Molecular Biology Seminar Series

Dr. Gavin Sherlock
Stanford University,
Lab Website

“Exploring the Join Distribution of Fitness Effects for Beneficial Mutations in Yeast.”

Friday, March 30, 2018
12:00 PM
RRI 101

Abstract: We previously developed a lineage tracking system to follow the dynamics of adaptive evolution of 500,000 isogenic haploid lineages of Saccharomyces cerevisiae under a glucose limited regime. By tracking the lineage tags over time, we showed that ~20,000 of the lineages gained a beneficial mutation during the experiment, which occurs over only 240 generations. Furthermore, we have also been able to generate a distribution of fitness effects for these lineages (Levy, Blundell et al, Nature (2015)). We isolated thousands of clones belonging to specific lineages, remeasured their fitness, and whole genome sequenced ~120 haploid clones from independent lineages that had gained beneficial mutations. We found that the RAS/cAMP/PKA pathway and the Tor pathway are frequently targets for adaptation under our conditions, uncovering almost 80 mutations in these pathways. In several cases where a gene has a paralog, beneficial mutations are recovered in one paralog significantly more frequently than that other. We have also found that even when mutations affect the same pathway, that the fitness conferred by mutations in a given gene tends to be specific for that gene, and distinct from the fitness effect of mutations in other genes in the pathway (Venkataram et al, Cell (2016)).

We next measured the fitness of these lineages under alternative conditions to determine in what phase of the growth cycle the beneficial mutations provide their fitness benefit, and whether there are within growth cycle fitness tradeoffs. By extending or shortening the length of exponential phase or stationary phase, we found that lineages carrying mutations from the same pathway show similar patterns of fitness change. Furthermore, Ras pathway mutants accrue fitness from spending time in the respiratory growth phase, but this fitness benefit is only manifested in the next growth cycle, as a shortening of lag phase. We also find that these mutants show deleterious effects in stationary phase, suggesting intrinsic tradeoffs between different parts of the growth cycle (Li et al., Current Biology (2018)).

Finally, to generalize beyond closely related experimental conditions, we have evolved both haploid and diploid yeast in several environments, using a double barcode approach, wherein the evolution condition is encoded in the second barcode. We have isolated adaptive clones from each of the conditions, then pooled them, and remeasured their fitness across each of the conditions, to understand how the ways in which beneficial mutants may either be generalists or specialists, and the ways in which they might tradeoff.