Dissecting the roles of ubiquitin in translation control

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Project Summary The long-term goal of the Silva Lab is to determine the molecular mechanism by which protein ubiquitination controls protein synthesis and cellular survival in response to oxidative stress. Oxidizers are constantly produced by a variety of endogenous and exogenous sources and translation is an essential cellular process that must be finely reprogrammed when cells are challenged with oxidizers. Failure to reprogram protein expression, accumulation of damaged proteins, and inadequate management of oxidizers are the underlying causes of a variety of neurodegenerative diseases, tumor progression, and the process of aging. Understanding and modulating stress defense pathways, such as translation, would provide new tools to promote healthier lives and fight diseases. In eukaryotes, a variety of defense pathways is regulated by ubiquitin. Protein ubiquitination is a prevalent post-translational modification initially characterized as the molecular marker for protein degradation. We have recently identified a new role for a poly-ubiquitin variant (K63-linked) in the regulation of protein synthesis during oxidative stress. Using molecular and proteomics approaches, our lab showed that ribosomes are the main target of K63 ubiquitin, K63 ubiquitin is essential for cellular viability, and that specific enzymes are involved in ribosomal ubiquitination and deubiquitination reactions. However, there is still a limited understanding of how K63 ubiquitin impacts ribosome activity and the protein expression program. This MIRA award will support the Silva Lab program of research, which will use a combination of large-scale, molecular, and computational approaches to understand each one of the steps necessary for regulation of translation by K63 ubiquitin. These steps include recognition of ribosome by ubiquitin enzymes, modification of individual ubiquitin sites, alteration of ribosome 3D structure, reconfiguration of translation landscape, and determination of the fate of ubiquitinated ribosomes. Defining the molecular mechanisms regulating such a fundamental biological process as protein synthesis is key to enhancing cellular resistance to stress and reshaping our understanding of gene expression control. This work will lead to an established and independent research program, future NIH research awards, expanded collaboration network, and interdisciplinary research within the NIGMS mission.