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Reversing Babel with GO Already Been Identified news & views Fauchon et al.2 could also be interpreted to taining pyruvate decarboxylase isoen- induction of these proteins. As with all suggest that these other stresses do not zymes, whereas non–plant-living yeasts good studies, the report by Fauchon et require such a drastic increase in glu- such as Candida albicans do not. With al.2 has provided us with many questions tathione levels for cell survival, pointing to a the availability of various microbial and and avenues for future research. pivotal role for glutathione in mediating other genome sequences, it should be 1. Avery, S.V. Adv. App. Microbiol. 49, 111–142 (2001). resistance to cadmium. possible to determine how general this 2. Fauchon, M. et al. Mol. Cell 9, 713–723 (2002). How general is this response? Does the response is. In particular, it would be 3. Westwater, J., McLaren, N.F., Dormer, U.H. & Jamieson, D.J. Yeast 19, 233–239 (2002). cadmium response occur in other yeast, interesting to focus on plant pathogens. 4. Jamieson, D.J.Yeast 14, 1511–1527. and more importantly in higher eukary- Equally intriguing is the finding that reg- 5. Wemmie, J.A., Szczypka, M.S., Thiele, D.J. & Moye- 2 Rowley, W.S. J. Biol. Chem. 269, 32592–32597 (1994). otes? Fauchon et al. suggest that the cad- ulation of the cadmium response by 6. Vido, K. et al. J. Biol. Chem. 276, 8469–8474 (2001). mium response could have evolved as a Met4p is not the whole story. It turns out 7. Meister, A. & Anderson, M.E. Annu. Rev. Biochem. strategy for protecting against toxic levels that many proteins, particularly those 52, 711–760 (1983). 8. Stephen, D.W. & Jamieson, D.J. Mol. Microbiol. 23, of heavy metals accumulated by the that are less abundant in the cell, are cad- 203–210 (1997). plants that yeast live on. They go on to mium-inducible in a Met4p-indepen- 9. Dormer, U.H. et al. J. Biol. Chem. 275, 32611–32616 (2000). point out that other plant-living yeasts, dent manner. It will be especially 10. Elskens, M.T., Jaspers, C.J. & Penninckx, M.J. J. Gen. such as Schizosaccharomyces pombe and interesting to examine in detail the fac- Microbiol. 137, 637–644 (1991). Pichia stipitis, possess low-sulfur-con- tors required for the cadmium-mediated 11. Grant, C.M., MacIver, F.H. & Dawes, I.W. Curr. Genet. 29, 511–515 (1996). which disease-causing mutations had Reversing Babel with GO already been identified. In 55 of the cases, the disease-related gene was iden- The Gene Ontology project allows biologists to share knowledge; a new study tified. As the authors point out, the demonstrates that GO terms can aid in the identification of candidate ‘disease’ genes. data-mining system is highly dependent on the information that is being mined. An untruth sometimes said about scien- And the Lord said, Thus, continued improvements in GO tists is that they lack artistic creativity. “Behold, they are one people, and they and its increased integration in data- As any reader of Nature Genetics can have all one language; and this is only the begin- bases will enhance the authors’ attest, scientific papers are rife with ning of what they will do; and nothing that they pro- data-mining system (available on creative language describing experi- pose to do will now be impossible for them. Come, let us the Genes2Disease website). mental data, natural phenomena go down, and there confuse their language, that they The efforts of the GO consortium and interpretation. So it’s likely that a may not understand one another’s speech.” are helping to lead us beyond a Babel- © http://genetics.nature.com Group 2002 Nature Publishing not a few biologists grumbled when the Genesis 11 like period and unify the field. And the Gene Ontology (GO) consortium tool reported by Perez-Iratxeta and col- announced its efforts to design a common leagues2 suggests that speaking the same language for describing the functions of terms are consistent, they are not com- language will have unexpected benefits. genes across organisms; a tool, it was plete, thereby allowing a dynamic vocab- —David Gresham claimed, that would serve to unify biol- ulary that evolves within the constraints 1. The Gene Ontology Consortium. Nature Genet. 25, 1 ogy . Some two years later, GO is begin- of the ontology. The consortium initially 25–29 (2000). 2. Perez-Iratxeta, C., Bork, P. & Andrade, M.A. Nature ning to realize its lofty goal and, included FlyBase, Mouse Genome Infor- Genet. 31, 316–319 (2002). moreover, it is being applied in unantici- matics and Saccaromyces Genome Data- 3. Gruber, T.R. Knowl. Acq. 5, 199–220 (1993). 4. Ashburner, M. et al. Genome Res. 11, 1425–1433 pated ways. The tool described by Car- base, but has subsequently grown to (2001). olina Perez-Iratxeta and colleagues2 on include the Arabidopsis Information page 316 is one such example. Resource, WormBase, PomBase, the Rat An ontology defines a controlled, con- Genome Database and DictyBase among sistent vocabulary to describe concepts others, which are now united by the use and relationships, thereby enabling of a single shared vocabulary4. knowledge-sharing3. The GO consor- Perez-Iratxeta and colleagues2 report tium was inspired by the recognition of a an approach in which they produce a bottleneck in the transfer of information score that links the functional annota- between those studying different model tion of proteins described using GO GO organisms, owing to the absence of a terms with the description of an inher- NG02 shared vocabulary4. To circumvent this ited disease using medical subject head- problem, they commenced development ing (MeSH; the National Library of of three ontologies applicable to all Science’s controlled vocabulary). Link- eukaryotes: the biological process in ing this score to information from Ref- I GENES which the gene product participates, the Seq yielded a list of most likely candidate molecular function of the gene product genes for 455 mapped diseases of and the cellular component within which unknown genetic defect. As a blind test, the gene product acts. Although GO the authors looked at 100 genes for Katie Ris 230 nature genetics • volume 31 • july 2002.
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