Transcript PowerPoint Presentation - Genomics, Proteomics and

Genomics, Proteomics and
Metabolomics
Genomics
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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
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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
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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 development
Aharoni 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
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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 posttranslational modification
Proteomic scheme
Peltier et al. 2000 Plant Cell 12:319-341
2-D gel to separate proteins
Peltier et al. 2000 Plant Cell 12:319-341
Analysis of spots with Mass
Spectrometry
Peltier et al. 2000 Plant Cell 12:319-341
Metabolomics
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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
Roessner et al. 2001 Plant Cell 13:11-29
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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
Transgenic and environmental
influences on some metabolites
Roessner et al. 2001 Plant Cell 13:11-29
Bioinformatics
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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 Analysis
Roessner 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
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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