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Sulatsky MI, Stepanenko OV, Stepanenko OV, Kuznetsova IM, Turoverov KK, Sulatskaya AI. Prediction of the Feasibility of Using the ≪Gold Standard≫ Thioflavin T to Detect Amyloid Fibril in Acidic Media. Anal Chem 2024; 96:2158-2164. [PMID: 38269442 DOI: 10.1021/acs.analchem.3c05118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
Ordered protein aggregates, amyloid fibrils, form toxic plaques in the human body in amyloidosis and neurodegenerative diseases and provide adaptive benefits to pathogens and to reduce the nutritional value of legumes. To identify the amyloidogenic properties of proteins and study the processes of amyloid fibril formation and degradation, the cationic dye thioflavin T (ThT) is the most commonly used. However, its use in acidic environments that induce amyloid formation in vitro can sometimes lead to misinterpretation of experimental results due to electrostatic repulsion. In this work, we show that calculating the net charge per residue of amyloidogenic proteins or peptides is a simple and effective approach for predicting whether their fibrils will interact with ThT at acidic pH. In particular, it was shown that at pH 2, proteins and peptides with a net charge per residue > +0.18 are virtually unstained by this fluorescent probe. The applicability of the proposed approach was demonstrated by predicting and experimentally confirming the absence of ThT interaction with amyloids formed from green fluorescent (sfGFP) and odorant-binding (bOBP) proteins, whose fibrillogenesis was first carried out in an acidic environment. Correct experimental evidence that the inability to detect these fibrils under acidic conditions is precisely because of the lack of dye binding to amyloids (and not their specific structure or the low fluorescence quantum yield of the bound dye) and that the number of ThT molecules associated with fibrils increases with decreasing acidity of the medium was obtained by using the equilibrium microdialysis approach.
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Affiliation(s)
- Maksim I Sulatsky
- Laboratory of cell morphology, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave., 194064 St. Petersburg, Russia
| | - Olesya V Stepanenko
- Laboratory of structural dynamics, stability and folding of proteins, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave., 194064 St. Petersburg, Russia
| | - Olga V Stepanenko
- Laboratory of structural dynamics, stability and folding of proteins, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave., 194064 St. Petersburg, Russia
| | - Irina M Kuznetsova
- Laboratory of structural dynamics, stability and folding of proteins, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave., 194064 St. Petersburg, Russia
| | - Konstantin K Turoverov
- Laboratory of structural dynamics, stability and folding of proteins, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave., 194064 St. Petersburg, Russia
| | - Anna I Sulatskaya
- Laboratory of structural dynamics, stability and folding of proteins, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave., 194064 St. Petersburg, Russia
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2
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Stepanenko OV, Sulatskaya AI, Sulatsky MI, Mikhailova EV, Kuznetsova IM, Turoverov KK, Stepanenko OV. Mammalian odorant-binding proteins are prone to form amorphous aggregates and amyloid fibrils. Int J Biol Macromol 2023; 253:126872. [PMID: 37722633 DOI: 10.1016/j.ijbiomac.2023.126872] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 09/06/2023] [Accepted: 09/10/2023] [Indexed: 09/20/2023]
Abstract
Odorant-binding proteins are involved in perceiving smell by capturing odorants within the protein's β-barrel. On the example of bovine odorant-binding protein (bOBP), the structural organization of such proteins and their ability to bind ligands under various conditions in vitro were examined. We found a tendency of bOBP to form oligomers and small amorphous aggregates without disturbing the integrity of protein monomers at physiological conditions. Changes in environmental parameters (increased temperature and pH) favored the formation of larger and dense supramolecular complexes that significantly reduce the binding of ligands by bOBP. The ability of bOBP to form fibrillar aggregates with the properties of amyloids, including high cytotoxicity, was revealed at sample stirring (even at physiological temperature and pH), at medium acidification or pre-solubilization with hexafluoroisopropanol. Fibrillogenesis of bOBP was initiated by the dissociation of the protein's supramolecular complexes into monomers and the destabilization of the protein's β-barrels without a significant destruction of its native β-strands.
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Affiliation(s)
- Olga V Stepanenko
- Laboratory of Structural Dynamics, Stability and folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave, 194064 St. Petersburg, Russia.
| | - Anna I Sulatskaya
- Laboratory of Structural Dynamics, Stability and folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave, 194064 St. Petersburg, Russia.
| | - Maksim I Sulatsky
- Laboratory of Cell Morphology, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave., 194064 St. Petersburg, Russia.
| | - Ekaterina V Mikhailova
- Laboratory of Structural Dynamics, Stability and folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave, 194064 St. Petersburg, Russia.
| | - Irina M Kuznetsova
- Laboratory of Structural Dynamics, Stability and folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave, 194064 St. Petersburg, Russia.
| | - Konstantin K Turoverov
- Laboratory of Structural Dynamics, Stability and folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave, 194064 St. Petersburg, Russia.
| | - Olesya V Stepanenko
- Laboratory of Structural Dynamics, Stability and folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave, 194064 St. Petersburg, Russia.
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3
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Matos GS, Vogt L, Santos RS, Devillars A, Yoshinaga MY, Miyamoto S, Schaffrath R, Montero-Lomeli M, Klassen R. Lipidome remodeling in response to nutrient replenishment requires the tRNA modifier Deg1/Pus3 in yeast. Mol Microbiol 2023; 120:893-905. [PMID: 37864403 DOI: 10.1111/mmi.15185] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 10/09/2023] [Accepted: 10/11/2023] [Indexed: 10/22/2023]
Abstract
In the yeast Saccharomyces cerevisiae, the absence of the pseudouridine synthase Pus3/Deg1, which modifies tRNA positions 38 and 39, results in increased lipid droplet (LD) content and translational defects. In addition, starvation-like transcriptome alterations and induced protein aggregation were observed. In this study, we show that the deg1 mutant increases specific misreading errors. This could lead to altered expression of the main regulators of neutral lipid synthesis which are the acetyl-CoA carboxylase (Acc1), an enzyme that catalyzes a key step in fatty acid synthesis, and its regulator, the Snf1/AMPK kinase. We demonstrate that upregulation of the neutral lipid content of LD in the deg1 mutant is achieved by a mechanism operating in parallel to the known Snf1/AMPK kinase-dependent phosphoregulation of Acc1. While in wild-type cells removal of the regulatory phosphorylation site (Ser-1157) in Acc1 results in strong upregulation of triacylglycerol (TG), but not steryl esters (SE), the deg1 mutation more specifically upregulates SE levels. In order to elucidate if other lipid species are affected, we compared the lipidomes of wild type and deg1 mutants, revealing multiple altered lipid species. In particular, in the exponential phase of growth, the deg1 mutant shows a reduction in the pool of phospholipids, indicating a compromised capacity to mobilize acyl-CoA from storage lipids. We conclude that Deg1 plays a key role in the coordination of lipid storage and mobilization, which in turn influences lipid homeostasis. The lipidomic effects in the deg1 mutant may be indirect outcomes of the activation of various stress responses resulting from protein aggregation.
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Affiliation(s)
- Gabriel Soares Matos
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Leonie Vogt
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Kassel, Germany
| | - Rosangela Silva Santos
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Aurélien Devillars
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Kassel, Germany
| | - Marcos Yukio Yoshinaga
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Sayuri Miyamoto
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Raffael Schaffrath
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Kassel, Germany
| | - Monica Montero-Lomeli
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Roland Klassen
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Kassel, Germany
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Kachkin DV, Lashkul VV, Gorsheneva NA, Fedotov SA, Rubel MS, Chernoff YO, Rubel AA. The Aβ42 Peptide and IAPP Physically Interact in a Yeast-Based Assay. Int J Mol Sci 2023; 24:14122. [PMID: 37762425 PMCID: PMC10531723 DOI: 10.3390/ijms241814122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/31/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Numerous studies have demonstrated that people with type 2 diabetes mellitus (associated with IAPP peptide aggregation) show an increased incidence of Alzheimer's disease (associated with Aβ aggregation), but the mechanism responsible for this correlation is presently unknown. Here, we applied a yeast-based model to study the interactions of IAPP with PrP (associated with TSEs) and with the Aβ42 peptide. We demonstrated that fluorescently tagged IAPP forms detergent-resistant aggregates in yeast cells. Using the FRET approach, we showed that IAPP and Aβ aggregates co-localize and physically interact in yeast cells. We also showed that this interaction is specific and that there is no interaction between IAPP and PrP in the yeast system. Our data confirmed a direct physical interaction between IAPP and Aβ42 aggregates in a living cell. Based on these findings, we hypothesize that this interaction may play a crucial role in seeding Aβ42 aggregation in T2DM patients, thereby promoting the development of AD.
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Affiliation(s)
- Daniel V. Kachkin
- Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg 199034, Russia; (D.V.K.); (S.A.F.)
| | - Veronika V. Lashkul
- Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg 199034, Russia; (D.V.K.); (S.A.F.)
| | - Natalia A. Gorsheneva
- Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg 199034, Russia; (D.V.K.); (S.A.F.)
| | - Sergey A. Fedotov
- Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg 199034, Russia; (D.V.K.); (S.A.F.)
- Pavlov Institute of Physiology, Russian Academy of Sciences, St. Petersburg 199034, Russia
| | - Maria S. Rubel
- Laboratory of DNA-Nanosensor Diagnostics, SCAMT Institute, ITMO University, St. Petersburg 191002, Russia;
| | - Yury O. Chernoff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA;
| | - Aleksandr A. Rubel
- Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg 199034, Russia; (D.V.K.); (S.A.F.)
- Pediatric Research and Clinical Center for Infectious Diseases, Department of Medical Microbiology and Molecular Epidemiology, St. Petersburg 197022, Russia
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5
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Jay-Garcia LM, Cornell JL, Howie RL, Faber QL, Salas A, Chernova TA, Chernoff YO. Yeast Chaperone Hsp70-Ssb Modulates a Variety of Protein-Based Heritable Elements. Int J Mol Sci 2023; 24:ijms24108660. [PMID: 37240005 DOI: 10.3390/ijms24108660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/03/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
Prions are transmissible self-perpetuating protein isoforms associated with diseases and heritable traits. Yeast prions and non-transmissible protein aggregates (mnemons) are frequently based on cross-β ordered fibrous aggregates (amyloids). The formation and propagation of yeast prions are controlled by chaperone machinery. Ribosome-associated chaperone Hsp70-Ssb is known (and confirmed here) to modulate formation and propagation of the prion form of the Sup35 protein [PSI+]. Our new data show that both formation and mitotic transmission of the stress-inducible prion form of the Lsb2 protein ([LSB+]) are also significantly increased in the absence of Ssb. Notably, heat stress leads to a massive accumulation of [LSB+] cells in the absence of Ssb, implicating Ssb as a major downregulator of the [LSB+]-dependent memory of stress. Moreover, the aggregated form of Gγ subunit Ste18, [STE+], behaving as a non-heritable mnemon in the wild-type strain, is generated more efficiently and becomes heritable in the absence of Ssb. Lack of Ssb also facilitates mitotic transmission, while lack of the Ssb cochaperone Hsp40-Zuo1 facilitates both spontaneous formation and mitotic transmission of the Ure2 prion, [URE3]. These results demonstrate that Ssb is a general modulator of cytosolic amyloid aggregation, whose effect is not restricted only to [PSI+].
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Affiliation(s)
- Lina M Jay-Garcia
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Joseph L Cornell
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Rebecca L Howie
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Quincy L Faber
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Abigail Salas
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Tatiana A Chernova
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Yury O Chernoff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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6
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Search and Identification of Amyloid Proteins. Methods Protoc 2023; 6:mps6010016. [PMID: 36827503 PMCID: PMC9967629 DOI: 10.3390/mps6010016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 02/08/2023] Open
Abstract
Amyloids are fibrillar proteins with a cross-β structure. Pathological amyloids are associated with the development of a number of incurable diseases, while functional amyloids regulate vital processes. The detection of unknown amyloids in living objects is a difficult task, and therefore the question of the prevalence and biological significance of amyloids remains open. We present a description of two methods, the combination of which makes it possible to find and identify amyloid proteins in the proteome of various organisms. The method of proteomic screening for amyloids allows the detection of the proteins that form SDS-resistant aggregates. SDS resistance is a general feature of amyloid fibrils. Protein aggregates resistant to SDS treatment can be collected by ultracentrifugation and further identified by mass spectrometry. However, in addition to amyloids, SDS-resistant aggregates contain some non-amyloid proteins. To test the amyloid properties of proteins identified by proteomic screening, we developed the method of fibril immunoprecipitation followed by Congo red staining and birefringence analysis. The methods of proteomic screening and immunoprecipitation of fibrillar proteins have been successfully tested and applied for the identification of amyloid proteins in yeast and vertebrates.
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Cuanalo-Contreras K, Schulz J, Mukherjee A, Park KW, Armijo E, Soto C. Extensive accumulation of misfolded protein aggregates during natural aging and senescence. Front Aging Neurosci 2023; 14:1090109. [PMID: 36778589 PMCID: PMC9909609 DOI: 10.3389/fnagi.2022.1090109] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/22/2022] [Indexed: 01/27/2023] Open
Abstract
Accumulation of misfolded protein aggregates is a hallmark event in many age-related protein misfolding disorders, including some of the most prevalent and insidious neurodegenerative diseases. Misfolded protein aggregates produce progressive cell damage, organ dysfunction, and clinical changes, which are common also in natural aging. Thus, we hypothesized that aging is associated to the widespread and progressive misfolding and aggregation of many proteins in various tissues. In this study, we analyzed whether proteins misfold, aggregate, and accumulate during normal aging in three different biological systems, namely senescent cells, Caenorhabditis elegans, and mouse tissues collected at different times from youth to old age. Our results show a significant accumulation of misfolded protein aggregates in aged samples as compared to young materials. Indeed, aged samples have between 1.3 and 2.5-fold (depending on the biological system) higher amount of insoluble proteins than young samples. These insoluble proteins exhibit the typical characteristics of disease-associated aggregates, including insolubility in detergents, protease resistance, and staining with amyloid-binding dye as well as accumulation in aggresomes. We identified the main proteins accumulating in the aging brain using proteomic studies. These results show that the aged brain contain large amounts of misfolded and likely non-functional species of many proteins, whose soluble versions participate in cellular pathways that play fundamental roles in preserving basic functions, such as protein quality control, synapsis, and metabolism. Our findings reveal a putative role for protein misfolding and aggregation in aging.
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Affiliation(s)
- Karina Cuanalo-Contreras
- Mitchell Center for Alzheimer’s Disease and Related Brain Disorders, Department of Neurology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Jonathan Schulz
- Mitchell Center for Alzheimer’s Disease and Related Brain Disorders, Department of Neurology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Abhisek Mukherjee
- Mitchell Center for Alzheimer’s Disease and Related Brain Disorders, Department of Neurology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Kyung-Won Park
- Mitchell Center for Alzheimer’s Disease and Related Brain Disorders, Department of Neurology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Enrique Armijo
- Mitchell Center for Alzheimer’s Disease and Related Brain Disorders, Department of Neurology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, United States,Facultad de Medicina, Universidad de los Andes, Santiago, Chile
| | - Claudio Soto
- Mitchell Center for Alzheimer’s Disease and Related Brain Disorders, Department of Neurology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, United States,Facultad de Medicina, Universidad de los Andes, Santiago, Chile,*Correspondence: Claudio Soto,
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8
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Saini PK, Dawitz H, Aufschnaiter A, Bondarev S, Thomas J, Amblard A, Stewart J, Thierry-Mieg N, Ott M, Pierrel F. The [PSI +] prion modulates cytochrome c oxidase deficiency caused by deletion of COX12. Mol Biol Cell 2022; 33:ar130. [PMID: 36129767 PMCID: PMC9727813 DOI: 10.1091/mbc.e21-10-0499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 09/09/2022] [Accepted: 09/13/2022] [Indexed: 02/04/2023] Open
Abstract
Cytochrome c oxidase (CcO) is a pivotal enzyme of the mitochondrial respiratory chain, which sustains bioenergetics of eukaryotic cells. Cox12, a peripheral subunit of CcO oxidase, is required for full activity of the enzyme, but its exact function is unknown. Here experimental evolution of a Saccharomyces cerevisiae Δcox12 strain for ∼300 generations allowed to restore the activity of CcO oxidase. In one population, the enhanced bioenergetics was caused by a A375V mutation in the cytosolic AAA+ disaggregase Hsp104. Deletion or overexpression of HSP104 also increased respiration of the Δcox12 ancestor strain. This beneficial effect of Hsp104 was related to the loss of the [PSI+] prion, which forms cytosolic amyloid aggregates of the Sup35 protein. Overall, our data demonstrate that cytosolic aggregation of a prion impairs the mitochondrial metabolism of cells defective for Cox12. These findings identify a new functional connection between cytosolic proteostasis and biogenesis of the mitochondrial respiratory chain.
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Affiliation(s)
- Pawan Kumar Saini
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Hannah Dawitz
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden
| | - Andreas Aufschnaiter
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden
| | - Stanislav Bondarev
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - Jinsu Thomas
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Amélie Amblard
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - James Stewart
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Nicolas Thierry-Mieg
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Martin Ott
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg 40530, Sweden
| | - Fabien Pierrel
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
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9
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Kachkin DV, Volkov KV, Sopova JV, Bobylev AG, Fedotov SA, Inge-Vechtomov SG, Galzitskaya OV, Chernoff YO, Rubel AA, Aksenova AY. Human RAD51 Protein Forms Amyloid-like Aggregates In Vitro. Int J Mol Sci 2022; 23:ijms231911657. [PMID: 36232958 PMCID: PMC9570251 DOI: 10.3390/ijms231911657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/21/2022] [Accepted: 09/26/2022] [Indexed: 12/30/2022] Open
Abstract
RAD51 is a central protein of homologous recombination and DNA repair processes that maintains genome stability and ensures the accurate repair of double-stranded breaks (DSBs). In this work, we assessed amyloid properties of RAD51 in vitro and in the bacterial curli-dependent amyloid generator (C-DAG) system. Resistance to ionic detergents, staining with amyloid-specific dyes, polarized microscopy, transmission electron microscopy (TEM), X-ray diffraction and other methods were used to evaluate the properties and structure of RAD51 aggregates. The purified human RAD51 protein formed detergent-resistant aggregates in vitro that had an unbranched cross-β fibrillar structure, which is typical for amyloids, and were stained with amyloid-specific dyes. Congo-red-stained RAD51 aggregates demonstrated birefringence under polarized light. RAD51 fibrils produced sharp circular X-ray reflections at 4.7 Å and 10 Å, demonstrating that they had a cross-β structure. Cytoplasmic aggregates of RAD51 were observed in cell cultures overexpressing RAD51. We demonstrated that a key protein that maintains genome stability, RAD51, has amyloid properties in vitro and in the C-DAG system and discussed the possible biological relevance of this observation.
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Affiliation(s)
- Daniel V. Kachkin
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Kirill V. Volkov
- Research Resource Center “Molecular and Cell Technologies”, Research Park, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
| | - Julia V. Sopova
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
- Center of Transgenesis and Genome Editing, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Alexander G. Bobylev
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 3 Institutskaya St., 142290 Moscow, Russia
| | - Sergei A. Fedotov
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Sergei G. Inge-Vechtomov
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Oxana V. Galzitskaya
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 3 Institutskaya St., 142290 Moscow, Russia
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Yury O. Chernoff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332-2000, USA
| | - Aleksandr A. Rubel
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
- Correspondence: (A.A.R.); (A.Y.A.)
| | - Anna Y. Aksenova
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
- Correspondence: (A.A.R.); (A.Y.A.)
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10
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NOS1AP Interacts with α-Synuclein and Aggregates in Yeast and Mammalian Cells. Int J Mol Sci 2022; 23:ijms23169102. [PMID: 36012368 PMCID: PMC9409085 DOI: 10.3390/ijms23169102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/11/2022] [Accepted: 08/11/2022] [Indexed: 11/24/2022] Open
Abstract
The NOS1AP gene encodes a cytosolic protein that binds to the signaling cascade component neuronal nitric oxide synthase (nNOS). It is associated with many different disorders, such as schizophrenia, post-traumatic stress disorder, autism, cardiovascular disorders, and breast cancer. The NOS1AP (also known as CAPON) protein mediates signaling within a complex which includes the NMDA receptor, PSD-95, and nNOS. This adapter protein is involved in neuronal nitric oxide (NO) synthesis regulation via its association with nNOS (NOS1). Our bioinformatics analysis revealed NOS1AP as an aggregation-prone protein, interacting with α-synuclein. Further investigation showed that NOS1AP forms detergent-resistant non-amyloid aggregates when overproduced. Overexpression of NOS1AP was found in rat models for nervous system injury as well as in schizophrenia patients. Thus, we can assume for the first time that the molecular mechanisms underlying these disorders include misfolding and aggregation of NOS1AP. We show that NOS1AP interacts with α-synuclein, allowing us to suggest that this protein may be implicated in the development of synucleinopathies and that its aggregation may explain the relationship between Parkinson’s disease and schizophrenia.
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11
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Seto EP, Hirsch AL, Schubert WW, Chandramowlishwaran P, Chernoff YO. Heat inactivation of stable proteinaceous particles for future sample return mission architecture. Front Microbiol 2022; 13:911091. [PMID: 36016789 PMCID: PMC9396123 DOI: 10.3389/fmicb.2022.911091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 07/05/2022] [Indexed: 12/02/2022] Open
Abstract
The National Aeronautics and Space Administration (NASA) and the European Space Agency (ESA) are studying how to improve the safety of future planetary science sample return missions that would bring back materials to Earth. Backward planetary protection requirements have been identified as a critical technology development focus in order to reduce the possibility of harm to Earth’s biosphere from such returned materials. In order to meet these challenges, NASA has identified the need for an appropriate suite of biological indicators (BIs) that would be used to develop, test, and ultimately validate sample return mission sterilization systems. Traditionally, BIs are defined as test systems composed of viable microorganisms that are inactivated when necessary conditions are met during sterilization procedures, providing a level of confidence in the process. BIs used traditionally at NASA have been driven by past mission requirements, mainly focused on spore-formers. However, spore-based BIs are insufficient as the only analog for a nominal case in sample return missions. NASA has directed sample return missions from habitable worlds to manage “potential extraterrestrial life and bioactive molecules” which requires investigation of a range of potential BIs. Thus, it is important to develop a mitigation strategy that addresses various known forms of biology, from complex organisms to biomolecular assemblies (including self-perpetuating non-nucleic acid containing structures). The current effort seeks to establish a BI that would address a stable biomolecule capable of replication. Additional engineering areas that may benefit from this information include applications of brazing, sealing, and impact heating, and atmospheric entry heating. Yeast aggregating proteins exhibit aggregation behavior similar to mammalian prion protein and have been successfully employed by researchers to understand fundamental prion properties such as aggregation and self-propagation. Despite also being termed “prions,” yeast proteins are not hazardous to humans and can be used as a cost effective and safer alternative to mammalian prions. We have shown that inactivation by dry heat is feasible for the prion formed by the yeast Sup35NM protein, although at higher temperature than for bacterial spores.
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Affiliation(s)
- Emily P. Seto
- Honeybee Robotics, Altadena, CA, United States
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
- *Correspondence: Emily P. Seto,
| | - Aspen L. Hirsch
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Wayne W. Schubert
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | | | - Yury O. Chernoff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
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12
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Kushnirov VV, Dergalev AA, Alieva MK, Alexandrov AI. Structural Bases of Prion Variation in Yeast. Int J Mol Sci 2022; 23:ijms23105738. [PMID: 35628548 PMCID: PMC9147965 DOI: 10.3390/ijms23105738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 05/13/2022] [Accepted: 05/18/2022] [Indexed: 12/04/2022] Open
Abstract
Amyloids are protein aggregates with a specific filamentous structure that are related to a number of human diseases, and also to some important physiological processes in animals and other kingdoms of life. Amyloids in yeast can stably propagate as heritable units, prions. Yeast prions are of interest both on their own and as a model for amyloids and prions in general. In this review, we consider the structure of yeast prions and its variation, how such structures determine the balance of aggregated and soluble prion protein through interaction with chaperones and how the aggregated state affects the non-prion functions of these proteins.
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13
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Ngo V, Karunatilleke NC, Brickenden A, Choy WY, Duennwald ML. Oxidative Stress-Induced Misfolding and Inclusion Formation of Nrf2 and Keap1. Antioxidants (Basel) 2022; 11:antiox11020243. [PMID: 35204126 PMCID: PMC8868093 DOI: 10.3390/antiox11020243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/24/2022] [Accepted: 01/24/2022] [Indexed: 12/30/2022] Open
Abstract
Cells that experience high levels of oxidative stress respond by inducing antioxidant proteins through activation of the protein transcription factor nuclear factor erythroid 2-related factor 2 (Nrf2). Nrf2 is negatively regulated by the E3 ubiquitin ligase Kelch-like ECH-associated protein 1 (Keap1), which binds to Nrf2 to facilitate its ubiquitination and ensuing proteasomal degradation under basal conditions. Here, we studied protein folding and misfolding in Nrf2 and Keap1 in yeast, mammalian cells, and purified proteins under oxidative stress conditions. Both Nrf2 and Keap1 are susceptible to protein misfolding and inclusion formation upon oxidative stress. We propose that the intrinsically disordered regions within Nrf2 and the high cysteine content of Keap1 contribute to their oxidation and the ensuing misfolding. Our work reveals previously unexplored aspects of Nrf2 and Keap1 regulation and/or dysregulation by oxidation-induced protein misfolding.
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Affiliation(s)
- Vy Ngo
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON N6A 3K7, Canada;
| | - Nadun C. Karunatilleke
- Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON N6A 3K7, Canada; (N.C.K.); (A.B.); (W.-Y.C.)
| | - Anne Brickenden
- Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON N6A 3K7, Canada; (N.C.K.); (A.B.); (W.-Y.C.)
| | - Wing-Yiu Choy
- Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON N6A 3K7, Canada; (N.C.K.); (A.B.); (W.-Y.C.)
| | - Martin L. Duennwald
- Department of Anatomy and Cell Biology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON N6A 3K7, Canada
- Correspondence:
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14
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Delfino L, Campesan S, Fedele G, Green EW, Giorgini F, Kyriacou CP, Rosato E. Visualization of Mutant Aggregates from Clock Neurons by Agarose Gel Electrophoresis (AGERA) in Drosophila melanogaster. Methods Mol Biol 2022; 2482:373-383. [PMID: 35610440 DOI: 10.1007/978-1-0716-2249-0_25] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The clock neurons of the fruit fly Drosophila melanogaster have become a useful model for expressing misfolded protein aggregates that accumulate in several human neurodegenerative diseases. One advantage of such an approach is that the behavioral effects can be readily quantified on circadian locomotor rhythms, sleep or activity levels via automated, highly reliable and objective procedures. Therefore, a rapid assay is required to visualize whether these neurons develop aggregates. Here we describe a modified immunoblot method, agarose gel electrophoresis (AGERA) that has been optimized for resolving aggregates from fly clock neurons.
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Affiliation(s)
- Laura Delfino
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Susanna Campesan
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Giorgio Fedele
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Edward W Green
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Flaviano Giorgini
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | | | - Ezio Rosato
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
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15
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Stepanenko OV, Sulatsky MI, Mikhailova EV, Kuznetsova IM, Turoverov KK, Stepanenko OV, Sulatskaya AI. New findings on GFP-like protein application as fluorescent tags: Fibrillogenesis, oligomerization, and amorphous aggregation. Int J Biol Macromol 2021; 192:1304-1310. [PMID: 34687761 DOI: 10.1016/j.ijbiomac.2021.10.107] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/19/2021] [Accepted: 10/14/2021] [Indexed: 10/20/2022]
Abstract
Green fluorescent proteins (GFP) are commonly used as fluorescent tags and biosensors in cell biology and medicine. However, the propensity of GFP-like proteins to aggregate and the consequence of intermolecular interaction for their application have not been thoroughly examined. In this work, alternative aggregation pathways of superfolder green fluorescent protein (sfGFP) were demonstrated using a spectroscopic and microscopic study of the samples prepared by equilibrium microdialysis. Besides oligomerization of native monomers, we showed for the first time the condition-specific formation by sfGFP of either amyloid fibrils (at increased temperature or acidity) or amorphous aggregates (at physiological conditions). Both types of sfGFP aggregates had lost green fluorescence and were toxic to cells. Thus, when using GFP-like proteins as fluorescent tags, one should take into account their high ability to form aggregates with lost unique visible fluorescence in the cellular environment, which affects cell viability. Moreover, the results of this work cast doubt on the correctness of the data on the fibrillogenesis of various amyloidogenic proteins obtained using their fusion with GFP-like proteins.
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Affiliation(s)
- Olga V Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - Maksim I Sulatsky
- Laboratory of Cell Morphology, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - Ekaterina V Mikhailova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - Irina M Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - Konstantin K Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia.
| | - Olesya V Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia.
| | - Anna I Sulatskaya
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
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16
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Danilov LG, Moskalenko SE, Matveenko AG, Sukhanova XV, Belousov MV, Zhouravleva GA, Bondarev SA. The Human NUP58 Nucleoporin Can Form Amyloids In Vitro and In Vivo. Biomedicines 2021; 9:biomedicines9101451. [PMID: 34680573 PMCID: PMC8533070 DOI: 10.3390/biomedicines9101451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/05/2021] [Accepted: 10/08/2021] [Indexed: 12/20/2022] Open
Abstract
Amyloids are fibrillar protein aggregates with a cross-β structure and unusual features, including high resistance to detergent or protease treatment. More than two hundred different proteins with amyloid or amyloid-like properties are already known. Several examples of nucleoporins (e.g., yeast Nup49, Nup100, Nup116, and human NUP153) are supposed to form amyloid fibrils. In this study, we demonstrated an ability of the human NUP58 nucleoporin to form amyloid aggregates in vivo and in vitro. Moreover, we found two forms of NUP58 aggregates: oligomers and polymers stabilized by disulfide bonds. Bioinformatic analysis revealed that all known orthologs of this protein are potential amyloids which possess several regions with conserved ability to aggregation. The biological role of nucleoporin amyloid formation is debatable. We suggest that it is a rather abnormal process, which is characteristic for many proteins implicated in phase separation.
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Affiliation(s)
- Lavrentii G. Danilov
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (L.G.D.); (S.E.M.); (A.G.M.); (X.V.S.); (M.V.B.)
| | - Svetlana E. Moskalenko
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (L.G.D.); (S.E.M.); (A.G.M.); (X.V.S.); (M.V.B.)
- St. Petersburg Branch, Vavilov Institute of General Genetics, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Andrew G. Matveenko
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (L.G.D.); (S.E.M.); (A.G.M.); (X.V.S.); (M.V.B.)
| | - Xenia V. Sukhanova
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (L.G.D.); (S.E.M.); (A.G.M.); (X.V.S.); (M.V.B.)
| | - Mikhail V. Belousov
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (L.G.D.); (S.E.M.); (A.G.M.); (X.V.S.); (M.V.B.)
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia
| | - Galina A. Zhouravleva
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (L.G.D.); (S.E.M.); (A.G.M.); (X.V.S.); (M.V.B.)
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
- Correspondence: or (G.A.Z.); or (S.A.B.)
| | - Stanislav A. Bondarev
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (L.G.D.); (S.E.M.); (A.G.M.); (X.V.S.); (M.V.B.)
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
- Correspondence: or (G.A.Z.); or (S.A.B.)
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17
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Kharkov BB, Podkorytov IS, Bondarev SA, Belousov MV, Salikov VA, Zhouravleva GA, Skrynnikov NR. The Role of Rotational Motion in Diffusion NMR Experiments on Supramolecular Assemblies: Application to Sup35NM Fibrils. Angew Chem Int Ed Engl 2021; 60:15445-15451. [PMID: 33891789 DOI: 10.1002/anie.202102408] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/19/2021] [Indexed: 11/08/2022]
Abstract
Pulsed-field gradient (PFG) NMR is an important tool for characterization of biomolecules and supramolecular assemblies. However, for micrometer-sized objects, such as amyloid fibrils, these experiments become difficult to interpret because in addition to translational diffusion they are also sensitive to rotational diffusion. We have constructed a mathematical theory describing the outcome of PFG NMR experiments on rod-like fibrils. To test its validity, we have studied the fibrils formed by Sup35NM segment of the prion protein Sup35. The interpretation of the PFG NMR data in this system is fully consistent with the evidence from electron microscopy. Contrary to some previously expressed views, the signals originating from disordered regions in the fibrils can be readily differentiated from the similar signals representing small soluble species (e.g. proteolytic fragments). This paves the way for diffusion-sorted NMR experiments on complex amyloidogenic samples.
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Affiliation(s)
- Boris B Kharkov
- Laboratory of Biomolecular NMR, St. Petersburg State University, 199034, St. Petersburg, Russia
| | - Ivan S Podkorytov
- Laboratory of Biomolecular NMR, St. Petersburg State University, 199034, St. Petersburg, Russia
| | - Stanislav A Bondarev
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034, St. Petersburg, Russia
| | - Mikhail V Belousov
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034, St. Petersburg, Russia.,Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608, St. Petersburg, Russia
| | - Vladislav A Salikov
- Laboratory of Biomolecular NMR, St. Petersburg State University, 199034, St. Petersburg, Russia
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034, St. Petersburg, Russia
| | - Nikolai R Skrynnikov
- Laboratory of Biomolecular NMR, St. Petersburg State University, 199034, St. Petersburg, Russia.,Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
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18
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Kharkov BB, Podkorytov IS, Bondarev SA, Belousov MV, Salikov VA, Zhouravleva GA, Skrynnikov NR. The Role of Rotational Motion in Diffusion NMR Experiments on Supramolecular Assemblies: Application to Sup35NM Fibrils. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Boris B. Kharkov
- Laboratory of Biomolecular NMR St. Petersburg State University 199034 St. Petersburg Russia
| | - Ivan S. Podkorytov
- Laboratory of Biomolecular NMR St. Petersburg State University 199034 St. Petersburg Russia
| | - Stanislav A. Bondarev
- Department of Genetics and Biotechnology St. Petersburg State University 199034 St. Petersburg Russia
| | - Mikhail V. Belousov
- Department of Genetics and Biotechnology St. Petersburg State University 199034 St. Petersburg Russia
- Laboratory for Proteomics of Supra-Organismal Systems All-Russia Research Institute for Agricultural Microbiology (ARRIAM) 196608 St. Petersburg Russia
| | - Vladislav A. Salikov
- Laboratory of Biomolecular NMR St. Petersburg State University 199034 St. Petersburg Russia
| | - Galina A. Zhouravleva
- Department of Genetics and Biotechnology St. Petersburg State University 199034 St. Petersburg Russia
| | - Nikolai R. Skrynnikov
- Laboratory of Biomolecular NMR St. Petersburg State University 199034 St. Petersburg Russia
- Department of Chemistry Purdue University West Lafayette IN 47907 USA
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19
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Matiiv AB, Trubitsina NP, Matveenko AG, Barbitoff YA, Zhouravleva GA, Bondarev SA. Amyloid and Amyloid-Like Aggregates: Diversity and the Term Crisis. BIOCHEMISTRY (MOSCOW) 2021; 85:1011-1034. [PMID: 33050849 DOI: 10.1134/s0006297920090035] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Active accumulation of the data on new amyloids continuing nowadays dissolves boundaries of the term "amyloid". Currently, it is most often used to designate aggregates with cross-β structure. At the same time, amyloids also exhibit a number of other unusual properties, such as: detergent and protease resistance, interaction with specific dyes, and ability to induce transition of some proteins from a soluble form to an aggregated one. The same features have been also demonstrated for the aggregates lacking cross-β structure, which are commonly called "amyloid-like" and combined into one group, although they are very diverse. We have collected and systematized information on the properties of more than two hundred known amyloids and amyloid-like proteins with emphasis on conflicting examples. In particular, a number of proteins in membraneless organelles form aggregates with cross-β structure that are morphologically indistinguishable from the other amyloids, but they can be dissolved in the presence of detergents, which is not typical for amyloids. Such paradoxes signify the need to clarify the existing definition of the term amyloid. On the other hand, the demonstrated structural diversity of the amyloid-like aggregates shows the necessity of their classification.
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Affiliation(s)
- A B Matiiv
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - N P Trubitsina
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - A G Matveenko
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - Y A Barbitoff
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia.,Bioinformatics Institute, St. Petersburg, 197342, Russia
| | - G A Zhouravleva
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia.,Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - S A Bondarev
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia. .,Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, 199034, Russia
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20
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Functional Mammalian Amyloids and Amyloid-Like Proteins. Life (Basel) 2020; 10:life10090156. [PMID: 32825636 PMCID: PMC7555005 DOI: 10.3390/life10090156] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/12/2020] [Accepted: 08/19/2020] [Indexed: 02/06/2023] Open
Abstract
Amyloids are highly ordered fibrous cross-β protein aggregates that are notorious primarily because of association with a variety of incurable human and animal diseases (termed amyloidoses), including Alzheimer’s disease (AD), Parkinson’s disease (PD), type 2 diabetes (T2D), and prion diseases. Some amyloid-associated diseases, in particular T2D and AD, are widespread and affect hundreds of millions of people all over the world. However, recently it has become evident that many amyloids, termed “functional amyloids,” are involved in various activities that are beneficial to organisms. Functional amyloids were discovered in diverse taxa, ranging from bacteria to mammals. These amyloids are involved in vital biological functions such as long-term memory, storage of peptide hormones and scaffolding melanin polymerization in animals, substrate attachment, and biofilm formation in bacteria and fungi, etc. Thus, amyloids undoubtedly are playing important roles in biological and pathological processes. This review is focused on functional amyloids in mammals and summarizes approaches used for identifying new potentially amyloidogenic proteins and domains.
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21
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Barbitoff YA, Matveenko AG, Bondarev SA, Maksiutenko EM, Kulikova AV, Zhouravleva GA. Quantitative assessment of chaperone binding to amyloid aggregates identifies specificity of Hsp40 interaction with yeast prion fibrils. FEMS Yeast Res 2020; 20:5831717. [PMID: 32379306 DOI: 10.1093/femsyr/foaa025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/05/2020] [Indexed: 12/18/2022] Open
Abstract
Yeast self-perpetuating protein aggregates (yeast prions) provide a framework to investigate the interaction of misfolded proteins with the protein quality control machinery. The major component of this system that facilitates propagation of all known yeast amyloid prions is the Hsp104 chaperone that catalyzes fibril fragmentation. Overproduction of Hsp104 cures some yeast prions via a fragmentation-independent mechanism. Importantly, major cytosolic chaperones of the Hsp40 group, Sis1 and Ydj1, oppositely affect yeast prion propagation, and are capable of stimulating different activities of Hsp104. In this work, we developed a quantitative method to investigate the Hsp40 binding to amyloid aggregates. We demonstrate that Sis1 binds fibrils formed by the Sup35NM protein with higher affinity compared to Ydj1. Moreover, the interaction of Sis1 with the fibrils formed by the other yeast prion protein, Rnq1, is orders of magnitude weaker. We show that the deletion of the dimerization domain of Sis1 (crucial for the curing of [PSI+] by excess Hsp104) decreases its affinity to both Sup35NM and Rnq1 fibrils. Taken together, these results suggest that tight binding of Hsp40 to the amyloid fibrils is likely to enhance aggregate malpartition instead of fibril fragmentation.
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Affiliation(s)
- Yury A Barbitoff
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab. 7/9, St. Petersburg, 199034 Russia
| | - Andrew G Matveenko
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab. 7/9, St. Petersburg, 199034 Russia
| | - Stanislav A Bondarev
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab. 7/9, St. Petersburg, 199034 Russia.,Laboratory of Amyloid Biology, St. Petersburg State University, Universitetskaya nab. 7/9, St. Petersburg, 199034 Russia
| | - Evgeniia M Maksiutenko
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab. 7/9, St. Petersburg, 199034 Russia.,St. Petersburg Branch, Vavilov Institute of General Genetics, Russian Academy of Sciences, Universitetskaya nab. 7/9, St. Petersburg, 199034 Russia
| | - Alexandra V Kulikova
- Peter the Great St. Petersburg Polytechnic University, Politekhnicheskaya ul. 29, St. Petersburg, 195251 Russia
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab. 7/9, St. Petersburg, 199034 Russia.,Laboratory of Amyloid Biology, St. Petersburg State University, Universitetskaya nab. 7/9, St. Petersburg, 199034 Russia
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22
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Villali J, Dark J, Brechtel TM, Pei F, Sindi SS, Serio TR. Nucleation seed size determines amyloid clearance and establishes a barrier to prion appearance in yeast. Nat Struct Mol Biol 2020; 27:540-549. [PMID: 32367069 PMCID: PMC7293557 DOI: 10.1038/s41594-020-0416-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 03/18/2020] [Indexed: 12/14/2022]
Abstract
Amyloid appearance is a rare event that is promoted in the presence of
other aggregated proteins. These aggregates were thought to act by templating
the formation of an assembly-competent nucleation seed, but we find an
unanticipated role for them in enhancing the persistence of amyloid after it
arises. Specifically, Saccharoymyces cerevisiae Rnq1 amyloid
reduces chaperone-mediated disassembly of Sup35 amyloid, promoting its
persistence in yeast. Mathematical modeling and corresponding in
vivo experiments link amyloid persistence to the conformationally
defined size of the Sup35 nucleation seed and suggest that amyloid is actively
cleared by disassembly below this threshold to suppress appearance of the
[PSI+] prion in vivo.
Remarkably, this framework resolves multiple known inconsistencies in the
appearance and curing of yeast prions. Thus, our observations establish the size
of the nucleation seed as a previously unappreciated characteristic of prion
variants that is key to understanding transitions between prion states.
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Affiliation(s)
- Janice Villali
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA.,Relay Therapeutics, Cambridge, MA, USA
| | - Jason Dark
- Department of Applied Mathematics, University of California, Merced, Merced, CA, USA
| | - Teal M Brechtel
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA
| | - Fen Pei
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA.,BioLegend, San Diego, CA, USA
| | - Suzanne S Sindi
- Department of Applied Mathematics, University of California, Merced, Merced, CA, USA.
| | - Tricia R Serio
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, USA.
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23
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Drozdova PB, Barbitoff YA, Belousov MV, Skitchenko RK, Rogoza TM, Leclercq JY, Kajava AV, Matveenko AG, Zhouravleva GA, Bondarev SA. Estimation of amyloid aggregate sizes with semi-denaturing detergent agarose gel electrophoresis and its limitations. Prion 2020; 14:118-128. [PMID: 32306832 PMCID: PMC7199750 DOI: 10.1080/19336896.2020.1751574] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Semi-denaturing detergent agarose gel electrophoresis (SDD-AGE) was proposed by Vitaly V. Kushnirov in the Michael D. Ter-Avanesyan’s laboratory as a method to compare sizes of amyloid aggregates. Currently, this method is widely used for amyloid investigation, but mostly as a qualitative approach. In this work, we assessed the possibilities and limitations of the quantitative analysis of amyloid aggregate size distribution using SDD-AGE results. For this purpose, we used aggregates of two well-characterized yeast amyloid-forming proteins, Sup35 and Rnq1, and developed a protocol to standardize image analysis and process the result. A detailed investigation of factors that may affect the results of SDD-AGE revealed that both the cell lysis method and electrophoresis conditions can substantially affect the estimation of aggregate size. Despite this, quantitative analysis of SDD-AGE results is possible when one needs to estimate and compare the size of aggregates on the same gel, or even in different experiments, if the experimental conditions are tightly controlled and additional standards are used.
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Affiliation(s)
- Polina B Drozdova
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia.,Institute of Biology, Irkutsk State University, Irkutsk, Russia
| | - Yury A Barbitoff
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - Mikhail V Belousov
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia.,Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
| | - Rostislav K Skitchenko
- International Research Institute of Bioengineering, ITMO University, St. Petersburg, Russia
| | - Tatyana M Rogoza
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia.,Vavilov Institute of General Genetics Russian Academy of Sciences, St. Petersburg Branch, St. Petersburg, Russia
| | - Jeremy Y Leclercq
- Centre de Recherche En Biologie Cellulaire De Montpellier, UMR 5237 CNRS, Montpellier, France
| | - Andrey V Kajava
- International Research Institute of Bioengineering, ITMO University, St. Petersburg, Russia.,Centre de Recherche En Biologie Cellulaire De Montpellier, UMR 5237 CNRS, Montpellier, France
| | - Andrew G Matveenko
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia.,Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, Russia
| | - Stanislav A Bondarev
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia.,Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, Russia
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24
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Trubitsina NP, Zemlyanko OM, Bondarev SA, Zhouravleva GA. Nonsense Mutations in the Yeast SUP35 Gene Affect the [ PSI+] Prion Propagation. Int J Mol Sci 2020; 21:E1648. [PMID: 32121268 PMCID: PMC7084296 DOI: 10.3390/ijms21051648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/20/2020] [Accepted: 02/26/2020] [Indexed: 11/16/2022] Open
Abstract
The essential SUP35 gene encodes yeast translation termination factor eRF3. Previously, we isolated nonsense mutations sup35-n and proposed that the viability of such mutants can be explained by readthrough of the premature stop codon. Such mutations, as well as the prion [PSI+], can appear in natural yeast populations, and their combinations may have different effects on the cells. Here, we analyze the effects of the compatibility of sup35-n mutations with the [PSI+] prion in haploid and diploid cells. We demonstrated that sup35-n mutations are incompatible with the [PSI+] prion, leading to lethality of sup35-n [PSI+] haploid cells. In diploid cells the compatibility of [PSI+] with sup35-n depends on how the corresponding diploid was obtained. Nonsense mutations sup35-21, sup35-74, and sup35-218 are compatible with the [PSI+] prion in diploid strains, but affect [PSI+] properties and lead to the formation of new prion variant. The only mutation that could replace the SUP35 wild-type allele in both haploid and diploid [PSI+] strains, sup35-240, led to the prion loss. Possibly, short Sup351-55 protein, produced from the sup35-240 allele, is included in Sup35 aggregates and destabilize them. Alternatively, single molecules of Sup351-55 can stick to aggregate ends, and thus interrupt the fibril growth. Thus, we can conclude that sup35-240 mutation prevents [PSI+] propagation and can be considered as a new pnm mutation.
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Affiliation(s)
- Nina P. Trubitsina
- Department of Genetics and Biotechnology, Saint Petersburg State University, 199034 St. Petersburg, Russia; (N.P.T.); (O.M.Z.); (S.A.B.)
| | - Olga M. Zemlyanko
- Department of Genetics and Biotechnology, Saint Petersburg State University, 199034 St. Petersburg, Russia; (N.P.T.); (O.M.Z.); (S.A.B.)
- Laboratory of Amyloid Biology, Saint Petersburg State University, 199034 St. Petersburg, Russia
| | - Stanislav A. Bondarev
- Department of Genetics and Biotechnology, Saint Petersburg State University, 199034 St. Petersburg, Russia; (N.P.T.); (O.M.Z.); (S.A.B.)
- Laboratory of Amyloid Biology, Saint Petersburg State University, 199034 St. Petersburg, Russia
| | - Galina A. Zhouravleva
- Department of Genetics and Biotechnology, Saint Petersburg State University, 199034 St. Petersburg, Russia; (N.P.T.); (O.M.Z.); (S.A.B.)
- Laboratory of Amyloid Biology, Saint Petersburg State University, 199034 St. Petersburg, Russia
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25
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Danilov LG, Matveenko AG, Ryzhkova VE, Belousov MV, Poleshchuk OI, Likholetova DV, Sokolov PA, Kasyanenko NA, Kajava AV, Zhouravleva GA, Bondarev SA. Design of a New [ PSI +]-No-More Mutation in SUP35 With Strong Inhibitory Effect on the [ PSI +] Prion Propagation. Front Mol Neurosci 2019; 12:274. [PMID: 31803017 PMCID: PMC6877606 DOI: 10.3389/fnmol.2019.00274] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 10/28/2019] [Indexed: 12/04/2022] Open
Abstract
A number of [PSI+]-no-more (PNM) mutations, eliminating [PSI+] prion, were previously described in SUP35. In this study, we designed and analyzed a new PNM mutation based on the parallel in-register β-structure of Sup35 prion fibrils suggested by the known experimental data. In such an arrangement, substitution of non-charged residues by charged ones may destabilize the fibril structure. We introduced Q33K/A34K amino acid substitutions into the Sup35 protein, corresponding allele was called sup35-M0. The mutagenized residues were chosen based on ArchCandy in silico prediction of high inhibitory effect on the amyloidogenic potential of Sup35. The experiments confirmed that Sup35-M0 leads to the elimination of [PSI+] with high efficiency. Our data suggested that the elimination of the [PSI+] prion is associated with the decreased aggregation properties of the protein. The new mutation can induce the prion with very low efficiency and is able to propagate only weak [PSI+] prion variants. We also showed that Sup35-M0 protein co-aggregates with the wild-type Sup35 in vivo. Moreover, our data confirmed the utility of the strategy of substitution of non-charged residues by charged ones to design new mutations to inhibit a prion formation.
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Affiliation(s)
- Lavrentii G Danilov
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - Andrew G Matveenko
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - Varvara E Ryzhkova
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - Mikhail V Belousov
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia.,Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), St. Petersburg, Russia
| | - Olga I Poleshchuk
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - Daria V Likholetova
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - Petr A Sokolov
- Department of Molecular Biophysics and Polymer Physics, St. Petersburg State University, St. Petersburg, Russia
| | - Nina A Kasyanenko
- Department of Molecular Biophysics and Polymer Physics, St. Petersburg State University, St. Petersburg, Russia
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Université Montpellier, Montpellier, France.,Institut de Biologie Computationnelle (IBC), Universitè Montpellier, Montpellier, France
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia.,Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, Russia
| | - Stanislav A Bondarev
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia.,Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, Russia
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26
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Kosolapova AO, Belousov MV, Sulatskaya AI, Belousova ME, Sulatsky MI, Antonets KS, Volkov KV, Lykholay AN, Shtark OY, Vasileva EN, Zhukov VA, Ivanova AN, Zykin PA, Kuznetsova IM, Turoverov KK, Tikhonovich IA, Nizhnikov AA. Two Novel Amyloid Proteins, RopA and RopB, from the Root Nodule Bacterium Rhizobium leguminosarum. Biomolecules 2019; 9:biom9110694. [PMID: 31690032 PMCID: PMC6920782 DOI: 10.3390/biom9110694] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 10/29/2019] [Accepted: 10/31/2019] [Indexed: 12/14/2022] Open
Abstract
Amyloids represent protein fibrils with a highly ordered spatial structure, which not only cause dozens of incurable human and animal diseases but also play vital biological roles in Archaea, Bacteria, and Eukarya. Despite the fact that association of bacterial amyloids with microbial pathogenesis and infectious diseases is well known, there is a lack of information concerning the amyloids of symbiotic bacteria. In this study, using the previously developed proteomic method for screening and identification of amyloids (PSIA), we identified amyloidogenic proteins in the proteome of the root nodule bacterium Rhizobium leguminosarum. Among 54 proteins identified, we selected two proteins, RopA and RopB, which are predicted to have β-barrel structure and are likely to be involved in the control of plant-microbial symbiosis. We demonstrated that the full-length RopA and RopB form bona fide amyloid fibrils in vitro. In particular, these fibrils are β-sheet-rich, bind Thioflavin T (ThT), exhibit green birefringence upon staining with Congo Red (CR), and resist treatment with ionic detergents and proteases. The heterologously expressed RopA and RopB intracellularly aggregate in yeast and assemble into amyloid fibrils at the surface of Escherichia coli. The capsules of the R. leguminosarum cells bind CR, exhibit green birefringence, and contain fibrils of RopA and RopB in vivo.
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Affiliation(s)
- Anastasiia O Kosolapova
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia.
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia.
| | - Mikhail V Belousov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia.
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia.
| | - Anna I Sulatskaya
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, 194064 St. Petersburg, Russia.
| | - Maria E Belousova
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia.
| | - Maksim I Sulatsky
- Laboratory of Cell Morphology, Institute of Cytology of the Russian Academy of Sciences, 194064 St. Petersburg, Russia.
| | - Kirill S Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia.
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia.
| | - Kirill V Volkov
- Research Resource Center "Molecular and Cell Technologies", Research Park, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia.
| | - Anna N Lykholay
- Research Resource Center "Molecular and Cell Technologies", Research Park, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia.
| | - Oksana Y Shtark
- Department of Biotechnology, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), St. Petersburg, 196608, Russia.
| | - Ekaterina N Vasileva
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia.
- Department of Biotechnology, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), St. Petersburg, 196608, Russia.
| | - Vladimir A Zhukov
- Department of Biotechnology, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), St. Petersburg, 196608, Russia.
| | - Alexandra N Ivanova
- Research Resource Center "Molecular and Cell Technologies", Research Park, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia.
- Komarov Botanical Institute RAS, 197376 Komarov Botanical Institute RAS, Russia.
| | - Pavel A Zykin
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia.
| | - Irina M Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, 194064 St. Petersburg, Russia.
| | - Konstantin K Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, 194064 St. Petersburg, Russia.
- Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia.
| | - Igor A Tikhonovich
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia.
- Department of Biotechnology, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), St. Petersburg, 196608, Russia.
| | - Anton A Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia.
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia.
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27
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Timchenko M, Abdullatypov A, Kihara H, Timchenko A. Effect of Single Amino Acid Substitutions by Asn and Gln on Aggregation Properties of Bence-Jones Protein BIF. Int J Mol Sci 2019; 20:ijms20205197. [PMID: 31635169 PMCID: PMC6834151 DOI: 10.3390/ijms20205197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 10/17/2019] [Accepted: 10/19/2019] [Indexed: 11/24/2022] Open
Abstract
The nature of renal amyloidosis involving Bence-Jones proteins in multiple myeloma is still unclear. The development of amyloidosis in neurodegenerative diseases is often associated with a high content of asparagine and glutamine residues in proteins forming amyloid deposits. To estimate the influence of Asn and Gln residues on the aggregation of Bence-Jones protein BIF, we obtained recombinant BIF and its mutants with the substitution of Tyr187→Asn (Y187N) in α-helix of CL domain, Lys170→Asn (K170N) and Ser157→Gln (S157Q) in CL domain loops, Arg109→Asn in VL-CL linker (R109N) and Asp29→Gln in VL domain loop (D29Q). The morphology of protein aggregates was studied at pH corresponding to the conditions in bloodstream (pH 7.2), distal (pH 6.5) and proximal renal tubules (pH 4.5) by atomic force microscopy (AFM) and small-angle X-ray scattering (SAXS). The Lys170→Asn replacement almost completely inhibits amyloidogenic activity. The Y187N forms fibril-like aggregates at all pH values. The Arg109→Asn replacement resulted in formation of fibril-like structures at pH 7.2 and 6.5 while the substitutions by Gln provoked formation of those structures only at pH 7.2. Therefore, the amyloidogenic properties are highly dependent on the location of Asn or Gln.
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Affiliation(s)
- Maria Timchenko
- Laboratory of NMR of Biosystems, Institute of Theoretical and Experimental Biophysics RAS, Pushchino 142290, Russia.
| | - Azat Abdullatypov
- Laboratory of Biotechnology and Physiology of Phototrophic Organisms, Institute of Basic Biological Problems RAS-a separate subdivision of PSCBR RAS (IBBP RAS), Pushchino 142290, Russia.
| | - Hiroshi Kihara
- Himeji-Hinomoto College, 890 Koro, Kodera-cho, Himeji 679-2151, Russia.
| | - Alexander Timchenko
- Laboratory of Protein Physics, Institute of Protein Research RAS, Pushchino 142290, Russia.
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28
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Howie RL, Jay-Garcia LM, Kiktev DA, Faber QL, Murphy M, Rees KA, Sachwani N, Chernoff YO. Role of the Cell Asymmetry Apparatus and Ribosome-Associated Chaperones in the Destabilization of a Saccharomyces cerevisiae Prion by Heat Shock. Genetics 2019; 212:757-771. [PMID: 31142614 PMCID: PMC6614889 DOI: 10.1534/genetics.119.302237] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 06/10/2019] [Indexed: 11/18/2022] Open
Abstract
Self-perpetuating transmissible protein aggregates, termed prions, are implicated in mammalian diseases and control phenotypically detectable traits in Saccharomyces cerevisiae Yeast stress-inducible chaperone proteins, including Hsp104 and Hsp70-Ssa that counteract cytotoxic protein aggregation, also control prion propagation. Stress-damaged proteins that are not disaggregated by chaperones are cleared from daughter cells via mother-specific asymmetric segregation in cell divisions following heat shock. Short-term mild heat stress destabilizes [PSI+ ], a prion isoform of the yeast translation termination factor Sup35 This destabilization is linked to the induction of the Hsp104 chaperone. Here, we show that the region of Hsp104 known to be required for curing by artificially overproduced Hsp104 is also required for heat-shock-mediated [PSI+ ] destabilization. Moreover, deletion of the SIR2 gene, coding for a deacetylase crucial for asymmetric segregation of heat-damaged proteins, also counteracts heat-shock-mediated destabilization of [PSI+ ], and Sup35 aggregates are colocalized with aggregates of heat-damaged proteins marked by Hsp104-GFP. These results support the role of asymmetric segregation in prion destabilization. Finally, we show that depletion of the heat-shock noninducible ribosome-associated chaperone Hsp70-Ssb decreases heat-shock-mediated destabilization of [PSI+ ], while disruption of a cochaperone complex mediating the binding of Hsp70-Ssb to the ribosome increases prion loss. Our data indicate that Hsp70-Ssb relocates from the ribosome to the cytosol during heat stress. Cytosolic Hsp70-Ssb has been shown to antagonize the function of Hsp70-Ssa in prion propagation, which explains the Hsp70-Ssb effect on prion destabilization by heat shock. This result uncovers the stress-related role of a stress noninducible chaperone.
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Affiliation(s)
- Rebecca L Howie
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332
| | | | - Denis A Kiktev
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332
- Laboratory of Amyloid Biology, St. Petersburg State University, Russia 199034
| | - Quincy L Faber
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Margaret Murphy
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Katherine A Rees
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Numera Sachwani
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Yury O Chernoff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332
- Laboratory of Amyloid Biology, St. Petersburg State University, Russia 199034
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29
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Senohrabkova L, Malcova I, Hasek J. An aggregation-prone mutant of eIF3a forms reversible assemblies escaping spatial control in exponentially growing yeast cells. Curr Genet 2019; 65:919-940. [PMID: 30715564 DOI: 10.1007/s00294-019-00940-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 01/14/2019] [Accepted: 01/17/2019] [Indexed: 10/27/2022]
Abstract
Cells have elaborated a complex strategy to maintain protein homeostasis under physiological as well as stress conditions with the aim to ensure the smooth functioning of vital processes and producing healthy offspring. Impairment of one of the most important processes in living cells, translation, might have serious consequences including various brain disorders in humans. Here, we describe a variant of the translation initiation factor eIF3a, Rpg1-3, mutated in its PCI domain that displays an attenuated translation efficiency and formation of reversible assemblies at physiological growth conditions. Rpg1-3-GFP assemblies are not sequestered within mother cells only as usual for misfolded-protein aggregates and are freely transmitted from the mother cell into the bud although they are of non-amyloid nature. Their bud-directed transmission and the active movement within the cell area depend on the intact actin cytoskeleton and the related molecular motor Myo2. Mutations in the Rpg1-3 protein render not only eIF3a but, more importantly, also the eIF3 core complex prone to aggregation that is potentiated by the limited availability of Hsp70 and Hsp40 chaperones. Our results open the way to understand mechanisms yeast cells employ to cope with malfunction and aggregation of essential proteins and their complexes.
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Affiliation(s)
- Lenka Senohrabkova
- Laboratory of Cell Reproduction, Institute of Microbiology of the CAS, Videnska 1083, 14220, Prague 4, Czech Republic
- First Faculty of Medicine, Charles University, Katerinska 42, 12108, Prague 2, Czech Republic
| | - Ivana Malcova
- Laboratory of Cell Reproduction, Institute of Microbiology of the CAS, Videnska 1083, 14220, Prague 4, Czech Republic.
| | - Jiri Hasek
- Laboratory of Cell Reproduction, Institute of Microbiology of the CAS, Videnska 1083, 14220, Prague 4, Czech Republic.
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30
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Abstract
This commentary describes scientific path and accomplishments of our late colleague, Prof. Michael D. Ter-Avanesyan, who made several seminal contributions into prion research.
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Affiliation(s)
- Vitaly V Kushnirov
- a Research Center of Biotechnology of Russian Academy of Sciences , A.N. Bach Institute of Biochemistry , Moscow , Russia
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31
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Galkin AP, Velizhanina ME, Sopova YV, Shenfeld AA, Zadorsky SP. Prions and Non-infectious Amyloids of Mammals - Similarities and Differences. BIOCHEMISTRY (MOSCOW) 2018; 83:1184-1195. [PMID: 30472956 DOI: 10.1134/s0006297918100048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Amyloids are highly ordered aggregates of protein fibrils exhibiting cross-β structure formed by intermolecular hydrogen bonds. Pathological amyloid deposition is associated with the development of several socially significant incurable human diseases. Of particular interest are infectious amyloids, or prions, that cause several lethal neurodegenerative diseases in humans and can be transmitted from one organism to another. Because of almost complete absence of criteria for infectious and non-infectious amyloids, there is a lack of consensus, especially, in the definition of similarities and differences between prions and non-infectious amyloids. In this review, we formulated contemporary molecular-biological criteria for identification of prions and non-infectious amyloids and focused on explaining the differences between these two types of molecules.
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Affiliation(s)
- A P Galkin
- St. Petersburg Branch of Vavilov Institute of General Genetics, Russian Academy of Sciences, St. Petersburg, 199034, Russia. .,St. Petersburg State University, Department of Genetics and Biotechnology, St. Petersburg, 199034, Russia
| | - M E Velizhanina
- St. Petersburg State University, Department of Genetics and Biotechnology, St. Petersburg, 199034, Russia
| | - Yu V Sopova
- St. Petersburg Branch of Vavilov Institute of General Genetics, Russian Academy of Sciences, St. Petersburg, 199034, Russia.,St. Petersburg State University, Department of Genetics and Biotechnology, St. Petersburg, 199034, Russia
| | - A A Shenfeld
- St. Petersburg Branch of Vavilov Institute of General Genetics, Russian Academy of Sciences, St. Petersburg, 199034, Russia.,St. Petersburg State University, Department of Genetics and Biotechnology, St. Petersburg, 199034, Russia
| | - S P Zadorsky
- St. Petersburg Branch of Vavilov Institute of General Genetics, Russian Academy of Sciences, St. Petersburg, 199034, Russia. .,St. Petersburg State University, Department of Genetics and Biotechnology, St. Petersburg, 199034, Russia
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32
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Urakov VN, Mitkevich OV, Dergalev AA, Ter-Avanesyan MD. The Pub1 and Upf1 Proteins Act in Concert to Protect Yeast from Toxicity of the [PSI⁺] Prion. Int J Mol Sci 2018; 19:E3663. [PMID: 30463309 PMCID: PMC6275000 DOI: 10.3390/ijms19113663] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 11/02/2018] [Accepted: 11/14/2018] [Indexed: 12/18/2022] Open
Abstract
The [PSI⁺] nonsense-suppressor determinant of Saccharomyces cerevisiae is based on the formation of heritable amyloids of the Sup35 (eRF3) translation termination factor. [PSI⁺] amyloids have variants differing in amyloid structure and in the strength of the suppressor phenotype. The appearance of [PSI⁺], its propagation and manifestation depend primarily on chaperones. Besides chaperones, the Upf1/2/3, Siw14 and Arg82 proteins restrict [PSI⁺] formation, while Sla2 can prevent [PSI⁺] toxicity. Here, we identify two more non-chaperone proteins involved in [PSI⁺] detoxification. We show that simultaneous lack of the Pub1 and Upf1 proteins is lethal to cells harboring [PSI⁺] variants with a strong, but not with a weak, suppressor phenotype. This lethality is caused by excessive depletion of the Sup45 (eRF1) termination factor due to its sequestration into Sup35 polymers. We also show that Pub1 acts to restrict excessive Sup35 prion polymerization, while Upf1 interferes with Sup45 binding to Sup35 polymers. These data allow consideration of the Pub1 and Upf1 proteins as a novel [PSI⁺] detoxification system.
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Affiliation(s)
- Valery N Urakov
- Bach Institute of Biochemistry, Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 119071 Moscow, Russia.
| | - Olga V Mitkevich
- Bach Institute of Biochemistry, Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 119071 Moscow, Russia.
| | - Alexander A Dergalev
- Bach Institute of Biochemistry, Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 119071 Moscow, Russia.
| | - Michael D Ter-Avanesyan
- Bach Institute of Biochemistry, Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 119071 Moscow, Russia
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33
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Timchenko MA, Timchenko AA. Influence of a Single Point Mutation in the Constant Domain of the Bence-Jones Protein bif on Its Aggregation Properties. BIOCHEMISTRY. BIOKHIMIIA 2018; 83:107-118. [PMID: 29618297 DOI: 10.1134/s0006297918020037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Multiple myeloma nephropathy occurs due to the aggregate formation by monoclonal immunoglobulin light chains (Bence-Jones proteins) in kidneys of patients with multiple myeloma. The mechanism of amyloid deposit formation is still unclear. Earlier, the key role in the fibril formation has been assigned to the variable domains that acquired amyloidogenic properties as a result of somatic mutations. However, fibril formation by the Bence-Jones protein BIF was found to be the function of its constant domain. The substitution of Ser177 by Asn in the constant domain of the BIF protein is most likely an inherited than a somatic mutation. To study the role of this mutation in amyloidogenesis, the recombinant Bence-Jones protein BIF and its mutant with the N177S substitution typical for the known immunoglobulin Cκ allotypes Km1, Km1,2, and Km3 were isolated. The morphology of aggregates formed by the recombinant proteins under conditions similar to those occurring during the protein transport in bloodstream and its filtration into the renal glomerulus, in the distal tubules, and in the proximal renal tubules was analyzed by atomic force microscopy. The nature of the aggregates formed by BIF and its N177S mutant during incubation for 14 days at 37°C strongly differed and depended on both pH and the presence of a reducing agent. BIF formed fibrils at pH 7.2, 6.5, and 10.1, while the N177S mutant formed fibrils only at alkaline pH 10.1. The refolding of both proteins in the presence of 5 mM dithiothreitol resulted in the formation of branched structures.
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Affiliation(s)
- M A Timchenko
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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34
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Drozdova P, Lipaeva P, Rogoza T, Zhouravleva G, Bondarev S. Overproduction of Sch9 leads to its aggregation and cell elongation in Saccharomyces cerevisiae. PLoS One 2018; 13:e0193726. [PMID: 29494682 PMCID: PMC5832320 DOI: 10.1371/journal.pone.0193726] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 02/16/2018] [Indexed: 11/25/2022] Open
Abstract
The Sch9 kinase of Saccharomyces cerevisiae is one of the major TOR pathway effectors and regulates diverse processes in the cell. Sch9 belongs to the AGC kinase family. In human, amplification of AGC kinase genes is connected with cancer. However, not much is known about the effects of Sch9 overproduction in yeast cells. To fill this gap, we developed a model system to monitor subcellular location and aggregation state of overproduced Sch9 or its regions fused to a fluorescent protein. With this system, we showed that Sch9-YFP forms detergent-resistant aggregates, and multiple protein regions are responsible for this. This finding corroborated the fact that Sch9-YFP is visualized as various fluorescent foci. In addition, we found that Sch9 overproduction caused cell elongation, and this effect was determined by its C-terminal region containing kinase domains. The constructs we present can be exploited to create superior yeast-based model systems to study processes behind kinase overproduction in cancers.
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Affiliation(s)
- Polina Drozdova
- Dept. of Genetics and Biotechnology, Saint Petersburg State University, St. Petersburg, Russia
| | - Polina Lipaeva
- Dept. of Genetics and Biotechnology, Saint Petersburg State University, St. Petersburg, Russia
| | - Tatyana Rogoza
- Dept. of Genetics and Biotechnology, Saint Petersburg State University, St. Petersburg, Russia
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, St. Petersburg, Russia
| | - Galina Zhouravleva
- Dept. of Genetics and Biotechnology, Saint Petersburg State University, St. Petersburg, Russia
- The Laboratory of Amyloid Biology, Saint Petersburg State University, St. Petersburg, Russia
| | - Stanislav Bondarev
- Dept. of Genetics and Biotechnology, Saint Petersburg State University, St. Petersburg, Russia
- The Laboratory of Amyloid Biology, Saint Petersburg State University, St. Petersburg, Russia
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35
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Al-Shabib NA, Khan JM, Malik A, Alsenaidy AM, Alsenaidy MA, Husain FM, Shamsi MB, Hidayathulla S, Khan RH. Negatively charged food additive dye “Allura Red” rapidly induces SDS-soluble amyloid fibril in beta-lactoglobulin protein. Int J Biol Macromol 2018; 107:1706-1716. [DOI: 10.1016/j.ijbiomac.2017.10.032] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 10/02/2017] [Accepted: 10/06/2017] [Indexed: 10/18/2022]
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36
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Belousov MV, Bondarev SA, Kosolapova AO, Antonets KS, Sulatskaya AI, Sulatsky MI, Zhouravleva GA, Kuznetsova IM, Turoverov KK, Nizhnikov AA. M60-like metalloprotease domain of the Escherichia coli YghJ protein forms amyloid fibrils. PLoS One 2018; 13:e0191317. [PMID: 29381728 PMCID: PMC5790219 DOI: 10.1371/journal.pone.0191317] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 01/03/2018] [Indexed: 12/31/2022] Open
Abstract
Amyloids are protein fibrils with a characteristic spatial structure. Amyloids were long perceived as the pathogens involved in a set of lethal diseases in humans and animals. In recent decades, it has become clear that amyloids represent a quaternary protein structure that is not only pathological but also functionally important and is widely used by different organisms, ranging from archaea to animals, to implement diverse biological functions. The greatest biological variety of amyloids is found in prokaryotes, where they control the formation of biofilms and cell wall sheaths, facilitate the overcoming of surface tension, and regulate the metabolism of toxins. Several amyloid proteins were identified in the important model, biotechnological and pathogenic bacterium Escherichia coli. In previous studies, using a method for the proteomic screening and identification of amyloids, we identified 61 potentially amyloidogenic proteins in the proteome of E. coli. Among these proteins, YghJ was the most enriched with bioinformatically predicted amyloidogenic regions. YghJ is a lipoprotein with a zinc metalloprotease M60-like domain that is involved in mucin degradation in the intestine as well as in proinflammatory responses. In this study, we analyzed the amyloid properties of the YghJ M60-like domain and demonstrated that it forms amyloid-like fibrils in vitro and in vivo.
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Affiliation(s)
- Mikhail V. Belousov
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab., St. Petersburg, Russian Federation
| | - Stanislav A. Bondarev
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab., St. Petersburg, Russian Federation
- Laboratory of Amyloid Biology, St. Petersburg State University, Universitetskaya nab., St. Petersburg, Russian Federation
| | - Anastasiia O. Kosolapova
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab., St. Petersburg, Russian Federation
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Podbelskogo sh., Pushkin, St. Petersburg, Russian Federation
| | - Kirill S. Antonets
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab., St. Petersburg, Russian Federation
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Podbelskogo sh., Pushkin, St. Petersburg, Russian Federation
| | - Anna I. Sulatskaya
- Institute of Cytology, Russian Academy of Science, St. Petersburg, Russian Federation
| | - Maksim I. Sulatsky
- Institute of Cytology, Russian Academy of Science, St. Petersburg, Russian Federation
| | - Galina A. Zhouravleva
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab., St. Petersburg, Russian Federation
- Laboratory of Amyloid Biology, St. Petersburg State University, Universitetskaya nab., St. Petersburg, Russian Federation
| | - Irina M. Kuznetsova
- Institute of Cytology, Russian Academy of Science, St. Petersburg, Russian Federation
| | - Konstantin K. Turoverov
- Institute of Cytology, Russian Academy of Science, St. Petersburg, Russian Federation
- Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya, St. Petersburg, Russian Federation
| | - Anton A. Nizhnikov
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab., St. Petersburg, Russian Federation
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Podbelskogo sh., Pushkin, St. Petersburg, Russian Federation
- Vavilov Institute of General Genetics, Russian Academy of Sciences, St Petersburg Branch, Universitetskaya nab., St. Petersburg, Russian Federation
- * E-mail:
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37
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Wickner RB, Kryndushkin D, Shewmaker F, McGlinchey R, Edskes HK. Study of Amyloids Using Yeast. Methods Mol Biol 2018; 1779:313-339. [PMID: 29886541 PMCID: PMC7337124 DOI: 10.1007/978-1-4939-7816-8_19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
We detail some of the genetic, biochemical, and physical methods useful in studying amyloids in yeast, particularly the yeast prions. These methods include cytoduction (cytoplasmic mixing), infection of cells with prion amyloids, use of green fluorescent protein fusions with amyloid-forming proteins for cytology, protein purification and amyloid formation, and electron microscopy of filaments.
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Affiliation(s)
- Reed B. Wickner
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes Digestive and Kidney Diseases, National Insititutes of Health, Bethesda, MD 20892-0830
| | - Dmitry Kryndushkin
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes Digestive and Kidney Diseases, National Insititutes of Health, Bethesda, MD 20892-0830,Dept. of Pharmacology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814
| | - Frank Shewmaker
- Dept. of Pharmacology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814
| | - Ryan McGlinchey
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes Digestive and Kidney Diseases, National Insititutes of Health, Bethesda, MD 20892-0830
| | - Herman K. Edskes
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes Digestive and Kidney Diseases, National Insititutes of Health, Bethesda, MD 20892-0830
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38
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Lomont JP, Rich KL, Maj M, Ho JJ, Ostrander JS, Zanni MT. Spectroscopic Signature for Stable β-Amyloid Fibrils versus β-Sheet-Rich Oligomers. J Phys Chem B 2017; 122:144-153. [PMID: 29220175 DOI: 10.1021/acs.jpcb.7b10765] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We use two-dimensional IR (2D IR) spectroscopy to explore fibril formation for the two predominant isoforms of the β-amyloid (Aβ1-40 and Aβ1-42) protein associated with Alzheimer's disease. Two-dimensional IR spectra resolve a transition at 1610 cm-1 in Aβ fibrils that does not appear in other Aβ aggregates, even those with predominantly β-sheet-structure-like oligomers. This transition is not resolved in linear IR spectroscopy because it lies under the broad band centered at 1625 cm-1, which is the traditional infrared signature for amyloid fibrils. The feature is prominent in 2D IR spectra because 2D lineshapes are narrower and scale nonlinearly with transition dipole strengths. Transmission electron microscopy measurements demonstrate that the 1610 cm-1 band is a positive identification of amyloid fibrils. Sodium dodecyl sulfate micelles that solubilize and disaggregate preaggregated Aβ samples deplete the 1625 cm-1 band but do not affect the 1610 cm-1 band, demonstrating that the 1610 cm-1 band is due to very stable fibrils. We demonstrate that the 1610 cm-1 transition arises from amide I modes by mutating out the only side-chain residue that could give rise to this transition, and we explore the potential structural origins of the transition by simulating 2D IR spectra based on Aβ crystal structures. It was not previously possible to distinguish stable Aβ fibrils from the less stable β-sheet-rich oligomers with infrared light. This 2D IR signature will be useful for Alzheimer's research on Aβ aggregation, fibril formation, and toxicity.
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Affiliation(s)
- Justin P Lomont
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Kacie L Rich
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Michał Maj
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Jia-Jung Ho
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Joshua S Ostrander
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Martin T Zanni
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
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39
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Antonets KS, Nizhnikov AA. Amyloids and prions in plants: Facts and perspectives. Prion 2017; 11:300-312. [PMID: 28960135 PMCID: PMC5639834 DOI: 10.1080/19336896.2017.1377875] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 09/02/2017] [Accepted: 09/05/2017] [Indexed: 02/07/2023] Open
Abstract
Amyloids represent protein fibrils that have highly ordered structure with unique physical and chemical properties. Amyloids have long been considered lethal pathogens that cause dozens of incurable diseases in humans and animals. Recent data show that amyloids may not only possess pathogenic properties but are also implicated in the essential biological processes in a variety of prokaryotes and eukaryotes. Functional amyloids have been identified in archaea, bacteria, fungi, and animals, including humans. Plants are one of the most poorly studied groups of organisms in the field of amyloid biology. Although amyloid properties have not been shown under native conditions for any plant protein, studies demonstrating amyloid properties for a set of plant proteins in vitro or in heterologous systems in vivo have been published in recent years. In this review, we systematize the data on the amyloidogenic proteins of plants and their functions and discuss the perspectives of identifying novel amyloids using bioinformatic and proteomic approaches.
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Affiliation(s)
- K. S. Antonets
- All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russian Federation
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russian Federation
| | - A. A. Nizhnikov
- All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russian Federation
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russian Federation
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40
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Keefer KM, Stein KC, True HL. Heterologous prion-forming proteins interact to cross-seed aggregation in Saccharomyces cerevisiae. Sci Rep 2017; 7:5853. [PMID: 28724957 PMCID: PMC5517628 DOI: 10.1038/s41598-017-05829-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 06/05/2017] [Indexed: 01/11/2023] Open
Abstract
The early stages of protein misfolding remain incompletely understood, as most mammalian proteinopathies are only detected after irreversible protein aggregates have formed. Cross-seeding, where one aggregated protein templates the misfolding of a heterologous protein, is one mechanism proposed to stimulate protein aggregation and facilitate disease pathogenesis. Here, we demonstrate the existence of cross-seeding as a crucial step in the formation of the yeast prion [PSI +], formed by the translation termination factor Sup35. We provide evidence for the genetic and physical interaction of the prion protein Rnq1 with Sup35 as a predominant mechanism leading to self-propagating Sup35 aggregation. We identify interacting sites within Rnq1 and Sup35 and determine the effects of breaking and restoring a crucial interaction. Altogether, our results demonstrate that single-residue disruption can drastically reduce the effects of cross-seeding, a finding that has important implications for human protein misfolding disorders.
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Affiliation(s)
- Kathryn M Keefer
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri, 63110, United States of America
| | - Kevin C Stein
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Heather L True
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri, 63110, United States of America.
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41
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Urakov VN, Mitkevich OV, Safenkova IV, Ter‐Avanesyan MD. Ribosome‐bound Pub1 modulates stop codon decoding during translation termination in yeast. FEBS J 2017; 284:1914-1930. [DOI: 10.1111/febs.14099] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 03/16/2017] [Accepted: 04/28/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Valery N. Urakov
- Federal Research Center ‘Fundamentals of Biotechnology’ of the Russian Academy of Sciences Bach Institute of Biochemistry Moscow Russia
| | - Olga V. Mitkevich
- Federal Research Center ‘Fundamentals of Biotechnology’ of the Russian Academy of Sciences Bach Institute of Biochemistry Moscow Russia
| | - Irina V. Safenkova
- Federal Research Center ‘Fundamentals of Biotechnology’ of the Russian Academy of Sciences Bach Institute of Biochemistry Moscow Russia
| | - Michael D. Ter‐Avanesyan
- Federal Research Center ‘Fundamentals of Biotechnology’ of the Russian Academy of Sciences Bach Institute of Biochemistry Moscow Russia
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42
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Barbitoff YA, Matveenko AG, Moskalenko SE, Zemlyanko OM, Newnam GP, Patel A, Chernova TA, Chernoff YO, Zhouravleva GA. To CURe or not to CURe? Differential effects of the chaperone sorting factor Cur1 on yeast prions are mediated by the chaperone Sis1. Mol Microbiol 2017; 105:242-257. [PMID: 28431189 DOI: 10.1111/mmi.13697] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2017] [Indexed: 02/06/2023]
Abstract
Yeast self-perpetuating protein aggregates (prions) provide a convenient model for studying various components of the cellular protein quality control system. Molecular chaperones and chaperone-sorting factors, such as yeast Cur1 protein, play key role in proteostasis via tight control of partitioning and recycling of misfolded proteins. In this study, we show that, despite the previously described ability of Cur1 to antagonize the yeast prion [URE3], it enhances propagation and phenotypic manifestation of another prion, [PSI+ ]. We demonstrate that both curing of [URE3] and enhancement of [PSI+ ] in the presence of excess Cur1 are counteracted by the cochaperone Hsp40-Sis1 in a dosage-dependent manner, and show that the effect of Cur1 on prions parallels effects of the attachment of nuclear localization signal to Sis1, indicating that Cur1 acts on prions via its previously reported ability to relocalize Sis1 from the cytoplasm to nucleus. This shows that the direction in which Cur1 influences a prion depends on how this specific prion responds to relocalization of Sis1.
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Affiliation(s)
- Yury A Barbitoff
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Andrew G Matveenko
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia.,Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg 199034, Russia.,St. Petersburg Branch, Vavilov Institute of General Genetics, Russian Academy of Sciences, St. Petersburg 199034, Russia
| | - Svetlana E Moskalenko
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia.,St. Petersburg Branch, Vavilov Institute of General Genetics, Russian Academy of Sciences, St. Petersburg 199034, Russia
| | - Olga M Zemlyanko
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia.,Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Gary P Newnam
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332-2000, USA
| | - Ayesha Patel
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332-2000, USA
| | - Tatiana A Chernova
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Yury O Chernoff
- Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg 199034, Russia.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332-2000, USA.,Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia
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43
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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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44
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Prions and the concept of polyprionic inheritance. Curr Genet 2017; 63:799-802. [PMID: 28260124 DOI: 10.1007/s00294-017-0685-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 02/11/2017] [Accepted: 02/14/2017] [Indexed: 12/16/2022]
Abstract
Discovery of prions-proteins that are able to convert between structurally distinct states, of which one or more is transmissible, led to the concept of "protein-based inheritance". According to this concept, the formation of prion fibrils causes DNA-independent heritable traits in microorganisms. Recently, we described a new and unusual type of prion inheritance. We showed that the yeast prions [PIN +] and [SWI +], like classical genes, demonstrate complementary interaction that causes a phenotypic change in yeast cells. Here, we discuss the possible mechanisms of such polyprionic inheritance and the perspectives in the identification of prions in various organisms using universal proteomic approaches.
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45
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Serpionov GV, Alexandrov AI, Ter-Avanesyan MD. Distinct mechanisms of mutant huntingtin toxicity in different yeast strains. FEMS Yeast Res 2016; 17:fow102. [PMID: 27915242 DOI: 10.1093/femsyr/fow102] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 10/17/2016] [Accepted: 12/01/2016] [Indexed: 11/12/2022] Open
Abstract
Expansion of polyglutamine stretches in several proteins causes neurodegenerative amyloidoses, including Huntington disease. In yeast, mutant huntingtin (mHtt) with a stretch of 103 glutamine residues (HttQ103) forms toxic aggregates. A range of yeast strains have been used to elucidate the mechanisms of mHtt toxicity, and have revealed perturbations of various unrelated processes. HttQ103 aggregates can induce aggregation of cellular proteins, many of which contain glutamine/asparagine-rich regions, including Sup35 and Def1. In the strain 74-D694 HttQ103, toxicity is related to aggregation-mediated depletion of soluble Sup35 and its interacting partner Sup45. Def1 was also implicated in mHtt toxicity, since its lack detoxified HttQ103 in another yeast strain, BY4741. Here we show that in BY4742, deletion of DEF1 lowers HttQ103 toxicity and decreases the amount of its polymers, but does not affect copolymerization of Sup35. Furthermore, in contrast to 74-D694, increasing the levels of soluble Sup35 and Sup45 does not alleviate toxicity of HttQ103 in BY4742. These data demonstrate a difference in the mechanisms underlying mHtt toxicity in different yeast strains and suggest that in humans with Huntington disease, neurons of different brain compartments and cells in other tissues can also be damaged by different mechanisms.
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Affiliation(s)
- Genrikh V Serpionov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Alexander I Alexandrov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Michael D Ter-Avanesyan
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
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46
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Matveenko AG, Drozdova PB, Belousov MV, Moskalenko SE, Bondarev SA, Barbitoff YA, Nizhnikov AA, Zhouravleva GA. SFP1-mediated prion-dependent lethality is caused by increased Sup35 aggregation and alleviated by Sis1. Genes Cells 2016; 21:1290-1308. [DOI: 10.1111/gtc.12444] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 09/14/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Andrew G. Matveenko
- St Petersburg Branch; Vavilov Institute of General Genetics of the Russian Academy of Sciences; St Petersburg Russia
- Department of Genetics and Biotechnology; Saint Petersburg State University; St Petersburg Russia
- Laboratory of Amyloid Biology; Saint Petersburg State University; St Petersburg Russia
| | - Polina B. Drozdova
- Department of Genetics and Biotechnology; Saint Petersburg State University; St Petersburg Russia
- Laboratory of Amyloid Biology; Saint Petersburg State University; St Petersburg Russia
| | - Mikhail V. Belousov
- Department of Genetics and Biotechnology; Saint Petersburg State University; St Petersburg Russia
| | - Svetlana E. Moskalenko
- St Petersburg Branch; Vavilov Institute of General Genetics of the Russian Academy of Sciences; St Petersburg Russia
- Department of Genetics and Biotechnology; Saint Petersburg State University; St Petersburg Russia
| | - Stanislav A. Bondarev
- Department of Genetics and Biotechnology; Saint Petersburg State University; St Petersburg Russia
- Laboratory of Amyloid Biology; Saint Petersburg State University; St Petersburg Russia
| | - Yury A. Barbitoff
- Department of Genetics and Biotechnology; Saint Petersburg State University; St Petersburg Russia
| | - Anton A. Nizhnikov
- St Petersburg Branch; Vavilov Institute of General Genetics of the Russian Academy of Sciences; St Petersburg Russia
- Department of Genetics and Biotechnology; Saint Petersburg State University; St Petersburg Russia
- All-Russia Research Institute for Agricultural Microbiology; Pushkin St Petersburg Russia
| | - Galina A. Zhouravleva
- Department of Genetics and Biotechnology; Saint Petersburg State University; St Petersburg Russia
- Laboratory of Amyloid Biology; Saint Petersburg State University; St Petersburg Russia
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Nizhnikov AA, Antonets KS, Inge-Vechtomov SG. Amyloids: from Pathogenesis to Function. BIOCHEMISTRY (MOSCOW) 2016; 80:1127-44. [PMID: 26555466 DOI: 10.1134/s0006297915090047] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The term "amyloids" refers to fibrillar protein aggregates with cross-β structure. They have been a subject of intense scrutiny since the middle of the previous century. First, this interest is due to association of amyloids with dozens of incurable human diseases called amyloidoses, which affect hundreds of millions of people. However, during the last decade the paradigm of amyloids as pathogens has changed due to an increase in understanding of their role as a specific variant of quaternary protein structure essential for the living cell. Thus, functional amyloids are found in all domains of the living world, and they fulfill a variety of roles ranging from biofilm formation in bacteria to long-term memory regulation in higher eukaryotes. Prions, which are proteins capable of existing under the same conditions in two or more conformations at least one of which having infective properties, also typically have amyloid features. There are weighty reasons to believe that the currently known amyloids are only a minority of their real number. This review provides a retrospective analysis of stages in the development of amyloid biology that during the last decade resulted, on one hand, in reinterpretation of the biological role of amyloids, and on the other hand, in the development of systems biology of amyloids, or amyloidomics.
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Affiliation(s)
- A A Nizhnikov
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, 199034, Russia.
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Serpionov GV, Alexandrov AI, Antonenko YN, Ter-Avanesyan MD. A protein polymerization cascade mediates toxicity of non-pathological human huntingtin in yeast. Sci Rep 2015; 5:18407. [PMID: 26673834 PMCID: PMC4682096 DOI: 10.1038/srep18407] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 11/18/2015] [Indexed: 12/21/2022] Open
Abstract
Several neurodegenerative amyloidoses, including Huntington disease, are caused by expansion of polyglutamine (polyQ) stretches in otherwise unrelated proteins. In a yeast model, an N-terminal fragment of mutant huntingtin with a stretch of 103 glutamine residues aggregates and causes toxicity, while its non-toxic wild type variant with a sequence of 25 glutamines (Htt25Q) does not aggregate. Here, we observed that non-toxic polymers of various proteins with glutamine-rich domains could seed polymerization of Htt25Q, which caused toxicity by seeding polymerization of the glutamine/asparagine-rich Sup35 protein thus depleting the soluble pools of this protein and its interacting partner, Sup45. Importantly, only polymers of Htt25Q, but not of the initial benign polymers, induced Sup35 polymerization, indicating an intermediary role of Htt25Q in cross-seeding Sup35 polymerization. These data provide a novel insight into interactions between amyloidogenic proteins and suggest a possible role for these interactions in the pathogenesis of Huntington and other polyQ diseases.
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Affiliation(s)
- Genrikh V Serpionov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences. 33, bld. 2 Leninsky Ave., Moscow 119071, Russia
| | - Alexander I Alexandrov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences. 33, bld. 2 Leninsky Ave., Moscow 119071, Russia
| | - Yuri N Antonenko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie gori, 1, bldg. 40, Moscow 119991, Russia
| | - Michael D Ter-Avanesyan
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences. 33, bld. 2 Leninsky Ave., Moscow 119071, Russia
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Lu X, Murphy RM. Asparagine Repeat Peptides: Aggregation Kinetics and Comparison with Glutamine Repeats. Biochemistry 2015. [PMID: 26204228 DOI: 10.1021/acs.biochem.5b00644] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amino acid repeat runs are common occurrences in eukaryotic proteins, with glutamine (Q) and asparagine (N) as particularly frequent repeats. Abnormal expansion of Q-repeat domains causes at least nine neurodegenerative disorders, most likely because expansion leads to protein misfolding, aggregation, and toxicity. The linkage between Q-repeats and disease has motivated several investigations into the mechanism of aggregation and the role of Q-repeat length in aggregation. Curiously, glutamine repeats are common in vertebrates, whereas N-repeats are virtually absent in vertebrates, but common in invertebrates. One hypothesis for the lack of N-repeats in vertebrates is biophysical; that is, there is strong selective pressure in higher organisms against aggregation-prone proteins. If true, then asparagine and glutamine repeats must differ substantially in their aggregation properties despite their chemical similarities. In this work, aggregation of peptides with asparagine repeats of variable length (12-24) were characterized and compared to that of similar peptides with glutamine repeats. As with glutamine, aggregation of N-repeat peptides was strongly length-dependent. Replacement of glutamine with asparagine caused a subtle shift in the conformation of the monomer, which strongly affected the rate of aggregation. Specifically, N-repeat peptides adopted β-turn structural elements, leading to faster self-assembly into globular oligomers and much more rapid conversion into fibrillar aggregates, compared to Q-repeat peptides. These biophysical differences may account for the differing biological roles of N- versus Q-repeat domains.
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Affiliation(s)
- Xiaomeng Lu
- †Biophysics Program and ‡Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Regina M Murphy
- †Biophysics Program and ‡Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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Nizhnikov AA, Alexandrov AI, Ryzhova TA, Mitkevich OV, Dergalev AA, Ter-Avanesyan MD, Galkin AP. Proteomic screening for amyloid proteins. PLoS One 2014; 9:e116003. [PMID: 25549323 PMCID: PMC4280166 DOI: 10.1371/journal.pone.0116003] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 12/02/2014] [Indexed: 11/18/2022] Open
Abstract
Despite extensive study, progress in elucidation of biological functions of amyloids and their role in pathology is largely restrained due to the lack of universal and reliable biochemical methods for their discovery. All biochemical methods developed so far allowed only identification of glutamine/asparagine-rich amyloid-forming proteins or proteins comprising amyloids that form large deposits. In this article we present a proteomic approach which may enable identification of a broad range of amyloid-forming proteins independently of specific features of their sequences or levels of expression. This approach is based on the isolation of protein fractions enriched with amyloid aggregates via sedimentation by ultracentrifugation in the presence of strong ionic detergents, such as sarkosyl or SDS. Sedimented proteins are then separated either by 2D difference gel electrophoresis or by SDS-PAGE, if they are insoluble in the buffer used for 2D difference gel electrophoresis, after which they are identified by mass-spectrometry. We validated this approach by detection of known yeast prions and mammalian proteins with established capacity for amyloid formation and also revealed yeast proteins forming detergent-insoluble aggregates in the presence of human huntingtin with expanded polyglutamine domain. Notably, with one exception, all these proteins contained glutamine/asparagine-rich stretches suggesting that their aggregates arose due to polymerization cross-seeding by human huntingtin. Importantly, though the approach was developed in a yeast model, it can easily be applied to any organism thus representing an efficient and universal tool for screening for amyloid proteins.
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Affiliation(s)
- Anton A. Nizhnikov
- Dept. of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia
- St. Petersburg Branch, Vavilov Institute of General Genetics of the Russian Academy of Sciences, St. Petersburg, Russia
| | | | - Tatyana A. Ryzhova
- Dept. of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia
- St. Petersburg Branch, Vavilov Institute of General Genetics of the Russian Academy of Sciences, St. Petersburg, Russia
| | - Olga V. Mitkevich
- A.N. Bach Institute of Biochemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Alexander A. Dergalev
- A.N. Bach Institute of Biochemistry of the Russian Academy of Sciences, Moscow, Russia
| | | | - Alexey P. Galkin
- Dept. of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia
- St. Petersburg Branch, Vavilov Institute of General Genetics of the Russian Academy of Sciences, St. Petersburg, Russia
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