Linkage mapping of yeast cross protection connects gene expression variation to a higher-order organismal trait

Abstract

Gene expression variation is extensive in nature, and is hypothesized to play a major role in shaping phenotypic diversity. However, connecting differences in gene expression across individuals to higher-order organismal traits is not trivial. In many cases, gene expression variation may be evolutionarily neutral, and in other cases expression variation may only affect phenotype under specific conditions. To understand connections between gene expression variation and stress defense phenotypes, we have been leveraging extensive natural variation in the gene expression response to acute ethanol in laboratory and wild Saccharomyces cerevisiae strains. Previous work found that the genetic architecture underlying these expression differences included dozens of “hotspot” loci that affected many transcripts in trans. In the present study, we provide new evidence that one of these expression QTL hotspot loci affects natural variation in one particular stress defense phenotype—ethanol-induced cross protection against severe doses of H2O2. A major causative polymorphism is in the heme-activated transcription factor Hap1p, which we show directly impacts cross protection, but not the basal H2O2 resistance of unstressed cells. This provides further support that distinct cellular mechanisms underlie basal and acquired stress resistance. We also show that Hap1p-dependent cross protection relies on novel regulation of cytosolic catalase T (Ctt1p) during ethanol stress in a wild oak strain. Because ethanol accumulation precedes aerobic respiration and accompanying reactive oxygen species formation, wild strains with the ability to anticipate impending oxidative stress would likely be at an advantage. This study highlights how strategically chosen traits that better correlate with gene expression changes can improve our power to identify novel connections between gene expression variation and higher-order organismal phenotypes.

Comparison of RNA isolation methods on RNA-Seq: implications for differential expression and meta-analyses

“…Six genes with either significantly higher (LAS17, SED1, PRY3) or lower (JNM1, EAF7, RRP36) abundance in the Phenol vs. Kit RNA-seq data were validated by real-time quantitative (q) PCR using the Maxima SYBR-qPCR Master Mix (Thermo Fisher Scientific) and a Bio-Rad CFX96 Touch Real-Time PCR Detection System as described [25]. Briefly, cDNA was synthesized from the same RNA samples used for RNA-seq using 10 μg total RNA, 3 μg anchored oligo-dT (T20VN), and SuperScript III (Thermo Fisher Scientific) according to the manufacturer's instructions.…”

Nutritional and Meiotic Induction of Heritable Stress Resistant States in Budding Yeast

“…For the sporulation/germination experiments we utilized an undomesticated wild strain isolated from Oak tree exudates while all of the haploid mitotic cell studies used the standard BY4742 strain background. Recent findings reveal genetic differences in acquired stress resistance of the exact strain backgrounds we employ here, and this will factor considerably in further studies 39 . Nevertheless, a plausible interpretation of our findings is that nutrient starvation underlies both the spore and haploid starved states.…”

Independent Mechanisms for Acquired Salt Tolerance versus Growth Resumption Induced by Mild Ethanol Pretreatment in Saccharomyces cerevisiae

“…In contrast, mild ethanol pretreatment did induce further ethanol resistance in the vast majority of wild yeast strains ( 11 ). Additionally, we recently discovered that mild ethanol stress can cross protect against oxidative stress in a wild oak strain ( 28 ). Because yeast in nature are likely to experience environmental shifts between high concentrations of sugars and high ethanol concentrations, we hypothesized that the inability of ethanol to cross protect against osmotic stress in S288c may be another aberrant acquired stress resistance phenotype in this strain background.…”

“…The acquired stress resistance assays were performed as described in reference 28 . Briefly, cells were grown overnight to saturation, subcultured into 30 ml fresh medium, and then grown for at least 8 generations into exponential phase (OD 600 of 0.3 to 0.6) to reset any cellular memory of starvation stress ( 39 ).…”

“…We have previously noted that S288c has an aberrant gene expression response to ethanol ( 11 , 27 ), which we hypothesized was responsible for the strain’s inability to acquire resistance to any other stresses following pretreatment with mild ethanol ( 10 , 11 ). We subsequently found that defective induction of antioxidant defenses in response to mild ethanol was responsible for S288c’s inability to acquire further hydrogen peroxide ( 28 ).…”