Evolution of cross-tolerance to metals in yeast

Abstract

Organisms often face multiple selective pressures simultaneously (e.g., mine tailings with multiple heavy metal contaminants), yet we know little about when adaptation to one stressor provides cross-tolerance or cross-intolerance to other stressors. To explore the potential for cross-tolerance, we first adapted Saccharomyces cerevisiae to high concentrations of six single metals in a short-term evolutionary rescue experiment. We then measured the cross-tolerance of each metal-adapted line in the other five metals. We generated and tested three predictors for the degree of cross-tolerance, based on the similarity between pairs of metal environments in (1) their physiochemical properties, (2) the overlap in genes known to impact tolerance to both metals, and (3) their co-occurrence in the environment. None of these predictors explained significant variation in cross-tolerance. Instead, we observed that adapted lines in one metal were frequently cross-tolerant to certain metals (manganese and nickel) and intolerant to others (cobalt and zinc). Furthermore, cross-tolerance between pairs of metals was not reciprocal, with mutations accumulating in one metal (e.g., copper) providing adaptation to another metal (e.g., manganese), but not vice versa. Evolved lines also differed in their degree of specialization, with lines evolved in manganese or copper more specialized to that metal, but lines evolved in cobalt or zinc more generally tolerant. To determine the genetic basis of these metal adaptations, we sequenced the genomes of 109 metal-adapted yeast lines. The SNP mutation spectrum was significantly different in cadmium, cobalt, and manganese than expected in a mutation accumulation experiment in S. cerevisiae. In addition, two lines were highly mutated, bearing defects in DNA repair genes (both in manganese). Thirteen genes exhibited parallel adaptation to different metals; three of these genes generated broad cross-tolerance. Several mutations were found in vacuolar transporter genes, suggesting an important role for vacuolar proteins in adapting to metal stress. Our results with these metal-adapted lines indicate that cross-tolerance is challenging to predict, depending on the combined stressors experienced and the nature of the mutations involved.