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Systems Analysis of Plant Metabolism through the Integration of Heterogeneous Data from Genetics, Informatics and Metabolomics

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Mechanisms behind regulation of plant metabolism

Genes and proteins involved in regulating metabolic pathways in tomato plants have been investigated by EU-funded plant biologists.


The networks of genes and proteins that coordinate the activity of metabolic pathways during plant development and stress response have been unravelled with the help of the SAMIT (Systems analysis of plant metabolism through the integration of heterogeneous data from genetics, informatics and metabolomics) project. Researchers first established the analytical tools required for comprehensive non-targeted assays of metabolites based on mass-spectrometry. In addition, a population of tomato mutant lines was generated that included a large number of dominant mutants. This mutant library was used for the identification of key components regulating metabolic pathways in plants. The population was screened for novel mutants and genes associated with the project’s research interests. Visual screening, high-throughput assays and non-targeted metabolite analysis were used to screen different metabolites using liquid chromatography - mass spectrometry (LC-MS). Screening was also conducted using a reverse genetic approach (from sequence to mutant) through the display of transposons, the DNA sequences that can change position within the genome thereby creating or reversing mutations. Data obtained from metabolome and transcriptome analyses was found to be the most useful for gene discovery during the project. For example, it was discovered that the entire biosynthetic pathway of anti-nutritional components in potatoes and other Solanacea species, which include tomatoes was composed of ten genes. SAMIT provided new knowledge on the genetic control of metabolic pathways, which was previously very limited. It successfully integrated genetic, gene expression, protein interaction and metabolic data to give greater insight into plant regulatory networks and their control of plant metabolism.


SAMIT, metabolic pathway, stress response, metabolites, liquid chromatography - mass spectrometry, transposon, metabolome, transcriptome

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