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1.  Prions are a common mechanism for phenotypic inheritance in wild yeasts 
Nature  2012;482(7385):363-368.
SUMMARY
The self-templating conformations of yeast prion proteins act as epigenetic elements of inheritance. Yeast prions might provide a mechanism for generating heritable phenotypic diversity that promotes survival in fluctuating environments and the evolution of new traits. However, this hypothesis is highly controversial. Prions that create new traits have not been found in wild strains, leading to the perception that they are rare “diseases” of laboratory cultivation. Here we biochemically test ~700 wild strains of Saccharomyces for [PSI+] or [MOT3+], and find these prions in many. They conferred diverse phenotypes that were frequently beneficial under selective conditions. Simple meiotic re-assortment of the variation harboured within a strain readily fixed one such trait, making it robust and prion-independent. Finally, we genetically screened for unknown prion elements. Fully one third of wild strains harboured them. These, too, created diverse, often beneficial phenotypes. Thus, prions broadly govern heritable traits in nature, in a manner that could profoundly expand adaptive opportunities.
doi:10.1038/nature10875
PMCID: PMC3319070  PMID: 22337056
2.  Genetic and epigenetic control of the efficiency and fidelity of cross-species prion transmission 
Molecular microbiology  2010;76(6):1483-1499.
Summary
Self-perpetuating amyloid-based protein isoforms (prions) transmit neurodegenerative diseases in mammals and phenotypic traits in yeast. Although mechanisms that control species-specificity of prion transmission are poorly understood, studies of closely related orthologs of yeast prion protein Sup35 demonstrate that cross-species prion transmission is modulated by both genetic (specific sequence elements) and epigenetic (prion variants, or “strains”) factors. Depending on the prion variant, the species barrier could be controlled at the level of either heterologous coaggregation or conversion of the aggregate-associated heterologous protein into a prion polymer. Sequence divergence influences cross-species transmission of different prion variants in opposing ways. The ability of a heterologous prion domain to either faithfully reproduce or irreversibly switch the variant-specific prion patterns depends on both sequence divergence and the prion variant. Sequence variations within different modules of prion domains contribute to transmission barriers in different cross-species combinations. Individual amino acid substitutions within short amyloidogenic stretches drastically alter patterns of cross-species prion conversion, implicating these stretches as major determinants of species specificity.
doi:10.1111/j.1365-2958.2010.07177.x
PMCID: PMC3025758  PMID: 20444092
amyloid; Saccharomyces bayanus; Saccharomyces cerevisiae; Saccharomyces paradoxus; yeast
3.  Dissection and Design of Yeast Prions 
PLoS Biology  2004;2(4):e86.
Many proteins can misfold into β-sheet-rich, self-seeding polymers (amyloids). Prions are exceptional among such aggregates in that they are also infectious. In fungi, prions are not pathogenic but rather act as epigenetic regulators of cell physiology, providing a powerful model for studying the mechanism of prion replication. We used prion-forming domains from two budding yeast proteins (Sup35p and New1p) to examine the requirements for prion formation and inheritance. In both proteins, a glutamine/asparagine-rich (Q/N-rich) tract mediates sequence-specific aggregation, while an adjacent motif, the oligopeptide repeat, is required for the replication and stable inheritance of these aggregates. Our findings help to explain why although Q/N-rich proteins are relatively common, few form heritable aggregates: prion inheritance requires both an aggregation sequence responsible for self-seeded growth and an element that permits chaperone-dependent replication of the aggregate. Using this knowledge, we have designed novel artificial prions by fusing the replication element of Sup35p to aggregation-prone sequences from other proteins, including pathogenically expanded polyglutamine.
Artificial prions - infectious, misfolded proteins - can be created by fusing the replication element of one prion to aggregation sequences from another
doi:10.1371/journal.pbio.0020086
PMCID: PMC374241  PMID: 15045026
4.  A systematic survey identifies prions and illuminates sequence features of prionogenic proteins 
Cell  2009;137(1):146-158.
SUMMARY
Prions are proteins that convert between structurally and functionally distinct states, one or more of which is transmissible. In yeast, this ability allows them to act as non-Mendelian elements of phenotypic inheritance. To further our understanding of prion biology, we conducted a bioinformatic proteome-wide survey for prionogenic proteins in S. cerevisiae, followed by experimental investigations of 100 prion candidates. We found an unexpected amino acid bias in aggregation-prone candidates and discovered that 19 of these could also form prions. At least one of these prion proteins, Mot3, produces a bona fide prion in its natural context that increases population-level phenotypic heterogeneity. The self-perpetuating states of these proteins present a vast source of heritable phenotypic variation that increases the adaptability of yeast populations to diverse environments.
doi:10.1016/j.cell.2009.02.044
PMCID: PMC2683788  PMID: 19345193
prion; amyloid; aggregation; non-Mendelian inheritance
5.  Infectious Fold and Amyloid Propagation in Podospora anserina 
Prion  2007;1(1):44-47.
Amyloid protein aggregation is involved in serious neurodegenerative disorders such as Alzheimer's disease and transmissible encephalopathies. The concept of an infectious protein (prion) being the scrapie agent was successfully validated for several yeast and fungi proteins. Ure2, Sup35 and Rnq1 in Saccharomyces cerevisiae and HET-s in Podospora anserina have been genetically and biochemically identified as prion proteins. Studies on these proteins have revealed critical information on the mechanisms of prions appearance and propagation. The prion phenotype correlates with the aggregation state of these particular proteins. In vitro, the recombinant prion proteins form amyloid fibers characterized by rich β sheet content. In a previous work on the HET-s prion protein Podospora, we demonstrated the infectivity of HET-s recombinant amyloid aggregates. More recently, the structural analysis of the HET-s prion domain associated with in vivo mutagenesis allowed us to propose a model for the infectious fold of the HET-s prion domain. Further investigations to complete this model are discussed in this review, as are relevant questions about the [Het-s] system of Podospora anserina.
PMCID: PMC2633707  PMID: 19164904
prion; HET-s; Podospora; amyloid; infectious; β sheet; mutagenesis; fold; propagation
6.  Neuroinvasion in Prion Diseases: The Roles of Ascending Neural Infection and Blood Dissemination 
Prion disorders are infectious, neurodegenerative diseases that affect humans and animals. Susceptibility to some prion diseases such as kuru or the new variant of Creutzfeldt-Jakob disease in humans and scrapie in sheep and goats is influenced by polymorphisms of the coding region of the prion protein gene, while other prion disorders such as fatal familial insomnia, familial Creutzfeldt-Jakob disease, or Gerstmann-Straussler-Scheinker disease in humans have an underlying inherited genetic basis. Several prion strains have been demonstrated experimentally in rodents and sheep. The progression and pathogenesis of disease is influenced by both genetic differences in the prion protein and prion strain. Some prion diseases only affect the central nervous system whereas others involve the peripheral organs prior to neuroinvasion. Many experiments undertaken in different species and using different prion strains have postulated common pathways of neuroinvasion. It is suggested that prions access the autonomic nerves innervating peripheral organs and tissues to finally reach the central nervous system. We review here published data supporting this view and additional data suggesting that neuroinvasion may concurrently or independently involve the blood vascular system.
doi:10.1155/2010/747892
PMCID: PMC2905956  PMID: 20652006
7.  Quaternary Structure of Pathological Prion Protein as a Determining Factor of Strain-Specific Prion Replication Dynamics 
PLoS Pathogens  2013;9(10):e1003702.
Prions are proteinaceous infectious agents responsible for fatal neurodegenerative diseases in animals and humans. They are essentially composed of PrPSc, an aggregated, misfolded conformer of the ubiquitously expressed host-encoded prion protein (PrPC). Stable variations in PrPSc conformation are assumed to encode the phenotypically tangible prion strains diversity. However the direct contribution of PrPSc quaternary structure to the strain biological information remains mostly unknown. Applying a sedimentation velocity fractionation technique to a panel of ovine prion strains, classified as fast and slow according to their incubation time in ovine PrP transgenic mice, has previously led to the observation that the relationship between prion infectivity and PrPSc quaternary structure was not univocal. For the fast strains specifically, infectivity sedimented slowly and segregated from the bulk of proteinase-K resistant PrPSc. To carefully separate the respective contributions of size and density to this hydrodynamic behavior, we performed sedimentation at the equilibrium and varied the solubilization conditions. The density profile of prion infectivity and proteinase-K resistant PrPSc tended to overlap whatever the strain, fast or slow, leaving only size as the main responsible factor for the specific velocity properties of the fast strain most infectious component. We further show that this velocity-isolable population of discrete assemblies perfectly resists limited proteolysis and that its templating activity, as assessed by protein misfolding cyclic amplification outcompetes by several orders of magnitude that of the bulk of larger size PrPSc aggregates. Together, the tight correlation between small size, conversion efficiency and duration of disease establishes PrPSc quaternary structure as a determining factor of prion replication dynamics. For certain strains, a subset of PrP assemblies appears to be the best template for prion replication. This has important implications for fundamental studies on prions.
Author Summary
Prions are infectious agents causing irremediably fatal neurodegenerative diseases in human and in farmed or wild animals. They are thought to be formed from abnormally folded assemblies (PrPSc) of the host-encoded prion protein (PrPC). Different PrPSc conformational variants associated with distinct biological phenotypes, or ‘strains,’ can propagate in the same host. To gain some structural information on the physical relationship between packing order (i.e. quaternary structure) and the strain-specific biological information, we previously subjected PrPSc assemblies from prion strains classified as fast or slow (according to their survival time in susceptible laboratory animals) to sedimentation velocity ultracentrifugation experiments. For the fast strains specifically, the most infectious assemblies sedimented slowly and partitioned from the bulk of PrPSc macromolecular complexes. By changing the solubilization and sedimentation conditions, we established here that a small PrPSc aggregation size and not a low density accounts for these hydrodynamic properties. We further showed that these small assemblies resist proteolytic digestion and outcompete by several orders of magnitude the larger-size assemblies in cell-free prion conversion assays. Thus PrPSc quaternary structure appears to be a determining factor of prion replication dynamics. For certain strains, a discrete subset of PrPSc assemblies appears to be the best template for prion replication.
doi:10.1371/journal.ppat.1003702
PMCID: PMC3795044  PMID: 24130496
8.  The NatA Acetyltransferase Couples Sup35 Prion Complexes to the [PSI+] Phenotype 
Molecular Biology of the Cell  2009;20(3):1068-1080.
Protein-only (prion) epigenetic elements confer unique phenotypes by adopting alternate conformations that specify new traits. Given the conformational flexibility of prion proteins, protein-only inheritance requires efficient self-replication of the underlying conformation. To explore the cellular regulation of conformational self-replication and its phenotypic effects, we analyzed genetic interactions between [PSI+], a prion form of the S. cerevisiae Sup35 protein (Sup35[PSI+]), and the three Nα-acetyltransferases, NatA, NatB, and NatC, which collectively modify ∼50% of yeast proteins. Although prion propagation proceeds normally in the absence of NatB or NatC, the [PSI+] phenotype is reversed in strains lacking NatA. Despite this change in phenotype, [PSI+] NatA mutants continue to propagate heritable Sup35[PSI+]. This uncoupling of protein state and phenotype does not arise through a decrease in the number or activity of prion templates (propagons) or through an increase in soluble Sup35. Rather, NatA null strains are specifically impaired in establishing the translation termination defect that normally accompanies Sup35 incorporation into prion complexes. The NatA effect cannot be explained by the modification of known components of the [PSI+] prion cycle including Sup35; thus, novel acetylated cellular factors must act to establish and maintain the tight link between Sup35[PSI+] complexes and their phenotypic effects.
doi:10.1091/mbc.E08-04-0436
PMCID: PMC2633373  PMID: 19073888
9.  The tip of the iceberg: RNA-binding proteins with prion-like domains in neurodegenerative disease 
Brain Research  2012;1462:61-80.
Prions are self-templating protein conformers that are naturally transmitted between individuals and promote phenotypic change. In yeast, prion-encoded phenotypes can be beneficial, neutral or deleterious depending upon genetic background and environmental conditions. A distinctive and portable ‘prion domain’ enriched in asparagine, glutamine, tyrosine and glycine residues unifies the majority of yeast prion proteins. Deletion of this domain precludes prionogenesis and appending this domain to reporter proteins can confer prionogenicity. An algorithm designed to detect prion domains has successfully identified 19 domains that can confer prion behavior. Scouring the human genome with this algorithm enriches a select group of RNA-binding proteins harboring a canonical RNA recognition motif (RRM) and a putative prion domain. Indeed, of 210 human RRM-bearing proteins, 29 have a putative prion domain, and 12 of these are in the top 60 prion candidates in the entire genome. Startlingly, these RNA-binding prion candidates are inexorably emerging, one by one, in the pathology and genetics of devastating neurodegenerative disorders, including: amyotrophic lateral sclerosis (ALS), frontotemporal lobar degeneration with ubiquitin-positive inclusions (FTLD-U), Alzheimer’s disease and Huntington’s disease. For example, FUS and TDP-43, which rank 1st and 10th among RRM-bearing prion candidates, form cytoplasmic inclusions in the degenerating motor neurons of ALS patients and mutations in TDP-43 and FUS cause familial ALS. Recently, perturbed RNA-binding proteostasis of TAF15, which is the 2nd ranked RRM-bearing prion candidate, has been connected with ALS and FTLD-U. We strongly suspect that we have now merely reached the tip of the iceberg. We predict that additional RNA-binding prion candidates identified by our algorithm will soon surface as genetic modifiers or causes of diverse neurodegenerative conditions. Indeed, simple prion-like transfer mechanisms involving the prion-like domains of RNA-binding proteins could underlie the classical non-cell-autonomous emanation of neurodegenerative pathology from originating epicenters to neighboring portions of the nervous system.
doi:10.1016/j.brainres.2012.01.016
PMCID: PMC3372647  PMID: 22445064
10.  Prion Protein Repeat Expansion Results in Increased Aggregation and Reveals Phenotypic Variability▿  
Molecular and Cellular Biology  2007;27(15):5445-5455.
Mammalian prion diseases are fatal neurodegenerative disorders dependent on the prion protein PrP. Expansion of the oligopeptide repeats (ORE) found in PrP is associated with inherited prion diseases. Patients with ORE frequently harbor PrP aggregates, but other factors may contribute to pathology, as they often present with unexplained phenotypic variability. We created chimeric yeast-mammalian prion proteins to examine the influence of the PrP ORE on prion properties in yeast. Remarkably, all chimeric proteins maintained prion characteristics. The largest repeat expansion chimera displayed a higher propensity to maintain a self-propagating aggregated state. Strikingly, the repeat expansion conferred increased conformational flexibility, as observed by enhanced phenotypic variation. Furthermore, the repeat expansion chimera displayed an increased rate of prion conversion, but only in the presence of another aggregate, the [RNQ+] prion. We suggest that the PrP ORE increases the conformational flexibility of the prion protein, thereby enhancing the formation of multiple distinct aggregate structures and allowing more frequent prion conversion. Both of these characteristics may contribute to the phenotypic variability associated with PrP repeat expansion diseases.
doi:10.1128/MCB.02127-06
PMCID: PMC1952097  PMID: 17548473
11.  Prion proteostasis 
Prion  2008;2(4):135-140.
Infectious amyloid forms of the release factor, Sup35, comprise the yeast prion [PSI+]. This protein-based unit of inheritance is an evolutionary capacitor able to release cryptic genetic variation during environmental stress and generate potentially beneficial phenotypes. Genetic data have uncovered a sophisticated proteostasis network that tightly regulates [PSI+] formation, propagation and elimination. Central to this network, is the AAA+ ATPase and protein disaggregase, Hsp104. Shifting the balance of the cytosolic Hsp70:Hsp40 chaperone machinery and associated nucleotide exchange factors also influences the [PSI+] prion cycle. Yet, a precise understanding of how these systems co-operate to directly modulate the protein folding events required for sustainable Sup35 prionogenesis has remained elusive. Here, we spotlight recent advances that begin to clarify this issue. We suggest that the Hsp70:Hsp40 chaperone machinery functions collectively as a rheostat that adjusts Hsp104's basic prion-remodeling activities.
PMCID: PMC2658762  PMID: 19242125
Sup35; prion; Hsp104; Hsp70; Hsp40; chaperone
12.  The Genetic Control of the Formation and Propagation of the [PSI+] Prion of Yeast 
Prion  2007;1(2):101-109.
It is over 40 years since it was first reported that the yeast Saccahromyces cerevisiae contains two unusual cytoplasmic ‘genetic’ elements: [PSI+] and [URE3]. Remarkably the underlying determinants are protein-based rather than nucleic acid-based, i.e., that they are prions, and we have already learnt much about their inheritance and phenotypic effects from the application of ‘classical’ genetic studies alongside the more modern molecular, cellular and biochemical approaches. Of particular value has been the exploitation of chemical mutagens and ‘antagonistic’ mutants which directly affect the replication and/or transmission of yeast prions. In this Chapter we describe what has emerged from the application of classical and molecular genetic studies, to the most intensively studied of the three native yeast prions, the [PSI+] prion.
PMCID: PMC2634449  PMID: 19164924
yeast; [PSI]; prion; SUP35/eRF3; SUP45/eRF1; antisuppressor; [PSI+] maintenance genes; Hsp104; prion antagonists
13.  Prions, protein homeostasis, and phenotypic diversity 
Trends in cell biology  2010;20(3):125-133.
Prions are fascinating but often misunderstood protein aggregation phenomena. The traditional association of the mammalian prion protein with disease has overshadowed a potentially more interesting attribute of prions - their ability to create protein-based molecular memories. In fungi, prions alter the relationship between genotype and phenotype in a heritable way that diversifies clonal populations. Recent findings in yeast indicate that prions may be much more common than previously realized. Moreover, prion-driven phenotypic diversity increases under stress, and can be amplified by the dynamic maturation of prion-initiating states. We argue that these qualities allow prions to act as bet-hedging devices that facilitate yeast’s adaptation to stressful environments, and may speed the evolution of new traits.
doi:10.1016/j.tcb.2009.12.003
PMCID: PMC2846750  PMID: 20071174
14.  Hsp104-Dependent Remodeling of Prion Complexes Mediates Protein-Only Inheritance  
PLoS Biology  2007;5(2):e24.
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.
Author Summary
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+].
doi:10.1371/journal.pbio.0050024
PMCID: PMC1779812  PMID: 17253904
15.  Prion and Nonprion Amyloids 
Prion  2007;1(3):179-184.
Yeast prion determinants are related to polymerization of some proteins into amyloid-like fibers. The [PSI+] determinant reflects polymerization of the Sup35 protein. Fragmentation of prion polymers by the Hsp104 chaperone represents a key step of the prion replication cycle. The frequency of fragmentation varies depending on the structure of the prion polymers and defines variation in the prion phenotypes, e.g., the suppressor strength of [PSI+] and stability of its inheritance. Besides [PSI+], overproduction of Sup35 can produce nonheritable phenotypically silent Sup35 amyloid-like polymers. These polymers are fragmented poorly and are present due to efficient seeding with the Rnq1 prion polymers, which occurs by several orders of magnitude more frequently than seeding of [PSI+] appearance. Such Sup35 polymers resemble human nonprion amyloids by their nonheritability, mode of appearance and increased size. Thus, a single protein, Sup35, can model both prion and nonprion amyloids. In yeast, these phenomena are distinguished by the frequency of polymer fragmentation. We argue that in mammals the fragmentation frequency also represents a key factor defining differing properties of prion and nonprion amyloids, including infectivity. By analogy with the Rnq1 seeding of nonheritable Sup35 polymers, the “species barrier” in prion transmission may be due to seeding by heterologous prion of nontransmissible type of amyloid, rather than due to the lack of seeding.
PMCID: PMC2634591  PMID: 19164899
amyloid; prion; Rnq1; Sup35; Ure2; translation termination; yeast
16.  Biochemical Properties of Highly Neuroinvasive Prion Strains 
PLoS Pathogens  2012;8(2):e1002522.
Infectious prions propagate from peripheral entry sites into the central nervous system (CNS), where they cause progressive neurodegeneration that ultimately leads to death. Yet the pathogenesis of prion disease can vary dramatically depending on the strain, or conformational variant of the aberrantly folded and aggregated protein, PrPSc. Although most prion strains invade the CNS, some prion strains cannot gain entry and do not cause clinical signs of disease. The conformational basis for this remarkable variation in the pathogenesis among strains is unclear. Using mouse-adapted prion strains, here we show that highly neuroinvasive prion strains primarily form diffuse aggregates in brain and are noncongophilic, conformationally unstable in denaturing conditions, and lead to rapidly lethal disease. These neuroinvasive strains efficiently generate PrPSc over short incubation periods. In contrast, the weakly neuroinvasive prion strains form large fibrillary plaques and are stable, congophilic, and inefficiently generate PrPSc over long incubation periods. Overall, these results indicate that the most neuroinvasive prion strains are also the least stable, and support the concept that the efficient replication and unstable nature of the most rapidly converting prions may be a feature linked to their efficient spread into the CNS.
Author Summary
Prion diseases are fatal neurodegenerative disorders that are also infectious. Prions are composed of a misfolded, aggregated form of a normal cellular protein that is highly expressed in neurons. Prion- infected individuals show variability in the clinical signs and brain regions that selectively accumulate prions, even within the same species expressing the same prion protein sequence. The basis of these divergent disease phenotypes is unclear, but is thought to be due to different conformations of the misfolded prion protein, known as strains. Here we characterized the neuropathology and biochemical properties of prion strains that efficiently or poorly invade the CNS from their peripheral entry site. We show that prion strains that efficiently invade the CNS also cause a rapidly terminal disease after an intracerebral exposure. These rapidly lethal strains were unstable when exposed to denaturants or high temperatures, and efficiently accumulated misfolded prion protein over a short incubation period in vivo. Our findings indicate that the most invasive, rapidly spreading strains are also the least conformationally stable.
doi:10.1371/journal.ppat.1002522
PMCID: PMC3271082  PMID: 22319450
17.  The yeast global transcriptional co-repressor protein Cyc8 can propagate as a prion 
Nature cell biology  2009;11(3):344-349.
Summary
Although many proteins can misfold into a self-seeding amyloid-like conformation1, only six are known to be infectious, i.e. prions; [PSI+], [PIN+], [URE3], [SWI+] and [HET-s] cause distinct heritable physiological changes in fungi2–4, while PrPSc causes infectious encephalopathies in mammals5. It is unknown if “protein-only” inheritance is limited to these exceptional cases, or represents a widespread mechanism of epigenetic control. Towards this goal, we now describe a new prion formed by the Cyc8 (Ssn6) protein of Saccharomyces cerevisiae. Analogous to other yeast prions, transient over-production of a glutamine-rich region of Cyc8 induced a heritable dominant cyc8− phenotype that is transmitted cytoplasmically and dependent on the chaperone Hsp104 and the continued presence of the Cyc8 protein. The evolutionarily conserved Cyc8-Tup1 global transcriptional repressor complex6 forms one of the largest gene regulatory circuits, controlling the expression of over 7% of yeast genes7. Our finding that Cyc8 can propagate as a prion, together with a recent report that Swi1 of the Swi-Snf global transcriptional regulatory complex also has a prion form4, shows that prionization can lead to mass activation or repression of yeast genes and is suggestive of a link between the epigenetic phenomena of chromatin remodeling and prion formation.
doi:10.1038/ncb1843
PMCID: PMC2667906  PMID: 19219034
18.  PrionHome: A Database of Prions and Other Sequences Relevant to Prion Phenomena 
PLoS ONE  2012;7(2):e31785.
Prions are units of propagation of an altered state of a protein or proteins; prions can propagate from organism to organism, through cooption of other protein copies. Prions contain no necessary nucleic acids, and are important both as both pathogenic agents, and as a potential force in epigenetic phenomena. The original prions were derived from a misfolded form of the mammalian Prion Protein PrP. Infection by these prions causes neurodegenerative diseases. Other prions cause non-Mendelian inheritance in budding yeast, and sometimes act as diseases of yeast. We report the bioinformatic construction of the PrionHome, a database of >2000 prion-related sequences. The data was collated from various public and private resources and filtered for redundancy. The data was then processed according to a transparent classification system of prionogenic sequences (i.e., sequences that can make prions), prionoids (i.e., proteins that propagate like prions between individual cells), and other prion-related phenomena. There are eight PrionHome classifications for sequences. The first four classifications are derived from experimental observations: prionogenic sequences, prionoids, other prion-related phenomena, and prion interactors. The second four classifications are derived from sequence analysis: orthologs, paralogs, pseudogenes, and candidate-prionogenic sequences. Database entries list: supporting information for PrionHome classifications, prion-determinant areas (where relevant), and disordered and compositionally-biased regions. Also included are literature references for the PrionHome classifications, transcripts and genomic coordinates, and structural data (including comparative models made for the PrionHome from manually curated alignments). We provide database usage examples for both vertebrate and fungal prion contexts. Using the database data, we have performed a detailed analysis of the compositional biases in known budding-yeast prionogenic sequences, showing that the only abundant bias pattern is for asparagine bias with subsidiary serine bias. We anticipate that this database will be a useful experimental aid and reference resource. It is freely available at: http://libaio.biol.mcgill.ca/prion.
doi:10.1371/journal.pone.0031785
PMCID: PMC3282748  PMID: 22363733
19.  Cooperative working of bacterial chromosome replication proteins generated by a reconstituted protein expression system 
Nucleic Acids Research  2013;41(14):7176-7183.
Replication of all living cells relies on the multirounds flow of the central dogma. Especially, expression of DNA replication proteins is a key step to circulate the processes of the central dogma. Here we achieved the entire sequential transcription–translation–replication process by autonomous expression of chromosomal DNA replication machineries from a reconstituted transcription–translation system (PURE system). We found that low temperature is essential to express a complex protein, DNA polymerase III, in a single tube using the PURE system. Addition of the 13 genes, encoding initiator, DNA helicase, helicase loader, RNA primase and DNA polymerase III to the PURE system gave rise to a DNA replication system by a coupling manner. An artificial genetic circuit demonstrated that the DNA produced as a result of the replication is able to provide genetic information for proteins, indicating the in vitro central dogma can sequentially undergo two rounds.
doi:10.1093/nar/gkt489
PMCID: PMC3737561  PMID: 23737447
20.  The influence of DNA sequence on epigenome-induced pathologies 
Clear cause-and-effect relationships are commonly established between genotype and the inherited risk of acquiring human and plant diseases and aberrant phenotypes. By contrast, few such cause-and-effect relationships are established linking a chromatin structure (that is, the epitype) with the transgenerational risk of acquiring a disease or abnormal phenotype. It is not entirely clear how epitypes are inherited from parent to offspring as populations evolve, even though epigenetics is proposed to be fundamental to evolution and the likelihood of acquiring many diseases. This article explores the hypothesis that, for transgenerationally inherited chromatin structures, “genotype predisposes epitype”, and that epitype functions as a modifier of gene expression within the classical central dogma of molecular biology. Evidence for the causal contribution of genotype to inherited epitypes and epigenetic risk comes primarily from two different kinds of studies discussed herein. The first and direct method of research proceeds by the examination of the transgenerational inheritance of epitype and the penetrance of phenotype among genetically related individuals. The second approach identifies epitypes that are duplicated (as DNA sequences are duplicated) and evolutionarily conserved among repeated patterns in the DNA sequence. The body of this article summarizes particularly robust examples of these studies from humans, mice, Arabidopsis, and other organisms. The bulk of the data from both areas of research support the hypothesis that genotypes predispose the likelihood of displaying various epitypes, but for only a few classes of epitype. This analysis suggests that renewed efforts are needed in identifying polymorphic DNA sequences that determine variable nucleosome positioning and DNA methylation as the primary cause of inherited epigenome-induced pathologies. By contrast, there is very little evidence that DNA sequence directly determines the inherited positioning of numerous and diverse post-translational modifications of histone side chains within nucleosomes. We discuss the medical and scientific implications of these observations on future research and on the development of solutions to epigenetically induced disorders.
doi:10.1186/1756-8935-5-11
PMCID: PMC3439399  PMID: 22818522
21.  A non Q/N-rich prion domain of a foreign prion, [Het-s], can propagate as a prion in yeast 
Molecular cell  2007;27(1):67-77.
Summary
Prions are self-propagating, infectious aggregates of misfolded proteins. The mammalian prion, PrPSc, causes fatal neurodegenerative disorders. Fungi also have prions. While yeast prions depend upon glutamine/asparagine(Q/N)-rich regions, the Podospora anserina HET-s and PrP prion proteins, lack such sequences. Nonetheless, we show that the HET-s prion domain fused to GFP propagates as a prion in yeast. Analogously to native yeast prions: transient overexpression of the HET-s fusion induces ring-like aggregates that propagate in daughter cells as cytoplasmically-inherited, detergent-resistant dot aggregates. Efficient dot propagation, but not ring formation, is dependent upon the Hsp104 chaperone. The yeast prion [PIN+] enhances HET-s ring formation, suggesting that prions with and without Q/N-rich regions interact. Finally, HET-s aggregates propagated in yeast are infectious when introduced into Podospora. To our knowledge, this is the first report of prion propagation in a truly foreign host. Since yeast can host non Q/N-rich prions, such native yeast prions may exist.
doi:10.1016/j.molcel.2007.05.027
PMCID: PMC1995001  PMID: 17612491
22.  Structural insights into a yeast prion illuminate nucleation and strain diversity 
Nature  2005;435(7043):765-772.
Self-perpetuating changes in the conformations of amyloidogenic proteins play vital roles in normal biology and disease. Despite intense research, amyloid architecture and conformational conversion remain poorly understood. Amyloid conformers of Sup35 are the molecular embodiment of the yeast prion [PSI+], which produces heritable changes in phenotype through self-perpetuating changes in protein folding. We determine the nature of Sup35’s cooperatively folded amyloid core and use this information to investigate central questions in prion biology. Specific segments of the amyloid core form intermolecular contacts in a ‘Head-to-Head’, ‘Tail-to-Tail’ fashion, while the Central Core is sequestered in intramolecular contacts. The “Head” acquires productive interactions first and these nucleate assembly. Variations in the length of the amyloid core and the nature of intermolecular interfaces are the structural basis of distinct prion “strains”, which produce variant phenotypes in vivo. These findings solve several problems in yeast prion biology and have broad implications for other amyloids.
doi:10.1038/nature03679
PMCID: PMC1405905  PMID: 15944694
23.  Genetic risk factors for variant Creutzfeldt–Jakob disease: a genome-wide association study 
Lancet Neurology  2009;8(1):57-66.
Summary
Background
Human and animal prion diseases are under genetic control, but apart from PRNP (the gene that encodes the prion protein), we understand little about human susceptibility to bovine spongiform encephalopathy (BSE) prions, the causal agent of variant Creutzfeldt–Jakob disease (vCJD).
Methods
We did a genome-wide association study of the risk of vCJD and tested for replication of our findings in samples from many categories of human prion disease (929 samples) and control samples from the UK and Papua New Guinea (4254 samples), including controls in the UK who were genotyped by the Wellcome Trust Case Control Consortium. We also did follow-up analyses of the genetic control of the clinical phenotype of prion disease and analysed candidate gene expression in a mouse cellular model of prion infection.
Findings
The PRNP locus was strongly associated with risk across several markers and all categories of prion disease (best single SNP [single nucleotide polymorphism] association in vCJD p=2·5×10−17; best haplotypic association in vCJD p=1×10−24). Although the main contribution to disease risk was conferred by PRNP polymorphic codon 129, another nearby SNP conferred increased risk of vCJD. In addition to PRNP, one technically validated SNP association upstream of RARB (the gene that encodes retinoic acid receptor beta) had nominal genome-wide significance (p=1·9×10−7). A similar association was found in a small sample of patients with iatrogenic CJD (p=0·030) but not in patients with sporadic CJD (sCJD) or kuru. In cultured cells, retinoic acid regulates the expression of the prion protein. We found an association with acquired prion disease, including vCJD (p=5·6×10−5), kuru incubation time (p=0·017), and resistance to kuru (p=2·5×10−4), in a region upstream of STMN2 (the gene that encodes SCG10). The risk genotype was not associated with sCJD but conferred an earlier age of onset. Furthermore, expression of Stmn2 was reduced 30-fold post-infection in a mouse cellular model of prion disease.
Interpretation
The polymorphic codon 129 of PRNP was the main genetic risk factor for vCJD; however, additional candidate loci have been identified, which justifies functional analyses of these biological pathways in prion disease.
Funding
The UK Medical Research Council.
doi:10.1016/S1474-4422(08)70265-5
PMCID: PMC2643048  PMID: 19081515
24.  Destruction or potentiation of different prions catalyzed by similar Hsp104 remodeling activities 
Molecular cell  2006;23(3):425-438.
Summary
Yeast prions are protein-based genetic elements that self-perpetuate changes in protein conformation and function. A protein-remodeling factor, Hsp104, controls the inheritance of several yeast prions, including those formed by Sup35 and Ure2. Perplexingly, deletion of Hsp104 eliminates Sup35 and Ure2 prions, whereas overexpression of Hsp104 purges cells of Sup35 prions, but not Ure2 prions. Here, we used pure components to dissect how Hsp104 regulates prion formation, growth, and division. For both Sup35 and Ure2, Hsp104 catalyzes de novo prion nucleation from soluble, native protein. Using a distinct mechanism, Hsp104 fragments both prions to generate new prion assembly surfaces. For Sup35, the fragmentation endpoint is an ensemble of non-infectious, amyloid-like aggregates and soluble protein that cannot replicate conformation. In vivid distinction, the endpoint of Ure2 fragmentation is short prion fibers with enhanced infectivity and self-replicating ability. These advances explain the distinct effects of Hsp104 on the inheritance of the two prions.
doi:10.1016/j.molcel.2006.05.042
PMCID: PMC1540446  PMID: 16885031
25.  Molecular Basis for Transmission Barrier and Interference between Closely Related Prion Proteins in Yeast* 
The Journal of Biological Chemistry  2011;286(18):15773-15780.
Replicating amyloids, called prions, are responsible for transmissible neurodegenerative diseases in mammals and some heritable phenotypes in fungi. The transmission of prions between species is usually inhibited, being highly sensitive to small differences in amino acid sequence of the prion-forming proteins. To understand the molecular basis of this prion interspecies barrier, we studied the transmission of the [PSI+] prion state from Sup35 of Saccharomyces cerevisiae to hybrid Sup35 proteins with prion-forming domains from four other closely related Saccharomyces species. Whereas all the hybrid Sup35 proteins could adopt a prion form in S. cerevisiae, they could not readily acquire the prion form from the [PSI+] prion of S. cerevisiae. Expression of the hybrid Sup35 proteins in S. cerevisiae [PSI+] cells often resulted in frequent loss of the native [PSI+] prion. Furthermore, all hybrid Sup35 proteins showed different patterns of interaction with the native [PSI+] prion in terms of co-polymerization, acquisition of the prion state, and induced prion loss, all of which were also dependent on the [PSI+] variant. The observed loss of S. cerevisiae [PSI+] can be related to inhibition of prion polymerization of S. cerevisiae Sup35 and formation of a non-heritable form of amyloid. We have therefore identified two distinct molecular origins of prion transmission barriers between closely sequence-related prion proteins: first, the inability of heterologous proteins to co-aggregate with host prion polymers, and second, acquisition by these proteins of a non-heritable amyloid fold.
doi:10.1074/jbc.M110.183889
PMCID: PMC3091186  PMID: 21454674
Amyloid; Prions; Protein Folding; Translation Release Factors; Yeast; Saccharomyces; Sup35; Prion Interference; Prion Species Barrier

Results 1-25 (671124)