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Genomics, Proteomics and Metabolomics

Genomics, Proteomics and Metabolomics. Genomics. The complete set of DNA found in each cell is known as the genome Most crop plant genomes have billions of nucleotide bases Arabidopsis thaliana has 120 million bases that encode approximately 25,000 genes

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Genomics, Proteomics and Metabolomics

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  1. Genomics, Proteomics and Metabolomics

  2. Genomics • The complete set of DNA found in each cell is known as the genome • Most crop plant genomes have billions of nucleotide bases • Arabidopsis thaliana has 120 million bases that encode approximately 25,000 genes • The entire Arabidopsis genome was sequenced in 2000

  3. Other Plant Genomes are being sequenced • Large scale sequencing: rice, alfalfa • Grass ESTs: rice, maize, barley, wheat, millet, sorghum, forage grasses • Dicot ESTs: alfalfa, bean, beet, cassava, cotton, lettuce, potato, rapeseed, soybean, sunflower, tomato, ice plant • Tree ESTs: apple, cherry, pine, poplar

  4. Functional Genomics • Determining the role of genes through gene disruption (knockouts, underexpression and overexpression • Many genes have multiple copies

  5. cDNA microarray for global transcript analysis Seki et al. 2001 Plant Cell 13:61-72

  6. Strawberry flavor development Aharoni et al. 2000 Plant Cell 12:647-661

  7. Strawberry gene involved in flavor during ripening Aharoni et al. 2000 Plant Cell 12:647-661

  8. Proteomics • The complete set of proteins found in each cell is known as the proteome • Approximately 25,000 proteins in a plant cell • Proteins concentration (and activity) may be different than gene expression due to post-translational modification

  9. Proteomic scheme Peltier et al. 2000 Plant Cell 12:319-341

  10. 2-D gel to separate proteins Peltier et al. 2000 Plant Cell 12:319-341

  11. Analysis of spots with Mass Spectrometry Peltier et al. 2000 Plant Cell 12:319-341

  12. Metabolomics • The complete set of metabolites (5000 +) found in each cell is known as the metabolome • Use high-throughput mass spectrometry to analyze the metabolic components of the cell • Useful for determining the effects of the environment or gene transformation on the metabolism of the plant

  13. Transgenic and Environmental Effects on Potato Roessner et al. 2001 Plant Cell 13:11-29 • Able to measure 88 metabolites in one sample • Used different transgenic plants altered in sucrose metabolism • Able to distinguish individual genotypes based upon their metabolic profile

  14. Transgenic and environmental influences on some metabolites Roessner et al. 2001 Plant Cell 13:11-29

  15. Bioinformatics • The analysis of large volumes of genomic, proteomic and metabolomic data requiring sophisticated algorithms and powerful computers • Rapidly evolving field with an extreme shortage of skilled workers to write programs and analyze data

  16. Hierarchical Cluster Analysis Roessner et al. 2001 Plant Cell 13:11-29

  17. Principal Component Analysis(PCA) Roessner et al. 2001 Plant Cell 13:11-29

  18. PCA to identify which metabolites are most different Roessner et al. 2001 Plant Cell 13:11-29

  19. Conclusions • Genomics, proteomics and metabolomics will give an integrated, wholistic view of the cell • Can be used to monitor or modify organisms in a comprehensive way • Bioinformatics will be the key to understanding the plethora of information and modeling the cell

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