Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology.

2.50
Hdl Handle:
http://hdl.handle.net/10033/48158
Title:
Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology.
Authors:
Puchałka, Jacek; Oberhardt, Matthew A; Godinho, Miguel; Bielecka, Agata; Regenhardt, Daniela; Timmis, Kenneth N; Papin, Jason A; Martins dos Santos, Vítor A P
Abstract:
A cornerstone of biotechnology is the use of microorganisms for the efficient production of chemicals and the elimination of harmful waste. Pseudomonas putida is an archetype of such microbes due to its metabolic versatility, stress resistance, amenability to genetic modifications, and vast potential for environmental and industrial applications. To address both the elucidation of the metabolic wiring in P. putida and its uses in biocatalysis, in particular for the production of non-growth-related biochemicals, we developed and present here a genome-scale constraint-based model of the metabolism of P. putida KT2440. Network reconstruction and flux balance analysis (FBA) enabled definition of the structure of the metabolic network, identification of knowledge gaps, and pin-pointing of essential metabolic functions, facilitating thereby the refinement of gene annotations. FBA and flux variability analysis were used to analyze the properties, potential, and limits of the model. These analyses allowed identification, under various conditions, of key features of metabolism such as growth yield, resource distribution, network robustness, and gene essentiality. The model was validated with data from continuous cell cultures, high-throughput phenotyping data, (13)C-measurement of internal flux distributions, and specifically generated knock-out mutants. Auxotrophy was correctly predicted in 75% of the cases. These systematic analyses revealed that the metabolic network structure is the main factor determining the accuracy of predictions, whereas biomass composition has negligible influence. Finally, we drew on the model to devise metabolic engineering strategies to improve production of polyhydroxyalkanoates, a class of biotechnologically useful compounds whose synthesis is not coupled to cell survival. The solidly validated model yields valuable insights into genotype-phenotype relationships and provides a sound framework to explore this versatile bacterium and to capitalize on its vast biotechnological potential.
Affiliation:
Synthetic and Systems Biology Group, Helmholtz Center for Infection Research (HZI), Braunschweig, Germany.
Citation:
Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology. 2008, 4 (10):e1000210 PLoS Comput. Biol.
Journal:
PLoS computational biology
Issue Date:
Oct-2008
URI:
http://hdl.handle.net/10033/48158
DOI:
10.1371/journal.pcbi.1000210
PubMed ID:
18974823
Additional Links:
http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000210
Type:
Article
Language:
en
ISSN:
1553-7358
Appears in Collections:
Publications of the RG Systems and synthetic biology (SSBI)

Full metadata record

DC FieldValue Language
dc.contributor.authorPuchałka, Jacek-
dc.contributor.authorOberhardt, Matthew A-
dc.contributor.authorGodinho, Miguel-
dc.contributor.authorBielecka, Agata-
dc.contributor.authorRegenhardt, Daniela-
dc.contributor.authorTimmis, Kenneth N-
dc.contributor.authorPapin, Jason A-
dc.contributor.authorMartins dos Santos, Vítor A P-
dc.date.accessioned2009-01-28T13:53:44Z-
dc.date.available2009-01-28T13:53:44Z-
dc.date.issued2008-10-
dc.identifier.citationGenome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology. 2008, 4 (10):e1000210 PLoS Comput. Biol.en
dc.identifier.issn1553-7358-
dc.identifier.pmid18974823-
dc.identifier.doi10.1371/journal.pcbi.1000210-
dc.identifier.urihttp://hdl.handle.net/10033/48158-
dc.description.abstractA cornerstone of biotechnology is the use of microorganisms for the efficient production of chemicals and the elimination of harmful waste. Pseudomonas putida is an archetype of such microbes due to its metabolic versatility, stress resistance, amenability to genetic modifications, and vast potential for environmental and industrial applications. To address both the elucidation of the metabolic wiring in P. putida and its uses in biocatalysis, in particular for the production of non-growth-related biochemicals, we developed and present here a genome-scale constraint-based model of the metabolism of P. putida KT2440. Network reconstruction and flux balance analysis (FBA) enabled definition of the structure of the metabolic network, identification of knowledge gaps, and pin-pointing of essential metabolic functions, facilitating thereby the refinement of gene annotations. FBA and flux variability analysis were used to analyze the properties, potential, and limits of the model. These analyses allowed identification, under various conditions, of key features of metabolism such as growth yield, resource distribution, network robustness, and gene essentiality. The model was validated with data from continuous cell cultures, high-throughput phenotyping data, (13)C-measurement of internal flux distributions, and specifically generated knock-out mutants. Auxotrophy was correctly predicted in 75% of the cases. These systematic analyses revealed that the metabolic network structure is the main factor determining the accuracy of predictions, whereas biomass composition has negligible influence. Finally, we drew on the model to devise metabolic engineering strategies to improve production of polyhydroxyalkanoates, a class of biotechnologically useful compounds whose synthesis is not coupled to cell survival. The solidly validated model yields valuable insights into genotype-phenotype relationships and provides a sound framework to explore this versatile bacterium and to capitalize on its vast biotechnological potential.en
dc.language.isoenen
dc.relation.urlhttp://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000210en
dc.titleGenome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology.en
dc.typeArticleen
dc.contributor.departmentSynthetic and Systems Biology Group, Helmholtz Center for Infection Research (HZI), Braunschweig, Germany.en
dc.identifier.journalPLoS computational biologyen
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