A combination of metabolome and transcriptome analyses reveals new targets of the Corynebacterium glutamicum nitrogen regulator AmtR

Journal of Biotechnology

Volumn 140, Issue 1-2, 2009, Pages 68-74

  Buchinger, Sebastian ^a   Strösser, Julia ^a   Rehm, Nadine ^b   Hänßler, Eva ^b   Hans, Stephan ^c   Bathe, Brigitte ^c   Schomburg, Dietmar ^a,d   Krämer, Reinhard ^a   Burkovski, Andreas ^b  

^a UNIVERSITY OF COLOGNE   (Germany)

^b UNIVERSITY OF ERLANGEN NUREMBERG   (Germany)

^c EVONIK DEGUSSA GMBH   (Germany)

^d TECHNICAL UNIVERSITY OF BRAUNSCHWEIG   (Germany)

Author keywords

AmtR; GC MS; Metabolome analysis; Nitrogen control; Transcriptomics

Indexed keywords

AMTR; GC-MS; METABOLOME ANALYSIS; NITROGEN CONTROL; TRANSCRIPTOMICS;

AMINES; AMINO ACIDS; BIOCHEMICAL ENGINEERING; BIOCHEMISTRY; ENCODING (SYMBOLS); GELATION; LAKES; LAWS AND LEGISLATION; METABOLISM; NITROGEN; ORGANIC ACIDS; PHYSIOLOGY;

GENE ENCODING;

AMINO ACID; CITRIC ACID; DIAMINOPIMELIC ACID; GLUTAMATE AMMONIA LIGASE; GLUTAMINE; LYSINE; MALATE DEHYDROGENASE (DECARBOXYLATING); MESSENGER RNA; MUTANT PROTEIN; NITROGEN TRANSCRIPTIONAL REGULATOR; PENTOSE PHOSPHATE; PROTEIN; SUCCINYLASE; TRANSCRIPTOME; UNCLASSIFIED DRUG;

AMINO ACID SYNTHESIS; ARTICLE; CARBON METABOLISM; CITRIC ACID CYCLE; CONTROLLED STUDY; CORYNEBACTERIUM GLUTAMICUM; ENZYME ACTIVITY; GENE CONTROL; GENE DELETION; GENE EXPRESSION REGULATION; GLYCOLYSIS; METABOLITE; METABOLOME; NONHUMAN; NUCLEOTIDE SEQUENCE; PENTOSE PHOSPHATE CYCLE; PRIORITY JOURNAL; WILD TYPE;

ACYLTRANSFERASES; BACTERIAL PROTEINS; BASE SEQUENCE; CORYNEBACTERIUM GLUTAMICUM; ELECTROPHORETIC MOBILITY SHIFT ASSAY; GAS CHROMATOGRAPHY-MASS SPECTROMETRY; GENE DELETION; GENE EXPRESSION PROFILING; GLUTAMATE-AMMONIA LIGASE; GLUTAMIC ACID; METABOLOMICS; MOLECULAR SEQUENCE DATA; REPRESSOR PROTEINS; RNA PROCESSING, POST-TRANSCRIPTIONAL;

CORYNEBACTERIUM GLUTAMICUM;

EID: 61649094948     PISSN: 01681656     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbiotec.2008.10.009     Document Type: Article

References (39)

1. Abe S., Takayama K., and Kinoshita S. Taxonomical studies on glutamic acid-producing bacteria. J. Gen. Microbiol. 13 (1967) 279-301
2. Beckers G., Nolden L., and Burkovski A. Glutamate synthase of Corynebacterium glutamicum is not essential for glutamate synthesis and is regulated by the nitrogen status. Microbiology 147 (2001) 2961-2970
3. Beckers G., Bendt A.K., Krämer R., and Burkovski A. Molecular identification of the urea uptake system and transcriptional analysis of urea transporter- and urease-encoding genes in Corynebacterium glutamicum. J. Bacteriol. 186 (2004) 7645-7652
4. Beckers G., Strösser J., Hildebrandt U., Kalinowski J., Farwick M., Krämer R., and Burkovski A. Regulation of AmtR-controlled gene expression in Corynebacterium glutamicum: mechanism and characterization of the AmtR regulon. Mol. Microbiol. 58 (2005) 580-595
5. Bendt A.K., Beckers G., Silberbach M., Wittmann A., and Burkovski A. Utilization of creatinine as an alternative nitrogen source in Corynebacterium glutamicum. Arch. Microbiol. 181 (2004) 443-450
6. Börner J., Buchinger S., and Schomburg D. A high-throughput method for microbial metabolome analysis using gas chromatography/mass spectrometry. Anal. Biochem. 367 (2007) 143-151
7. Botzenhardt J., Morbach S., and Krämer R. Activity regulation of the betaine transporter BetP of Corynebacterium glutamicum in response to osmotic compensation. Biochim. Biophys. Acta 1667 (2004) 229-240
8. Burkovski A. Nitrogen metabolism and its regulation. In: Bott M., and Eggeling L. (Eds). Handbook of Corynebacterium glutamicum (2005), CRC Press LLC, Boca Raton, FL 333-349
9. Burkovski A. Proteomics of Corynebacterium glutamicum: essential industrial bacterium. Methods Biochem. Anal. 49 (2006) 137-147
10. Burkovski A. Nitrogen control in Corynebacterium glutamicum: proteins, mechanisms, signals. J. Microbiol. Biotechnol. 17 (2007) 187-194
11. Gourdon P., Boucher M.-F., Lindley N., and Guyonvarch A. Cloning of the malic enzyme gene from Corynebacterium glutamicum and role of the enzyme in lactate metabolism. Appl. Environ. Microbiol. 66 (2000) 2981-2987
12. Hänßler E., and Burkovski A. Molecular mechanisms of nitrogen control in corynebacteria. In: Burkovski A. (Ed). Corynebacteria: Genomics and Molecular Biology (2008), Caister Academic Press, Norwich 183-201
13. Hüser A., Becker A., Brune I., Dondrup M., Kalinowski J., Plassmeier J., Pühler A., Wiegräbe I., and Tauch A. Development of a Corynebacterium glutamicum DNA microarray and validation by genome-wide expression profiling during growth with propionate as carbon source. J. Biotechnol. 106 (2003) 269-286
14. Ikeda M., and Nakagawa S. The Corynebacterium glutamicum genome: features and impacts on biotechnological processes. Appl. Microbiol. Biotechnol. 62 (2003) 99-109
15. Jakoby M., Tesch M., Sahm H., Krämer R., and Burkovski A. Isolation of the Corynebacterium glutamicum glnA gene encoding glutamine synthetase I. FEMS Microbiol. Lett. 154 (1997) 81-88
16. Jakoby M., Krämer R., and Burkovski A. Nitrogen regulation in Corynebacterium glutamicum: isolation of genes involved and biochemical characterization of corresponding proteins. FEMS Microbiol. Lett. 173 (1999) 303-310
17. Jakoby M., Nolden L., Meier-Wagner J., Krämer R., and Burkovski A. AmtR, a global repressor in the nitrogen regulation system of Corynebacterium glutamicum. Mol. Microbiol. 37 (2000) 964-977
18. Kalinowski J., Bathe B., 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., Rückert C., Sahm H., Wendisch V.F., Wiegräbe I., and 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. 104 (2003) 5-25
19. Koch D.J., Rückert C., Rey D.A., Mix A., Pühler A., and Kalinowski J. Role of the ssu and seu genes of Corynebacterium glutamicum ATCC 13032 in utilization of sulfonates and sulfonate esters as sulfur sources. Appl. Environ. Microbiol. 71 (2005) 6104-6114
20. 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
21. Krömer J.O., Sorgenfrei O., Klopprogge K., Heinzle E., and Wittmann C. In-depth profiling of lysine-producing Corynebacterium glutamicum by combined analysis of the transcriptome, metabolome, and fluxome. J. Bacteriol. 186 (2004) 1769-1784
22. Kronemeyer W., Peekhaus N., Krämer R., Eggeling L., and Sahm H. Structure of the gluABCD cluster encoding the glutamate uptake system of Corynebacterium glutamicum. J. Bacteriol. 177 (1995) 1152-1158
23. Meers J.L., Tempest D.W., and Brown C.M. Glutamine(amide): 2-oxoglutarate amino transferase oxido-reductase (NADP); an enzyme involved in the synthesis of glutamate by some bacteria. J. Gen. Microbiol. 64 (1970) 187-194
24. Merkens H., Beckers G., Wirtz A., and Burkovski A. Vanillate metabolism in Corynebacterium glutamicum. Curr. Microbiol. 51 (2005) 59-65
25. Nampoothiri K.M., Hoischen C., Bathe B., Möckel B., Pfefferle W., Krumbach K., Sahm H., and Eggeling L. Expression of genes of lipid synthesis and altered lipid composition modulates l-glutamate efflux of Corynebacterium glutamicum. Appl. Microbiol. Biotechnol. 58 (2002) 89-96
26. Nolden L., Beckers G., Möckel B., Pfefferle W., Nampoothiri K.M., Krämer R., and Burkovski A. Urease of Corynebacterium glutamicum: organization of corresponding genes and investigation of activity. FEMS Microbiol. Lett. 189 (2000) 305-310
27. Nolden L., Farwick M., Krämer R., and Burkovski A. Glutamine synthetases in Corynebacterium glutamicum: transcriptional control and regulation of activity. FEMS Microbiol. Lett. 201 (2001) 91-98
28. Nolden L., Ngouoto-Nkili C.-E., Bendt A.K., Krämer R., and Burkovski A. Sensing nitrogen limitation in Corynebacterium glutamicum: the role of glnK and glnD. Mol. Microbiol. 42 (2001) 1281-1295
29. Schaffer S., and Burkovski A. Genome-based approaches: proteomics. In: Bott M., and Eggeling L. (Eds). Handbook of Corynebacterium glutamicum (2005), CRC Press LLC, Boca Raton, FL 99-118
30. Schilling O., Frick O., Herzberg C., Ehrenreich A., Heinzle E., Wittmann C., and Stülke J. Transcriptional and metabolomic responses of Bacillus subtilis to the availability of organic acids: transcription regulation is important but not sufficient to account for metabolic adaptation. Appl. Environ. Microbiol. 73 (2007) 499-507
31. Shapiro B.M., and Stadtman E.R. The regulation of glutamine synthesis in microorganisms. Annu. Rev. Microbiol. 24 (1970) 504-521
32. Strelkov S., von Elstermann M., and Schomburg D. Comprehensive analysis of metabolites in Corynebacterium glutamicum by gas chromatography/mass spectrometry. Biol. Chem. 385 (2004) 853-861
33. Strösser J., Lüdke A., Schaffer S., Krämer R., and Burkovski A. Regulation of GlnK activity: modification, membrane sequestration, and proteolysis as regulatory principles in the network of nitrogen control in Corynebacterium glutamicum. Mol. Microbiol. 54 (2004) 132-147
34. Takors R., Bathe B., Rieping M., Hans S., Kelle R., and Huthmacher K. Systems biology for industrial strains and fermentation processes-example: amino acids. J. Biotechnol. 129 (2007) 181-190
35. Udaka S. Screening method for microorganisms accumulating metabolites and its use in the isolation of Micrococcus glutamicus. J. Bacteriol. 79 (1960) 745-755
36. Udaka S. The discovery of Corynebacterium glutamicum and birth of amino acid fermentation industry in Japan. In: Burkovski A. (Ed). Corynebacteria: Genomics and Molecular Biology (2008), Caister Academic Press, Norwich 1-6
37. van den Dool H., and Kratz P.D. A generalization of the retention index system including linear temperature programmed gas-liquid partition chromatography. J. Chromatogr. 11 (1963) 463-471
38. Wehrmann A., Phillipp B., Sahm H., and Eggeling L. Different modes of diaminopimelate synthesis and their role in cell wall integrity: a study with Corynebacterium glutamicum. J. Bacteriol. 180 (1998) 182-184
39. Wendisch V.F. Genome-wide expression analysis in Corynebacterium glutamicum using DNA microarrays. J. Biotechnol. 104 (2003) 273-285