Information Technology Reference
In-Depth Information
In 1992 a European consortium led by a British scientist Steve Oliver sequenced the
first eukaryotic chromosome, chromosome III of the
S. cerevisiae
[31]. This led to the
creation of a world wide consortium which, under the leadership of a Belgian scientist
André Goffeau, succeeded in deciphering the entire genome of
S. cerevisiae
using a
structured, or ordered, approach [23]. The sequence of 12,068 kilobases defines 5,885
potential protein-encoding genes. Approximately 140 of these are ribosomal RNA, 40
genes encode small nuclear RNA molecules, while 275 are transfer RNA genes. In
addition, the complete sequence provides information about the higher order organisation
of the yeast's 16 chromosomes and allows some insight into their evolutionary history. The
major problem to be tackled with during the next stage of the yeast genome project is to
elucidate the biological functions of all these genes.
Having the sequence is one thing, but understanding it is quite another. From
approximately 6,200 genes of
S. cerevisiae
the function of one-third could be assigned from
either previous knowledge or because of a high degree of homology to genes of a known
function. Other third could not be unambiguously assigned but has features that at least
give some clues to their function. The most surprising discovery was that the last third of
genes was of totally unknown function, and was often called orphan genes. This has lead to
the world-wide effort to understand the function of all the genes in
S. cerevisiae
, that is
European Functional Analysis Network project - the EUROFAN - headed once again by
Steve Oliver. This project has grown again into an even bigger project, the so-called Yeast
Deletion Project. In one of the published report of the Yeast Deletion Project from five
years ago, genomic locations of 1,620 nonessential and 356 essential genes were presented.
The distribution of functional classes of essential and nonessential ORFs using the criteria
from the Munich information Centre for Protein Sequences was also shown [32].
Completion of the
S. cerevisiae
genome has opened an opportunity for developing
new approaches for the evaluation of small molecules and their interaction with living cells
in which yeast genome or proteome was used as the unit of function. The Miami conference
'Exploiting Yeast Molecular biology for Therapeutics', summarised by Charles Brenner, has
highlighted the latest developments in applied yeast technologies for drug discovery [33]. A
number of yeast genes and their corresponding products were identified by classical genetic
approaches that began with identification of mutant phenotype and progressed 'forward' to
the gene and the product. A number of other genes were discovered by 'reverse' genetic
approaches, in which mutants were obtained last. The original reverse genetic experiments
were fractionation-based; one purified a protein of interest, sequenced it partially, and then
cloned and disrupted the corresponding gene. More recently, reverse genetic approaches
have been driven by identification of homologous sequences. The availability of complete
genomic information has made possible a new type of reverse genetics based on a novel
fractionation schemes. These novel fractionation schemes allowed scientists to start asking
questions such as: given a substrate - find the enzyme, given an enzyme - validate it as a
drug target, given a target - find a drug, given a drug - find the target and given a
pathogenic fungus - find a drug target.
One of the examples of the application of functional genomics in the discovery of
novel drugs was the search for 'disinactivators' of human potassium channels. Inactivation
of such channels might be associated with sizes and hippocampal ischaemia. For that
reason, small molecules that block the association of specific ¬ and ß subunits were
considered to have therapeutic potential. Sequencing of human genome allowed the
identification of genes for ¬ and ß subunits of human potassium channels. The yeast two-
hybrid interaction system was constructed to produce growth inhibition, such that drugs
that block the interaction restore growth. The new screen for potassium channel
disinactivators involved more than 170,000 compounds and has apparently identified a
