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Fine-tuning tomato agronomic properties by computational genome redesign

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Fine-tuning tomato agronomic properties by computational genome redesign

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Carrera Montesinos, J.; Fernández Del Carmen, MA.; Fernández Muñoz, R.; Rambla Nebot, JL.; Pons Puig, C.; Jaramillo Rosales, A.; Elena Fito, SF.... (2012). Fine-tuning tomato agronomic properties by computational genome redesign. PLoS Computational Biology. 8(6):1002528-1002528. https://doi.org/10.1371/journal.pcbi.1002528

Por favor, use este identificador para citar o enlazar este ítem: http://hdl.handle.net/10251/59169

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Título: Fine-tuning tomato agronomic properties by computational genome redesign
Autor: Carrera Montesinos, Javier Fernández Del Carmen, María Asunción Fernández Muñoz, Rafael Rambla Nebot, Jose Luis Pons Puig, Clara Jaramillo Rosales, Alfonso Elena Fito, Santiago Fco Granell Richart, Antonio
Entidad UPV: 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
Fecha difusión:
Resumen:
[EN] 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 ...[+]
Palabras clave: Lean manufacturing , Transcriptomic data , Metabolomic data , Phenomic data
Derechos de uso: Reserva de todos los derechos
Fuente:
PLoS Computational Biology. (issn: 1553-734X ) (eissn: 1553-7358 )
DOI: 10.1371/journal.pcbi.1002528
Editorial:
Public Library of Science
Versión del editor: http://dx.doi.org/10.1371/journal.pcbi.1002528
Código del Proyecto:
info:eu-repo/grantAgreement/EC/FP7/043338/EU/
info:eu-repo/grantAgreement/MEC//TIN2006-12860/
info:eu-repo/grantAgreement/EC/FP7/265505/EU/Paving the Way for Future Emerging DNA-based Technologies: Computer-Aided Design and Manufacturing of DNA libraries/
info:eu-repo/grantAgreement/EC/FP6/16214/EU/High Quality Solanaceous Crops for Consumers, Processors and Producers by Exploration of Natural Biodiversity/EU-SOL/
info:eu-repo/grantAgreement/MICINN//BFU2009-06993/ES/Biologia Evolutiva Y De Sistemas De La Emergencia De Fitovirus De Rna/
Agradecimientos:
This work was supported by grant TIN2006-12860 from the Spanish Ministerio de Ciencia e Innovacion), the Structural Funds of the European Regional Development Fund (ERDF), FP7-ICT-043338 (BACTOCOM), the FP7-ICT-265505 ...[+]
Tipo: Artículo

References

Endy, D. (2005). Foundations for engineering biology. Nature, 438(7067), 449-453. doi:10.1038/nature04342

Knight, T. F. (2005). Engineering novel life. Molecular Systems Biology, 1(1). doi:10.1038/msb4100028

Andrianantoandro, E., Basu, S., Karig, D. K., & Weiss, R. (2006). Synthetic biology: new engineering rules for an emerging discipline. Molecular Systems Biology, 2(1). doi:10.1038/msb4100073 [+]
Endy, D. (2005). Foundations for engineering biology. Nature, 438(7067), 449-453. doi:10.1038/nature04342

Knight, T. F. (2005). Engineering novel life. Molecular Systems Biology, 1(1). doi:10.1038/msb4100028

Andrianantoandro, E., Basu, S., Karig, D. K., & Weiss, R. (2006). Synthetic biology: new engineering rules for an emerging discipline. Molecular Systems Biology, 2(1). doi:10.1038/msb4100073

Feist, A. M., Herrgård, M. J., Thiele, I., Reed, J. L., & Palsson, B. Ø. (2008). Reconstruction of biochemical networks in microorganisms. Nature Reviews Microbiology, 7(2), 129-143. doi:10.1038/nrmicro1949

Di Bernardo, D., Thompson, M. J., Gardner, T. S., Chobot, S. E., Eastwood, E. L., Wojtovich, A. P., … Collins, J. J. (2005). Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks. Nature Biotechnology, 23(3), 377-383. doi:10.1038/nbt1075

Carrera, J., Rodrigo, G., & Jaramillo, A. (2009). Model-based redesign of global transcription regulation. Nucleic Acids Research, 37(5), e38-e38. doi:10.1093/nar/gkp022

Carrera, J., Rodrigo, G., Jaramillo, A., & Elena, S. F. (2009). Reverse-engineering the Arabidopsis thaliana transcriptional network under changing environmental conditions. Genome Biology, 10(9), R96. doi:10.1186/gb-2009-10-9-r96

Faith, J. J., Hayete, B., Thaden, J. T., Mogno, I., Wierzbowski, J., Cottarel, G., … Gardner, T. S. (2007). Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles. PLoS Biology, 5(1), e8. doi:10.1371/journal.pbio.0050008

Bonneau, R., Facciotti, M. T., Reiss, D. J., Schmid, A. K., Pan, M., Kaur, A., … Baliga, N. S. (2007). A Predictive Model for Transcriptional Control of Physiology in a Free Living Cell. Cell, 131(7), 1354-1365. doi:10.1016/j.cell.2007.10.053

Tagkopoulos, I., Liu, Y.-C., & Tavazoie, S. (2008). Predictive Behavior Within Microbial Genetic Networks. Science, 320(5881), 1313-1317. doi:10.1126/science.1154456

Covert, M. W., Knight, E. M., Reed, J. L., Herrgard, M. J., & Palsson, B. O. (2004). Integrating high-throughput and computational data elucidates bacterial networks. Nature, 429(6987), 92-96. doi:10.1038/nature02456

Endy, D., & Brent, R. (2001). Modelling cellular behaviour. Nature, 409(6818), 391-395. doi:10.1038/35053181

Joyce, A. R., & Palsson, B. Ø. (2006). The model organism as a system: integrating «omics» data sets. Nature Reviews Molecular Cell Biology, 7(3), 198-210. doi:10.1038/nrm1857

Burgard, A. P., Pharkya, P., & Maranas, C. D. (2003). Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnology and Bioengineering, 84(6), 647-657. doi:10.1002/bit.10803

Segre, D., Vitkup, D., & Church, G. M. (2002). Analysis of optimality in natural and perturbed metabolic networks. Proceedings of the National Academy of Sciences, 99(23), 15112-15117. doi:10.1073/pnas.232349399

Rocha, M., Maia, P., Mendes, R., Pinto, J. P., Ferreira, E. C., Nielsen, J., … Rocha, I. (2008). Natural computation meta-heuristics for the in silico optimization of microbial strains. BMC Bioinformatics, 9(1). doi:10.1186/1471-2105-9-499

Meyer, R. C., Steinfath, M., Lisec, J., Becher, M., Witucka-Wall, H., Torjek, O., … Altmann, T. (2007). The metabolic signature related to high plant growth rate in Arabidopsis thaliana. Proceedings of the National Academy of Sciences, 104(11), 4759-4764. doi:10.1073/pnas.0609709104

Mounet, F., Moing, A., Garcia, V., Petit, J., Maucourt, M., Deborde, C., … Lemaire-Chamley, M. (2009). Gene and Metabolite Regulatory Network Analysis of Early Developing Fruit Tissues Highlights New Candidate Genes for the Control of Tomato Fruit Composition and Development. Plant Physiology, 149(3), 1505-1528. doi:10.1104/pp.108.133967

Garcia, V., Stevens, R., Gil, L., Gilbert, L., Gest, N., Petit, J., … Rothan, C. (2009). An integrative genomics approach for deciphering the complex interactions between ascorbate metabolism and fruit growth and composition in tomato. Comptes Rendus Biologies, 332(11), 1007-1021. doi:10.1016/j.crvi.2009.09.013

Schauer, N., Semel, Y., Roessner, U., Gur, A., Balbo, I., Carrari, F., … Fernie, A. R. (2006). Comprehensive metabolic profiling and phenotyping of interspecific introgression lines for tomato improvement. Nature Biotechnology, 24(4), 447-454. doi:10.1038/nbt1192

Osorio, S., Alba, R., Damasceno, C. M. B., Lopez-Casado, G., Lohse, M., Zanor, M. I., … Fernie, A. R. (2011). Systems Biology of Tomato Fruit Development: Combined Transcript, Protein, and Metabolite Analysis of Tomato Transcription Factor (nor, rin) and Ethylene Receptor (Nr) Mutants Reveals Novel Regulatory Interactions. Plant Physiology, 157(1), 405-425. doi:10.1104/pp.111.175463

Rohrmann, J., Tohge, T., Alba, R., Osorio, S., Caldana, C., McQuinn, R., … Fernie, A. R. (2011). Combined transcription factor profiling, microarray analysis and metabolite profiling reveals the transcriptional control of metabolic shifts occurring during tomato fruit development. The Plant Journal, 68(6), 999-1013. doi:10.1111/j.1365-313x.2011.04750.x

Sabeti, P. C., Varilly, P., Fry, B., Lohmueller, J., Hostetter, E., … Lander, E. S. (2007). Genome-wide detection and characterization of positive selection in human populations. Nature, 449(7164), 913-918. doi:10.1038/nature06250

Daetwyler, H. D., Villanueva, B., Bijma, P., & Woolliams, J. A. (2007). Inbreeding in genome-wide selection. Journal of Animal Breeding and Genetics, 124(6), 369-376. doi:10.1111/j.1439-0388.2007.00693.x

Martin-Magniette, M.-L., Aubert, J., Bar-Hen, A., Elftieh, S., Magniette, F., Renou, J.-P., & Daudin, J.-J. (2008). Normalization for triple-target microarray experiments. BMC Bioinformatics, 9(1). doi:10.1186/1471-2105-9-216

Riedelsheimer, C., Czedik-Eysenberg, A., Grieder, C., Lisec, J., Technow, F., Sulpice, R., … Melchinger, A. E. (2012). Genomic and metabolic prediction of complex heterotic traits in hybrid maize. Nature Genetics, 44(2), 217-220. doi:10.1038/ng.1033

Shah, R., & Ward, P. T. (2002). Lean manufacturing: context, practice bundles, and performance. Journal of Operations Management, 21(2), 129-149. doi:10.1016/s0272-6963(02)00108-0

Rosati, C., Diretto, G., & Giuliano, G. (2009). Biosynthesis and Engineering of Carotenoids and Apocarotenoids in Plants: State of the Art and Future Prospects. Biotechnology and Genetic Engineering Reviews, 26(1), 139-162. doi:10.5661/bger-26-139

E., F., Y., L., L., C.-G., A., G., M., S., T., P., … D., Z. (2002). Two tightly linked QTLs modify tomato sugar content via different physiological pathways. Molecular Genetics and Genomics, 266(5), 821-826. doi:10.1007/s00438-001-0599-4

Cong, B., Barrero, L. S., & Tanksley, S. D. (2008). Regulatory change in YABBY-like transcription factor led to evolution of extreme fruit size during tomato domestication. Nature Genetics, 40(6), 800-804. doi:10.1038/ng.144

Wang, H., Schauer, N., Usadel, B., Frasse, P., Zouine, M., Hernould, M., … Bouzayen, M. (2009). Regulatory Features Underlying Pollination-Dependent and -Independent Tomato Fruit Set Revealed by Transcript and Primary Metabolite Profiling. The Plant Cell, 21(5), 1428-1452. doi:10.1105/tpc.108.060830

Klee, H. J. (2010). Improving the flavor of fresh fruits: genomics, biochemistry, and biotechnology. New Phytologist, 187(1), 44-56. doi:10.1111/j.1469-8137.2010.03281.x

Minoia, S., Petrozza, A., D’Onofrio, O., Piron, F., Mosca, G., Sozio, G., … Carriero, F. (2010). A new mutant genetic resource for tomato crop improvement by TILLING technology. BMC Research Notes, 3(1). doi:10.1186/1756-0500-3-69

Bogdanove, A. J., & Voytas, D. F. (2011). TAL Effectors: Customizable Proteins for DNA Targeting. Science, 333(6051), 1843-1846. doi:10.1126/science.1204094

Hetherington, S. E., Smillie, R. M., & Davies, W. J. (1998). Photosynthetic activities of vegetative and fruiting tissues of tomato. Journal of Experimental Botany, 49(324), 1173-1181. doi:10.1093/jxb/49.324.1173

Fridman, E. (2004). Zooming In on a Quantitative Trait for Tomato Yield Using Interspecific Introgressions. Science, 305(5691), 1786-1789. doi:10.1126/science.1101666

Agius, F., González-Lamothe, R., Caballero, J. L., Muñoz-Blanco, J., Botella, M. A., & Valpuesta, V. (2003). Engineering increased vitamin C levels in plants by overexpression of a D-galacturonic acid reductase. Nature Biotechnology, 21(2), 177-181. doi:10.1038/nbt777

Cahoon, E. B., Hall, S. E., Ripp, K. G., Ganzke, T. S., Hitz, W. D., & Coughlan, S. J. (2003). Metabolic redesign of vitamin E biosynthesis in plants for tocotrienol production and increased antioxidant content. Nature Biotechnology, 21(9), 1082-1087. doi:10.1038/nbt853

Ye, X. (2000). Engineering the Provitamin A (-Carotene) Biosynthetic Pathway into (Carotenoid-Free) Rice Endosperm. Science, 287(5451), 303-305. doi:10.1126/science.287.5451.303

Aharoni, A., & Galili, G. (2011). Metabolic engineering of the plant primary–secondary metabolism interface. Current Opinion in Biotechnology, 22(2), 239-244. doi:10.1016/j.copbio.2010.11.004

Alba, J. M., Montserrat, M., & Fernández-Muñoz, R. (2008). Resistance to the two-spotted spider mite (Tetranychus urticae) by acylsucroses of wild tomato (Solanum pimpinellifolium) trichomes studied in a recombinant inbred line population. Experimental and Applied Acarology, 47(1), 35-47. doi:10.1007/s10493-008-9192-4

Zanor, M. I., Rambla, J.-L., Chaïb, J., Steppa, A., Medina, A., Granell, A., … Causse, M. (2009). Metabolic characterization of loci affecting sensory attributes in tomato allows an assessment of the influence of the levels of primary metabolites and volatile organic contents. Journal of Experimental Botany, 60(7), 2139-2154. doi:10.1093/jxb/erp086

Lytovchenko, A., Eickmeier, I., Pons, C., Osorio, S., Szecowka, M., Lehmberg, K., … Fernie, A. R. (2011). Tomato Fruit Photosynthesis Is Seemingly Unimportant in Primary Metabolism and Ripening But Plays a Considerable Role in Seed Development. Plant Physiology, 157(4), 1650-1663. doi:10.1104/pp.111.186874

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