Control analysis of the eukaryotic cell cycle using gene copy-number series in yeast tetraploids

Abstract

BackgroundIn the model eukaryote, Saccharomyces cerevisiae, previous experiments have identified those genes that exert the most significant control over cell growth rate. These genes are termed HFC for high flux control. Such genes are overrepresented within pathways controlling the mitotic cell cycle.ResultsWe postulated that the increase/decrease in growth rate is due to a change in the rate of progression through specific cell cycle steps. We extended and further developed an existing logical model of the yeast cell cycle in order elucidate how the HFC genes modulated progress through the cycle. This model can simulate gene dosage-variation and calculate the cycle time, determine the order and relative speed at which events occur, and predict arrests and failures to correctly execute a step. To experimentally test our model’s predictions, we constructed a tetraploid series of deletion mutants for a set of eight genes that control the G2/M transition. This system allowed us to vary gene copy number through more intermediate levels than previous studies and examine the impact of copy-number variation on growth, cell-cycle phenotype, and response to different cellular stresses.ConclusionsFor the majority of strains, the predictions agreed with experimental observations, validating our model and its use for further predictions. Where simulation and experiment diverged, we uncovered both novel tetraploid-specific phenotypes and a switch in the determinative execution point of a key cell-cycle regulator, the Cdc28 kinase, from the G1/S to the S/G2 boundaries.

Advances and challenges in logical modeling of cell cycle regulation: perspective for multi-scale, integrative yeast cell models

“…The three studies that will be presented in the following, Todd and Helikar (2012), Alcasabas et al. (2013) and Rubinstein et al. (2013), have their foundations in the work of Li, Fauré or Irons.…”

“…To test the effect of growth, sequential deletions of alleles in tetraploid yeast cells were conducted, with mutants expressing 0%, 25%, 50% and 75% of the wild-type dosage, corresponding to 0, 1, 2 and 3 gene copies (Alcasabas et al. 2013). The gene dosages were then modeled by probabilities.…”

“…This trajectory has 31 steps and, thus, establishes a time against which the behaviors of deletion mutants may be compared (Alcasabas et al. 2013). In the stochastic model, trajectories will differ over each iteration.…”

“…The model predicted a phenotypic difference in growth rate between deletion mutants with low copy numbers for CLB1 and CLB2 cyclin genes—which regulate the timing of cell division together with the kinase Cdk1—that was observed experimentally (Alcasabas et al. 2013). Furthermore, the model shows that different dosages of the kinase Cdk1 can result in phenotypic variation.…”

“…In particular, the growth rate predicted for the low copy numbers of SWE1 , negative regulator of the Cdk1 kinase, was slower as compared to the experimental observation (Alcasabas et al. 2013). …”