PhD Oral Exam - Walters Aji Tebung, Biochemistry

When studying for a doctoral degree (PhD), candidates submit a thesis that provides a critical review of the current state of knowledge of the thesis subject as well as the student’s own contributions to the subject. The distinguishing criterion of doctoral graduate research is a significant and original contribution to knowledge.

Once accepted, the candidate presents the thesis orally. This oral exam is open to the public.

Abstract

The prediction of protein function based on the role of orthologous proteins in other species is a common practice in life sciences. While such predictions prove accurate in some cases, a growing number of structurally orthologous proteins with different roles have been reported. Functional differences among structurally orthologous transcription factors create what has been termed transcriptional rewiring. We have characterized some zinc cluster transcription factors (ZCFs) in Candida albicans (C. albicans) including Ppr1, Stb5 and Put3. We identified cases of total rewiring, partial rewiring and functional conservation (no rewiring) but with some regulatory fine-tuning between C. albicans and S. cerevisiae for the ZCFs Ppr1, Stb5 and Put3 respectively.

We show that Ppr1 regulates purine catabolism in C. albicans, which is different from its role in S. cerevisiae where it regulates pyrimidine biosynthesis. We identified that Ppr1 rewired at Naumovozyma castellii in the phylogeny, and propose that Ppr1 rewiring is a result of cellular adaptations to permit growth in hypoxic conditions. In another study, we report that Stb5 has gone from regulating drug efflux pumps and glyoxylate cycle enzymes in C. albicans, to only regulating drug efflux pumps in S. cerevisiae. The glyoxylate cycle is required for C. albicans virulence, and our stb5 null mutants showed sensitivity to the echinocandin class of antifungal drugs. We therefore propose Stb5 as a potential drug target against candidiasis. Finally, we discovered that Put3 has conserved its role in regulating proline catabolism between C. albicans and S. cerevisiae. However, unlike the case of S. cerevisiae where Put3 can only activate transcription of proline catabolism genes in the absence of rich nitrogen sources, there is no equivalent restriction in C. albicans where Put3 preserves its ability to activate proline degradation even in the presence of the rich nitrogen source ammonium sulfate, thus allowing for the use of proline as a carbon source. The robust ability of C. albicans to obtain nutrients from a variety of sources adds to its efficiency as a pathogen.

These studies correlate transcriptional rewiring to species requirements, where different species adapt available transcription factors to meet their specific needs.