sugars by a synthetic yeast platform. Nature 505:7482 (2014), 239–243, 10.1038/nature12771.
33. Frandsen, K.E.H., Simmons, T.J., Dupree, P., Poulsen, J.-C.N., Hemsworth, G.R., Ciano, L., Johnston, E.M., Tovborg, M., Johansen, K.S., von Freiesleben, P., Marmuse, L., Fort, S., Cottaz, S., Driguez, H., Henrissat, B., Lenfant, N., Tuna, F., Baldansuren, A., Davies, G.J., Lo Leggio, L., Walton, P.H., The molecular basis of polysaccharide cleavage by lytic polysaccharide monooxygenases. Nat. Chem. Biol., 12, 2016, 10.1038/nchembio.2029.
34. Frank, S., Lawrence, A.D., Prentice, M.B., Warren, M.J., Bacterial microcompartments moving into a synthetic biological world. J. Biotechnol. 163:2 (2013), 273–279, 10.1016/j.jbiotec.2012.09.002.
35. Gacesa, P., Alginates. Carbohydr. Polym. 8:3 (1988), 161–182, 10.1016/0144-8617(88)90001-X.
36. Gandhi, S., Salleh, A.B., Rahman, R.N.Z.R.A., Chor Leow, T., Oslan, S.N., Expression and characterization of Geobacillus stearothermophilus SR74 recombinant α -amylase in Pichia pastoris. BioMed Res. Int. 2015 (2015), 1–9, 10.1155/2015/529059.
37. Gao, D., Luan, Y., Wang, Q., Liang, Q., Qi, Q., Construction of cellulose-utilizing Escherichia coli based on a secretable cellulase. Microb. Cell Fact., 14(1), 2015, 159, 10.1186/s12934-015-0349-7.
38. Gaugue, I., Oberto, J., Putzer, H., Plumbridge, J., The use of amino sugars by Bacillus subtilis: presence of a unique operon for the catabolism of glucosamine. PLoS One, 8(5), 2013, e63025, 10.1371/journal.pone.0063025.
39. Gonzalez, C.F., Proudfoot, M., Brown, G., Korniyenko, Y., Mori, H., Savchenko, A.V., Yakunin, A.F., Molecular basis of formaldehyde detoxification: characterization of two S-formylglutathione hydrolases from Escherichia coli, FrmB and YeiG. J. Biol. Chem. 281:20 (2006), 14514–14522, 10.1074/jbc.M600996200.
40. Gopinath, V., Meiswinkel, T.M., Wendisch, V.F., Nampoothiri, K.M., Amino acid production from rice straw and wheat bran hydrolysates by recombinant pentose-utilizing Corynebacterium glutamicum. Appl. Microbiol. Biotechnol. 92:5 (2011), 985–996, 10.1007/s00253-011-3478-x.
41. Groenewald, M., Boekhout, T., Neuveglise, C., Gaillardin, C., van Dijck, P.W.M., Wyss, M., Yarrowia lipolytica: safety assessment of an oleaginous yeast with a great industrial potential. Crit. Rev. Microbiol. 40:3 (2014), 187–206, 10.3109/1040841X.2013.770386.
42. Gu, Y., Ding, Y., Ren, C., Sun, Z., Rodionov, D.A., Zhang, W.,.. Jiang, W., Reconstruction of xylose utilization pathway and regulons in Firmicutes. BMC Genomics 11:1 (2010), 1–14, 10.1186/1471-2164-11-255.
43. Guimarães, P.M.R., Teixeira, J.A., Domingues, L., Fermentation of lactose to bio-ethanol by yeasts as part of integrated solutions for the valorisation of cheese whey. Biotechnol. Adv. 28:3 (2010), 375–384, 10.1016/j.biotechadv.2010.02.002.
44. Gutheil, W.G., Holmquist, B., Vallee, B.L., Purification, characterization, and partial sequence of the glutathione-dependent formaldehyde dehydrogenase from Escherichia coli: a class III alcohol dehydrogenase. Biochemistry 31:2 (1992), 475–481, 10.1021/bi00117a025.
45. Hadiati, A., Krahn, I., Lindner, S.N., Wendisch, V.F., Engineering of Corynebacterium glutamicum for growth and production of L-ornithine, L-lysine, and lycopene from hexuronic acids. Bioresour. Bioprocess. 1:1 (2014), 1–10, 10.1186/s40643-014-0025-5.
46. Hahn-Hägerdal, B., Karhumaa, K., Jeppsson, M., Gorwa-Grauslund, M.F., Metabolic engineering for pentose utilization in Saccharomyces cerevisiae. Biofuels, 2007, Springer, Berlin, Heidelberg, 147–177, 10.1007/10_2007_062.
47. Hamid, R., Khan, M.A., Ahmad, M., Ahmad, M.M., Abdin, M.Z., Musarrat, J., Javed, S., Chitinases: an update. J. Pharm. Bioallied Sci. 5:1 (2013), 21–29, 10.4103/0975-7406.106559.
48. Hansen, L.H., Sorensen, S.J., Jensen, L.B., Chromosomal insertion of the entire Escherichia coli lactose operon, into two strains of Pseudomonas, using a modified mini-Tn5 delivery system. Gene 186:2 (1997), 167–173, 10.1016/S0378-1119(96)00688-9.
49. Hashimoto, W., Miyake, O., Momma, K., Kawai, S., Murata, K., Molecular identification of oligoalginate lyase of Sphingomonas sp. strain A1 as one of the enzymes required for complete depolymerization of alginate. J. Bacteriol. 182:16 (2000), 4572–4577, 10.1128/jb.182.16.4572-4577.2000.
50. Herring, C.D., Blattner, F.R., Global transcriptional effects of a suppressor tRNA and the inactivation of the regulator FrmR. J. Bacteriol. 186:20 (2004), 6714–6720, 10.1128/JB.186.20.6714-6720.2004.
51. Holmberg, C., Beijer, L., Rutberg, B., Rutberg, L., Glycerol catabolism in Bacillus subtilis: nucleotide sequence of the genes encoding glycerol kinase (glpK) and glycerol-3-phosphate dehydrogenase (glpD). J. Gen. Microbiol. 136:12 (1990), 2367–2375, 10.1099/00221287-136-12-2367.
52. 2 fixation of Chloroflexus aurantiacus. Arch. Microbiol. 145:2 (1986), 173–180, 10.1007/Bf00446776.
53. Huber, H., Gallenberger, M., Jahn, U., Eylert, E., Berg, I.A., Kockelkorn, D.,.. Fuchs, G., A dicarboxylate/4-hydroxybutyrate autotrophic carbon assimilation cycle in the hyperthermophilic archaeum Ignicoccus hospitalis. Proc. Natl. Acad. Sci. U. S. A. 105:22 (2008), 7851–7856, 10.1073/pnas.0801043105.
54. Hyeon, J.E., Jeon, W.J., Whang, S.Y., Han, S.O., Production of minicellulosomes for the enhanced hydrolysis of cellulosic substrates by recombinant Corynebacterium glutamicum. Enzyme Microb. Technol. 48:4–5 (2011), 371–377, 10.1016/j.enzmictec.2010.12.014.
55. Innis, M.A., Holland, M.J., McCabe, P.C., Cole, G.E., Wittman, V.P., Tal, R.,.. Meade, J.H., Expression, glycosylation, and secretion of an aspergillus glucoamylase by Saccharomyces cerevisiae. Science 228:4695 (1985), 21–26, 10.1126/science.228.4695.21.
56. Inoue, A., Nishiyama, R., Mochizuki, S., Ojima, T., Identification of a 4-deoxy-L-erythro-5-hexoseulose uronic acid reductase, FlRed, in an alginolytic bacterium Flavobacterium sp. strain UMI-01. Mar. Drugs 13:1 (2015), 493–508, 10.3390/md13010493.
57. Joentgen, W., Müller, N., Mitschker, A., Schmidt, H., Polyaspartic acids. Biopolymers Online, 2005, Wiley-VCH Verlag GmbH & Co. KGaA, 10.1002/3527600035.bpol7007.
58. Kabisch, J., Pratzka, I., Meyer, H., Albrecht, D., Lalk, M., Ehrenreich, A., Schweder, T., Metabolic engineering of Bacillus subtilis for growth on overflow metabolites. Microb. Cell Fact., 12(1), 2013, 72, 10.1186/1475-2859-12-72.
59. Kang, M.-K., Lee, J., Um, Y., Lee, T.S., Bott, M., Park, S.J., Woo, H.M., Synthetic biology platform of CoryneBrick vectors for gene expression in Corynebacterium glutamicum and its application to xylose utilization. Appl. Microbiol. Biotechnol. 98:13 (2014), 5991–6002, 10.1007/s00253-014-5714-7.
60. Kawaguchi, H., Verte, A.A., Okino, S., Inui, M., Yukawa, H., Yukawa, H., Mol, J., Engineering of a xylose metabolic pathway in Corynebacterium glutamicum. Appl. Environ. Microbiol. 72:5 (2006), 3418–3428, 10.1128/AEM.72.5.3418.
61. Kawaguchi, H., Sasaki, M., Vertès, A.A., Inui, M., Yukawa, H., Engineering of an L-arabinose metabolic pathway in Corynebacterium glutamicum. Appl. Microbiol. Biotechnol. 77:5 (2008), 1053–1062, 10.1007/s00253-007-1244-x.
62. Keyhani, N.O., Roseman, S., Wild-type Escherichia coli grows on the chitin disaccharide, N,N′-diacetylchitobiose, by expressing the cel operon. Proc. Natl. Acad. Sci. U. S. A. 94:26 (1997), 14367–14371, 10.1073/pnas.94.26.14367.
63. Khanna, S., Goyal, A., Moholkar, V.S., Microbial conversion of glycerol: present status and future prospects. Crit. Rev. Biotechnol. 32:3 (2012), 235–262, 10.3109/07388551.2011.604839.
64. Kim, S.J., Hyeon, J.E., Jeon, S.D., Choi, G.W., Han, S.O., Bi-functional cellulases complexes displayed on the cell surface of Corynebacterium glutamicum increase hydrolysis of lignocelluloses at elevated temperature. Enzyme Microb. Technol. 66 (2014), 67–73, 10.1016/j.enzmictec.2014.08.010.
65. Kim, E.-M., Um, Y., Bott, M., Woo, H.M., Engineering of Corynebacterium glutamicum for growth and succinate production from levoglucosan, a pyrolytic sugar substrate. FEMS Microbiol. Lett., 362(19), 2015, fnv161, 10.1093/femsle/fnv161.
66. Kiran, S., Dhar, K.S., Wendisch, V.F., Nampoothiri, K.M., Engineering of Corynebacterium glutamicum for Xylitol Production from Lignocellulosic Pentose Sugars. J. Biotechnol., 2016, 10.1016/j.jbiotec.2016.05.011 accepted.
67. Kircher, M., Sustainability of biofuels and renewable chemicals production from biomass. Curr. Opin. Chem. Biol. 29 (2015), 26–31, 10.1016/j.cbpa.2015.07.010.
68. Knoshaug, E.P., Franden, M.A., Stambuk, B.U., Zhang, M., Singh, A., Utilization and transport of L-arabinose by non-Saccharomyces yeasts. Cellulose 16:4 (2009), 729–741, 10.1007/s10570-009-9319-8.
69. Kondo, A., Ishii, J., Hara, K.Y., Hasunuma, T., Matsuda, F., Development of microbial cell factories for bio-refinery through synthetic bioengineering. J. Biotechnol. 163:2 (2013), 204–216, 10.1016/j.jbiotec.2012.05.021.
70. Koopman, F.W., De Winde, J.H., Ruijssenaars, H.J., C1 compounds as auxiliary substrate for engineered Pseudomonas putida S12. Appl. Microbiol. Biotechnol. 83:4 (2009), 705–713, 10.1007/s00253-009-1922-y.
71. Kornberg, H.L., Madsen, N.B., The metabolism of C2 compounds in microorganisms. 3. Synthesis of malate from acetate via the glyoxylate cycle. Biochem. J. 68:3 (1958), 549–557, 10.1042/bj0680549.
72. Krispin, O., Allmansberger, R., The Bacillus subtilis galE gene is essential in the presence of glucose and galactose. J. Bacteriol. 180:8 (1998), 2265–2270.
73. La Grange, D.C., Pretorius, I.S., Claeyssens, M., van Zyl, W.H., Degradation of xylan to D-xylose by recombinant Saccharomyces cerevisiae coexpressing the Aspergillus niger β-xylosidase (xlnD) and the Trichoderma reesei xylanase II (xyn2) genes. Appl. Environ. Microbiol. 67:12 (2001), 5512–5519, 10.1128/AEM.67.12.5512-5519.2001.
74. Lan, E.I., Liao, J.C., Microbial synthesis of n-butanol, isobutanol, and other higher alcohols from diverse resources. Bioresour. Technol. 135 (2013), 339–349, 10.1016/j.biortech.2012.09.104.
75. Lange, J.P., Renewable feedstocks: the problem of catalyst deactivation and its mitigation. Angew. Chem. Int. Ed. 54:45 (2015), 13187–13197, 10.1002/anie.201503595.
76. Larsen, S., Weaver, J., de Sa Campos, K., Bulahan, R., Nguyen, J., Grove, H.,.. Lin-Cereghino, G.P., Mutant strains of Pichia pastoris with enhanced secretion of recombinant proteins. Biotechnol. Lett. 35:11 (2013), 1925–1935, 10.1007/s10529-013-1290-7.
77. Layton, D.S., Ajjarapu, A., Choi, D.W., Jarboe, L.R., Engineering ethanologenic Escherichia coli for levoglucosan utilization. Bioresour. Technol. 102:17 (2011), 8318–8322, 10.1016/j.biortech.2011.06.011.
78. Lazar, Z., Gamboa-Melendez, H., Le Coq, A.-M.C.-, Neuveglise, C., Nicaud, J.-M., Awakening the endogenous Leloir pathway for efficient galactose utilization by Yarrowia lipolytica. Biotechnol. Biofuels, 8, 2015, 185, 10.1186/s13068-015-0370-4.
79. Lazarev, D., Puskarz, I., Breaker, R.R., Substrate specificity and reaction kinetics of an X-motif ribozyme. RNA 9:6 (2003), 688–697, 10.1261/rna.2600503.
80. Lessmeier, L., Hoefener, M., Wendisch, V.F., Formaldehyde degradation in Corynebacterium glutamicum involves acetaldehyde dehydrogenase and mycothiol-dependent formaldehyde dehydrogenase. Microbiology (United Kingdom) 159:PART 12 (2013), 2651–2662, 10.1099/mic.0.072413-0.
81. Lessmeier, L., Pfeifenschneider, J., Carnicer, M., Heux, S., Portais, J.C., Wendisch, V.F., Production of carbon-13-labeled cadaverine by engineered Corynebacterium glutamicum using carbon-13-labeled methanol as co-substrate. Appl. Microbiol. Biotechnol. 99:23 (2015), 10163–10176, 10.1007/s00253-015-6906-5.
82. Li, Z., Wu, J., Zhang, B., Wang, F., Ye, X., Huang, Y.,.. Cui, Z., AmyM, a novel maltohexaose-forming α-amylase from Corallococcus sp. strain EGB. Appl. Environ. Microbiol. 81:6 (2015), 1977–1987, 10.1128/AEM.03934-14.
83. Lidstrom, M.E., Stirling, D.I., Methylotrophs: genetics and commercial applications. Annu. Rev. Microbiol. 44 (1990), 27–58.
84. Lidstrom, M.E., Genetics of carbon metabolism in methylotrophic bacteria. FEMS Microbiol. Rev. 7:3–4 (1990), 431–436, 10.1111/j.1574-6968.1990.tb04949.x.
85. Lim, H.G., Seo, S.W., Jung, G.Y., Engineered Escherichia coli for simultaneous utilization of galactose and glucose. Bioresour. Technol. 135 (2013), 564–567, 10.1016/j.biortech.2012.10.124.
86. Lindner, S.N., Meiswinkel, T.M., Panhorst, M., Youn, J.W., Wiefel, L., Wendisch, V.F., Glycerol-3-phosphatase of Corynebacterium glutamicum. J. Biotechnol. 159:3 (2012), 216–224, 10.1016/j.jbiotec.2012.02.003.
87. Linger, J.G., Hobdey, S.E., Franden, M.A., Fulk, E.M., Beckham, G.T., Conversion of levoglucosan and cellobiosan by Pseudomonas putida KT2440. Metab. Eng. Commun. 3 (2016), 24–29, 10.1016/j.meteno.2016.01.005.
88. Litsanov, B., Brocker, M., Bott, M., Glycerol as a substrate for aerobic succinate production in minimal medium with Corynebacterium glutamicum. Microb. Biotechnol. 6:2 (2013), 189–195, 10.1111/j.1751-7915.2012.00347.x.
89. Liu, G., Yue, L., Chi, Z., Yu, W., Chi, Z., Madzak, C., The surface display of the alginate lyase on the cells of Yarrowia lipolytica for hydrolysis of alginate. Mar. Biotechnol. 11:5 (2009), 619–626, 10.1007/s10126-009-9178-1.
90. Liu, L., Liu, Y., Shin, H., Chen, R., Li, J., Du, G., Chen, J., Microbial production of glucosamine and N-acetylglucosamine: advances and perspectives. Appl. Microbiol. Biotechnol. 97:14 (2013), 6149–6158, 10.1007/s00253-013-4995-6.
91. Liu, Z., Inokuma, K., Ho, S.-H., Haan, R., Hasunuma, den, van Zyl, T., Kondo, W.H., Combined cell-surface display- and secretion-based strategies for production of cellulosic ethanol with Saccharomyces cerevisiae. Biotechnol. Biofuels, 8(1), 2015, 162, 10.1186/s13068-015-0344-6.
92. Loc, N.H., Thi, N., Hoa, Q., Thi, P., Cuc, K., Quang, H.T., Expression of chitinase (chi42) gene from Trichoderma asperellum in Saccharomyces cerevisiae. Ann. Biol. Res. 4:9 (2013), 15–19.
93. Müller, J.E.N., Heggeset, T.M.B., Wendisch, V.F., Vorholt, J.A., Brautaset, T., Methylotrophy in the thermophilic Bacillus methanolicus, basic insights and application for commodity production from methanol. Appl. Microbiol. Biotechnol. 99:2 (2015), 535–551, 10.1007/s00253-014-6224-3.
94. Müller, J.E.N., Meyer, F., Litsanov, B., Kiefer, P., Potthoff, E., Heux, S.,.. Vorholt, J.A., Engineering Escherichia coli for methanol conversion. Metab. Eng. 28 (2015), 190–201, 10.1016/j.ymben.2014.12.008.
95. Mackerras, A.H., de Chazal, N.M., Smith, G.D., Transient accumulations of cyanophycin in Anabaena cylindrica and Synechocystis 6308. Microbiology 136:10 (1990), 2057–2065, 10.1099/00221287-136-10-2057.
96. Majewski, R.A., Domach, M.M., Simple constrained-optimization view of acetate overflow in Escherichia coli. Biotechnol. Bioeng 35 (1990), 732–738, 10.1002/bit.260350711.
97. Marx, C.J., Bringel, F., Chistoserdova, L., Moulin, L., Farhan Ul Haque, M., Fleischman, D.E.,.. Vuilleumier, S., Complete genome sequences of six strains of the genus Methylobacterium. J. Bacteriol. 194:17 (2012), 4746–4748, 10.1128/JB.01009-12.
98. Matano, C., Uhde, A., Youn, J.W., Maeda, T., Clermont, L., Marin, K.,.. Seibold, G.M., Engineering of Corynebacterium glutamicum for growth and L-lysine and lycopene production from N-acetyl glucosamine. Appl. Microbiol. Biotechnol. 98 (2014), 5633–5643, 10.1007/s00253-014-5676-9.
99. Mattozzi, M. d., Ziesack, M., Voges, M.J., Silver, P.A., Way, J.C., Expression of the sub-pathways of the Chloroflexus aurantiacus 3-hydroxypropionate carbon fixation bicycle in E. coli: Toward horizontal transfer of autotrophic growth. Metab. Eng. 16:1 (2013), 130–139, 10.1016/j.ymben.2013.01.005.
100. May, C.D., Industrial pectins: sources, production and applications. Carbohydr. Polym. 12:1 (1990), 79–99, 10.1016/0144-8617(90)90105-2.
101. Meijnen, J.P., De Winde, J.H., Ruijssenaars, H.J., Engineering Pseudomonas putida S12 for efficient utilization of D-xylose and L-arabinose. Appl. Environ. Microbiol. 74:16 (2008), 5031–5037, 10.1128/AEM.00924-08.
102. Meijnen, J.P., De Winde, J.H., Ruijssenaars, H.J., Establishment of oxidative D-xylose metabolism in Pseudomonas putida S12. Appl. Environ. Microbiol. 75:9 (2009), 2784–2791, 10.1128/AEM.02713-08.
103. Meiswinkel, T.M., Gopinath, V., Lindner, S.N., Nampoothiri, K.M., Wendisch, V.F., Accelerated pentose utilization by Corynebacterium glutamicum for accelerated production of lysine, glutamate, ornithine and putrescine. Microbiol. Biotechnol. 6 (2013), 131–140, 10.1111/1751-7915.12001.
104. Meiswinkel, T.M., Rittmann, D., Lindner, S.N., Wendisch, V.F., Crude glycerol-based production of amino acids and putrescine by Corynebacterium glutamicum. Bioresour. Technol. 145 (2013), 254–258, 10.1016/j.biortech.2013.02.053.
105. Meng, D.C., Shi, Z.Y., Wu, L.P., Zhou, Q., Wu, Q., Chen, J.C., Chen, G.Q., Production and characterization of poly(3-hydroxypropionate-co-4-hydroxybutyrate) with fully controllable structures by recombinant Escherichia coli containing an engineered pathway. Metab. Eng. 14:4 (2012), 317–324, 10.1016/j.ymben.2012.04.003.
106. Monti, M.R., Smania, A.M., Fabro, G., Alvarez, M.E., Argarana, C.E., Engineering Pseudomonas fluorescens for biodegradation of 2,4-dinitrotoluene. Appl. Environ. Microbiol. 71:12 (2005), 8864–8872, 10.1128/AEM.71.12.8864-8872.2005.
107. Murai, T., Ueda, M., Yamamura, M., Atomi, H., Shibasaki, Y., Kamasawa, N.,.. Tanaka, A., Construction of a starch-utilizing yeast by cell surface engineering. Appl. Environ. Microbiol. 63:4 (1997), 1362–1366.
108. Murray, A., Rathbone, A.J., Ray, D.E., Novel protein targets for organophosphorus pesticides in rat brain. Environ. Toxicol. Pharmacol. 19:3 (2005), 451–454, 10.1016/j.etap.2004.12.006.
109. Naerdal, I., Pfeifenschneider, J., Brautaset, T., Wendisch, V.F., Methanol-based cadaverine production by genetically engineered Bacillus methanolicus strains. Microbiol. Biotechnol. 8:2 (2015), 342–350, 10.1111/1751-7915.12257.
110. Nakano, K., Rischke, M., Sato, S., Märkl, H., Influence of acetic acid on the growth of Escherichia coli K12 during high-cell-density cultivation in a dialysis reactor. Appl. Microbiol. Biotechnol. 48:5 (1997), 597–601, 10.1007/s002530051101.
111. Nikel, P.I., Romero-Campero, F.J., Zeidman, J.A., Goñi-Moreno, Á., de Lorenzo, V., The glycerol-dependent metabolic persistence of Pseudomonas putida KT2440 reflects the regulatory logic of the GlpR repressor. mBio 6:2 (2015), e00340–15, 10.1128/mBio.00340-15.
112. Obst, M., Oppermann-Sanio, F.B., Luftmann, H., Steinbüchel, A., Isolation of cyanophycin-degrading bacteria, cloning and characterization of an extracellular cyanophycinase gene (cphE) from Pseudomonas anguilliseptica strain BI. J. Biol. Chem. 277:28 (2002), 25096–25105, 10.1074/jbc.M112267200.
113. Obst, M., Sallam, A., Luftmann, H., Steinbüchel, A., Isolation and characterization of gram-positive cyanophycin-degrading bacteria. Kinetic studies on cyanophycin depolymerase activity in aerobic bacteria. Biomacromolecules 5:1 (2004), 153–161, 10.1021/bm034281p.
114. Ochiai, A., Yamasaki, M., Mikami, B., Hashimoto, W., Murata, K., Crystallization and preliminary X-ray analysis of an exotype alginate lyase Atu3025 from Agrobacterium tumefaciens strain C58, a member of polysaccharide lyase family 15. Acta Crystallogr. Sect. F: Struct. Biol. Cryst. Commun. 62:Pt 5 (2006), 486–488, 10.1107/S1744309106014333.
115. Ochsner, A.M., Sonntag, F., Buchhaupt, M., Schrader, J., Vorholt, J.A., Methylobacterium extorquens: methylotrophy and biotechnological applications. Appl. Microbiol. Biotechnol. 99:2 (2014), 517–534, 10.1007/s00253-014-6240-3.
116. Okamoto, S., Chin, T., Nagata, K., Takahashi, T., Ohara, H., Aso, Y., Production of itaconic acid in Escherichia coli expressing recombinant α-amylase using starch as substrate. J. Biosci. Bioeng. 119:5 (2015), 548–553, 10.1016/j.jbiosc.2014.10.021.
117. Olah, G.A., Goeppert, A., Prakash, G.K.S., 2009. Beyond Oil and Gas: The Methanol Economy: Second Edition. Beyond Oil and Gas: The Methanol Economy: Second Edition, pp. 1–334. doi:10.1002/9783527627806.
118. Olah, G.A., Towards oil independence through renewable methanol chemistry. Angew. Chem. Int. Ed. 52:1 (2013), 104–107, 10.1002/anie.201204995.
119. Onaca, C., Kieninger, M., Engesser, K.H., Altenbuchner, J., Degradation of alkyl methyl ketones by Pseudomonas veronii MEK700. J. Bacteriol. 189:10 (2007), 3759–3767, 10.1128/JB.01279-06.
120. Orita, I., Sakamoto, N., Kato, N., Yurimoto, H., Sakai, Y., Bifunctional enzyme fusion of 3-hexulose-6-phosphate synthase and 6-phospho-3-hexuloisomerase. Appl. Microbiol. Biotechnol. 76:2 (2007), 439–445, 10.1007/s00253-007-1023-8.
121. Peng, S., Chu, Z., Lu, J., Li, D., Wang, Y., Yang, S., Zhang, Y., Co-expression of chaperones from P. furiosus enhanced the soluble expression of the recombinant hyperthermophilic α-amylase in E. coli. Cell Stress Chaperones 21:3 (2016), 477–484, 10.1007/s12192-016-0675-7.
122. Poust, S., Piety, J., Bar-Even, A., Louw, C., Baker, D., Keasling, J.D., Siegel, J.B., Mechanistic analysis of an engineered enzyme that catalyzes the formose reaction. ChemBioChem 16:13 (2015), 1950–1954, 10.1002/cbic.201500228.
123. Preiss, J., Ashwell, G., Alginic acid metabolism in bacteria: II. The enzymatic reduction of 4-deoxy-I-erythro-5-hexoseulose uronic acid to 2-keto-3-deoxy-D-gluconic acid. J. Biol. Chem. 237:2 (1962), 317–321.
124. Prosen, E.M., Radlein, D., Piskorz, J., Scott, D.S., Legge, R.L., Microbial utilization of levoglucosan in wood pyrolysate as a carbon and energy source. Biotechnol. Bioeng. 42:4 (1993), 538–541, 10.1002/bit.260420419.
125. Qi, X., Zha, J., Liu, G.-G., Zhang, W., Li, B.-Z., Yuan, Y.-J., Heterologous xylose isomerase pathway and evolutionary engineering improve xylose utilization in Saccharomyces cerevisiae. Front. Microbiol., 6, 2015, 1165, 10.3389/fmicb.2015.01165.
126. Qiao, Y., Peng, Q., Yan, J., Wang, H., Ding, H., Shi, B., Gene cloning and enzymatic characterization of alkali-tolerant type I pullulanase from Exiguobacterium acetylicum. Lett. Appl. Microbiol. 60:1 (2015), 52–59, 10.1111/lam.12333.
127. Radek, A., Krumbach, K., Gätgens, J., Wendisch, V.F., Wiechert, W., Bott, M.,.. Marienhagen, J., Engineering of Corynebacterium glutamicum for minimized carbon loss during utilization of D-xylose containing substrates. J. Biotechnol. 192:Part (2014), 156–160, 10.1016/j.jbiotec.2014.09.026.
128. Reinscheid, D.J., Eikmanns, B.J., Sahm, H., 1994. Characterization of the isocitrate lyase gene from Corynebacterium glutamicum and biochemical analysis of the enzyme, 176 (12), 3474–3483.
129. Rhee, M.S., Wei, L., Sawhney, N., Rice, J.D., St John, F.J., Hurlbert, J.C., Preston, J.F., Engineering the xylan utilization system in Bacillus subtilis for production of acidic Xylooligosaccharides. Appl. Environ. Microbiol. 80:3 (2014), 917–927, 10.1128/aem.03246-13.
130. Richard, P., Hilditch, S., D-Galacturonic acid catabolism in microorganisms and its biotechnological relevance. Appl. Microbiol. Biotechnol. 82:4 (2009), 597–604, 10.1007/s00253-009-1870-6.
131. Richter, R., Hejazi, M., Kraft, R., Ziegler, K., Lockau, W., Cyanophycinase, a peptidase degrading the cyanobacterial reserve material multi-L-arginyl-poly-L-aspartic acid (cyanophycin). Eur. J. Biochem. 263:1 (1999), 163–169, 10.1046/j.1432-1327.1999.00479.x.
132. Rittmann, D., Lindner, S.N., Wendisch, V.F., Engineering of a glycerol utilization pathway for amino acid production by Corynebacterium glutamicum. Appl. Environ. Microbiol. 74:20 (2008), 6216–6222, 10.1128/AEM.00963-08.
133. Roberts, G.A.F., Chitin Chemistry. 1992, Macmillan, London, 10.1007/978-1-349-11545-7_1.
134. Russell, A.J., Berberich, J.a., Drevon, G.F., Koepsel, R.R., Biomaterials for mediation of chemical and biological warfare agents. Annu. Rev. Biomed. Eng. 5 (2003), 1–27, 10.1146/annurev.bioeng.5.121202.125602.
135. Sa-Nogueira, I., Nogueira, T.V., Soares, S., de Lencastre, H., The Bacillus subtilis L-arabinose (ara) operon: nucleotide sequence, genetic organization and expression. Microbiology 143:Part 3 (1997), 957–969, 10.1099/00221287-143-3-957.
136. Sallam, A., Kalkandzhiev, D., Steinbüchel, A., Production optimization of cyanophycinase ChpE (al) from Pseudomonas alcaligenes DIP1. AMB Express, 1, 2011, 38, 10.1186/2191-0855-1-38.
137. Sasaki, M., Jojima, T., Inui, M., Yukawa, H., Simultaneous utilization of D-cellobiose, D-glucose, and D-xylose by recombinant Corynebacterium glutamicum under oxygen-deprived conditions. Appl. Microbiol. Biotechnol. 81:4 (2008), 691–699, 10.1007/s00253-008-1703-z.
138. Sasaki, M., Jojima, T., Kawaguchi, H., Inui, M., Yukawa, H., Engineering of pentose transport in Corynebacterium glutamicum to improve simultaneous utilization of mixed sugars. Appl. Microbiol. Biotechnol. 85:1 (2009), 105–115, 10.1007/s00253-009-2065-x.
139. Schauer, N.L., Ferry, J.G., Metabolism of formate in Methanobacterium formicicum. J. Bacteriol. 142:3 (1980), 800–807.
140. Schneider, J., Niermann, K., Wendisch, V.F., Production of the amino acids L-glutamate, L-lysine, L-ornithine and L-arginine from arabinose by recombinant Corynebacterium glutamicum. J. Biotechnol., 154, 2011, 10.1016/j.jbiotec.2010.07.009.
141. Schroeter, R., Voigt, B., Jürgen, B., Methling, K., Pöther, D.C., Schäfer, H.,.. Schweder, T., The peroxide stress response of Bacillus licheniformis. Proteomics 11:14 (2011), 2851–2866, 10.1002/pmic.201000461.
142. Schwanborn, M., Joentgen, W., Chemical synthesis of polyaspartates. A biodegradable alternative to currently used polycarboxylate homo-and copolymers. Chim. Oggi 16:11–12 (1998), 36–40.
143. Seibold, G., Auchter, M., Berens, S., Kalinowski, J., Eikmanns, B.J., Utilization of soluble starch by a recombinant Corynebacterium glutamicum strain: growth and lysine production. J. Biotechnol. 124:2 (2006), 381–391, 10.1016/j.jbiotec.2005.12.027.
144. Seo, J.-S., Keum, Y.-S., Li, Q.X., Bacterial degradation of aromatic compounds. Int. J. Environ. Res. Public Health 6:1 (2009), 278–309, 10.3390/ijerph6010278.
145. 2-fixing photorespiratory bypass into a cyanobacterium. J. Biol. Chem. 289:14 (2014), 9493–9500, 10.1074/jbc.C113.543132.
146. Shin, J.W., Lee, O.K., Park, H.H., Kim, H.S., Lee, E.Y., Molecular characterization of a novel oligoalginate lyase consisting of AlgL- and heparinase II/III-like domains from Stenotrophomonas maltophilia KJ-2 and its application to alginate saccharification. Korean J. Chem. Eng. 32:5 (2015), 917–924, 10.1007/s11814-014-0282-1.
147. Siegel, J.B., Smith, A.L., Poust, S., Wargacki, A.J., Bar-Even, A., Louw, C.,.. Baker, D., Computational protein design enables a novel one-carbon assimilation pathway. Proc. Natl. Acad. Sci. U. S. A. 112:12 (2015), 3704–3709, 10.1073/pnas.1500545112.
148. Simon, R.D., Weathers, P., Determination of the structure of the novel polypeptide containing aspartic acid and arginine which is found in cyanobacteria. Biochim. Biophys. Acta 420:1 (1976), 165–176, 10.1016/0005-2795(76)90355-X.
149. Šmejkalová, H., Erb, T.J., Fuchs, G., Methanol assimilation in Methylobacterium extorquens AM1: Demonstration of all enzymes and their regulation. PLoS One, 5(10), 2010, e13001, 10.1371/journal.pone.0013001.
150. Smith, J.E., Anderson, J.G., Senior, E., Aidoo, K., Bioprocessing of lignocelluloses. Phil. Trans. R. Soc. Lond. 321 (1987), 507–521.
151. Sonntag, F., Kroner, C., Lubuta, P., Peyraud, R., Horst, A., Buchhaupt, M., Schrader, J., Engineering Methylobacterium extorquens for de novo synthesis of the sesquiterpenoid α-humulene from methanol. Metab. Eng. 32 (2015), 82–94, 10.1016/j.ymben.2015.09.004.
152. Spadoni, S., Zabotina, O., Di Matteo, A., Mikkelsen, J.D., Cervone, F., De Lorenzo, G.,.. Bellincampi, D., Polygalacturonase-inhibiting protein interacts with pectin through a binding site formed by four clustered residues of arginine and lysine. Plant Physiol. 141:2 (2006), 557–564, 10.1104/pp.106.076950.
153. Sriamornsak, P., Chemistry of pectin and its pharmaceutical uses: a review. Silpakorn Univ. Int. J. 3:1–2 (2003), 206–228.
154. Srisimarat, W., Murakami, S., Pongsawasdi, P., Krusong, K., Crystallization and preliminary X-ray crystallographic analysis of the amylomaltase from Corynebacterium glutamicum. Acta Crystallogr. Sect. F: Struct. Biol. Cryst. Commun. 69:9 (2013), 1004–1006, 10.1107/S1744309113020319.
155. Starr, M.P., Chatterjee, A.K., Starr, P.B., Buchanan, G.E., Enzymatic degradation of polygalacturonic acid by Yersinia and Klebsiella species in relation to clinical laboratory procedures. J. Clin. Microbiol. 6:4 (1977), 379–386.
156. Subtil, T., Boles, E., Improving L-arabinose utilization of pentose fermenting Saccharomyces cerevisiae cells by heterologous expression of L-arabinose transporting sugar transporters. Biotechnol. Biofuels, 4, 2011, 38, 10.1186/1754-6834-4-38.
157. Swinnen, S., Ho, P.-W., Klein, M., Nevoigt, E., Genetic determinants for enhanced glycerol growth of Saccharomyces cerevisiae. Metab. Eng. 36 (2016), 68–79, 10.1016/j.ymben.2016.03.003.
158. Takase, R., Ochiai, A., Mikami, B., Hashimoto, W., Murata, K., Molecular identification of unsaturated uronate reductase prerequisite for alginate metabolism in Sphingomonas sp. A1. Biochim. Biophys. Acta 1804:9 (2010), 1925–1936, 10.1016/j.bbapap.2010.05.010.
159. Takase, R., Mikami, B., Kawai, S., Murata, K., Hashimoto, W., Structure-based conversion of the coenzyme requirement of a short-chain dehydrogenase/reductase involved in bacterial alginate metabolism. J. Biol. Chem. 289:48 (2014), 33198–33214, 10.1074/jbc.M114.585661.
160. Takeda, H., Yoneyama, F., Kawai, S., Hashimoto, W., Murata, K., Bioethanol production from marine biomass alginate by metabolically engineered bacteria. Energy Environ. Sci. 4:7 (2011), 2575–2581, 10.1039/C1EE01236C.
161. Tanaka, T., Kondo, A., Cell surface engineering of industrial microorganisms for biorefining applications. Biotechnol. Adv. 33:7 (2015), 1403–1411, 10.1016/j.biotechadv.2015.06.002.
162. Tanimura, K., Takashima, S., Matsumoto, T., Tanaka, T., Kondo, A., 2,3-Butanediol production from cellobiose using exogenous β-glucosidase-expressing Bacillus subtilis. Appl. Microbiol. Biotechnol., 2016, 1–9, 10.1007/s00253-016-7326-x.
163. Tateno, T., Fukuda, H., Kondo, A., Production of L-lysine from starch by Corynebacterium glutamicum displaying α-amylase on its cell surface. Appl. Microbiol. Biotechnol. 74:6 (2007), 1213–1220, 10.1007/s00253-006-0766-y.
164. Tateno, T., Okada, Y., Tsuchidate, T., Tanaka, T., Fukuda, H., Kondo, A., Direct production of cadaverine from soluble starch using Corynebacterium glutamicum coexpressing α-amylase and lysine decarboxylase. Appl. Microbiol. Biotechnol. 82:1 (2009), 115–121, 10.1007/s00253-008-1751-4.
165. Teramoto, H., Shirai, T., Inui, M., Yukawa, H., Identification of a gene encoding a transporter essential for utilization of C4 dicarboxylates in Corynebacterium glutamicum. Appl. Environ. Microbiol. 74:17 (2008), 5290–5296, 10.1128/AEM.00832-08.
166. Thomas, C.M., Süss-Fink, G., Ligand effects in the rhodium-catalyzed carbonylation of methanol. Coord. Chem. Rev. 243:1–2 (2003), 125–142, 10.1016/S0010-8545(03)00051-1.
167. Thomas, F., Lundqvist, L.C.E., Jam, M., Jeudy, A., Barbeyron, T., Sandström, C.,.. Czjzek, M., Comparative characterization of two marine alginate lyases from Zobellia galactanivorans reveals distinct modes of action and exquisite adaptation to their natural substrate. J. Biol. Chem. 288:32 (2013), 23021–23037, 10.1074/jbc.M113.467217.
168. Tsuchidate, T., Tateno, T., Okai, N., Tanaka, T., Ogino, C., Kondo, A., Glutamate production from β-glucan using endoglucanase-secreting Corynebacterium glutamicum. Appl. Microbiol. Biotechnol. 90:3 (2011), 895–901, 10.1007/s00253-011-3116-7.
169. Tsuge, Y., Tateno, T., Sasaki, K., Hasunuma, T., Tanaka, T., Kondo, A., Direct production of organic acids from starch by cell surface-engineered Corynebacterium glutamicum in anaerobic conditions. AMB Express, 3(1), 2013, 72, 10.1186/2191-0855-3-72.
170. Uhde, A., Youn, J.W., Maeda, T., Clermont, L., Matano, C., Kramer, R.,.. Marin, K., Glucosamine as carbon source for amino acid-producing Corynebacterium glutamicum. Appl. Microbiol. Biotechnol. 97:4 (2013), 1679–1687, 10.1007/s00253-012-4313-8.
171. Uhde, A., Brühl, N., Goldbeck, O., Matano, C., Gurow, O., Rückert, C.,.. Seibold, G.M., Transcription of sialic acid catabolism genes in Corynebacterium glutamicum is subject to catabolite repression and control by the transcriptional repressor NanR. J. Bacteriol., 2016.
172. van Maris, A.J.A., Abbott, D.A., Bellissimi, E., van den Brink, J., Kuyper, M., Luttik, M.A.H.,.. Pronk, J.T., Alcoholic fermentation of carbon sources in biomass hydrolysates by Saccharomyces cerevisiae: current status. Antonie Van Leeuwenhoek 90:4 (2006), 391–418, 10.1007/s10482-006-9085-7.
173. Van Rensburg, P., Van Zyl, W.H., Pretorius, I.S., Engineering yeast for efficient cellulose degradation. Yeast 14:1 (1998), 67–76, 10.1002/(SICI)1097-0061(19980115)14:1<67:AID-YEA200>3.0.CO;2-T.
174. Viktor, M.J., Rose, S.H., van Zyl, W.H., Viljoen-Bloom, M., Raw starch conversion by Saccharomyces cerevisiae expressing Aspergillus tubingensis amylases. Biotechnol. Biofuels, 6(1), 2013, 167, 10.1186/1754-6834-6-167.
175. Voigt, B., Le, T.H., Jürgen, B., Albrecht, D., Ehrenreich, A., Veith, B.,.. Schweder, T., The glucose and nitrogen starvation response of Bacillus licheniformis. Proteomics 7:3 (2007), 413–423, 10.1002/pmic.200600556.
176. Vongpichayapaiboon, T., Pongsawasdi, P., Krusong, K., Optimization of large-ring cyclodextrin production from starch by amylomaltase from Corynebacterium glutamicum and effect of organic solvent on product size. J. Appl. Microbiol. 120:4 (2016), 912–920, 10.1111/jam.13087.
177. Vorholt, J.A., Cofactor-dependent pathways of formaldehyde oxidation in methylotrophic bacteria. Arch. Microbiol. 178:4 (2002), 239–249, 10.1007/s00203-002-0450-2.
178. Vuilleumier, S., Chistoserdova, L., Lee, M.C., Bringel, F., Lajus, A., Yang, Z.,.. Lidstrom, M.E., Methylobacterium genome sequences: a reference blueprint to investigate microbial metabolism of C1 compounds from natural and industrial sources. PLoS One, 4(5), 2009, e5584, 10.1371/journal.pone.0005584.
179. Walker, A.W., Keasling, J.D., Metabolic engineering of Pseudomonas putida for the utilization of parathion as a carbon and energy source. Biotechnol. Bioeng. 78:7 (2002), 715–721, 10.1002/bit.10251.
180. Wanarska, M., Kur, J., A method for the production of D-tagatose using a recombinant Pichia pastoris strain secreting β-D-galactosidase from Arthrobacter chlorophenolicus and a recombinant L-arabinose isomerase from Arthrobacter sp. 22c. Microb. Cell Fact., 11, 2012, 113, 10.1186/1475-2859-11-113.
181. Wang, Q., Liu, C., Xian, M., Zhang, Y., Zhao, G., Biosynthetic pathway for poly(3-hydroxypropionate) in recombinant Escherichia coli. J. Microbiol. 50:4 (2012), 693–697, 10.1007/s12275-012-2234-y.
182. Wang, D.M., Kim, H.T., Yun, E.J., Kim, D.H., Park, Y.-C., Woo, H.C., Kim, K.H., Optimal production of 4-deoxy-L-erythro-5-hexoseulose uronic acid from alginate for brown macro algae saccharification by combining endo- and exo-type alginate lyases. Bioprocess Biosyst. Eng. 37:10 (2014), 2105–2111, 10.1007/s00449-014-1188-3.
183. Wang, W., Wei, H., Alahuhta, M., Chen, X., Hyman, D., Johnson, D.K., Himmel, M.E., Heterologous expression of xylanase enzymes in lipogenic yeast Yarrowia lipolytica. PLoS One, 9(12), 2014, e111443, 10.1371/journal.pone.0111443.
184. Wargacki, A.J., Leonard, E., Win, M.N., Regitsky, D.D., Santos, C.N., Kim, P.B.,.. Yoshikuni, Y., An engineered microbial platform for direct biofuel production from brown macroalgae. Science 335:6066 (2012), 308–313, 10.1126/science.1214547.
185. Wendisch, V.F., Bott, M., Eikmanns, B.J., Metabolic engineering of Escherichia coli and Corynebacterium glutamicum for biotechnological production of organic acids and amino acids. Curr. Opin. Microbiol. 9:3 (2006), 268–274, 10.1016/j.mib.2006.03.001.
186. Wendisch, V.F., Jorge, J.M.P., Pérez-García, F., Sgobba, E., Updates on industrial production of amino acids using Corynebacterium glutamicum. World J. Microbiol. Biotechnol., 32(6), 2016, 105, 10.1007/s11274-016-2060-1.
187. Wendland, J., Schaub, Y., Walther, A., N-Acetylglucosamine utilization by Saccharomyces cerevisiae based on expression of Candida albicans NAG genes. Appl. Environ. Microbiol. 75:18 (2009), 5840–5845, 10.1128/AEM.00053-09.
188. Willats, W.G.T., McCartney, L., Mackie, W., Knox, J.P., Pectin: cell biology and prospects for functional analysis. Plant Mol. Biol. 47:1 (2001), 9–27, 10.1023/A:1010662911148.
189. Wisselink, H.W., Toirkens, M.J., del Rosario Franco Berriel, M., Winkler, A.A., van Dijken, J.P., Pronk, J.T., van Maris, A.J.A., Engineering of Saccharomyces cerevisiae for efficient anaerobic alcoholic fermentation of L-arabinose. Appl. Environ. Microbiol. 73:15 (2007), 4881–4891, 10.1128/aem.00177-07.
190. Wisselink, H.W., Toirkens, M.J., Wu, Q., Pronk, J.T., van Maris, A.J., Novel evolutionary engineering approach for accelerated utilization of glucose, xylose, and arabinose mixtures by engineered Saccharomyces cerevisiae strains. Appl. Environ. Microbiol. 75:4 (2009), 907–914, 10.1128/aem.02268-08.
191. Witthoff, S., Eggeling, L., Bott, M., Polen, T., Corynebacterium glutamicum harbours a molybdenum cofactor-dependent formate dehydrogenase which alleviates growth inhibition in the presence of formate. Microbiology (United Kingdom) 158:9 (2012), 2428–2439, 10.1099/mic.0.059196-0.
192. Witthoff, S., Mühlroth, A., Marienhagen, J., Bott, M., Muhlroth, A., Marienhagen, J., Bott, M., C1 metabolism in Corynebacterium glutamicum: an endogenous pathway for oxidation of methanol to carbon dioxide. Appl. Environ. Microbiol. 79:22 (2013), 6974–6983, 10.1128/AEM.02705-13.
193. Wong, T.Y., Preston, L.A., Schiller, N.L., Alginate lyase: review of major sources and enzyme characteristics, structure-function analysis, biological roles, and applications. Annu. Rev. Microbiol. 54:1 (2000), 289–340, 10.1146/annurev.micro.54.1.289.
194. Xia, T., Eiteman, M.A., Altman, E., Simultaneous utilization of glucose, xylose and arabinose in the presence of acetate by a consortium of Escherichia coli strains. Microb. Cell Fact., 11(1), 2012, 77, 10.1186/1475-2859-11-77.
195. Yao, W., Chu, C., Deng, X., Zhang, Y., Liu, M., Zheng, P., Sun, Z., Display of α-amylase on the surface of Corynebacterium glutamicum cells by using NCgl1221 as the anchoring protein, and production of glutamate from starch. Arch. Microbiol. 191:10 (2009), 751–759, 10.1007/s00203-009-0506-7.
196. Yim, S.S., Choi, J.W., Lee, S.H., Jeong, K.J., Modular optimization of a hemicellulose-utilizing pathway in Corynebacterium glutamicum for consolidated bioprocessing of hemicellulosic biomass. ACS Synth. Biol. 5:4 (2016), 334–343, 10.1021/acssynbio.5b00228.
197. Yonemoto, Y., Murata, K., Kimura, A., Yamaguchi, H., Okayama, K., Bacterial alginate lyase: characterization of alginate lyase-producing bacteria and purification of the enzyme. J. Ferment. Bioeng. 72:3 (1991), 152–157, 10.1016/0922-338X(91)90208-X.
198. Yoon, S.-H., Moon, T.S., Iranpour, P., Lanza, A.M., Prather, K.J., Cloning and characterization of uronate dehydrogenases from two pseudomonads and Agrobacterium tumefaciens strain C58. J. Bacteriol. 191:5 (2009), 1565–1573, 10.1128/JB.00586-08.
199. Youn, J.W., Jolkver, E., Kramer, R., Marin, K., Wendisch, V.F., Identification and characterization of the dicarboxylate uptake system DccT in Corynebacterium glutamicum. J. Bacteriol. 190:19 (2008), 6458–6466, 10.1128/JB.00780-08.
200. Youn, J.W., Jolkver, E., Kramer, R., Marin, K., Wendisch, V.F., Characterization of the dicarboxylate transporter DctA in Corynebacterium glutamicum. J. Bacteriol. 191:17 (2009), 5480–5488, 10.1128/JB.00640-09.
201. Yurimoto, H., Oku, M., Sakai, Y., Yeast methylotrophy: metabolism, gene regulation and peroxisome homeostasis. Int. J. Microbiol. 2011 (2011), 1–8, 10.1155/2011/101298.
202. 2 fixation cycle in Chloroflexus aurantiacus. Proc. Natl. Acad. Sci. U. S. A. 106:50 (2009), 21317–21322, 10.1073/pnas.0908356106.
203. Zhang, X.-Z., Sathitsuksanoh, N., Zhu, Z., Percival Zhang, Y.-H., One-step production of lactate from cellulose as the sole carbon source without any other organic nutrient by recombinant cellulolytic Bacillus subtilis. Metab. Eng. 13:4 (2011), 364–372, 10.1016/j.ymben.2011.04.003.
204. Zhou, Q., Shi, Z.Y., Meng, D.C., Wu, Q., Chen, J.C., Chen, G.Q., Production of 3-hydroxypropionate homopolymer and poly(3-hydroxypropionate-co-4-hydroxybutyrate) copolymer by recombinant Escherichia coli. Metab. Eng. 13:6 (2011), 777–785, 10.1016/j.ymben.2011.10.002.