Analysis of the [RNQ+] prion reveals stability of amyloid fibers as the key determinant of yeast prion variant propagation

Disease-associated mutations within the yeast DNAJB6 homolog Sis1 slow conformer-specific substrate processing and can be corrected by the modulation of nucleotide exchange factors

Molecular chaperones, or heat shock proteins (HSPs), protect against the toxic misfolding and aggregation of proteins. As such, mutations or deficiencies within the chaperone network can lead to disease. Dominant mutations within DNAJB6 (Hsp40)-an Hsp70 co-chaperone-lead to a protein aggregation-linked myopathy termed Limb-Girdle Muscular Dystrophy Type D1 (LGMDD1). Here, we used the yeast prion model client in conjunction with in vitro chaperone activity assays to gain mechanistic insights into the molecular basis of LGMDD1. Here, we show how mutations analogous to those found in LGMDD1 affect Sis1 (a functional homolog of human DNAJB6) function by altering the structure of client protein aggregates, interfering with the Hsp70 ATPase cycle, dimerization and substrate processing; poisoning the function of wild-type protein. These results uncover the mechanisms through which LGMDD1-associated mutations alter chaperone activity, and provide insights relevant to potential therapeutic interventions.

Extracellular Vesicles-Encapsulated Yeast Prions and What They Can Tell Us about the Physical Nature of Propagons

The yeast Saccharomyces cerevisiae hosts an ensemble of protein-based heritable traits, most of which result from the conversion of structurally and functionally diverse cytoplasmic proteins into prion forms. Among these, [PSI⁺], [URE3] and [PIN⁺] are the most well-documented prions and arise from the assembly of Sup35p, Ure2p and Rnq1p, respectively, into insoluble fibrillar assemblies. Yeast prions propagate by molecular chaperone-mediated fragmentation of these aggregates, which generates small self-templating seeds, or propagons. The exact molecular nature of propagons and how they are faithfully transmitted from mother to daughter cells despite spatial protein quality control are not fully understood. In [PSI⁺] cells, Sup35p forms detergent-resistant assemblies detectable on agarose gels under semi-denaturant conditions and cytosolic fluorescent puncta when the protein is fused to green fluorescent protein (GFP); yet, these macroscopic manifestations of [PSI⁺] do not fully correlate with the infectivity measured during growth by the mean of protein infection assays. We also discovered that significant amounts of infectious Sup35p particles are exported via extracellular (EV) and periplasmic (PV) vesicles in a growth phase and glucose-dependent manner. In the present review, I discuss how these vesicles may be a source of actual propagons and a suitable vehicle for their transmission to the bud.

Protein-based inheritance

Epigenetic mechanisms of inheritance have come to occupy a prominent place in our understanding of living systems, primarily eukaryotes. There has been considerable and lively discussion of the possible evolutionary significance of transgenerational epigenetic inheritance. One particular type of epigenetic inheritance that has not figured much in general discussions is that based on conformational changes in proteins, where proteins with altered conformations can act as templates to propagate their own structure. An increasing number of such proteins - prions and prion-like - are being discovered. Phenotypes due to the structurally altered proteins are transmitted along with their structures. This review discusses the properties and implications of "classical" amyloid-forming prions, as well as the broader class of proteins with intrinsically disordered domains, which are proving to have fascinating properties that appear to play important roles in cell organisation and function, especially during stress responses.

[PIN+]ing down the mechanism of prion appearance

Prions are conformationally flexible proteins capable of adopting a native state and a spectrum of alternative states associated with a change in the function of the protein. These alternative states are prone to assemble into amyloid aggregates, which provide a structure for self-replication and transmission of the underlying conformer and thereby the emergence of a new phenotype. Amyloid appearance is a rare event in vivo, regulated by both the aggregation propensity of prion proteins and their cellular environment. How these forces normally intersect to suppress amyloid appearance and the ways in which these restrictions can be bypassed to create protein-only phenotypes remain poorly understood. The most widely studied and perhaps most experimentally tractable system to explore the mechanisms regulating amyloid appearance is the [PIN⁺] prion of Saccharomyces cerevisiae. [PIN⁺] is required for the appearance of the amyloid state for both native yeast proteins and for human proteins expressed in yeast. These observations suggest that [PIN⁺] facilitates the bypass of amyloid regulatory mechanisms by other proteins in vivo. Several models of prion appearance are compatible with current observations, highlighting the complexity of the process and the questions that must be resolved to gain greater insight into the mechanisms regulating these events.

Prion Variants of Yeast are Numerous, Mutable, and Segregate on Growth, Affecting Prion Pathogenesis, Transmission Barriers, and Sensitivity to Anti-Prion Systems

The known amyloid-based prions of Saccharomyces cerevisiae each have multiple heritable forms, called "prion variants" or "prion strains". These variants, all based on the same prion protein sequence, differ in their biological properties and their detailed amyloid structures, although each of the few examined to date have an in-register parallel folded β sheet architecture. Here, we review the range of biological properties of yeast prion variants, factors affecting their generation and propagation, the interaction of prion variants with each other, the mutability of prions, and their segregation during mitotic growth. After early differentiation between strong and weak stable and unstable variants, the parameters distinguishing the variants has dramatically increased, only occasionally correlating with the strong/weak paradigm. A sensitivity to inter- and intraspecies barriers, anti-prion systems, and chaperone deficiencies or excesses and other factors all have dramatic selective effects on prion variants. Recent studies of anti-prion systems, which cure prions in wild strains, have revealed an enormous array of new variants, normally eliminated as they arise and so not previously studied. This work suggests that defects in the anti-prion systems, analogous to immune deficiencies, may be at the root of some human amyloidoses.

Broadening the functionality of a J-protein/Hsp70 molecular chaperone system

By binding to a multitude of polypeptide substrates, Hsp70-based molecular chaperone systems perform a range of cellular functions. All J-protein co-chaperones play the essential role, via action of their J-domains, of stimulating the ATPase activity of Hsp70, thereby stabilizing its interaction with substrate. In addition, J-proteins drive the functional diversity of Hsp70 chaperone systems through action of regions outside their J-domains. Targeting to specific locations within a cellular compartment and binding of specific substrates for delivery to Hsp70 have been identified as modes of J-protein specialization. To better understand J-protein specialization, we concentrated on Saccharomyces cerevisiae SIS1, which encodes an essential J-protein of the cytosol/nucleus. We selected suppressors that allowed cells lacking SIS1 to form colonies. Substitutions changing single residues in Ydj1, a J-protein, which, like Sis1, partners with Hsp70 Ssa1, were isolated. These gain-of-function substitutions were located at the end of the J-domain, suggesting that suppression was connected to interaction with its partner Hsp70, rather than substrate binding or subcellular localization. Reasoning that, if YDJ1 suppressors affect Ssa1 function, substitutions in Hsp70 itself might also be able to overcome the cellular requirement for Sis1, we carried out a selection for SSA1 suppressor mutations. Suppressing substitutions were isolated that altered sites in Ssa1 affecting the cycle of substrate interaction. Together, our results point to a third, additional means by which J-proteins can drive Hsp70's ability to function in a wide range of cellular processes-modulating the Hsp70-substrate interaction cycle.

Heterologous prion-forming proteins interact to cross-seed aggregation in Saccharomyces cerevisiae

The early stages of protein misfolding remain incompletely understood, as most mammalian proteinopathies are only detected after irreversible protein aggregates have formed. Cross-seeding, where one aggregated protein templates the misfolding of a heterologous protein, is one mechanism proposed to stimulate protein aggregation and facilitate disease pathogenesis. Here, we demonstrate the existence of cross-seeding as a crucial step in the formation of the yeast prion [PSI ⁺], formed by the translation termination factor Sup35. We provide evidence for the genetic and physical interaction of the prion protein Rnq1 with Sup35 as a predominant mechanism leading to self-propagating Sup35 aggregation. We identify interacting sites within Rnq1 and Sup35 and determine the effects of breaking and restoring a crucial interaction. Altogether, our results demonstrate that single-residue disruption can drastically reduce the effects of cross-seeding, a finding that has important implications for human protein misfolding disorders.

The natural history of yeast prions

Although prions were first discovered through their link to severe brain degenerative diseases in animals, the emergence of prions as regulators of the phenotype of the yeast Saccharomyces cerevisiae and the filamentous fungus Podospora anserina has revealed a new facet of prion biology. In most cases, fungal prions are carried without apparent detriment to the host cell, representing a novel form of epigenetic inheritance. This raises the question of whether or not yeast prions are beneficial survival factors or actually gives rise to a "disease state" that is selected against in nature. To date, most studies on the impact of fungal prions have focused on laboratory-cultivated "domesticated" strains of S. cerevisiae. At least eight prions have now been described in this species, each with the potential to impact on a wide range of cellular processes. The discovery of prions in nondomesticated strains of S. cerevisiae and P. anserina has confirmed that prions are not simply an artifact of "domestication" of this species. In this review, I describe what we currently know about the phenotypic impact of fungal prions. I then describe how the interplay between host genotype and the prion-mediated changes can generate a wide array of phenotypic diversity. How such prion-generated diversity may be of benefit to the host in survival in a fluctuating, often hazardous environment is then outlined. Prion research has now entered a new phase in which we must now consider their biological function and evolutionary significance in the natural world.

Structural variants of yeast prions show conformer-specific requirements for chaperone activity

Molecular chaperones monitor protein homeostasis and defend against the misfolding and aggregation of proteins that is associated with protein conformational disorders. In these diseases, a variety of different aggregate structures can form. These are called prion strains, or variants, in prion diseases, and cause variation in disease pathogenesis. Here, we use variants of the yeast prions [RNQ+] and [PSI+] to explore the interactions of chaperones with distinct aggregate structures. We found that prion variants show striking variation in their relationship with Hsp40s. Specifically, the yeast Hsp40 Sis1 and its human orthologue Hdj1 had differential capacities to process prion variants, suggesting that Hsp40 selectivity has likely changed through evolution. We further show that such selectivity involves different domains of Sis1, with some prion conformers having a greater dependence on particular Hsp40 domains. Moreover, [PSI+] variants were more sensitive to certain alterations in Hsp70 activity as compared to [RNQ+] variants. Collectively, our data indicate that distinct chaperone machinery is required, or has differential capacity, to process different aggregate structures. Elucidating the intricacies of chaperone-client interactions, and how these are altered by particular client structures, will be crucial to understanding how this system can go awry in disease and contribute to pathological variation.

Extensive diversity of prion strains is defined by differential chaperone interactions and distinct amyloidogenic regions

Amyloidogenic proteins associated with a variety of unrelated diseases are typically capable of forming several distinct self-templating conformers. In prion diseases, these different structures, called prion strains (or variants), confer dramatic variation in disease pathology and transmission. Aggregate stability has been found to be a key determinant of the diverse pathological consequences of different prion strains. Yet, it remains largely unclear what other factors might account for the widespread phenotypic variation seen with aggregation-prone proteins. Here, we examined a set of yeast prion variants of the [RNQ+] prion that differ in their ability to induce the formation of another yeast prion called [PSI+]. Remarkably, we found that the [RNQ+] variants require different, non-contiguous regions of the Rnq1 protein for both prion propagation and [PSI+] induction. This included regions outside of the canonical prion-forming domain of Rnq1. Remarkably, such differences did not result in variation in aggregate stability. Our analysis also revealed a striking difference in the ability of these [RNQ+] variants to interact with the chaperone Sis1. Thus, our work shows that the differential influence of various amyloidogenic regions and interactions with host cofactors are critical determinants of the phenotypic consequences of distinct aggregate structures. This helps reveal the complex interdependent factors that influence how a particular amyloid structure may dictate disease pathology and progression.

Extracellular environment modulates the formation and propagation of particular amyloid structures

Amyloidogenic proteins, including prions, assemble into multiple forms of structurally distinct fibres. The [PSI(+)] prion, endogenous to the yeast Saccharomyces cerevisiae, is a dominantly inherited, epigenetic modifier of phenotypes. [PSI(+)] formation relies on the coexistence of another prion, [RNQ(+)]. Here, in order to better define the role of amyloid diversity on cellular phenotypes, we investigated how physiological and environmental changes impact the generation and propagation of diverse protein conformations from a single polypeptide. Utilizing the yeast model system, we defined extracellular factors that influence the formation of a spectrum of alternative self-propagating amyloid structures of the Sup35 protein, called [PSI(+)] variants. Strikingly, exposure to specific stressful environments dramatically altered the variants of [PSI(+)] that formed de novo. Additionally, we found that stress also influenced the association between the [PSI(+)] and [RNQ(+)] prions in a way that it superceded their typical relationship. Furthermore, changing the growth environment modified both the biochemical properties and [PSI(+)]-inducing capabilities of the [RNQ(+)] template. These data suggest that the cellular environment contributes to both the generation and the selective propagation of specific amyloid structures, providing insight into a key feature that impacts phenotypic diversity in yeast and the cross-species transmission barriers characteristic of prion diseases.

Wild yeast harbour a variety of distinct amyloid structures with strong prion-inducing capabilities

Variation in amyloid structures profoundly influences a wide array of pathological phenotypes in mammalian protein conformation disorders and dominantly inherited phenotypes in yeast. Here, we describe, for the first time, naturally occurring, self-propagating, structural variants of a prion protein isolated from wild strains of the yeast Saccharomyces cerevisiae. Variants of the [RNQ⁺] prion propagating in a variety of wild yeast differ biochemically, in their intracellular distributions, and in their ability to promote formation of the [PSI⁺] prion. [PSI⁺] is an epigenetic regulator of cellular phenotype and adaptability. Strikingly, we find that most natural [RNQ⁺] variants induced [PSI⁺] at high frequencies and the majority of [PSI⁺] variants elicited strong cellular phenotypes. We hypothesize that the presence of an efficient [RNQ⁺] template primes the cell for [PSI⁺] formation in order to induce [PSI⁺] in conditions where it would be advantageous. These studies utilize naturally occurring structural variants to expand our understanding of the consequences of diverse prion conformations on cellular phenotypes.

Spontaneous variants of the [RNQ+] prion in yeast demonstrate the extensive conformational diversity possible with prion proteins

Prion strains (or variants) are structurally distinct amyloid conformations arising from a single polypeptide sequence. The existence of prion strains has been well documented in mammalian prion diseases. In many cases, prion strains manifest as variation in disease progression and pathology, and in some cases, these prion strains also show distinct biochemical properties. Yet, the underlying basis of prion propagation and the extent of conformational possibilities available to amyloidogenic proteins remain largely undefined. Prion proteins in yeast that are also capable of maintaining multiple self-propagating structures have provided much insight into prion biology. Here, we explore the vast structural diversity of the yeast prion [RNQ+] in Saccharomyces cerevisiae. We screened for the formation of [RNQ+] in vivo, allowing us to calculate the rate of spontaneous formation as ~2.96x10^-6, and successfully isolate several different [RNQ+] variants. Through a comprehensive set of biochemical and biological analyses, we show that these prion variants are indeed novel. No individual property or set of properties, including aggregate stability and size, was sufficient to explain the physical basis and range of prion variants and their resulting cellular phenotypes. Furthermore, all of the [RNQ+] variants that we isolated were able to facilitate the de novo formation of the yeast prion [PSI+], an epigenetic determinant of translation termination. This supports the hypothesis that [RNQ+] acts as a functional amyloid in regulating the formation of [PSI+] to produce phenotypic diversity within a yeast population and promote adaptation. Collectively, this work shows the broad spectrum of available amyloid conformations, and thereby expands the foundation for studying the complex factors that interact to regulate the propagation of distinct aggregate structures.

Low activity of select Hsp104 mutants is sufficient to propagate unstable prion variants

The molecular chaperone network plays a critical role in the formation and propagation of self-replicating yeast prions. Not only do individual prions differ in their requirements for certain chaperones, but structural variants of the same prion can also display distinct dependences on the chaperone machinery, specifically Hsp104. The AAA+ ATPase Hsp104 is a disaggregase required for the maintenance of most known yeast prions. As a key component in the propagation of prions, understanding how Hsp104 differs in its interaction with specific variants is crucial to understanding how prion variants may be selected or evolve. Here, we investigate two novel mutations in Hsp104, hsp104-G254D, and hsp104-G730D, which allow us to elucidate some mechanistic features of Hsp104 disaggregation and its requirement for activity in propagating specific prion variants. Both Hsp104 mutants propagate the [PSI+] prion to some extent, but show a high rate of prion loss. Both Hsp104-G254D and Hsp104-G730D display reduced biochemical activity, yet differ in their ability to efficiently resolubilize disordered, heat-aggregated substrates. Additionally, both mutants impair weak [PSI+] propagation, but are capable of propagating the less stable strong [PSI+] variant to some extent. One of the Hsp104 mutants also has the ability to propagate one variant of the [RNQ+] prion. Thus, our data suggest that changes in Hsp104 activity limit substrate disaggregation in a manner that depends more on the stability of the substrate than the nature of the aggregated species.

Exploring the basis of [PIN(+)] variant differences in [PSI(+)] induction

Certain soluble proteins can form amyloid-like prion aggregates. Indeed, the same protein can make different types of aggregates, called variants. Each variant is heritable because it attracts soluble homologous protein to join its aggregate, which is then broken into seeds (propagons) and transmitted to daughter cells. [PSI(+)] and [PIN(+)] are respectively prion forms of Sup35 and Rnq1. Curiously, [PIN(+)] enhances the de novo induction of [PSI(+)]. Different [PIN(+)] variants do this to dramatically different extents. Here, we investigate the mechanism underlying this effect. Consistent with a heterologous prion cross-seeding model, different [PIN(+)] variants preferentially promoted the appearance of different variants of [PSI(+)]. However, we did not detect this specificity in vitro. Also, [PIN(+)] variant cross-seeding efficiencies were not proportional to the level of Rnq1 coimmunocaptured with Sup35 or to the number of [PIN(+)] propagons characteristic for that variant. This leads us to propose that [PIN(+)] variants differ in the cross-seeding quality of their seeds, following the Sup35/[PIN(+)] binding step.

Strain phenomenon in protein aggregation: Interplay between sequence and conformation

Studies of yeast and mammalian prions introduced the idea that the protein aggregates can exist in multiple stable conformations that can be propagated by seeding. These conformational states (aka strains) were shown to have distinct physical (secondary structure, stability) and biological (cytotoxicity, infectivity) properties. For mammalian prions they were also tied to differences in disease pathology and incubation time. It was later shown that this phenomenon is not limited to prion proteins, and distinct conformational states of amyloid fibrils and oligomers derived from a variety of proteins can be propagated both in vitro and in vivo. Moreover, in some cases these conformations were preserved even when propagated into a protein with a different sequence. There is now an increasing body of evidence that strain phenomenon is a generic feature of protein aggregation, and characteristic features of amyloid strains can be transmitted between unrelated sequences.

Patterns of [PSI (+) ] aggregation allow insights into cellular organization of yeast prion aggregates

The yeast prion phenomenon is very widespread and mounting evidence suggests that it has an impact on cellular regulatory mechanisms related to phenotypic responses to changing environments. Studying the aggregation patterns of prion amyloids during different stages of the prion life cycle is a first key step to understand major principles of how and where cells generate, organize and turn-over prion aggregates. The induction of the [PSI (+) ] state involves the actin cytoskeleton and quality control compartments such as the Insoluble Protein Deposit (IPOD). An initially unstable transitional induction state can be visualized by overexpression of the prion determinant and displays characteristic large ring- and ribbon-shaped aggregates consisting of poorly fragmented bundles of very long prion fibrils. In the mature prion state, the aggregation pattern is characterized by highly fragmented, shorter prion fibrils that form aggregates, which can be visualized through tagging with fluorescent proteins. The number of aggregates formed varies, ranging from a single large aggregate at the IPOD to multiple smaller ones, depending on several parameters discussed. Aggregate units below the resolution of light microscopy that are detectable by fluorescence correlation spectroscopy are in equilibrium with larger aggregates in this stage and can mediate faithful inheritance of the prion state. Loss of the prion state is often characterized by reduced fragmentation of prion fibrils and fewer, larger aggregates.

Fungal prions

For both mammalian and fungal prion proteins, conformational templating drives the phenomenon of protein-only infectivity. The conformational conversion of a protein to its transmissible prion state is associated with changes to host cellular physiology. In mammals, this change is synonymous with disease, whereas in fungi no notable detrimental effect on the host is typically observed. Instead, fungal prions can serve as epigenetic regulators of inheritance in the form of partial loss-of-function phenotypes. In the presence of environmental challenges, the prion state [PRION(+)], with its resource for phenotypic plasticity, can be associated with a growth advantage. The growing number of yeast proteins that can switch to a heritable [PRION(+)] form represents diverse and metabolically penetrating cellular functions, suggesting that the [PRION(+)] state in yeast is a functional one, albeit rarely found in nature. In this chapter, we introduce the biochemical and genetic properties of fungal prions, many of which are shared by the mammalian prion protein PrP, and then outline the major contributions that studies on fungal prions have made to prion biology.

Amyloid structure: conformational diversity and consequences

Many, perhaps most, proteins, are capable of forming self-propagating, β-sheet (amyloid) aggregates. Amyloid-like aggregates are found in a wide range of diseases and underlie prion-based inheritance. Despite intense interest in amyloids, structural details have only recently begun to be revealed as advances in biophysical approaches, such as hydrogen-deuterium exchange, X-ray crystallography, solid-state nuclear magnetic resonance (SSNMR), and cryoelectron microscopy (cryoEM), have enabled high-resolution insights into their molecular organization. Initial studies found that despite the highly divergent primary structure of different amyloid-forming proteins, amyloids from different sources share many structural similarities. With higher-resolution information, however, it has become clear that, on the molecular level, amyloids comprise a wide diversity of structures. Particularly surprising has been the finding that identical polypeptides can fold into multiple, distinct amyloid conformations and that this structural diversity can lead to distinct heritable prion states or strains.

The [RNQ+] prion: a model of both functional and pathological amyloid

The formation of fibrillar amyloid is most often associated with protein conformational disorders such as prion diseases, Alzheimer disease and Huntington disease. Interestingly, however, an increasing number of studies suggest that amyloid structures can sometimes play a functional role in normal biology. Several proteins form self-propagating amyloids called prions in the budding yeast Saccharomyces cerevisiae. These unique elements operate by creating a reversible, epigenetic change in phenotype. While the function of the non-prion conformation of the Rnq1 protein is unclear, the prion form, [RNQ+], acts to facilitate the de novo formation of other prions to influence cellular phenotypes. The [RNQ+] prion itself does not adversely affect the growth of yeast, but the overexpression of Rnq1p can form toxic aggregated structures that are not necessarily prions. The [RNQ+] prion is also involved in dictating the aggregation and toxicity of polyglutamine proteins ectopically expressed in yeast. Thus, the [RNQ+] prion provides a tractable model that has the potential to reveal significant insight into the factors that dictate how amyloid structures are initiated and propagated in both physiological and pathological contexts.

Fungal prions: structure, function and propagation

Prions are not uniquely associated with rare fatal neurodegenerative diseases in the animal kingdom; prions are also found in fungi and in particular the yeast Saccharomyces cerevisiae. As with animal prions, fungal prions are proteins able to exist in one or more self-propagating alternative conformations, but show little primary sequence relationship with the mammalian prion protein PrP. Rather, fungal prions represent a relatively diverse collection of proteins that participate in key cellular processes such as transcription and translation. Upon switching to their prion form, these proteins can generate stable, sometimes beneficial, changes in the host cell phenotype. Much has already been learnt about prion structure, and propagation and de novo generation of the prion state through studies in yeast and these findings are reviewed here.

The [RNQ+] prion: a model of both functional and pathological amyloid

The formation of fibrillar amyloid is most often associated with protein conformational disorders such as prion diseases, Alzheimer disease and Huntington disease. Interestingly, however, an increasing number of studies suggest that amyloid structures can sometimes play a functional role in normal biology. Several proteins form self-propagating amyloids called prions in the budding yeast Saccharomyces cerevisiae. These unique elements operate by creating a reversible, epigenetic change in phenotype. While the function of the non-prion conformation of the Rnq1 protein is unclear, the prion form, [RNQ+], acts to facilitate the de novo formation of other prions to influence cellular phenotypes. The [RNQ+] prion itself does not adversely affect the growth of yeast, but the overexpression of Rnq1p can form toxic aggregated structures that are not necessarily prions. The [RNQ+] prion is also involved in dictating the aggregation and toxicity of polyglutamine proteins ectopically expressed in yeast. Thus, the [RNQ+] prion provides a tractable model that has the potential to reveal significant insight into the factors that dictate how amyloid structures are initiated and propagated in both physiological and pathological contexts.