Epigenetics of stress-induced genome instability in the human fungal pathogen Candida albicans

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Candida albicans is an opportunistic fungus (a form of yeast) that normally lives on the human body without causing any harm. However, C. albicans can cause devastating diseases especially in immunocompromised patients who have undergone organ transplants, chemotherapy, or HIV treatment. During infections, C. albicans colonises several parts of our body and therefore needs to thrive in the many different environments found in the body. For example, pathogenic C. albicans survives high temperatures (i.e. fever) and drug resistant C. albicans strains thrive in the presence of anti-fungal drugs. The main goal of this proposal is to answer the key question: How can C. albicans adapt to such different environments?In all living organisms, the genome contains the information (genes) needed to build the organism and allow it to grow and develop. In most organisms, genome organisation must be maintained to ensure the right balance of genes (and therefore of the instructions for making our body function correctly).This is different in C. albicans: this fungus, like many other human fungal pathogens, has a flexible genome. This means that its genome structure changes and that C.albicans can live without the right proportion of its genes or even lose a part of a chromosome. Importantly, C. albicans' genome flexibility is enhanced when C. albicans encounters hostile environments (such as for example drug treatments) this allows selection of new genome organisations with a combination of genes that allow survival in these hostile environments. My laboratory has discovered that genome flexibility originates by breaking the DNA at specific DNA sites: the TRE hotspots. Identical TRE sites are found at each of C. albicans chromosomes and therefore, once broken, TRE sites can interact and fuse with each other. As a result, the C. albicans genome can rearrange itself, causing loss of some sequences and duplication of others. It can also bring two separate sections of the genome together. Work from my laboratory has demonstrated that the DNA packaging (chromatin) of TRE sites can direct or stop breaks at TRE hotspots.It is unknown what makes TRE sites special. This is impossible to predict because TRE hotspots are not found in other organisms and therefore it is not possible to guess their function. In this proposal, we will use our expertise in chromatin and C. albicans biology to answer 3 key questions:1. Why are TRE sites of DNA breaks?We will use genetics and genomics to determine why TRE hotspots are sites of DNA breakage. 2. How does the DNA packaging control TRE breaks?We hypothesise that the DNA packaging of TRE hotspots changes in different environments. This allows TRE hotspots to be exposed in hostile environments and to be protected in unstressed cells. 3. What are the consequences of TRE breaks?We will use CRISPR/Cas9 genome editing to generate a library of C. albicans strains carrying all the possible combination of TRE genomic shuffling. We will test which of these genomic organisation are beneficial for C. albicans virulence (ie how efficiently it causes infection).Understanding how TRE hotspots work will help the development of strategies to block genome flexibility stopping infections and drug resistance. Importantly, TRE DNA sequences are not found in humans and therefore blocking DNA shuffling at these sites will not have any deleterious effect in our body.