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Proteogenomics to Study the Anaerobic Degradation of Aromatic Compounds and Hydrocarbons

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Rabus,  R.
Department of Microbiology, Max Planck Institute for Marine Microbiology, Max Planck Society;

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Trautwein,  K.
Department of Microbiology, Max Planck Institute for Marine Microbiology, Max Planck Society;

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Citation

Rabus, R., & Trautwein, K. (2010). Proteogenomics to Study the Anaerobic Degradation of Aromatic Compounds and Hydrocarbons. In K. N. Timmis (Ed.), Handbook of Hydrocarbon and Lipid Microbiology (pp. 4385-4405). Heidelberg: Springer-Verlag Berlin.


Cite as: http://hdl.handle.net/21.11116/0000-0001-CB7A-2
Abstract
The tools of modern genomics and proteomics (proteogenomics) are revolutionizing all aspects of biological research, having also opened new possibilities in the field of anaerobic biodegradation. The presently applied proteogenomic technologies are summarized. Insights into anaerobic biodegradation enabled by the new approaches include the identification of novel alkyl/arylsuccinate synthases for anaerobic n-alkane and 2-methylnaphthalene activation, and the regulation of catabolic pathways in the anaerobic aromatic compound degrading denitrifying bacterium “Aromatoleum aromaticum” strain EbN1. A key step in the proteomic workflow is the detection of substrate-specifically formed proteins (enzyme candidates for the studied degradation pathway) coupled to the quantitative determination of changes in their abundance. Two-dimensional difference gel electrophoresis (2D DIGE) is the current benchmark for gel-based differential protein profiling. The basic principle and experimental procedures of the 2D DIGE technology are described.