title: GB3.0: a platform for plant bio-design that connects functional DNA elements with associated biological data.
abstract: 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.
authors.affiliation: Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain.
authors.forename: Marta
authors.initials: M
authors.lastname: Vazquez-Vilar
authors.affiliation: Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain.
authors.forename: Alfredo
authors.initials: A
authors.lastname: Quijano-Rubio
authors.affiliation: Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain.
authors.forename: Asun
authors.initials: A
authors.lastname: Fernandez-Del-Carmen
authors.affiliation: Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain.
authors.forename: Alejandro
authors.initials: A
authors.lastname: Sarrion-Perdigones
authors.affiliation: Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain.
authors.forename: Rocio
authors.initials: R
authors.lastname: Ochoa-Fernandez
authors.affiliation: Centro de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain.
authors.forename: Peio
authors.initials: P
authors.lastname: Ziarsolo
authors.affiliation: Centro de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain.
authors.forename: José
authors.initials: J
authors.lastname: Blanca
authors.affiliation: Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain.
authors.forename: Antonio
authors.initials: A
authors.lastname: Granell
authors.affiliation: Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain.
authors.forename: Diego
authors.initials: D
authors.lastname: Orzaez
mesh_terms: D019295:Computational Biology / Q000379:methods*; D018744:DNA, Plant; D015870:Gene Expression; D018506:Gene Expression Regulation, Plant; D017930:Genes, Reporter; D010944:Plants / Q000235:genetics* / Q000378:metabolism*; D011401:Promoter Regions, Genetic; D011523:Protoplasts / Q000378:metabolism; D012984:Software; D014158:Transcription, Genetic; D014584:User-Computer Interface; D064878:Web Browser
chemical_list: D018744:DNA, Plant