Composition-based prediction and rational manipulation of prion-like domain recruitment to stress granules

Abstract

Mutations in a number of stress granule-associated proteins have been linked to various neurodegenerative diseases. Several of these mutations are found in aggregation-prone prion-like domains (PrLDs) within these proteins. In this work, we examine the sequence features governing PrLD localization to stress granules upon stress. We demonstrate that many yeast PrLDs are sufficient for stress-induced assembly into microscopically visible foci that colocalize with stress granule markers. Additionally, compositional biases exist among PrLDs that assemble upon stress, and these biases are consistent across different stressors. Using these biases, we have developed a composition-based prediction method that accurately predicts PrLD assembly into foci upon heat shock. We show that compositional changes alter PrLD assembly behavior in a predictable manner, while scrambling primary sequence has little effect on PrLD assembly and recruitment to stress granules. Furthermore, we were able to design synthetic PrLDs that were efficiently recruited to stress granules, and found that aromatic amino acids, which have previously been linked to PrLD phase separation, were dispensable for this recruitment. These results highlight the flexible sequence requirements for stress granule recruitment and suggest that PrLD localization to stress granules is driven primarily by amino acid composition, rather than primary sequence.

Tumor suppressor protein p53 expressed in yeast can remain diffuse, form a prion, or form unstable liquid-like droplets

“…Unlike amyloid-like prion aggregates, liquid droplets are not stable. They often appear and disappear in the cell in response to protein-specific stress triggers ( Boeynaems et al., 2018 ; Boncella et al., 2020 ; Buchan et al., 2011 ; Chakravarty and Jarosz, 2018 ; Grousl et al., 2013 ; Itakura et al., 2018 ; Jin et al., 2017 ; Lee et al., 2018 ; Narayanaswamy et al., 2009 ). In particular, P-bodies, highly conserved RNA-protein granules that increase in number to help cells divert resources to survival in response to stress, have been shown to be liquid-like droplets in yeast ( Kroschwald et al., 2015 ).…”

From Prions to Stress Granules: Defining the Compositional Features of Prion-Like Domains That Promote Different Types of Assemblies

“…One example of these constraints has emerged from studies of interactions between Sup35 and the chaperone Hsp104. Maintenance of prions over multiple rounds [10,58] versus stress granule recruitment [73]. It is important to note that this figure represents general trends that were observed in these screens and, therefore, may not reflect the behavior of all PrLDs.…”

“…Other PrLDs have been similarly linked to the formation of various other membraneless organelles [ 123 , 124 , 125 ]. Additionally, in both yeast and mammalian cells, various PrLDs are actually sufficient for recruitment to stress granules [ 26 , 73 , 126 , 127 ].…”

“…It is important to note that these possibilities are not mutually exclusive. The fact that various PrLDs are necessary [ 22 , 137 ] and/or sufficient [ 73 , 126 ] for stress granule recruitment suggests a direct role for some PrLDs in promoting the recruitment of their respective proteins to stress granules. However, these studies do not indicate whether these PrLDs engage in heterotypic or homotypic interactions within stress granules.…”

Defining the Caprin-1 interactome in unstressed and stressed conditions

“…There has been considerable effort invested to identify and understand the proteomic (13, 14) and transcriptomic (15, 16) composition of SGs (14, 17–20). Most of these studies have used G3BP1, a core SG protein, to define the SG proteome (19).…”