PhD Oral Exam - Raha Parvizi Omran, Biology

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 yeast Candida albicans is a commensal member of the gastrointestinal and urogenital tracts of most healthy humans. However, its capacity to function as an opportunistic pathogen allows it to cause systematic infections of immunocompromised individuals. Over the past two decades, the C. albicans zinc cluster transcription factor family (ZCFs) has been a fascinating subject of research – with studies identifying their roles in virulence, morphogenesis, biofilm formation, drug resistance and many other cellular processes. An understanding of these ZCFs may reveal new targets for therapeutic strategies.

My work focused on generating genome-wide transcriptional profiling for a large subset of 35 ZCF gain-of-function mutants (GOF) to elucidate the transcriptional profiles among the ZCFs, and on investigating in depth the function of some specific ZCFs in the fungal pathogen.

Transcriptional profiling revealed the target genes that are activated by the ZCF-GOF mutants and provided insight into the underlying roles of the factors. My study focused on establishing the transcriptional regulatory relationship among the ZCFs and understanding the function of some uncharacterized ZCFs. I achieved the first goal in collaboration with M. Hallett's lab. The network approach often shows a specific ZCF-GOF caused activation of expression of other ZCFs, which highlights the extensive interactions among ZCFs. We suggest that most expression changes can be the result of downstream long-term adaptive responses that induce the expression of intimidating transcription factors.

In chapter 2, I selected a set of 35 ZCF which mostly are uncharacterized, or little is known about them to functionally explore their function using RNA-based transcriptional profiling in collaboration with the M. Hallett lab.

In chapter 3, I characterized a new element involved in hyphal development regulation as a previously unstudied Candida-specific ZCF encoded by CaORF19.1604 that I named Rha1 (Regulator of Hyphal Activity). I identified Rha1 through screening a ZCF-GOF library and noting the Rha1-GOF strain was in a filamentous form under yeast growth conditions. I have characterized Rha1 inactivation mutants and GOF alleles, and I explored the Rha1 regulatory network involving Brg1 and Ume6, which are upregulated hyphal activators that appeared in the Rha1-GOF profile to show that Rha1 affects hyphal gene expression and connects to the Brg1/Ume6/Nrg1 regulatory circuit.
In chapter 4, I investigated the role of ZCF4 in cell wall biogenesis, filamentation, biofilm formation, and drug resistance. I explored the ZCF4 function after noting its upregulation in most of the activated ZCF profiles. Zcf4-GOF showed a severe filamentation defect on serum-based medium but exhibited normal filamentation under other cues. I have showed that ZCF4 influenced filamentation is nutrient dependent.

In chapter 5, I showed the robust ability of C. albicans to use proline as a carbon and nitrogen source by describing CaPut3 as a proline catabolism regulator. The functional studies demonstrated Put3 has a conserved role in regulating proline catabolism between C. albicans and Saccharomyces cerevisiae, but CaPut3 initiates the degradation of proline even in the presence of rich nitrogen source such as ammonium sulphate.

Collectively, this study established a framework and generated a robust transcriptional data from an activated set of 35 ZCFs to help understand the biology of C. albicans, an important human pathogen.