Bioinformatics Advance Access originally published online on November 13, 2008
Bioinformatics 2009 25(1):90-97; doi:10.1093/bioinformatics/btn589
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Decomposition of complex microbial behaviors into resource-based stress responses
Department of Chemical and Biological Engineering, Center for Biofilm Engineering and Thermal Biology Institute, Montana State University, Bozeman, MT 59717, USA
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Abstract |
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Motivation: Highly redundant metabolic networks and experimental data from cultures likely adapting simultaneously to multiple stresses can complicate the analysis of cellular behaviors. It is proposed that the explicit consideration of these factors is critical to understanding the competitive basis of microbial strategies.
Results: Wide ranging, seemingly unrelated Escherichia coli physiological fluxes can be simply and accurately described as linear combinations of a few ecologically relevant stress adaptations. These strategies were identified by decomposing the central metabolism of E.coli into elementary modes (mathematically defined biochemical pathways) and assessing the resource investment cost–benefit properties for each pathway. The approach capitalizes on the inherent tradeoffs related to investing finite resources like nitrogen into different pathway enzymes when the pathways have varying metabolic efficiencies. The subset of ecologically competitive pathways represented 0.02% of the total permissible pathways. The biological relevance of the assembled strategies was tested against 10 000 randomly constructed pathway subsets. None of the randomly assembled collections were able to describe all of the considered experimental data as accurately as the cost-based subset. The results suggest these metabolic strategies are biologically significant. The current descriptions were compared with linear programming (LP)-based flux descriptions using the Euclidean distance metric. The current study's pathway subset described the experimental fluxes with better accuracy than the LP results without having to test multiple objective functions or constraints and while providing additional ecological insight into microbial behavior. The assembled pathways seem to represent a generalized set of strategies that can describe a wide range of microbial responses and hint at evolutionary processes where a handful of successful metabolic strategies are utilized simultaneously in different combinations to adapt to diverse conditions.
Contact: rossc{at}biofilms.montana.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Associate Editor: Limsoon Wong
Received on August 10, 2008; revised on November 10, 2088; accepted on November 10, 2088
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