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Abstract

mRNA and protein clump—or condense—in response to cellular stress across the tree of eukaryotic life. Yet, despite decades of inquiry and its universal evolutionary conservation, the function of stress-induced condensation remains enigmatic. The aim of this thesis is to gain insights into this fundamental phenomenon, using both cell biological and reductionist biophysical perspectives. Outstanding issues in the field of mRNA condensation are disagreements of which transcripts condense in response to stress, mechanistic understanding of how mRNA condenses and accumulates into microscopically visible stress granules, and the functional consequences of mRNA condensation. Outstanding issues in the field of protein condensation are a lack of high resolution understanding of the structures of condensates, how the structures of condensates may differ in different stress contexts, and how Nature encodes condensation into a protein’s primary sequence. Furthermore, how organisms modulate condensation by altering the chemical environment of the cell remains understudied.In Chapter 2, I summarize our understanding of stress-induced condensation of mRNA and protein, detail active areas of inquiry, and raise grand challenges plaguing the field from answering these questions. In Chapter 3, we interrogate mRNAs condensation during stress using budding yeast as a model organism. I show that most mRNAs condense following exposure to multiple divergent stresses. Rather than length being the defining predicter of mRNA condensation, we find that transcriptionally induced mRNAs escape condensation. Mechanistic work reveals that an increased abundance of ribosome-free mRNA is not sufficient to explain stress-induced mRNA condensation. Rather than simply being a byproduct of stress-triggered translational downregulation, our data supports a model in which mRNA condensation helps focus the cell’s translational machinery to produce proteins needed to mount its stress response. In Chapter 4, I probe the molecular mechanisms of protein condensation using polyadenylate- binding protein (Pab1 in budding yeast) as a model. I advance our understanding of Pab1 condensation mechanism by identifying putative, specific crosslinks connecting Pab1 protomers in the condensate. Supporting the thermodynamic specificity model of Pab1 condensation, I use HDX-MS to probe the hydrogen bond networks of Pab1 condensates formed at different temperatures and find that different condensation onset temperatures causes different condensate structures. HDX-MS study of Pab1 condensates from orthologs with different condensation onset temperatures informs how Nature encodes condensation in primary sequence. In Chapter 5, I investigate how Nature may utilize transition metal signaling to modu- lation condensation. Using Pab1 from budding yeast as a model system, I find that Zn2+ specifically promotes Pab1 condensation. Transition metals may be a broadly applicable class of signaling molecules, aiding the cell to transduce stress signals into condensate formation.

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