Week 2: What am I doing?

The Silva lab researches how cells respond to stressful environments. When cells are put in a stressful environment, many of their proteins are damaged. Damaged proteins can result in many adverse consequences for the cell, so in times of stress the cell works to remove these proteins. Eukaryotes have evolved special machinery to recognize and tag damaged proteins using ubiquitin. Ubiquitin is a short protein used to post-translationally modify other proteins and can signal many different things such as degradation of the tagged protein.  Ubiquitin accumulate in the cell, possibly resulting in negative outcomes. This accumulation and disruption of the proteasome degradation system is thought to be related to neurodegenerative diseases like Parkinson’s and Alzheimer’s disease. However, very little is understood about how the ubiquitin proteasome system is related to disease and many ubiquitin pathways and targets remain to be characterized. Additionally, stress intensity can also impact the efficiency of the proteasome.  At low levels of stress, efficiency can increase whereas at highs levels, the proteasome’s functionality is reduced. However, the causes for this response are not well understood. The Silva lab’s research focuses on characterizing ubiquitination pathways and their corresponding cellular responses as a result of oxidative stress.

My project relates to one specific kind of ubiquitin modification, Lysine 48 (K48) ubiquitination. This tag serves as a signal for protein degradation. My project focuses on characterizing K48 ubiquitination levels in cells experiencing oxidative stress. Some of the big questions of my research project are what enzymes are involved, specifically the E2 and corresponding E3 enzymes that ubiquitinate proteins. As well as what are the targets for K48, how K48 ubiquitination of ribosomes vary in stressful environments, and how these modifications impact translation. My current project is taking many different approaches to characterizing the usage of K48 ubiquitin in response to stress. I’ve started out this research experience looking at general levels of K48 ubiquitination in wild type yeast cells under different levels of oxidative stress. After this initial experiment, I’m studying K48 levels in mutant yeast stains that lack E2 enzyme genes in order to test which enzymes are important to the K48 ubiquitination process. After this, I will explore how the proteasome activity and deubiquitinating enzymes in the cell are affected by oxidative stress and then how the frequency of K48 modified ribosomes changes in a stressful environment. Characterizing this pathway could provide greater insight into the biological underpinnings of serious neurodegenerative diseases and help this area of research be one step closer to finding a cure.

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