Unformatted text preview: Strains grown for 0 (red)
or 60 generations (green)
in minimal media Given a set of deletions for all genes in the genome, each can be
tested and phenotyped.
This is being done for budding yeast using a large number of
criteria. Since at present many genes do not display a phenotype
when disrupted and you can always add new selection criteria,
it is an on going analysis.
For whole set, 18.7% of genes are essential on rich yeast media.
The information is available for every gene as part of the SGD
information pages Fig. 2 from Winzeler et al (1999) When disrupting or deleting a gene by homologous
recombination a unique molecular tag (DNA sequence) can
be added to each locus.
locus kanamycinR plus barcode tags Example of real tag structure (Giaever et al., 2002) Elizabeth A.Winzeler, Daniel. D. Shoemaker, Anna Astromoff,
Hong Liang, et al. Functional Characterization of the
Saccharomyces cerevisiae Genome by Gene Deletion and
Parallel Analysis. Science. 285 : 901-906. (1999) Since each gene is uniquely tagged they can be mixed together,
put under some type of genetic selection and then analyzed by
microarray. Relative growth rates in rich vs minimal media for genes
On chromosome XIII
Fig. 3 from Winzeler et al. 1999 The complete deletion set has been tested by this means.
Whole genome parallel analysis (Giaever et al., 2002 Nature.
418:387-91) Used six conditions:
•Sorbitol Using highly sensitive comparison of 500 strains, 40% show
quantitative growth defects. •Galactose
•Nystatin 1 Growth rates under
selection Previous studies done on haploid strains. If one asks
the same sorts of questions regarding heterozygous
diploids then about 3% of genes generate a fitness
defect. (Giaever et al., 2005) Fig.2
Giaever et al, 2002 If you couple these results to
microarray expression data
from stressed populations.. Plots of levels under stress
vs. fitness defect under the
Fig. 4 from Giaever et al.,
2002 “We found that in galactose, less than 7% of the
genes that exhibited a significant increase in mRNA
expression also exhibited a significant decrease in
fitness. In the case of pH 8, 1 M NaCl and 1.5 M
sorbitol, 3.0%, 0.88% and 0.34%, respectively, of
the genes that exhibited a significant increase in
mRNA expression also exhibited a significant
decrease in fitness.” Giaever et al., 2002 2 ...
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