Sophie Shaw. BSc (Hons), AHEA

Department: Microbes, Plants and Disease Research Group
Discipline: Biosciences

Project Summary

Project Title: Functional Significance of Differential Allele Expression in the Yeast Candida albicans. As a diploid organism, each strain of the yeast Candida albicans has two alleles at a genetic locus. The diploid sequence of the wild type strain revealed a high level heterozygosity between alleles with 78% of polymorphisms leading to non-synonymous substitutions. This leads to the hypothesis that these alleles could be producing functionally different proteins. RNA sequencing of this wild type strain has shown that, for 233 genes, alleles are differentially expressed. The initial aim of my research was to take this data and construct heterozygous knockout mutants in the wild type strain SC5314. This produced strains where one of the allele has been replaced by an antibiotic resistance marker. These strains were used to observe the phenotypic contributions of each allele under various conditions. This work is testing the hypothesis that alleles could differ in function, and that this is linked to the differences seen in allele expression. 

Expression levels of proteins produced by different alleles has also been monitored using tagged strains and western blotting protocols. This is helping us to investigate the relationship between RNA expression levels and protein expression levels. 

I have developed a bioinformatics pipeline that uses existing RNA-sequencing for the Illumina platform to investigate the extent of differential allele expression in the wild type strain of C. albicans under different conditions; for example in its hyphal form or during exposure to stress. This will show whether levels of allele expression change to adapt to changing environments. I am now looking at implementing this pipeline for different sequencing platforms. 

Final areas of research which I aim to undertake as I approach the end of my PhD are the analysis of the control of this differential expression by studying both structural factors and cis- and trans- acting transcription factors that dictate gene expression; and to investigate gene sequence in clinical isolates to investigate the evolution of these differentially expression alleles.

Supervisory Team

Supervisor 1 - Dr. Mark Ramsdale Supervisor 2 - Dr. Jamie Stevens