Trends in Biotechnology
Systematic functional analysis of the yeast genome
Section snippets
Generation of specific deletion mutants
In order to determine the function of novel yeast genes using a systematic and hierarchical approach, a large European research network called EUROFAN (European functional analysis network) has been established[7]; parallel activities are also under way in Canada, Japan and the USA. The first aim of these projects is the production of a complete set of 6000 single-gene deletion mutants covering all the open reading-frames (ORFs) revealed by the complete S. cerevisiae genome sequence. Such a
The transcriptome
The quantitative analysis of expression levels of a novel gene under a variety of physiological or developmental conditions is a powerful tool in the elucidation of gene function, when compared with the expression patterns of functionally characterized genes. One approach to the efficient analysis of gene expression on a genome-wide scale is the use of SAGE (serial analysis of gene expression) technology[13], which was employed by Velculescu and co-workers[14]to determine the complete set of
The proteome
Another route to the elucidation of gene function is the analysis of all yeast proteins synthesized under a given set of conditions, the so-called proteome[20]. The yeast proteome is being defined by two-dimensional gel electrophoresis[21]using mass spectrometry to identify the proteins within the spots on the gel22, 23. By taking full advantage of the complete genome sequence, it should be possible to determine a single protein fragment of unique mass in order to identify a yeast protein. The
Quantitative phenotypic analysis
One reason for taking a quantitative approach to the analysis of gene function is that there is a growing number of genes found by systematic genome sequencing projects that have homologues of unknown function in a number of species but that had not been discovered by classical molecular genetics. It is possible that these genes have been missed because quantitative, rather than qualitative, data are required to reveal their phenotypic effect. Another reason to consider a quantitative approach
The metabolome
The second type of data required for the MCA approach is the measurement of the change in the relative concentrations of metabolites as the result of the deletion or overexpression of a gene. In contrast to the determination of flux-control coefficients, where very sensitive and discriminatory analytical tools are required, the determination of effective metabolite-concentration-control coefficients requires analyses that are very comprehensive in their scope, because (for any particular novel
Conclusion
It is evident that a wide range of experimental approaches are being developed for use in S. cerevisiae that will allow functional genomics to build up an integrative view of the workings of a simple eukaryotic cell. This should enable a deeper understanding of more-complex eukaryotes, both by the identification of orthologous genes in the different species and also by the expression of foreign coding sequences in yeast for complementation or two-hybrid analyses. However, many of these
Acknowledgements
Work on yeast genome analysis in SGO's laboratory has been supported by the European Commission (in both the Yeast Genome Sequencing Network and EUROFAN), the BBSRC, the Wellcome Trust, Pfizer Central Research, Applied Biosystems, Amersham International and Zeneca. FB is grateful to Pfizer Central Research for the provision of a postgraduate research studentship. Work on the analysis of metabolism in DBK's laboratory is supported by the BBSRC, GlaxoWellcome and Bruker.
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