Stress-Induced Expression is Enriched for Evolutionarily Young Genes in Diverse Budding Yeasts

Abstract

<jats:title>Abstract</jats:title><jats:p>The Saccharomycotina subphylum (budding yeasts) spans more than 400 million years of evolution and includes species that thrive in many of Earth’s harsh environments. Characterizing species that grow in harsh conditions could enable the design of more robust yeast strains for biotechnology. However, tolerance to stressful conditions is a multifactorial response, which is difficult to understand since many of the genes involved are as yet uncharacterized. In this work, three divergent yeast species were grown under multiple stressful conditions to identify stress-induced genes. For each condition, duplicated and non-conserved genes were significantly enriched for stress responsiveness compared to single-copy conserved genes. To understand this further, we developed a sorting method that considers evolutionary origin and duplication timing to assign an evolutionary age to each gene. Subsequent analysis of the sets of genes that changed expression revealed a relationship between stress-induced genes and the youngest gene set, regardless of the species or stress in question. These young genes are rarely essential for growth and evolve rapidly, which may facilitate their functionalization for stress tolerance and may explain their stress-induced expression. These findings show that systems-level analyses that consider gene age can expedite the identification of stress tolerance genes.</jats:p>

Identification of a novel gene required for competitive growth at high temperature in the thermotolerant yeast Kluyveromyces marxianus

“…The main aim of this study was to generate data to address the hypothesis put forward in a previous study that evolutionary young genes could be involved in adaption to growth under adverse conditions [37]. We did this by investigating genes that were upregulated during steady-state growth at high temperature in K. marxianus.…”

“…Differential gene expression (DE) analysis was performed on the previously published RNA-seq dataset of strain CBS 6556 [37].…”

Comparison of Different Label-free Techniques for the Semi-absolute Quantification of Protein Abundance

“…Each set of conditions was independently replicated three times, resulting in a total of 15 samples (5 conditions x 3 replicates). Sampling was carried out as described elsewhere [32].…”

Development of a Ribosome Profiling Protocol to Study Translation in the yeast Kluyveromyces marxianus

“…Aspects that have been studied include growth and ethanol production on alternative sugar substrates such as xylose (Schabort et al 2016;Kwon et al 2019) and inulin (Gao et al 2015); ethanol tolerance during adaptive laboratory evolution (Mo et al 2019); response to growth inhibitors derived from lignocellulosic substrates (Wang et al 2018) and the ability to grow at high temperatures (Fu et al 2019). Recently, mainly using transcriptome analysis, we determined that young genes specific to K. marxianus are enriched in the response to stresses such as high temperature, low pH and high osmolarity (Doughty et al 2020).…”

“…2019). Recently, mainly using transcriptome analysis, we determined that young genes specific to K. marxianus are enriched in the response to stresses such as high temperature, low pH and high osmolarity (Doughty et al . 2020).…”