Abstract
The Saccharomycotina subphylum (budding yeasts) spans 400 million years of evolution and includes species that thrive in diverse environments. To study niche-adaptation, we identify changes in gene expression in three divergent yeasts grown in the presence of various stressors. Duplicated and non-conserved genes are significantly more likely to respond to stress than genes that are conserved as single-copy orthologs. Next, we develop a sorting method that considers evolutionary origin and duplication timing to assign an evolutionary age to each gene. Subsequent analysis reveals that genes that emerged in recent evolutionary time are enriched amongst stress-responsive genes for each species. This gene expression pattern suggests that budding yeasts share a stress adaptation mechanism, whereby selective pressure leads to functionalization of young genes to improve growth in adverse conditions. Further characterization of young genes from species that thrive in harsh environments can inform the design of more robust strains for biotechnology.
Highlights
The Saccharomycotina subphylum spans 400 million years of evolution and includes species that thrive in diverse environments
We analyze stress conditions to assess gene expression changes after stress adaptation in three diverse budding yeast species, one of which is well characterized (S. cerevisiae), and two that are less-well-characterized (K. marxianus and Y. lipolytica). The goal of this analysis is to identify common systems-level trends that are shared between each species stress responses. This analysis discovers that each organism displays a consistent response at the level of gene expression that is characterized by the enrichment of stress responsive genes amongst certain categories: namely, genes of unknown function and recently duplicated and taxonomically restricted genes
S. cerevisiae, K. marxianus, and Y. lipolytica were exposed to stress conditions that are present in natural environments, such as those caused by environmental temperature variation and growth on sugar-rich or acidic substrates[22]
Summary
The Saccharomycotina subphylum (budding yeasts) spans 400 million years of evolution and includes species that thrive in diverse environments. Researchers have employed systems biology to characterize the transcriptome and/or proteome-wide stressinduced changes[13,14,16,17,18] These approaches have identified biological processes that exhibit altered expression in response to stress exposure, which builds upon and relates to previous research into gene functions (e.g., GO term enrichment analysis). We analyze stress conditions to assess gene expression changes after stress adaptation in three diverse budding yeast species, one of which is well characterized (S. cerevisiae), and two that are less-well-characterized (K. marxianus and Y. lipolytica) The goal of this analysis is to identify common systems-level trends that are shared between each species stress responses. We propose that the gene sorting method we developed provides a path forward for more rapid identification of stress response genes in environmentally robust yeast, thereby accelerating understanding of niche adaption in budding yeasts
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