1
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Auxier B, Zhang J, Marquez FR, Senden K, van den Heuvel J, Aanen DK, Snelders E, Debets AJM. The Narrow Footprint of Ancient Balancing Selection Revealed by Heterokaryon Incompatibility Genes in Aspergillus fumigatus. Mol Biol Evol 2024; 41:msae079. [PMID: 38652808 PMCID: PMC11138114 DOI: 10.1093/molbev/msae079] [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: 05/31/2023] [Revised: 04/03/2024] [Accepted: 04/11/2024] [Indexed: 04/25/2024] Open
Abstract
In fungi, fusion between individuals leads to localized cell death, a phenomenon termed heterokaryon incompatibility. Generally, the genes responsible for this incompatibility are observed to be under balancing selection resulting from negative frequency-dependent selection. Here, we assess this phenomenon in Aspergillus fumigatus, a human pathogenic fungus with a very low level of linkage disequilibrium as well as an extremely high crossover rate. Using complementation of auxotrophic mutations as an assay for hyphal compatibility, we screened sexual progeny for compatibility to identify genes involved in this process, called het genes. In total, 5/148 (3.4%) offspring were compatible with a parent and 166/2,142 (7.7%) sibling pairs were compatible, consistent with several segregating incompatibility loci. Genetic mapping identified five loci, four of which could be fine mapped to individual genes, of which we tested three through heterologous expression, confirming their causal relationship. Consistent with long-term balancing selection, trans-species polymorphisms were apparent across several sister species, as well as equal allele frequencies within A. fumigatus. Surprisingly, a sliding window genome-wide population-level analysis of an independent dataset did not show increased Tajima's D near these loci, in contrast to what is often found surrounding loci under balancing selection. Using available de novo assemblies, we show that these balanced polymorphisms are restricted to several hundred base pairs flanking the coding sequence. In addition to identifying the first het genes in an Aspergillus species, this work highlights the interaction of long-term balancing selection with rapid linkage disequilibrium decay.
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Affiliation(s)
- Ben Auxier
- Laboratory of Genetics, Wageningen University & Research, Wageningen, the Netherlands
| | - Jianhua Zhang
- Laboratory of Genetics, Wageningen University & Research, Wageningen, the Netherlands
| | | | - Kira Senden
- Laboratory of Genetics, Wageningen University & Research, Wageningen, the Netherlands
| | - Joost van den Heuvel
- Laboratory of Genetics, Wageningen University & Research, Wageningen, the Netherlands
| | - Duur K Aanen
- Laboratory of Genetics, Wageningen University & Research, Wageningen, the Netherlands
| | - Eveline Snelders
- Laboratory of Genetics, Wageningen University & Research, Wageningen, the Netherlands
| | - Alfons J M Debets
- Laboratory of Genetics, Wageningen University & Research, Wageningen, the Netherlands
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2
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Son M, Han S, Lee S. Prions in Microbes: The Least in the Most. J Microbiol 2023; 61:881-889. [PMID: 37668956 DOI: 10.1007/s12275-023-00070-4] [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: 06/29/2023] [Revised: 07/31/2023] [Accepted: 08/04/2023] [Indexed: 09/06/2023]
Abstract
Prions are infectious proteins that mostly replicate in self-propagating amyloid conformations (filamentous protein polymers) and consist of structurally altered normal soluble proteins. Prions can arise spontaneously in the cell without any clear reason and are generally considered fatal disease-causing agents that are only present in mammals. However, after the seminal discovery of two prions, [PSI+] and [URE3], in the eukaryotic model microorganism Saccharomyces cerevisiae, at least ten more prions have been discovered, and their biological and pathological effects on the host, molecular structure, and the relationship between prions and cellular components have been studied. In a filamentous fungus model, Podospora anserina, a vegetative incomparability-related [Het-s] prion that directly triggers cell death during anastomosis (hyphal fusion) was discovered. These prions in eukaryotic microbes have extended our understanding to overcome most fatal human prion/amyloid diseases. A prokaryotic microorganism (Clostridium botulinum) was reported to have a prion analog. The transcriptional regulators of C. botulinum-Rho can be converted into the self-replicating prion form ([RHO-X-C+]), which may affect global transcription. Here, we outline the major issues with prions in microbes and the lessons learned from the relatively uncovered microbial prion world.
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Affiliation(s)
- Moonil Son
- Department of Microbiology, Pusan National University, Busan, 46241, Republic of Korea.
- Department of Integrated Biological Science, Pusan National University, Busan, 46241, Republic of Korea.
- Microbiological Resource Research Institute, Pusan National University, Busan, 46241, Republic of Korea.
| | - Sia Han
- Department of Integrated Biological Science, Pusan National University, Busan, 46241, Republic of Korea
| | - Seyeon Lee
- Department of Integrated Biological Science, Pusan National University, Busan, 46241, Republic of Korea
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3
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Anti-Prion Systems in Saccharomyces cerevisiae Turn an Avalanche of Prions into a Flurry. Viruses 2022; 14:v14091945. [PMID: 36146752 PMCID: PMC9503967 DOI: 10.3390/v14091945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/01/2022] [Accepted: 08/06/2022] [Indexed: 11/16/2022] Open
Abstract
Prions are infectious proteins, mostly having a self-propagating amyloid (filamentous protein polymer) structure consisting of an abnormal form of a normally soluble protein. These prions arise spontaneously in the cell without known reason, and their effects were generally considered to be fatal based on prion diseases in humans or mammals. However, the wide array of prion studies in yeast including filamentous fungi revealed that their effects can range widely, from lethal to very mild (even cryptic) or functional, depending on the nature of the prion protein and the specific prion variant (or strain) made by the same prion protein but with a different conformation. This prion biology is affected by an array of molecular chaperone systems, such as Hsp40, Hsp70, Hsp104, and combinations of them. In parallel with the systems required for prion propagation, yeast has multiple anti-prion systems, constantly working in the normal cell without overproduction of or a deficiency in any protein, which have negative effects on prions by blocking their formation, curing many prions after they arise, preventing prion infections, and reducing the cytotoxicity produced by prions. From the protectors of nascent polypeptides (Ssb1/2p, Zuo1p, and Ssz1p) to the protein sequesterase (Btn2p), the disaggregator (Hsp104), and the mysterious Cur1p, normal levels of each can cure the prion variants arising in its absence. The controllers of mRNA quality, nonsense-mediated mRNA decay proteins (Upf1, 2, 3), can cure newly formed prion variants by association with a prion-forming protein. The regulator of the inositol pyrophosphate metabolic pathway (Siw14p) cures certain prion variants by lowering the levels of certain organic compounds. Some of these proteins have other cellular functions (e.g., Btn2), while others produce an anti-prion effect through their primary role in the normal cell (e.g., ribosomal chaperones). Thus, these anti-prion actions are the innate defense strategy against prions. Here, we outline the anti-prion systems in yeast that produce innate immunity to prions by a multi-layered operation targeting each step of prion development.
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4
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Siemer AB. What makes functional amyloids work? Crit Rev Biochem Mol Biol 2022; 57:399-411. [PMID: 35997712 PMCID: PMC9588633 DOI: 10.1080/10409238.2022.2113030] [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: 01/25/2022] [Revised: 06/29/2022] [Accepted: 08/10/2022] [Indexed: 01/27/2023]
Abstract
Although first described in the context of disease, cross-β (amyloid) fibrils have also been found as functional entities in all kingdoms of life. However, what are the specific properties of the cross-β fibril motif that convey biological function, make them especially suited for their particular purpose, and distinguish them from other fibrils found in biology? This review approaches these questions by arguing that cross-β fibrils are highly periodic, stable, and self-templating structures whose formation is accompanied by substantial conformational change that leads to a multimerization of their core and framing sequences. A discussion of each of these properties is followed by selected examples of functional cross-β fibrils that show how function is usually achieved by leveraging many of these properties.
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Affiliation(s)
- Ansgar B Siemer
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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5
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Seuma M, Bolognesi B. Understanding and evolving prions by yeast multiplexed assays. Curr Opin Genet Dev 2022; 75:101941. [PMID: 35777350 DOI: 10.1016/j.gde.2022.101941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/19/2022] [Accepted: 05/27/2022] [Indexed: 11/15/2022]
Abstract
Yeast genetics made it possible to derive the first fundamental insights into prion composition, conformation, and propagation. Fast-forward 30 years and the same model organism is now proving an extremely powerful tool to comprehensively explore the impact of mutations in prion sequences on their function, toxicity, and physical properties. Here, we provide an overview of novel multiplexed strategies where deep mutagenesis is combined to a range of tailored selection assays in yeast, which are particularly amenable for investigating prions and prion-like sequences. By mimicking evolution in a flask, these multiplexed approaches are revealing mechanistic insights on the consequences of prion self-assembly, while also reporting on the structure prion sequences adopt in vivo.
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Affiliation(s)
- Mireia Seuma
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain. https://twitter.com/@mseumaar
| | - Benedetta Bolognesi
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain.
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6
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Daskalov A, El Mammeri N, Lends A, Shenoy J, Lamon G, Fichou Y, Saad A, Martinez D, Morvan E, Berbon M, Grélard A, Kauffmann B, Ferber M, Bardiaux B, Habenstein B, Saupe SJ, Loquet A. Structures of Pathological and Functional Amyloids and Prions, a Solid-State NMR Perspective. Front Mol Neurosci 2021; 14:670513. [PMID: 34276304 PMCID: PMC8280340 DOI: 10.3389/fnmol.2021.670513] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 05/26/2021] [Indexed: 12/20/2022] Open
Abstract
Infectious proteins or prions are a remarkable class of pathogens, where pathogenicity and infectious state correspond to conformational transition of a protein fold. The conformational change translates into the formation by the protein of insoluble amyloid aggregates, associated in humans with various neurodegenerative disorders and systemic protein-deposition diseases. The prion principle, however, is not limited to pathogenicity. While pathological amyloids (and prions) emerge from protein misfolding, a class of functional amyloids has been defined, consisting of amyloid-forming domains under natural selection and with diverse biological roles. Although of great importance, prion amyloid structures remain challenging for conventional structural biology techniques. Solid-state nuclear magnetic resonance (SSNMR) has been preferentially used to investigate these insoluble, morphologically heterogeneous aggregates with poor crystallinity. SSNMR methods have yielded a wealth of knowledge regarding the fundamentals of prion biology and have helped to solve the structures of several prion and prion-like fibrils. Here, we will review pathological and functional amyloid structures and will discuss some of the obtained structural models. We will finish the review with a perspective on integrative approaches combining solid-state NMR, electron paramagnetic resonance and cryo-electron microscopy, which can complement and extend our toolkit to structurally explore various facets of prion biology.
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Affiliation(s)
- Asen Daskalov
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Nadia El Mammeri
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Alons Lends
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | | | - Gaelle Lamon
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Yann Fichou
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Ahmad Saad
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Denis Martinez
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Estelle Morvan
- CNRS, INSERM, IECB, UMS 3033, University of Bordeaux, Pessac, France
| | - Melanie Berbon
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Axelle Grélard
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Brice Kauffmann
- CNRS, INSERM, IECB, UMS 3033, University of Bordeaux, Pessac, France
| | | | | | | | - Sven J. Saupe
- CNRS, IBGC UMR 5095, University of Bordeaux, Bordeaux, France
| | - Antoine Loquet
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
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7
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Auxier B, Scholtmeijer K, van Peer AF, Baars JJP, Debets AJM, Aanen DK. Cytoplasmic Mixing, Not Nuclear Coexistence, Can Explain Somatic Incompatibility in Basidiomycetes. Microorganisms 2021; 9:1248. [PMID: 34201361 PMCID: PMC8229728 DOI: 10.3390/microorganisms9061248] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 12/03/2022] Open
Abstract
Nonself recognition leading to somatic incompatibility (SI) is commonly used by mycologists to distinguish fungal individuals. Despite this, the process remains poorly understood in basidiomycetes as all current models of SI are based on genetic and molecular research in ascomycete fungi. Ascomycete fungi are mainly found in a monokaryotic stage, with a single type of haploid nuclei, and only briefly during mating do two genomes coexist in heterokaryotic cells. The sister phylum, Basidiomycota, differs in several relevant aspects. Basidiomycete fungi have an extended heterokaryotic stage, and SI is generally observed between heterokaryons instead of between homokaryons. Additionally, considerable nuclear migration occurs during a basidiomycete mating reaction, introducing a nucleus into a resident homokaryon with cytoplasmic mixing limited to the fused or neighboring cells. To accommodate these differences, we describe a basidiomycete model for nonself recognition using post-translational modification, based on a reader-writer system as found in other organisms. This post-translational modification combined with nuclear migration allows for the coexistence of two genomes in one individual while maintaining nonself recognition during all life stages. Somewhat surprisingly, this model predicts localized cell death during mating, which is consistent with previous observations but differs from the general assumptions of basidiomycete mating. This model will help guide future research into the mechanisms behind basidiomycete nonself recognition.
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Affiliation(s)
- Ben Auxier
- Laboratory of Genetics, Wageningen University and Research, 6708 PB Wageningen, The Netherlands;
| | - Karin Scholtmeijer
- Mushroom Group, Plant Breeding Department, Wageningen University and Research, 6708 PB Wageningen, The Netherlands; (K.S.); (A.F.v.P.); (J.J.P.B.)
| | - Arend F. van Peer
- Mushroom Group, Plant Breeding Department, Wageningen University and Research, 6708 PB Wageningen, The Netherlands; (K.S.); (A.F.v.P.); (J.J.P.B.)
| | - Johan J. P. Baars
- Mushroom Group, Plant Breeding Department, Wageningen University and Research, 6708 PB Wageningen, The Netherlands; (K.S.); (A.F.v.P.); (J.J.P.B.)
- CNC Grondstoffen, P.O. Box 13, 6590 AA Gennep, The Netherlands
| | - Alfons J. M. Debets
- Laboratory of Genetics, Wageningen University and Research, 6708 PB Wageningen, The Netherlands;
| | - Duur K. Aanen
- Laboratory of Genetics, Wageningen University and Research, 6708 PB Wageningen, The Netherlands;
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8
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Assembling the right type of switch: Protein condensation to signal cell death. Curr Opin Cell Biol 2021; 69:55-61. [PMID: 33461073 DOI: 10.1016/j.ceb.2020.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/30/2020] [Accepted: 12/12/2020] [Indexed: 11/22/2022]
Abstract
Protein phase transitions are particularly amenable for cell signalling as these highly cooperative processes allow cells to make binary decisions in response to relatively small intracellular changes. The different processes of condensate formation and the distinct material properties of the resulting condensates provide a dictionary to modulate a range of decisions on cell fate. We argue that, on the one hand, the reversibility of liquid demixing offers a chance to arrest cell growth under specific circumstances. On the other hand, the transition to amyloids is better suited for terminal decisions such as those leading to apoptosis and necrosis. Here, we review recent examples of both scenarios, highlighting how mutations in signalling proteins affect the formation of biomolecular condensates with drastic effects on cell survival.
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9
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Hervás R, Oroz J. Mechanistic Insights into the Role of Molecular Chaperones in Protein Misfolding Diseases: From Molecular Recognition to Amyloid Disassembly. Int J Mol Sci 2020; 21:ijms21239186. [PMID: 33276458 PMCID: PMC7730194 DOI: 10.3390/ijms21239186] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 11/29/2020] [Accepted: 11/29/2020] [Indexed: 12/14/2022] Open
Abstract
Age-dependent alterations in the proteostasis network are crucial in the progress of prevalent neurodegenerative diseases, such as Alzheimer’s, Parkinson’s, or amyotrophic lateral sclerosis, which are characterized by the presence of insoluble protein deposits in degenerating neurons. Because molecular chaperones deter misfolded protein aggregation, regulate functional phase separation, and even dissolve noxious aggregates, they are considered major sentinels impeding the molecular processes that lead to cell damage in the course of these diseases. Indeed, members of the chaperome, such as molecular chaperones and co-chaperones, are increasingly recognized as therapeutic targets for the development of treatments against degenerative proteinopathies. Chaperones must recognize diverse toxic clients of different orders (soluble proteins, biomolecular condensates, organized protein aggregates). It is therefore critical to understand the basis of the selective chaperone recognition to discern the mechanisms of action of chaperones in protein conformational diseases. This review aimed to define the selective interplay between chaperones and toxic client proteins and the basis for the protective role of these interactions. The presence and availability of chaperone recognition motifs in soluble proteins and in insoluble aggregates, both functional and pathogenic, are discussed. Finally, the formation of aberrant (pro-toxic) chaperone complexes will also be disclosed.
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Affiliation(s)
- Rubén Hervás
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA;
| | - Javier Oroz
- Rocasolano Institute for Physical Chemistry, Spanish National Research Council (IQFR-CSIC), Serrano 119, E-28006 Madrid, Spain
- Correspondence: ; Tel.: +34-915619400
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10
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Das M, Bhargava BL. Exploring the candidates for a new protein folding - cross-α amyloid - in available protein databases. Phys Chem Chem Phys 2020; 22:23725-23734. [PMID: 33057523 DOI: 10.1039/d0cp03256e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Amyloid fibrils are formed from the assembly of soluble proteins and are responsible for many diseases. They are known to have a cross-β structure, where the fibril runs perpendicular to the β-sheets. A new type of tertiary structure formed by the aggregation of peptides in their α-helical form, in naturally occurring as well as synthetic peptides, termed cross-α amyloid has been reported recently. We have studied the interactions responsible for the formation of these cross-α amyloids and proposed a model to determine the peptides that could form these structures. Eight such peptides obtained using the model have been shown to form a cross-α structure using molecular dynamics simulations. The formation of a cross-α structure from eight copies of a randomly chosen peptide and its stability over a microsecond simulation have been demonstrated. A software named Cross-Alpha-Det has been developed that can determine whether a protein can form a cross-α structure from its secondary structure.
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Affiliation(s)
- Mitradip Das
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai, 400005, India. and School of Chemical Sciences, National Institute of Science Education and Research - Bhubaneswar, HBNI, Jatni, Odisha 752050, India.
| | - B L Bhargava
- School of Chemical Sciences, National Institute of Science Education and Research - Bhubaneswar, HBNI, Jatni, Odisha 752050, India.
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11
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Functional Mammalian Amyloids and Amyloid-Like Proteins. Life (Basel) 2020; 10:life10090156. [PMID: 32825636 PMCID: PMC7555005 DOI: 10.3390/life10090156] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/12/2020] [Accepted: 08/19/2020] [Indexed: 02/06/2023] Open
Abstract
Amyloids are highly ordered fibrous cross-β protein aggregates that are notorious primarily because of association with a variety of incurable human and animal diseases (termed amyloidoses), including Alzheimer’s disease (AD), Parkinson’s disease (PD), type 2 diabetes (T2D), and prion diseases. Some amyloid-associated diseases, in particular T2D and AD, are widespread and affect hundreds of millions of people all over the world. However, recently it has become evident that many amyloids, termed “functional amyloids,” are involved in various activities that are beneficial to organisms. Functional amyloids were discovered in diverse taxa, ranging from bacteria to mammals. These amyloids are involved in vital biological functions such as long-term memory, storage of peptide hormones and scaffolding melanin polymerization in animals, substrate attachment, and biofilm formation in bacteria and fungi, etc. Thus, amyloids undoubtedly are playing important roles in biological and pathological processes. This review is focused on functional amyloids in mammals and summarizes approaches used for identifying new potentially amyloidogenic proteins and domains.
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12
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Dixson JD, Azad RK. Prions: Roles in Development and Adaptive Evolution. J Mol Evol 2020; 88:427-434. [PMID: 32388713 DOI: 10.1007/s00239-020-09944-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 04/28/2020] [Indexed: 12/14/2022]
Abstract
Prions are often considered as anomalous proteins associated primarily with disease rather than as a fundamental source of diversity within biological proteomes. Whereas this longstanding viewpoint has its genesis in the discovery of the original namesake prions as causative agents of several complex diseases, the underlying assumption of a strict disease basis for prions could not be further from the truth. Prions and the spectrum of functions they comprise, likely represent one of the largest paradigm shifts concerning molecular-encoded phenotypic diversity since identification of DNA as the principle molecule of heredity. The ability of prions to recruit similar proteins to alternate conformations may engender a reservoir of diversity supplementing the genetic diversity resulting from stochastic mutations of DNA and subsequent natural selection. Here we present several currently known prions and how many of their functions as well as modes of transmission are intricately linked to adaptation from an evolutionary perspective. Further, the stability of some prion conformations across generations indicates that heritable prion-based adaptation is a reality.
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Affiliation(s)
- Jamie D Dixson
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, 76203, USA
| | - Rajeev K Azad
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, 76203, USA.
- Department of Mathematics, University of North Texas, Denton, TX, 76203, USA.
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13
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Kulkarni M, Stolp ZD, Hardwick JM. Targeting intrinsic cell death pathways to control fungal pathogens. Biochem Pharmacol 2019; 162:71-78. [PMID: 30660496 DOI: 10.1016/j.bcp.2019.01.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 01/11/2019] [Indexed: 02/07/2023]
Abstract
Fungal pathogens pose an increasing threat to public health. Limited clinical drug regimens and emerging drug-resistant isolates challenge infection control. The global burden of human fungal pathogens is estimated at 1 billion infections and 1.5 million deaths annually. In addition, plant fungal pathogens increasingly threaten global food resources. Novel strategies are needed to combat emerging fungal diseases and pan-resistant fungi. An untapped mechanistically novel approach is to pharmacologically activate the intrinsic cell death pathways encoded by pathogenic fungi. This strategy is analogous to new anti-cancer therapeutics now entering the clinic. Here we summarize the best understood examples of cell death mechanisms encoded by pathogenic fungi, contrast these to mammalian cell death pathways, and highlight the gaps in knowledge towards identifying potential death effectors as druggable targets.
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Affiliation(s)
- Madhura Kulkarni
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, USA
| | - Zachary D Stolp
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, USA
| | - J Marie Hardwick
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, USA; Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, USA.
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14
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Johnston A, Wang Z. Necroptosis: MLKL Polymerization. JOURNAL OF NATURE AND SCIENCE 2018; 4:e513. [PMID: 30294675 PMCID: PMC6173486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Necroptosis is a subtype of regulated necrosis that occurs when caspases are inhibited or fail to activate. Stimulus of cell death receptors results in a signaling cascade that triggers caspase independent, immunogenic cell death. The core pathway relies on receptor interacting protein kinase (RIPK) 1 and 3, which interact through their receptor homotypic interacting motif (RHIM) domains, and form amyloid-like structures termed the necrosome. RIPK3 recruits and phosphorylates mixed lineage kinase domain-like pseudokinase (MLKL), the terminal mediator in the necroptotic pathway. MLKL polymerizes to form a second amyloid-like structure that causes cell membrane disruption resulting in cell death. Although the core necroptosis pathway has been elucidated, the details of MLKL membrane translocation and membrane disruption remain an open area of research.
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Affiliation(s)
- Andrea Johnston
- Department of Molecular Biology, UT Southwestern, 6000 Harry Hines Blvd., NA8.202, Dallas, Texas 75390, USA
| | - Zhigao Wang
- Department of Molecular Biology, UT Southwestern, 6000 Harry Hines Blvd., NA8.202, Dallas, Texas 75390, USA
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15
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3D structure determination of amyloid fibrils using solid-state NMR spectroscopy. Methods 2018; 138-139:26-38. [DOI: 10.1016/j.ymeth.2018.03.014] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/28/2018] [Accepted: 03/30/2018] [Indexed: 01/08/2023] Open
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16
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Abstract
In the last decade, multiple reports have established that amyloids can bear important functional roles in a variety of biological processes and in distant taxonomic clades. In filamentous fungi, amyloids are involved in a signal transducing mechanism in which a group of NOD-like receptors (NLRs) controls downstream effector proteins to induce a programmed cell death reaction. A structurally characterized example of fungal signal-transducing amyloid is the prion-forming domain (PFD) of the HET-S toxin from Podospora anserina. Amyloid-mediated programmed cell death is equally reported in metazoans in the context of innate immunity and antiviral response. The cell death reaction, described as programmed necrosis, is dependent on an amyloid-forming RHIM motif (RIP homotypic interaction motif). An evolutionary link between the RHIM and the PFD signaling amyloids has been previously reported. Our recent study ties further the signaling amyloids in fungi and metazoans, reporting a fungal signal-transducing domain with amyloid and prion-like properties, which shows significant sequence similarity to the metazoan RHIM motif. Here, I discuss the expanding class of the signal-transducing amyloids and reflect on the possible evolutionary scenarios of their diversification.
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Affiliation(s)
- Asen Daskalov
- a Department of Plant and Microbial Biology , University of California , Berkeley , CA , USA
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17
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Abstract
In this review, we detail our current knowledge of PrPSc structure on the basis of structural and computational studies. We discuss the progress toward an atomic resolution description of PrPSc and results from the broader field of amyloid studies that may further inform our knowledge of this structure. Moreover, we summarize work that investigates the role of PrPSc structure in its toxicity, transmissibility, and species specificity. We look forward to an atomic model of PrPSc, which is expected to bring diagnostics and/or therapeutics to the field of prion disease.
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Affiliation(s)
- Jose A Rodriguez
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095
| | - Lin Jiang
- Department of Neurology, Molecular Biology Institute (MBI), and Brain Research Institute (BRI), David Geffen School of Medicine, University of California, Los Angeles, California 90095
| | - David S Eisenberg
- Department of Biological Chemistry, UCLA-DOE Institute for Genomics and Proteomics, Howard Hughes Medical Institute, University of California, Los Angeles, California 90095
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18
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Kraus A. Proline and lysine residues provide modulatory switches in amyloid formation: Insights from prion protein. Prion 2017; 10:57-62. [PMID: 26864641 DOI: 10.1080/19336896.2015.1132138] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Amyloidogenic proteins have an increased propensity to reorganize into the highly structured, β sheet rich structures that characterize amyloid. The probability of attaining these highly structured assemblies is influenced by multiple factors, including amino acid composition and environmental conditions. Evolutionary selection for amino acid sequences that prevent amyloid formation could further modulate amyloid-forming propensity. Indeed, we have recently identified specific proline and lysine residues, contained within a highly conserved central region of prion protein (PrP), that impede PrP amyloid formation in vitro. These prolines are mutated in certain forms of the human familial genetic disease, Gerstmann-Straüssler-Schneiker (GSS) syndrome. Here, I discuss the influence of these proline and lysine residues on PrP amyloid formation and how such anti-amyloidogenic primary amino acid sequences might be modulated to influence protein amyloidogenicity.
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Affiliation(s)
- Allison Kraus
- a Laboratory of Persistant Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health , Hamilton , MT , USA
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19
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Abstract
The [Het-s] prion of the fungus Podospora anserina is a well-studied model system to elucidate the action of prions and beyond. The [Het-s] prion works as an activation trigger of a cell death execution protein termed HET-S. Amyloid transconformation of the prion-forming region of HET-S induces activation of its pore-forming cell death execution HeLo domain. The prion motif functions in a signal transduction process by which a nucleotide-binding oligomerization domain (NOD)-like receptor termed NWD2 controls the HET-S cell death effector. This prion motif thus corresponds to a functional amyloid motif, allowing a conformational crosstalk between homologous motif domains in signal transduction processes that appears to be widespread from the fungal to the mammalian animal kingdoms. This review aims to establish a structure-activity relationship of the HET-S/s prion system and sets it in the context of its wider biological significance.
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Affiliation(s)
- Roland Riek
- Laboratory of Physical Chemistry, ETH Zürich, 8093 Zürich, Switzerland
| | - Sven J Saupe
- Institut de Biochimie et de Génétique Cellulaire UMR 5095, CNRS - Université de Bordeaux, 33077 Bordeaux, France
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20
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Strom NB, Bushley KE. Two genomes are better than one: history, genetics, and biotechnological applications of fungal heterokaryons. Fungal Biol Biotechnol 2016; 3:4. [PMID: 28955463 PMCID: PMC5611628 DOI: 10.1186/s40694-016-0022-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Accepted: 04/11/2016] [Indexed: 02/08/2023] Open
Abstract
Heterokaryosis is an integral part of the parasexual cycle used by predominantly asexual fungi to introduce and maintain genetic variation in populations. Research into fungal heterokaryons began in 1912 and continues to the present day. Heterokaryosis may play a role in the ability of fungi to respond to their environment, including the adaptation of arbuscular mycorrhizal fungi to different plant hosts. The parasexual cycle has enabled advances in fungal genetics, including gene mapping and tests of complementation, dominance, and vegetative compatibility in predominantly asexual fungi. Knowledge of vegetative compatibility groups has facilitated population genetic studies and enabled the design of innovative methods of biocontrol. The vegetative incompatibility response has the potential to be used as a model system to study biological aspects of some human diseases, including neurodegenerative diseases and cancer. By combining distinct traits through the formation of artificial heterokaryons, fungal strains with superior properties for antibiotic and enzyme production, fermentation, biocontrol, and bioremediation have been produced. Future biotechnological applications may include site-specific biocontrol or bioremediation and the production of novel pharmaceuticals.
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Affiliation(s)
- Noah B Strom
- Department of Plant Biology, University of Minnesota, 826 Biological Sciences, 1445 Gortner Avenue, Saint Paul, MN 55108 USA
| | - Kathryn E Bushley
- Department of Plant Biology, University of Minnesota, 826 Biological Sciences, 1445 Gortner Avenue, Saint Paul, MN 55108 USA
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21
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Habenstein B, Loquet A. Solid-state NMR: An emerging technique in structural biology of self-assemblies. Biophys Chem 2016; 210:14-26. [DOI: 10.1016/j.bpc.2015.07.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 07/08/2015] [Indexed: 12/13/2022]
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22
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Daskalov A, Habenstein B, Martinez D, Debets AJM, Sabaté R, Loquet A, Saupe SJ. Signal transduction by a fungal NOD-like receptor based on propagation of a prion amyloid fold. PLoS Biol 2015; 13:e1002059. [PMID: 25671553 PMCID: PMC4344463 DOI: 10.1371/journal.pbio.1002059] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 12/29/2014] [Indexed: 01/09/2023] Open
Abstract
In the fungus Podospora anserina, the [Het-s] prion induces programmed cell death by activating the HET-S pore-forming protein. The HET-s β-solenoid prion fold serves as a template for converting the HET-S prion-forming domain into the same fold. This conversion, in turn, activates the HET-S pore-forming domain. The gene immediately adjacent to het-S encodes NWD2, a Nod-like receptor (NLR) with an N-terminal motif similar to the elementary repeat unit of the β-solenoid fold. NLRs are immune receptors controlling cell death and host defense processes in animals, plants and fungi. We have proposed that, analogously to [Het-s], NWD2 can activate the HET-S pore-forming protein by converting its prion-forming region into the β-solenoid fold. Here, we analyze the ability of NWD2 to induce formation of the β-solenoid prion fold. We show that artificial NWD2 variants induce formation of the [Het-s] prion, specifically in presence of their cognate ligands. The N-terminal motif is responsible for this prion induction, and mutations predicted to affect the β-solenoid fold abolish templating activity. In vitro, the N-terminal motif assembles into infectious prion amyloids that display a structure resembling the β-solenoid fold. In vivo, the assembled form of the NWD2 N-terminal region activates the HET-S pore-forming protein. This study documenting the role of the β-solenoid fold in fungal NLR function further highlights the general importance of amyloid and prion-like signaling in immunity-related cell fate pathways. The fungus Podospora anserina uses a prion amyloid fold as a signal transduction device between a Nod-like receptor and a downstream cell death execution protein. Although amyloids are best known as protein aggregates that are responsible for fatal neurodegenerative diseases, amyloid structures can also fulfill functional roles in cells. In particular, the controlled formation of amyloid structures appears to be involved in different signaling processes in the context of programmed cell death and host defense. The [Het-s] prion of the filamentous fungus Podospora anserina is a model system in which the 3-D structure of the prion form has been solved. The [Het-s] prion works as an activation switch for a second protein termed HET-S. HET-S is a pore-forming protein that is activated when the [Het-s] prion causes its C-terminal domain to adopt an amyloid-like fold. The protein encoded by the gene adjacent to het-S is a Nod-like receptor (NLR) called NWD2. NLRs are immune receptors that control host defense and cell death processes in plants, animals, and fungi. We show that NWD2 can template the formation of the [Het-s] prion fold in a ligand-controlled manner. NWD2 has an N-terminal motif homologous to the HET-S/s prion-forming region; we find that this region is both necessary and sufficient for its prion-inducing activity, and our functional and structural approaches reveal that the N-terminal region of NWD2 adopts a fold closely related to that of the HET-S/s prion. This study illustrates how the controlled formation of a prion amyloid fold can be used in a signaling process whereby a Nod-like receptor protein activates a downstream cell death execution domain.
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Affiliation(s)
- Asen Daskalov
- Non-self recognition in Fungi, Institut de Biochimie et de Génétique Cellulaire, UMR 5095, CNRS—Université de Bordeaux, Bordeaux, France
| | - Birgit Habenstein
- Institute of Chemistry & Biology of Membranes & Nanoobjects, CNRS, CBMN, UMR 5248, Pessac, France
| | - Denis Martinez
- Institute of Chemistry & Biology of Membranes & Nanoobjects, CNRS, CBMN, UMR 5248, Pessac, France
| | - Alfons J. M. Debets
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg, Wageningen, The Netherlands
| | - Raimon Sabaté
- Institut de Nanociència i nanotecnologia, Departament Fisicoquímica, Universitat de Barcelona, Joan XXIII s/n, Barcelona, Spain
| | - Antoine Loquet
- Institute of Chemistry & Biology of Membranes & Nanoobjects, CNRS, CBMN, UMR 5248, Pessac, France
| | - Sven J. Saupe
- Non-self recognition in Fungi, Institut de Biochimie et de Génétique Cellulaire, UMR 5095, CNRS—Université de Bordeaux, Bordeaux, France
- * E-mail:
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23
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Dyrka W, Lamacchia M, Durrens P, Kobe B, Daskalov A, Paoletti M, Sherman DJ, Saupe SJ. Diversity and variability of NOD-like receptors in fungi. Genome Biol Evol 2014; 6:3137-58. [PMID: 25398782 PMCID: PMC4986451 DOI: 10.1093/gbe/evu251] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Nucleotide-binding oligomerization domain (NOD)-like receptors (NLRs) are intracellular receptors that control innate immunity and other biotic interactions in animals and plants. NLRs have been characterized in plant and animal lineages, but in fungi, this gene family has not been systematically described. There is however previous indications of the involvement of NLR-like genes in nonself recognition and programmed cell death in fungi. We have analyzed 198 fungal genomes for the presence of NLRs and have annotated a total of 5,616 NLR candidates. We describe their phylogenetic distribution, domain organization, and evolution. Fungal NLRs are characterized by a great diversity of domain organizations, suggesting frequently occurring combinatorial assortments of different effector, NOD and repeat domains. The repeat domains are of the WD, ANK, and TPR type; no LRR motifs were found. As previously documented for WD-repeat domains of fungal NLRs, TPR, and ANK repeats evolve under positive selection and show highly conserved repeats and repeat length polymorphism, suggesting the possibility of concerted evolution of these repeats. We identify novel effector domains not previously found associated with NLRs, whereas others are related to effector domains of plant or animals NLRs. In particular, we show that the HET domain found in fungal NLRs may be related to Toll/interleukin-1 receptor domains found in animal and plant immune receptors. This description of fungal NLR repertoires reveals both similarities and differences with plant and animals NLR collections, highlights the importance of domain reassortment and repeat evolution and provides a novel entry point to explore the evolution of NLRs in eukaryotes.
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Affiliation(s)
- Witold Dyrka
- INRIA-Université Bordeaux-CNRS, MAGNOME, Talence, France
| | - Marina Lamacchia
- Institut de Biochimie et de Génétique Cellulaire, UMR 5095, CNRS-Université de Bordeaux, France
| | - Pascal Durrens
- INRIA-Université Bordeaux-CNRS, MAGNOME, Talence, France
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Centre for Infectious Disease Research, University of Queensland, Brisbane, Queensland, Australia
| | - Asen Daskalov
- Institut de Biochimie et de Génétique Cellulaire, UMR 5095, CNRS-Université de Bordeaux, France
| | - Matthieu Paoletti
- Institut de Biochimie et de Génétique Cellulaire, UMR 5095, CNRS-Université de Bordeaux, France
| | | | - Sven J Saupe
- Institut de Biochimie et de Génétique Cellulaire, UMR 5095, CNRS-Université de Bordeaux, France
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24
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Daskalov A, Gantner M, Wälti MA, Schmidlin T, Chi CN, Wasmer C, Schütz A, Ceschin J, Clavé C, Cescau S, Meier B, Riek R, Saupe SJ. Contribution of specific residues of the β-solenoid fold to HET-s prion function, amyloid structure and stability. PLoS Pathog 2014; 10:e1004158. [PMID: 24945274 PMCID: PMC4055769 DOI: 10.1371/journal.ppat.1004158] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 04/15/2014] [Indexed: 01/12/2023] Open
Abstract
The [Het-s] prion of the fungus Podospora anserina represents a good model system for studying the structure-function relationship in amyloid proteins because a high resolution solid-state NMR structure of the amyloid prion form of the HET-s prion forming domain (PFD) is available. The HET-s PFD adopts a specific β-solenoid fold with two rungs of β-strands delimiting a triangular hydrophobic core. A C-terminal loop folds back onto the rigid core region and forms a more dynamic semi-hydrophobic pocket extending the hydrophobic core. Herein, an alanine scanning mutagenesis of the HET-s PFD was conducted. Different structural elements identified in the prion fold such as the triangular hydrophobic core, the salt bridges, the asparagines ladders and the C-terminal loop were altered and the effect of these mutations on prion function, fibril structure and stability was assayed. Prion activity and structure were found to be very robust; only a few key mutations were able to corrupt structure and function. While some mutations strongly destabilize the fold, many substitutions in fact increase stability of the fold. This increase in structural stability did not influence prion formation propensity in vivo. However, if an Ala replacement did alter the structure of the core or did influence the shape of the denaturation curve, the corresponding variant showed a decreased prion efficacy. It is also the finding that in addition to the structural elements of the rigid core region, the aromatic residues in the C-terminal semi-hydrophobic pocket are critical for prion propagation. Mutations in the latter region either positively or negatively affected prion formation. We thus identify a region that modulates prion formation although it is not part of the rigid cross-β core, an observation that might be relevant to other amyloid models.
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Affiliation(s)
- Asen Daskalov
- Institut de Biochimie et de Génétique Cellulaire, Unité Mixte de Recherche 5095, Centre National de la Recherche Scientifique Université de Bordeaux, Bordeaux, France
| | - Matthias Gantner
- Laboratory of Physical Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Marielle Aulikki Wälti
- Laboratory of Physical Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Thierry Schmidlin
- Laboratory of Physical Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Celestine N. Chi
- Laboratory of Physical Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Christian Wasmer
- Laboratory of Physical Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Anne Schütz
- Laboratory of Physical Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Johanna Ceschin
- Institut de Biochimie et de Génétique Cellulaire, Unité Mixte de Recherche 5095, Centre National de la Recherche Scientifique Université de Bordeaux, Bordeaux, France
| | - Corinne Clavé
- Institut de Biochimie et de Génétique Cellulaire, Unité Mixte de Recherche 5095, Centre National de la Recherche Scientifique Université de Bordeaux, Bordeaux, France
| | - Sandra Cescau
- Institut de Biochimie et de Génétique Cellulaire, Unité Mixte de Recherche 5095, Centre National de la Recherche Scientifique Université de Bordeaux, Bordeaux, France
| | - Beat Meier
- Laboratory of Physical Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Roland Riek
- Laboratory of Physical Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Sven J. Saupe
- Institut de Biochimie et de Génétique Cellulaire, Unité Mixte de Recherche 5095, Centre National de la Recherche Scientifique Université de Bordeaux, Bordeaux, France
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25
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Van der Nest MA, Olson A, Lind M, Vélëz H, Dalman K, Brandström Durling M, Karlsson M, Stenlid J. Distribution and evolution of het gene homologs in the basidiomycota. Fungal Genet Biol 2013; 64:45-57. [PMID: 24380733 DOI: 10.1016/j.fgb.2013.12.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 12/04/2013] [Accepted: 12/20/2013] [Indexed: 12/24/2022]
Abstract
In filamentous fungi a system known as somatic incompatibility (SI) governs self/non-self recognition. SI is controlled by a regulatory signaling network involving proteins encoded at the het (heterokaryon incompatible) loci. Despite the wide occurrence of SI, the molecular identity and structure of only a small number of het genes and their products have been characterized in the model fungi Neurospora crassa and Podospora anserina. Our aim was to identify and study the distribution and evolution of putative het gene homologs in the Basidiomycota. For this purpose we used the information available for the model fungi to identify homologs of het genes in other fungi, especially the Basidiomycota. Putative het-c, het-c2 and un-24 homologs, as well as sequences containing the NACHT, HET or WD40 domains present in the het-e, het-r, het-6 and het-d genes were identified in certain members of the Ascomycota and Basidiomycota. The widespread phylogenetic distribution of certain het genes may reflect the fact that the encoded proteins are involved in fundamental cellular processes other than SI. Although homologs of het-S were previously known only from the Sordariomycetes (Ascomycota), we also identified a putative homolog of this gene in Gymnopus luxurians (Basidiomycota, class Agaricomycetes). Furthermore, with the exception of un-24, all of the putative het genes identified occurred mostly in a multi-copy fashion, some with lineage and species-specific expansions. Overall our results indicated that gene duplication followed by gene loss and/or gene family expansion, as well as multiple events of domain fusion and shuffling played an important role in the evolution of het gene homologs of Basidiomycota and other filamentous fungi.
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Affiliation(s)
- M A Van der Nest
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden.
| | - A Olson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - M Lind
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - H Vélëz
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - K Dalman
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - M Brandström Durling
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - M Karlsson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - J Stenlid
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
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