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GB3.0: a platform for plant bio-design that connects functional DNA elements with associated biological data

Vázquez-Vilar, Marta ; Quijano-Rubio, Alfredo ; Fernández Del Carmen, María Asunción ; Sarrion-Perdigones, Alejandro ; Ochoa-Fernández, Rocío ; Ziarsolo Areitioaurtena, Pello ; Blanca Postigo, José Miguel ; Granell Richart, Antonio ; Orzáez Calatayud, Diego Vicente

Oxford University Press 2017

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  • Título:
    GB3.0: a platform for plant bio-design that connects functional DNA elements with associated biological data
  • Autor: Vázquez-Vilar, Marta ; Quijano-Rubio, Alfredo ; Fernández Del Carmen, María Asunción ; Sarrion-Perdigones, Alejandro ; Ochoa-Fernández, Rocío ; Ziarsolo Areitioaurtena, Pello ; Blanca Postigo, José Miguel ; Granell Richart, Antonio ; Orzáez Calatayud, Diego Vicente
  • Assuntos: BIOQUIMICA Y BIOLOGIA MOLECULAR ; Genetic dna engineering integrase ; GENETICA ; Luciferases plants genetics transcriptional activation syntax ; MICROBIOLOGIA ; Transcription
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  • Descrição: This is a pre-copyedited, author-produced version of an article accepted for publication in Nucleic Acids Research following peer review. The version of record Vázquez-Vilar, M.; Quijano-Rubio, A.; Fernandez Del Carmen, MA.; Sarrion-Perdigones, A.; Ochoa-Fernández, R.; Ziarsolo Areitioaurtena, P.; Blanca Postigo, JM... (2017). GB3.0: a platform for plant bio-design that connects functional DNA elements with associated biological data. Nucleic Acids Research. 45(4):2196-2209. doi:10.1093/nar/gkw1326 is available online at: http://doi.org/10.1093/nar/gkw1326. [EN] Modular DNA assembly simplifies multigene engineering in Plant Synthetic Biology. Furthermore, the recent adoption of a common syntax to facilitate the exchange of plant DNA parts (phytobricks) is a promising strategy to speed up genetic engineering. Following this lead, here, we present a platform for plant biodesign that incorporates functional descriptions of phytobricks obtained under pre-defined experimental conditions, and systematically registers the resulting information as metadata for documentation. To facilitate the handling of functional descriptions, we developed a new version (v3.0) of the GoldenBraid (GB) webtool that integrates the experimental data and displays it in the form of datasheets. We report the use of the Luciferase/Renilla (Luc/Ren) transient agroinfiltration assay in Nicotiana benthamiana as a standard to estimate relative transcriptional activities conferred by regulatory phytobricks, and show the consistency and reproducibility of this method in the characterization of a synthetic phytobrick based on the CaMV35S promoter. Furthermore, we illustrate the potential for combinatorial optimization and incremental innovation of the GB3.0 platform in two separate examples, (i) the development of a collection of orthogonal transcriptional regulators based on phiC31 integrase and (ii) the design of a small genetic circuit that connects a glucocorticoid switch to a MYB/bHLH transcriptional activation module. Spanish Ministry of Economy and Competitiveness [BIO2013-42193-R and BIO2016-78601-R projects to A.G. and D.O.]. Funding for open access charge: Spanish Ministry of Economy and Competitiveness [BIO2013-42193-R and BIO2016-78601-R projects to A.G. and D.O.]. Vázquez-Vilar, M.; Quijano-Rubio, A.; Fernández Del Carmen, MA.; Sarrion-Perdigones, A.; Ochoa-Fernández, R.; Ziarsolo Areitioaurtena, P.; Blanca Postigo, JM... (2017). GB3.0: a platform for plant bio-design that connects functional DNA elements with associated biological data. 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  • Editor: Oxford University Press
  • Data de criação/publicação: 2017
  • Idioma: Inglês
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