Curing of yeast [PSI+] prion by guanidine inactivation of Hsp104 does not require cell division

Hsp70 Binding to the N-terminal Domain of Hsp104 Regulates [PSI+] Curing by Hsp104 Overexpression

Hsp104 propagates the yeast prion [PSI+], the infectious form of Sup35, by severing the prion seeds, but when Hsp104 is overexpressed, it cures [PSI+] in a process that is not yet understood but may be caused by trimming, which removes monomers from the ends of the amyloid fibers. This curing was shown to depend on both the N-terminal domain of Hsp104 and the expression level of various members of the Hsp70 family, which raises the question as to whether these effects of Hsp70 are due to it binding to the Hsp70 binding site that was identified in the N-terminal domain of Hsp104, a site not involved in prion propagation. Investigating this question, we now find, first, that mutating this site prevents both the curing of [PSI+] by Hsp104 overexpression and the trimming activity of Hsp104. Second, we find that depending on the specific member of the Hsp70 family binding to the N-terminal domain of Hsp104, both trimming and the curing caused by Hsp104 overexpression are either increased or decreased in parallel. Therefore, the binding of Hsp70 to the N-terminal domain of Hsp104 regulates both the rate of [PSI+] trimming by Hsp104 and the rate of [PSI+] curing by Hsp104 overexpression.

Recent Insights on Alzheimer's Disease Originating from Yeast Models

In this review article, yeast model-based research advances regarding the role of Amyloid-β (Aβ), Tau and frameshift Ubiquitin UBB+1 in Alzheimer’s disease (AD) are discussed. Despite having limitations with regard to intercellular and cognitive AD aspects, these models have clearly shown their added value as complementary models for the study of the molecular aspects of these proteins, including their interplay with AD-related cellular processes such as mitochondrial dysfunction and altered proteostasis. Moreover, these yeast models have also shown their importance in translational research, e.g., in compound screenings and for AD diagnostics development. In addition to well-established Saccharomyces cerevisiae models, new upcoming Schizosaccharomyces pombe, Candida glabrata and Kluyveromyces lactis yeast models for Aβ and Tau are briefly described. Finally, traditional and more innovative research methodologies, e.g., for studying protein oligomerization/aggregation, are highlighted.

Study of Amyloids Using Yeast

We detail some of the genetic, biochemical, and physical methods useful in studying amyloids in yeast, particularly the yeast prions. These methods include cytoduction (cytoplasmic mixing), infection of cells with prion amyloids, use of green fluorescent protein fusions with amyloid-forming proteins for cytology, protein purification and amyloid formation, and electron microscopy of filaments.

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.

Differences in the curing of [PSI+] prion by various methods of Hsp104 inactivation

[PSI⁺] yeast, containing the misfolded amyloid conformation of Sup35 prion, is cured by inactivation of Hsp104. There has been controversy as to whether inactivation of Hsp104 by guanidine treatment or by overexpression of the dominant negative Hsp104 mutant, Hsp104-2KT, cures [PSI⁺] by the same mechanism– inhibition of the severing of the prion seeds. Using live cell imaging of Sup35-GFP, overexpression of Hsp104-2KT caused the foci to increase in size, then decrease in number, and finally disappear when the cells were cured, similar to that observed in cells cured by depletion of Hsp104. In contrast, guanidine initially caused an increase in foci size but then the foci disappeared before the cells were cured. By starving the yeast to make the foci visible in cells grown with guanidine, the number of cells with foci was found to correlate exactly with the number of [PSI⁺] cells, regardless of the curing method. Therefore, the fluorescent foci are the prion seeds required for maintenance of [PSI⁺] and inactivation of Hsp104 cures [PSI⁺] by preventing severing of the prion seeds. During curing with guanidine, the reduction in seed size is an Hsp104-dependent effect that cannot be explained by limited severing of the seeds. Instead, in the presence of guanidine, Hsp104 retains an activity that trims or reduces the size of the prion seeds by releasing Sup35 molecules that are unable to form new prion seeds. This Hsp104 activity may also occur in propagating yeast.

Study of amyloids using yeast

We detail some of the genetic, biochemical, and physical methods useful in studying amyloids in yeast, particularly the yeast prions. These methods include cytoduction (cytoplasmic mixing), infection of cells with prion amyloids, use of green fluorescent protein fusions with amyloid-forming proteins for cytology, protein purification and amyloid formation, and electron microscopy of filaments.

Insight into molecular basis of curing of [PSI+] prion by overexpression of 104-kDa heat shock protein (Hsp104)

Yeast prions are a powerful model for understanding the dynamics of protein aggregation associated with a number of human neurodegenerative disorders. The AAA+ protein disaggregase Hsp104 can sever the amyloid fibrils produced by yeast prions. This action results in the propagation of "seeds" that are transmitted to daughter cells during budding. Overexpression of Hsp104 eliminates the [PSI+] prion but not other prions. Using biochemical methods we identified Hsp104 binding sites in the highly charged middle domain of Sup35, the protein determinant of [PSI+]. Deletion of a short segment of the middle domain (amino acids 129-148) diminishes Hsp104 binding and strongly affects the ability of the middle domain to stimulate the ATPase activity of Hsp104. In yeast, [PSI+] maintained by Sup35 lacking this segment, like other prions, is propagated by Hsp104 but cannot be cured by Hsp104 overexpression. These results provide new insight into the enigmatic specificity of Hsp104-mediated curing of yeast prions and sheds light on the limitations of the ability of Hsp104 to eliminate aggregates produced by other aggregation-prone proteins.

Single-particle tracking of quantum dot-conjugated prion proteins inside yeast cells

Yeast is a model eukaryote with a variety of biological resources. Here we developed a method to track a quantum dot (QD)-conjugated protein in the budding yeast Saccharomyces cerevisiae. We chemically conjugated QDs with the yeast prion Sup35, incorporated them into yeast spheroplasts, and tracked the motions by conventional two-dimensional or three-dimensional tracking microscopy. The method paves the way toward the individual tracking of proteins of interest inside living yeast cells.

Pathogenic polyglutamine tracts are potent inducers of spontaneous Sup35 and Rnq1 amyloidogenesis

The glutamine/asparagine (Q/N)-rich yeast prion protein Sup35 has a low intrinsic propensity to spontaneously self-assemble into ordered, beta-sheet-rich amyloid fibrils. In yeast cells, de novo formation of Sup35 aggregates is greatly facilitated by high protein concentrations and the presence of preformed Q/N-rich protein aggregates that template Sup35 polymerization. Here, we have investigated whether aggregation-promoting polyglutamine (polyQ) tracts can stimulate the de novo formation of ordered Sup35 protein aggregates in the absence of Q/N-rich yeast prions. Fusion proteins with polyQ tracts of different lengths were produced and their ability to spontaneously self-assemble into amlyloid structures was analyzed using in vitro and in vivo model systems. We found that Sup35 fusions with pathogenic (>or=54 glutamines), as opposed to non-pathogenic (19 glutamines) polyQ tracts efficiently form seeding-competent protein aggregates. Strikingly, polyQ-mediated de novo assembly of Sup35 protein aggregates in yeast cells was independent of pre-existing Q/N-rich protein aggregates. This indicates that increasing the content of aggregation-promoting sequences enhances the tendency of Sup35 to spontaneously self-assemble into insoluble protein aggregates. A similar result was obtained when pathogenic polyQ tracts were linked to the yeast prion protein Rnq1, demonstrating that polyQ sequences are generic inducers of amyloidogenesis. In conclusion, long polyQ sequences are powerful molecular tools that allow the efficient production of seeding-competent amyloid structures.

Amyloid oligomers: diffuse oligomer-based transmission of yeast prions

Prions are infectious proteins, in which self-propagating amyloid conformations of proteins are transmitted. The budding yeast Saccharomyces cerevisiae, one of the best-studied model eukaryotes, also has prions, and thus provides a tractable model system with which to understand the mechanisms of prion phenomena. The yeast prions are protein-based heritable elements, such as [PSI(+)], in which aggregates of prion proteins are transmitted to daughter cells in a non-Mendelian manner. Although the genetic approaches preceded the yeast prion studies, recent investigations of the dynamic aspects of the prion proteins have unraveled the molecular mechanisms by which prions are propagated and transmitted. In particular, several lines of evidence have revealed that the oligomeric species of prion proteins dispersed in the cytoplasm are critical for the transmission. This review summarizes the topics on the transmissible entities of yeast prions, focusing mainly on the Sup35 protein in [PSI(+)].

Single mother-daughter pair analysis to clarify the diffusion properties of yeast prion Sup35 in guanidine-HCl-treated [PSI] cells

The yeast prion [PSI(+)] is a protein-based heritable element, in which aggregates of Sup35 protein are transmitted to daughter cells in a non-Mendelian manner. To elucidate the mechanism of the transmission, we have developed methods to directly analyse the dynamics of Sup35 fused with GFP in single mother-daughter pairs. As it is known that the treatment of yeast cells with guanidine hydrochloride (GuHCl) cures [PSI(+)] by perturbing Hsp104, a prion-remodelling factor, we analysed the diffusion profiles of Sup35-GFP in GuHCl-treated [PSI(+)] cells using fluorescence correlation spectroscopy (FCS). FCS analyses revealed that Sup35-GFP diffusion in the daughter cells was faster; that is, the Sup35-GFP particle was smaller, than that in the mother [PSI(+)] cells, and it eventually reached the diffusion profiles in [psi(-)] cells. We then analysed the flux of Sup35-GFP oligomers from mother to daughter [PSI(+)] cells in the presence of GuHCl, using a modified fluorescent recovery after photobleaching technique, and found that the flux of the diffuse oligomers was completely inhibited. The noninvasive methods described here can be applied to other protein-based transmissible systems inside living cells.

Application of GFP-labeling to study prions in yeast

Fluorescent live cell imaging has recently been used in numerous studies to examine prions in yeast. These fluorescence studies take advantage of the fact that unlike the normally folded form, the misfolded amyloid form of the prion protein is aggregated. The studies have used fluorescence to identify new prions, to study the transmission of prion from mother to daughter, and to understand the role of molecular chaperones in this transmission. The use of fluorescence imaging complements the more standard methods used to study prion propagation. This review discusses the various studies that have taken advantage of fluorescence imaging technique particularly in regard to understanding the transmission and curing of the [PSI(+)], the prion form of the translation termination factor Sup35p.

Cell division is essential for elimination of the yeast [PSI+] prion by guanidine hydrochloride

Guanidine hydrochloride (Gdn.HCl) blocks the propagation of yeast prions by inhibiting Hsp104, a molecular chaperone that is absolutely required for yeast prion propagation. We had previously proposed that ongoing cell division is required for Gdn.HCl-induced loss of the [PSI+] prion. Subsequently, Wu et al.[Wu Y, Greene LE, Masison DC, Eisenberg E (2005) Proc Natl Acad Sci USA 102:12789-12794] claimed to show that Gdn.HCl can eliminate the [PSI+] prion from alpha-factor-arrested cells leading them to propose that in Gdn.HCl-treated cells the prion aggregates are degraded by an Hsp104-independent mechanism. Here we demonstrate that the results of Wu et al. can be explained by an unusually high rate of alpha-factor-induced cell death in the [PSI+] strain (780-1D) used in their studies. What appeared to be no growth in their experiments was actually no increase in total cell number in a dividing culture through a counterbalancing level of cell death. Using media-exchange experiments, we provide further support for our original proposal that elimination of the [PSI+] prion by Gdn.HCl requires ongoing cell division and that prions are not destroyed during or after the evident curing phase.

Prion stability

The rate of spontaneous change from psi(-) to the psi(+) condition, determined in yeast by states of the Sup35p protein, is briefly discussed together with the conditions necessary for such change to occur. Conditions that promote and which affect the rate of induction of psi(+) in Sup35p and of other prion-forming proteins to their respective prion forms are also discussed. These include the influence of the amount of non-prion protein, the presence of other prions, the activity of chaperones, and brief descriptions of the role of native sequences in the proteins and how alteration of sequences in prion-forming proteins influences the rate of induction of [prion(+)] and amyloid forms. The second part of this article discusses the conditions which affect the reversion of psi(+) to psi-, including factors which affect the copy-number of prion "seeds" or propagons and their partition. The principal factor discussed is the activity of the chaperone Hsp104, but the existence of other factors, such protein sequence and of other, less well-studied agents is touched upon and comparisons are made, as appropriate, with studies with other yeast prions. We conclude with a discussion of models of maintenance, in particular that of Tanaka et al. published in Nature (2006), which provides much insight into the phenotypic and genetic parameters of the numerous "variants" of prions increasingly being described in the literature.

Approximations for expected generation number

A deterministic formula is commonly used to approximate the expected generation number of a population of growing cells. However, this can give misleading results because it does not allow for natural variation in the times that individual cells take to reproduce. Here we present more accurate approximations for both symmetric and asymmetric cell division. Based on the first two moments of the generation time distribution, these approximations are also robust. We illustrate the improved approximations using data that arise from monitoring individual yeast cells under a microscope and also demonstrate how the approximations can be used when such detailed data are not available.

Hsp104-dependent remodeling of prion complexes mediates protein-only inheritance

Inheritance of phenotypic traits depends on two key events: replication of the determinant of that trait and partitioning of these copies between mother and daughter cells. Although these processes are well understood for nucleic acid–based genes, the mechanisms by which protein-only or prion-based genetic elements direct phenotypic inheritance are poorly understood. Here, we report a process crucial for inheritance of the Saccharomyces cerevisiae prion [PSI⁺], a self-replicating conformer of the Sup35 protein. By tightly controlling expression of a Sup35-GFP fusion, we directly observe remodeling of existing Sup35^[PSI+] complexes in vivo. This dynamic change in Sup35^[PSI+] is lost when the molecular chaperone Hsp104, a factor essential for propagation of all yeast prions, is functionally impaired. The loss of Sup35^[PSI+] remodeling by Hsp104 decreases the mobility of these complexes in the cytosol, creates a segregation bias that limits their transmission to daughter cells, and consequently diminishes the efficiency of conversion of newly made Sup35 to the prion form. Our observations resolve several seemingly conflicting reports on the mechanism of Hsp104 action and point to a single Hsp104-dependent event in prion propagation.

The inheritance of phenotypic traits (the observable characteristics of the organism) is a fundamental process in biology. Most phenotypes are controlled by a cell's genes, and a particular phenotype becomes heritable when this underlying genetic information is copied and transmitted to progeny. In contrast, another group of phenotypes appears to be inherited through a protein-only, or prion, mechanism in which the structure of a protein rather than its sequence is the molecular determinant of the phenotype. It is thought that the presence of a prion in a cell forces conversion of a normal cellular protein into a differently folded shape (the prion form), which simultaneously deprives the cell of the protein's normal function and causes the prion-folded protein to aggregate within the cell. However, prion inheritance (how prions are passed down to daughter cells) remains poorly understood.

Using the yeast prion [PSI⁺] as a model system, we have elucidated a process necessary for protein-only inheritance. Here we show that the molecular chaperone Hsp104, a factor necessary for the inheritance of all known yeast prions, plays a single primary role in generating additional templates for protein-state replication. In the absence of this activity, existing prion templates are inefficiently transferred to daughter cells. As a consequence, the rate of protein-state replication is greatly decreased, and the protein-based phenotype is progressively lost.

The authors examine the role of the molecular chaperone Hsp104 in controlling inheritance of the prion form of Sup35^[PSI+].

Prion propagation: the role of protein dynamics

The transfer of phenotypes from one individual to another is a fundamental aspect of biology. In addition to traditional nucleic acid-based genetic determinants, unique proteins known as prions can also act as elements of inheritance, infectivity, and disease. Nucleic acids and proteins encode genetic information in distinct ways, either in the sequence of bases in DNA or RNA or in the three dimensional structure of the polypeptide chain. Given these differences in the nature of the genetic repository, the mechanisms underlying the transmission of nucleic acid-based and protein-based phenotypes are necessarily distinct. While the appearance, persistence and transfer of nucleic acid determinants require the synthesis of new polymers, recent studies indicate that prions are propagated through dynamic transitions in the structure of existing protein.

Dynamics of yeast prion aggregates in single living cells

Prions are propagating proteins that are ordered protein aggregates, in which the phenotypic trait is retained in the altered protein conformers. To understand the dynamics of the prion aggregates in living cells, we directly monitored the fate of the aggregates using an on-chip single-cell cultivation system as well as fluorescence correlation spectroscopy (FCS). Single-cell imaging revealed that the visible foci of yeast prion Sup35 fused with GFP are dispersed throughout the cytoplasm during cell growth, but retain the prion phenotype. FCS showed that [PSI+] cells, irrespective of the presence of foci, contain diffuse oligomers, which are transmitted to their daughter cells. Single-cell observations of the oligomer-based transmission provide a link between previous in vivo and in vitro analyses of the prion and shed light on the relationship between the protein conformation and the phenotype.

Application of photobleaching for measuring diffusion of prion proteins in cytosol of yeast cells

Measurement of fluorescence recovery after photobleaching (FRAP) is a non-invasive technique for studying protein dynamics in real time in living cells. FRAP studies are carried out on proteins tagged with green fluorescent protein (GFP) or one of its spectral variants. Illumination with high intensity laser light irreversibly bleaches the GFP fluorescence but has no effect on protein function. By photobleaching a limited region of the cytoplasm, the rate of fluorescence recovery provides a measure of the rate of protein diffusion. A detailed description of the FRAP technique is given, including its application to measuring the mobility of GFP-tagged Sup35p in [psi(-)] and [PSI(+)] cells.

The [PSI+] prion of yeast: A problem of inheritance

The [PSI(+)] prion of the yeast Saccharomyces cerevisiae was first identified by Brian Cox some 40 years ago as a non-Mendelian genetic element that modulated the efficiency of nonsense suppression. Following the suggestion by Reed Wickner in 1994 that such elements might be accounted for by invoking a prion-based model, it was subsequently established that the [PSI(+)] determinant was the prion form of the Sup35p protein. In this article, we review how a combination of classical genetic approaches and modern molecular and biochemical methods has provided conclusive evidence of the prion basis of the [PSI(+)] determinant. In so doing we have tried to provide a historical context, but also describe the results of more recent experiments aimed at elucidating the mechanism by which the [PSI(+)] (and other yeast prions) are efficiently propagated in dividing cells. While understanding of the [PSI(+)] prion and its mode of propagation has, and will continue to have, an impact on mammalian prion biology nevertheless the very existence of a protein-based mechanism that can have a beneficial impact on a cell's fitness provides equally sound justification to fully explore yeast prions.