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 The entire Arabidopsis genome was sequenced in

2000

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

Functional Genomics

Determining the role of genes through gene disruption (knockouts, underexpression and overexpression

Many genes have multiple copies

cDNA microarray for global transcript analysis

Seki et al. 2001 Plant Cell 13:61-72

Strawberry flavor developmentAharoni et al. 2000 Plant Cell 12:647-661

Strawberry gene involved in flavor during ripening

Aharoni et al. 2000 Plant Cell 12:647-661

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

Proteomic schemePeltier et al. 2000 Plant Cell 12:319-341

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

Analysis of spots with Mass Spectrometry

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

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

Transgenic and Environmental Effects on Potato

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

Roessner et al. 2001 Plant Cell 13:11-29

Transgenic and environmental influences on some metabolites

Roessner et al. 2001 Plant Cell 13:11-29

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

Hierarchical Cluster AnalysisRoessner et al. 2001 Plant Cell 13:11-29

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

PCA to identify which metabolites are most different

Roessner et al. 2001 Plant Cell 13:11-29

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