1
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Garai S, Raizada A, Kumar V, Sopory SK, Pareek A, Singla-Pareek SL, Kaur C. In silico analysis of fungal prion-like proteins for elucidating their role in plant-fungi interactions. Arch Microbiol 2024; 206:308. [PMID: 38896139 DOI: 10.1007/s00203-024-04040-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 06/07/2024] [Accepted: 06/09/2024] [Indexed: 06/21/2024]
Abstract
Prion-like proteins (PrLPs) have emerged as beneficial molecules with implications in adaptive responses. These proteins possess a conserved prion-like domain (PrLD) which is an intrinsically disordered region capable of adopting different conformations upon perceiving external stimuli. Owing to changes in protein conformation, functional characteristics of proteins harboring PrLDs get altered thereby, providing a unique mode of protein-based regulation. Since PrLPs are ubiquitous in nature and involved in diverse functions, through this study, we aim to explore the role of such domains in yet another important physiological process viz. plant-microbe interactions to get insights into the mechanisms dictating cross-kingdom interactions. We have evaluated the presence and functions of PrLPs in 18 different plant-associated fungi of agricultural importance to unravel their role in plant-microbe interactions. Of the 241,997 proteins scanned, 3,820 (~ 1.6%) were identified as putative PrLPs with pathogenic fungi showing significantly higher PrLP density than their beneficial counterparts. Further, through GO enrichment analysis, we could predict several PrLPs from pathogenic fungi to be involved in virulence and formation of stress granules. Notably, PrLPs involved in (retro)transposition were observed exclusively in pathogenic fungi. We even analyzed publicly available data for the expression alterations of fungal PrLPs upon their interaction with their respective hosts which revealed perturbation in the levels of some PrLP-encoding genes during interactions with plants. Overall, our work sheds light into the probable role of prion-like candidates in plant-fungi interaction, particularly in context of pathogenesis, paving way for more focused studies for validating their role.
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Affiliation(s)
- Sampurna Garai
- Plant Stress Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Avi Raizada
- National Agri-Food Biotechnology Institute, Mohali, 140306, Punjab, India
| | - Vijay Kumar
- National Agri-Food Biotechnology Institute, Mohali, 140306, Punjab, India
| | - Sudhir K Sopory
- Plant Stress Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Ashwani Pareek
- National Agri-Food Biotechnology Institute, Mohali, 140306, Punjab, India
| | - Sneh L Singla-Pareek
- Plant Stress Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Charanpreet Kaur
- National Agri-Food Biotechnology Institute, Mohali, 140306, Punjab, India.
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2
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Eraña H, Sampedro-Torres-Quevedo C, Charco JM, Díaz-Domínguez CM, Peccati F, San-Juan-Ansoleaga M, Vidal E, Gonçalves-Anjo N, Pérez-Castro MA, González-Miranda E, Piñeiro P, Fernández-Veiga L, Galarza-Ahumada J, Fernández-Muñoz E, Perez de Nanclares G, Telling G, Geijo M, Jiménez-Osés G, Castilla J. A Protein Misfolding Shaking Amplification-based method for the spontaneous generation of hundreds of bona fide prions. Nat Commun 2024; 15:2112. [PMID: 38459071 PMCID: PMC10923866 DOI: 10.1038/s41467-024-46360-2] [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: 10/13/2023] [Accepted: 02/23/2024] [Indexed: 03/10/2024] Open
Abstract
Prion diseases are a group of rapidly progressing neurodegenerative disorders caused by the misfolding of the endogenous prion protein (PrPC) into a pathogenic form (PrPSc). This process, despite being the central event underlying these disorders, remains largely unknown at a molecular level, precluding the prediction of new potential outbreaks or interspecies transmission incidents. In this work, we present a method to generate bona fide recombinant prions de novo, allowing a comprehensive analysis of protein misfolding across a wide range of prion proteins from mammalian species. We study more than 380 different prion proteins from mammals and classify them according to their spontaneous misfolding propensity and their conformational variability. This study aims to address fundamental questions in the prion research field such as defining infectivity determinants, interspecies transmission barriers or the structural influence of specific amino acids and provide invaluable information for future diagnosis and therapy applications.
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Affiliation(s)
- Hasier Eraña
- Center for Cooperative Research in Biosciences (CIC BioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
- Centro de Investigación Biomédica en Red de Enfermedades infecciosas (CIBERINFEC), Carlos III National Health Institute, Madrid, Spain
- ATLAS Molecular Pharma S. L, Derio, Spain
| | | | - Jorge M Charco
- Center for Cooperative Research in Biosciences (CIC BioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
- Centro de Investigación Biomédica en Red de Enfermedades infecciosas (CIBERINFEC), Carlos III National Health Institute, Madrid, Spain
- ATLAS Molecular Pharma S. L, Derio, Spain
| | - Carlos M Díaz-Domínguez
- Center for Cooperative Research in Biosciences (CIC BioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
- Centro de Investigación Biomédica en Red de Enfermedades infecciosas (CIBERINFEC), Carlos III National Health Institute, Madrid, Spain
| | - Francesca Peccati
- Center for Cooperative Research in Biosciences (CIC BioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Maitena San-Juan-Ansoleaga
- Center for Cooperative Research in Biosciences (CIC BioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Enric Vidal
- IRTA. Programa de Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA). Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Catalonia, Spain
- Unitat mixta d'Investigació IRTA-UAB en Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA). Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Catalonia, Spain
| | - Nuno Gonçalves-Anjo
- Center for Cooperative Research in Biosciences (CIC BioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Miguel A Pérez-Castro
- Center for Cooperative Research in Biosciences (CIC BioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Ezequiel González-Miranda
- Center for Cooperative Research in Biosciences (CIC BioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Patricia Piñeiro
- Center for Cooperative Research in Biosciences (CIC BioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Leire Fernández-Veiga
- Center for Cooperative Research in Biosciences (CIC BioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Josu Galarza-Ahumada
- Center for Cooperative Research in Biosciences (CIC BioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Eva Fernández-Muñoz
- Center for Cooperative Research in Biosciences (CIC BioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Guiomar Perez de Nanclares
- Molecular (Epi)Genetics Laboratory, Bioaraba Health Research Institute, Araba University Hospital, Vitoria-Gasteiz, Spain
| | - Glenn Telling
- Prion Research Center, Colorado State University, Fort Collins, CO, USA
| | - Mariví Geijo
- Animal Health Department, NEIKER-Basque Institute for Agricultural Research and Development. Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Gonzalo Jiménez-Osés
- Center for Cooperative Research in Biosciences (CIC BioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Joaquín Castilla
- Center for Cooperative Research in Biosciences (CIC BioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades infecciosas (CIBERINFEC), Carlos III National Health Institute, Madrid, Spain.
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain.
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3
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Hall D. MIL-CELL: a tool for multi-scale simulation of yeast replication and prion transmission. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:673-704. [PMID: 37670150 PMCID: PMC10682183 DOI: 10.1007/s00249-023-01679-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/08/2023] [Accepted: 08/14/2023] [Indexed: 09/07/2023]
Abstract
The single-celled baker's yeast, Saccharomyces cerevisiae, can sustain a number of amyloid-based prions, the three most prominent examples being [URE3], [PSI+], and [PIN+]. In the laboratory, haploid S. cerevisiae cells of a single mating type can acquire an amyloid prion in one of two ways (i) spontaneous nucleation of the prion within the yeast cell, and (ii) receipt via mother-to-daughter transmission during the cell division cycle. Similarly, prions can be lost due to (i) dissolution of the prion amyloid by its breakage into non-amyloid monomeric units, or (ii) preferential donation/retention of prions between the mother and daughter during cell division. Here we present a computational tool (Monitoring Induction and Loss of prions in Cells; MIL-CELL) for modelling these four general processes using a multiscale approach describing both spatial and kinetic aspects of the yeast life cycle and the amyloid-prion behavior. We describe the workings of the model, assumptions upon which it is based and some interesting simulation results pertaining to the wave-like spread of the epigenetic prion elements through the yeast population. MIL-CELL is provided as a stand-alone GUI executable program for free download with the paper. MIL-CELL is equipped with a relational database allowing all simulated properties to be searched, collated and graphed. Its ability to incorporate variation in heritable properties means MIL-CELL is also capable of simulating loss of the isogenic nature of a cell population over time. The capability to monitor both chronological and reproductive age also makes MIL-CELL potentially useful in studies of cell aging.
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Affiliation(s)
- Damien Hall
- WPI Nano Life Science Institute, Kanazawa University, Kakumamachi, Kanazawa, Ishikawa, 920-1164, Japan.
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4
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Comment on Billant et al. p53, A Victim of the Prion Fashion. Cancers 2021, 13, 269. Cancers (Basel) 2023; 15:cancers15010309. [PMID: 36612305 PMCID: PMC9818150 DOI: 10.3390/cancers15010309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/27/2022] [Accepted: 12/27/2022] [Indexed: 01/04/2023] Open
Abstract
The p53 tumor suppressor is a central protein in the fight against cancer [...].
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5
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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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Miller SC, Wegrzynowicz AK, Cole SJ, Hayward RE, Ganser SJ, Hines JK. Hsp40/JDP Requirements for the Propagation of Synthetic Yeast Prions. Viruses 2022; 14:v14102160. [PMID: 36298715 PMCID: PMC9611480 DOI: 10.3390/v14102160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/22/2022] [Accepted: 09/27/2022] [Indexed: 11/05/2022] Open
Abstract
Yeast prions are protein-based transmissible elements, most of which are amyloids. The chaperone protein network in yeast is inexorably linked to the spreading of prions during cell division by fragmentation of amyloid prion aggregates. Specifically, the core “prion fragmentation machinery” includes the proteins Hsp104, Hsp70 and the Hsp40/J-domain protein (JDP) Sis1. Numerous novel amyloid-forming proteins have been created and examined in the yeast system and occasionally these amyloids are also capable of continuous Hsp104-dependent propagation in cell populations, forming synthetic prions. However, additional chaperone requirements, if any, have not been determined. Here, we report the first instances of a JDP-Hsp70 system requirement for the propagation of synthetic prions. We utilized constructs from a system of engineered prions with prion-forming domains (PrDs) consisting of a polyQ stretch interrupted by a single heterologous amino acid interspersed every fifth residue. These “polyQX” PrDs are fused to the MC domains of Sup35, creating chimeric proteins of which a subset forms synthetic prions in yeast. For four of these prions, we show that SIS1 repression causes prion loss in a manner consistent with Sis1′s known role in prion fragmentation. PolyQX prions were sensitive to Sis1 expression levels to differing degrees, congruent with the variability observed among native prions. Our results expand the scope known Sis1 functionality, demonstrating that Sis1 acts on amyloids broadly, rather than through specific protein–protein interactions with individual yeast prion-forming proteins.
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7
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Ho AT, Hurst LD. Stop codon usage as a window into genome evolution: mutation, selection, biased gene conversion and the TAG paradox. Genome Biol Evol 2022; 14:6648529. [PMID: 35867377 PMCID: PMC9348620 DOI: 10.1093/gbe/evac115] [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] [Accepted: 07/17/2022] [Indexed: 11/16/2022] Open
Abstract
Protein coding genes terminate with one of three stop codons (TAA, TGA, or TAG) that, like synonymous codons, are not employed equally. With TGA and TAG having identical nucleotide content, analysis of their differential usage provides an unusual window into the forces operating on what are ostensibly functionally identical residues. Across genomes and between isochores within the human genome, TGA usage increases with G + C content but, with a common G + C → A + T mutation bias, this cannot be explained by mutation bias-drift equilibrium. Increased usage of TGA in G + C-rich genomes or genomic regions is also unlikely to reflect selection for the optimal stop codon, as TAA appears to be universally optimal, probably because it has the lowest read-through rate. Despite TAA being favored by selection and mutation bias, as with codon usage bias G + C pressure is the prime determinant of between-species TGA usage trends. In species with strong G + C-biased gene conversion (gBGC), such as mammals and birds, the high usage and conservation of TGA is best explained by an A + T → G + C repair bias. How to explain TGA enrichment in other G + C-rich genomes is less clear. Enigmatically, across bacterial and archaeal species and between human isochores TAG usage is mostly unresponsive to G + C pressure. This unresponsiveness we dub the TAG paradox as currently no mutational, selective, or gBGC model provides a well-supported explanation. That TAG does increase with G + C usage across eukaryotes makes the usage elsewhere yet more enigmatic. We suggest resolution of the TAG paradox may provide insights into either an unknown but common selective preference (probably at the DNA/RNA level) or an unrecognized complexity to the action of gBGC.
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Affiliation(s)
- Alexander T Ho
- Milner Centre for Evolution, University of Bath, Bath, UK
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8
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Sakaguchi S, Hara H. The first non-prion pathogen identified: neurotropic influenza virus. Prion 2022; 16:1-6. [PMID: 34978525 PMCID: PMC8741280 DOI: 10.1080/19336896.2021.2015224] [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] [Indexed: 11/13/2022] Open
Abstract
The cellular isoform of prion protein, designated PrPC, is a membrane glycoprotein expressed most abundantly in the brain, particularly by neurons, and its conformational conversion into the abnormally folded, amyloidogenic isoform, PrPSc, is an underlying mechanism in the pathogenesis of prion diseases, a group of neurodegenerative disorders in humans and animals. Most cases of these diseases are sporadic and their aetiologies are unknown. We recently found that a neurotropic strain of influenza A virus (IAV/WSN) caused the conversion of PrPC into PrPSc and the subsequent formation of infectious prions in mouse neuroblastoma cells after infection. These results show that IAV/WSN is the first non-prion pathogen capable of inducing the conversion of PrPC into PrPSc and propagating infectious prions in cultured neuronal cells, and also provide the intriguing possibility that IAV infection in neurons might be a cause of or be associated with sporadic prion diseases. Here, we present our findings of the IAV/WSN-induced conversion of PrPC into PrPSc and subsequent propagation of infectious prions, and also discuss the biological significance of the conversion of PrPC into PrPSc in virus infections.
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Affiliation(s)
- Suehiro Sakaguchi
- Division of Molecular Neurobiology, The Institute for Enzyme Research (KOSOKEN), Tokushima University, Tokushima 770-8503, Japan
| | - Hideyuki Hara
- Division of Molecular Neurobiology, The Institute for Enzyme Research (KOSOKEN), Tokushima University, Tokushima 770-8503, Japan
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Gene Amplification as a Mechanism of Yeast Adaptation to Nonsense Mutations in Release Factor Genes. Genes (Basel) 2021; 12:genes12122019. [PMID: 34946968 PMCID: PMC8701342 DOI: 10.3390/genes12122019] [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: 10/16/2021] [Revised: 12/13/2021] [Accepted: 12/15/2021] [Indexed: 11/17/2022] Open
Abstract
Protein synthesis (translation) is one of the fundamental processes occurring in the cells of living organisms. Translation can be divided into three key steps: initiation, elongation, and termination. In the yeast Saccharomyces cerevisiae, there are two translation termination factors, eRF1 and eRF3. These factors are encoded by the SUP45 and SUP35 genes, which are essential; deletion of any of them leads to the death of yeast cells. However, viable strains with nonsense mutations in both the SUP35 and SUP45 genes were previously obtained in several groups. The survival of such mutants clearly involves feedback control of premature stop codon readthrough; however, the exact molecular basis of such feedback control remain unclear. To investigate the genetic factors supporting the viability of these SUP35 and SUP45 nonsense mutants, we performed whole-genome sequencing of strains carrying mutant sup35-n and sup45-n alleles; while no common SNPs or indels were found in these genomes, we discovered a systematic increase in the copy number of the plasmids carrying mutant sup35-n and sup45-n alleles. We used the qPCR method which confirmed the differences in the relative number of SUP35 and SUP45 gene copies between strains carrying wild-type or mutant alleles of SUP35 and SUP45 genes. Moreover, we compare the number of copies of the SUP35 and SUP45 genes in strains carrying different nonsense mutant variants of these genes as a single chromosomal copy. qPCR results indicate that the number of mutant gene copies is increased compared to the wild-type control. In case of several sup45-n alleles, this was due to a disomy of the entire chromosome II, while for the sup35-218 mutation we observed a local duplication of a segment of chromosome IV containing the SUP35 gene. Taken together, our results indicate that gene amplification is a common mechanism of adaptation to nonsense mutations in release factor genes in yeast.
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Wei J, Ho G, Takamatsu Y, Masliah E, Hashimoto M. Therapeutic Potential of α-Synuclein Evolvability for Autosomal Recessive Parkinson's Disease. PARKINSON'S DISEASE 2021; 2021:6318067. [PMID: 34858569 PMCID: PMC8632460 DOI: 10.1155/2021/6318067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 10/20/2021] [Accepted: 11/03/2021] [Indexed: 06/13/2023]
Abstract
The majority of Parkinson's disease (PD) is sporadic in elderly and is characterized by α-synuclein (αS) aggregation and other alterations involving mitochondria, ubiquitin-proteasome, and autophagy. The remaining are familial PD associated with gene mutations of either autosomal dominant or recessive inheritances. However, the former ones are similar to sporadic PD, and the latter ones are accompanied by impaired mitophagy during the reproductive stage. Since no radical therapies are available for PD, the objective of this paper is to discuss a mechanistic role for amyloidogenic evolvability, a putative physiological function of αS, among PD subtypes, and the potential relevance to therapy. Presumably, αS evolvability might benefit familial PD due to autosomal dominant genes and also sporadic PD during reproduction, which may manifest as neurodegenerative diseases through antagonistic pleiotropy mechanism in aging. Indeed, there are some reports describing that αS prevents apoptosis and mitochondrial alteration under the oxidative stress conditions, notwithstanding myriads of papers on the neuropathology of αS. Importantly, β-synuclein (βS), the nonamyloidogenic homologue of αS, might buffer against evolvability of αS protofibrils associated with neurotoxicity. Finally, it is intriguing to predict that increased αS evolvability through suppression of βS expression might protect against autosomal recessive PD. Collectively, further studies are warranted to better understand αS evolvability in PD pathogenesis, leading to rational therapy development.
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Affiliation(s)
- Jianshe Wei
- Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
- Institute for Brain Sciences Research, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Gilbert Ho
- PCND Neuroscience Research Institute, Poway 92064, CA, USA
| | - Yoshiki Takamatsu
- Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Eliezer Masliah
- Division of Neurosciences, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Makoto Hashimoto
- Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
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11
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Ho AT, Hurst LD. Effective Population Size Predicts Local Rates but Not Local Mitigation of Read-through Errors. Mol Biol Evol 2021; 38:244-262. [PMID: 32797190 PMCID: PMC7783166 DOI: 10.1093/molbev/msaa210] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
In correctly predicting that selection efficiency is positively correlated with the effective population size (Ne), the nearly neutral theory provides a coherent understanding of between-species variation in numerous genomic parameters, including heritable error (germline mutation) rates. Does the same theory also explain variation in phenotypic error rates and in abundance of error mitigation mechanisms? Translational read-through provides a model to investigate both issues as it is common, mostly nonadaptive, and has good proxy for rate (TAA being the least leaky stop codon) and potential error mitigation via "fail-safe" 3' additional stop codons (ASCs). Prior theory of translational read-through has suggested that when population sizes are high, weak selection for local mitigation can be effective thus predicting a positive correlation between ASC enrichment and Ne. Contra to prediction, we find that ASC enrichment is not correlated with Ne. ASC enrichment, although highly phylogenetically patchy, is, however, more common both in unicellular species and in genes expressed in unicellular modes in multicellular species. By contrast, Ne does positively correlate with TAA enrichment. These results imply that local phenotypic error rates, not local mitigation rates, are consistent with a drift barrier/nearly neutral model.
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Affiliation(s)
- Alexander T Ho
- Milner Centre for Evolution, University of Bath, Bath, United Kingdom
- Corresponding author: E-mail:
| | - Laurence D Hurst
- Milner Centre for Evolution, University of Bath, Bath, United Kingdom
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12
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Andreychuk YV, Zadorsky SP, Zhuk AS, Stepchenkova EI, Inge-Vechtomov SG. Relationship between Type I and Type II Template Processes: Amyloids and Genome Stability. Mol Biol 2020. [DOI: 10.1134/s0026893320050027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Abstract
Stalled protein synthesis produces defective nascent chains that can harm cells. In response, cells degrade these nascent chains via a process called ribosome-associated quality control (RQC). Here, we review the irregularities in the translation process that cause ribosomes to stall as well as how cells use RQC to detect stalled ribosomes, ubiquitylate their tethered nascent chains, and deliver the ubiquitylated nascent chains to the proteasome. We additionally summarize how cells respond to RQC failure.
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Affiliation(s)
- Cole S Sitron
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany;
| | - Onn Brandman
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA;
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14
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Rodnina MV, Korniy N, Klimova M, Karki P, Peng BZ, Senyushkina T, Belardinelli R, Maracci C, Wohlgemuth I, Samatova E, Peske F. Translational recoding: canonical translation mechanisms reinterpreted. Nucleic Acids Res 2020; 48:1056-1067. [PMID: 31511883 PMCID: PMC7026636 DOI: 10.1093/nar/gkz783] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/21/2019] [Accepted: 08/30/2019] [Indexed: 01/15/2023] Open
Abstract
During canonical translation, the ribosome moves along an mRNA from the start to the stop codon in exact steps of one codon at a time. The collinearity of the mRNA and the protein sequence is essential for the quality of the cellular proteome. Spontaneous errors in decoding or translocation are rare and result in a deficient protein. However, dedicated recoding signals in the mRNA can reprogram the ribosome to read the message in alternative ways. This review summarizes the recent advances in understanding the mechanisms of three types of recoding events: stop-codon readthrough, –1 ribosome frameshifting and translational bypassing. Recoding events provide insights into alternative modes of ribosome dynamics that are potentially applicable to other non-canonical modes of prokaryotic and eukaryotic translation.
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Affiliation(s)
- Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Natalia Korniy
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Mariia Klimova
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Prajwal Karki
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Bee-Zen Peng
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Tamara Senyushkina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Riccardo Belardinelli
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Cristina Maracci
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Ingo Wohlgemuth
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Ekaterina Samatova
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Frank Peske
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
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15
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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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16
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Ho AT, Hurst LD. In eubacteria, unlike eukaryotes, there is no evidence for selection favouring fail-safe 3' additional stop codons. PLoS Genet 2019; 15:e1008386. [PMID: 31527909 PMCID: PMC6764699 DOI: 10.1371/journal.pgen.1008386] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 09/27/2019] [Accepted: 08/27/2019] [Indexed: 12/23/2022] Open
Abstract
Errors throughout gene expression are likely deleterious, hence genomes are under selection to ameliorate their consequences. Additional stop codons (ASCs) are in-frame nonsense ‘codons’ downstream of the primary stop which may be read by translational machinery should the primary stop have been accidentally read through. Prior evidence in several eukaryotes suggests that ASCs are selected to prevent potentially-deleterious consequences of read-through. We extend this evidence showing that enrichment of ASCs is common but not universal for single cell eukaryotes. By contrast, there is limited evidence as to whether the same is true in other taxa. Here, we provide the first systematic test of the hypothesis that ASCs act as a fail-safe mechanism in eubacteria, a group with high read-through rates. Contra to the predictions of the hypothesis we find: there is paucity, not enrichment, of ASCs downstream; substitutions that degrade stops are more frequent in-frame than out-of-frame in 3’ sequence; highly expressed genes are no more likely to have ASCs than lowly expressed genes; usage of the leakiest primary stop (TGA) in highly expressed genes does not predict ASC enrichment even compared to usage of non-leaky stops (TAA) in lowly expressed genes, beyond downstream codon +1. Any effect at the codon immediately proximal to the primary stop can be accounted for by a preference for a T/U residue immediately following the stop, although if anything, TT- and TC- starting codons are preferred. We conclude that there is no compelling evidence for ASC selection in eubacteria. This presents an unusual case in which the same error could be solved by the same mechanism in eukaryotes and prokaryotes but is not. We discuss two possible explanations: that, owing to the absence of nonsense mediated decay, bacteria may solve read-through via gene truncation and in eukaryotes certain prion states cause raised read-through rates. In all organisms, gene expression is error-prone. One such error, translational read-through, occurs where the primary stop codon of an expressed gene is missed by the translational machinery. Failure to terminate is likely to be costly, hence genomes are under selection to prevent this from happening. One proposed error-proofing strategy involves in-frame proximal additional stop codons (ASCs) which may act as a ‘fail-safe’ mechanism by providing another opportunity for translation to terminate. There is evidence for ASC enrichment in several eukaryotes. We extend this evidence showing it to be common but not universal in single celled eukaryotes. However, the situation in bacteria is poorly understood, despite bacteria having high read-through rates. Here, we test the fail-safe hypothesis within a broad range of bacteria. To our surprise, we find that not only are ASCs not enriched, but they may even be selected against. This provides evidence for an unusual circumstance where eukaryotes and prokaryotes could solve the same problem the same way but don’t. What are we to make of this? We suggest that if read-through is the problem, ASCs are not necessarily the expected solution. Owing to the absence of nonsense-mediated decay, a process that makes gene truncation in eukaryotes less viable, we propose bacteria may rescue a leaky stop by mutation that creates a new stop upstream. Alternatively, raised read-through rates in some particular conditions in eukaryotes might explain the difference.
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Affiliation(s)
- Alexander T. Ho
- Milner Centre for Evolution, University of Bath, Bath, United Kingdom
- * E-mail:
| | - Laurence D. Hurst
- Milner Centre for Evolution, University of Bath, Bath, United Kingdom
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17
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Park S, Park SK, Watanabe N, Hashimoto T, Iwatsubo T, Shelkovnikova TA, Liebman SW. Calcium-responsive transactivator (CREST) toxicity is rescued by loss of PBP1/ATXN2 function in a novel yeast proteinopathy model and in transgenic flies. PLoS Genet 2019; 15:e1008308. [PMID: 31390360 PMCID: PMC6699716 DOI: 10.1371/journal.pgen.1008308] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 08/19/2019] [Accepted: 07/12/2019] [Indexed: 12/26/2022] Open
Abstract
Proteins associated with familial neurodegenerative disease often aggregate in patients’ neurons. Several such proteins, e.g. TDP-43, aggregate and are toxic when expressed in yeast. Deletion of the ATXN2 ortholog, PBP1, reduces yeast TDP-43 toxicity, which led to identification of ATXN2 as an amyotrophic lateral sclerosis (ALS) risk factor and therapeutic target. Likewise, new yeast neurodegenerative disease models could facilitate identification of other risk factors and targets. Mutations in SS18L1, encoding the calcium-responsive transactivator (CREST) chromatin-remodeling protein, are associated with ALS. We show that CREST is toxic in yeast and forms nuclear and occasionally cytoplasmic foci that stain with Thioflavin-T, a dye indicative of amyloid-like protein. Like the yeast chromatin-remodeling factor SWI1, CREST inhibits silencing of FLO genes. Toxicity of CREST is enhanced by the [PIN+] prion and reduced by deletion of the HSP104 chaperone required for the propagation of many yeast prions. Likewise, deletion of PBP1 reduced CREST toxicity and aggregation. In accord with the yeast data, we show that the Drosophila ortholog of human ATXN2, dAtx2, is a potent enhancer of CREST toxicity. Downregulation of dAtx2 in flies overexpressing CREST in retinal ganglion cells was sufficient to largely rescue the severe degenerative phenotype induced by human CREST. Overexpression caused considerable co-localization of CREST and PBP1/ATXN2 in cytoplasmic foci in both yeast and mammalian cells. Thus, co-aggregation of CREST and PBP1/ATXN2 may serve as one of the mechanisms of PBP1/ATXN2-mediated toxicity. These results extend the spectrum of ALS associated proteins whose toxicity is regulated by PBP1/ATXN2, suggesting that therapies targeting ATXN2 may be effective for a wide range of neurodegenerative diseases. Mutations in the calcium-responsive transactivator (CREST) protein have been shown to cause amyotrophic lateral sclerosis (ALS). Here we show that the human CREST protein expressed in yeast forms largely nuclear aggregates and is toxic. We also show that the HSP104 chaperone required for propagation of yeast prions is likewise required for CREST toxicity. Furthermore deletion of HSP104 affects CREST aggregation. ATXN2, previously shown to modify ALS toxicity caused by mutations in the TDP-43 encoding gene, also modifies toxicity of CREST expressed in either yeast or flies. In addition, deletion of the yeast ATXN2 ortholog reduces CREST aggregation. These results extend the spectrum of ALS associated proteins whose toxicity is regulated by ATXN2, suggesting that therapies targeting ATXN2 may be effective for a wide range of neurodegenerative diseases.
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Affiliation(s)
- Sangeun Park
- Department of Pharmacology, University of Nevada, Reno, Untied States of America
| | - Sei-Kyoung Park
- Department of Pharmacology, University of Nevada, Reno, Untied States of America
| | | | | | | | | | - Susan W. Liebman
- Department of Pharmacology, University of Nevada, Reno, Untied States of America
- * E-mail:
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18
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Alexandrov AI, Grosfeld EV, Dergalev AA, Kushnirov VV, Chuprov-Netochin RN, Tyurin-Kuzmin PA, Kireev II, Ter-Avanesyan MD, Leonov SV, Agaphonov MO. Analysis of novel hyperosmotic shock response suggests 'beads in liquid' cytosol structure. Biol Open 2019; 8:bio044529. [PMID: 31285266 PMCID: PMC6679407 DOI: 10.1242/bio.044529] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 06/25/2019] [Indexed: 12/11/2022] Open
Abstract
Proteins can aggregate in response to stresses, including hyperosmotic shock. Formation and disassembly of aggregates is a relatively slow process. We describe a novel instant response of the cell to hyperosmosis, during which chaperones and other proteins form numerous foci with properties uncharacteristic of classical aggregates. These foci appeared/disappeared seconds after shock onset/removal, in close correlation with cell volume changes. Genome-wide and targeted testing revealed chaperones, metabolic enzymes, P-body components and amyloidogenic proteins in the foci. Most of these proteins can form large assemblies and for some, the assembled state was pre-requisite for participation in foci. A genome-wide screen failed to identify genes whose absence prevented foci participation by Hsp70. Shapes of and interconnections between foci, revealed by super-resolution microscopy, indicated that the foci were compressed between other entities. Based on our findings, we suggest a new model of cytosol architecture as a collection of numerous gel-like regions suspended in a liquid network. This network is reduced in volume in response to hyperosmosis and forms small pockets between the gel-like regions.
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Affiliation(s)
- Alexander I Alexandrov
- Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Bach Institute of Biochemistry, Leninsky Ave. 33, bld. 2, Moscow 119071, Russia
- A.N. Belozersky Institute of Physico-chemical Biology, M.V. Lomonosov Moscow State University, Leninskie gori 1, bldg 40, Moscow 119234, Russia
| | - Erika V Grosfeld
- Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Bach Institute of Biochemistry, Leninsky Ave. 33, bld. 2, Moscow 119071, Russia
- Chair of Molecular and Cell Biology, Moscow Institute of Physics and Technology (State University), Institutskiy per. 9, Dolgoprudny, Moscow Region 141701, Russia
| | - Alexander A Dergalev
- Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Bach Institute of Biochemistry, Leninsky Ave. 33, bld. 2, Moscow 119071, Russia
| | - Vitaly V Kushnirov
- Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Bach Institute of Biochemistry, Leninsky Ave. 33, bld. 2, Moscow 119071, Russia
| | - Roman N Chuprov-Netochin
- School of Biological and Medical Physics, Moscow Institute of Physics and Technology (State University), Institutskiy per. 9, Dolgoprudny, Moscow Region 141701, Russia
| | - Pyotr A Tyurin-Kuzmin
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, M.V. Lomonosov Moscow State University, Lomonosovskiy pr., 27 bldg 1, Moscow 119192, Russia
| | - Igor I Kireev
- A.N. Belozersky Institute of Physico-chemical Biology, M.V. Lomonosov Moscow State University, Leninskie gori 1, bldg 40, Moscow 119234, Russia
- V. I. Kulakov National Medical Research Center for Obstetrics, Gynecology, and Perinatology, Moscow 117198, Russia
- Faculty of Biology, M. V. Lomonosov Moscow State University, Moscow 119234, Russia
| | - Michael D Ter-Avanesyan
- Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Bach Institute of Biochemistry, Leninsky Ave. 33, bld. 2, Moscow 119071, Russia
| | - Sergey V Leonov
- School of Biological and Medical Physics, Moscow Institute of Physics and Technology (State University), Institutskiy per. 9, Dolgoprudny, Moscow Region 141701, Russia
- Institute of Cell Biophysics of the Russian Academy of Sciences, Institutskaya str., 3, Moscow Region, 142290 Puschino, Russia
| | - Michael O Agaphonov
- Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Bach Institute of Biochemistry, Leninsky Ave. 33, bld. 2, Moscow 119071, Russia
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19
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Avni A, Swasthi HM, Majumdar A, Mukhopadhyay S. Intrinsically disordered proteins in the formation of functional amyloids from bacteria to humans. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2019; 166:109-143. [PMID: 31521230 DOI: 10.1016/bs.pmbts.2019.05.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Amyloids are nanoscopic ordered self-assemblies of misfolded proteins that are formed via aggregation of partially unfolded or intrinsically disordered proteins (IDPs) and are commonly linked to devastating human diseases. An enlarging body of recent research has demonstrated that certain amyloids can be beneficial and participate in a wide range of physiological functions from bacteria to humans. These amyloids are termed as functional amyloids. Like disease-associated amyloids, a vast majority of functional amyloids are derived from a range of IDPs or hybrid proteins containing ordered domains and intrinsically disordered regions (IDRs). In this chapter, we describe an account of recent studies on the aggregation behavior of IDPs resulting in the formation of functional amyloids in a diverse range of organisms from bacteria to human. We also discuss the strategies that are used by these organisms to regulate the spatiotemporal amyloid assembly in their physiological functions.
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Affiliation(s)
- Anamika Avni
- Centre for Protein Science, Design and Engineering, Department of Biological Sciences, and Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India
| | - Hema M Swasthi
- Centre for Protein Science, Design and Engineering, Department of Biological Sciences, and Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India
| | - Anupa Majumdar
- Centre for Protein Science, Design and Engineering, Department of Biological Sciences, and Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India
| | - Samrat Mukhopadhyay
- Centre for Protein Science, Design and Engineering, Department of Biological Sciences, and Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India.
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20
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Antonets KS, Belousov MV, Belousova ME, Nizhnikov AA. The Gln3 Transcriptional Regulator of Saccharomyces cerevisiae Manifests Prion-Like Properties upon Overproduction. BIOCHEMISTRY (MOSCOW) 2019; 84:441-451. [DOI: 10.1134/s0006297919040126] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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21
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Nelson P, Masel J. Evolutionary Capacitance Emerges Spontaneously during Adaptation to Environmental Changes. Cell Rep 2018; 25:249-258. [DOI: 10.1016/j.celrep.2018.09.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 04/26/2018] [Accepted: 09/04/2018] [Indexed: 11/28/2022] Open
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22
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Jennings LK, Ahmed I, Munn AL, Carroll AR. Yeast-based screening of natural product extracts results in the identification of prion inhibitors from a marine sponge. Prion 2018; 12:234-244. [PMID: 30165789 PMCID: PMC6277187 DOI: 10.1080/19336896.2018.1513315] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/16/2018] [Accepted: 08/07/2018] [Indexed: 10/28/2022] Open
Abstract
One of the major medical challenges of the twenty-first century is the treatment of incurable and fatal neurodegenerative disorders caused by misfolded prion proteins. Since the discovery of these diseases a number of studies have been conducted to identify small molecules for their treatment, however to date no curative treatment is available. These studies can be highly expensive and time consuming, but more recent experimental approaches indicate a significant application for yeast prions in these studies. We therefore used yeast prions to optimize previous high-throughput methods for the cheaper, easier and more rapid screening of natural extracts. Through this approach we aimed to identify natural yeast-prion inhibitors that could be useful in the development of novel treatment strategies for neurodegenerative disorders. We screened 500 marine invertebrate extracts from temperate waters in Australia allowing the identification of yeast-prion inhibiting extracts. Through the bioassay-driven chemical investigation of an active Suberites sponge extract, a group of bromotyrosine derivatives were identified as potent yeast-prion inhibitors. This study outlines the importance of natural products and yeast prions as a first-stage screen for the identification of new chemically diverse and bioactive compounds.
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Affiliation(s)
- Laurence K. Jennings
- School of Environment and Science, Environmental Futures Research Institute, Griffith University (Gold Coast campus), Southport, QLD 4222, Australia
| | - Ishtiaq Ahmed
- School of Medical Science, Understanding Chronic Conditions Program, Menzies Health Institute Queensland, Griffith University (Gold Coast campus), Southport, QLD 4222, Australia
| | - Alan L. Munn
- School of Medical Science, Understanding Chronic Conditions Program, Menzies Health Institute Queensland, Griffith University (Gold Coast campus), Southport, QLD 4222, Australia
| | - Anthony R. Carroll
- School of Environment and Science, Environmental Futures Research Institute, Griffith University (Gold Coast campus), Southport, QLD 4222, Australia
- Griffith Institute for Drug Discovery, Griffith University (Brisbane Innovation Park), Nathan, QLD 4111, Australia
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23
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Chakravarty AK, Jarosz DF. More than Just a Phase: Prions at the Crossroads of Epigenetic Inheritance and Evolutionary Change. J Mol Biol 2018; 430:4607-4618. [PMID: 30031007 DOI: 10.1016/j.jmb.2018.07.017] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 07/08/2018] [Accepted: 07/16/2018] [Indexed: 12/11/2022]
Abstract
A central tenet of molecular biology is that heritable information is stored in nucleic acids. However, this paradigm has been overturned by a group of proteins called "prions." Prion proteins, many of which are intrinsically disordered, can adopt multiple conformations, at least one of which has the capacity to self-template. This unusual folding landscape drives a form of extreme epigenetic inheritance that can be stable through both mitotic and meiotic cell divisions. Although the first prion discovered-mammalian PrP-is the causative agent of debilitating neuropathies, many additional prions have now been identified that are not obviously detrimental and can even be adaptive. Intrinsically disordered regions, which endow proteins with the bulk property of "phase-separation," can also be drivers of prion formation. Indeed, many protein domains that promote phase separation have been described as prion-like. In this review, we describe how prions lie at the crossroads of phase separation, epigenetic inheritance, and evolutionary adaptation.
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Affiliation(s)
- Anupam K Chakravarty
- Department of Chemical and Systems Biology, Stanford University, 269 Campus Drive, Stanford, CA 94305, United States
| | - Daniel F Jarosz
- Department of Chemical and Systems Biology, Stanford University, 269 Campus Drive, Stanford, CA 94305, United States; Department of Developmental Biology, Stanford University, 269 Campus Drive, Stanford, CA 94305, United States.
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24
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Lian HY, Lin KW, Yang C, Cai P. Generation and propagation of yeast prion [URE3] are elevated under electromagnetic field. Cell Stress Chaperones 2018; 23:581-594. [PMID: 29214607 PMCID: PMC6045541 DOI: 10.1007/s12192-017-0867-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 11/24/2017] [Accepted: 11/27/2017] [Indexed: 12/13/2022] Open
Abstract
In this study, we studied the effect of 2.0 GHz radio frequency electromagnetic field (RF-EMF) and 50 Hz extremely low frequency electromagnetic field (ELF-EMF) exposure on prion generation and propagation using two budding yeast strains, NT64C and SB34, as model organisms. Under exposure to RF-EMF or ELF-EMF, the de novo generation and propagation of yeast prions [URE3] were elevated in both strains. The elevation increased over time, and the effects of ELF-EMF occurred in a dose-dependent manner. The transcription and expression levels of the molecular chaperones Hsp104, Hsp70-Ssa1/2, and Hsp40-Ydj1 were not statistically significantly changed after exposure. Furthermore, the levels of ROS, as well as the activities of superoxide dismutase (SOD) and catalase (CAT), were significantly elevated after short-term, but not long-term exposure. This work demonstrated for the first time that EMF exposure could elevate the de novo generation and propagation of yeast prions and supports the hypothesis that ROS may play a role in the effects of EMF on protein misfolding. The effects of EMF on protein folding and ROS levels may mediate the broad effects of EMF on cell function.
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Affiliation(s)
- Hui-Yong Lian
- Xiamen Key Laboratory of Physical Environment, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, People's Republic of China.
- College of Life Sciences and Ecology, Hainan Tropical Ocean University, 1 Yucai Road, Sanya, 572022, People's Republic of China.
| | - Kang-Wei Lin
- Xiamen Key Laboratory of Physical Environment, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, People's Republic of China
- University of the Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, People's Republic of China
| | - Chuanjun Yang
- Xiamen Key Laboratory of Physical Environment, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, People's Republic of China
| | - Peng Cai
- Xiamen Key Laboratory of Physical Environment, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, People's Republic of China.
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25
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Astor MT, Kamiya E, Sporn ZA, Berger SE, Hines JK. Variant-specific and reciprocal Hsp40 functions in Hsp104-mediated prion elimination. Mol Microbiol 2018; 109:41-62. [PMID: 29633387 PMCID: PMC6099457 DOI: 10.1111/mmi.13966] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2018] [Indexed: 01/02/2023]
Abstract
The amyloid-based prions of Saccharomyces cerevisiae are heritable aggregates of misfolded proteins, passed to daughter cells following fragmentation by molecular chaperones including the J-protein Sis1, Hsp70 and Hsp104. Overexpression of Hsp104 efficiently cures cell populations of the prion [PSI+ ] by an alternative Sis1-dependent mechanism that is currently the subject of significant debate. Here, we broadly investigate the role of J-proteins in this process by determining the impact of amyloid polymorphisms (prion variants) on the ability of well-studied Sis1 constructs to compensate for Sis1 and ask whether any other S. cerevisiae cytosolic J-proteins are also required for this process. Our comprehensive screen, examining all 13 members of the yeast cytosolic/nuclear J-protein complement, uncovered significant variant-dependent genetic evidence for a role of Apj1 (antiprion DnaJ) in this process. For strong, but not weak [PSI+ ] variants, depletion of Apj1 inhibits Hsp104-mediated curing. Overexpression of either Apj1 or Sis1 enhances curing, while overexpression of Ydj1 completely blocks it. We also demonstrated that Sis1 was the only J-protein necessary for the propagation of at least two weak [PSI+ ] variants and no J-protein alteration, or even combination of alterations, affected the curing of weak [PSI+ ] variants, suggesting the possibility of biochemically distinct, variant-specific Hsp104-mediated curing mechanisms.
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Affiliation(s)
| | - Erina Kamiya
- Department of ChemistryLafayette CollegeEastonPAUSA
| | - Zachary A. Sporn
- Department of ChemistryLafayette CollegeEastonPAUSA
- Present address:
Geisinger Commonwealth School of MedicineScrantonPAUSA
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Verma M, Girdhar A, Patel B, Ganguly NK, Kukreti R, Taneja V. Q-Rich Yeast Prion [ PSI+] Accelerates Aggregation of Transthyretin, a Non-Q-Rich Human Protein. Front Mol Neurosci 2018; 11:75. [PMID: 29593496 PMCID: PMC5859028 DOI: 10.3389/fnmol.2018.00075] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 02/26/2018] [Indexed: 11/30/2022] Open
Abstract
Interactions amongst different amyloid proteins have been proposed as a probable mechanism of aggregation and thus an important risk factor for the onset as well as progression of various neurodegenerative disorders including Alzheimer's, Parkinson's, Huntington's, and Amyotrophic Lateral Sclerosis. Evidences suggest that transthyretin (TTR), a plasma protein associated with transthyretin amyloidosis or familial polyneuropathy (FAP) interacts with heterologous amyloid proteins including amyloid beta and islet amyloid polypeptide. In addition, recent clinical studies have revealed the presence of systemic polyneuropathy associated with FAP mutations in patients with spinocerebral ataxia, amyotrophic lateral sclerosis, and new familial systematic prion disease. Hence, it is important to investigate the interactions amongst different amyloid proteins to gain better insight into the pathology of amyloid disorders. Yeast has been an excellent model system to study interaction/ cross-seeding between heterologous amyloid proteins, more because of presence of endogenous yeast prions. Here, we examined interactions of non-glutamine (non-Q)-rich transthyretin, with glutamine (Q)-rich yeast prion protein Sup35. We established aggregation of an engineered double (F87M/L110M) mutant M-TTR-GFP in yeast. This mutant is monomeric and readily formed aggregates compared to WT-TTR-GFP in yeast at acidic pH. Interestingly, aggregation of M-TTR-GFP was significantly enhanced in presence of [PSI+], an endogenous prion form of Sup35. Different variants of [PSI+] seeded M-TTR-GFP with different efficiencies and curing of [PSI+] (losing the prion form) in these strains reduced aggregation. Moreover, overexpression of prion domain of Sup35 fused to RFP (NM-RFP) also increased M-TTR-GFP aggregation. M-TTR-GFP and NM-RFP aggregates co-localized in perivacuolar and juxtranuclear region. Sup35 protein was even immunocaptured in M-TTR-GFP aggregates. However, M-TTR-GFP overexpression did not induce Sup35 aggregation. Thus, it appears to be a unidirectional interaction between these two amyloid proteins. However, no affect on M-TTR-GFP aggregation was observed due to another yeast prion, [PIN+]. Our findings thus show the molecular interaction of transthyretin with yeast prion and support that sequence similarity is not the prime requirement for heterologous amyloid interactions.
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Affiliation(s)
- Meenakshi Verma
- Genomics and Molecular Medicine, Institute of Genomics and Integrative Biology, Council of Scientific & Industrial Research (CSIR), New Delhi, India.,Department of Research, Sir Ganga Ram Hospital, New Delhi, India
| | | | - Basant Patel
- Department of Biotechnology, IIT Hyderabad, New Delhi, India
| | - Nirmal K Ganguly
- Department of Research, Sir Ganga Ram Hospital, New Delhi, India
| | - Ritushree Kukreti
- Genomics and Molecular Medicine, Institute of Genomics and Integrative Biology, Council of Scientific & Industrial Research (CSIR), New Delhi, India
| | - Vibha Taneja
- Department of Research, Sir Ganga Ram Hospital, New Delhi, India
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Abstract
Prion-like proteins overlap with intrinsically disordered and low-complexity sequence families. These proteins are widespread, especially among mRNA-binding proteins. A salient feature of these proteins is the ability to form protein assemblies with distinct biophysical and functional properties. While prion-like proteins are involved in myriad of cellular processes, we propose potential roles for protein assemblies in regulated protein synthesis. Since proteins are the ultimate functional output of gene expression, when, where, and how much of a particular protein is made dictates the functional state of a cell. Recent finding suggests that the prion-like proteins offer unique advantages in translation regulation and also raises questions regarding formation and regulation of protein assemblies.
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Affiliation(s)
- Liying Li
- Stowers Institute for Medical Research, 1000E 50(th) Street, Kansas City, MO 64110, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, Kansas 66160, USA
| | - J P McGinnis
- Stowers Institute for Medical Research, 1000E 50(th) Street, Kansas City, MO 64110, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, Kansas 66160, USA
| | - Kausik Si
- Stowers Institute for Medical Research, 1000E 50(th) Street, Kansas City, MO 64110, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, Kansas 66160, USA.
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Franzmann TM, Jahnel M, Pozniakovsky A, Mahamid J, Holehouse AS, Nüske E, Richter D, Baumeister W, Grill SW, Pappu RV, Hyman AA, Alberti S. Phase separation of a yeast prion protein promotes cellular fitness. Science 2018. [DOI: 10.1126/science.aao5654 eaao5654] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Biophysical responses of proteins to stress
Much recent work has focused on liquid-liquid phase separation as a cellular response to changing physicochemical conditions. Because phase separation responds critically to small changes in conditions such as pH, temperature, or salt, it is in principle an ideal way for a cell to measure and respond to changes in the environment. Small pH changes could, for instance, induce phase separation of compartments that store, protect, or inactivate proteins. Franzmann
et al.
used the yeast translation termination factor Sup35 as a model for a phase separation–induced stress response. Lowering the pH induced liquid-liquid phase separation of Sup35. The resulting liquid compartments subsequently hardened into gels, which sequestered the termination factor. Raising the pH triggered dissolution of the gels, concomitant with translation restart. Protecting Sup35 in gels could provide a fitness advantage to recovering yeast cells that must restart the translation machinery after stress.
Science
, this issue p.
eaao5654
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Affiliation(s)
- Titus M. Franzmann
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Marcus Jahnel
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
- Biotec, Technische Universität Dresden, Tatzberg 47/48, 01307 Dresden, Germany
| | - Andrei Pozniakovsky
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Julia Mahamid
- European Molecular Biology Laboratory, Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Alex S. Holehouse
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Elisabeth Nüske
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Doris Richter
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Wolfgang Baumeister
- Max Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Stephan W. Grill
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
- Biotec, Technische Universität Dresden, Tatzberg 47/48, 01307 Dresden, Germany
| | - Rohit V. Pappu
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Anthony A. Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
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29
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Franzmann TM, Jahnel M, Pozniakovsky A, Mahamid J, Holehouse AS, Nüske E, Richter D, Baumeister W, Grill SW, Pappu RV, Hyman AA, Alberti S. Phase separation of a yeast prion protein promotes cellular fitness. Science 2018; 359:359/6371/eaao5654. [DOI: 10.1126/science.aao5654] [Citation(s) in RCA: 395] [Impact Index Per Article: 65.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 11/27/2017] [Indexed: 12/13/2022]
Abstract
Despite the important role of prion domains in neurodegenerative disease, their physiological function has remained enigmatic. Previous work with yeast prions has defined prion domains as sequences that form self-propagating aggregates. Here, we uncovered an unexpected function of the canonical yeast prion protein Sup35. In stressed conditions, Sup35 formed protective gels via pH-regulated liquid-like phase separation followed by gelation. Phase separation was mediated by the N-terminal prion domain and regulated by the adjacent pH sensor domain. Phase separation promoted yeast cell survival by rescuing the essential Sup35 translation factor from stress-induced damage. Thus, prion-like domains represent conserved environmental stress sensors that facilitate rapid adaptation in unstable environments by modifying protein phase behavior.
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Abstract
The field described as 'epigenetics' has captured the imagination of scientists and the lay public. Advances in our understanding of chromatin and gene regulatory mechanisms have had impact on drug development, fueling excitement in the lay public about the prospects of applying this knowledge to address health issues. However, when describing these scientific advances as 'epigenetic', we encounter the problem that this term means different things to different people, starting within the scientific community and amplified in the popular press. To help researchers understand some of the misconceptions in the field and to communicate the science accurately to each other and the lay audience, here we review the basis for many of the assumptions made about what are currently referred to as epigenetic processes.
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31
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Nizhnikov AA, Antonets KS, Bondarev SA, Inge-Vechtomov SG, Derkatch IL. Prions, amyloids, and RNA: Pieces of a puzzle. Prion 2017; 10:182-206. [PMID: 27248002 DOI: 10.1080/19336896.2016.1181253] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Amyloids are protein aggregates consisting of fibrils rich in β-sheets. Growth of amyloid fibrils occurs by the addition of protein molecules to the tip of an aggregate with a concurrent change of a conformation. Thus, amyloids are self-propagating protein conformations. In certain cases these conformations are transmissible / infectious; they are known as prions. Initially, amyloids were discovered as pathological extracellular deposits occurring in different tissues and organs. To date, amyloids and prions have been associated with over 30 incurable diseases in humans and animals. However, a number of recent studies demonstrate that amyloids are also functionally involved in a variety of biological processes, from biofilm formation by bacteria, to long-term memory in animals. Interestingly, amyloid-forming proteins are highly overrepresented among cellular factors engaged in all stages of mRNA life cycle: from transcription and translation, to storage and degradation. Here we review rapidly accumulating data on functional and pathogenic amyloids associated with mRNA processing, and discuss possible significance of prion and amyloid networks in the modulation of key cellular functions.
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Affiliation(s)
- Anton A Nizhnikov
- a Dept. of Genetics and Biotechnology , St. Petersburg State University , St. Petersburg , Russia.,b Vavilov Institute of General Genetics of the Russian Academy of Sciences, St. Petersburg Branch , St. Petersburg , Russia.,c All-Russia Research Institute for Agricultural Microbiology , St. Petersburg , Russia
| | - Kirill S Antonets
- a Dept. of Genetics and Biotechnology , St. Petersburg State University , St. Petersburg , Russia.,b Vavilov Institute of General Genetics of the Russian Academy of Sciences, St. Petersburg Branch , St. Petersburg , Russia
| | - Stanislav A Bondarev
- a Dept. of Genetics and Biotechnology , St. Petersburg State University , St. Petersburg , Russia
| | - Sergey G Inge-Vechtomov
- a Dept. of Genetics and Biotechnology , St. Petersburg State University , St. Petersburg , Russia.,b Vavilov Institute of General Genetics of the Russian Academy of Sciences, St. Petersburg Branch , St. Petersburg , Russia
| | - Irina L Derkatch
- d Department of Neuroscience , College of Physicians and Surgeons of Columbia University, Columbia University , New York , NY , USA
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Antonets KS, Kliver SF, Polev DE, Shuvalova AR, Andreeva EA, Inge-Vechtomov SG, Nizhnikov AA. Distinct mechanisms of phenotypic effects of inactivation and prionization of Swi1 protein in Saccharomyces cerevisiae. BIOCHEMISTRY (MOSCOW) 2017; 82:1147-1157. [DOI: 10.1134/s0006297917100078] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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33
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Overexpression of the essential Sis1 chaperone reduces TDP-43 effects on toxicity and proteolysis. PLoS Genet 2017; 13:e1006805. [PMID: 28531192 PMCID: PMC5460882 DOI: 10.1371/journal.pgen.1006805] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 06/06/2017] [Accepted: 05/05/2017] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease characterized by selective loss of motor neurons with inclusions frequently containing the RNA/DNA binding protein TDP-43. Using a yeast model of ALS exhibiting TDP-43 dependent toxicity, we now show that TDP-43 overexpression dramatically alters cell shape and reduces ubiquitin dependent proteolysis of a reporter construct. Furthermore, we show that an excess of the Hsp40 chaperone, Sis1, reduced TDP-43’s effect on toxicity, cell shape and proteolysis. The strength of these effects was influenced by the presence of the endogenous yeast prion, [PIN+]. Although overexpression of Sis1 altered the TDP-43 aggregation pattern, we did not detect physical association of Sis1 with TDP-43, suggesting the possibility of indirect effects on TDP-43 aggregation. Furthermore, overexpression of the mammalian Sis1 homologue, DNAJB1, relieves TDP-43 mediated toxicity in primary rodent cortical neurons, suggesting that Sis1 and its homologues may have neuroprotective effects in ALS. Many neurodegenerative diseases are associated with aggregation of specific proteins. Thus we are interested in factors that influence the aggregation and how the aggregated proteins are associated with pathology. Here, we study a protein called TDP-43 that is frequently aggregated in the neurons of patients with amyotrophic lateral sclerosis (ALS). TDP-43 aggregates and is toxic when expressed in yeast, providing a useful model for ALS. Remarkably, a protein that modified TDP-43 toxicity in yeast successfully predicted a new ALS susceptibility gene in humans. We now report a new modifier of TDP-43 toxicity, Sis1. We show that expression of TDP-43 in yeast inhibits degradation of damaged protein, while overexpression of Sis1 restores degradation. Thus suggests a link between protein degradation and TDP-43 toxicity. Furthermore we show that a mammalian protein similar to Sis1 reduces TDP-43 toxicity in primary rodent neurons. This identifies the mammalian Sis1-like gene as a new ALS therapeutic target and possible susceptibility gene.
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34
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Antonets KS, Sargsyan HM, Nizhnikov AA. A Glutamine/Asparagine-Rich Fragment of Gln3, but not the Full-Length Protein, Aggregates in Saccharomyces cerevisiae. BIOCHEMISTRY (MOSCOW) 2017; 81:407-13. [PMID: 27293098 DOI: 10.1134/s0006297916040118] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The amino acid sequence of protein Gln3 in yeast Saccharomyces cerevisiae has a region enriched with Gln (Q) and Asn (N) residues. In this study, we analyzed the effects of overexpression of Gln3 and its Q/N-rich fragment fused with yellow fluorescent protein (YFP). Being overexpressed, full-length Gln3-YFP does not form aggregates, inhibits vegetative growth, and demonstrates nuclear localization, while the Q/N-rich fragment (Gln3QN) fused with YFP forms aggregates that do not colocalize with the nucleus and do not affect growth of the cells. Although detergent-resistant aggregates of Gln3QN are formed in the absence of yeast prions, the aggregation of Gln3QN significantly increases in the presence of [PIN(+)] prion, while in the presence of two prions, [PSI(+)] and [PIN(+)], the percentage of cells with Gln3QN aggregates is significantly lower than in the strain bearing only [PIN(+)]. Data on colocalization demonstrate that this effect is mediated by interaction between Gln3QN aggregates and [PSI(+)] and [PIN(+)] prions.
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Affiliation(s)
- K S Antonets
- St. Petersburg State University, Department of Genetics and Biotechnology, St. Petersburg, 199034, Russia.
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35
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Tikhodeyev ON, Tarasov OV, Bondarev SA. Allelic variants of hereditary prions: The bimodularity principle. Prion 2017; 11:4-24. [PMID: 28281926 PMCID: PMC5360123 DOI: 10.1080/19336896.2017.1283463] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 01/04/2017] [Accepted: 01/10/2017] [Indexed: 12/26/2022] Open
Abstract
Modern biology requires modern genetic concepts equally valid for all discovered mechanisms of inheritance, either "canonical" (mediated by DNA sequences) or epigenetic. Applying basic genetic terms such as "gene" and "allele" to protein hereditary factors is one of the necessary steps toward these concepts. The basic idea that different variants of the same prion protein can be considered as alleles has been previously proposed by Chernoff and Tuite. In this paper, the notion of prion allele is further developed. We propose the idea that any prion allele is a bimodular hereditary system that depends on a certain DNA sequence (DNA determinant) and a certain epigenetic mark (epigenetic determinant). Alteration of any of these 2 determinants may lead to establishment of a new prion allele. The bimodularity principle is valid not only for hereditary prions; it seems to be universal for any epigenetic hereditary factor.
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Affiliation(s)
- Oleg N. Tikhodeyev
- Department of Genetics & Biotechnology, Saint-Petersburg State University, Saint-Petersburg, Russia
| | - Oleg V. Tarasov
- Department of Genetics & Biotechnology, Saint-Petersburg State University, Saint-Petersburg, Russia
- Saint-Petersburg Scientific Center of RAS, Saint-Petersburg, Russia
| | - Stanislav A. Bondarev
- Department of Genetics & Biotechnology, Saint-Petersburg State University, Saint-Petersburg, Russia
- The Laboratory of Amyloid Biology, Saint-Petersburg State University, Saint-Petersburg, Russia
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36
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Antonets KS, Volkov KV, Maltseva AL, Arshakian LM, Galkin AP, Nizhnikov AA. Proteomic Analysis of Escherichia coli Protein Fractions Resistant to Solubilization by Ionic Detergents. BIOCHEMISTRY (MOSCOW) 2016; 81:34-46. [PMID: 26885581 DOI: 10.1134/s0006297916010041] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Amyloids are protein fibrils adopting structure of cross-beta spine exhibiting either pathogenic or functionally significant properties. In prokaryotes, there are several groups of functional amyloids; however, all of them were identified by specialized approaches that do not reveal all cellular amyloids. Here, using our previously developed PSIA (Proteomic Screening and Identification of Amyloids) approach, we have conducted a proteomic screening for candidates for novel amyloid-forming proteins in Escherichia coli as one of the most important model organisms and biotechnological objects. As a result, we identified 61 proteins in fractions resistant to treatment with ionic detergents. We found that a fraction of proteins bearing potentially amyloidogenic regions predicted by bioinformatics algorithms was 3-5-fold more abundant among the identified proteins compared to those observed in the entire E. coli proteome. Almost all identified proteins contained potentially amyloidogenic regions, and four of them (BcsC, MukB, YfbK, and YghJ) have asparagine- and glutamine-rich regions underlying a crucial feature of many known amyloids. In this study, we demonstrate for the first time that at the proteome level there is a correlation between experimentally demonstrated detergent-resistance of proteins and potentially amyloidogenic regions predicted by bioinformatics approaches. The data obtained enable further comprehensive characterization of entirety of amyloids (or amyloidome) in bacterial cells.
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Affiliation(s)
- K S Antonets
- St. Petersburg State University, Department of Genetics and Biotechnology, St. Petersburg, 199034, 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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38
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Affiliation(s)
- Kausik Si
- Stowers Institute for Medical Research, Kansas City, Missouri 64110;
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39
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Moosavi B, Mousavi B, Yang GF. Actin, Membrane Trafficking and the Control of Prion Induction, Propagation and Transmission in Yeast. Traffic 2015; 17:5-20. [PMID: 26503767 DOI: 10.1111/tra.12344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 10/23/2015] [Accepted: 10/23/2015] [Indexed: 12/16/2022]
Abstract
The model eukaryotic yeast Saccharomyces cerevisiae has proven a useful model system in which prion biogenesis and elimination are studied. Several yeast prions exist in budding yeast and a number of studies now suggest that these alternate protein conformations may play important roles in the cell. During the last few years cellular factors affecting prion induction, propagation and elimination have been identified. Amongst these, proteins involved in the regulation of the actin cytoskeleton and dynamic membrane processes such as endocytosis have been found to play a critical role not only in facilitating de novo prion formation but also in prion propagation. Here we briefly review prion formation and maintenance with special attention given to the cellular processes that require the functionality of the actin cytoskeleton.
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Affiliation(s)
- Behrooz Moosavi
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, P.R. China
| | - Bibimaryam Mousavi
- Laboratory of Organometallics, Catalysis and Ordered Materials, State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan, P.R. China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, P.R. China
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40
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Troisi EM, Rockman ME, Nguyen PP, Oliver EE, Hines JK. Swa2, the yeast homolog of mammalian auxilin, is specifically required for the propagation of the prion variant [URE3-1]. Mol Microbiol 2015; 97:926-41. [PMID: 26031938 PMCID: PMC4689296 DOI: 10.1111/mmi.13076] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/31/2015] [Indexed: 01/09/2023]
Abstract
Yeast prions require a core set of chaperone proteins including Sis1, Hsp70 and Hsp104 to generate new amyloid templates for stable propagation, yet emerging studies indicate that propagation of some prions requires additional chaperone activities, demonstrating chaperone specificity beyond the common amyloid requirements. To comprehensively assess such prion-specific requirements for the propagation of the [URE3] prion variant [URE3-1], we screened 12 yeast cytosolic J-proteins, and here we report a novel role for the J-protein Swa2/Aux1. Swa2 is the sole yeast homolog of the mammalian protein auxilin, which, like Swa2, functions in vesicle-mediated endocytosis by disassembling the structural lattice formed by the protein clathrin. We found that, in addition to Sis1, [URE3-1] is specifically dependent upon Swa2, but not on any of the 11 other J-proteins. Further, we show that [URE3-1] propagation requires both a functional J-domain and the tetratricopeptide repeat (TPR) domain, but surprisingly does not require Swa2-clathrin binding. Because the J-domain of Swa2 can be replaced with the J-domains of other proteins, our data strongly suggest that prion-chaperone specificity arises from the Swa2 TPR domain and supports a model where Swa2 acts through Hsp70, most likely to provide additional access points for Hsp104 to promote prion template generation.
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Affiliation(s)
| | | | - Phil P Nguyen
- Department of Chemistry, Lafayette College, Easton, PA, USA
| | - Emily E Oliver
- Department of Chemistry, Lafayette College, Easton, PA, USA
| | - Justin K Hines
- Department of Chemistry, Lafayette College, Easton, PA, USA
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41
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Arslan F, Hong JY, Kanneganti V, Park SK, Liebman SW. Heterologous aggregates promote de novo prion appearance via more than one mechanism. PLoS Genet 2015; 11:e1004814. [PMID: 25568955 PMCID: PMC4287349 DOI: 10.1371/journal.pgen.1004814] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 10/09/2014] [Indexed: 12/12/2022] Open
Abstract
Prions are self-perpetuating conformational variants of particular proteins. In yeast, prions cause heritable phenotypic traits. Most known yeast prions contain a glutamine (Q)/asparagine (N)-rich region in their prion domains. [PSI+], the prion form of Sup35, appears de novo at dramatically enhanced rates following transient overproduction of Sup35 in the presence of [PIN+], the prion form of Rnq1. Here, we establish the temporal de novo appearance of Sup35 aggregates during such overexpression in relation to other cellular proteins. Fluorescently-labeled Sup35 initially forms one or a few dots when overexpressed in [PIN+] cells. One of the dots is perivacuolar, colocalizes with the aggregated Rnq1 dot and grows into peripheral rings/lines, some of which also colocalize with Rnq1. Sup35 dots that are not near the vacuole do not always colocalize with Rnq1 and disappear by the time rings start to grow. Bimolecular fluorescence complementation failed to detect any interaction between Sup35-VN and Rnq1-VC in [PSI+][PIN+] cells. In contrast, all Sup35 aggregates, whether newly induced or in established [PSI+], completely colocalize with the molecular chaperones Hsp104, Sis1, Ssa1 and eukaryotic release factor Sup45. In the absence of [PIN+], overexpressed aggregating proteins such as the Q/N-rich Pin4C or the non-Q/N-rich Mod5 can also promote the de novo appearance of [PSI+]. Similar to Rnq1, overexpressed Pin4C transiently colocalizes with newly appearing Sup35 aggregates. However, no interaction was detected between Mod5 and Sup35 during [PSI+] induction in the absence of [PIN+]. While the colocalization of Sup35 and aggregates of Rnq1 or Pin4C are consistent with the model that the heterologous aggregates cross-seed the de novo appearance of [PSI+], the lack of interaction between Mod5 and Sup35 leaves open the possibility of other mechanisms. We also show that Hsp104 is required in the de novo appearance of [PSI+] aggregates in a [PIN+]-independent pathway. Certain proteins can misfold into β-sheet-rich, self-seeding aggregates. Such proteins appear to be associated with neurodegenerative diseases such as prion, Alzheimer's and Parkinson's. Yeast prions also misfold into self-seeding aggregates and provide a good model to study how these rogue polymers first appear. De novo prion appearance can be made very frequent in yeast by transient overexpression of the prion protein in the presence of heterologous prions or prion-like aggregates. Here, we show that the aggregates of one such newly induced prion are initially formed in a dot-like structure near the vacuole. These dots then grow into rings at the periphery of the cell prior to becoming smaller rings surrounding the vacuole and maturing into the characteristic heritable prion tiny dots found throughout the cytoplasm. We found considerable colocalization of two heterologous prion/prion-like aggregates with the newly appearing prion protein aggregates, which is consistent with the prevalent model that existing prion aggregates can cross-seed the de novo aggregation of a heterologous prion protein. However, we failed to find any physical interaction between another heterologous aggregating protein and the newly appearing prion aggregates it stimulated to appear, which is inconsistent with cross-seeding.
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Affiliation(s)
- Fatih Arslan
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada, United States of America
| | - Joo Y. Hong
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada, United States of America
| | - Vydehi Kanneganti
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada, United States of America
| | - Sei-Kyoung Park
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada, United States of America
| | - Susan W. Liebman
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada, United States of America
- * E-mail:
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Distinct amino acid compositional requirements for formation and maintenance of the [PSI⁺] prion in yeast. Mol Cell Biol 2014; 35:899-911. [PMID: 25547291 DOI: 10.1128/mcb.01020-14] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Multiple yeast prions have been identified that result from the structural conversion of proteins into a self-propagating amyloid form. Amyloid-based prion activity in yeast requires a series of discrete steps. First, the prion protein must form an amyloid nucleus that can recruit and structurally convert additional soluble proteins. Subsequently, maintenance of the prion during cell division requires fragmentation of these aggregates to create new heritable propagons. For the Saccharomyces cerevisiae prion protein Sup35, these different activities are encoded by different regions of the Sup35 prion domain. An N-terminal glutamine/asparagine-rich nucleation domain is required for nucleation and fiber growth, while an adjacent oligopeptide repeat domain is largely dispensable for prion nucleation and fiber growth but is required for chaperone-dependent prion maintenance. Although prion activity of glutamine/asparagine-rich proteins is predominantly determined by amino acid composition, the nucleation and oligopeptide repeat domains of Sup35 have distinct compositional requirements. Here, we quantitatively define these compositional requirements in vivo. We show that aromatic residues strongly promote both prion formation and chaperone-dependent prion maintenance. In contrast, nonaromatic hydrophobic residues strongly promote prion formation but inhibit prion propagation. These results provide insight into why some aggregation-prone proteins are unable to propagate as prions.
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43
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Nizhnikov AA, Antonets KS, Inge-Vechtomov SG, Derkatch IL. Modulation of efficiency of translation termination in Saccharomyces cerevisiae. Prion 2014; 8:247-60. [PMID: 25486049 DOI: 10.4161/pri.29851] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Nonsense suppression is a readthrough of premature termination codons. It typically occurs either due to the recognition of stop codons by tRNAs with mutant anticodons, or due to a decrease in the fidelity of translation termination. In the latter case, suppressors usually promote the readthrough of different types of nonsense codons and are thus called omnipotent nonsense suppressors. Omnipotent nonsense suppressors were identified in yeast Saccharomyces cerevisiae in 1960s, and most of subsequent studies were performed in this model organism. Initially, omnipotent suppressors were localized by genetic analysis to different protein- and RNA-encoding genes, mostly the components of translational machinery. Later, nonsense suppression was found to be caused not only by genomic mutations, but also by epigenetic elements, prions. Prions are self-perpetuating protein conformations usually manifested by infectious protein aggregates. Modulation of translational accuracy by prions reflects changes in the activity of their structural proteins involved in different aspects of protein synthesis. Overall, nonsense suppression can be seen as a "phenotypic mirror" of events affecting the accuracy of the translational machine. However, the range of proteins participating in the modulation of translation termination fidelity is not fully elucidated. Recently, the list has been expanded significantly by findings that revealed a number of weak genetic and epigenetic nonsense suppressors, the effect of which can be detected only in specific genetic backgrounds. This review summarizes the data on the nonsense suppressors decreasing the fidelity of translation termination in S. cerevisiae, and discusses the functional significance of the modulation of translational accuracy.
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Affiliation(s)
- Anton A Nizhnikov
- a Department of Genetics and Biotechnology ; St. Petersburg State University ; St. Petersburg , Russia
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44
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Luckgei N, Schütz AK, Habenstein B, Bousset L, Sourigues Y, Melki R, Meier BH, Böckmann A. Solid-state NMR sequential assignments of the amyloid core of Sup35pNM. BIOMOLECULAR NMR ASSIGNMENTS 2014; 8:365-370. [PMID: 23934139 DOI: 10.1007/s12104-013-9518-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 08/01/2013] [Indexed: 06/02/2023]
Abstract
Sup35pNM represents the N-terminal and middle (M) domains of the yeast Saccharomyces cerevisiae prion Sup35p. This fragment is commonly used for structural and functional studies of Sup35p. We here present a solid-state NMR study of fibrils formed by this fragment and show that sequential assignments can be obtained for the rigid and well-ordered parts of the protein using 3D spectroscopy. We describe in detail the sequential assignment of the 22 residues yielding strong, narrow signals with chemical shifts that correspond mostly to β-sheet secondary-structured amino acids that form the fibril core.
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Affiliation(s)
- Nina Luckgei
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS/Université de Lyon, 1, 7 passage du Vercors, 69367, Lyon, France
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45
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Schütz AK, Habenstein B, Luckgei N, Bousset L, Sourigues Y, Nielsen AB, Melki R, Böckmann A, Meier BH. Solid-state NMR sequential assignments of the amyloid core of full-length Sup35p. BIOMOLECULAR NMR ASSIGNMENTS 2014; 8:349-356. [PMID: 23943018 DOI: 10.1007/s12104-013-9515-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 08/01/2013] [Indexed: 06/02/2023]
Abstract
Sup35p is a yeast prion and is responsible for the [PSI(+)] trait in Saccharomyces cerevisiae. With 685 amino acids, full-length soluble and fibrillar Sup35p are challenging targets for structural biology as they cannot be investigated by X-ray crystallography or NMR in solution. We present solid-state NMR studies of fibrils formed by the full-length Sup35 protein. We detect an ordered and rigid core of the protein that gives rise to narrow and strong peaks, while large parts of the protein show either static disorder or dynamics on time scales which interfere with dipolar polarization transfer or shorten the coherence lifetime. Thus, only a small subset of resonances is observed in 3D spectra. Here we describe in detail the sequential assignments of the 22 residues for which resonances are observed in 3D spectra: their chemical shifts mostly corresponding to β-sheet secondary structure. We suspect that these residues form the amyloid core of the fibril.
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Affiliation(s)
- Anne K Schütz
- Physical Chemistry, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093, Zurich, Switzerland
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46
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Yang Z, Stone DE, Liebman SW. Prion-promoted phosphorylation of heterologous amyloid is coupled with ubiquitin-proteasome system inhibition and toxicity. Mol Microbiol 2014; 93:1043-56. [PMID: 25039275 DOI: 10.1111/mmi.12716] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2014] [Indexed: 11/30/2022]
Abstract
Many neurodegenerative diseases are associated with conversion of a soluble protein into amyloid deposits, but how this is connected to toxicity remains largely unknown. Here, we explore mechanisms of amyloid associated toxicity using yeast. [PIN(+)], the prion form of the Q/N-rich Rnq1 protein, was known to enhance aggregation of heterologous proteins, including the overexpressed Q/N-rich amyloid forming domain of Pin4 (Pin4C), and Pin4C aggregates were known to attract chaperones, including Sis1. Here we show that in [PIN(+)] but not [pin(-)] cells, overexpression of Pin4C is deadly and linked to hyperphosphorylation of aggregated Pin4C. Furthermore, Pin4C aggregation, hyperphosphorylation and toxicity are simultaneously reversed by Sis1 overexpression. Toxicity may result from proteasome overload because hyperphosphorylated Pin4C aggregation is associated with reduced degradation of a ubiquitin-protein degradation reporter. Finally, hyperphosphorylation of endogenous full-length Pin4 was also facilitated by [PIN(+)], revealing that a prion can regulate post-translational modification of another protein.
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Affiliation(s)
- Zi Yang
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA
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47
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Functional diversification of hsp40: distinct j-protein functional requirements for two prions allow for chaperone-dependent prion selection. PLoS Genet 2014; 10:e1004510. [PMID: 25058638 PMCID: PMC4109904 DOI: 10.1371/journal.pgen.1004510] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 05/30/2014] [Indexed: 01/22/2023] Open
Abstract
Yeast prions are heritable amyloid aggregates of functional yeast proteins; their propagation to subsequent cell generations is dependent upon fragmentation of prion protein aggregates by molecular chaperone proteins. Mounting evidence indicates the J-protein Sis1 may act as an amyloid specificity factor, recognizing prion and other amyloid aggregates and enabling Ssa and Hsp104 to act in prion fragmentation. Chaperone interactions with prions, however, can be affected by variations in amyloid-core structure resulting in distinct prion variants or ‘strains’. Our genetic analysis revealed that Sis1 domain requirements by distinct variants of [PSI+] are strongly dependent upon overall variant stability. Notably, multiple strong [PSI+] variants can be maintained by a minimal construct of Sis1 consisting of only the J-domain and glycine/phenylalanine-rich (G/F) region that was previously shown to be sufficient for cell viability and [RNQ+] prion propagation. In contrast, weak [PSI+] variants are lost under the same conditions but maintained by the expression of an Sis1 construct that lacks only the G/F region and cannot support [RNQ+] propagation, revealing mutually exclusive requirements for Sis1 function between these two prions. Prion loss is not due to [PSI+]-dependent toxicity or dependent upon a particular yeast genetic background. These observations necessitate that Sis1 must have at least two distinct functional roles that individual prions differentially require for propagation and which are localized to the glycine-rich domains of the Sis1. Based on these distinctions, Sis1 plasmid-shuffling in a [PSI+]/[RNQ+] strain permitted J-protein-dependent prion selection for either prion. We also found that, despite an initial report to the contrary, the human homolog of Sis1, Hdj1, is capable of [PSI+] prion propagation in place of Sis1. This conservation of function is also prion-variant dependent, indicating that only one of the two Sis1-prion functions may have been maintained in eukaryotic chaperone evolution. Multiple neurodegenerative disorders such as Alzheimer's, Parkinson's and Creutzfeldt-Jakob disease are associated with the accumulation of fibrous protein aggregates collectively termed ‘amyloid.’ In the baker's yeast Saccharomyces cerevisiae, multiple proteins form intracellular amyloid aggregates known as yeast prions. Yeast prions minimally require a core set of chaperone proteins for stable propagation in yeast, including the J-protein Sis1, which appears to be required for the propagation of all yeast prions and functioning similarly in each case. Here we present evidence which challenges the notion of a universal function for Sis1 in prion propagation and asserts instead that Sis1's function in the maintenance of at least two prions, [RNQ+] and [PSI+], is distinct and mutually exclusive for some prion variants. We also find that the human homolog of Sis1, called Hdj1, has retained the ability to support some, but not all yeast prions, indicating a partial conservation of function. Because yeast chaperones have the ability to both bind and fragment amyloids in vivo, further investigations into these prion-specific properties of Sis1 and Hdj1 will likely lead to new insights into the biological management of protein misfolding.
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48
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Singh N, Haldar S, Tripathi AK, Horback K, Wong J, Sharma D, Beserra A, Suda S, Anbalagan C, Dev S, Mukhopadhyay CK, Singh A. Brain iron homeostasis: from molecular mechanisms to clinical significance and therapeutic opportunities. Antioxid Redox Signal 2014; 20:1324-63. [PMID: 23815406 PMCID: PMC3935772 DOI: 10.1089/ars.2012.4931] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Iron has emerged as a significant cause of neurotoxicity in several neurodegenerative conditions, including Alzheimer's disease (AD), Parkinson's disease (PD), sporadic Creutzfeldt-Jakob disease (sCJD), and others. In some cases, the underlying cause of iron mis-metabolism is known, while in others, our understanding is, at best, incomplete. Recent evidence implicating key proteins involved in the pathogenesis of AD, PD, and sCJD in cellular iron metabolism suggests that imbalance of brain iron homeostasis associated with these disorders is a direct consequence of disease pathogenesis. A complete understanding of the molecular events leading to this phenotype is lacking partly because of the complex regulation of iron homeostasis within the brain. Since systemic organs and the brain share several iron regulatory mechanisms and iron-modulating proteins, dysfunction of a specific pathway or selective absence of iron-modulating protein(s) in systemic organs has provided important insights into the maintenance of iron homeostasis within the brain. Here, we review recent information on the regulation of iron uptake and utilization in systemic organs and within the complex environment of the brain, with particular emphasis on the underlying mechanisms leading to brain iron mis-metabolism in specific neurodegenerative conditions. Mouse models that have been instrumental in understanding systemic and brain disorders associated with iron mis-metabolism are also described, followed by current therapeutic strategies which are aimed at restoring brain iron homeostasis in different neurodegenerative conditions. We conclude by highlighting important gaps in our understanding of brain iron metabolism and mis-metabolism, particularly in the context of neurodegenerative disorders.
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Affiliation(s)
- Neena Singh
- 1 Department of Pathology, Case Western Reserve University , Cleveland, Ohio
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49
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Exploring the basis of [PIN(+)] variant differences in [PSI(+)] induction. J Mol Biol 2013; 425:3046-59. [PMID: 23770111 DOI: 10.1016/j.jmb.2013.06.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 05/07/2013] [Accepted: 06/07/2013] [Indexed: 01/12/2023]
Abstract
Certain soluble proteins can form amyloid-like prion aggregates. Indeed, the same protein can make different types of aggregates, called variants. Each variant is heritable because it attracts soluble homologous protein to join its aggregate, which is then broken into seeds (propagons) and transmitted to daughter cells. [PSI(+)] and [PIN(+)] are respectively prion forms of Sup35 and Rnq1. Curiously, [PIN(+)] enhances the de novo induction of [PSI(+)]. Different [PIN(+)] variants do this to dramatically different extents. Here, we investigate the mechanism underlying this effect. Consistent with a heterologous prion cross-seeding model, different [PIN(+)] variants preferentially promoted the appearance of different variants of [PSI(+)]. However, we did not detect this specificity in vitro. Also, [PIN(+)] variant cross-seeding efficiencies were not proportional to the level of Rnq1 coimmunocaptured with Sup35 or to the number of [PIN(+)] propagons characteristic for that variant. This leads us to propose that [PIN(+)] variants differ in the cross-seeding quality of their seeds, following the Sup35/[PIN(+)] binding step.
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50
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Oishi K, Kurahashi H, Pack CG, Sako Y, Nakamura Y. A bipolar functionality of Q/N-rich proteins: Lsm4 amyloid causes clearance of yeast prions. Microbiologyopen 2013; 2:415-30. [PMID: 23512891 PMCID: PMC3684756 DOI: 10.1002/mbo3.83] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Revised: 02/13/2013] [Accepted: 02/19/2013] [Indexed: 12/11/2022] Open
Abstract
Prions are epigenetic modifiers that cause partially loss-of-function phenotypes of the proteins in Saccharomyces cerevisiae. The molecular chaperone network that supports prion propagation in the cell has seen a great progress in the last decade. However, the cellular machinery to activate or deactivate the prion states remains an enigma, largely due to insufficient knowledge of prion-regulating factors. Here, we report that overexpression of a [PSI+]-inducible Q/N-rich protein, Lsm4, eliminates the three major prions [PSI+], [URE3], and [RNQ+]. Subcloning analysis revealed that the Q/N-rich region of Lsm4 is responsible for the prion loss. Lsm4 formed an amyloid in vivo, which seemed to play a crucial role in the prion elimination. Fluorescence correlation spectroscopy analysis revealed that in the course of the Lsm4-driven [PSI+] elimination, the [PSI+] aggregates undergo a size increase, which ultimately results in the formation of conspicuous foci in otherwise [psi−]-like mother cells. We also found that the antiprion activity is a general property of [PSI+]-inducible factors. These data provoked a novel “unified” model that explains both prion induction and elimination by a single scheme.
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Affiliation(s)
- Keita Oishi
- Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
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