Metabolic modeling and analysis of the metabolic switch in <it>Streptomyces coelicolor</it>
<p>Abstract</p> <p>Background</p> <p>The transition from exponential to stationary phase in <it>Streptomyces coelicolor </it>is accompanied by a major metabolic switch and results in a strong activation of secondary metabolism. Here we have explored the unde...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2010-03-01
|
| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/11/202 |
| _version_ | 1818353504626933760 |
|---|---|
| author | Wellington Elizabeth MH Hodgson David A Merlo Maria E Alam Mohammad T Takano Eriko Breitling Rainer |
| author_facet | Wellington Elizabeth MH Hodgson David A Merlo Maria E Alam Mohammad T Takano Eriko Breitling Rainer |
| author_sort | Wellington Elizabeth MH |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>The transition from exponential to stationary phase in <it>Streptomyces coelicolor </it>is accompanied by a major metabolic switch and results in a strong activation of secondary metabolism. Here we have explored the underlying reorganization of the metabolome by combining computational predictions based on constraint-based modeling and detailed transcriptomics time course observations.</p> <p>Results</p> <p>We reconstructed the stoichiometric matrix of <it>S. coelicolor</it>, including the major antibiotic biosynthesis pathways, and performed flux balance analysis to predict flux changes that occur when the cell switches from biomass to antibiotic production. We defined the model input based on observed fermenter culture data and used a dynamically varying objective function to represent the metabolic switch. The predicted fluxes of many genes show highly significant correlation to the time series of the corresponding gene expression data. Individual mispredictions identify novel links between antibiotic production and primary metabolism.</p> <p>Conclusion</p> <p>Our results show the usefulness of constraint-based modeling for providing a detailed interpretation of time course gene expression data.</p> |
| first_indexed | 2024-12-13T19:10:35Z |
| format | Article |
| id | doaj.art-92ff542eca92468f9757bdf7cbe250eb |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-13T19:10:35Z |
| publishDate | 2010-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-92ff542eca92468f9757bdf7cbe250eb2022-12-21T23:34:26ZengBMCBMC Genomics1471-21642010-03-0111120210.1186/1471-2164-11-202Metabolic modeling and analysis of the metabolic switch in <it>Streptomyces coelicolor</it>Wellington Elizabeth MHHodgson David AMerlo Maria EAlam Mohammad TTakano ErikoBreitling Rainer<p>Abstract</p> <p>Background</p> <p>The transition from exponential to stationary phase in <it>Streptomyces coelicolor </it>is accompanied by a major metabolic switch and results in a strong activation of secondary metabolism. Here we have explored the underlying reorganization of the metabolome by combining computational predictions based on constraint-based modeling and detailed transcriptomics time course observations.</p> <p>Results</p> <p>We reconstructed the stoichiometric matrix of <it>S. coelicolor</it>, including the major antibiotic biosynthesis pathways, and performed flux balance analysis to predict flux changes that occur when the cell switches from biomass to antibiotic production. We defined the model input based on observed fermenter culture data and used a dynamically varying objective function to represent the metabolic switch. The predicted fluxes of many genes show highly significant correlation to the time series of the corresponding gene expression data. Individual mispredictions identify novel links between antibiotic production and primary metabolism.</p> <p>Conclusion</p> <p>Our results show the usefulness of constraint-based modeling for providing a detailed interpretation of time course gene expression data.</p>http://www.biomedcentral.com/1471-2164/11/202 |
| spellingShingle | Wellington Elizabeth MH Hodgson David A Merlo Maria E Alam Mohammad T Takano Eriko Breitling Rainer Metabolic modeling and analysis of the metabolic switch in <it>Streptomyces coelicolor</it> BMC Genomics |
| title | Metabolic modeling and analysis of the metabolic switch in <it>Streptomyces coelicolor</it> |
| title_full | Metabolic modeling and analysis of the metabolic switch in <it>Streptomyces coelicolor</it> |
| title_fullStr | Metabolic modeling and analysis of the metabolic switch in <it>Streptomyces coelicolor</it> |
| title_full_unstemmed | Metabolic modeling and analysis of the metabolic switch in <it>Streptomyces coelicolor</it> |
| title_short | Metabolic modeling and analysis of the metabolic switch in <it>Streptomyces coelicolor</it> |
| title_sort | metabolic modeling and analysis of the metabolic switch in it streptomyces coelicolor it |
| url | http://www.biomedcentral.com/1471-2164/11/202 |
| work_keys_str_mv | AT wellingtonelizabethmh metabolicmodelingandanalysisofthemetabolicswitchinitstreptomycescoelicolorit AT hodgsondavida metabolicmodelingandanalysisofthemetabolicswitchinitstreptomycescoelicolorit AT merlomariae metabolicmodelingandanalysisofthemetabolicswitchinitstreptomycescoelicolorit AT alammohammadt metabolicmodelingandanalysisofthemetabolicswitchinitstreptomycescoelicolorit AT takanoeriko metabolicmodelingandanalysisofthemetabolicswitchinitstreptomycescoelicolorit AT breitlingrainer metabolicmodelingandanalysisofthemetabolicswitchinitstreptomycescoelicolorit |