- -

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

RiuNet: Institutional repository of the Polithecnic University of Valencia

Share/Send to

Cited by

Statistics

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

Show full item 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

Por favor, use este identificador para citar o enlazar este ítem: http://hdl.handle.net/10251/102491

Files in this item

Item Metadata

Title: GB3.0: a platform for plant bio-design that connects functional DNA elements with associated biological data
Author: 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
UPV Unit: Universitat Politècnica de València. Instituto Universitario Mixto de Biología Molecular y Celular de Plantas - Institut Universitari Mixt de Biologia Molecular i Cel·lular de Plantes
Universitat Politècnica de València. Departamento de Biotecnología - Departament de Biotecnologia
Universitat Politècnica de València. Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana - Institut Universitari de Conservació i Millora de l'Agrodiversitat Valenciana
Issued date:
Abstract:
[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 ...[+]
Subjects: Transcription , Genetic dna engineering integrase , Luciferases plants genetics transcriptional activation syntax
Copyrigths: Reserva de todos los derechos
Source:
Nucleic Acids Research. (issn: 0305-1048 )
DOI: 10.1093/nar/gkw1326
Publisher:
Oxford University Press
Publisher version: http://doi.org/10.1093/nar/gkw1326
Description: 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.
Thanks:
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 ...[+]
Type: Artículo

References

Dalal, J., Yalamanchili, R., La Hovary, C., Ji, M., Rodriguez-Welsh, M., Aslett, D., … Qu, R. (2015). A novel gateway-compatible binary vector series (PC-GW) for flexible cloning of multiple genes for genetic transformation of plants. Plasmid, 81, 55-62. doi:10.1016/j.plasmid.2015.06.003

Cha-aim, K., Fukunaga, T., Hoshida, H., & Akada, R. (2009). Reliable fusion PCR mediated by GC-rich overlap sequences. Gene, 434(1-2), 43-49. doi:10.1016/j.gene.2008.12.014

Nour-Eldin, H. H., Geu-Flores, F., & Halkier, B. A. (2010). USER Cloning and USER Fusion: The Ideal Cloning Techniques for Small and Big Laboratories. Methods in Molecular Biology, 185-200. doi:10.1007/978-1-60761-723-5_13 [+]
Dalal, J., Yalamanchili, R., La Hovary, C., Ji, M., Rodriguez-Welsh, M., Aslett, D., … Qu, R. (2015). A novel gateway-compatible binary vector series (PC-GW) for flexible cloning of multiple genes for genetic transformation of plants. Plasmid, 81, 55-62. doi:10.1016/j.plasmid.2015.06.003

Cha-aim, K., Fukunaga, T., Hoshida, H., & Akada, R. (2009). Reliable fusion PCR mediated by GC-rich overlap sequences. Gene, 434(1-2), 43-49. doi:10.1016/j.gene.2008.12.014

Nour-Eldin, H. H., Geu-Flores, F., & Halkier, B. A. (2010). USER Cloning and USER Fusion: The Ideal Cloning Techniques for Small and Big Laboratories. Methods in Molecular Biology, 185-200. doi:10.1007/978-1-60761-723-5_13

Engler, C., Kandzia, R., & Marillonnet, S. (2008). A One Pot, One Step, Precision Cloning Method with High Throughput Capability. PLoS ONE, 3(11), e3647. doi:10.1371/journal.pone.0003647

Blake, W. J., Chapman, B. A., Zindal, A., Lee, M. E., Lippow, S. M., & Baynes, B. M. (2010). Pairwise selection assembly for sequence-independent construction of long-length DNA. Nucleic Acids Research, 38(8), 2594-2602. doi:10.1093/nar/gkq123

De Paoli, H. C., Tuskan, G. A., & Yang, X. (2016). An innovative platform for quick and flexible joining of assorted DNA fragments. Scientific Reports, 6(1). doi:10.1038/srep19278

Engler, C., Gruetzner, R., Kandzia, R., & Marillonnet, S. (2009). Golden Gate Shuffling: A One-Pot DNA Shuffling Method Based on Type IIs Restriction Enzymes. PLoS ONE, 4(5), e5553. doi:10.1371/journal.pone.0005553

Weber, E., Engler, C., Gruetzner, R., Werner, S., & Marillonnet, S. (2011). A Modular Cloning System for Standardized Assembly of Multigene Constructs. PLoS ONE, 6(2), e16765. doi:10.1371/journal.pone.0016765

Sarrion-Perdigones, A., Falconi, E. E., Zandalinas, S. I., Juárez, P., Fernández-del-Carmen, A., Granell, A., & Orzaez, D. (2011). GoldenBraid: An Iterative Cloning System for Standardized Assembly of Reusable Genetic Modules. PLoS ONE, 6(7), e21622. doi:10.1371/journal.pone.0021622

Patron, N. J., Orzaez, D., Marillonnet, S., Warzecha, H., Matthewman, C., Youles, M., … Rogers, C. (2015). Standards for plant synthetic biology: a common syntax for exchange ofDNAparts. New Phytologist, 208(1), 13-19. doi:10.1111/nph.13532

Liu, W., & Stewart, C. N. (2015). Plant synthetic biology. Trends in Plant Science, 20(5), 309-317. doi:10.1016/j.tplants.2015.02.004

Wang, Y.-H., Wei, K. Y., & Smolke, C. D. (2013). Synthetic Biology: Advancing the Design of Diverse Genetic Systems. Annual Review of Chemical and Biomolecular Engineering, 4(1), 69-102. doi:10.1146/annurev-chembioeng-061312-103351

Engler, C., Youles, M., Gruetzner, R., Ehnert, T.-M., Werner, S., Jones, J. D. G., … Marillonnet, S. (2014). A Golden Gate Modular Cloning Toolbox for Plants. ACS Synthetic Biology, 3(11), 839-843. doi:10.1021/sb4001504

Canton, B., Labno, A., & Endy, D. (2008). Refinement and standardization of synthetic biological parts and devices. Nature Biotechnology, 26(7), 787-793. doi:10.1038/nbt1413

Sarrion-Perdigones, A., Vazquez-Vilar, M., Palaci, J., Castelijns, B., Forment, J., Ziarsolo, P., … Orzaez, D. (2013). GoldenBraid 2.0: A Comprehensive DNA Assembly Framework for Plant Synthetic Biology. PLANT PHYSIOLOGY, 162(3), 1618-1631. doi:10.1104/pp.113.217661

Orzaez, D., Medina, A., Torre, S., Fernández-Moreno, J. P., Rambla, J. L., Fernández-del-Carmen, A., … Granell, A. (2009). A Visual Reporter System for Virus-Induced Gene Silencing in Tomato Fruit Based on Anthocyanin Accumulation. Plant Physiology, 150(3), 1122-1134. doi:10.1104/pp.109.139006

Yoo, S.-D., Cho, Y.-H., & Sheen, J. (2007). Arabidopsis mesophyll protoplasts: a versatile cell system for transient gene expression analysis. Nature Protocols, 2(7), 1565-1572. doi:10.1038/nprot.2007.199

Schneider, C. A., Rasband, W. S., & Eliceiri, K. W. (2012). NIH Image to ImageJ: 25 years of image analysis. Nature Methods, 9(7), 671-675. doi:10.1038/nmeth.2089

Gutiérrez, S., Yvon, M., Thébaud, G., Monsion, B., Michalakis, Y., & Blanc, S. (2010). Dynamics of the Multiplicity of Cellular Infection in a Plant Virus. PLoS Pathogens, 6(9), e1001113. doi:10.1371/journal.ppat.1001113

Vazquez-Vilar, M., Sarrion-Perdigones, A., Ziarsolo, P., Blanca, J., Granell, A., & Orzaez, D. (2015). Software-Assisted Stacking of Gene Modules Using GoldenBraid 2.0 DNA-Assembly Framework. Plant Functional Genomics, 399-420. doi:10.1007/978-1-4939-2444-8_20

Vazquez-Vilar, M., Bernabé-Orts, J. M., Fernandez-del-Carmen, A., Ziarsolo, P., Blanca, J., Granell, A., & Orzaez, D. (2016). A modular toolbox for gRNA–Cas9 genome engineering in plants based on the GoldenBraid standard. Plant Methods, 12(1). doi:10.1186/s13007-016-0101-2

Quinn, J. Y., Cox, R. S., Adler, A., Beal, J., Bhatia, S., Cai, Y., … Sauro, H. M. (2015). SBOL Visual: A Graphical Language for Genetic Designs. PLOS Biology, 13(12), e1002310. doi:10.1371/journal.pbio.1002310

Thorpe, H. M., Wilson, S. E., & Smith, M. C. M. (2000). Control of directionality in the site-specific recombination system of the Streptomyces phage phiC31. Molecular Microbiology, 38(2), 232-241. doi:10.1046/j.1365-2958.2000.02142.x

Khaleel, T., Younger, E., McEwan, A. R., Varghese, A. S., & Smith, M. C. M. (2011). A phage protein that binds φC31 integrase to switch its directionality. Molecular Microbiology, 80(6), 1450-1463. doi:10.1111/j.1365-2958.2011.07696.x

Ort, D. R., Merchant, S. S., Alric, J., Barkan, A., Blankenship, R. E., Bock, R., … Zhu, X. G. (2015). Redesigning photosynthesis to sustainably meet global food and bioenergy demand. Proceedings of the National Academy of Sciences, 112(28), 8529-8536. doi:10.1073/pnas.1424031112

Smolke, C. D. (2009). Building outside of the box: iGEM and the BioBricks Foundation. Nature Biotechnology, 27(12), 1099-1102. doi:10.1038/nbt1209-1099

Cambray, G., Mutalik, V. K., & Arkin, A. P. (2011). Toward rational design of bacterial genomes. Current Opinion in Microbiology, 14(5), 624-630. doi:10.1016/j.mib.2011.08.001

Mutalik, V. K., Guimaraes, J. C., Cambray, G., Mai, Q.-A., Christoffersen, M. J., Martin, L., … Arkin, A. P. (2013). Quantitative estimation of activity and quality for collections of functional genetic elements. Nature Methods, 10(4), 347-353. doi:10.1038/nmeth.2403

Cambray, G., Guimaraes, J. C., Mutalik, V. K., Lam, C., Mai, Q.-A., Thimmaiah, T., … Endy, D. (2013). Measurement and modeling of intrinsic transcription terminators. Nucleic Acids Research, 41(9), 5139-5148. doi:10.1093/nar/gkt163

Mutalik, V. K., Guimaraes, J. C., Cambray, G., Lam, C., Christoffersen, M. J., Mai, Q.-A., … Endy, D. (2013). Precise and reliable gene expression via standard transcription and translation initiation elements. Nature Methods, 10(4), 354-360. doi:10.1038/nmeth.2404

Bartley, B., Beal, J., Clancy, K., Misirli, G., Roehner, N., Oberortner, E., … Sauro, H. (2015). Synthetic Biology Open Language (SBOL) Version 2.0.0. Journal of Integrative Bioinformatics, 12(2). doi:10.1515/jib-2015-272

Angov, E. (2011). Codon usage: Nature’s roadmap to expression and folding of proteins. Biotechnology Journal, 6(6), 650-659. doi:10.1002/biot.201000332

Hillson, N. J., Rosengarten, R. D., & Keasling, J. D. (2011). j5 DNA Assembly Design Automation Software. ACS Synthetic Biology, 1(1), 14-21. doi:10.1021/sb2000116

Brazma, A., Hingamp, P., Quackenbush, J., Sherlock, G., Spellman, P., Stoeckert, C., … Vingron, M. (2001). Minimum information about a microarray experiment (MIAME)—toward standards for microarray data. Nature Genetics, 29(4), 365-371. doi:10.1038/ng1201-365

Taylor, C. F., Paton, N. W., Lilley, K. S., Binz, P.-A., Julian, R. K., Jones, A. R., … Hermjakob, H. (2007). The minimum information about a proteomics experiment (MIAPE). Nature Biotechnology, 25(8), 887-893. doi:10.1038/nbt1329

Yang, Y., Li, R., & Qi, M. (2000). In vivo analysis of plant promoters and transcription factors by agroinfiltration of tobacco leaves. The Plant Journal, 22(6), 543-551. doi:10.1046/j.1365-313x.2000.00760.x

Kapila, J., De Rycke, R., Van Montagu, M., & Angenon, G. (1997). An Agrobacterium-mediated transient gene expression system for intact leaves. Plant Science, 122(1), 101-108. doi:10.1016/s0168-9452(96)04541-4

Schaumberg, K. A., Antunes, M. S., Kassaw, T. K., Xu, W., Zalewski, C. S., Medford, J. I., & Prasad, A. (2015). Quantitative characterization of genetic parts and circuits for plant synthetic biology. Nature Methods, 13(1), 94-100. doi:10.1038/nmeth.3659

Dafny-Yelin, M., & Tzfira, T. (2007). Delivery of Multiple Transgenes to Plant Cells. Plant Physiology, 145(4), 1118-1128. doi:10.1104/pp.107.106104

TZFIRA, T. (2004). Agrobacterium T-DNA integration: molecules and models. Trends in Genetics, 20(8), 375-383. doi:10.1016/j.tig.2004.06.004

De Buck, S., De Wilde, C., Van Montagu, M., & Depicker, A. (2000). Determination of the T-DNA Transfer and the T-DNA Integration Frequencies upon Cocultivation ofArabidopsis thalianaRoot Explants. Molecular Plant-Microbe Interactions, 13(6), 658-665. doi:10.1094/mpmi.2000.13.6.658

Konermann, S., Brigham, M. D., Trevino, A. E., Joung, J., Abudayyeh, O. O., Barcena, C., … Zhang, F. (2014). Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Nature, 517(7536), 583-588. doi:10.1038/nature14136

Gilbert, L. A., Horlbeck, M. A., Adamson, B., Villalta, J. E., Chen, Y., Whitehead, E. H., … Weissman, J. S. (2014). Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation. Cell, 159(3), 647-661. doi:10.1016/j.cell.2014.09.029

Moore, I., Samalova, M., & Kurup, S. (2006). Transactivated and chemically inducible gene expression in plants. The Plant Journal, 45(4), 651-683. doi:10.1111/j.1365-313x.2006.02660.x

Butelli, E., Titta, L., Giorgio, M., Mock, H.-P., Matros, A., Peterek, S., … Martin, C. (2008). Enrichment of tomato fruit with health-promoting anthocyanins by expression of select transcription factors. Nature Biotechnology, 26(11), 1301-1308. doi:10.1038/nbt.1506

Müller, K., Siegel, D., Rodriguez Jahnke, F., Gerrer, K., Wend, S., Decker, E. L., … Zurbriggen, M. D. (2014). A red light-controlled synthetic gene expression switch for plant systems. Mol. BioSyst., 10(7), 1679-1688. doi:10.1039/c3mb70579j

Davuluri, G. R., van Tuinen, A., Fraser, P. D., Manfredonia, A., Newman, R., Burgess, D., … Bowler, C. (2005). Fruit-specific RNAi-mediated suppression of DET1 enhances carotenoid and flavonoid content in tomatoes. Nature Biotechnology, 23(7), 890-895. doi:10.1038/nbt1108

Zhang, Y., Butelli, E., Alseekh, S., Tohge, T., Rallapalli, G., Luo, J., … Martin, C. (2015). Multi-level engineering facilitates the production of phenylpropanoid compounds in tomato. Nature Communications, 6(1). doi:10.1038/ncomms9635

Ori, N., Juarez, M. T., Jackson, D., Yamaguchi, J., Banowetz, G. M., & Hake, S. (1999). Leaf Senescence Is Delayed in Tobacco Plants Expressing the Maize Homeobox Gene knotted1 under the Control of a Senescence-Activated Promoter. The Plant Cell, 11(6), 1073-1080. doi:10.1105/tpc.11.6.1073

Azuma, M., Morimoto, R., Hirose, M., Morita, Y., Hoshino, A., Iida, S., … Shiratake, K. (2015). A petal‐specific In MYB 1 promoter from Japanese morning glory: a useful tool for molecular breeding of floricultural crops. Plant Biotechnology Journal, 14(1), 354-363. doi:10.1111/pbi.12389

Paine, J. A., Shipton, C. A., Chaggar, S., Howells, R. M., Kennedy, M. J., Vernon, G., … Drake, R. (2005). Improving the nutritional value of Golden Rice through increased pro-vitamin A content. Nature Biotechnology, 23(4), 482-487. doi:10.1038/nbt1082

Houmard, N. M., Mainville, J. L., Bonin, C. P., Huang, S., Luethy, M. H., & Malvar, T. M. (2007). High-lysine corn generated by endosperm-specific suppression of lysine catabolism using RNAi. Plant Biotechnology Journal, 5(5), 605-614. doi:10.1111/j.1467-7652.2007.00265.x

Padidam, M. (2003). Chemically regulated gene expression in plants. Current Opinion in Plant Biology, 6(2), 169-177. doi:10.1016/s1369-5266(03)00005-0

Kinkema, M., Geijskes, R. J., Shand, K., Coleman, H. D., De Lucca, P. C., Palupe, A., … Sainz, M. B. (2013). An improved chemically inducible gene switch that functions in the monocotyledonous plant sugar cane. Plant Molecular Biology, 84(4-5), 443-454. doi:10.1007/s11103-013-0140-2

[-]

This item appears in the following Collection(s)

Show full item record