title: Abundant gene-by-environment interactions in gene expression reaction norms to copper within Saccharomyces cerevisiae.
abstract: Genetic variation for plastic phenotypes potentially contributes phenotypic variation to populations that can be selected during adaptation to novel ecological contexts. However, the basis and extent of plastic variation that manifests in diverse environments remains elusive. Here, we characterize copper reaction norms for mRNA abundance among five Saccharomyces cerevisiae strains to 1) describe population variation across the full range of ecologically relevant copper concentrations, from starvation to toxicity, and 2) to test the hypothesis that plastic networks exhibit increased population variation for gene expression. We find that although the vast majority of the variation is small in magnitude (considerably <2-fold), not just some, but most genes demonstrate variable expression across environments, across genetic backgrounds, or both. Plastically expressed genes included both genes regulated directly by copper-binding transcription factors Mac1 and Ace1 and genes indirectly responding to the downstream metabolic consequences of the copper gradient, particularly genes involved in copper, iron, and sulfur homeostasis. Copper-regulated gene networks exhibited more similar behavior within the population in environments where those networks have a large impact on fitness. Nevertheless, expression variation in genes like Cup1, important to surviving copper stress, was linked with variation in mitotic fitness and in the breadth of differential expression across the genome. By revealing a broader and deeper range of population variation, our results provide further evidence for the interconnectedness of genome-wide mRNA levels, their dependence on environmental context and genetic background, and the abundance of variation in gene expression that can contribute to future evolution.
authors.affiliation: Department of Ecology and Evolutionary Biology, Yale University, USA.
authors.forename: Andrea
authors.initials: A
authors.lastname: Hodgins-Davis
authors.forename: Aleksandra B
authors.initials: AB
authors.lastname: Adomas
authors.forename: Jonas
authors.initials: J
authors.lastname: Warringer
authors.forename: Jeffrey P
authors.initials: JP
authors.lastname: Townsend
mesh_terms: D016000:Cluster Analysis; D003300:Copper / Q000378:metabolism / Q000494:pharmacology*; D004268:DNA-Binding Proteins / Q000235:genetics / Q000502:physiology; D004305:Dose-Response Relationship, Drug; D020869:Gene Expression Profiling; D015966:Gene Expression Regulation, Fungal / Q000187:drug effects*; D059647:Gene-Environment Interaction; D005800:Genes, Fungal; D014644:Genetic Variation / Q000502:physiology; D053858:Metabolic Networks and Pathways / Q000187:drug effects / Q000235:genetics; D046228:Microarray Analysis; D009687:Nuclear Proteins / Q000235:genetics / Q000502:physiology; D012441:Saccharomyces cerevisiae / Q000187:drug effects* / Q000235:genetics* / Q000254:growth & development; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism / Q000502:physiology; D014157:Transcription Factors / Q000235:genetics / Q000502:physiology; D059467:Transcriptome / Q000187:drug effects / Q000235:genetics
chemical_list: C060256:CUP2 protein, S cerevisiae; D004268:DNA-Binding Proteins; C084954:MAC1 protein, S cerevisiae; D009687:Nuclear Proteins; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors; D003300:Copper