Genomics, Proteomics and Metabolomics

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

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

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

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

Strawberry flavor development Aharoni et al Plant Cell 12:

Strawberry gene involved in flavor during ripening Aharoni et al Plant Cell 12:

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

Proteomic scheme Peltier et al Plant Cell 12:

2-D gel to separate proteins Peltier et al Plant Cell 12:

Analysis of spots with Mass Spectrometry Peltier et al Plant Cell 12:

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

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

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

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

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

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

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

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