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Fine-tuning tomato agronomic properties by computational genome redesign

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Papin, Jason A., Carrera, Javier, Fernández del Carmen, Asun, Fernández-Muñoz, Rafael, Rambla, Jose Luis, Pons, Clara, Jaramillo, Alfonso, Elena, Santiago F. and Granell, Antonio (2012) Fine-tuning tomato agronomic properties by computational genome redesign. PLoS Computational Biology, 8 (6). e1002528. doi:10.1371/journal.pcbi.1002528

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Official URL: http://dx.doi.org/10.1371/journal.pcbi.1002528

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Abstract

Considering cells as biofactories, we aimed to optimize its internal processes by using the same engineering principles that large industries are implementing nowadays: lean manufacturing. We have applied reverse engineering computational methods to transcriptomic, metabolomic and phenomic data obtained from a collection of tomato recombinant inbreed lines to formulate a kinetic and constraint-based model that efficiently describes the cellular metabolism from expression of a minimal core of genes. Based on predicted metabolic profiles, a close association with agronomic and organoleptic properties of the ripe fruit was revealed with high statistical confidence. Inspired in a synthetic biology approach, the model was used for exploring the landscape of all possible local transcriptional changes with the aim of engineering tomato fruits with fine-tuned biotechnological properties. The method was validated by the ability of the proposed genomes, engineered for modified desired agronomic traits, to recapitulate experimental correlations between associated metabolites.

Item Type: Journal Article
Subjects: Q Science > QH Natural history
Divisions: Faculty of Science > Life Sciences (2010- )
Library of Congress Subject Headings (LCSH): Synthetic biology, Lean Manufacturing, Genomes, Systems biology, Plant genomes
Journal or Publication Title: PLoS Computational Biology
Publisher: Public Library of Science
ISSN: 1553-7358
Official Date: 12 June 2012
Dates:
DateEvent
12 June 2012Published
Volume: 8
Number: 6
Article Number: e1002528
DOI: 10.1371/journal.pcbi.1002528
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Restricted or Subscription Access
Funder: Actions Thématiques Incitatives de Genopole (ATIGE), Fondation pour la Recherche Medicale, Genoma España
RIOXX Funder/Project Grant:
Project/Grant IDRIOXX Funder NameFunder ID
TIN2006-12860Ministerio de Ciencia e Innovaciónhttp://dx.doi.org/10.13039/501100004837
UNSPECIFIEDEuropean Regional Development Fundhttp://dx.doi.org/10.13039/501100008530
FP7-ICT-043338 (BACTOCOM)Seventh Framework Programmehttp://dx.doi.org/10.13039/100011102
FP7-ICT-265505 (CADMAD)Seventh Framework Programmehttp://dx.doi.org/10.13039/100011102
BFU2009-06993Ministerio de Ciencia e Innovaciónhttp://dx.doi.org/10.13039/501100004837
FOOD-CT-2006-016214European Commissionhttp://dx.doi.org/10.13039/501100000780

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