A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory

20 p.-5 fig.4 tab.

Detalles Bibliográficos
Autores: Nogales, Juan, Palsson, Bernhard Ø, Thiele, Ines
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2008
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/8268
Acceso en línea:http://hdl.handle.net/10261/8268
Access Level:acceso abierto
Palabra clave:Pseudomonas putida KT2440
Genome-scale reconstruction
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spelling A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factoryNogales, JuanPalsson, Bernhard ØThiele, InesPseudomonas putida KT2440Genome-scale reconstruction20 p.-5 fig.4 tab.Background Pseudomonas putida is the best studied pollutant degradative bacteria and is harnessed by industrial biotechnology to synthesize fine chemicals. Since the publication of P. putida KT2440's genome, some in silico analyses of its metabolic and biotechnology capacities have been published. However, global understanding of the capabilities of P. putida KT2440 requires the construction of a metabolic model that enables the integration of classical experimental data along with genomic and high-throughput data. The constraint-based reconstruction and analysis (COBRA) approach has been successfully used to build and analyze in silico genome-scale metabolic reconstructions. Results We present a genome-scale reconstruction of P. putida KT2440's metabolism, iJN746, which was constructed based on genomic, biochemical, and physiological information. This manually-curated reconstruction accounts for 746 genes, 950 reactions, and 911 metabolites. iJN746 captures biotechnologically relevant pathways, including polyhydroxyalkanoate synthesis and catabolic pathways of aromatic compounds (e.g., toluene, benzoate, phenylacetate, nicotinate), not described in other metabolic reconstructions or biochemical databases. The predictive potential of iJN746 was validated using experimental data including growth performance and gene deletion studies. Furthermore, in silico growth on toluene was found to be oxygen-limited, suggesting the existence of oxygen-efficient pathways not yet annotated in P. putida's genome. Moreover, we evaluated the production efficiency of polyhydroxyalkanoates from various carbon sources and found fatty acids as the most prominent candidates, as expected. Conclusion Here we presented the first genome-scale reconstruction of P. putida, a biotechnologically interesting all-surrounder. Taken together, this work illustrates the utility of iJN746 as i) a knowledge-base, ii) a discovery tool, and iii) an engineering platform to explore P. putida's potential in bioremediation and bioplastic production.JN is the recipients of an I3P predoctoral Fellowship from the Consejo Superior de Investigaciones Científicas (CSIC) and JN stay in San Diego was supported by a short term I3P fellowship.Peer reviewedBioMed Central200820082008info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersion1642188 bytesapplication/pdfhttp://hdl.handle.net/10261/8268reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Ingléshttp://dx.doi.org/10.1186/1752-0509-2-79info:eu-repo/semantics/openAccessoai:digital.csic.es:10261/82682026-05-22T06:33:51Z
dc.title.none.fl_str_mv A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory
title A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory
spellingShingle A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory
Nogales, Juan
Pseudomonas putida KT2440
Genome-scale reconstruction
title_short A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory
title_full A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory
title_fullStr A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory
title_full_unstemmed A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory
title_sort A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory
dc.creator.none.fl_str_mv Nogales, Juan
Palsson, Bernhard Ø
Thiele, Ines
author Nogales, Juan
author_facet Nogales, Juan
Palsson, Bernhard Ø
Thiele, Ines
author_role author
author2 Palsson, Bernhard Ø
Thiele, Ines
author2_role author
author
dc.subject.none.fl_str_mv Pseudomonas putida KT2440
Genome-scale reconstruction
topic Pseudomonas putida KT2440
Genome-scale reconstruction
description 20 p.-5 fig.4 tab.
publishDate 2008
dc.date.none.fl_str_mv 2008
2008
2008
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/8268
url http://hdl.handle.net/10261/8268
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv http://dx.doi.org/10.1186/1752-0509-2-79
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
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dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
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score 15,811543

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