DOCSLIB.ORG

Polarization Transfer Dynamics in Multi-Spin Systems Using the DREAM Scheme

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Polarization Transfer Dynamics in Multi-Spin Systems Using the DREAM Scheme Research Collection Doctoral Thesis Polarization transfer dynamics in multi-spin systems using the DREAM scheme Author(s): Westfeld, Thomas Publication Date: 2010 Permanent Link: https://doi.org/10.3929/ethz-a-006410379 Rights / License: In Copyright - Non-Commercial Use Permitted This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library DISS. ETH NO. 19196 Polarization Transfer Dynamics in Multi-Spin Systems Using the DREAM Scheme A dissertation submitted to ETH ZÜRICH for the degree of Doctor of Sciences presented by THOMAS WESTFELD born September 9, 1979 citizen of the Federal Republic of Germany accepted on the recommendation of Prof. Dr. Beat H. Meier, examiner Prof. Dr. Roland Riek, co-examiner 2010 Meiner Mutter nanos gigantium humeris insidentes Bernardus Carnotensis Contents Abbreviations ix Abstract xi Zusammenfassung xiii 1. General Introduction 1 1.1. Quantum-mechanical Framework of NMR . ............. 1 1.1.1. Hamiltonians in NMR . ..................... 1 1.1.2. Describing the Outcome of an NMR Experiment ......... 5 1.1.3. Average-Hamiltonian Theory . ................. 6 1.1.4. Spherical-Tensor Representations and Rotations ......... 7 1.1.5. Magic-Angle Spinning . ..................... 9 1.1.6. Adiabatic Fast-Passage . ..................... 13 1.2. NMR on Biomolecules . ......................... 15 1.2.1. Liquid-State NMR . ......................... 15 1.2.2. Solid-State NMR . ......................... 17 1.3. The Assignment Problem . ......................... 21 I. Solid-State NMR Studies of the Prion Protein HET-s (156-289) 25 2. Introduction To Prion Proteins and Amyloids 27 2.1. Discovery of Prions . ............................. 27 2.2. Replication of Prions and Amyloid Fiber Formation . ......... 28 2.3. Amyloid diseases . ............................. 30 2.4. Fungal Prions ................................. 31 v vi Contents 2.5. The HET-s Prion . ............................. 32 2.5.1. Biological Background . ..................... 32 2.5.2. Solid-state NMR Studies on HET-s(218–289) . ......... 33 2.5.3. The HET-s(156–289) Prion . ..................... 34 3. Experimental 37 3.1. Bacterial Strains . ............................. 37 3.2. Protein Expression and Purification..................... 37 3.2.1. Transformation of pET24-HET-s(156–289) Vector ......... 37 3.2.2. Expression of U-13C,15N HET-s (156-289) ............. 37 3.2.3. Expression of HET-s(156–289) Using Auto-Induction . 38 3.2.4. Cell Work-Up and Lysis . ..................... 38 3.2.5. Purification.............................. 39 3.2.6. SDS–PAGE . ............................. 39 3.2.7. Fibrilization and Sample Preparation . ............. 39 3.2.8. Preparation of Low Temperature Samples ............. 40 3.3. Electron Microscopy ............................. 40 3.4. NMR Experiments . ............................. 40 3.4.1. Solid-State NMR Experiments . ................. 40 3.4.2. Data Processing and Data Analysis ................. 43 4. Results 45 4.1. Expression of HET-s(156–289) . ..................... 45 4.1.1. Expression of U-13C,15N HET-s (156-289) ............. 45 4.1.2. Expression of HET-s(156–289) Using Auto-induction . 45 4.1.3. Refolding and Fibrilization of HET-s(156–289) . ......... 47 4.2. Solid-State NMR studies . ......................... 47 4.2.1. Comparing HET-s(218–289) and HET-s(156–289) ......... 47 4.2.2. Chemical Shift Mapping . ..................... 56 4.2.3. Low-Temperature Measurements . ................. 56 4.2.4. Using non Dipolar-Based Experiments . ............. 62 5. Discussion 67 5.1. Solid-state NMR Spectra of HET-s(156–289) . ............. 67 5.2. J-BasedSpectra................................ 69 Contents vii 6. Conclusion 71 II. The DREAM Experiment in Multi-Spin Systems 73 7. Introduction to the DREAM Experiment 75 7.1. Theoretical Description . ......................... 76 7.1.1. The HORROR Experiment . ..................... 76 7.1.2. From HORROR to DREAM ..................... 80 7.1.3. DREAM in Multi-Spin Systems . ................. 83 7.2. Simulation Strategies ............................. 85 7.3. DREAMing Away . ............................. 87 8. Experimental 91 8.1. Simulation of DREAM Transfer . ..................... 91 8.1.1. Simulating the Mixing Using Time-Slicing . ......... 92 8.1.2. Simulating the Mixing Using Floquet Theory . ......... 92 8.2. Experimental DREAM Spectra . ..................... 93 8.2.1. DREAM Spectra of Single Amino Acids . ............. 93 8.2.2. DREAM Spectra of Ubiquitin . ................. 94 8.2.3. Data Evaluation . ......................... 94 9. Results 97 9.1. Simulation Strategies ............................. 97 9.2. Transfer Efficiency Dependence on Carrier Position and RF Field . 99 9.3. Cross Peak Patterns in Protein Spectra . ................. 104 9.3.1. Experimental DREAM Spectra . ................. 104 9.3.2. Simulated DREAM Spectra ..................... 105 9.3.3. Comparing Simulated and Experimental DREAM Spectra . 105 10.Discussion 115 10.1. Simulation Strategies of DREAM Spectra ................. 115 10.2. Transfer Efficiency Dependence on Carrier Position and RF Field . 117 10.3. Cross Peak Patterns in Protein Spectra . ................. 120 viii Contents 11.Conclusion 123 12.Outlook 125 Bibliography 129 Acknowledgements 143 Curriculum Vitae 145 Publications 147 Abbreviations 1D One dimensional 2D Two dimensional APHH CP Adiabatic-passage Hartmann-Hahn cross-polarization AHT Average Hamiltonian theory BSE Bovine spongiform encephalopathy CJD Creutzfeldt-Jakob disease CP Cross-polarization CSA Chemical shift anisotropy DARR Dipolar assisted rotational resonance DNA Deoxyribonucleic acid DREAM Dipolar recoupling enhanced by amplitude modulation FT Fourier transform GFP Green fluorescent protein GSS Gerstmann-Sträussler syndrome HORROR Homonuclear rotary-resonance INEPT Insensitive nuclei enhanced by polarization transfer LAB Laboratory frame MAS Magic-angle spinning MiByte Mebibyte (1 Mebibyte = 10242 byte) MOL Molecular fixed frame MRI Magnetic resonance imaging NMR Nuclear magnetic resonance NOE Nuclear Overhauser effect λ = OD600 Optical density at wavelength 600 nm PAS Principle axis frame ppm Parts per million Prion Proteinaceous infectious particle ix x Contents RF Radio frequency RNA Ribonucleic acid ROT Rotor fixed frame SDS Sodium dodecyl sulfate STEM Scanning transmission electron microscopy TOBSY Through-bond spectroscopy TPPM Two pulse phase modulation WiW WURST–inverse–WURST WURST Wideband, uniform rate, and smooth truncation XiX x–inverse–x Abstract In this thesis two projects are presented which demonstrate the application of solid- state NMR on prion proteins and the characteristics of a polarization transfer method in the context of biomolecular NMR. Prion proteins are linked with a number of neurodegenerative diseases such as bovine spongiform encephalopathy (BSE) in cattle or chronic wasting disease (CWD) in mule deer and elk. In humans known prion diseases are the Creutzfeldt-Jakob dis- ease, the Gerstmann-Sträussler syndrome and kuru. The protein is therefore trans- formed from a soluble state into an infectious prion state in which it aggregates to amyloid plaques which consist of protein fibrils. The prion protein HET-s studied in this work is from the filamentous fungus Po- dospora anserina. In this organism the prion is involved in the recognition of the com- patibility of other species before cell fusion. In this case the prion is not pathogenic, but has an important function for the fungus. Amyloids are not soluble and do not form crystals which make them inaccessible for standard protein structure determination techniques such as X-ray crystallogra- phy or liquid-state NMR. However solid-state NMR studies have been applied suc- cessfully to gain insight into the structure of prions. In the first project of this work a C-terminal fragment of HET-s from residue 156 to 289 is studied. This fragment can be divided into a prion forming domain from residue 218 to 289 and roughly the same number of residues which are located in the globular part of the protein from residue 156 to 217. It has been shown that the prion forming domain alone is able for form amyloid fibril which are infectious to the fungus but is not active with respect to its function to distinguish between compatible and non compatible cell fusion partners. In contrast the fragment studied here is in this respect biologically active. To characterize this fragment the protein was produced recombinantely by expres- sion in E.coli. The uniformly 13C and 15N labeled sample was then used to collect xi xii Abstract different 2D correlation spectra at ambient and low temperature. This data was com- pared to the analogous spectra of the prion forming domain alone. It was possible to show that the prion forming domain has the same structure in HET-s(156–289) and HET-s(218–289) . The additional residues are visible in the spectrum at positions in- dicating that they are in a random coil. There are also resonances observed which indicate that some residues are in an alpha-helical conformation. The weak signal in- tensity and the observed random-coil chemical shift indicate that the part belonging to the globular domain of HET-s(156–289) is structurally disordered. The second project of this thesis demonstrates how a method for reintroducing the dipolar coupling in solid-state NMR under Magic Angle Spinning (MAS) can be tailored to facilitate the analysis of protein spectra. MAS is averaging
Load more

Recommended publications
  • Prpsc Prions State of the Art
    Sc PrP Prions State of the Art Edited by Joaquín Castilla and Jesús R. Requena Printed Edition of the Special Issue Published in Pathogens www.mdpi.com/journal/pathogens PrPSc Prions: State of the Art Sc PrP Prions: State of the Art Special Issue Editors Joaqu´ınCastilla Jes ´usR. Requena MDPI • Basel • Beijing • Wuhan • Barcelona • Belgrade Special Issue Editors Joaqu´ın Castilla Jes us´ R. Requena CIC bioGUNE University of Santiago de Compostela Spain Spain Editorial Office MDPI St. Alban-Anlage 66 Basel, Switzerland This is a reprint of articles from the Special Issue published online in the open access journal Pathogens (ISSN 2076-0817) from 2017 to 2018 (available at: https://www.mdpi.com/journal/pathogens/ special issues/prions study) For citation purposes, cite each article independently as indicated on the article page online and as indicated below: LastName, A.A.; LastName, B.B.; LastName, C.C. Article Title. Journal Name Year, Article Number, Page Range. ISBN 978-3-03897-308-9 (Pbk) ISBN 978-3-03897-309-6 (PDF) Cover image courtesy of Jesus´ R. Requena and Joaqu´ın Castilla. Articles in this volume are Open Access and distributed under the Creative Commons Attribution (CC BY) license, which allows users to download, copy and build upon published articles even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. The book taken as a whole is c 2018 MDPI, Basel, Switzerland, distributed under the terms and conditions of the Creative Commons license CC BY-NC-ND (http://creativecommons.org/licenses/by-nc-nd/4.0/).
    [Show full text]
  • Podospora Anserina Bibliography N° 10 - Additions
    Fungal Genetics Reports Volume 50 Article 15 Podospora anserina bibliography n° 10 - Additions Robert Debuchy Université Paris-Sud Follow this and additional works at: https://newprairiepress.org/fgr This work is licensed under a Creative Commons Attribution-Share Alike 4.0 License. Recommended Citation Debuchy, R. (2003) "Podospora anserina bibliography n° 10 - Additions," Fungal Genetics Reports: Vol. 50, Article 15. https://doi.org/10.4148/1941-4765.1161 This Special Paper is brought to you for free and open access by New Prairie Press. It has been accepted for inclusion in Fungal Genetics Reports by an authorized administrator of New Prairie Press. For more information, please contact [email protected]. Podospora anserina bibliography n° 10 - Additions Abstract Podospora anserina is a coprophilous fungus growing on herbivore dung. It is a pseudohomothallic species in which ascus development results, as in Neurospora tetrasperma but through a different process, in the formation of four large ascospores containing nuclei of both mating types. This special paper is available in Fungal Genetics Reports: https://newprairiepress.org/fgr/vol50/iss1/15 Debuchy: Podospora anserina bibliography n° 10 - Additions Number 50, 2003 27 Podospora anserina bibliography n/ 10 - Additions Robert Debuchy, Institut de Génétique et Microbiologie UMR 8621, Bâtiment 400, Université Paris-Sud, 91405 Orsay cedex, France. Fungal Genet. Newsl. 50: 27-36. Podospora anserina is a coprophilous fungus growing on herbivore dung. It is a pseudohomothallic species in which ascus development results, as in Neurospora tetrasperma but through a different process, in the formation of four large ascospores containing nuclei of both mating types. These ascospores give self-fertile strains.
    [Show full text]
  • Prions As Protein-Based Genetic Elements
    14 Aug 2002 14:0 AR AR168-MI56-28.tex AR168-MI56-28.sgm LaTeX2e(2002/01/18) P1: IBD 10.1146/annurev.micro.56.013002.100603 Annu. Rev. Microbiol. 2002. 56:703–41 doi: 10.1146/annurev.micro.56.013002.100603 Copyright c 2002 by Annual Reviews. All rights reserved First published online as a Review in Advance on July 15, 2002 PRIONS AS PROTEIN-BASED GENETIC ELEMENTS Susan M. Uptain1 and Susan Lindquist2 1Howard Hughes Medical Institute, Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois 60637; e-mail: [email protected] 2Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Biology, Nine Cambridge Center, Cambridge, Massachusetts 02142; e-mail: lindquist [email protected] Key Words Sup35, Ure2, HET-s, Rnq1, amyloid ■ Abstract Fungal prions are fascinating protein-based genetic elements. They alter cellular phenotypes through self-perpetuating changes in protein conformation and are cytoplasmically partitioned from mother cell to daughter. The four prions of Saccharomyces cerevisiae and Podospora anserina affect diverse biological pro- cesses: translational termination, nitrogen regulation, inducibility of other prions, and heterokaryon incompatibility. They share many attributes, including unusual genetic behaviors, that establish criteria to identify new prions. Indeed, other fungal traits that baffled microbiologists meet some of these criteria and might be caused by prions. Recent research has provided notable insight about how prions are induced and prop- agated and their many biological roles. The ability to become a prion appears to be evolutionarily conserved in two cases. [PSI+] provides a mechanism for genetic vari- ation and phenotypic diversity in response to changing environments.
    [Show full text]
  • Ribosomal RNA Modulates Aggregation of the Podospora Prion Protein HET-S
    International Journal of Molecular Sciences Article Ribosomal RNA Modulates Aggregation of the Podospora Prion Protein HET-s Yanhong Pang y, Petar Kovachev and Suparna Sanyal * Department of Cell and Molecular Biology, Uppsala University, Box-596, Biomedical Center, 751 24 Uppsala, Sweden; [email protected] (Y.P.); [email protected] (P.K.) * Correspondence: [email protected] Present address: Department of Molecular Sciences, Uppsala Biocenter, Swedish University of Agricultural y Sciences, 750 07 Uppsala, Sweden. Received: 25 August 2020; Accepted: 28 August 2020; Published: 1 September 2020 Abstract: The role of the nucleic acids in prion aggregation/disaggregation is becoming more and more evident. Here, using HET-s prion from fungi Podospora anserina (P. anserina) as a model system, we studied the role of RNA, particularly of different domains of the ribosomal RNA (rRNA), in its aggregation process. Our results using Rayleigh light scattering, Thioflavin T (ThT) binding, transmission electron microscopy (TEM) and cross-seeding assay show that rRNA, in particular the domain V of the major rRNA from the large subunit of the ribosome, substantially prevents insoluble amyloid and amorphous aggregation of the HET-s prion in a concentration-dependent manner. Instead, it facilitates the formation of the soluble oligomeric “seeds”, which are capable of promoting de novo HET-s aggregation. The sites of interactions of the HET-s prion protein on domain V rRNA were identified by primer extension analysis followed by UV-crosslinking, which overlap with the sites previously identified for the protein-folding activity of the ribosome (PFAR). This study clarifies a missing link between the rRNA-based PFAR and the mode of propagation of the fungal prions.
    [Show full text]
  • Drivers of Evolutionary Change in Podospora Anserina
    Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 1923 Drivers of evolutionary change in Podospora anserina SANDRA LORENA AMENT-VELÁSQUEZ ACTA UNIVERSITATIS UPSALIENSIS ISSN 1651-6214 ISBN 978-91-513-0921-7 UPPSALA urn:nbn:se:uu:diva-407766 2020 Dissertation presented at Uppsala University to be publicly examined in Ekmansalen, Evolutionary Biology Centre (EBC), Norbyvägen 18D, Uppsala, Tuesday, 19 May 2020 at 10:00 for the degree of Doctor of Philosophy (Faculty of Theology). The examination will be conducted in English. Faculty examiner: Professor Bengt Olle Bengtsson (Lund University). Abstract Ament-Velásquez, S. L. 2020. Drivers of evolutionary change in Podospora anserina. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 1923. 63 pp. Uppsala: Acta Universitatis Upsaliensis. ISBN 978-91-513-0921-7. Genomic diversity is shaped by a myriad of forces acting in different directions. Some genes work in concert with the interests of the organism, often shaped by natural selection, while others follow their own interests. The latter genes are considered “selfish”, behaving either neutrally to the host, or causing it harm. In this thesis, I focused on genes that have substantial fitness effects on the fungus Podospora anserina and relatives, but whose effects are very contrasting. In Papers I and II, I explored the evolution of a particular type of selfish genetic elements that cause meiotic drive. Meiotic drivers manipulate the outcome of meiosis to achieve overrepresentation in the progeny, thus increasing their likelihood of invading and propagating in a population. In P. anserina there are multiple meiotic drivers but their genetic basis was previously unknown.
    [Show full text]
  • How Do Yeast Cells Contend with Prions?
    International Journal of Molecular Sciences Review How Do Yeast Cells Contend with Prions? Reed B. Wickner *, Herman K. Edskes, Moonil Son, Songsong Wu and Madaleine Niznikiewicz Laboratory of Biochemistry and Genetics, National Institute of Diabetes Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0830, USA; [email protected] (H.K.E.); [email protected] (M.S.); [email protected] (S.W.); [email protected] (M.N.) * Correspondence: [email protected]; Tel.: +1-301-496-3452 Received: 15 June 2020; Accepted: 30 June 2020; Published: 3 July 2020 Abstract: Infectious proteins (prions) include an array of human (mammalian) and yeast amyloid diseases in which a protein or peptide forms a linear β-sheet-rich filament, at least one functional amyloid prion, and two functional infectious proteins unrelated to amyloid. In Saccharomyces cerevisiae, at least eight anti-prion systems deal with pathogenic amyloid yeast prions by (1) blocking their generation (Ssb1,2, Ssz1, Zuo1), (2) curing most variants as they arise (Btn2, Cur1, Hsp104, Upf1,2,3, Siw14), and (3) limiting the pathogenicity of variants that do arise and propagate (Sis1, Lug1). Known mechanisms include facilitating proper folding of the prion protein (Ssb1,2, Ssz1, Zuo1), producing highly asymmetric segregation of prion filaments in mitosis (Btn2, Hsp104), competing with the amyloid filaments for prion protein monomers (Upf1,2,3), and regulation of levels of inositol polyphosphates (Siw14). It is hoped that the discovery of yeast anti-prion systems and elucidation of their mechanisms will facilitate finding analogous or homologous systems in humans, whose manipulation may be useful in treatment.
    [Show full text]
  • Signature Redacted. Amy E
    A genetic platform for the study of protein perturbation and prion-based inheritance by Gregory A. Newby B.S., Biological Sciences Carnegie Mellon University (2009) SUBMITTED TO THE DEPARTMENT OF BIOLOGY IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY AT THE MASSACHUSETTS INSTITUTE OF TECHNOLOGY June 2017 Massachusetts Institute of Technology 2017. All rights reserved. Signature redacted Signature of Author................................. Department of Biology redacted C e rtifie d B y .. Signature ............... I.R..... F..... / Gerald R. Fink Professor of Biology Acting Thesis Supervisor in Place of Susan Lipdquist (deceased) Accepted By............ Signature redacted. Amy E. Keating MASSACHUSETTS INSTITUTE Professor of Biology OF TECHNOLOGY Chair, Graduate Student Committee MAY 2 3 2017 LIBRARIES I 1 2 A genetic platform for the study of protein perturbation and prion-based inheritance By Gregory Arthur Newby Submitted to the Department of Biology in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Biology SUMMARY Proteins mediate every cellular process. In order for life to exist, each protein must be finely tuned to carry out its function at the proper time and place. Because the environment is dynamic and often unpredictable, the regulation of proteins must be responsive to environmental stimuli. Mutations, age, and severe or repeated insults can decrease the quality of protein regulation, leading to disease. The study of protein regulation and its dysfunction in disease are of vital importance. Regulatory and disease phenomena involving protein assembly or aggregation are common but currently understudied on account of their intractability with existing techniques. In order to equip scientists with better tools to tackle these difficult phenomena, my collaborators Ahmad Khalil and Szilvia Kiriakov (Boston University) and I developed the yTRAP platform (standing for: yeast transcriptional reporters of aggregating proteins).
    [Show full text]
  • The Role of RNA in Prion Aggregation and Disease
    Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 1620 The role of RNA in prion aggregation and disease PETAR STEFANOV KOVACHEV ACTA UNIVERSITATIS UPSALIENSIS ISSN 1651-6214 ISBN 978-91-513-0208-9 UPPSALA urn:nbn:se:uu:diva-338857 2018 Dissertation presented at Uppsala University to be publicly examined in A1:107a, BMC, Husargatan 3, Uppsala, Friday, 2 March 2018 at 09:00 for the degree of Doctor of Philosophy. The examination will be conducted in English. Faculty examiner: Associate professor Magnus Wolf-Watz (Department of Chemistry, Umeå University). Abstract Kovachev, P. S. 2018. The role of RNA in prion aggregation and disease. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 1620. 81 pp. Uppsala: Acta Universitatis Upsaliensis. ISBN 978-91-513-0208-9. As humanity evolved to witness an exceptionally high standard of living, Alzheimer’s, cancer and diabetes gradually replaced infections as the main limiting factors in longevity. It is both disturbing and captivating that such degenerative conditions are caused by the most ubiquitous biomolecule – the protein. Indeed, proteins are not only the most functional, but also the least understood of the cellular biopolymers. It is then not surprising that many severe human ailments are associated with aberrant proteostasis. The key, causative mechanism of proteinopathy is protein aggregation. Naturally occurring and sometimes functional, aggregation is an auxiliary pathway in protein folding. In the context of a crowded cellular environment, folding and aggregation are the least and one of the least understood molecular processes, respectively. Unravelling one can help deconstruct the other and vice versa, but also can provide mechanistic insight on degenerative proteinopathies.
    [Show full text]
  • What Makes a Prion: Infectious Proteins from Animals to Yeast Kyle S
    University of New Hampshire University of New Hampshire Scholars' Repository Life Sciences Faculty Scholarship Life Sciences 10-20-2016 What Makes a Prion: Infectious Proteins From Animals to Yeast Kyle S. MacLea University of New Hampshire, Manchester, [email protected] Follow this and additional works at: https://scholars.unh.edu/unhmbiology_facpub Recommended Citation MacLea, K.S. What makes a prion: Infectious proteins from animals to yeast. Int Rev Cell Mol Biol, 329:227-276, doi: 10.1016/ bs.ircmb.2016.08.012, 2017. This Article is brought to you for free and open access by the Life Sciences at University of New Hampshire Scholars' Repository. It has been accepted for inclusion in Life Sciences Faculty Scholarship by an authorized administrator of University of New Hampshire Scholars' Repository. For more information, please contact [email protected]. 1 What Makes a Prion: Infectious Proteins From Animals to Yeast 2 3 Kyle S. MacLea 4 5 Department of Life Sciences, University of New Hampshire, Manchester, New Hampshire 6 7 8 9 10 11 Running title: Infectious Proteins from Animals to Yeast 12 13 14 15 Corresponding Author: Dr. Kyle S. MacLea 16 Department of Life Sciences 17 University of New Hampshire 18 Manchester, NH 03101 19 20 Tel: 603-641-4129 21 Fax: 603-641-4303 22 e-mail: [email protected] 23 24 25 2 Tables, 4 Figures 26 27 28 Abbreviations: TSE, transmissible spongiform encephalopathy; BSE, bovine spongiform 29 encephalopathy; CWD, chronic wasting disease; CJD, Creutzfeldt-Jakob disease; FFI, 30 fatal familial insomnia; MBM, meat and bone meal; ALS, amyotrophic lateral sclerosis; 31 FTLD, frontotemporal lobar degeneration; MSA, multiple system atrophy; TMV, tobacco 32 mosaic virus; PrP, prion protein; PFD, prion-forming domain; PrLD, prion-like domain; 33 ND, nucleation domain; ORD, oligopeptide repeat domain; PrP, mammalian prion 34 protein; HMM, hidden Markov model; GFP, green fluorescent protein; ORF, open 35 reading frame.
    [Show full text]
  • The HET-S/S Prion Motif in the Control of Programmed Cell Death
    Downloaded from http://cshperspectives.cshlp.org/ on September 30, 2021 - Published by Cold Spring Harbor Laboratory Press The HET-S/s Prion Motif in the Control of Programmed Cell Death Roland Riek1 and Sven J. Saupe2 1Laboratory of Physical Chemistry, ETH Zu¨rich, 8093 Zu¨rich, Switzerland 2Institut de Biochimie et de Ge´ne´tique Cellulaire UMR 5095, CNRS - Universite´ de Bordeaux, 33077 Bordeaux, France Correspondence: [email protected]; [email protected] The [Het-s] prion of the fungus Podospora anserina is a well-studied model system to eluci- date the action of prions and beyond. The [Het-s] prion works as an activation trigger of a cell death execution protein termed HET-S. Amyloid transconformation of the prion-forming region of HET-S induces activation of its pore-forming cell death execution HeLo domain. The prion motif functions in a signal transduction process by which a nucleotide-binding oligomerization domain (NOD)-like receptor termed NWD2 controls the HET-S cell death effector. This prion motif thus corresponds to a functional amyloid motif, allowing a confor- mational crosstalk between homologous motif domains in signal transduction processes that appears to be widespread from the fungal to the mammalian animal kingdoms. This review aims to establish a structure–activity relationship of the HET-S/s prion system and sets it in the context of its wider biological significance. myloids are generally perceived as patholog- Podospora anserina. Upon prion formation, the Aical protein aggregates because they cause HET-s prion-forming domain (PFD) under- devastating neurodegenerative diseases in hu- goes a transition from an unordered flexible mans (Jucker and Walker 2013).
    [Show full text]
  • On the Evolution of Allorecognition and Somatic Fusion in Ascomycete Filamentous Fungi
    On the evolution of allorecognition and somatic fusion in ascomycete filamentous fungi Eric Bastiaans Thesis committee Promotor Prof. Dr B.J. Zwaan Professor of Genetics Wageningen University Co-promotors Dr D.K. Aanen Assistant professor, Laboratory of Genetics Wageningen University Dr A.J.M. Debets Associate professor, Laboratory of Genetics Wageningen University Other members Prof. Dr T.W. Kuyper, Wageningen University Prof. Dr H. Wösten, Utrecht University Prof. Dr N.P.R. Anten, Wageningen University Prof. Dr L. Sundström, University of Helsinki, Finland This research was conducted under the auspices of the C.T. de Wit Graduate School for Production Ecology and Resource Conservation On the evolution of allorecognition and somatic fusion in ascomycete filamentous fungi Eric Bastiaans Thesis submitted in fulfilment of the requirements for the degree of doctor at Wageningen University by the authority of the Rector Magnificus Prof. Dr M.J. Kropff, in the presence of the Thesis Committee appointed by the Academic Board to be defended in public on Wednesday 27 May 2015 at 4 p.m. in the Aula. Eric Bastiaans On the evolution of allorecognition and somatic fusion in ascomycete filamentous fungi 128 pages. PhD thesis, Wageningen University, Wageningen, NL (2015) With references, with summaries in Dutch and English ISBN 978-94-6257-297-3 Contents Chapter 1 7 General introduction Chapter 2 19 Experimental demonstration of the benefits of somatic fusion and the consequences for allorecognition Chapter 3 35 High relatedness protects multicellular
    [Show full text]
  • Discovery and Characterization of Prions in Saccharomyces Cerevisiae
    Discovery and Characterization of Prions in Saccharomyces cerevisiae by Randal A. Halfmann B.S. Genetics Texas A&M University, 2004 Submitted to the Department of Biology in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY IN BIOLOGY at the MASSACHUSETTS INSTITUTE OF TECHNOLOGY FEBRUARY 2011 © 2011 Randal A. Halfmann. All rights reserved. The author hereby grants to MIT permission to reproduce and to distribute publicly paper and electronic copies of this thesis document in whole or in part in any medium now known or hereafter created Signature of Author:_________________________________________________________________________________ Department of Biology December 3, 2010 Certified by:___________________________________________________________________________________________ Susan L. Lindquist Professor of Biology Thesis Supervisor Accepted by:__________________________________________________________________________________________ Stephen P. Bell Professor of Biology Co-Chair, Biology Graduate Committee 1 2 Discovery and Characterization of Prions in Saccharomyces cerevisiae by Randal A. Halfmann Submitted to the Department of Biology in partial fulfillment of the requirements for the Degree of Doctor of Philosophy in Biology ABSTRACT Some protein aggregates can perpetuate themselves in a self-templating protein-misfolding reaction. These aggregates, or prions, are the infectious agents behind diseases like Kuru and mad- cow disease. In yeast, however, prions act as epigenetic elements that confer heritable alternative phenotypes. Prion-forming proteins create bistable molecular systems whose semi-stochastic switching between functional states increases phenotypic diversity within cell populations. My thesis work explores the idea that rather than being detrimental, prions may commonly act to their host’s advantage. To broaden the known range of prion phenomena in S. cerevisiae, I, together with a postdoctoral fellow in our lab, systematically surveyed the yeast proteome for prion-forming proteins.
    [Show full text]