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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
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 | |||||||||||||||||||||
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| 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: |
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| 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: |
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