Pathway identification combining metabolic flux and functional genomics analyses: Acetate and propionate activation by Corynebacterium glutamicum

Journal of Biotechnology

Volumn 140, Issue 1-2, 2009, Pages 75-83

  Veit, Andrea ^a   Rittmann, Doris ^a   Georgi, Tobias ^a   Youn, Jung Won ^c   Eikmanns, Bernhard J ^b   Wendisch, Volker F ^c  

^a FORSCHUNGSZENTRUM JÜLICH   (Germany)

^b UNIVERSITY OF ULM   (Germany)

^c UNIVERSITY OF MÜNSTER   (Germany)

Author keywords

Acetate activation; Amino acid production; CoA transferase; Corynebacterium glutamicum; Propionate activation

Indexed keywords

ACETATE ACTIVATION; AMINO ACID PRODUCTION; COA TRANSFERASE; CORYNEBACTERIUM GLUTAMICUM; PROPIONATE ACTIVATION;

AMINATION; AMINES; AMINO ACIDS; FATTY ACIDS; GENE ENCODING; GLUCOSE; METABOLISM; NUCLEIC ACIDS; ORGANIC ACIDS; STRAIN;

ENZYMES;

ACETATE KINASE; ACETIC ACID; ACETYL COENZYME A; CARBON 13; COENZYME A TRANSFERASE; GLUCOSE; GLYOXYLIC ACID; PHOSPHATE ACETYLTRANSFERASE; PHOSPHOENOLPYRUVATE CARBOXYLASE; PROPIONIC ACID; PYRUVATE CARBOXYLASE; SHORT CHAIN FATTY ACID;

AMINO ACID SYNTHESIS; ARTICLE; BACTERIAL GROWTH; BACTERIAL STRAIN; CARBON SOURCE; CATALYSIS; CITRIC ACID CYCLE; CONTROLLED STUDY; CORYNEBACTERIUM GLUTAMICUM; DNA MICROARRAY; FUNCTIONAL GENOMICS; GENE EXPRESSION; GLYCOLYSIS; ISOTOPE LABELING; NONHUMAN; OPERON; PRIORITY JOURNAL; PROTEIN PURIFICATION;

ACETATE KINASE; ACETATES; AMINO ACIDS; BACTERIAL PROTEINS; CARBON ISOTOPES; COENZYME A-TRANSFERASES; CORYNEBACTERIUM GLUTAMICUM; GENE EXPRESSION PROFILING; GENOMICS; GLUCOSE; ISOTOPE LABELING; METABOLIC NETWORKS AND PATHWAYS; MUTATION; PHOSPHATE ACETYLTRANSFERASE; PROPIONATES;

CORYNEBACTERIUM GLUTAMICUM;

EID: 61649119614     PISSN: 01681656     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbiotec.2008.12.014     Document Type: Article

References (62)

1. Arndt A., Auchter M., Ishige T., Wendisch V.F., and Eikmanns B.J. Ethanol catabolism in Corynebacterium glutamicum. J. Mol. Microbiol. Biotechnol. 15 (2008) 222-233 http://dx.doi.org/10.1159/000107370
2. Arndt A., and Eikmanns B.J. The alcohol dehydrogenase gene adhA in Corynebacterium glutamicum is subject to carbon catabolite repression. J. Bacteriol. 189 (2007) 7408-7416
3. Arndt A., and Eikmanns B.J. Regulation of carbon metabolism in Corynebacterium glutamicum. In: Burkovski A. (Ed). Corynebacteria: Genomics and Molecular Biology (2008), Caister Academic Press, Wymondham, UK 155-182
4. Bendt A.K., Burkovski A., Schaffer S., Bott M., Farwick M., and Hermann T. Towards a phosphoproteome map of Corynebacterium glutamicum. Proteomics 3 (2003) 1637-1646
5. Blombach B., Schreiner M.E., Bartek T., Oldiges M., and Eikmanns B.J. Corynebacterium glutamicum tailored for high-yield l-valine production. Appl. Microbiol. Biotechnol. 79 (2008) 471-479
6. Blombach B., Schreiner M.E., Holatko J., Bartek T., Oldiges M., and Eikmanns B.J. l-valine production with pyruvate dehydrogenase complex-deficient Corynebacterium glutamicum. Appl. Environ. Microbiol. 73 (2007) 2079-2084
7. Blombach B., Schreiner M.E., Moch M., Oldiges M., and Eikmanns B.J. Effect of pyruvate dehydrogenase complex deficiency on l-lysine production with Corynebacterium glutamicum. Appl. Microbiol. Biotechnol. 76 (2007) 615-623
8. Bock A.K., Glasemacher J., Schmidt R., and Schönheit P. Purification and characterization of two extremely thermostable enzymes, phosphate acetyltransferase and acetate kinase, from the hyperthermophilic eubacterium Thermotoga maritima. J. Bacteriol. 181 (1999) 1861-1867
9. Claes W.A., Pühler A., and Kalinowski J. Identification of two prpDBC gene clusters in Corynebacterium glutamicum and their involvement in propionate degradation via the 2-methylcitrate cycle. J. Bacteriol. 184 (2002) 2728-2739
10. Cremer J., Eggeling L., and Sahm H. Cloning of the dapA dapB cluster of the lysine-secreting bacterium Corynebacterium glutamicum. Mol. Gen. Genet. 220 (1990) 478-480
11. Dominguez H., et al. Modified carbon flux during oxygen limited growth of Corynebacterium glutamicum and the consequences for amino acid overproduction. Biotechnol. Lett. 15 (1993) 449-454
12. Dominguez H., Rollin C., Guyonvarch A., Guerquin-Kern J.L., Cocaign-Bousquet M., and Lindley N.D. Carbon-flux distribution in the central metabolic pathways of Corynebacterium glutamicum during growth on fructose. Eur. J. Biochem. 254 (1998) 96-102
13. Ebbighausen H., Weil B., and Krämer R. Carrier-mediated acetate uptake in Corynebacterium glutamicum. Arch. Microbiol. 155 (1991) 505-510
14. Eikmanns B.J., Metzger M., Reinscheid D., Kircher M., and Sahm H. Amplification of three threonine biosynthesis genes in Corynebacterium glutamicum and its influence on carbon flux in different strains. Appl. Microbiol. Biotechnol. 34 (1991) 617-622
15. Fukaya M., Takemura H., Okumura H., Kawamura Y., Horinouchi S., and Beppu T. Cloning of genes responsible for acetic acid resistance in Acetobacter aceti. J. Bacteriol. 172 (1990) 2096-2104
16. Gerstmeir R., Wendisch V.F., Schnicke S., Ruan H., Farwick M., Reinscheid D., and Eikmanns B.J. Acetate metabolism and its regulation in Corynebacterium glutamicum. J. Biotechnol. 104 (2003) 99-122
17. Gornall A.G., Bardawill C.J., and David M.M. Determination of serum proteins by means of biuret reaction. J. Biol. Chem. 177 (1949) 751-766
18. Haller T., Buckel T., Retey J., and Gerlt J.A. Discovering new enzymes and metabolic pathways: conversion of succinate to propionate by Escherichia coli. Biochemistry 39 (2000) 4622-4629
19. Horswill A.R., and Escalante-Semerena J.C. The prpE gene of Salmonella typhimurium LT2 encodes propionyl-CoA synthetase. Microbiology 145 (1999) 1381-1388
20. Ishige T., Krause M., Bott M., Wendisch V.F., and Sahm H. The phosphate starvation stimulon of Corynebacterium glutamicum determined by DNA microarray analyses. J. Bacteriol. 185 (2003) 4519-4529
21. Jakoby M., Ngouto-Nkili C.E., and Burkovski A. Construction and application of new Corynebacterium glutamicum vectors. Biotechnol. Tech. 13 (1999) 437-441
22. Jolkver, E., Emer, D., Ballan, S., Krämer, R., Eikmanns, B.J., Marin K. 2008. Identification and Characterization of a Bacterial Transport System for the Uptake of Pyruvate, Propionate, and Acetate in Corynebacterium glutamicum. J. Bacteriol. Nov 21. [Epub ahead of print].
23. Kalinowski J., Bathe B., Bartels D., Bischoff N., Bott M., Burkovski A., Dusch N., Eggeling L., Eikmanns B.J., Gaigalat L., et al. The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of l-aspartate-derived amino acids and vitamins. J. Biotechnol. 104 (2003) 5-25
24. Kinoshita S., and Tanaka K. Glutamic acid. In: Yamada K., Kinoshita S., Tsunoda T., and Aida K. (Eds). The microbial production of amino acids (1972), Halsted Press, New York, NY, USA 263-324
25. Krämer R., and Lambert C. Uptake of glutamate in Corynebacterium glutamicum. 2. Evidence for a primary active transport system. Eur. J. Biochem. 194 (1990) 937-944
26. Lange C., Rittmann D., Wendisch V.F., Bott M., and Sahm H. Global expression profiling and physiological characterization of Corynebacterium glutamicum grown in the presence of l-valine. Appl. Environ. Microbiol. 69 (2003) 2521-2532
27. Lin E.C.C. Dissimilatory pathways for sugars, polyols and carboxylates. In: Neidhardt F.C., Curtiss III R., Ingraham J.L., Lin E.C.C., Low K.B., Magasanik B., Reznikoff W.S., Riley M., Schaechter M., and Umbarger H.E. (Eds). Escherichia coli and Salmonella: Cellular and Molecular Biology. 2nd ed. (1996), ASM Press, Washington, DC 307-342
28. Marx A., de Graaf A.A., Wiechert W., Eggeling L., and Sahm H. Determination of the fluxes in the central metabolism of Corynebacterium glutamicum by nuclear magnetic resonance spetroscopy combined with metabolite balancing. Biotechnol. Bioeng. 49 (1996) 111-129
29. Merkens H., Beckers G., Wirtz A., and Burkovski A. Vanillate metabolism in Corynebacterium glutamicum. Curr. Microbiol. 51 (2005) 59-65
30. Munoz-Elias E.J., and McKinney J.D. Mycobacterium tuberculosis isocitrate lyases 1 and 2 are jointly required for in vivo growth and virulence. Nat. Med. 1 (2005) 638-644
31. Netzer R., Peters-Wendisch P., Eggeling L., and Sahm H. Cometabolism of a nongrowth substrate: l-serine utilization by Corynebacterium glutamicum. Appl. Environ. Microbiol. 70 (2004) 7148-7155
32. Paegle L., and Ruklisha M. Lysine synthesis control in Corynebacterium glutamicum RC 115 in mixed substrate (glucose-acetate) medium. J. Biotechnol. 104 (2003) 123-128
33. Palacios S., Starai V.J., and Escalante-Semerena J.C. Propionyl coenzyme A Is a common intermediate in the 1,2-propanediol and propionate catabolic pathways needed for expression of the prpBCDE operon during growth of Salmonella enterica on 1,2-propanediol. J. Bacteriol. 185 (2003) 2802-2810
34. Peters-Wendisch P.G., Eikmanns B.J., Thierbach G., Bachmann B., and Sahm H. Phosphoenolpyruvate carboxylase in Corynebacterium glutamicum is dispensable for growth and lysine production. FEMS Microbiol. Lett. 112 (1993) 269-274
35. Polen T., and Wendisch V.F. Genomewide expression analysis in amino acid-producing bacteria using DNA microarrays. Appl. Biochem. Biotechnol. 118 (2004) 215-232
36. Rado T.A., and Hoch J.A. Phosphotransacetylase from Bacillus subtilis: purification and physiological studies. Biochim. Biophys. Acta 321 (1973) 114-125
37. Reinscheid D.J., Eikmanns B.J., and Sahm H. Characterization of the isocitrate lyase gene from Corynebacterium glutamicum and biochemical analysis of the enzyme. J. Bacteriol. 176 (1994) 3474-3483
38. Reinscheid D.J., Eikmanns B.J., and Sahm H. Malate synthase from Corynebacterium glutamicum: sequence analysis of the gene and biochemical characterization of the enzyme. Microbiology 140 (1994) 3099-3108
39. Reinscheid D.J., Schnicke S., Rittmann D., Zahnow U., Sahm H., and Eikmanns B.J. Cloning, sequence analysis, expression and inactivation of the Corynebacterium glutamicum pta-ack operon encoding phosphotransacetylase and acetate kinase. Microbiology 145 (1999) 503-513
40. Riedel C., Rittmann D., Dangel P., Möckel B., Petersen S., Sahm H., and Eikmanns B.J. 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 (2001) 573-583
41. Rittmann D., Schaffer S., Wendisch V.F., and Sahm H. Fructose-1,6-bisphosphatase from Corynebacterium glutamicum: expression and deletion of the fbp gene and biochemical characterization of the enzyme. Arch. Microbiol. 180 (2003) 285-292
42. Sambrook J., and Russell D. Molecular Cloning. A Laboratory Manual. 3rd ed. (2001), Cold Spring Harbor Laboratoy Press, Cold Spring Harbor, NY
43. Schäfer A., Tauch A., Jäger W., Kalinowski J., Thierbach G., and Pühler A. Small mobilizable multi-purpose cloning vectors derived from the Escherichia coli plasmids pK18 and pK19: selection of defined deletions in the chromosome of Corynebacterium glutamicum. Gene 145 (1994) 69-73
44. Schaffer S., Weil B., Nguyen V.D., Dongmann G., Gunther K., Nickolaus M., Hermann T., and Bott M. A high-resolution reference map for cytoplasmic and membrane-associated proteins of Corynebacterium glutamicum. Electrophoresis 22 (2001) 4404-4422
45. Scherf U., and Buckel W. Purification and properties of 4-hydroxybutyrate coenzyme A transferase from Clostridium aminobutyricum. Appl. Environ. Microbiol. 57 (1991) 2699-2702
46. Schreiner M.E., and Eikmanns B.J. Pyruvate:quinone oxidoreductase from Corynebacterium glutamicum: purification and biochemical characterization. J. Bacteriol. 187 (2005) 862-871
47. Shiio I., and Miyajima R. Concerted inhibition and its reversal by end products of aspartate kinase in Brevibacterium flavum. J. Biochem. (Tokyo) 65 (1969) 849-859
48. Shimizu H., and Hirasawa T. Production of Glutamate and Glutamate-Related Amino Acids: MolecularMechanism Analysis and Metabolic Engineering. In: Wendisch V.F. (Ed). Amino Acid Biosynthesis-Pathways, Regulation and Metabolic Engineering (2007), Springer, Heidelberg, Germany 10.1007/7171_2006_064
49. Sohling B., and Gottschalk G. Molecular analysis of the anaerobic succinate degradation pathway in Clostridium kluyveri. J. Bacteriol. 178 (1996) 871-880
50. Sonntag K., Eggeling L., De Graaf A.A., and Sahm H. Flux partitioning in the split pathway of lysine synthesis in Corynebacterium glutamicum. Quantification by 13C- and 1H-NMR spectroscopy. Eur. J. Biochem. 213 (1993) 1325-1331
51. Stadtman E.R. Phosphotransacetylase from Clostridium kluyveri. In: Colowick S.P., and Kaplan N.O. (Eds). Methods in Enzymology vol 1 (1955), Academic Press, New York pp.596-599
52. Tabuchi T., Serizawa N., and Ohmono S. Isolation and identification of (-)-methylcitric acid and 2-methyl-cis-aconitic acid from the culture of Candida lipolytica. Agric. Biol. Chem. 38 (1974) 2565-2566
53. Textor S., Wendisch V.F., De Graaf A.A., Müller U., Linder M.I., Linder D., and Buckel W. Propionate oxidation in Escherichia coli: evidence for operation of a methylcitrate cycle in bacteria. Arch. Microbiol. 168 (1997) 428-436
54. Wendisch V.F. Genome-wide expression analysis in Corynebacterium glutamicum using DNA microarrays. J. Biotechnol. 104 (2003) 273-285
55. Wendisch V.F. Genetic regulation of Corynebacterium glutamicum metabolism. J. Microbiol. Biotechnol. 16 (2006) 999
56. 1H nuclear magnetic resonance. Anal. Biochem. 245 (1997) 196-202
57. Wendisch V.F., de Graaf A.A., Sahm H., and Eikmanns B.J. Quantitative determination of metabolic fluxes during coutilization of two carbon sources: comparative analyses with Corynebacterium glutamicum during growth on acetate and/or glucose. J. Bacteriol. 182 (2000) 3088-3096
58. Wendisch V.F., Spies M., Reinscheid D.J., Schnicke S., Sahm H., and Eikmanns B.J. Regulation of acetate metabolism in Corynebacterium glutamicum: transcriptional control of the isocitrate lyase and malate synthase genes. Arch. Microbiol. 168 (1997) 262-269
59. Wiechert W., and de Graaf A.A. Bidirectional reaction steps in metabolic networks: I. modeling and simulation of carbon isotope labeling experiments. Biotechnol. Bioeng. 55 (1997) 101-111
60. Wiechert W., Siefke C., de Graaf A.A., and Marx A. Bidirectional reaction steps in metabolic networks: II. flux estimation and staistical analysis. Biotechnol. Bioeng. 55 (1997) 118-135
61. Wittmann C., and Becker J. The l-Lysine Story: From Metabolic Pathways to Industrial Production. In: Wendisch V.F. (Ed). Amino Acid Biosynthesis-Pathways, Regulation and Metabolic Engineering (2007), Springer, Heidelberg, Germany 10.1007/7171_2006_089
62. Yasuda K., Jojima T., Suda M., Okino S., Inui M., and Yukawa H. Analyses of the acetate-producing pathways in Corynebacterium glutamicum under oxygen-deprived conditions. Appl. Microbiol. Biotechnol. 77 (2007) 853-860