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Kamali-Jamil R, Vázquez-Fernández E, Tancowny B, Rathod V, Amidian S, Wang X, Tang X, Fang A, Senatore A, Hornemann S, Dudas S, Aguzzi A, Young HS, Wille H. The ultrastructure of infectious L-type bovine spongiform encephalopathy prions constrains molecular models. PLoS Pathog 2021; 17:e1009628. [PMID: 34061899 PMCID: PMC8195424 DOI: 10.1371/journal.ppat.1009628] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 06/11/2021] [Accepted: 05/10/2021] [Indexed: 11/18/2022] Open
Abstract
Bovine spongiform encephalopathy (BSE) is a prion disease of cattle that is caused by the misfolding of the cellular prion protein (PrPC) into an infectious conformation (PrPSc). PrPC is a predominantly α-helical membrane protein that misfolds into a β-sheet rich, infectious state, which has a high propensity to self-assemble into amyloid fibrils. Three strains of BSE prions can cause prion disease in cattle, including classical BSE (C-type) and two atypical strains, named L-type and H-type BSE. To date, there is no detailed information available about the structure of any of the infectious BSE prion strains. In this study, we purified L-type BSE prions from transgenic mouse brains and investigated their biochemical and ultrastructural characteristics using electron microscopy, image processing, and immunogold labeling techniques. By using phosphotungstate anions (PTA) to precipitate PrPSc combined with sucrose gradient centrifugation, a high yield of proteinase K-resistant BSE amyloid fibrils was obtained. A morphological examination using electron microscopy, two-dimensional class averages, and three-dimensional reconstructions revealed two structural classes of L-type BSE amyloid fibrils; fibrils that consisted of two protofilaments with a central gap and an average width of 22.5 nm and one-protofilament fibrils that were 10.6 nm wide. The one-protofilament fibrils were found to be more abundant compared to the thicker two-protofilament fibrils. Both fibrillar assemblies were successfully decorated with monoclonal antibodies against N- and C-terminal epitopes of PrP using immunogold-labeling techniques, confirming the presence of polypeptides that span residues 100-110 to 227-237. The fact that the one-protofilament fibrils contain both N- and C-terminal PrP epitopes constrains molecular models for the structure of the infectious conformer in favour of a compact four-rung β-solenoid fold.
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Affiliation(s)
- Razieh Kamali-Jamil
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
| | - Ester Vázquez-Fernández
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
| | - Brian Tancowny
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
| | - Vineet Rathod
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
| | - Sara Amidian
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
| | - Xiongyao Wang
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
| | - Xinli Tang
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
| | - Andrew Fang
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
| | - Assunta Senatore
- Institute of Neuropathology, University of Zürich, Zürich, Switzerland
| | - Simone Hornemann
- Institute of Neuropathology, University of Zürich, Zürich, Switzerland
| | - Sandor Dudas
- Canadian BSE Reference Laboratory, Canadian Food Inspection Agency, Lethbridge Laboratory, Lethbridge, Alberta, Canada
| | - Adriano Aguzzi
- Institute of Neuropathology, University of Zürich, Zürich, Switzerland
| | - Howard S. Young
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Holger Wille
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Alberta, Canada
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Sevillano AM, Fernández-Borges N, Younas N, Wang F, R. Elezgarai S, Bravo S, Vázquez-Fernández E, Rosa I, Eraña H, Gil D, Veiga S, Vidal E, Erickson-Beltran ML, Guitián E, Silva CJ, Nonno R, Ma J, Castilla J, R. Requena J. Recombinant PrPSc shares structural features with brain-derived PrPSc: Insights from limited proteolysis. PLoS Pathog 2018; 14:e1006797. [PMID: 29385212 PMCID: PMC5809102 DOI: 10.1371/journal.ppat.1006797] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 02/12/2018] [Accepted: 12/08/2017] [Indexed: 11/18/2022] Open
Abstract
Very solid evidence suggests that the core of full length PrPSc is a 4-rung β-solenoid, and that individual PrPSc subunits stack to form amyloid fibers. We recently used limited proteolysis to map the β-strands and connecting loops that make up the PrPSc solenoid. Using high resolution SDS-PAGE followed by epitope analysis, and mass spectrometry, we identified positions ~116/118, 133-134, 141, 152-153, 162, 169 and 179 (murine numbering) as Proteinase K (PK) cleavage sites in PrPSc. Such sites likely define loops and/or borders of β-strands, helping us to predict the threading of the β-solenoid. We have now extended this approach to recombinant PrPSc (recPrPSc). The term recPrPSc refers to bona fide recombinant prions prepared by PMCA, exhibiting infectivity with attack rates of ~100%. Limited proteolysis of mouse and bank vole recPrPSc species yielded N-terminally truncated PK-resistant fragments similar to those seen in brain-derived PrPSc, albeit with varying relative yields. Along with these fragments, doubly N- and C-terminally truncated fragments, in particular ~89/97-152, were detected in some recPrPSc preparations; similar fragments are characteristic of atypical strains of brain-derived PrPSc. Our results suggest a shared architecture of recPrPSc and brain PrPSc prions. The observed differences, in particular the distinct yields of specific PK-resistant fragments, are likely due to differences in threading which result in the specific biochemical characteristics of recPrPSc. Furthermore, recombinant PrPSc offers exciting opportunities for structural studies unachievable with brain-derived PrPSc.
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Affiliation(s)
- Alejandro M. Sevillano
- CIMUS Biomedical Research Institute and Department of Medical Sciences University of Santiago de Compostela-IDIS, Santiago de Compostela, Spain
- * E-mail: (AMS); (JRR)
| | | | - Neelam Younas
- CIMUS Biomedical Research Institute and Department of Medical Sciences University of Santiago de Compostela-IDIS, Santiago de Compostela, Spain
| | - Fei Wang
- Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, Michigan, United States of America
| | | | - Susana Bravo
- Proteomics Lab, IDIS, Santiago de Compostela, Spain
| | | | - Isaac Rosa
- CIMUS Biomedical Research Institute and Department of Medical Sciences University of Santiago de Compostela-IDIS, Santiago de Compostela, Spain
| | | | | | - Sonia Veiga
- CIMUS Biomedical Research Institute and Department of Medical Sciences University of Santiago de Compostela-IDIS, Santiago de Compostela, Spain
| | - Enric Vidal
- Priocat Laboratory, Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Barcelona, Catalonia, Spain
| | | | - Esteban Guitián
- Mass spectrometry Core Facility, RIAIDT, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Christopher J. Silva
- USDA, ARS Western Regional Research Center, Albany, California, United States of America
| | - Romolo Nonno
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | - Jiyan Ma
- Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, Michigan, United States of America
| | | | - Jesús R. Requena
- CIMUS Biomedical Research Institute and Department of Medical Sciences University of Santiago de Compostela-IDIS, Santiago de Compostela, Spain
- * E-mail: (AMS); (JRR)
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Vázquez-Fernández E, Alonso J, Pastrana MA, Ramos A, Stitz L, Vidal E, Dynin I, Petsch B, Silva CJ, Requena JR. Structural organization of mammalian prions as probed by limited proteolysis. PLoS One 2012. [PMID: 23185550 PMCID: PMC3502352 DOI: 10.1371/journal.pone.0050111] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Elucidation of the structure of PrPSc continues to be one major challenge in prion research. The mechanism of propagation of these infectious agents will not be understood until their structure is solved. Given that high resolution techniques such as NMR or X-ray crystallography cannot be used, a number of lower resolution analytical approaches have been attempted. Thus, limited proteolysis has been successfully used to pinpoint flexible regions within prion multimers (PrPSc). However, the presence of covalently attached sugar antennae and glycosylphosphatidylinositol (GPI) moieties makes mass spectrometry-based analysis impractical. In order to surmount these difficulties we analyzed PrPSc from transgenic mice expressing prion protein (PrP) lacking the GPI membrane anchor. Such animals produce prions that are devoid of the GPI anchor and sugar antennae, and, thereby, permit the detection and location of flexible, proteinase K (PK) susceptible regions by Western blot and mass spectrometry-based analysis. GPI-less PrPSc samples were digested with PK. PK-resistant peptides were identified, and found to correspond to molecules cleaved at positions 81, 85, 89, 116, 118, 133, 134, 141, 152, 153, 162, 169 and 179. The first 10 peptides (to position 153), match very well with PK cleavage sites we previously identified in wild type PrPSc. These results reinforce the hypothesis that the structure of PrPSc consists of a series of highly PK-resistant β-sheet strands connected by short flexible PK-sensitive loops and turns. A sizeable C-terminal stretch of PrPSc is highly resistant to PK and therefore perhaps also contains β-sheet secondary structure.
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Affiliation(s)
- Ester Vázquez-Fernández
- CIMUS Biomedical Research Institute, University of Santiago de Compostela-IDIS, Santiago de Compostela, Spain
- * E-mail: (EVF); (JRR)
| | - Jana Alonso
- Proteomics Unit, IDIS, Santiago de Compostela, Spain
| | - Miguel A. Pastrana
- CIMUS Biomedical Research Institute, University of Santiago de Compostela-IDIS, Santiago de Compostela, Spain
| | - Adriana Ramos
- CIMUS Biomedical Research Institute, University of Santiago de Compostela-IDIS, Santiago de Compostela, Spain
| | - Lothar Stitz
- Institute of Immunology, Friedrich Loeffler Institut, Tübingen, Germany
| | - Enric Vidal
- Priocat Laboratory, Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Barcelona, Spain
| | - Irina Dynin
- Western Regional Research Center, USDA, Albany, California, United States of America
| | - Benjamin Petsch
- Institute of Immunology, Friedrich Loeffler Institut, Tübingen, Germany
| | - Christopher J. Silva
- Western Regional Research Center, USDA, Albany, California, United States of America
| | - Jesús R. Requena
- CIMUS Biomedical Research Institute, University of Santiago de Compostela-IDIS, Santiago de Compostela, Spain
- Department of Medicine, University of Santiago de Compostela, Santiago de Compostela, Spain
- * E-mail: (EVF); (JRR)
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Sajnani G, Silva CJ, Ramos A, Pastrana MA, Onisko BC, Erickson ML, Antaki EM, Dynin I, Vázquez-Fernández E, Sigurdson CJ, Carter JM, Requena JR. PK-sensitive PrP is infectious and shares basic structural features with PK-resistant PrP. PLoS Pathog 2012; 8:e1002547. [PMID: 22396643 PMCID: PMC3291653 DOI: 10.1371/journal.ppat.1002547] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Accepted: 01/10/2012] [Indexed: 11/25/2022] Open
Abstract
One of the main characteristics of the transmissible isoform of the prion protein (PrPSc) is its partial resistance to proteinase K (PK) digestion. Diagnosis of prion disease typically relies upon immunodetection of PK-digested PrPSc following Western blot or ELISA. More recently, researchers determined that there is a sizeable fraction of PrPSc that is sensitive to PK hydrolysis (sPrPSc). Our group has previously reported a method to isolate this fraction by centrifugation and showed that it has protein misfolding cyclic amplification (PMCA) converting activity. We compared the infectivity of the sPrPSc versus the PK-resistant (rPrPSc) fractions of PrPSc and analyzed the biochemical characteristics of these fractions under conditions of limited proteolysis. Our results show that sPrPSc and rPrPSc fractions have comparable degrees of infectivity and that although they contain different sized multimers, these multimers share similar structural properties. Furthermore, the PK-sensitive fractions of two hamster strains, 263K and Drowsy (Dy), showed strain-dependent differences in the ratios of the sPrPSc to the rPrPSc forms of PrPSc. Although the sPrPSc and rPrPSc fractions have different resistance to PK-digestion, and have previously been shown to sediment differently, and have a different distribution of multimers, they share a common structure and phenotype. Prion diseases are protein misfolding disorders. Different strains of prions are known to have variable resistance to proteinase K (PK) digestion. Furthermore, the same strain possesses both a PK sensitive (sPrPSc) and PK resistant (rPrPSc) aggregate of PrP. We developed methods to isolate the sPrPSc from rPrPSc fraction of the 263K strain of hamster-adapted scrapie. Both fractions were infectious, but have different physico-chemical properties. When we analyzed the lesion targets in the brain produced by each fraction they were essentially identical, suggesting that they were the same strain. The biochemical differences in the phenotypes of these two fractions are due to different sized multimers that share common structural properties. Furthermore, the comparison of the sensitive fractions of two hamster strains, 263K and Drowsy (Dy), showed strain-dependent differences in the ratios of the PK-sensitive to the PK-resistant forms of PrPSc.
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Affiliation(s)
- Gustavo Sajnani
- Department of Medicine, School of Medicine, University of Santiago de Compostela, Santiago de Compostela, Galiza, Spain.
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Gong B, Ramos A, Vázquez-Fernández E, Silva CJ, Alonso J, Liu Z, Requena JR. Probing structural differences between PrP(C) and PrP(Sc) by surface nitration and acetylation: evidence of conformational change in the C-terminus. Biochemistry 2011; 50:4963-72. [PMID: 21526750 DOI: 10.1021/bi102073j] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We used two chemical modifiers, tetranitromethane (TNM) and acetic anhydride (Ac(2)O), which specifically target accessible tyrosine and lysine residues, respectively, to modify recombinant Syrian hamster PrP(90-231) [rSHaPrP(90-231)] and SHaPrP 27-30, the proteinase K-resistant core of PrP(Sc) isolated from brain of scrapie-infected Syrian hamsters. Our aim was to find locations of conformational change. Modified proteins were subjected to in-gel proteolytic digestion with trypsin or chymotrypsin and subsequent analysis by mass spectrometry (MALDI-TOF). Several differences in chemical reactivity were observed. With TNM, the most conspicuous reactivity difference seen involves peptide E(221)-R(229) (containing Y(225) and Y(226)), which in rSHaPrP(90-231) was much more extensively modified than in SHaPrP 27-30; peptide H(111)-R(136), containing Y(128), was also more modified in rSHaPrP(90-231). Conversely, peptides Y(149)-R(151), Y(157)-R(164), and R(151)-Y(162) suffered more extensive modification in SHaPrP 27-30. Acetic anhydride modified very extensively peptide G(90)-K(106), containing K(101), K(104), K(106), and the amino terminus, in both rSHaPrP(90-231) and SHaPrP 27-30. These results suggest that (1) SHaPrP 27-30 exhibits important conformational differences in the C-terminal region with respect to rSHaPrP(90-231), resulting in the loss of solvent accessibility of Y(225) and Y(226), very solvent-exposed in the latter conformation; because other results suggest preservation of the two C-terminal helices, this might mean that these are tightly packed in SHaPrP 27-30. (2) On the other hand, tyrosines contained in the stretch spanning approximately Y(149)-R(164) are more accessible in SHaPrP 27-30, suggesting rearrangements in α-helix H1 and the short β-sheet of rSHaPrP(90-231). (3) The amino-terminal region of SHaPrP 27-30 is very accessible. These data should help in the validation and construction of structural models of PrP(Sc).
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Affiliation(s)
- Binbin Gong
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Animal Science and Veterinary Medicine, Jilin University, Changchun, PR China
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López-Vizcaíno ME, Vidal-Rodeiro CL, Santiago-Pérez MI, Vázquez-Fernández E, Hervada-Vidal X. An evaluation of spatio-temporal models for the estimation of the mortality relative risk from breast cancer in Galicia, Spain. J Cancer Epidemiol Prev 2003; 7:181-93. [PMID: 12846489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
BACKGROUND Disease mapping is now a big focus of interest in the area of Public Health, and the geographical distribution of a disease has an important role in understanding its origin or its causes. The purpose of this work is to review and evaluate different techniques to map the mortality risk of a disease in small geographical areas. METHODS Three different methods have been studied. The first one is a classical approach consisting of mapping SMRs, which are maximum likelihood estimates of the relative risk under a Poisson model of death counts. In a second step we consider Poisson and negative binomial regression to fit the rates and finally we use a Bayesian approach that assumes a hierarchical model where the death counts follow a Poisson distribution conditioned by the prior information. These methods have been applied to the study of geographical variation in female breast cancer mortality from 1976 to 1999 in the districts of Galicia, Spain. RESULTS Mapping the SMRs using the first method has important drawbacks and there are difficulties to distinguish the mortality pattern. With the second method we achieved some improvements. The Bayesian methodology produces smoother maps with a clear mortality pattern. DISCUSSION These methods are powerful tools for identifying areas with elevated risk. The Bayesian methodology has many advantages over the other methods that had been analysed in this work.
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Vidal-Rodeiro CL, Santiago-Pérez MI, Paz-Esquete J, López-Vizcaíno ME, Cerdeira-Caramés S, Hervada-Vidal X, Vázquez-Fernández E. [Space-time distribution of suicide in Galicia, Spain [1976-1998]]. Gac Sanit 2001; 15:389-97. [PMID: 11734151 DOI: 10.1016/s0213-9111(01)71592-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
OBJECTIVE To study the space-time distribution of suicide in Galicia from 1976 to 1998, taking into account gender, age, season and method of suicide. METHODS For each sex crude and age-adjusted rates per province and age-specific rates per period (1978-84, 1985-91, 1992-98) were calculated. To estimate mortality risk and time trends in the municipalities, a Bayesian hierarchical model was used. RESULTS In the last few years mortality from suicide has increase considerably. Age-adjusted rates of 6 per 105 at the beginning of the study rose to 10 per 105 at the end. The increase was greatest among men. The higher rates were observed in the elderly, although in terms of time trends the highest increase occurred among adolescents and young adults. In both sexes the main method of suicide was hanging. Less common methods were jumping from a height and shooting. The greatest number of suicides took place during the spring and summer months. In terms of spatial distribution, a high number of suicides were committed in the province of Lugo; in the municipalities, mortality risk decreased from North to South and an inverse temporal trend was observed in both sexes. This differed from the space-time patterns of suicides committed using methods other than hanging. CONCLUSIONS Suicide is an important health problem in Galicia not only because to its magnitude but also because of the increasing rates, especially among young people. Geographical and temporal analysis can identify priority areas where preventive policies should be implemented.
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Affiliation(s)
- C L Vidal-Rodeiro
- Servicio de Información sobre Saúde Pública. Dirección Xeral de Saúde Pública. Consellería de Sanidade e Servicios Sociais. Xunta de Galicia
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