Misfolding-prone proteins are reversibly sequestered to an Hsp42-associated granule upon chronological aging

Abstract

Alteration of protein localization is an important strategy for cells to regulate protein homeostasis upon environmental stresses. In the budding yeast , many proteins relocalize and form cytosolic granules during chronological aging. However, the functions and exact components of these protein granules remain uncharacterized in most cases. In this study, we performed a genome-wide analysis of protein localization in stationary phase cells, leading to the discovery of 307 granule-forming proteins and the identification of new components in the Hsp42-stationary phase granule (Hsp42-SPG), P-bodies, Ret2 granules and actin bodies. We further characterized the Hsp42-SPG, which contains the largest number of protein components, including many molecular chaperones, metabolic enzymes and regulatory proteins. Formation of the Hsp42-SPG efficiently downregulates the activities of sequestered components, which can be differentially released from the granule based on environmental cues. We found a similar structure in the pre-whole genome duplication yeast species,, suggesting that the Hsp42-SPG is a common machinery allowing chronologically aged cells to contend with changing environments when available energy is limited. This article has an associated First Person interview with the first author of the paper.

Spatial Organization of Proteasome Aggregates in the Regulation of Proteasome Homeostasis

“…It was also demonstrated that under carbon starvation, Hsp42-SPGs co-immunoprecipitates with Ssa1-TAP and not Hsp42-TAP (Lee et al, 2018). This may indicate that under carbon starvation stress, Hsp42 is predominantly insoluble, while Ssa1 (Shiber et al, 2013) and the other SPG components (Lee et al, 2018), similar to PSGs (Enenkel, 2018), are soluble. Taken together, these results imply that Hsp42 may preferentially sequester insoluble proteins.…”

“…Attempts to identify additional proteins that aggregate similarly to PSGs, and might form a PSG scaffold, were described in two independent studies. Both used an arrayed GFP clone collection of S. cerevisiae tagged open reading frames (Huh et al, 2003) to systematically follow the reorganization of yeast proteins under carbon starvation (Gu et al, 2017;Lee et al, 2018). Other than Ubi4, Ubp6, Blm10 and the proteasome subunits themselves, none of the detected protein aggregates were reversable upon carbon addition, or co-localized with PSGs (Gu et al, 2017;Lee et al, 2018).…”

“…Hsp42 is crucial for the assembly of proteins that have a role in epigenetics, metabolic enzymes and molecular chaperones, during the stationary phase. These granules were termed Hsp42-Sationary phase granules (SPGs) (Liu et al, 2012;Lee et al, 2016Lee et al, , 2018, and their presence was shown to promote cell survival during stress (Liu et al, 2012;Lee et al, 2016Lee et al, , 2018. It was also demonstrated that under carbon starvation, Hsp42-SPGs co-immunoprecipitates with Ssa1-TAP and not Hsp42-TAP (Lee et al, 2018).…”

“…These granules were termed Hsp42-Sationary phase granules (SPGs) (Liu et al, 2012;Lee et al, 2016Lee et al, , 2018, and their presence was shown to promote cell survival during stress (Liu et al, 2012;Lee et al, 2016Lee et al, , 2018. It was also demonstrated that under carbon starvation, Hsp42-SPGs co-immunoprecipitates with Ssa1-TAP and not Hsp42-TAP (Lee et al, 2018). This may indicate that under carbon starvation stress, Hsp42 is predominantly insoluble, while Ssa1 (Shiber et al, 2013) and the other SPG components (Lee et al, 2018), similar to PSGs (Enenkel, 2018), are soluble.…”

“…During unfolding stress, the S. cerevisiae Hsps, Hsp42, and Hsp26, associate with substrates in a partially unfolded intermediate state, maintaining them in a ready-to-refold conformation close to the native structure (Haslbeck et al, 2004(Haslbeck et al, , 2005. Hsp42 co-aggregates with diverse misfolded substrates under different stress conditions, including heat stress (Specht et al, 2011), proteasome inhibition (Peters et al, 2015(Peters et al, , 2016Marshall et al, 2016), cellular quiescence (Liu et al, 2012), and cellular aging (Saarikangas and Barral, 2015;Lee et al, 2018). Such co-aggregation is employed to actively control the formation of CytoQs and promote the coalescence of multiple small CytoQs into a small number of assemblies of larger size at specific cellular sites (Specht et al, 2011;Escusa-Toret et al, 2013).…”