MSEA: metabolite set enrichment analysis in the MeltDB metabolomics software platform: metabolic profiling of Corynebacterium glutamicum as an example
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Gene set enrichment analysis (GSEA) has been successfully employed in transcriptomics and proteomics research for over 5 years. We have applied a modified GSEA approach to metabolomics, called metabolite set enrichment analysis (MSEA), and have integrated this method into the MeltDB platform. With the novel integrated functionality, we evaluate the applicability of the approach for metabolomics research by analyzing the metabolic profiles of industrial amino acid producer strains of Corynebacterium glutamicum. Metabolite sets are obtained from metabolic pathways defined in the KEGG and the newly created CglCyc databases. In the first experiment using MSEA, the metabolic profiling analyses compared glucose- and acetate-grown strains, and, in the second, a production strain series in which the carbon flow is shifted step-wise from the lysine pathway to the branching threonine, isoleucine, and methionine pathways. By identifying changes of the metabolic profile MSEA was able to identify the metabolic pathways activated while utilizing different carbon sources or those that have been genetically modified. The presented experimental results are publicly available at http://meltdb.cebitec.uni-bielefeld.de.
KeywordsMetabolite set enrichment analysis Corynebacterium glutamicum
HN and LJS acknowledge the financial support of the SysLogics Project (BMBF 0315275A) and MP that of the SysMAP Project (BMBF 0313704). NK acknowledges the support by a fellowship from the CLIB-Graduate Cluster Industrial Biotechnology. The authors wish to thank the BRF team for expert technical support. Furthermore, the authors thank Daniel Stephen Brooks (Department of Philosophy, University of Bielefeld, Germany) and John Quimby (Massachusetts Institute of Technology, Sinskey Laboratory, Cambridge, USA) for carefully reading the manuscript and helping with wording and phrasing.
- Drysch, A., El Massaoudi, M., Mack, C., et al. (2003). Production process monitoring by serial mapping of microbial carbon flux distributions using a novel sensor reactor approach: II–(13)C-labeling-based metabolic flux analysis and l-lysine production. Metabolic Engineering, 5(2), 96–107.PubMedCrossRefGoogle Scholar
- Dunn, W. B., & Ellis, D. I. (2005). Metabolomics: Current analytical platforms and methodologies. Trends in Analytical Chemistry, 4, 285–294.Google Scholar
- Guillouet, S., Rodal, A. A., An, G. H., et al. (2001). Metabolic redirection of carbon flow toward isoleucine by expressing a catabolic threonine dehydratase in a threonine-overproducing Corynebacterium glutamicum. Applied Microbiology and Biotechnology, 57(5–6), 667–673.PubMedCrossRefGoogle Scholar
- Hansmeier, N., Chao, T. C., Puhler, A., Tauch, A., & Kalinowski, J. (2006). The cytosolic, cell surface and extracellular proteomes of the biotechnologically important soil bacterium Corynebacterium efficiens YS-314 in comparison to those of Corynebacterium glutamicum ATCC 13032. Proteomics, 6(1), 233–250.PubMedCrossRefGoogle Scholar
- Hüser, A. T., Chassagnole, C., Lindley, N. D., et al. (2005). Rational design of a Corynebacterium glutamicum pantothenate production strain and its characterization by metabolic flux analysis and genome-wide transcriptional profiling. Applied and Environmental Microbiology, 71(6), 3255–3268.PubMedCrossRefGoogle Scholar
- Kanehisa, M., Goto, S., Hattori, M. et al. (2006). From genomics to chemical genomics: New developments in KEGG. Nucleic Acids Research, 34(Database issue), D354–D357.Google Scholar
- Leuchtenberger, W. (1996) Amino acids: Technical production and use. In H. J. Rehm, G. Reed, A. Pühler, & P. Stadler (Eds.), Biotechnology (pp. 466–502). Weinheim: VCH.Google Scholar
- Persicke, M., Plassmeier, J., Neuweger, H. et al. (2010). Size exclusion chromatography-an improved method to harvest Corynebacterium glutamicum cells for the analysis of cytosolic metabolites. Journal of Biotechnology. doi: 10.1016/j.jbiotec.2010.08.016.
- Plassmeier, J., Barsch, A., Persicke, M., Niehaus, K., & Kalinowski, J. (2007). Investigation of central carbon metabolism and the 2-methylcitrate cycle in Corynebacterium glutamicum by metabolic profiling using gas chromatography-mass spectrometry. Journal of Biotechnology, 130(4), 354–363.PubMedCrossRefGoogle Scholar
- Rey, D. A., Nentwich, S. S., Koch, D. J., et al. (2005). The McbR repressor modulated by the effector substance S-adenosylhomocysteine controls directly the transcription of a regulon involved in sulphur metabolism of Corynebacterium glutamicum ATCC 13032. Molecular Microbiology, 56(4), 871–887.PubMedCrossRefGoogle Scholar
- Rey, D. A., Pühler, A., & Kalinowski, J. (2003). The putative transcriptional repressor McbR, member of the TetR-family, is involved in the regulation of the metabolic network directing the synthesis of sulfur containing amino acids in Corynebacterium glutamicum. Journal of Biotechnology, 103(1), 51–65.PubMedCrossRefGoogle Scholar
- Stavrum, A. K., Petersen, K., Jonassen, I., & Dysvik, B. (2008). Analysis of gene-expression data using J-Express. Current Protocols in Bioinformatics, Chap. 7, Unit 7.3.Google Scholar
- Wendisch, V. F., de Graaf, A. A., Sahm, H., & Eikmanns, B. J. (2000). Quantitative determination of metabolic fluxes during coutilization of two carbon sources: comparative analyses with Corynebacterium glutamicum during growth on acetate and/or glucose. Journal of Bacteriology, 182(11), 3088–3096.PubMedCrossRefGoogle Scholar