A Systems Biology Approach to the Elucidation of Metabolic Networks Underlying Health Based Quality Traits in Tomato Fruit.

Lead Research Organisation: University of Nottingham
Department Name: Sch of Biosciences


'We are what we eat' is a phrase that has been used for many years to describe the importance of good dietary components. Although this may not be strictly true, it has been shown that diets rich in fruits and vegetables are beneficial to human well-being and health. The beneficial effects of fruits and vegetables have been attributed to the synergistic effects of various phytochemicals present. Many of these compounds like carotenoids, vitamins E and C, as well as flavonoids and phenylpropanoids are potent antioxidants, with the ability to dissipate damaging reactive molecules produced by the body's metabolism. Tomato fruit are a major dietary source of important antioxidants such as carotenoids (especially the red-coloured lycopene of ripe fruit). The consumers demands for improved aesthetic and nutritional quality has lead to increased efforts to increase the levels of these compounds in crop plants. Recently tomato varieties have been produced that contain high levels of multiple antioxidants. These varieties were produced by manipulating the plants ability to perceive light, in this instance GM technology was used. Although this technology is not acceptable presently to the consumer the plants do provide a valuable research tool to study the underlying events leading to nutritional enhancement in crop plants such as tomato. In the present proposal we aim to use modern techniques to determine the chemical composition and genes expressed in these tomato varieties as their fruit develops and ripens. A mathematical approach will then be used to collate, integrate and decipher the information. The collective data will reveal the interaction between the genes and metabolites in these tomato varieties from which a dynamic model can be constructed. This approach is termed a systems approach because it does not look at specific molecule entities but how they interact in a cell. The dynamic models showing the genes and molecules interacting will enable us to determine cascades of events occurring in the cell from which putative master regulators can be identified. These regulators will be tested by transient expression in the tomato fruit cells to see if they can elevate health related phytochemical in tomato fruit. The knowledge acquired will enable show to apply modern non-GM plant breeding techniques to produce improved tomato varieties that are nutrient rich and more beneficial to human health.

Technical Summary

Diets rich in fruits and vegetables are beneficial to human well-being and health. These health promoting properties have been attributed to the synergistic effects of various phytochemicals, such as carotenoids, vitamins E and C, flavonoids and phenylpropanoids. Todays consumer demands improved nutritional quality and several strategies have been employed to create nutrient-rich foods. Ripe tomato fruit contain significant basal levels of several health promoting phytochemicals. Recently the manipulation in tomato of a signal transduction component involved in light perception, namely De /Etiolated-1 (DET-1) has lead to tomato varieties with unparalleled simultaneous elevation of multiple classes of health-related compounds. This experimental system will form the basis of the proposed project. Using a developmental and ripening series of tomato fruits derived from RNAi-suppressed DET-1, transcriptomic and metabolomic analyses have been performed. A systems biology approach will be used to integrate and de-convolute these datasets, elucidating gene to gene, metabolite to metabolite, gene to metabolite, as well as gene/metabolite to cellular properties and phenotype correlations. Time Series Network Inference (TSNI) and Bayesian approaches will be employed to decipher the cascade of molecular and metabolic events that leads to these important chemotypes. Collectively these data will enable the identification of putative regulatory and biosynthetic genes that contribute to DET-1 chemotypes/phenoypes. Functional testing of these putative regulators and their role in the networks predicted will be carried out using Virus VIGS and TILLING approaches to down regulate the target genes, or Agrobacterium infiltration to over-express gene products. The datasets derived from functional testing will be analysed to refine and extend our predictive models of the networks underlying health based traits conferred by DET-1 down regulation.


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Description This was a relatively small part of a larger project BB/F005644/1 led from RHUL by Professor Peter Bramley at RHUL. The Nottingham co-PIs contributed 12 PDRA months. The PDRA then spent another two years on a complementary ESB-LINK award BB/F005458 PI Professor Charlie Hodgman.
The main outputs of this 1 year project were
1) Inferred networks hypothesised 2 transcription factors (TFs) with overarching control of aspects of secondary metabolism. On subsequent laboratory testing in the TFs had lethal phenotypes owing to hyper-accumulation of secondary metabolites in callus in tissue culture. Other transgenics generated at the same time including vector-only controls did not show this phenotype. Further work using a fruit specific promoter produced viable transgenic plants from modulation of expression of one of the TFs and these had enhanced levels of important secondary metabolites in the fruits. Homozygous lines are being generated and this material will then be fully characterised and the work submitted for publication in collaboration with the RHUL team.
2) Refined mathematical models of the effect of DET1 on chromatin structure and consequent effects upon gene regulation of metabolite levels have been constructed. These will be used to predict further key regulatory components of secondary metabolism.
Exploitation Route The PDRA contributed to a patent application WO2012041856 and a paper published in Plant Physiology (Pan et al, 2013). We expect to submit for publication a new fruit ripening network and network viewer to which this award contributed along with BB/F005458
Sectors Agriculture, Food and Drink

Description Interaction on map-based cloning of ripening genes and the mechanistic basis of fruit ripening 
Organisation Cornell University
Country United States 
Sector Academic/University 
PI Contribution Sharing of data and ideas relating to the mechanisms controlling fruit ripening
Collaborator Contribution Provision of ideas and resources including access to data. This has resulted in a number of important papers and the collaboration has helped to formulate the now accepted model for the biological basis of fruit ripening
Impact The Tomato Genome Consortium (including Seymour GB) (2012).The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635-641 Seymour GB, Ryder CD, Cevik V, Hammond JP, Popovich A, King GJ, Vrebalov J, Giovannoni JJ and Manning K (2011). A SEPALLATA gene is involved in the development and ripening of strawberry (Fragaria × ananassa Duch.) fruit, a non-climacteric tissue. J. Exp. Bot: 62, 1179-1188. Vrebalov, J., Pan, I.L., Matas Arroyo., A.J., McQuinn, R., Chung, M-Y., Poole, M., Rose, J., Seymour, G., Grandillo, S., Giovannoni, J., Irish, V.F. (2009) Freshy fruit expansion and ripening are regulated by the tomato SHATTERPROOF gene TAGL1. Plant Cell 21 3041-3062. Manning K., Tor, M., Poole M., Hong, Y.,Thompson, A.J., King G., Giovannoni, J. and Seymour, G.B. (2006). A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening. Nature Genetics, 38: 948-952.
Description The present invention relates to a transcription factor gene that plays a key role in Solanaceae fruit ripening. Plants overexpressing the gene have fruits with deeper pigmentation and ripen more rapidly than controls. The invention also relates to transgenic plants comprising said gene, and methods of making said plants. 
IP Reference WO2012041856 
Protection Patent application published
Year Protection Granted 2012
Licensed Yes
Impact Enhancing colour and health promoting phytochemicals in fruit crops. The application will directly impact tomato and pepper breeding
Description Public Lecture, University of Nottingham 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact Public lecture, entitled "Genetic secrets of the tomato",

knowledge transfer
Year(s) Of Engagement Activity 2008
Description Systems Biology Showcase at Nottingham 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Hodgman led and Seymour contributed to a Systems Biology showcase (Sep 2010) which included visitors from major agri-food companies.

Support for future grant applications from industry partners
Year(s) Of Engagement Activity 2010