Temporal expression-based analysis of metabolism.
Metabolic flux is frequently rerouted through cellular metabolism in response to dynamic changes in the intra- and extra-cellular environment. Capturing the mechanisms underlying these metabolic transitions in quantitative and predictive models is a prominent challenge in systems biology. Progress i...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2012-01-01
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| Series: | PLoS Computational Biology |
| Online Access: | http://europepmc.org/articles/PMC3510039?pdf=render |
| _version_ | 1818296363082842112 |
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| author | Sara B Collins Ed Reznik Daniel Segrè |
| author_facet | Sara B Collins Ed Reznik Daniel Segrè |
| author_sort | Sara B Collins |
| collection | DOAJ |
| description | Metabolic flux is frequently rerouted through cellular metabolism in response to dynamic changes in the intra- and extra-cellular environment. Capturing the mechanisms underlying these metabolic transitions in quantitative and predictive models is a prominent challenge in systems biology. Progress in this regard has been made by integrating high-throughput gene expression data into genome-scale stoichiometric models of metabolism. Here, we extend previous approaches to perform a Temporal Expression-based Analysis of Metabolism (TEAM). We apply TEAM to understanding the complex metabolic dynamics of the respiratorily versatile bacterium Shewanella oneidensis grown under aerobic, lactate-limited conditions. TEAM predicts temporal metabolic flux distributions using time-series gene expression data. Increased predictive power is achieved by supplementing these data with a large reference compendium of gene expression, which allows us to take into account the unique character of the distribution of expression of each individual gene. We further propose a straightforward method for studying the sensitivity of TEAM to changes in its fundamental free threshold parameter θ, and reveal that discrete zones of distinct metabolic behavior arise as this parameter is changed. By comparing the qualitative characteristics of these zones to additional experimental data, we are able to constrain the range of θ to a small, well-defined interval. In parallel, the sensitivity analysis reveals the inherently difficult nature of dynamic metabolic flux modeling: small errors early in the simulation propagate to relatively large changes later in the simulation. We expect that handling such "history-dependent" sensitivities will be a major challenge in the future development of dynamic metabolic-modeling techniques. |
| first_indexed | 2024-12-13T04:02:21Z |
| format | Article |
| id | doaj.art-446885182f004584ae20f80abfc5e960 |
| institution | Directory Open Access Journal |
| issn | 1553-734X 1553-7358 |
| language | English |
| last_indexed | 2024-12-13T04:02:21Z |
| publishDate | 2012-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj.art-446885182f004584ae20f80abfc5e9602022-12-22T00:00:23ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582012-01-01811e100278110.1371/journal.pcbi.1002781Temporal expression-based analysis of metabolism.Sara B CollinsEd ReznikDaniel SegrèMetabolic flux is frequently rerouted through cellular metabolism in response to dynamic changes in the intra- and extra-cellular environment. Capturing the mechanisms underlying these metabolic transitions in quantitative and predictive models is a prominent challenge in systems biology. Progress in this regard has been made by integrating high-throughput gene expression data into genome-scale stoichiometric models of metabolism. Here, we extend previous approaches to perform a Temporal Expression-based Analysis of Metabolism (TEAM). We apply TEAM to understanding the complex metabolic dynamics of the respiratorily versatile bacterium Shewanella oneidensis grown under aerobic, lactate-limited conditions. TEAM predicts temporal metabolic flux distributions using time-series gene expression data. Increased predictive power is achieved by supplementing these data with a large reference compendium of gene expression, which allows us to take into account the unique character of the distribution of expression of each individual gene. We further propose a straightforward method for studying the sensitivity of TEAM to changes in its fundamental free threshold parameter θ, and reveal that discrete zones of distinct metabolic behavior arise as this parameter is changed. By comparing the qualitative characteristics of these zones to additional experimental data, we are able to constrain the range of θ to a small, well-defined interval. In parallel, the sensitivity analysis reveals the inherently difficult nature of dynamic metabolic flux modeling: small errors early in the simulation propagate to relatively large changes later in the simulation. We expect that handling such "history-dependent" sensitivities will be a major challenge in the future development of dynamic metabolic-modeling techniques.http://europepmc.org/articles/PMC3510039?pdf=render |
| spellingShingle | Sara B Collins Ed Reznik Daniel Segrè Temporal expression-based analysis of metabolism. PLoS Computational Biology |
| title | Temporal expression-based analysis of metabolism. |
| title_full | Temporal expression-based analysis of metabolism. |
| title_fullStr | Temporal expression-based analysis of metabolism. |
| title_full_unstemmed | Temporal expression-based analysis of metabolism. |
| title_short | Temporal expression-based analysis of metabolism. |
| title_sort | temporal expression based analysis of metabolism |
| url | http://europepmc.org/articles/PMC3510039?pdf=render |
| work_keys_str_mv | AT sarabcollins temporalexpressionbasedanalysisofmetabolism AT edreznik temporalexpressionbasedanalysisofmetabolism AT danielsegre temporalexpressionbasedanalysisofmetabolism |