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Harnessing the Dark Side of Protein Folding: Manipulating Aggregation for Recombinant Protein Production

Final Report Summary - DARKSIDE (Harnessing the Dark Side of Protein Folding: Manipulating Aggregation for Recombinant Protein Production)

The goal of the project was to examine the pathways regulating protein aggregation, and to understand and exploit the regulation of these mechanisms to control protein translation for commercial and biomedical purposes. Protein aggregation is a common occurrence under stress, and plays a pathological role in many human diseases. It is also, however, an important regulatory mechanism in cells, in its own right. Not all aggregates are harmful, and many types of aggregates and protein assemblies play a beneficial role in stress response and stress memory. We set out to discover the regulatory hubs for controlling protein aggregation phenomena in cells, focusing primarily on the unicellular organism, budding yeast. Our goals included the identification of mechanisms diverting misfolded proteins to insoluble aggregates, so as to free up more chaperone resources for productive protein folding, and the identification of novel beneficial functions of protein aggregates and assemblies.

During the course of this project, we were indeed able to illuminate several novel mechanisms regulating protein expression in response to stress, particularly metabolic stress. We characterized a mechanism for targeting manifolded proteins to aggregates, as well as a beneficial survival mechanism that exploits the aggregation property of some proteins to facilitate cell recovery from stress.

The completion of this project has created several novel methodologies and resources for the yeast community, including effective BioID in yeast, and efficient modular chromosomal integration of vectors. In addition to the progress that we have made in understanding the active aggregation pathways in yeast, we have also uncovered a novel mechanism that can be exploited to control the metabolism of yeast used for recombinant protein production. Finally, beyond the scope of the project, this metabolic regulation by functional protein aggregates open new avenues for studying neurodegenerative diseases.