Post genomic analysis of biological systems: an evolutionary perspective of the protein network complexity in hybrid species

Access to files

•   FULL-TEXT.PDF (pdf)

Abstract

Saccharomyces yeasts are ideal candidates for genomic and evolutionary studies in eukaryotes due to their small genome, short generation time and availability of genomic data. Species freely hybridize producing viable but largely sterile cells. A hybridization event can be a swift mechanism for evolutionary innovation that if successful, may produce individuals fitter than either parents. It is largely unclear which mechanisms contribute to such hybrid vigour. This thesis investigated three mechanisms by which a natural hybrid may utilise one or both subgenomes to its advantage: recombination, the formation of chimeric protein complexes and the inheritance of mitochondrial DNA. Three strains of Saccharomyces pastorianus, a natural hybrid of Saccharomyces cerevisiae and Saccharomyces eubayanus, used in the lager fermentation process were sequenced using a NGS SOLiD platform. An analysis of recombination between each subgenome revealed the presence of 30 breakpoints, 28 of which are found within coding regions. Two breakpoints, present within the genes XRN1 and HSP82 have been reused in all three strains of S. pastorianus. This thesis investigated the formation of chimeric protein complexes in S. pastorianus by determining the configuration of protein complex-forming gene pairs to see whether they were mainly uni-specific, with all members belonging to the same parent, or chimeric, comprising one member from each parental species. A total of 21 pairwise protein complexes were found to be obligatorily chimeric in three strains of S. pastorianus. We used PCR-mediated gene deletion to recreate chimeric protein complexes in laboratory hybrids of S. cerevisiae and S. uvarum. The allelic configuration of one protein-complex forming gene pair, MLP2 and SPC110, impacted the growth of hybrid strains in a temperature-dependent manner.Finally, we looked at the mitochondrial inheritance in hybrids. Yeast hybrids can initially inherit mitochondrial DNA (mtDNA) from both parents, but rapidly become homoplasmic. To investigate the mechanisms influencing mtDNA inheritance, strains of Saccharomyces cerevisiae and Saccharomyces uvarum were crossed under different environmental conditions. The majority of hybrids inherited S. cerevisiae mtDNA when crossed in glycerol, a carbon source that can only be respired by yeast, in a range of temperatures. Those crossed in glucose, a fermentable source, did not show a preference for the inheritance of mtDNA at 30°, but at 10°C preferentially inherited S. uvarum mtDNA. In subsequent growth assays, hybrids with S. cerevisiae mtDNA grew better than those with S. uvarum mtDNA at 30°C and 20°C. However, at 10°C, the reverse was true: hybrids with S. uvarum mtDNA grew better that those with S. cerevisiae mtDNA, although only in glycerol. Overall this works sheds light on the molecular mechanisms contributing to fitness and evolutionary vigour in yeast hybrids.

Additional content not available electronically

1) Read_depth_analysis.xlsxTable D1a and D1b. Hierarchical cluster analysis of read depth of S. cerevisiae regions and S. eubayanus regions of S. pastorianus chromosomes2) RNA_expression_data.xlsxTable D2: Differential expression of alleles between HScMT, HSuMT, S. cerevisiae and S. uvarum strains grown at 30°C in glycerol.3) 2-micron_SNPS.xlsxTable D3: Single nucleotide polymorphisms between S. cerevisiae and S. pastorianus 2-micron plasmid sequence.4) RawCounts_ScMito.xlsxTable D4: S. cerevisiae mtDNA-encoded reads derived from the total RNA extraction of each hybrid strain at 28°C in YPGly

Keyword(s)

Chimeric genes; Chimeric protein complexes; Hybrid vigour; Lager yeast; Mitochondrial inheritance; MtDNA; Next-generation sequencing; Recombination; S. pastorianus; Yeast

Bibliographic metadata

Institutional metadata

Record metadata