Gene expression differences and functional diversification of glycolytic gene paralogs in Saccharomyces cerevisiae

Abstract

Genomes of all organisms are full of genes that duplicated and then subsequently diversified in function during evolution. A primary goal of evolutionary genetics is to mechanistically understand how genes evolve following duplication such that both copies become essential and retained by evolution across millions of years of evolutionary time. In my research, I used the evolution and diversification of the three TDH genes within Saccharomyces cerevisiae, to investigate this question. The TDH gene duplicates (TDH1, TDH2, TDH3) are involved in the fundamental process of glycolysis, through which sugars are converted to energy, and specifically catalyze the conversion of glyceraldehyde-3-phosphate in this pathway. My research asks explicitly if the three TDH genes have diverged with respect to their effects on growth rate and whether this divergence happened through changes in the gene promoter or the protein-coding region. I first measured the effect of each TDH gene on growth rate by using CRISPR-Cas9 to delete them individually and in combination. I then determined whether the divergence between genes was because of changes in the gene promoters or the protein-coding sequences by swapping the promoters and protein-coding sequences between the TDH genes and measuring growth rate. My data shows that the TDH duplicates have diverged in some functions but retained other conserved functions. Further, my data shows that most functional differentiation between the TDH genes, with respect to effects on growth rate, occurred through changes in the promoter that alters gene expression. However, I also discovered that the TDH paralogs may have roles beyond glycolysis and fermentative growth. To investigate this, fluorescent microscopy was used to determine if the subfunctionalization of TDH regulatory sequences over evolutionary time was followed by the neofunctionalization of protein-coding sequences.