Published online 24 April 2008 | Nature | doi:10.1038/news.2008.776


Plant proteins mapped

New 'omics' tools fuel plant-biology research.

All about Arabidopsis: researchers have compiled several 'omic' databases.Punchstock

The first plant-wide catalogue of the proteins produced by by the weed Arabidopsis thaliana has yielded an inventory of more than 13,000 proteins.

Although researchers have investigated the 'proteome' of individual compartments within plant cells, such as chloroplasts, Sacha Baginsky and his colleagues are the first to tackle the proteome of an entire plant. “Our goal was to identify all proteins that are expressed in the genome,” says Baginsky, a plant biologist at the Swiss Federal Institute of Technology in Zurich.

The map captures proteins created in different plant organs and at various developmental stages — samples were taken from roots, leaves, flower buds and fully developed flowers, for example. The team estimates that they captured about half of the proteins thought to be made by the plant.

This draft version of the plant's proteome, published today in Science1, should help researchers to interpret the plant's genome. At present, computer models are used to determine which regions of the genome correspond to genes that encode proteins, and what proteins they produce. These predictions are useful, but not always accurate: 57 of the 13,000 proteins identified in the new sweep weren't predicted by models.

Whole lot of omics

Since the Arabidopsis genome was published in 2000, several other plants — including rice and, most recently, papaya (see Papaya genome project bears fruit) — have also been sequenced. But the diminutive weed Arabidopsis remains the most mature of the plant model systems.

Earlier this year, two labs sequenced the Arabidopsis epigenome: all the sequences in the genome that may be chemically modified by the addition of a methyl group, which can in turn affect gene expression2,3. Information about the transcriptome – all the RNA molecules, the intermediate between DNA and protein, produced by the genome – has also been steadily accumulating.

And more ‘omes’ are on the way: several research groups are busy cranking out the plant metabolome, a collection of all the metabolites produced by plants, as well as the plant interactome, the network of physical interactions between proteins.

The interplay of these ‘omic’ data sets promises to propel plant biology forwards into an era of quantitative modelling called systems biology, says Baginsky. “These tools really give you the systems level of understanding that is the ultimate goal,” he says.


Comprehensive approach

Steven Jacobsen, a plant biologist at the University of California, Los Angeles, adds that the growing set of Arabidopsis databases is speeding up the day-to-day work of classical genetics.

Researchers can now search a database to determine whether their gene of interest is methylated, for example, rather than carrying out the sometimes tricky experiments themselves. Jacobsen himself has used the transcriptome to help identify genes of interest in mutant Arabidopsis plants. The database, containing the results of 2,000 gene-expression experiments, revealed a gene variant that seemed to match their mutant's characteristics. “We thought ‘well that’s probably our gene’ and it was,” he says. 

  • References

    1. Baerenfaller, K. et al. Science doi:10.1126/science.1157956 (2008).
    2. Cokus, S. J. et al. Nature 452, 215-219 (2008). | Article | PubMed | ChemPort |
    3. Lister, R. et al. Cell doi:10.1016/j.cell.2008.03.029 (2008).
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