PhD Oral Exam - Idowu Bello-Osagie, 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

Aspergillus niger is a filamentous ascomycete fungus that is commonly found in soil and decomposing plant matter. It harbours a vast array of genes that regulate both primary and secondary metabolisms. It efficiently metabolizes a variety of plant polysaccharides using an extensive array of genes encoding extracellular enzymes. In the recent past, fungal genomes, including that of A. niger, have been sequenced, and deduced amino acid sequences from many gene models exhibit various degrees of similarity to aromatic compounds-degrading genes of bacterial origin. Despite the advances in genome sequencing, there is a large gap in the fundamental understanding of catabolic pathways for plant-derived aromatic compounds in fungi. Many of the genes encoding aromatic compound-degrading enzymes in fungi have not been identified, and in some cases, some of these pathway intermediates remain unknown in filamentous fungi. As part of an ongoing effort to comprehend the genes involved in the degradation of aromatics in A. niger. I have investigated in vivo the genes encoding enzymes in the pathway of two aromatic compounds, namely gentisate and resveratrol. In the first research chapter, I investigated the role of genes involved in the catabolism of gentisate in A. niger using multiple approaches of sequence homology to functionally characterize gentisate pathway genes in bacteria, as well as transcriptome analysis. This initially identified two gene clusters (NRRL3_05234–NRRL3_05237 and NRRL3_10244–NRRL3_10250) encoding enzymes with similar functions. Further investigation through gene knock-out studies, functional complementation test, and the detection of pathway intermediates using LC-MS identified genes in the first gene cluster (ΔNRRL3_05234–NRRL3_05237) as the genes that catalyze gentisate in A. niger. Of note is the identification of a gene (miaA) with no homology to known bacteria gentisate pathway gene but was found to be indispensable in the catabolism of gentisate in the conversion of maleylpyruvate to fumarylpyruvate. With these approaches, I was able to confirm and refine the assignment of these genes and their roles in the catabolism of gentisate in A. niger. The second research chapter is the result of the attempt to assign roles to the second gene cluster (NRRL3_10244- 10250). Using similar approaches as stated above, excluding the functional complementation tests and transcriptome analysis, I identified the genes and their role in the resveratrol catabolic pathway in A. niger.