Exploring the roles of genes that provide resistance to cold temperatures in the Saccharomyces genus

  • Javier Pinto Aguirre

Student thesis: Phd


The understanding of the molecular mechanisms that affect the adaption of microbial species at different temperatures is essential to appreciate how biodiversity originates and how it can be maintained in a constantly changing environment. The Saccharomyces genus is an ideal group to study interspecific ecological traits, especially temperature, since it consists of a monophyletic group of species with high levels of sequence similarity within the Ascomycota phylum. The Saccharomyces genus is composed of eight species with a wide range of optimal growth temperatures and can be divided into thermo-tolerant, generalist and cold-tolerant. Saccharomyces species that share the same habitat (sympatry) may have optimum growth temperature, suggesting a partitioning of thermal niche possibly to avoid exploitative competition. In this study, the cellular role of a group of genes identified as key elements to provide optimal growth at cold temperatures by computational modelling and large-scale studies were investigated. Homozygote mutants of ADH3, GUT2, NMA1, YND1, ADH5 and FAA1, in all eight species belonging to the Saccharomyces genus were created. Upon deletion of these genes, S. kudriavzevii and S. arboricola displayed the most compromised fitness when compared with the other species. The level of expression of these genes in their native species at different temperature was determined. A significantly higher expression at cold for S. paradoxus, S. kudriavzevii and S. jurei compared to S. cerevisiae was observed. Different combinations of double mutants were also constructed, and the fitness scored in the different species. The double mutants ΔADH3/ΔADH3 and ΔYND1/ΔYND1 in S. paradoxus, S. uvarum and S. kudriavzevii, showed the greatest fitness impairment at cold. Interestingly, most of the genetic interactions in the double mutants showed positive and negative epistasis in S. cerevisiae and S. kudriavzevii, respectively. Also, interactions of ncRNAs with the genes under study to infer epigenetic mechanisms that are involved in cold-tolerance were evaluated. To tease apart the role of promoters (i.e. gene expression) from the allele type (i.e. genetic) in cold-adaptation, either the ADH3 and YND1 alelles or their promoters in S. cerevisiae, S. paradoxus, S. jurei and S. eubayanus with alelles or promoters belonging to the cold-tolerant species S. kudriavzevii were replaced independently. Fitness improvement was detected at cold temperature in the strains carrying S. kudriavzevii promoter for both ADH3 and YND1, whereas fitness was lower when the alleles were swapped, suggesting strength of expression is crucial in maintaining growth at cold temperatures over the type of allele. Additionally, different conditions for isolating yeast wild strains were explored, finding that cold-tolerant yeast species had higher fitness over thermotolerant and generalist in oak (Quercus) and spruce (Picea) infused media, and at low temperature S. eubayanus was the species which showed the best performance. Field studies were carried out to attempt to isolate S. eubayanus. The location of Scottish Highlands Forest was chosen based on maximum probability model based on climate data. No Saccharomyces species were isolated, instead species belonging to the genus Nakazawea were the most representative among the yeast isolates. Overall, this study contributes to understanding the importance of a non-essential group of genes in adaptation to cold temperatures and the role of promoter and allele type on cold adaptation in Saccharomyces species. It also, sheds light on the type of epistasis among the candidate genes in different species background.
Date of Award31 Dec 2022
Original languageEnglish
Awarding Institution
  • The University of Manchester
SupervisorDaniela Delneri (Supervisor) & Jean-Marc Schwartz (Supervisor)


  • Gene function
  • Cold temperature
  • Saccharomyces
  • Adaptation
  • Biodiversity
  • Transcription

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