Genetic basis of haloperidol resistance, laboratory evolution of thermotolerance in Saccharomyces yeast

Abstract

The genetic basis of most heritable traits is complex. Inhibitory compounds and their effects in model organisms have been used in many studies to gain insights into the genetic architecture underlying quantitative traits. However, the differential effect of compound concentration has not been explored in detail. In this thesis, I used a large segregant panel between two genetically divergent S. cerevisiae yeast strains, BY4724 and RM11_1a, to study the genetic basis of variation in response to different doses of a drug. Linkage analysis revealed a highly dose-dependent genetic architecture of resistance to the drug haloperidol. I showed that a major QTL affecting resistance across all concentrations of haloperidol was caused by polymorphisms in SWH1, a homologue of human oxysterol binding protein. I further identified complex interactions between the alleles of genes SWH1, MKT1, and IRA2 that were most pronounced at 200 µM haloperidol in the RM background.

Next, we describe the laboratory evolution of thermotolerant S. bayanus, a yeast that diverged from S. cerevisiae nearly 20 million years ago. Unlike S. cerevisiae, which exhibits a maximal growth rate at 30ºC, S. bayanus prefers lower temperatures (~18-20ºC). To explore the genetic determinants that enhance S. bayanus growth at higher temperatures, we developed an evolution strategy and identified seven independent clones whose maximal growth rate increased 33-250% over the ancestral strain at 34ºC following 500 generations. Whole genome sequencing of evolved strains revealed, on average, four non-synonymous mutations in protein coding genes. We identified two causal gene variants, a truncation of UTH1 at residue 284, and a double mutant of YML108W (E52D and N54I), which enhanced S. bayanus growth at high temperatures. Mutations linked to SCH9, CDC25, and CDC27 can also promote thermotolerance in S. bayanus. All seven evolved S. bayanus strains showed increased resistance to actin inhibitor latruncilin B, and became more sensitive to benomyl, a microtubule inhibitor, demonstrating the presence of integrated genetic networks regulating diverse stresses in S. bayanus.

Finally, we present a systematic quantification of reproductive isolation between S. paradoxus subpopulations, and identify subpopulation level phenotypes, illustrating the prospects for using quantitative genetics to study natural populations.