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PhD Defense - Yonghyun (John) Kim

You are cordially invited to the dissertation defense of Yonghyun (John) Kim.

Date: October 10, 2008
Time: 2:00pm
Location: BIOL 004

Some refreshments will be provided.

TITLE: Proteomic Identification of Novel Regulators and Effectors of Osmoadaptaion and Autophagy of Model Filamentous Fungi Aspergillus nidulans

The genus Aspergillus is an important grouping of filamentous fungi for study, as it contains a number of species which are either extremely helpful (e.g., in the bioprocess industry) or harmful (e.g., human/animal/crop pathogens). Here, we focus on a representative, model species, Aspergillus nidulans, and study a key cellular process called autophagy. Autophagy (more specifically, macroautophagy) is an important cellular mechanism by which cells first degrade and subsequently recycle portions of the cytosol when there is limited nutrient supply. Autophagy proteins (and regulation of their expression) are highly conserved from yeast to man, and thus our study has potentially broad implications for all eukaryotes. Currently, only a few studies exist which have characterized autophagy in fungi. To further this understanding, we employed proteomic analysis, a systems biology tool which provides a panoptic, large-scale profiling of protein expression level changes. Our broad goal here was to utilize proteomic analysis to develop a better fundamental understanding of protein expression associated with autophagy in filamentous fungi. When fully developed, this understanding may allow us to intelligently manipulate fungi at the molecular level to harness increased benefit from fungi used in the bioprocess industry and diminish detriment from pathogenic fungi.

We began by establishing one of the first, published A. nidulans proteome maps. We did this while studying osmoadaptation, which has been tied to autophagy and is a relatively well understood stress response. This study also served to validate our proteomic experimental approach. Our analysis identified a number of novel proteins that were, for the first time, linked with osmoadaptation. Next, we studied differences in protein expression patterns when A. nidulans is grown in the presence of two known inducers of autophagy, carbon starvation and rapamycin treatment. Our data suggest that some downstream effectors are shared between the rapamycin-regulated pathways and carbon-starvation regulated pathways (e.g. polar growth, cell wall degradation), that the mechanism by which they are regulated are seemingly different (e.g. 14-3-3 ArtA involved in regulating polar growth during carbon-starvation but not during rapamycin treatment), and that there are other effectors which are distinct between the two inducers (e.g. reduced amino acid biosynthesis only observed in carbon-starvation). Our final study builds on this theme by reporting the time-dependent response of an autophagy-impaired mutant (ΔAtg8) exposed to rapamycin. Our proteomic data suggest that A. nidulans, when challenged with rapamycin, upregulates gluconeogenesis, the pentose phosphate pathway, amino acid biosynthesis, secretory pathway, polarized growth, and ribosome turnover even without a fully functioning autophagy pathway. Taken together, these data imply that rapamycin-mediated effectors are distinct from those of autophagy.