Development of a Corynebacterium glutamicum DNA microarray and validation by genome-wide expression profiling during growth with propionate as carbon source

Hüser AT, Becker A, Brune I, Dondrup M, Kalinowski J, Plassmeier J, Pühler A, Wiegräbe I, Tauch A (2003)
JOURNAL OF BIOTECHNOLOGY 106(2-3): 269-286.

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Zeitschriftenaufsatz | Veröffentlicht | Englisch
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Abstract / Bemerkung
A DNA microarray was developed to analyse global gene expression of the amino acid-producing bacterium Corynebacterium glutamicum. PCR products representing 93.4% of the predicted C. glutamicum genes were prepared and spotted in quadruplicate onto 3-aminopropyltrimethoxysilane-coated glass slides. The applicability of the C. glutamicum DNA microarray was demonstrated by co-hybridisation with fluorescently labelled cDNA probes. Analysis of the technical variance revealed that C. glutamicum genes detected with different intensities resulting in ratios greater than 1.52 or smaller than -1.52 can be regarded as differentially expressed with a confidence level of greater than 95%. In a validation example, we measured changes of the mRNA levels during growth of C. glutamicum with acetate and propionate as carbon sources. Acetate-grown C glutamicum cultures were used as reference. At the 95% confidence interval, 117 genes revealed increased transcript levels in the presence of propionate, while 43 genes showed a decreased expression compared with the acetate-grown culture. Global expression profiling confirmed the induction of the prpD2B2C2 gene cluster already known to be essential for propionate degradation via the 2-methylcitrate cycle. Besides many genes of unknown function, the paralogous prpD1B1C1 gene cluster as well as fasI-B (encoding fatty-acid synthase IB), dtsR1 and dtsR2 (components of acyl-CoA carboxylases), gluABCD (glutamate transport system), putP (proline transport system), and pyc (pyruvate carboxylase) showed significantly increased expression levels. Differential expression of these genes was confirmed by real-time reverse transcription (RT) PCR assays. (C) 2003 Elsevier B.V. All rights reserved.
Erscheinungsjahr
Zeitschriftentitel
JOURNAL OF BIOTECHNOLOGY
Band
106
Zeitschriftennummer
2-3
Seite
269-286
ISSN
PUB-ID

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Hüser AT, Becker A, Brune I, et al. Development of a Corynebacterium glutamicum DNA microarray and validation by genome-wide expression profiling during growth with propionate as carbon source. JOURNAL OF BIOTECHNOLOGY. 2003;106(2-3):269-286.
Hüser, A. T., Becker, A., Brune, I., Dondrup, M., Kalinowski, J., Plassmeier, J., Pühler, A., et al. (2003). Development of a Corynebacterium glutamicum DNA microarray and validation by genome-wide expression profiling during growth with propionate as carbon source. JOURNAL OF BIOTECHNOLOGY, 106(2-3), 269-286. doi:10.1016/j.jbiotec.2003.08.006
Hüser, A. T., Becker, A., Brune, I., Dondrup, M., Kalinowski, J., Plassmeier, J., Pühler, A., Wiegräbe, I., and Tauch, A. (2003). Development of a Corynebacterium glutamicum DNA microarray and validation by genome-wide expression profiling during growth with propionate as carbon source. JOURNAL OF BIOTECHNOLOGY 106, 269-286.
Hüser, A.T., et al., 2003. Development of a Corynebacterium glutamicum DNA microarray and validation by genome-wide expression profiling during growth with propionate as carbon source. JOURNAL OF BIOTECHNOLOGY, 106(2-3), p 269-286.
A.T. Hüser, et al., “Development of a Corynebacterium glutamicum DNA microarray and validation by genome-wide expression profiling during growth with propionate as carbon source”, JOURNAL OF BIOTECHNOLOGY, vol. 106, 2003, pp. 269-286.
Hüser, A.T., Becker, A., Brune, I., Dondrup, M., Kalinowski, J., Plassmeier, J., Pühler, A., Wiegräbe, I., Tauch, A.: Development of a Corynebacterium glutamicum DNA microarray and validation by genome-wide expression profiling during growth with propionate as carbon source. JOURNAL OF BIOTECHNOLOGY. 106, 269-286 (2003).
Hüser, Andrea T., Becker, Anke, Brune, Iris, Dondrup, Michael, Kalinowski, Jörn, Plassmeier, Jens, Pühler, Alfred, Wiegräbe, I., and Tauch, Andreas. “Development of a Corynebacterium glutamicum DNA microarray and validation by genome-wide expression profiling during growth with propionate as carbon source”. JOURNAL OF BIOTECHNOLOGY 106.2-3 (2003): 269-286.

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Hovey R, Lentes S, Ehrenreich A, Salmon K, Saba K, Gottschalk G, Gunsalus RP, Deppenmeier U., Mol Genet Genomics 273(3), 2005
PMID: 15902489
Adaptation of Corynebacterium glutamicum to ammonium limitation: a global analysis using transcriptome and proteome techniques.
Silberbach M, Schäfer M, Hüser AT, Kalinowski J, Pühler A, Krämer R, Burkovski A., Appl Environ Microbiol 71(5), 2005
PMID: 15870326
EMMA: a platform for consistent storage and efficient analysis of microarray data.
Dondrup M, Goesmann A, Bartels D, Kalinowski J, Krause L, Linke B, Rupp O, Sczyrba A, Pühler A, Meyer F., J Biotechnol 106(2-3), 2003
PMID: 14651856

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