Chaperone functional specificity promotes yeast prion diversity

Abstract

While prions are protein-based infectious agents, yeast prions are protein-based genetic elements of the baker's yeast Saccharomyces cerevisiae [1]. Most yeast prions are amyloid protein aggregates that spread during mitosis through the cytosolic transmission of small, self-templating pieces called propagons. Propagons continue to recruit free protein monomers, perpetuating the prion phenotype in daughter cells [2]. Similar to the reliance of viruses upon host replication machinery, propagation of yeast prions to subsequent cell generations is dependent upon the fragmentation of aggregates by a core set of cellular chaperone proteins to create new propagons. The following three proteins make up the core "prion-chaperone machinery": the hexameric disaggregase Hsp104, the cytosolic Hsp70 Ssa, and the Hsp40 (also and hereafter called a "J protein") Sis1 [2]. Propagon generation is dependent upon the severing of amyloid fibers by Hsp104, which requires the upstream action of the Hsp70 Ssa and Sis1 to first bind to amyloids and unfold a portion of the protein, either exposing it or directly transferring it to Hsp104 [3][4][5][6][7][8]. Here, we will focus on the role of J proteins in promoting the propagation of a wide variety of yeast prions with the aim of better understanding how amyloid diversity is dependent on diverse chaperone activities. Yeast prion structures are diverse and chaperone requirements are heterologousPrions can also form distinct amyloid structures (structural polymorphisms) called "strains" in mammalian systems and "variants" in yeast [2,9]. These polymorphisms dictate species transmission barriers and disease pathology in mammals, and the intensity of prion-associated phenotypes and stability in mitosis in yeast [9][10][11][12][13]. Recently, we and others have demonstrated that prion-chaperone requirements are heterogeneous and, in contrast to Hsp104 and Hsp70, which have general roles, J proteins appear to represent a prion-specific component of the prion propagation machinery. Most notable has been a direct demonstration that the persistence of distinct prion variants is dependent on the action of different molecular chaperones, of which here we will focus exclusively on the J-protein component. These findings suggest that distinct amyloid structures have unique features that are differentiable by chaperone proteins, revealing a previously unappreciated level of additional complexity that may be exploitable for therapeutic intervention.

Variant‐specific and reciprocal Hsp40 functions in Hsp104‐mediated prion elimination

“…Our finding, that neither of two distinct weak [ PSI + ] variants require a second J‐protein, negates this hypothesis. Rather, these results indicate that the requirement (or lack thereof) for additional chaperone action may be the result of more fundamental differences between prions and prion‐forming proteins apart from variation in the final amyloid structure, for example, sequence elements, or more likely amino acid composition of the prion‐forming protein, as we have suggested before (Hines and Craig, ; Killian and Hines, ).…”

“…If so, then weak variants of other prions that also have low propagon numbers may share these requirements for prion propagation. Indeed, recent work has demonstrated significant variation of the J‐protein requirements among variants of the same prion (Harris et al ., ; Stein and True, a,b; Sporn and Hines, ; Killian and Hines, ). Our finding, that neither of two distinct weak [ PSI + ] variants require a second J‐protein, negates this hypothesis.…”

“…For example, in the case of [ PSI + ], weak variants tend to have larger amyloid fibers with fewer free ends, resulting in fewer transmissible aggregates to propagate the prion as well as a greater amount of soluble Sup35 (Liebman and Chernoff, ). Prion variants often have distinct requirements of chaperone activity, particularly with respect to J‐protein activity, for stable propagation (Derkatch et al ., ; Hines et al ., a, Prusiner, ; Stein and True, a,b; Harris et al ., ; Sporn and Hines, ; Schilke et al ., ; Killian and Hines, ). The J‐protein Sis1 is specifically required for the propagation of at least four yeast prions and has been shown to be the sole cytosolic J‐protein required for the propagation of strong [ PSI + ] variants (Sondheimer et al ., ; Higurashi et al ., ; Tipton et al ., ; Hines et al ., b; Schilke et al ., ).…”

Three J-proteins impact Hsp104-mediated variant-specific prion elimination: a new critical role for a low-complexity domain

“…Prior to our investigation, four cytosolic J-proteins were implicated in prion biology: Sis1, Apj1, Swa2, and Ydj1 (Kryndushkin et al 2002;Bradley et al 2002;Lian et al 2007;Hines et al 2011a;Hines and Craig 2011;Troisi et al 2015;Verma et al 2017;Oliver et al 2017;Killian and Hines 2018). Given 13 J-proteins at least partially inhabit the yeast cytosol (Sahi and Craig 2007) and three (Sis1, Ydj1, and Swa2) have been found to play critical roles in prion propagation, we hypothesized that other J-proteins may be involved in Hsp104-mediated curing of [PSI + ].…”

“…One of these J-proteins, Sis1, is essential for both cell survival and propagation of the four best-studied yeast prions: [PSI + ], [RNQ + ], [URE3], and [SWI + ] (Luke et al 1991;Sondheimer et al 2001;Aron et al 2007;Higurashi et al 2008;Hines et al 2011b). Specific chaperone requirements for propagation are largely differentiable among different prions and prion variants, particularly with respect to domain requirements of J-proteins (Derkatch et al 1996;Hines et al 2011a;Prusiner 2013;Stein and True 2014;Sporn and Hines 2015;Schilke et al 2017;Killian and Hines 2018;Killian et al 2019). In addition to Sis1, three other J-proteins-Ydj1, Swa2, and Apj1-have been previously implicated in prion biology.…”