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Schepers J, Carter Z, Kritsiligkou P, Grant CM. Methionine Sulfoxide Reductases Suppress the Formation of the [ PSI+] Prion and Protein Aggregation in Yeast. Antioxidants (Basel) 2023; 12:antiox12020401. [PMID: 36829961 PMCID: PMC9952077 DOI: 10.3390/antiox12020401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/01/2023] [Accepted: 02/03/2023] [Indexed: 02/11/2023] Open
Abstract
Prions are self-propagating, misfolded forms of proteins associated with various neurodegenerative diseases in mammals and heritable traits in yeast. How prions form spontaneously into infectious amyloid-like structures without underlying genetic changes is poorly understood. Previous studies have suggested that methionine oxidation may underlie the switch from a soluble protein to the prion form. In this current study, we have examined the role of methionine sulfoxide reductases (MXRs) in protecting against de novo formation of the yeast [PSI+] prion, which is the amyloid form of the Sup35 translation termination factor. We show that [PSI+] formation is increased during normal and oxidative stress conditions in mutants lacking either one of the yeast MXRs (Mxr1, Mxr2), which protect against methionine oxidation by reducing the two epimers of methionine-S-sulfoxide. We have identified a methionine residue (Met124) in Sup35 that is important for prion formation, confirming that direct Sup35 oxidation causes [PSI+] prion formation. [PSI+] formation was less pronounced in mutants simultaneously lacking both MXR isoenzymes, and we show that the morphology and biophysical properties of protein aggregates are altered in this mutant. Taken together, our data indicate that methionine oxidation triggers spontaneous [PSI+] prion formation, which can be alleviated by methionine sulfoxide reductases.
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Affiliation(s)
- Jana Schepers
- Institute of Pathobiochemistry, University Medical Center of the Johannes Gutenberg University Mainz, Duesbergweg 6, 55099 Mainz, Germany
| | - Zorana Carter
- Division of Molecular and Cellular Function, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK
| | - Paraskevi Kritsiligkou
- Division of Redox Regulation, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Chris M. Grant
- Division of Molecular and Cellular Function, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK
- Correspondence:
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Genomic Diversity of a Globally Used, Live Attenuated Mycoplasma Vaccine. Microbiol Spectr 2022; 10:e0284522. [PMID: 36318012 PMCID: PMC9769879 DOI: 10.1128/spectrum.02845-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The Mycoplasma synoviae live attenuated vaccine strain MS-H (Vaxsafe MS; Bioproperties Pty., Ltd., Australia) is commonly used around the world to prevent chronic infections caused by M. synoviae in birds and to minimize economic losses in the poultry industry. MS-H is a temperature-sensitive strain that is generated via the chemical mutagenesis of a virulent M. synoviae isolate, 86079/7NS. 32 single nucleotide polymorphisms have been found in the genome of MS-H compared to that of 86079/7NS, including 25 in predicted coding sequences (CDSs). There is limited information on the stability of these mutations in MS-H in vitro during the propagation of the vaccine manufacturing process or in vivo after the vaccination of chickens. Here, we performed a comparative analysis of MS-H genomes after in vitro and in vivo passages under different circumstances. Studying the dynamics of the MS-H population can provide insights into the factors that potentially affect the health of vaccinated birds. The genomes of 11 in vitro laboratory passages and 138 MS-H bird reisolates contained a total of 254 sequence variations. Of these, 39 variations associated with CDSs were detected in more than one genome (range = 2 to 62, median = 2.5), suggesting that these sequences are particularly prone to mutations. From the 25 CDSs containing previously characterized variations between MS-H and 86079/7NS, 7 were identified in the MS-H reisolates and progenies examined here. In conclusion, the MS-H genome contains individual regions that are prone to mutations that enable the restoration of the genotype or the phenotype of wild-type 86079/7NS in those regions. However, accumulated mutations in these regions are rare. IMPORTANCE Preventative measures, such as vaccination, are commonly used for the control of mycoplasmal infections in poultry. A live attenuated vaccine strain (Vaxsafe MS; MS-H; Bioproperties Pty. Ltd., Australia) is used for the prevention of disease caused by M. synoviae in many countries. However, information on the stability of previously characterized mutations in the MS-H genome is limited. In this study, we performed a comparative analysis of the whole-genome sequences of MS-H seeds used for vaccine manufacturing, commercial batches of the vaccine, cultures minimally passaged under small-scale laboratory and large-scale manufacturing conditions, MS-H reisolated from specific-pathogen-free (SPF) chickens that were vaccinated under controlled conditions, and MS-H reisolated from vaccinated commercial poultry flocks around the world. This study provides a comprehensive assessment of genome stability in MS-H after in vitro and in vivo passages under different circumstances and suggests that most of the mutations in the attenuated MS-H vaccine strain are stable.
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Anti-Prion Systems in Saccharomyces cerevisiae Turn an Avalanche of Prions into a Flurry. Viruses 2022; 14:v14091945. [PMID: 36146752 PMCID: PMC9503967 DOI: 10.3390/v14091945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/01/2022] [Accepted: 08/06/2022] [Indexed: 11/16/2022] Open
Abstract
Prions are infectious proteins, mostly having a self-propagating amyloid (filamentous protein polymer) structure consisting of an abnormal form of a normally soluble protein. These prions arise spontaneously in the cell without known reason, and their effects were generally considered to be fatal based on prion diseases in humans or mammals. However, the wide array of prion studies in yeast including filamentous fungi revealed that their effects can range widely, from lethal to very mild (even cryptic) or functional, depending on the nature of the prion protein and the specific prion variant (or strain) made by the same prion protein but with a different conformation. This prion biology is affected by an array of molecular chaperone systems, such as Hsp40, Hsp70, Hsp104, and combinations of them. In parallel with the systems required for prion propagation, yeast has multiple anti-prion systems, constantly working in the normal cell without overproduction of or a deficiency in any protein, which have negative effects on prions by blocking their formation, curing many prions after they arise, preventing prion infections, and reducing the cytotoxicity produced by prions. From the protectors of nascent polypeptides (Ssb1/2p, Zuo1p, and Ssz1p) to the protein sequesterase (Btn2p), the disaggregator (Hsp104), and the mysterious Cur1p, normal levels of each can cure the prion variants arising in its absence. The controllers of mRNA quality, nonsense-mediated mRNA decay proteins (Upf1, 2, 3), can cure newly formed prion variants by association with a prion-forming protein. The regulator of the inositol pyrophosphate metabolic pathway (Siw14p) cures certain prion variants by lowering the levels of certain organic compounds. Some of these proteins have other cellular functions (e.g., Btn2), while others produce an anti-prion effect through their primary role in the normal cell (e.g., ribosomal chaperones). Thus, these anti-prion actions are the innate defense strategy against prions. Here, we outline the anti-prion systems in yeast that produce innate immunity to prions by a multi-layered operation targeting each step of prion development.
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Wickner RB, Edskes HK, Son M, Wu S. Anti-Prion Systems Block Prion Transmission, Attenuate Prion Generation, Cure Most Prions as They Arise and Limit Prion-Induced Pathology in Saccharomyces cerevisiae. BIOLOGY 2022; 11:biology11091266. [PMID: 36138748 PMCID: PMC9495834 DOI: 10.3390/biology11091266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/08/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary Virus and bacterial infections are opposed by their hosts at many levels. Similarly, we find that infectious proteins (prions) are severely restricted by an array of host systems, acting independently to prevent infection, generation, propagation and the ill effects of yeast prions. These ‘anti-prion systems’ work in normal cells without the overproduction or deficiency of any components. DNA repair systems reverse the effects of DNA damage, with only a rare lesion propagated as a mutation. Similarly, the combined effects of several anti-prion systems cure and block the generation of all but 1 in about 5000 prions arising. We expect that application of our approach to mammalian cells will detect analogous or even homologous systems that will be useful in devising therapy for human amyloidoses, most of which are prions. Abstract All variants of the yeast prions [PSI+] and [URE3] are detrimental to their hosts, as shown by the dramatic slowing of growth (or even lethality) of a majority, by the rare occurrence in wild isolates of even the mildest variants and by the absence of reproducible benefits of these prions. To deal with the prion problem, the host has evolved an array of anti-prion systems, acting in normal cells (without overproduction or deficiency of any component) to block prion transmission from other cells, to lower the rates of spontaneous prion generation, to cure most prions as they arise and to limit the damage caused by those variants that manage to elude these (necessarily) imperfect defenses. Here we review the properties of prion protein sequence polymorphisms Btn2, Cur1, Hsp104, Upf1,2,3, ribosome-associated chaperones, inositol polyphosphates, Sis1 and Lug1, which are responsible for these anti-prion effects. We recently showed that the combined action of ribosome-associated chaperones, nonsense-mediated decay factors and the Hsp104 disaggregase lower the frequency of [PSI+] appearance as much as 5000-fold. Moreover, while Btn2 and Cur1 are anti-prion factors against [URE3] and an unrelated artificial prion, they promote [PSI+] prion generation and propagation.
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Amyloid particles facilitate surface-catalyzed cross-seeding by acting as promiscuous nanoparticles. Proc Natl Acad Sci U S A 2021; 118:2104148118. [PMID: 34462352 PMCID: PMC8433567 DOI: 10.1073/pnas.2104148118] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Amyloid seeds are nanometer-sized protein particles that accelerate amyloid assembly as well as propagate and transmit the amyloid protein conformation associated with a wide range of protein misfolding diseases. However, seeded amyloid growth through templated elongation at fibril ends cannot explain the full range of molecular behaviors observed during cross-seeded formation of amyloid by heterologous seeds. Here, we demonstrate that amyloid seeds can accelerate amyloid formation via a surface catalysis mechanism without propagating the specific amyloid conformation associated with the seeds. This type of seeding mechanism is demonstrated through quantitative characterization of the cross-seeded assembly reactions involving two nonhomologous and unrelated proteins: the human Aβ42 peptide and the yeast prion-forming protein Sup35NM. Our results demonstrate experimental approaches to differentiate seeding by templated elongation from nontemplated amyloid seeding and rationalize the molecular mechanism of the cross-seeding phenomenon as a manifestation of the aberrant surface activities presented by amyloid seeds as nanoparticles.
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Wang W, Ventura S. Prion domains as a driving force for the assembly of functional nanomaterials. Prion 2020; 14:170-179. [PMID: 32597308 PMCID: PMC7518758 DOI: 10.1080/19336896.2020.1785659] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/11/2020] [Accepted: 06/12/2020] [Indexed: 01/06/2023] Open
Abstract
Amyloids display a highly ordered fibrillar structure. Many of these assemblies appear associated with human disease. However, the controllable, stable, tunable, and robust nature of amyloid fibrils can be exploited to build up remarkable nanomaterials with a wide range of applications in biomedicine and biotechnology. Functional prions constitute a particular class of amyloids. These transmissible proteins exhibit a modular architecture, with a disordered prion domain responsible for the assembly and one or more globular domains that account for the activity. Importantly, the original globular protein can be replaced with any protein of interest, without compromising the fibrillation potential. These genetic fusions form fibrils in which the globular domain remains folded, rendering functional nanostructures. However, in some cases, steric hindrance restricts the activity of these fibrils. This limitation can be solved by dissecting prion domains into shorter sequences that keep their self-assembling properties while allowing better access to the active protein in the fibrillar state. In this review, we will discuss the properties of prion-like functional nanomaterials and the amazing applications of these biocompatible fibrillar arrangements.
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Affiliation(s)
- Weiqiang Wang
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
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Lyke DR, Dorweiler JE, Manogaran AL. The three faces of Sup35. Yeast 2019; 36:465-472. [PMID: 30963611 DOI: 10.1002/yea.3392] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 03/07/2019] [Accepted: 03/26/2019] [Indexed: 12/30/2022] Open
Abstract
Sup35p is an essential protein in yeast that functions in complex with Sup45p for efficient translation termination. Although some may argue that this function is the only important attribute of Sup35p, there are two additional known facets of Sup35p's biology that may provide equally important functions for yeast; both of which involve various strategies for coping with stress. Recently, the N-terminal and middle regions (NM) of Sup35p, which are not required for translation termination function, have been found to provide stress-sensing abilities and facilitate the phase separation of Sup35p into biomolecular condensates in response to transient stress. Interestingly, the same NM domain is also required for Sup35p to misfold and enter into aggregates associated with the [PSI+ ] prion. Here, we review these three different states or "faces" of Sup35p. For each, we compare the functionality and necessity of different Sup35p domains, including the role these domains play in facilitating interactions with important protein partners, and discuss the potential ramifications that each state affords yeast cells under varying environmental conditions.
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Affiliation(s)
- Douglas R Lyke
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin
| | - Jane E Dorweiler
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin
| | - Anita L Manogaran
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin
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Serio TR. [PIN+]ing down the mechanism of prion appearance. FEMS Yeast Res 2019; 18:4923032. [PMID: 29718197 PMCID: PMC5889010 DOI: 10.1093/femsyr/foy026] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 03/03/2018] [Indexed: 11/13/2022] Open
Abstract
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.
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Affiliation(s)
- Tricia R Serio
- The University of Massachusetts-Amherst, Department of Biochemistry and Molecular Biology, 240 Thatcher Rd, N360, Amherst, MA 01003, USA
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9
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Wisniewski BT, Sharma J, Legan ER, Paulson E, Merrill SJ, Manogaran AL. Toxicity and infectivity: insights from de novo prion formation. Curr Genet 2018; 64:117-123. [PMID: 28856415 PMCID: PMC5777878 DOI: 10.1007/s00294-017-0736-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 08/15/2017] [Accepted: 08/17/2017] [Indexed: 02/07/2023]
Abstract
Prions are infectious misfolded proteins that assemble into oligomers and large aggregates, and are associated with neurodegeneration. It is believed that the oligomers contribute to cytotoxicity, although genetic and environmental factors have also been shown to have additional roles. The study of the yeast prion [PSI +] has provided valuable insights into how prions form and why they are toxic. Our recent work suggests that SDS-resistant oligomers arise and remodel early during the prion formation process, and lysates containing these newly formed oligomers are infectious. Previous work shows that toxicity is associated with prion formation and this toxicity is exacerbated by deletion of the VPS5 gene. Here, we show that newly made oligomer formation and infectivity of vps5∆ lysates are similar to wild-type strains. However using green fluorescent protein fusions, we observe that the assembly of fluorescent cytoplasmic aggregates during prion formation is different in vps5∆ strains. Instead of large immobile aggregates, vps5∆ strains have an additional population of small mobile foci. We speculate that changes in the cellular milieu in vps5∆ strains may reduce the cell's ability to efficiently recruit and sequester newly formed prion particles into central deposition sites, resulting in toxicity.
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Affiliation(s)
- Brett T Wisniewski
- Department of Biological Sciences, Marquette University, P.O. Box 1881, Milwaukee, WI, 53201-1881, USA
| | - Jaya Sharma
- Department of Biological Sciences, Marquette University, P.O. Box 1881, Milwaukee, WI, 53201-1881, USA
| | - Emily R Legan
- Department of Biological Sciences, Marquette University, P.O. Box 1881, Milwaukee, WI, 53201-1881, USA
| | - Emily Paulson
- Department of Mathematics, Statistics and Computer Science, Marquette University, Milwaukee, WI, 53201, USA
| | - Stephen J Merrill
- Department of Mathematics, Statistics and Computer Science, Marquette University, Milwaukee, WI, 53201, USA
| | - Anita L Manogaran
- Department of Biological Sciences, Marquette University, P.O. Box 1881, Milwaukee, WI, 53201-1881, USA.
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Harvey ZH, Chen Y, Jarosz DF. Protein-Based Inheritance: Epigenetics beyond the Chromosome. Mol Cell 2017; 69:195-202. [PMID: 29153393 DOI: 10.1016/j.molcel.2017.10.030] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 10/01/2017] [Accepted: 10/20/2017] [Indexed: 12/23/2022]
Abstract
Epigenetics refers to changes in phenotype that are not rooted in DNA sequence. This phenomenon has largely been studied in the context of chromatin modification. Yet many epigenetic traits are instead linked to self-perpetuating changes in the individual or collective activity of proteins. Most such proteins are prions (e.g., [PSI+], [URE3], [SWI+], [MOT3+], [MPH1+], [LSB+], and [GAR+]), which have the capacity to adopt at least one conformation that self-templates over long biological timescales. This allows them to serve as protein-based epigenetic elements that are readily broadcast through mitosis and meiosis. In some circumstances, self-templating can fuel disease, but it also permits access to multiple activity states from the same polypeptide and transmission of that information across generations. Ensuing phenotypic changes allow genetically identical cells to express diverse and frequently adaptive phenotypes. Although long thought to be rare, protein-based epigenetic inheritance has now been uncovered in all domains of life.
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Affiliation(s)
- Zachary H Harvey
- Department of Chemical and Systems Biology, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA 94305, USA
| | - Yiwen Chen
- Department of Chemical and Systems Biology, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA 94305, USA
| | - Daniel F Jarosz
- Department of Chemical and Systems Biology, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA 94305, USA.
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Abstract
Prions are misfolded, aggregated, infectious proteins found in a range of organisms from mammals to bacteria. In mammals, prion formation is difficult to study because misfolding and aggregation take place prior to symptom presentation. The study of the yeast prion [PSI+], which is the misfolded infectious form of Sup35p, provides a tractable system to monitor prion formation in real time. Recently, we showed that the de novo formation of prion aggregates begins with the appearance of highly mobile cytoplasmic foci, called early foci, which assemble into larger ring or dot structures. We also observed SDS-resistant oligomers during formation, and lysates containing newly formed oligomers can convert [psi−] cells to the [PSI+] state, suggesting that these oligomers have infectious potential. Here, we further characterize two aspects of prion formation: spatial sequestration of early foci and oligomerization of endogenous Sup35p. Our data provides important insights into the process of prion formation and explores the minimal oligomer requirement for infectivity.
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Affiliation(s)
- Douglas R Lyke
- a Department of Biological Sciences , Marquette University , Milwaukee , WI , USA
| | - Anita L Manogaran
- a Department of Biological Sciences , Marquette University , Milwaukee , WI , USA
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12
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Sharma J, Wisniewski BT, Paulson E, Obaoye JO, Merrill SJ, Manogaran AL. De novo [PSI +] prion formation involves multiple pathways to form infectious oligomers. Sci Rep 2017; 7:76. [PMID: 28250435 PMCID: PMC5427932 DOI: 10.1038/s41598-017-00135-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 02/09/2017] [Indexed: 11/09/2022] Open
Abstract
Prion and other neurodegenerative diseases are associated with misfolded protein assemblies called amyloid. Research has begun to uncover common mechanisms underlying transmission of amyloids, yet how amyloids form in vivo is still unclear. Here, we take advantage of the yeast prion, [PSI +], to uncover the early steps of amyloid formation in vivo. [PSI +] is the prion form of the Sup35 protein. While [PSI +] formation is quite rare, the prion can be greatly induced by overexpression of the prion domain of the Sup35 protein. This de novo induction of [PSI +] shows the appearance of fluorescent cytoplasmic rings when the prion domain is fused with GFP. Our current work shows that de novo induction is more complex than previously thought. Using 4D live cell imaging, we observed that fluorescent structures are formed by four different pathways to yield [PSI +] cells. Biochemical analysis of de novo induced cultures indicates that newly formed SDS resistant oligomers change in size over time and lysates made from de novo induced cultures are able to convert [psi -] cells to [PSI +] cells. Taken together, our findings suggest that newly formed prion oligomers are infectious.
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Affiliation(s)
- Jaya Sharma
- Department of Biological Sciences, Marquette University, Milwaukee, WI, 53201, USA
| | - Brett T Wisniewski
- Department of Biological Sciences, Marquette University, Milwaukee, WI, 53201, USA
| | - Emily Paulson
- Department of Mathematics, Statistics and Computer Science, Marquette University, Milwaukee, WI, 53201, USA
| | - Joanna O Obaoye
- Department of Biological Sciences, Marquette University, Milwaukee, WI, 53201, USA
| | - Stephen J Merrill
- Department of Mathematics, Statistics and Computer Science, Marquette University, Milwaukee, WI, 53201, USA
| | - Anita L Manogaran
- Department of Biological Sciences, Marquette University, Milwaukee, WI, 53201, USA.
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13
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MacLea KS. What Makes a Prion: Infectious Proteins From Animals to Yeast. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 329:227-276. [PMID: 28109329 DOI: 10.1016/bs.ircmb.2016.08.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
While philosophers in ancient times had many ideas for the cause of contagion, the modern study of infective agents began with Fracastoro's 1546 proposal that invisible "spores" spread infectious disease. However, firm categorization of the pathogens of the natural world would need to await a mature germ theory that would not arise for 300 years. In the 19th century, the earliest pathogens described were bacteria and other cellular microbes. By the close of that century, the work of Ivanovsky and Beijerinck introduced the concept of a virus, an infective particle smaller than any known cell. Extending into the early-mid-20th century there was an explosive growth in pathogenic microbiology, with a cellular or viral cause identified for nearly every transmissible disease. A few occult pathogens remained to be discovered, including the infectious proteins (prions) proposed by Prusiner in 1982. This review discusses the prions identified in mammals, yeasts, and other organisms, focusing on the amyloid-based prions. I discuss the essential biochemical properties of these agents and the application of this knowledge to diseases of protein misfolding and aggregation, as well as the utility of yeast as a model organism to study prion and amyloid proteins that affect human and animal health. Further, I summarize the ideas emerging out of these studies that the prion concept may go beyond proteinaceous infectious particles and that prions may be a subset of proteins having general nucleating or seeding functions involved in noninfectious as well as infectious pathogenic protein aggregation.
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Affiliation(s)
- K S MacLea
- University of New Hampshire, Manchester, NH, United States.
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14
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Abstract
The year 2015 sees the fiftieth anniversary of the publication of a research paper that underpins much of our understanding of fungal prion biology, namely "ψ, a cytoplasmic suppressor of super-suppressor in yeast" by Brian Cox. Here we show how our understanding of the molecular nature of the [PSI(+)] determinant evolved from an 'occult' determinant to a transmissible amyloid form of a translation termination factor. We also consider the impact studies on [PSI] have had--and continue to have--on prion research. To demonstrate this, leading investigators in the yeast prion field who have made extensive use of the [PSI(+)] trait in their research, provide their own commentaries on the discovery and significance of [PSI].
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Affiliation(s)
- Mick F Tuite
- a Kent Fungal Group; School of Biosciences; University of Kent ; Canterbury , Kent , UK
| | - Gemma L Staniforth
- a Kent Fungal Group; School of Biosciences; University of Kent ; Canterbury , Kent , UK
| | - Brian S Cox
- a Kent Fungal Group; School of Biosciences; University of Kent ; Canterbury , Kent , UK
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15
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Abstract
Yeast and fungal prions are infectious proteins, most being self-propagating amyloids of normally soluble proteins. Their effects range from a very mild detriment to lethal, with specific effects dependent on the prion protein and the specific prion variant ("prion strain"). The prion amyloids of Sup35p, Ure2p, and Rnq1p are in-register, parallel, folded β-sheets, an architecture that naturally suggests a mechanism by which a protein can template its conformation, just as DNA or RNA templates its sequence. Prion propagation is critically affected by an array of chaperone systems, most notably the Hsp104/Hsp70/Hsp40 combination, which is responsible for generating new prion seeds from old filaments. The Btn2/Cur1 antiprion system cures most [URE3] prions that develop, and the Ssb antiprion system blocks [PSI+] generation.
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Affiliation(s)
- Reed B Wickner
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0830
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16
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Abstract
The molecular basis by which fungal and mammalian prions arise spontaneously is poorly understood. A number of different environmental stress conditions are known to increase the frequency of yeast [PSI(+)] prion formation in agreement with the idea that conditions which cause protein misfolding may promote the conversion of normally soluble proteins to their amyloid forms. A recent study from our laboratory has shown that the de novo formation of the [PSI(+)] prion is significantly increased in yeast mutants lacking key antioxidants suggesting that endogenous reactive oxygen species are sufficient to promote prion formation. Our findings strongly implicate oxidative damage of Sup35 as an important trigger for the formation of the heritable [PSI(+)] prion in yeast. This review discusses the mechanisms by which the direct oxidation of Sup35 might lead to structural transitions favoring conversion to the transmissible amyloid-like form. This is analogous to various environmental factors which have been proposed to trigger misfolding of the mammalian prion protein (PrP(C)) into the aggregated scrapie form (PrP(Sc)).
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Affiliation(s)
- Chris M Grant
- a Faculty of Life Sciences; University of Manchester ; Manchester , UK
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17
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Wickner RB, Kelly AC. Prions are affected by evolution at two levels. Cell Mol Life Sci 2016; 73:1131-44. [PMID: 26713322 PMCID: PMC4762734 DOI: 10.1007/s00018-015-2109-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 11/30/2015] [Accepted: 12/01/2015] [Indexed: 12/30/2022]
Abstract
Prions, infectious proteins, can transmit diseases or be the basis of heritable traits (or both), mostly based on amyloid forms of the prion protein. A single protein sequence can be the basis for many prion strains/variants, with different biological properties based on different amyloid conformations, each rather stably propagating. Prions are unique in that evolution and selection work at both the level of the chromosomal gene encoding the protein, and on the prion itself selecting prion variants. Here, we summarize what is known about the evolution of prion proteins, both the genes and the prions themselves. We contrast the one known functional prion, [Het-s] of Podospora anserina, with the known disease prions, the yeast prions [PSI+] and [URE3] and the transmissible spongiform encephalopathies of mammals.
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Affiliation(s)
- Reed B Wickner
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes Digestive and Kidney Diseases, National Institutes of Health, Bldg. 8, Room 225, 8 Center Drive MSC 0830, Bethesda, MD, 20892-0830, USA.
| | - Amy C Kelly
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes Digestive and Kidney Diseases, National Institutes of Health, Bldg. 8, Room 225, 8 Center Drive MSC 0830, Bethesda, MD, 20892-0830, USA.
- NCAUR, Agricultural Research Service, U.S. Department of Agriculture, 1815 N. University St., Peoria, IL, 61604, USA.
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18
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Speldewinde SH, Doronina VA, Grant CM. Autophagy protects against de novo formation of the [PSI+] prion in yeast. Mol Biol Cell 2015; 26:4541-51. [PMID: 26490118 PMCID: PMC4678013 DOI: 10.1091/mbc.e15-08-0548] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 10/14/2015] [Indexed: 11/11/2022] Open
Abstract
The molecular basis by which prions arise spontaneously is poorly understood. The present data point toward oxidative protein damage as one of the triggers of de novo prion formation. Autophagy functions to clear oxidatively damaged proteins before their conversion to the prion form. Prions are self-propagating, infectious proteins that underlie several neurodegenerative diseases. The molecular basis underlying their sporadic formation is poorly understood. We show that autophagy protects against de novo formation of [PSI+], which is the prion form of the yeast Sup35 translation termination factor. Autophagy is a cellular degradation system, and preventing autophagy by mutating its core components elevates the frequency of spontaneous [PSI+] formation. Conversely, increasing autophagic flux by treating cells with the polyamine spermidine suppresses prion formation in mutants that normally show a high frequency of de novo prion formation. Autophagy also protects against the de novo formation of another prion, namely the Rnq1/[PIN+] prion, which is not related in sequence to the Sup35/[PSI+] prion. We show that growth under anaerobic conditions in the absence of molecular oxygen abrogates Sup35 protein damage and suppresses the high frequency of [PSI+] formation in an autophagy mutant. Autophagy therefore normally functions to remove oxidatively damaged Sup35, which accumulates in cells grown under aerobic conditions, but in the absence of autophagy, damaged/misfolded Sup35 undergoes structural transitions favoring its conversion to the propagatable [PSI+] form.
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Affiliation(s)
- Shaun H Speldewinde
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Victoria A Doronina
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Chris M Grant
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
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19
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Abstract
A prion is an infectious protein horizontally transmitting a disease or trait without a required nucleic acid. Yeast and fungal prions are nonchromosomal genes composed of protein, generally an altered form of a protein that catalyzes the same alteration of the protein. Yeast prions are thus transmitted both vertically (as genes composed of protein) and horizontally (as infectious proteins, or prions). Formation of amyloids (linear ordered β-sheet-rich protein aggregates with β-strands perpendicular to the long axis of the filament) underlies most yeast and fungal prions, and a single prion protein can have any of several distinct self-propagating amyloid forms with different biological properties (prion variants). Here we review the mechanism of faithful templating of protein conformation, the biological roles of these prions, and their interactions with cellular chaperones, the Btn2 and Cur1 aggregate-handling systems, and other cellular factors governing prion generation and propagation. Human amyloidoses include the PrP-based prion conditions and many other, more common amyloid-based diseases, several of which show prion-like features. Yeast prions increasingly are serving as models for the understanding and treatment of many mammalian amyloidoses. Patients with different clinical pictures of the same amyloidosis may be the equivalent of yeasts with different prion variants.
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20
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Abstract
The unusual genetic properties of the non-chromosomal genetic elements [URE3] and [PSI+] led to them being identified as prions (infectious proteins) of Ure2p and Sup35p respectively. Ure2p and Sup35p, and now several other proteins, can form amyloid, a linear ordered polymer of protein monomers, with a part of each molecule, the prion domain, forming the core of this β-sheet structure. Amyloid filaments passed to a new cell seed the conversion of the normal form of the protein into the same amyloid form. The cell's phenotype is affected, usually from the deficiency of the normal form of the protein. Solid-state NMR studies indicate that the yeast prion amyloids are in-register parallel β-sheet structures, in which each residue (e.g. Asn35) forms a row along the filament long axis. The favourable interactions possible for aligned identical hydrophilic and hydrophobic residues are believed to be the mechanism for propagation of amyloid conformation. Thus, just as DNA mediates inheritance by templating its own sequence, these proteins act as genes by templating their conformation. Distinct isolates of a given prion have different biological properties, presumably determined by differences between the amyloid structures. Many lines of evidence indicate that the Saccharomyces cerevisiae prions are pathological disease agents, although the example of the [Het-s] prion of Podospora anserina shows that a prion can have beneficial aspects.
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21
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Doronina VA, Staniforth GL, Speldewinde SH, Tuite MF, Grant CM. Oxidative stress conditions increase the frequency of de novo formation of the yeast [PSI+] prion. Mol Microbiol 2015; 96:163-74. [PMID: 25601439 PMCID: PMC4407919 DOI: 10.1111/mmi.12930] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/08/2015] [Indexed: 01/09/2023]
Abstract
Prions are self‐perpetuating amyloid protein aggregates which underlie various neurodegenerative diseases in mammals and heritable traits in yeast. The molecular basis of how yeast and mammalian prions form spontaneously into infectious amyloid‐like structures is poorly understood. We have explored the hypothesis that oxidative stress is a general trigger for prion formation using the yeast [PSI+] prion, which is the altered conformation of the Sup35 translation termination factor. We show that the frequency of [PSI+] prion formation is elevated under conditions of oxidative stress and in mutants lacking key antioxidants. We detect increased oxidation of Sup35 methionine residues in antioxidant mutants and show that overexpression of methionine sulphoxide reductase abrogates both the oxidation of Sup35 and its conversion to the [PSI+] prion. [PSI+] prion formation is particularly elevated in a mutant lacking the Sod1 Cu,Zn‐superoxide dismutase. We have used fluorescence microscopy to show that the de novo appearance of [PSI+] is both rapid and increased in frequency in this mutant. Finally, electron microscopy analysis of native Sup35 reveals that similar fibrillar structures are formed in both the wild‐type and antioxidant mutants. Together, our data indicate that oxidative stress is a general trigger of [PSI+] formation, which can be alleviated by antioxidant defenses.
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Affiliation(s)
- Victoria A Doronina
- Faculty of Life Sciences, University of Manchester, The Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
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22
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Abstract
A prion is an infectious protein horizontally transmitting a disease or trait without a required nucleic acid. Yeast and fungal prions are nonchromosomal genes composed of protein, generally an altered form of a protein that catalyzes the same alteration of the protein. Yeast prions are thus transmitted both vertically (as genes composed of protein) and horizontally (as infectious proteins, or prions). Formation of amyloids (linear ordered β-sheet-rich protein aggregates with β-strands perpendicular to the long axis of the filament) underlies most yeast and fungal prions, and a single prion protein can have any of several distinct self-propagating amyloid forms with different biological properties (prion variants). Here we review the mechanism of faithful templating of protein conformation, the biological roles of these prions, and their interactions with cellular chaperones, the Btn2 and Cur1 aggregate-handling systems, and other cellular factors governing prion generation and propagation. Human amyloidoses include the PrP-based prion conditions and many other, more common amyloid-based diseases, several of which show prion-like features. Yeast prions increasingly are serving as models for the understanding and treatment of many mammalian amyloidoses. Patients with different clinical pictures of the same amyloidosis may be the equivalent of yeasts with different prion variants.
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23
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Arslan F, Hong JY, Kanneganti V, Park SK, Liebman SW. Heterologous aggregates promote de novo prion appearance via more than one mechanism. PLoS Genet 2015; 11:e1004814. [PMID: 25568955 PMCID: PMC4287349 DOI: 10.1371/journal.pgen.1004814] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 10/09/2014] [Indexed: 12/12/2022] Open
Abstract
Prions are self-perpetuating conformational variants of particular proteins. In yeast, prions cause heritable phenotypic traits. Most known yeast prions contain a glutamine (Q)/asparagine (N)-rich region in their prion domains. [PSI+], the prion form of Sup35, appears de novo at dramatically enhanced rates following transient overproduction of Sup35 in the presence of [PIN+], the prion form of Rnq1. Here, we establish the temporal de novo appearance of Sup35 aggregates during such overexpression in relation to other cellular proteins. Fluorescently-labeled Sup35 initially forms one or a few dots when overexpressed in [PIN+] cells. One of the dots is perivacuolar, colocalizes with the aggregated Rnq1 dot and grows into peripheral rings/lines, some of which also colocalize with Rnq1. Sup35 dots that are not near the vacuole do not always colocalize with Rnq1 and disappear by the time rings start to grow. Bimolecular fluorescence complementation failed to detect any interaction between Sup35-VN and Rnq1-VC in [PSI+][PIN+] cells. In contrast, all Sup35 aggregates, whether newly induced or in established [PSI+], completely colocalize with the molecular chaperones Hsp104, Sis1, Ssa1 and eukaryotic release factor Sup45. In the absence of [PIN+], overexpressed aggregating proteins such as the Q/N-rich Pin4C or the non-Q/N-rich Mod5 can also promote the de novo appearance of [PSI+]. Similar to Rnq1, overexpressed Pin4C transiently colocalizes with newly appearing Sup35 aggregates. However, no interaction was detected between Mod5 and Sup35 during [PSI+] induction in the absence of [PIN+]. While the colocalization of Sup35 and aggregates of Rnq1 or Pin4C are consistent with the model that the heterologous aggregates cross-seed the de novo appearance of [PSI+], the lack of interaction between Mod5 and Sup35 leaves open the possibility of other mechanisms. We also show that Hsp104 is required in the de novo appearance of [PSI+] aggregates in a [PIN+]-independent pathway. Certain proteins can misfold into β-sheet-rich, self-seeding aggregates. Such proteins appear to be associated with neurodegenerative diseases such as prion, Alzheimer's and Parkinson's. Yeast prions also misfold into self-seeding aggregates and provide a good model to study how these rogue polymers first appear. De novo prion appearance can be made very frequent in yeast by transient overexpression of the prion protein in the presence of heterologous prions or prion-like aggregates. Here, we show that the aggregates of one such newly induced prion are initially formed in a dot-like structure near the vacuole. These dots then grow into rings at the periphery of the cell prior to becoming smaller rings surrounding the vacuole and maturing into the characteristic heritable prion tiny dots found throughout the cytoplasm. We found considerable colocalization of two heterologous prion/prion-like aggregates with the newly appearing prion protein aggregates, which is consistent with the prevalent model that existing prion aggregates can cross-seed the de novo aggregation of a heterologous prion protein. However, we failed to find any physical interaction between another heterologous aggregating protein and the newly appearing prion aggregates it stimulated to appear, which is inconsistent with cross-seeding.
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Affiliation(s)
- Fatih Arslan
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada, United States of America
| | - Joo Y. Hong
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada, United States of America
| | - Vydehi Kanneganti
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada, United States of America
| | - Sei-Kyoung Park
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada, United States of America
| | - Susan W. Liebman
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada, United States of America
- * E-mail:
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24
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Abstract
Multiple prion elements, which are transmitted as heritable protein conformations and often linked to distinct phenotypes, have been identified in the budding yeast, Saccharomyces cerevisiae. It has been shown that overproduction of a prion protein Swi1 can promote the de novo conversion of another yeast prion [PSI(+)] when Sup35 is co-overproduced. However, the mechanism underlying this Pin(+) ([PSI(+)] inducible) activity is not clear. Moreover, how the Swi1 prion ([SWI(+)]) interacts with other yeast prions is unknown. Here, we demonstrate that the Pin(+) activity associated with Swi1 overproduction is independent of Rnq1 expression or [PIN(+)] conversion. We also show that [SWI(+)] enhances the appearance of [PSI(+)] and [PIN(+)]. However, [SWI(+)] significantly compromises the Pin(+) activity of [PIN(+)] when they coexist. We further demonstrate that a single yeast cell can harbor three prions, [PSI(+)], [PIN(+)], and [SWI(+)], simultaneously. However, under this condition, [SWI(+)] is significantly destabilized. While the propensity to aggregate underlies prionogenesis, Swi1 and Rnq1 aggregates resulting from overproduction are usually nonheritable. Conversely, prion protein aggregates formed in nonoverexpressing conditions or induced by preexisting prion(s) are more prionogenic. For [PSI(+)] and [PIN(+)] de novo formation, heterologous "facilitators," such as preexisting [SWI(+)] aggregates, colocalize only with the newly formed ring-/rod-shaped Sup35 or Rnq1 aggregates, but not with the dot-shaped mature prion aggregates. Their colocalization frequency is coordinated with their prion inducibility, indicating that prion-prion interactions mainly occur at the early initiation stage. Our results provide supportive evidence for the cross-seeding model of prionogenesis and highlight a complex interaction network among prions in yeast.
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25
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Tyedmers J. Patterns of [PSI (+) ] aggregation allow insights into cellular organization of yeast prion aggregates. Prion 2012; 6:191-200. [PMID: 22449721 DOI: 10.4161/pri.18986] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
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.
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Affiliation(s)
- Jens Tyedmers
- Center for Molecular Biology of the University of Heidelberg (ZMBH, Heidelberg, Germany.
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26
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Affiliation(s)
- Reed B Wickner
- Laboratory of Biochemistry and Genetics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892-0830, USA.
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27
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Manogaran AL, Hong JY, Hufana J, Tyedmers J, Lindquist S, Liebman SW. Prion formation and polyglutamine aggregation are controlled by two classes of genes. PLoS Genet 2011; 7:e1001386. [PMID: 21625618 PMCID: PMC3098188 DOI: 10.1371/journal.pgen.1001386] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Accepted: 04/14/2011] [Indexed: 11/20/2022] Open
Abstract
Prions are self-perpetuating aggregated proteins that are not limited to mammalian systems but also exist in lower eukaryotes including yeast. While much work has focused around chaperones involved in prion maintenance, including Hsp104, little is known about factors involved in the appearance of prions. De novo appearance of the [PSI+] prion, which is the aggregated form of the Sup35 protein, is dramatically enhanced by transient overexpression of SUP35 in the presence of the prion form of the Rnq1 protein, [PIN+]. When fused to GFP and overexpressed in [ps−] [PIN+] cells, Sup35 forms fluorescent rings, and cells with these rings bud off [PSI+] daughters. We investigated the effects of over 400 gene deletions on this de novo induction of [PSI+]. Two classes of gene deletions were identified. Class I deletions (bug1Δ, bem1Δ, arf1Δ, and hog1Δ) reduced the efficiency of [PSI+] induction, but formed rings normally. Class II deletions (las17Δ, vps5Δ, and sac6Δ) inhibited both [PSI+] induction and ring formation. Furthermore, class II deletions reduced, while class I deletions enhanced, toxicity associated with the expanded glutamine repeats of the huntingtin protein exon 1 that causes Huntington's disease. This suggests that prion formation and polyglutamine aggregation involve a multi-phase process that can be inhibited at different steps. Certain proteins that exist in functional unaggregated conformers can also form self-perpetuating infectious aggregates called prions. Here we investigate factors involved in the initial switch to the prion form. De novo appearance of the [PSI+] prion, which is the aggregated form of the Sup35 protein, is dramatically enhanced by overexpression of the SUP35 gene in the presence of the prion form of the Rnq1 protein, [PIN+]. When tagged with green fluorescent protein and transiently overexpressed in [psi−] [PIN+] cells, Sup35 forms fluorescent rings, and cells with these rings give rise to daughter cells that are [PSI+]. Here, we investigate factors required for this induction of [PSI+]. Analyses of over 400 gene deletions revealed two classes that reduce [PSI+] induction: one class forms fluorescent rings normally, and the other does not. Interestingly, the former class enhanced, while the latter class reduced, toxicity associated with the expanded polyglutamine repeats of the huntingtin protein exon 1 that causes Huntington's disease. These results suggest that prion formation and polyglutamine aggregation involve a multi-phase process that can be inhibited at different steps.
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Affiliation(s)
- Anita L. Manogaran
- Department of Biological Sciences, Laboratory for Molecular Biology, University of Illinois at Chicago, Chicago, Illinois, United States of America
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States of America
| | - Joo Y. Hong
- Department of Biological Sciences, Laboratory for Molecular Biology, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Joan Hufana
- Department of Biological Sciences, Laboratory for Molecular Biology, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Jens Tyedmers
- Zentrum fuer Molekulare Biologie Heidelberg, DKFZ-ZMBH-Alliance, Universitaet Heidelberg, Heidelberg, Germany
- Whitehead Institute for Biomedical Research and Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research and Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Susan W. Liebman
- Department of Biological Sciences, Laboratory for Molecular Biology, University of Illinois at Chicago, Chicago, Illinois, United States of America
- * E-mail:
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28
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Palmer KJ, Ridout MS, Morgan BJT. Kinetic models of guanidine hydrochloride-induced curing of the yeast [PSI+] prion. J Theor Biol 2011; 274:1-11. [PMID: 21184760 DOI: 10.1016/j.jtbi.2010.12.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2009] [Revised: 12/15/2010] [Accepted: 12/15/2010] [Indexed: 11/30/2022]
Abstract
A population of [PSI(+)] Saccharomyces cerevisiae cells can be cured of the [PSI(+)] prion by the addition of guanidine hydrochloride (GdnHCl). In this paper we extend existing nucleated polymerisation simulation models to investigate the mechanisms that might underlie curing. Our results are consistent with the belief that prions are dispersed through the cells at division following GdnHCl addition. A key feature of the simulation model is that the probability that a polymer is transmitted from mother to daughter during cell division is dependent upon the length of the polymer. The model is able to reproduce the essential features of data from several different experimental protocols involving addition and removal of GdnHCl.
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Affiliation(s)
- K J Palmer
- School of Mathematics, Statistics and Actuarial Science, University of Kent, Canterbury, Kent CT2 7NF, United Kingdom
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29
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Tuite MF, Marchante R, Kushnirov V. Fungal prions: structure, function and propagation. Top Curr Chem (Cham) 2011; 305:257-98. [PMID: 21717344 DOI: 10.1007/128_2011_172] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
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.
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Affiliation(s)
- Mick F Tuite
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK.
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30
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Non-Mendelian determinant [ISP+] in yeast is a nuclear-residing prion form of the global transcriptional regulator Sfp1. Proc Natl Acad Sci U S A 2010; 107:10573-7. [PMID: 20498075 DOI: 10.1073/pnas.1005949107] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four protein-based genetic determinants or prions-[SWI(+)], [MCA], [OCT(+)], and [MOT3(+)]-are recent additions to the list of well-known Saccharomyces cerevisiae prions, [PSI(+)], [URE3], and [PIN(+)]. A rapid expansion of this list may indicate that many yeast proteins can convert into heritable prion forms and underscores a problem of prion input into cellular physiology. Here, we prove that the global transcriptional regulator Sfp1 can become a prion corresponding to the prion-like determinant [ISP(+)] described earlier. We show that SFP1 deletion causes an irreversible [ISP(+)] loss, whereas increased SFP1 expression induces [ISP(+)] appearance. Cells that display the [ISP(+)] phenotype contain the aggregated form of Sfp1. Indeed, these aggregates demonstrate a nuclear location. We also show that the phenotypic manifestation of Sfp1 prionization differs from the manifestation of SFP1 deletion. These properties and others distinguish [ISP(+)] from yeast prions described to date.
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31
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The spontaneous appearance rate of the yeast prion [PSI+] and its implications for the evolution of the evolvability properties of the [PSI+] system. Genetics 2009; 184:393-400. [PMID: 19917766 DOI: 10.1534/genetics.109.110213] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Epigenetically inherited aggregates of the yeast prion [PSI+] cause genomewide readthrough translation that sometimes increases evolvability in certain harsh environments. The effects of natural selection on modifiers of [PSI+] appearance have been the subject of much debate. It seems likely that [PSI+] would be at least mildly deleterious in most environments, but this may be counteracted by its evolvability properties on rare occasions. Indirect selection on modifiers of [PSI+] is predicted to depend primarily on the spontaneous [PSI+] appearance rate, but this critical parameter has not previously been adequately measured. Here we measure this epimutation rate accurately and precisely as 5.8 x 10(-7) per generation, using a fluctuation test. We also determine that genetic "mimics" of [PSI+] account for up to 80% of all phenotypes involving general nonsense suppression. Using previously developed mathematical models, we can now infer that even in the absence of opportunities for adaptation, modifiers of [PSI+] are only weakly deleterious relative to genetic drift. If we assume that the spontaneous [PSI+] appearance rate is at its evolutionary optimum, then opportunities for adaptation are inferred to be rare, such that the [PSI+] system is favored only very weakly overall. But when we account for the observed increase in the [PSI+] appearance rate in response to stress, we infer much higher overall selection in favor of [PSI+] modifiers, suggesting that [PSI+]-forming ability may be a consequence of selection for evolvability.
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32
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Abstract
Reversible phenotypic switching can be caused by a number of different mechanisms including epigenetic inheritance systems and DNA-based contingency loci. Previous work has shown that reversible switching systems may be favored by natural selection. Many switches can be characterized as "on/off" where the "off" state constitutes a temporary and reversible loss of function. Loss-of-function phenotypes corresponding to the "off" state can be produced in many different ways, all yielding identical fitness in the short term. In the long term, however, a switch-induced loss of function can be reversed, whereas many loss-of-function mutations, especially deletions, cannot. We refer to these loss-of-function mutations as "irreversible mimics" of the reversible switch. Here, we develop a model in which a reversible switch evolves in the presence of both irreversible mimics and metapopulation structure. We calculate that when the rate of appearance of irreversible mimics exceeds the migration rate, the evolved reversible switching rate will exceed the bet-hedging rate predicted by panmictic models.
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Affiliation(s)
- Alex K Lancaster
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
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33
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Griswold CK, Masel J. Complex adaptations can drive the evolution of the capacitor [PSI], even with realistic rates of yeast sex. PLoS Genet 2009; 5:e1000517. [PMID: 19521499 PMCID: PMC2686163 DOI: 10.1371/journal.pgen.1000517] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2009] [Accepted: 05/13/2009] [Indexed: 02/02/2023] Open
Abstract
The [PSI+] prion may enhance evolvability by revealing previously cryptic genetic variation, but it is unclear whether such evolvability properties could be favored by natural selection. Sex inhibits the evolution of other putative evolvability mechanisms, such as mutator alleles. This paper explores whether sex also prevents natural selection from favoring modifier alleles that facilitate [PSI+] formation. Sex may permit the spread of “cheater” alleles that acquire the benefits of [PSI+] through mating without incurring the cost of producing [PSI+] at times when it is not adaptive. Using recent quantitative estimates of the frequency of sex in Saccharomyces paradoxus, we calculate that natural selection for evolvability can drive the evolution of the [PSI+] system, so long as yeast populations occasionally require complex adaptations involving synergistic epistasis between two loci. If adaptations are always simple and require substitution at only a single locus, then the [PSI+] system is not favored by natural selection. Obligate sex might inhibit the evolution of [PSI+]-like systems in other species. Can evolvability evolve? One obvious way to evolve faster is via mutator alleles that increase the mutation rate. Unfortunately, recombination will rapidly separate a mutator allele from the advantageous alleles that it creates. Mutators, therefore, gain very little benefit from promoting adaptations and are thought not to evolve in sexual organisms. Here we find that the [PSI+] prion, unlike mutator alleles, will evolve to promote evolvability in sexual yeast species. Together with previous laboratory studies of [PSI+]–mediated adaptation, and with bioinformatic studies consistent with [PSI+]–mediated adaptation in the wild, our theoretical results firmly establish [PSI+] as a model system for the evolution of evolvability. We also shed light on the importance of complex adaptations involving multiple genes. Adaptations involving multiple simultaneous genes drive the evolution of evolvability in this system. This work is an important proof of principle, showing that evolvability can sometimes evolve under realistic conditions.
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Affiliation(s)
- Cortland K. Griswold
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, United States of America
| | - Joanna Masel
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, United States of America
- * E-mail:
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34
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Alberti S, Halfmann R, King O, Kapila A, Lindquist S. A systematic survey identifies prions and illuminates sequence features of prionogenic proteins. Cell 2009; 137:146-58. [PMID: 19345193 DOI: 10.1016/j.cell.2009.02.044] [Citation(s) in RCA: 768] [Impact Index Per Article: 51.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2008] [Revised: 02/09/2009] [Accepted: 02/25/2009] [Indexed: 02/01/2023]
Abstract
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.
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Affiliation(s)
- Simon Alberti
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
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35
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Tyedmers J, Madariaga ML, Lindquist S. Prion switching in response to environmental stress. PLoS Biol 2009; 6:e294. [PMID: 19067491 PMCID: PMC2586387 DOI: 10.1371/journal.pbio.0060294] [Citation(s) in RCA: 203] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Accepted: 10/14/2008] [Indexed: 02/07/2023] Open
Abstract
Evolution depends on the manner in which genetic variation is translated into new phenotypes. There has been much debate about whether organisms might have specific mechanisms for "evolvability," which would generate heritable phenotypic variation with adaptive value and could act to enhance the rate of evolution. Capacitor systems, which allow the accumulation of cryptic genetic variation and release it under stressful conditions, might provide such a mechanism. In yeast, the prion [PSI(+)] exposes a large array of previously hidden genetic variation, and the phenotypes it thereby produces are advantageous roughly 25% of the time. The notion that [PSI(+)] is a mechanism for evolvability would be strengthened if the frequency of its appearance increased with stress. That is, a system that mediates even the haphazard appearance of new phenotypes, which have a reasonable chance of adaptive value would be beneficial if it were deployed at times when the organism is not well adapted to its environment. In an unbiased, high-throughput, genome-wide screen for factors that modify the frequency of [PSI(+)] induction, signal transducers and stress response genes were particularly prominent. Furthermore, prion induction increased by as much as 60-fold when cells were exposed to various stressful conditions, such as oxidative stress (H2O2) or high salt concentrations. The severity of stress and the frequency of [PSI(+)] induction were highly correlated. These findings support the hypothesis that [PSI(+)] is a mechanism to increase survival in fluctuating environments and might function as a capacitor to promote evolvability.
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Affiliation(s)
- Jens Tyedmers
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Maria Lucia Madariaga
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
- Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * To whom correspondence should be addressed. E-mail:
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36
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Abstract
The [PSI(+)] prion causes widespread readthrough translation and is rare in natural populations of Saccharomyces, despite the fact that sex is expected to cause it to spread. Using the recently estimated rate of Saccharomyces outcrossing, we calculate the strength of selection necessary to maintain [PSI(+)] at levels low enough to be compatible with data. Using the best available parameter estimates, we find selection against [PSI(+)] to be significant. Inference regarding selection on modifiers of [PSI(+)] appearance depends on obtaining more precise and accurate estimates of the product of yeast effective population size N(e) and the spontaneous rate of [PSI(+)] appearance m. The ability to form [PSI(+)] has persisted in yeast over a long period of evolutionary time, despite a diversity of modifiers that could abolish it. If mN(e) < 1, this may be explained by insufficiently strong selection. If mN(e) > 1, then selection should favor the spread of [PSI(+)] resistance modifiers. In this case, rare conditions where [PSI(+)] is adaptive may permit its persistence in the face of negative selection.
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37
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Abstract
Amyloidogenesis is the aggregation of soluble proteins into structurally conserved fibers. Amyloid fibers are distinguished by their resistance to proteinase K, tinctorial properties and beta-sheet-rich secondary structure. Amyloid formation is a hallmark of many human diseases including Alzheimer's, Huntington's and the prion diseases. Therefore, understanding amyloidogenesis will provide insights into the development of therapeutics that target these debilitating diseases. A new class of ;functional' amyloids promises a unique glimpse at how nature has harnessed the amyloid fiber to accomplish important physiological tasks. Functional amyloids are produced by organisms spanning all aspects of cellular life. Herein we review amyloidogenesis, with special attention focused on the similarities and differences between the best characterized disease-associated amyloidogenic protein amyloid-beta and the formation of several functional amyloids. The implications of studying functional amyloidogenesis and the strategies organisms employ to limit exposure to toxic intermediates will also be discussed.
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Affiliation(s)
- Neal D Hammer
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109-0620, USA
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38
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Abstract
Prions were originally defined as infectious agents of protein nature, which caused neurodegenerative diseases in animals and humans. The prion concept implies that the infectious agent is a protein in special conformation that can be transmitted to the normal molecules of the same protein through protein-protein interactions. Until the 1990s, the prion phenomenon was associated with the single protein named PrP. Discovery of prions in lower eukaryotes, the yeast Saccharomyces cerevisiae and fungus Podospora anserina, suggests that prions have wider significance. Prions of lower eukaryotes are not related to diseases; their propagation caused by aggregation of prion-like proteins underlies the inheritance of phenotypic traits and most likely has adaptive significance. This review covers prions of mammals and lower eukaryotes, mechanisms of their appearance de novo and maintenance, structure of prion particles, and prospects for the treatment of prion diseases. Recent data concerning the search for new prion-like proteins is included. The paper focuses on the [PSI+] prion of S. cerevisiae, since at present it is the most investigated one. The biological significance of prions is discussed.
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Affiliation(s)
- I S Shkundina
- Russian Cardiology Research-Industrial Center, 3-ya Cherepkovskaya ul. 15A, 121552 Moscow, Russia
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39
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Abstract
The term prion has been used to describe self-replicating protein conformations that can convert other protein molecules of the same primary structure into its prion conformation. Several different proteins have now been found to exist as prions in Saccharomyces cerevisiae. Surprisingly, these heterologous prion proteins have a strong influence on each others' appearance and propagation, which may result from structural similarity between the prions. Both positive and negative effects of a prion on the de novo appearance of a heterologous prion have been observed in genetic studies. Other examples of reported interactions include mutual or unilateral inhibition and destabilization when two prions are present together in a single cell. In vitro work showing that one purified prion stimulates the conversion of a purified heterologous protein into a prion form, suggests that facilitation of de novo prion formation by heterologous prions in vivo is a result of a direct interaction between the prion proteins (a cross-seeding mechanism) and does not require other cellular components. However, other cellular structures, e.g., the cytoskeleton, may provide a scaffold for these interactions in vivo and chaperones can further facilitate or inhibit this process. Some negative prion-prion interactions may also occur via a direct interaction between the prion proteins. Another explanation is a competition between the prions for cellular factors involved in prion propagation or differential effects of chaperones stimulated by one prion on the heterologous prions.
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Affiliation(s)
- Irina L Derkatch
- Department of Microbiology, New York University School of Medicine, New York University Medical Center, New York, New York 10016, USA.
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40
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Abstract
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.
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Affiliation(s)
- Brian S Cox
- Department of Biosciences, University of Kent, Canterbury, Kent, UK
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41
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Tuite MF, Cox BS. The genetic control of the formation and propagation of the [PSI+] prion of yeast. Prion 2007; 1:101-9. [PMID: 19164924 DOI: 10.4161/pri.1.2.4665] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
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.
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Affiliation(s)
- Mick F Tuite
- Department of Biosciences, University of Kent, Canterbury, Kent, UK.
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42
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Wickner RB, Edskes HK, Shewmaker F, Nakayashiki T, Engel A, McCann L, Kryndushkin D. Yeast prions: evolution of the prion concept. Prion 2007; 1:94-100. [PMID: 19164928 DOI: 10.4161/pri.1.2.4664] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Prions (infectious proteins) analogous to the scrapie agent have been identified in Saccharomyces cerevisiae and Podospora anserina based on their special genetic characteristics. Each is a protein acting as a gene, much like nucleic acids have been shown to act as enzymes. The [URE3], [PSI(+)], [PIN(+)] and [Het-s] prions are self-propagating amyloids of Ure2p, Sup35p, Rnq1p and the HET-s protein, respectively. The [beta] and [C] prions are enzymes whose precursor activation requires their own active form. [URE3] and [PSI(+)] are clearly diseases, while [Het-s] and [beta] carry out normal cell functions. Surprisingly, the prion domains of Ure2p and Sup35p can be randomized without loss of ability to become a prion. Thus amino acid content and not sequence determine these prions. Shuffleability also suggests amyloids with a parallel in-register beta-sheet structure.
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Affiliation(s)
- Reed B Wickner
- Laboratory of Biochemistry and Genetics, The National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0830, USA.
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43
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Abstract
According to classical evolutionary theory, phenotypic variation originates from random mutations that are independent of selective pressure. However, recent findings suggest that organisms have evolved mechanisms to influence the timing or genomic location of heritable variability. Hypervariable contingency loci and epigenetic switches increase the variability of specific phenotypes; error-prone DNA replicases produce bursts of variability in times of stress. Interestingly, these mechanisms seem to tune the variability of a given phenotype to match the variability of the acting selective pressure. Although these observations do not undermine Darwin's theory, they suggest that selection and variability are less independent than once thought.
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Affiliation(s)
- Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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44
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Masel J, King OD, Maughan H. The loss of adaptive plasticity during long periods of environmental stasis. Am Nat 2006; 169:38-46. [PMID: 17206583 PMCID: PMC1766558 DOI: 10.1086/510212] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2005] [Accepted: 08/14/2006] [Indexed: 11/03/2022]
Abstract
Adaptive plasticity allows populations to adjust rapidly to environmental change. If this is useful only rarely, plasticity may undergo mutational degradation and be lost from a population. We consider a population of constant size N undergoing loss of plasticity at functional mutation rate m and with selective advantage s associated with loss. Environmental change events occur at rate theta per generation, killing all individuals that lack plasticity. The expected time until loss of plasticity in a fluctuating environment is always at least tau, the expected time until loss of plasticity in a static environment. When mN > 1 and N theta >> 1, we find that plasticity will be maintained for an average of at least 10(8) generations in a single population, provided tau > 18/theta. In a metapopulation, plasticity is retained under the more lenient condition tau > 1.3/theta, irrespective of mN, for a modest number of demes. We calculate both exact and approximate solutions for tau and find that it is linearly dependent only on the logarithm of N, and so, surprisingly, both the population size and the number of demes in the metapopulation make little difference to the retention of plasticity. Instead, tau is dominated by the term 1/(m+s/2).
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Affiliation(s)
- Joanna Masel
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA.
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45
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Liebman SW, Bagriantsev SN, Derkatch IL. Biochemical and genetic methods for characterization of [PIN+] prions in yeast. Methods 2006; 39:23-34. [PMID: 16793281 DOI: 10.1016/j.ymeth.2006.04.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2006] [Accepted: 04/24/2006] [Indexed: 10/24/2022] Open
Abstract
The glutamine- and asparagine-rich Rnq1p protein in Saccharomyces cerevisiae can exist in the cell as a soluble monomer or in one of several aggregated, infectious, prion forms called [PIN(+)]. Interest in [PIN(+)] is heightened by its ability to promote the conversion of other proteins into a prion or an aggregated amyloid state. However, little is known about the function of Rnq1p, which makes it difficult to assay the phenotypes associated with its normal vs. prion forms. In this chapter, we describe methods used to detect [PIN(+)] and distinguish between different variations of the prion. Genetic methods are based on the ability of the [PIN(+)] prion to facilitate the appearance of another yeast prion, [PSI(+)], which has an easily detectable phenotype. Biochemical methods exploit the fact that the [PIN(+)] prion exists in the yeast cytosol in the form of large aggregates, composed of SDS-stable subparticles. Sucrose gradient centrifugation, agarose SDS electrophoresis and GFP fusions are used to distinguish between aggregates and subparticles from different [PIN(+)] variants.
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Affiliation(s)
- Susan W Liebman
- Department of Biological Sciences, Laboratory for Molecular Biology, University of Illinois, Chicago, IL 60607, USA
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46
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Wickner RB, Edskes HK, Shewmaker F. How to find a prion: [URE3], [PSI+] and [β]. Methods 2006; 39:3-8. [PMID: 16793280 DOI: 10.1016/j.ymeth.2006.04.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2006] [Accepted: 04/24/2006] [Indexed: 11/16/2022] Open
Abstract
Infectious proteins (prions) in yeast or other microorganisms can be identified by genetic methods of rather general applicability. Infection in yeast means transfer by cytoplasmic mixing (cytoduction), a property of all non-chromosomal genetic elements whether plasmids, viruses, or prions. Prions can be diagnosed by reversible curability, increased occurrence when the corresponding protein is overproduced, a requirement for the gene for the corresponding protein for propagation, and, in some cases, similarity of phenotype of: (a) mutations in the gene for the protein and (b) the presence of the prion. This approach is illustrated with [URE3], an amyloid-based prion of the regulator of nitrogen catabolism, Ure2p and [PSI(+)] as a prion of the translation termination factor Sup35p. The prion concept is not limited to infectious amyloids, but includes proteins whose active form is necessary for the activation of the inactive precursor. We detail methods used in studies of [URE3] and [beta], a self-activating protease, some of which are of broad application.
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Affiliation(s)
- Reed B Wickner
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0830, USA.
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47
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King CY, Wang HL, Chang HY. Transformation of yeast by infectious prion particles. Methods 2006; 39:68-71. [PMID: 16759879 DOI: 10.1016/j.ymeth.2006.04.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2006] [Accepted: 04/24/2006] [Indexed: 11/28/2022] Open
Abstract
We present methods to prepare infectious Sup35 protein aggregates and use them for genetic transformation of yeast. The protein aggregates are prepared from bacterially expressed recombinant protein, which is converted to amyloid fibers by extended incubation or by nucleated growth using yeast prion particles as seeds. The aggregates are introduced into yeast by a modified spheroplast transformation protocol. The phenotype of the yeast transformants is further characterized by robust prion strain typing methods. The methodology can be used to introduce different [PSI(+)] particles to many laboratory yeast genetic backgrounds. It can be adapted for applications in other yeast prion systems as well.
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Affiliation(s)
- Chih-Yen King
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.
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48
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Tuite MF, Cox BS. The [PSI+] prion of yeast: A problem of inheritance. Methods 2006; 39:9-22. [PMID: 16757178 DOI: 10.1016/j.ymeth.2006.04.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2006] [Accepted: 04/24/2006] [Indexed: 10/24/2022] Open
Abstract
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.
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Affiliation(s)
- Mick F Tuite
- Protein Science Group, Department of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK.
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49
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Abstract
Cryptic genetic variation accumulates under weakened selection and has been proposed as a source of evolutionary innovations. Weakened selection may, however, also lead to the accumulation of strongly deleterious or lethal alleles, swamping the effect of any potentially adaptive alleles when they are revealed. Here I model variation that is partially shielded from selection, assuming that unconditionally deleterious variation is more strongly deleterious than variation that is potentially adaptive in a future environment. I find that cryptic genetic variation can be substantially enriched for potential adaptations under a broad range of realistic parameter values, including those applicable to alternative splices and readthrough products generated by the yeast prion [PSI+]. This enrichment is dramatically stronger when multiple simultaneous changes are required to generate a potentially adaptive phenotype. Cryptic genetic variation is likely to be an effective source of useful adaptations at a time of environmental change, relative to an equivalent source of variation that has not spent time in a hidden state.
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Affiliation(s)
- Joanna Masel
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA.
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50
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Wickner RB, Edskes HK, Ross ED, Pierce MM, Shewmaker F, Baxa U, Brachmann A. Prions of yeast are genes made of protein: amyloids and enzymes. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2005; 69:489-96. [PMID: 16117685 DOI: 10.1101/sqb.2004.69.489] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- R B Wickner
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0830, USA
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