Investigation of glycolysis and pyruvate branching of three lactic acid bacteria

Challenge: Comparative analyses, as demonstrated by comparative genomics and bioinformatics, are extremely powerful for (i) transfer of information from (experimentally) well-studied organisms to the other organisms, and (ii) when coupled to functional and phenotypic information, insight in the relative importance of components to the observed differences and simalities. The central principle of this proposal is that important aspects of the functional differences between organisms derive not only from the differences in genetic components (which underlies comparative genomics) but also from the interactions between their components (see Fig. 1). Therefore, this project will develop Comparative Systems Biology (CSB).
Model system: The project focuses on three relatively simple and highly related microorganisms, which nevertheless exhibit stark and important differences in their functional relationship with human beings: These organisms are homofermentative lactic acid bacteria, namely Lactococcus lactis, the major microorganism used in the dairy industry, Enterococcus faecalis, a major (fecal) contaminant in food and water as well as a
contributor to food fermentation, and Streptococcus pyogenes, an important human pathogen. These organisms have similar primary metabolism, but persist in completely different environments (milk, faeces, blood). Lactococcus lactis will be used as the reference microorganism, since: (i) it is by far the best studied lactic acid bacterium, (ii) three different genomes have been sequenced, (iii) a kinetic model has been developed for its complete glycolysis including some branching pathways, (iv) genetic and metabolic engineering tools are available and (v) a functional genomics platform has been set-up including DNA microarray and metabolic databases.
Deliverables: The specific deliverables of this project will be
(i) a thorough understanding of the differences and similarities in systems biology (components and how these components interact) between these three organisms and the extent to which these differences contribute to the organisms being different functionally (Fig. 1).
(ii) generic methods and tools for transfer of systems biology knowledge from one organism to another by comparative analysis.
This multidisciplinary approach will result in mathematical, comprehensive, models that quantitatively describe the catabolic (product formation) response of lactic acid bacteria under different, industrially relevant, conditions. These models will help in the design of strategies that optimise functional activities such as acidification and flavour production, but also strategies to control or reduce growth of undesirable contaminants and pathogens.
Methodology: The project will focus on carbon metabolism and its response to aeration, change of sugar-source, addition of heme and elimination of the crucial metabolic enzyme, lactate dehydrogenase. Cells will be grown in a non-nutrient-limited turbidostat that will allow maximal growth under defined conditions. The major regulatory events at the genetic level (adaptive mutations), the transcription, translation, enzymatic and metabolic level up to the final output (functional) level, will be quantified and then integrated in iterations between experimentation (all~omics) and modeling (network structure, flux balances, dynamics, control, regulation). The detailed knowledge from the reference strain L lactis will be used to accelerate the model development of the other two, less-well studied, organisms (contributing to deliverable ii in that process).

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Created: 15th Feb 2010 at 13:38

Last updated: 22nd Nov 2011 at 20:12

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