From zero to hero-Design-based systems metabolic engineering of Corynebacterium glutamicum for l-lysine production

Metabolic Engineering

Volumn 13, Issue 2, 2011, Pages 159-168

  Becker, Judith ^a   Zelder, Oskar ^b   Häfner, Stefan ^b   Schröder, Hartwig ^b   Wittmann, Christoph ^a  

^a TECHNICAL UNIVERSITY OF BRAUNSCHWEIG   (Germany)

^b BASF SE   (Germany)

Author keywords

In silico design; Metabolic flux analysis; Rational strain optimization; Systems biology

Indexed keywords

BIO-PRODUCTION; CARBON FLUXES; CORYNEBACTERIUM GLUTAMICUM; ENGINEERING PROCESS; FED-BATCH CULTURES; GENES ENCODING; GLUCOSE UPTAKE; HIGH YIELD; IN-SILICO; L-LYSINE; L-LYSINE PRODUCTION; LYSINE PRODUCTION; METABOLIC ENGINEERING; METABOLIC ENZYMES; METABOLIC FLUX ANALYSIS; RATIONAL STRAIN OPTIMIZATION; SYSTEMS BIOLOGY; WILD TYPES;

AMINO ACIDS; BATCH CELL CULTURE; DESIGN; GLUCOSE; INDUSTRIAL APPLICATIONS; OPTIMIZATION;

METABOLISM;

LYSINE; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE;

ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; BACTERIUM CULTURE; COMPUTER MODEL; CORYNEBACTERIUM GLUTAMICUM; FED BATCH CULTURE; FERMENTATION; GLUCOSE TRANSPORT; METABOLIC ENGINEERING; NONHUMAN; PRIORITY JOURNAL;

CORYNEBACTERIUM GLUTAMICUM; FERMENTATION; GENETIC ENGINEERING; GLUCOSE; INDUSTRIAL MICROBIOLOGY; LYSINE; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL;

CORYNEBACTERIUM GLUTAMICUM;

EID: 79952106791     PISSN: 10967176     EISSN: 10967184     Source Type: Journal    
DOI: 10.1016/j.ymben.2011.01.003     Document Type: Article

References (58)

1. Anastassiadis S. l-lysine fermentation. Recent Pat. Biotechnol. 2007, 1:11-24.
2. Becker J., Buschke N., Bücker R., Wittmann C. Systems level engineering of Corynebacterium glutamicum-reprogramming translational efficiency for superior production. Eng. Life Sci. 2010, 10:430-438.
3. Becker J., Heinzle E., Klopprogge C., Zelder O., Wittmann C. 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. 2005, 71:8587-8596.
4. Becker J., Klopprogge C., Herold A., Zelder O., Bolten C.J., Wittmann C. Metabolic flux engineering of l-lysine production in Corynebacterium glutamicum-over expression and modification of G6P dehydrogenase. J. Biotechnol. 2007, 132:99-109.
5. Becker J., Klopprogge C., Schröder H., Wittmann C. Metabolic engineering of the tricarboxylic acid cycle for improved lysine production by Corynebacterium glutamicum. Appl. Environ. Microbiol. 2009, 75:7866-7869.
6. Becker J., Klopprogge C., Wittmann C. Metabolic responses to pyruvate kinase deletion in lysine producing Corynebacterium glutamicum. Microb. Cell Fact. 2008, 7:8.
7. Bolten C.J., Heinzle E., Müller R., Wittmann C. Investigation of the central carbon metabolism of Sorangium cellulosum: metabolic network reconstruction and quantification of pathway fluxes. J. Microbiol. Biotechnol. 2009, 19:23-36.
8. Bradford M.M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 1976, 72:248-254.
9. Brautaset T., Jakobsen O.M., Josefsen K.D., Flickinger M.C., Ellingsen T.E. Bacillus methanolicus: a candidate for industrial production of amino acids from methanol at 50degrees C. Appl. Microbiol. Biotechnol. 2007, 74:22-34.
10. Contador C.A., Rizk M.L., Asenjo J.A., Liao J.C. Ensemble modeling for strain development of l-lysine-producing Escherichia coli. Metab. Eng. 2009, 11:221-233.
11. Cremer J., Eggeling L., Sahm H. Control of the lysine biosynthesis sequence in Corynebacterium glutamicum as analyzed by overexpression of the individual corresponding genes. Appl. Environ. Microbiol. 1991, 57(6):1746-1752.
12. Cremer J., Treptow C., Eggeling L., Sahm H. Regulation of enzymes of lysine biosynthesis in Corynebacterium glutamicum. J. Gen. Microbiol. 1988, 134:3221-3229.
13. Emmerling M., Dauner M., Ponti A., Fiaux J., Hochuli M., Szyperski T., Wuthrich K., Bailey J.E., Sauer U. Metabolic flux responses to pyruvate kinase knockout in Escherichia coli. J. Bacteriol. 2002, 184:152-164.
14. Gasent-Ramirez J.M., Benitez T. Lysine-overproducing mutants of Saccharomyces cerevisiae baker's yeast isolated in continuous culture. Appl. Environ. Microbiol. 1997, 63:4800-4806.
15. Gunji Y., Yasueda H. Enhancement of l-lysine production in methylotroph Methylophilus methylotrophus by introducing a mutant LysE exporter. J. Biotechnol. 2006, 127:1-13.
16. Hirao T., Nakano T., Azuma T., Sugimoto M., Nakanishi T. l-Lysine production in continuous culture of an l-lysine hyperproducing mutant of Corynebacterium glutamicum. Appl. Microbiol. Biotechnol. 1989, 32:269-273.
17. Ikeda M. Amino acid production processes. Adv. Biochem. Eng. Biotechnol. 2003, 79:1-35.
18. Ikeda M., Ohnishi J., Hayashi M., Mitsuhashi S. A genome-based approach to create a minimally mutated Corynebacterium glutamicum strain for efficient l-lysine production. J. Ind. Microbiol. Biotechnol. 2006, 33:610-615.
19. Jäger W., Schäfer A., Pühler A., Labes G., Wohlleben W. Expression of the Bacillus subtilis sacB gene leads to sucrose sensitivity in the gram-positive bacterium Corynebacterium glutamicum but not in Streptomyces lividans. J. Bacteriol. 1992, 174:5462-5465.
20. Kalinowski J., Bathe B., Bartels D., Bischoff N., Bott M., Burkovski A., Dusch N., Eggeling L., Eikmanns B.J., Gaigalat L., Goesmann A., Hartmann M., Huthmacher K., Krämer R., Linke B., McHardy A.C., Meyer F., Möckel B., Pfefferle W., Pühler A., Rey D.A., Rückert C., Rupp O., Sahm H., Wendisch V.F., Wiegrabe I., Tauch A. The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins. J. Biotechnol. 2003, 104:5-25.
21. Kelle R., Hermann T., Bathe B. l-Lysine Production. Handbook of Corynebacterium glutamicum 2005, 465-488. CRC Press, Boca Raton. L. Eggeling, M. Bott (Eds.).
22. Kiefer P., Heinzle E., Zelder O., Wittmann C. Comparative metabolic flux analysis of lysine-producing Corynebacterium glutamicum cultured on glucose or fructose. Appl. Environ. Microbiol. 2004, 70:229-239.
23. Kind S., Jeong W.K., Schröder H., Wittmann C. Systems-wide metabolic pathway engineering in Corynebacterium glutamicum for bio-based production of diaminopentane. Metab. Eng. 2010, 12:341-351.
24. Kjeldsen K.R., Nielsen J. In silico genome-scale reconstruction and validation of the Corynebacterium glutamicum metabolic network. Biotechnol. Bioeng. 2009, 102:583-597.
25. Koffas M., Stephanopoulos G. Strain improvement by metabolic engineering: lysine production as a case study for systems biology. Curr. Opin. Biotechnol. 2005, 16:361-366.
26. Koffas M.A., Jung G.Y., Stephanopoulos G. Engineering metabolism and product formation in Corynebacterium glutamicum by coordinated gene overexpression. Metab. Eng. 2003, 5:32-41.
27. Kojima, H., Ogawa, Y., Kawamura, K., Sano, K., 1999. Production of l-lysine by fermentation, Japan.
28. Kröger, B., Zelder, O., Klopprogge, C., Schröder, H., Haefner, S., 2005. P EF-TU Expression units, Germany.
29. Krömer J.O., Fritz M., Heinzle E., Wittmann C. In vivo quantification of intracellular amino acids and intermediates of the methionine pathway in Corynebacterium glutamicum. Anal. Biochem. 2005, 340:171-173.
30. Lee K.H., Park J.H., Kim T.Y., Kim H.U., Lee S.Y. Systems metabolic engineering of Escherichia coli for l-threonine production. Mol. Syst. Biol. 2007, 3:149.
31. Lee S.Y., Park J.H. Integration of systems biology with bioprocess engineering: l-threonine production by systems metabolic engineering of Escherichia coli. Adv. Biochem. Eng. Biotechno. 2010.
32. Leuchtenberger W. Amino Acids-Technical Production and Use. Biotechnology 1996, vol. 6:465-502. VCH, Weinheim, Germany.
33. Leuchtenberger W., Huthmacher K., Drauz K. Biotechnological production of amino acids and derivatives: current status and prospects. Appl. Microbiol. Biotechnol. 2005, 69:1-8.
34. Marx A., Hans S., Möckel B., Bathe B., de Graaf A.A. Metabolic phenotype of phosphoglucose isomerase mutants of Corynebacterium glutamicum. J. Biotechnol. 2003, 104:185-197.
35. Melzer G., Esfandabadi M.E., Franco-Lara E., Wittmann C. Flux design: in silico design of cell factories based on correlation of pathway fluxes to desired properties. BMC Syst. Biol. 2009, 3:120.
36. Murakami, Y., Miwa, H., Nakamori, S., 1992. Fermentative production of l-lysine. Japan.
37. Nakayama K., Araki K., Kase H. Microbial production of essential amino acid with Corynebacterium glutamicum mutants. Adv. Exp. Med. Biol. 1978, 105:649-661.
38. Netzer R., Krause M., Rittmann D., Peters-Wendisch P.G., Eggeling L., Wendisch V.F., Sahm H. Roles of pyruvate kinase and malic enzyme in Corynebacterium glutamicum for growth on carbon sources requiring gluconeogenesis. Arch. Microbiol. 2004, 182:354-363.
39. Ohnishi J., Katahira R., Mitsuhashi S., Kakita S., Ikeda M. A novel gnd mutation leading to increased l-lysine production in Corynebacterium glutamicum. FEMS Microbiol. Lett. 2005, 242:265-274.
40. Ohnishi J., Mitsuhashi S., Hayashi M., Ando S., Yokoi H., Ochiai K., Ikeda M. A novel methodology employing Corynebacterium glutamicum genome information to generate a new l-lysine-producing mutant. Appl. Microbiol. Biotechnol. 2002, 58:217-223.
41. Olano C., Lombo F., Mendez C., Salas J.A. Improving production of bioactive secondary metabolites in actinomycetes by metabolic engineering. Metab. Eng. 2008, 10:281-292.
42. Park J.H., Lee S.Y., Kim T.Y., Kim H.U. Application of systems biology for bioprocess development. Trends Biotechnol. 2008, 26:404-412.
43. Park S.D., Lee J.Y., Sim S.Y., Kim Y., Lee H.S. Characteristics of methionine production by an engineered Corynebacterium glutamicum strain. Metab. Eng. 2007, 9:327-336.
44. Peters-Wendisch P.G., Schiel B., Wendisch V.F., Katsoulidis E., Möckel B., Sahm H., Eikmanns B.J. Pyruvate carboxylase is a major bottleneck for glutamate and lysine production by Corynebacterium glutamicum. J. Mol. Microbiol. Biotechnol. 2001, 3:295-300.
45. Petersen S., Mack C., de Graaf A.A., Riedel C., Eikmanns B.J., Sahm H. Metabolic consequences of altered phosphoenolpyruvate carboxykinase activity in Corynebacterium glutamicum reveal anaplerotic regulation mechanisms in vivo. Metab. Eng. 2001, 3:344-361.
46. Sawada K., Zen-In S., Wada M., Yokota A. Metabolic changes in a pyruvate kinase gene deletion mutant of Corynebacterium glutamicum ATCC 13032. Metab. Eng 2010.
47. Shiio I., Miyajima R., Sano K. Genetically desensitized aspartate kinase to the concerted feedback inhibition in Brevibacterium flavum. J. Biochem. (Tokyo). 1970, 68:701-710.
48. Shinfuku Y., Sorpitiporn N., Sono M., Furusawa C., Hirasawa T., Shimizu H. Development and experimental verification of a genome-scale metabolic model for Corynebacterium glutamicum. Microb. Cell Fact. 2009, 8:43.
49. Tyo K.E., Kocharin K., Nielsen J. Toward design-based engineering of industrial microbes. Curr. Opin. Microbiol. 2010, 13:255-262.
50. van Winden W.A., Wittmann C., Heinzle E., Heijnen J.J. Correcting mass isotopomer distributions for naturally occurring isotopes. Biotechnol. Bioeng. 2002, 80:477-479.
51. Wittmann C. Metabolic flux analysis using mass spectrometry. Adv. Biochem. Eng. Biotechnol. 2002, 74:39-64.
52. Wittmann C. Fluxome analysis using GC-MS. Microb. Cell Fact. 2007, 6:6.
53. Wittmann C. Analysis and Engineering of Metabolic Pathway Fluxes in Corynebacterium glutamicum. Adv. Biochem. Eng. Biotechnol. 2010, 120:21-49.
54. Wittmann C., Becker J. The l-lysine story: from metabolic pathways to industrial production. Amino Acid Biosynthesis-Pathways, Regulation And Metabolic Engineering 2007, vol. 5:39-70. Springer, Berlin/ Heidelberg.
55. Wittmann C., de Graaf A. Metabolic flux analysis in Corynebacterium glutamicum. Handbook of Corynebacterium glutamicum 2005, 277-304. CRC Press, Boca Raton. L. Eggeling, M. Bott (Eds.).
56. Wittmann C., Hans M., Heinzle E. In vivo analysis of intracellular amino acid labelings by GC/MS. Anal. Biochem. 2002, 307:379-382.
57. Wittmann C., Heinzle E. Genealogy profiling through strain improvement by using metabolic network analysis: metabolic flux genealogy of several generations of lysine-producing Corynebacteria. Appl. Environ. Microbiol. 2002, 68:5843-5859.
58. Yokota A., Lindley N.D. Central metabolism: sugar uptake and conversion. Handbook of Corynebacterium glutamicum 2005, 215-240. CRC Press, Boca Raton. L. Eggeling, M. Bott (Eds.).