E-TABM-892 - Transcription profiling of yeast mutant at fast growth rates

Status
Released on 1 December 2010, last updated on 2 May 2014
Organism
Saccharomyces cerevisiae
Samples (52)
Arrays (2)
Protocols (7)
Description
Our approach for the identification and quantification of growth control by the components of yeast cells relies on two complementary screens: In the first, growth rate is changed and the effect on the concentration of cell components is measured (Castrillo et al. 2007, Genome Biology, 6,4). In the second, the concentration of the components is changed (by reducing gene copy number) and the effect on growth rate is measured (Delneri et al., 2008, Nat Gen, 40, 113). The heterozygous deletant (hemizygote) library we use is composed of diploid mutants each lacking one copy of a different gene (Giaever et al., 2002, Nature, 418, 387). When such a pool of mutants is grown in competition, some will grow slower than the others due to their particular mutation. Over time, the proportion of these mutants in the population will decrease – a phenotype termed `haploinsufficient’. Conversely, some mutants will have a growth-rate advantage and so will increase their proportion in the population; we call these strains `haploproficient’. Screening a pool of hemizygotes for their haploinsufficiency (HI)/haploproficiency (HP) phenotypes thus identifies cellular components that have high flux control (HFC) over growth rate. We found that genes that are major controllers of growth rate under nutrient-limitation are not, themselves, subject to growth rate control of their transcription. In this study we have investigated the generality of this rule, first by identifying HFC genes in turbidostat culture, where biomass concentration sets the rate of nutrient addition, growing at the maximum rate (mmax=0.32h-1) permitted by the complex defined medium (FPM) employed. And to study growth-rate effects, competition experiments were performed at higher growth rates (D=0.2h-1 and 0.3h-1) in nitrogen-limited chemostats and, to control for the effect of nitrogen limitation, in FPM using a chemostat at D=0.3h-1 (Pir et al., manuscript in preparation)
Experiment types
transcription profiling by array, co-expression, ex vivo, time series
Contact
Citation
Controls and Barriers to Rapid Growth in Yeast. Pir et al.
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-TABM-892.idf.txt
Sample and data relationshipE-TABM-892.sdrf.txt
Raw data (1)E-TABM-892.raw.1.zip
Processed data (1)E-TABM-892.processed.1.zip
Array designsA-AFFY-118.adf.txt, A-AFFY-153.adf.txt
Links