Mining and modelling the genome of yeast industrial hybrids

Student thesis: Phd

Abstract

First, to study the genome plasticity of Saccharomyces pastorianus strains, we developed HybridMine, a new user-friendly, open-source tool for functional annotation of hybrid aneuploid genomes of any species by predicting parental alleles including paralogs. This methodology is instrumental to understand the fate of duplicate genes following a whole genome duplication event and is applicable to all hybrid organisms with known parents. We investigated the phylogenetic relationship of the inherited Saccharomyces cerevisiae-like and Saccharomyces eubayanus-like genes for four strains of S. pastorianus, CBS 1513, CBS 1503, CBS 1538 and WS 34/70. As expected, the almost tetraploid Group II strain (WS 34/70) has the higher number of redundant genes. Out of the three Group I S. pastorianus strains studied, CBS 1538 shows the highest loss of the S. cerevisiae genome, and the lowest amount of redundant functional genes. Interestingly, the low amount of genetic redundancy in this case comes primarily by the loss of the S. cerevisiae-like genes. Next, we studied cis-trans regulation in natural yeast hybrids focusing on the analysis of the expression network of S. pastorianus CBS 1513 to identify alleles bias transcription under different environmental conditions. We identified temperature-dependent media-independent genes and showed that 35% have their regulation dependent on extracellular leucine uptake, suggesting an interplay between leucine metabolism and temperature response. Moreover, the analysis of the expression of ortholog parental alleles unveiled that the majority of the genes express preferentially one parental allele over the other, and that S. eubayanus-like alleles are significantly over-represented among the genes involved in cold acclimatisation. Our expression data indicates that the majority of the protein complexes established in the hybrid are likely to be either exclusively chimeric or uni-specific, and that the genetic redundancy is discouraged, a scenario supporting the gene-balance hypothesis during hybrid evolution. Finally, we constructed iSP_1513, a GSMM of S. pastorianus CBS 1513 strain, commonly referred to as the ”Carlsberg yeast”. This GSMM represents an important step towards understanding the metabolic capabilities of natural yeast hybrids and will enable a top-down approach to predict the evolution of metabolic pathways and to aid strain optimisation as well as media engineering for production processes. The iSP_1513 model was built based on the Yeast8 model and takes into account the functional redundancy caused by the presence of orthologous parental genes in the Gene-Protein-Reaction (GPR) rules. It comprises 4062 reactions, 1808 genes, and 2747 metabolites across 14 compartments and an inter-compartment. Essentiality datasets, metabolite secretion, as well as growth data on various carbohydrates, were used to validate this model. Flux Balance Analysis and Flux Variability analysis have been used to predict growth in different environments. The effect of high and low temperatures on metabolite production and on the parental sub-genome activity have been investigated by mapping transcriptome data. Overall, the construction of the iSP_1513 is of biotechnological importance and allows the use of computational approaches to design new strains of yeasts with improved phenotypic traits and optimised production processes for craft beer production. The model also enables researchers to explore the metabolic capabilities of S. pastorianus hybrids and better understand how they produce complex flavours and aromas.
Date of Award1 Aug 2024
Original languageEnglish
Awarding Institution
  • The University of Manchester
SupervisorDaniela Delneri (Supervisor) & Jean-Marc Schwartz (Supervisor)

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