1
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Moreira SM, Chyou TY, Wade JT, Brown CM. Diversification of the Rho transcription termination factor in bacteria. Nucleic Acids Res 2024:gkae582. [PMID: 38966992 DOI: 10.1093/nar/gkae582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 06/17/2024] [Accepted: 06/24/2024] [Indexed: 07/06/2024] Open
Abstract
Correct termination of transcription is essential for gene expression. In bacteria, factor-dependent termination relies on the Rho factor, that classically has three conserved domains. Some bacteria also have a functional insertion region. However, the variation in Rho structure among bacteria has not been analyzed in detail. This study determines the distribution, sequence conservation, and predicted features of Rho factors with diverse domain architectures by analyzing 2730 bacterial genomes. About half (49.8%) of the species analyzed have the typical Escherichia coli like Rho while most of the other species (39.8%) have diverse, atypical forms of Rho. Besides conservation of the main domains, we describe a duplicated RNA-binding domain present in specific species and novel variations in the bicyclomycin binding pocket. The additional regions observed in Rho proteins exhibit remarkable diversity. Commonly, however, they have exceptional amino acid compositions and are predicted to be intrinsically disordered, to undergo phase separation, or have prion-like behavior. Phase separation has recently been shown to play roles in Rho function and bacterial fitness during harsh conditions in one species and this study suggests a more widespread role. In conclusion, diverse atypical Rho factors are broadly distributed among bacteria, suggesting additional cellular roles.
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Affiliation(s)
- Sofia M Moreira
- Department of Biochemistry, University of Otago, Dunedin, Otago 9054, New Zealand
| | - Te-Yuan Chyou
- Department of Biochemistry, University of Otago, Dunedin, Otago 9054, New Zealand
| | - Joseph T Wade
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY 12222, USA
| | - Chris M Brown
- Department of Biochemistry, University of Otago, Dunedin, Otago 9054, New Zealand
- Genetics Otago, University of Otago, Dunedin, Otago 9054, New Zealand
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2
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Khalili K, Farzam F, Dabirmanesh B, Khajeh K. Prediction of protein aggregation. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 206:229-263. [PMID: 38811082 DOI: 10.1016/bs.pmbts.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
The scientific community is very interested in protein aggregation because of its involvement in several neurodegenerative diseases and its significance in industry. Remarkably, fibrillar aggregates are utilized naturally for constructing structural scaffolds or creating biological switches and may be intentionally designed to construct versatile nanomaterials. Consequently, there is a significant need to rationalize and predict protein aggregation. Researchers have developed various computational methodologies and algorithms to predict protein aggregation and understand its underlying mechanics. This chapter aims to summarize the significant advancements in computational methods, accessible resources, and prospective developments in the field of in silico research. We assess the existing computational tools for predicting protein aggregation propensities, detecting areas that are prone to sequential and structural aggregation, analyzing the effects of mutations on protein aggregation, or identifying prion-like domains.
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Affiliation(s)
- Kavyan Khalili
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Farnoosh Farzam
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Bahareh Dabirmanesh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Khosro Khajeh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
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3
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Pintado-Grima C, Bárcenas O, Ventura S. Expanding the Landscape of Amyloid Sequences with CARs-DB: A Database of Polar Amyloidogenic Peptides from Disordered Proteins. Methods Mol Biol 2024; 2714:171-185. [PMID: 37676599 DOI: 10.1007/978-1-0716-3441-7_10] [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] [Indexed: 09/08/2023]
Abstract
Several databases collecting amyloidogenic regions have been released to provide information on protein sequences able to form amyloid fibrils. However, most of these resources are built with data from experiments that detect highly hydrophobic stretches located within transiently exposed protein segments. We recently demonstrated that cryptic amyloidogenic regions (CARs) of polar nature have the potential to form amyloid fibrils in vitro. Given the underrepresentation of these types of sequences in current amyloid databases, we developed CARs-DB, the first repository that collects thousands of predicted CARs from intrinsically disordered regions. This protocol chapter describes how to use CARs-DB to search for sequences of interest that might be connected to disease or functional protein-protein interactions. In addition, we provide study cases to illustrate the database's features to users. The CARs-DB is readily accessible at http://carsdb.ppmclab.com/ .
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Affiliation(s)
- Carlos Pintado-Grima
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Oriol Bárcenas
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain.
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4
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Kumar A, Dixson J, Azad RK. RNA-Seq Analysis of Mammalian Prion Disease. Methods Mol Biol 2024; 2812:367-377. [PMID: 39068373 DOI: 10.1007/978-1-0716-3886-6_20] [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] [Indexed: 07/30/2024]
Abstract
A protein, which can attain a prion state, differs from standard proteins in terms of structural conformation and aggregation propensity. High-throughput sequencing technology provides an opportunity to gain insight into the prion disease condition when coupled with single-cell RNA-Seq analysis to reveal transcriptional changes during prion-based pathogenicity. In this chapter, we present a protocol for RNA-Seq analysis of mammalian prion disease using a single-cell RNA sequencing dataset procured from the NCBI GEO database. This protocol is a tool that can assist researchers in characterizing mammalian prion disease in a reproducible and reusable manner. Further, the resulting output has the potential to provide transcript biomarkers for mammalian prion diseases, which can be employed for diagnostic and prognostic purposes.
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Affiliation(s)
- Ambarish Kumar
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA
| | - Jamie Dixson
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA
| | - Rajeev K Azad
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA.
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5
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Fuentes-Jiménez DA, Salinas LS, Morales-Oliva E, Ramírez-Ramírez VA, Arciniega M, Navarro RE. Two predicted α-helices within the prion-like domain of TIAR-1 play a crucial role in its association with stress granules in Caenorhabditis elegans. Front Cell Dev Biol 2023; 11:1265104. [PMID: 38161334 PMCID: PMC10757852 DOI: 10.3389/fcell.2023.1265104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/14/2023] [Indexed: 01/03/2024] Open
Abstract
Stress granules (SGs) are sites for mRNA storage, protection, and translation repression. TIA1 and TIAR1 are two RNA-binding proteins that are key players in SGs formation in mammals. TIA1/TIAR have a prion-like domain (PrD) in their C-terminal that promotes liquid-phase separation. Lack of any TIA1/TIAR has severe consequences in mice. However, it is not clear whether the failure to form proper SGs is the cause of any of these problems. We disrupted two predicted α-helices within the prion-like domain of the Caenohabditis elegans TIA1/TIAR homolog, TIAR-1, to test whether its association with SGs is important for the nematode. We found that tiar-1 PrD mutant animals continued to form TIAR-1 condensates under stress in the C. elegans gonad. Nonetheless, TIAR-1 condensates appeared fragile and disassembled quickly after stress. Apparently, the SGs continued to associate regularly as observed with CGH-1, an SG marker. Like tiar-1-knockout nematodes, tiar-1 PrD mutant animals exhibited fertility problems and a shorter lifespan. Notwithstanding this, tiar-1 PrD mutant nematodes were no sensitive to stress. Our data demonstrate that the predicted prion-like domain of TIAR-1 is important for its association with stress granules. Moreover, this domain may also play a significant role in various TIAR-1 functions unrelated to stress, such as fertility, embryogenesis and lifespan.
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Affiliation(s)
- D. A. Fuentes-Jiménez
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - L. S. Salinas
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - E. Morales-Oliva
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - V. A. Ramírez-Ramírez
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - M. Arciniega
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - R. E. Navarro
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
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6
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Zajkowski T, Lee MD, Sharma S, Vallota-Eastman A, Kuska M, Malczewska M, Rothschild LJ. Conserved functions of prion candidates suggest a primeval role of protein self-templating. Proteins 2023; 91:1298-1315. [PMID: 37519023 DOI: 10.1002/prot.26558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 06/14/2023] [Accepted: 07/07/2023] [Indexed: 08/01/2023]
Abstract
Amyloid-based prions have simple structures, a wide phylogenetic distribution, and a plethora of functions in contemporary organisms, suggesting they may be an ancient phenomenon. However, this hypothesis has yet to be addressed with a systematic, computational, and experimental approach. Here we present a framework to help guide future experimental verification of candidate prions with conserved functions to understand their role in the early stages of evolution and potentially in the origins of life. We identified candidate prions in all high-quality proteomes available in UniProt computationally, assessed their phylogenomic distributions, and analyzed candidate-prion functional annotations. Of the 27 980 560 proteins scanned, 228 561 were identified as candidate prions (~0.82%). Among these candidates, there were 84 Gene Ontology (GO) terms conserved across the three domains of life. We found that candidate prions with a possible role in adaptation were particularly well-represented within this group. We discuss unifying features of candidate prions to elucidate the primeval roles of prions and their associated functions. Candidate prions annotated as transcription factors, DNA binding, and kinases are particularly well suited to generating diverse responses to changes in their environment and could allow for adaptation and population expansion into more diverse environments. We hypothesized that a relationship between these functions and candidate prions could be evolutionarily ancient, even if individual prion domains themselves are not evolutionarily conserved. Candidate prions annotated with these universally occurring functions potentially represent the oldest extant prions on Earth and are therefore excellent experimental targets.
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Affiliation(s)
- Tomasz Zajkowski
- Universities Space Research Association at NASA Ames Research Center, Mountain View, California, USA
- Polish Astrobiology Society, Warsaw, Poland
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, USA
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Michael D Lee
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- KBR, NASA Ames Research Center, Mountain View, California, USA
| | - Siddhant Sharma
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- School of Chemistry, University of New South Wales, Sydney, Australia
| | - Alec Vallota-Eastman
- Department of Earth Science, University of California, Santa Barbara, California, USA
| | - Mikołaj Kuska
- Polish Astrobiology Society, Warsaw, Poland
- Department of Biophysics, Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Małgorzata Malczewska
- Polish Astrobiology Society, Warsaw, Poland
- Department of Biophysics, Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Lynn J Rothschild
- Space Science and Astrobiology Division, NASA Ames Research Center, Mountain View, California, USA
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7
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Josefson R, Kumar N, Hao X, Liu B, Nyström T. The GET pathway is a major bottleneck for maintaining proteostasis in Saccharomyces cerevisiae. Sci Rep 2023; 13:9285. [PMID: 37286562 DOI: 10.1038/s41598-023-35666-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 05/18/2023] [Indexed: 06/09/2023] Open
Abstract
A hallmark of aging in a variety of organisms is a breakdown of proteostasis and an ensuing accumulation of protein aggregates and inclusions. However, it is not clear if the proteostasis network suffers from a uniform breakdown during aging or if some distinct components act as bottlenecks especially sensitive to functional decline. Here, we report on a genome-wide, unbiased, screen for single genes in young cells of budding yeast required to keep the proteome aggregate-free under non-stress conditions as a means to identify potential proteostasis bottlenecks. We found that the GET pathway, required for the insertion of tail-anchored (TA) membrane proteins in the endoplasmic reticulum, is such a bottleneck as single mutations in either GET3, GET2 or GET1 caused accumulation of cytosolic Hsp104- and mitochondria-associated aggregates in nearly all cells when growing at 30 °C (non-stress condition). Further, results generated by a second screen identifying proteins aggregating in GET mutants and analyzing the behavior of cytosolic reporters of misfolding, suggest that there is a general collapse in proteostasis in GET mutants that affects other proteins than TA proteins.
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Affiliation(s)
- Rebecca Josefson
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Navinder Kumar
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Xinxin Hao
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Beidong Liu
- Department of Chemistry and Molecular Biology, Faculty of Science, University of Gothenburg, Gothenburg, Sweden
| | - Thomas Nyström
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
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8
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Pintado-Grima C, Santos J, Iglesias V, Manglano-Artuñedo Z, Pallarès I, Ventura S. Exploring cryptic amyloidogenic regions in prion-like proteins from plants. FRONTIERS IN PLANT SCIENCE 2023; 13:1060410. [PMID: 36726678 PMCID: PMC9885169 DOI: 10.3389/fpls.2022.1060410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 12/19/2022] [Indexed: 06/18/2023]
Abstract
Prion-like domains (PrLDs) are intrinsically disordered regions (IDRs) of low sequence complexity with a similar composition to yeast prion domains. PrLDs-containing proteins have been involved in different organisms' regulatory processes. Regions of moderate amyloid propensity within IDRs have been shown to assemble autonomously into amyloid fibrils. These sequences tend to be rich in polar amino acids and often escape from the detection of classical bioinformatics screenings that look for highly aggregation-prone hydrophobic sequence stretches. We defined them as cryptic amyloidogenic regions (CARs) and recently developed an integrated database that collects thousands of predicted CARs in IDRs. CARs seem to be evolutionary conserved among disordered regions because of their potential to stablish functional contacts with other biomolecules. Here we have focused on identifying and characterizing CARs in prion-like proteins (pCARs) from plants, a lineage that has been poorly studied in comparison with other prionomes. We confirmed the intrinsic amyloid potential for a selected pCAR from Arabidopsis thaliana and explored functional enrichments and compositional bias of pCARs in plant prion-like proteins.
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Affiliation(s)
- Carlos Pintado-Grima
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Jaime Santos
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Valentín Iglesias
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
- Barcelona Institute for Global Health, Barcelona Centre for International Health Research (ISGlobal, Hospital Clínic-Universitat de Barcelona), Barcelona, Spain
- Nanomalaria Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Zoe Manglano-Artuñedo
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Irantzu Pallarès
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Salvador Ventura
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
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9
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Zhao Y, Pogue AI, Alexandrov PN, Butler LG, Li W, Jaber VR, Lukiw WJ. Alteration of Biomolecular Conformation by Aluminum-Implications for Protein Misfolding Disease. Molecules 2022; 27:5123. [PMID: 36014365 PMCID: PMC9412470 DOI: 10.3390/molecules27165123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/01/2022] [Accepted: 08/04/2022] [Indexed: 11/16/2022] Open
Abstract
The natural element aluminum possesses a number of unique biochemical and biophysical properties that make this highly neurotoxic species deleterious towards the structural integrity, conformation, reactivity and stability of several important biomolecules. These include aluminum's (i) small ionic size and highly electrophilic nature, having the highest charge density of any metallic cation with a Z2/r of 18 (ionic charge +3, radius 0.5 nm); (ii) inclination to form extremely stable electrostatic bonds with a tendency towards covalency; (iii) ability to interact irreversibly and/or significantly slow down the exchange-rates of complex aluminum-biomolecular interactions; (iv) extremely dense electropositive charge with one of the highest known affinities for oxygen-donor ligands such as phosphate; (v) presence as the most abundant metal in the Earth's biosphere and general bioavailability in drinking water, food, medicines, consumer products, groundwater and atmospheric dust; and (vi) abundance as one of the most commonly encountered intracellular and extracellular metallotoxins. Despite aluminum's prevalence and abundance in the biosphere it is remarkably well-tolerated by all plant and animal species; no organism is known to utilize aluminum metabolically; however, a biological role for aluminum has been assigned in the compaction of chromatin. In this Communication, several examples are given where aluminum has been shown to irreversibly perturb and/or stabilize the natural conformation of biomolecules known to be important in energy metabolism, gene expression, cellular homeostasis and pathological signaling in neurological disease. Several neurodegenerative disorders that include the tauopathies, Alzheimer's disease and multiple prion disorders involve the altered conformation of naturally occurring cellular proteins. Based on the data currently available we speculate that one way aluminum contributes to neurological disease is to induce the misfolding of naturally occurring proteins into altered pathological configurations that contribute to the neurodegenerative disease process.
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Affiliation(s)
- Yuhai Zhao
- LSU Neuroscience Center, Louisiana State University Health Science Center, New Orleans, LA 70112, USA
- Department of Cell Biology & Anatomy, LSU Health Science Center, New Orleans, LA 70112, USA
| | | | | | - Leslie G. Butler
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Wenhong Li
- Department of Pharmacology, Jiangxi University of TCM, Nanchang 330004, China
| | - Vivian R. Jaber
- LSU Neuroscience Center, Louisiana State University Health Science Center, New Orleans, LA 70112, USA
| | - Walter J. Lukiw
- LSU Neuroscience Center, Louisiana State University Health Science Center, New Orleans, LA 70112, USA
- Alchem Biotek Research, Toronto, ON M5S 1A8, Canada
- Russian Academy of Medical Sciences, 113152 Moscow, Russian
- Department of Ophthalmology, LSU Health Science Center, New Orleans, LA 70112, USA
- Department Neurology, LSU Health Science Center, New Orleans, LA 70112, USA
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10
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Computational methods to predict protein aggregation. Curr Opin Struct Biol 2022; 73:102343. [PMID: 35240456 DOI: 10.1016/j.sbi.2022.102343] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/20/2021] [Accepted: 01/17/2022] [Indexed: 01/13/2023]
Abstract
In most cases, protein aggregation stems from the establishment of non-native intermolecular contacts. The formation of insoluble protein aggregates is associated with many human diseases and is a major bottleneck for the industrial production of protein-based therapeutics. Strikingly, fibrillar aggregates are naturally exploited for structural scaffolding or to generate molecular switches and can be artificially engineered to build up multi-functional nanomaterials. Thus, there is a high interest in rationalizing and forecasting protein aggregation. Here, we review the available computational toolbox to predict protein aggregation propensities, identify sequential or structural aggregation-prone regions, evaluate the impact of mutations on aggregation or recognize prion-like domains. We discuss the strengths and limitations of these algorithms and how they can evolve in the next future.
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11
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DMSO and TMAO-Differences in Interactions in Aqueous Solutions of the K-Peptide. Int J Mol Sci 2022; 23:ijms23031872. [PMID: 35163792 PMCID: PMC8836737 DOI: 10.3390/ijms23031872] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/01/2022] [Accepted: 02/04/2022] [Indexed: 02/06/2023] Open
Abstract
Interactions between a solvent and their co-solute molecules in solutions of peptides are crucial for their stability and structure. The K-peptide is a synthetic fragment of a larger hen egg white lysozyme protein that is believed to be able to aggregate into amyloid structures. In this study, a complex experimental and theoretical approach is applied to study systems comprising the peptide, water, and two co-solutes: trimethylamide N-oxide (TMAO) or dimethyl sulfoxide (DMSO). Information about their interactions in solutions and on the stability of the K-peptide was obtained by FTIR spectroscopy and differential scanning microcalorimetry. The IR spectra of various osmolyte-water-model-peptide complexes were simulated with the DFT method (B3LYP/6-311++G(d,p)). The FTIR results indicate that both solutes are neutral for the K-peptide in solution. Both co-solutes affect the peptide to different degrees, as seen in the shape of its amide I band, and have different influences on its thermal stability. DFT calculations helped simplify the experimental data for easier interpretation.
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12
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Dixson JD, Azad RK. A Protocol for Prion Discovery in Plants. Methods Mol Biol 2022; 2396:215-226. [PMID: 34786686 DOI: 10.1007/978-1-0716-1822-6_16] [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] [Indexed: 06/13/2023]
Abstract
Recently a likely prion was found in the proteome of Arabidopsis thaliana based on inclusive compositional similarity to known yeast prion-like domains (PrLDs) and gene ontology analysis. A total of 474 proteins in the Arabidopsis thaliana proteome showed significant compositional similarity to known PrLDs in yeast warranting further analysis. In this chapter, we describe the use and limitations of the PLAAC (Prion-Like Amino Acid Composition) software for the identification of prions, specifically as it has recently been applied to identifying the first prion in plants. Our interest in this method, though presented from a plant-based perspective here, is broad and is primarily in using the method for comparative assessment with novel prion identification algorithms currently under development in our lab. This chapter is not meant to serve as a replete description of the architecture and use of HMM in prion prediction in general but is intended to serve as a reference for implementation and interpretation of output from PLAAC and its application to plant proteomes.
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Affiliation(s)
- Jamie D Dixson
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA
| | - Rajeev K Azad
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA.
- Department of Mathematics, University of North Texas, Denton, TX, USA.
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13
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Abstract
Protein assembly into β-sheet-rich amyloid structures is a general biophysical phenomenon that has significant biological consequences, most notable for their prominent association with neurodegenerative diseases, including Alzheimer's, Huntington's, or Parkinson's diseases. The assembly of amyloid structures is driven by short sequences called amyloid motifs. In many neurodegenerative diseases, intrinsically disordered proteins (IDPs) self-assemble through amyloid motifs, but these motifs are present in all proteins, including folded globular proteins. Importantly, mechanistic knowledge is lacking for how IDPs, which do not adopt a stable tertiary structure, mask these amyloidogenic motifs to mitigate or slow the formation of β-sheet-rich amyloid structures that cause disease. Our recent work has shown that local structural elements can modify the aggregation propensity of amyloid motifs in the intrinsically disordered microtubule-associated protein tau by adopting metastable β-hairpin-like structures that shield the amyloid motif, and disease-causing mutations change the conformation, thus increase aggregation propensity (Chen, Nat Commun 10:2493, 2019). Here we describe a protocol that correlates experimentally determined aggregation propensities for peptides measured by the Thioflavin T (ThT) fluorescence aggregation assay with their conformational ensembles derived from Groningen machine chemical simulations (GROMACS). Integration of experiment and simulation will help uncover structural rules behind changes in conformation that modulate protein aggregation. We anticipate that our general protocol will help identify key interactions in local structures that engage amyloid-forming motifs in IDPs which influence aggregation behavior.
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Affiliation(s)
- Sofia Bali
- Molecular Biophysics Graduate Program, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Lukasz A Joachimiak
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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14
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Behbahanipour M, García-Pardo J, Ventura S. Decoding the role of coiled-coil motifs in human prion-like proteins. Prion 2021; 15:143-154. [PMID: 34428113 PMCID: PMC8386614 DOI: 10.1080/19336896.2021.1961569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 07/22/2021] [Accepted: 07/25/2021] [Indexed: 11/28/2022] Open
Abstract
Prions are self-propagating proteins that cause fatal neurodegenerative diseases in humans. However, increasing evidence suggests that eukaryotic cells exploit prion conformational conversion for functional purposes. A recent study delineated a group of twenty prion-like proteins in humans, characterized by the presence of low-complexity glutamine-rich sequences with overlapping coiled-coil (CCs) motifs. This is the case of Mediator complex subunit 15 (MED15), which is overexpressed in a wide range of human cancers. Biophysical studies demonstrated that the prion-like domain (PrLD) of MED15 forms homodimers in solution, sustained by CCs interactions. Furthermore, the same coiled-coil (CC) region plays a crucial role in the PrLD structural transition to a transmissible β-sheet amyloid state. In this review, we discuss the role of CCs motifs and their contribution to amyloid transitions in human prion-like domains (PrLDs), while providing a comprehensive overview of six predicted human prion-like proteins involved in transcription, gene expression, or DNA damage response and associated with human disease, whose PrLDs contain or overlap with CCs sequences. Finally, we try to rationalize how these molecular signatures might relate to both their function and involvement in disease.
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Affiliation(s)
- Molood Behbahanipour
- Institut De Biotecnologia I De Biomedicina (Ibb) and Departament De Bioquímica I Biologia Molecular, Universitat Autónoma De Barcelona, Barcelona, Spain
| | - Javier García-Pardo
- Institut De Biotecnologia I De Biomedicina (Ibb) and Departament De Bioquímica I Biologia Molecular, Universitat Autónoma De Barcelona, Barcelona, Spain
| | - Salvador Ventura
- Institut De Biotecnologia I De Biomedicina (Ibb) and Departament De Bioquímica I Biologia Molecular, Universitat Autónoma De Barcelona, Barcelona, Spain
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15
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Xu X, Zheng C, Lu D, Song CP, Zhang L. Phase separation in plants: New insights into cellular compartmentalization. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1835-1855. [PMID: 34314106 DOI: 10.1111/jipb.13152] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/16/2021] [Indexed: 05/16/2023]
Abstract
A fundamental challenge for cells is how to coordinate various biochemical reactions in space and time. To achieve spatiotemporal control, cells have developed organelles that are surrounded by lipid bilayer membranes. Further, membraneless compartmentalization, a process induced by dynamic physical association of biomolecules through phase transition offers another efficient mechanism for intracellular organization. While our understanding of phase separation was predominantly dependent on yeast and animal models, recent findings have provided compelling evidence for emerging roles of phase separation in plants. In this review, we first provide an overview of the current knowledge of phase separation, including its definition, biophysical principles, molecular features and regulatory mechanisms. Then we summarize plant-specific phase separation phenomena and describe their functions in plant biological processes in great detail. Moreover, we propose that phase separation is an evolutionarily conserved and efficient mechanism for cellular compartmentalization which allows for distinct metabolic processes and signaling pathways, and is especially beneficial for the sessile lifestyle of plants to quickly and efficiently respond to the changing environment.
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Affiliation(s)
- Xiumei Xu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Canhui Zheng
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Dandan Lu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Chun-Peng Song
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Lixin Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
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16
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Iglesias V, Santos J, Santos-Suárez J, Pintado-Grima C, Ventura S. SGnn: A Web Server for the Prediction of Prion-Like Domains Recruitment to Stress Granules Upon Heat Stress. Front Mol Biosci 2021; 8:718301. [PMID: 34490351 PMCID: PMC8416484 DOI: 10.3389/fmolb.2021.718301] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/09/2021] [Indexed: 11/15/2022] Open
Abstract
Proteins bearing prion-like domains (PrLDs) are essential players in stress granules (SG) assembly. Analysis of data on heat stress-induced recruitment of yeast PrLDs to SG suggests that this propensity might be connected with three defined protein biophysical features: aggregation propensity, net charge, and the presence of free cysteines. These three properties can be read directly in the PrLDs sequences, and their combination allows to predict protein recruitment to SG under heat stress. On this basis, we implemented SGnn, an online predictor of SG recruitment that exploits a feed-forward neural network for high accuracy classification of the assembly behavior of PrLDs. The simplicity and precision of our strategy should allow its implementation to identify heat stress-induced SG-forming proteins in complete proteomes.
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Affiliation(s)
- Valentín Iglesias
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Jaime Santos
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Juan Santos-Suárez
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Carlos Pintado-Grima
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
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17
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Gil‐Garcia M, Iglesias V, Pallarès I, Ventura S. Prion-like proteins: from computational approaches to proteome-wide analysis. FEBS Open Bio 2021; 11:2400-2417. [PMID: 34057308 PMCID: PMC8409284 DOI: 10.1002/2211-5463.13213] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 05/07/2021] [Accepted: 05/28/2021] [Indexed: 12/16/2022] Open
Abstract
Prions are self-perpetuating proteins able to switch between a soluble state and an aggregated-and-transmissible conformation. These proteinaceous entities have been widely studied in yeast, where they are involved in hereditable phenotypic adaptations. The notion that such proteins could play functional roles and be positively selected by evolution has triggered the development of computational tools to identify prion-like proteins in different kingdoms of life. These algorithms have succeeded in screening multiple proteomes, allowing the identification of prion-like proteins in a diversity of unrelated organisms, evidencing that the prion phenomenon is well conserved among species. Interestingly enough, prion-like proteins are not only connected with the formation of functional membraneless protein-nucleic acid coacervates, but are also linked to human diseases. This review addresses state-of-the-art computational approaches to identify prion-like proteins, describes proteome-wide analysis efforts, discusses these unique proteins' functional role, and illustrates recently validated examples in different domains of life.
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Affiliation(s)
- Marcos Gil‐Garcia
- Departament de Bioquímica i Biologia MolecularInstitut de Biotecnologia i de BiomedicinaUniversitat Autònoma de BarcelonaSpain
| | - Valentín Iglesias
- Departament de Bioquímica i Biologia MolecularInstitut de Biotecnologia i de BiomedicinaUniversitat Autònoma de BarcelonaSpain
| | - Irantzu Pallarès
- Departament de Bioquímica i Biologia MolecularInstitut de Biotecnologia i de BiomedicinaUniversitat Autònoma de BarcelonaSpain
| | - Salvador Ventura
- Departament de Bioquímica i Biologia MolecularInstitut de Biotecnologia i de BiomedicinaUniversitat Autònoma de BarcelonaSpain
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18
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Peccati F, Sodupe M. Atomistic insights into the structure of heptapeptide nanofibers. J Chem Phys 2021; 155:055101. [PMID: 34364337 DOI: 10.1063/5.0048988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Artificial amyloid-like nanofibers formed from short peptides are emerging as new supramolecular structures for catalysis and advanced materials. In this work, we analyze, by means of computational approaches, the preferred atomistic fibrillar architectures that result from the self-assembly of polar NY7, NF7, SY7, SF7, and GY7 peptides into steric zippers formed by two β-sheets (describing an individual steric zipper) and by four β-sheets. For all heptapeptides, except GY7, parallel β-sheet organizations with polar residues packed at the steric zipper appear to be the preferred assemblies for the two β-sheets system due to the formation of a strong network of hydrogen bonds. For GY7, however, an antiparallel organization with glycine at the steric zipper is the most stable one. The preferred architecture is mostly conserved when enlarging our model from two to four β-sheets. The present work shows that the relative stability of different architectures results from a delicate balance between peptide composition, side chain hydrophobicity, and non-covalent interactions at the interface and provides the basis for a rational design of new improved artificial prion-inspired materials.
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Affiliation(s)
- Francesca Peccati
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Mariona Sodupe
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
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19
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Cascarina SM, Kaplan JP, Elder MR, Brookbank L, Ross ED. Generalizable Compositional Features Influencing the Proteostatic Fates of Polar Low-Complexity Domains. Int J Mol Sci 2021; 22:ijms22168944. [PMID: 34445649 PMCID: PMC8396281 DOI: 10.3390/ijms22168944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/11/2021] [Accepted: 08/16/2021] [Indexed: 11/25/2022] Open
Abstract
Protein aggregation is associated with a growing list of human diseases. A substantial fraction of proteins in eukaryotic proteomes constitutes a proteostasis network—a collection of proteins that work together to maintain properly folded proteins. One of the overarching functions of the proteostasis network is the prevention or reversal of protein aggregation. How proteins aggregate in spite of the anti-aggregation activity of the proteostasis machinery is incompletely understood. Exposed hydrophobic patches can trigger degradation by the ubiquitin-proteasome system, a key branch of the proteostasis network. However, in a recent study, we found that model glycine (G)-rich or glutamine/asparagine (Q/N)-rich prion-like domains differ in their susceptibility to detection and degradation by this system. Here, we expand upon this work by examining whether the features controlling the degradation of our model prion-like domains generalize broadly to G-rich and Q/N-rich domains. Experimentally, native yeast G-rich domains in isolation are sensitive to the degradation-promoting effects of hydrophobic residues, whereas native Q/N-rich domains completely resist these effects and tend to aggregate instead. Bioinformatic analyses indicate that native G-rich domains from yeast and humans tend to avoid degradation-promoting features, suggesting that the proteostasis network may act as a form of selection at the molecular level that constrains the sequence space accessible to G-rich domains. However, the sensitivity or resistance of G-rich and Q/N-rich domains, respectively, was not always preserved in their native protein contexts, highlighting that proteins can evolve other sequence features to overcome the intrinsic sensitivity of some LCDs to degradation.
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20
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Garai S, Citu, Singla-Pareek SL, Sopory SK, Kaur C, Yadav G. Complex Networks of Prion-Like Proteins Reveal Cross Talk Between Stress and Memory Pathways in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:707286. [PMID: 34381483 PMCID: PMC8350573 DOI: 10.3389/fpls.2021.707286] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 06/29/2021] [Indexed: 08/01/2023]
Abstract
Prions are often considered as molecular memory devices, generating reproducible memory of a conformational change. Prion-like proteins (PrLPs) have been widely demonstrated to be present in plants, but their role in plant stress and memory remains unexplored. In this work, we report the widespread presence of PrLPs in plants through a comprehensive meta-analysis of 39 genomes representing major taxonomic groups. We find diverse functional roles associated with these proteins in various species and term the full complement of PrLPs in a genome as its "prionome." In particular, we found the rice prionome being significantly enriched in transposons/retrotransposons (Ts/RTRs) and identified over 60 rice PrLPs that were differentially regulated in stress and developmental responses. This prompted us to explore whether and to what extent PrLPs may build stress memory. By integrating the available rice interactome, transcriptome, and regulome data sets, we could find links between stress and memory pathways that would not have otherwise been discernible. Regulatory inferences derived from the superimposition of these data sets revealed a complex network and cross talk between PrLPs, transcription factors (TFs), and the genes involved in stress priming. This integrative meta-analysis connects transient and transgenerational memory mechanisms in plants with PrLPs, suggesting that plant memory may rely upon protein-based signals in addition to chromatin-based epigenetic signals. Taken together, our work provides important insights into the anticipated role of prion-like candidates in stress and memory, paving the way for more focused studies for validating the role of the identified PrLPs in memory acclimation.
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Affiliation(s)
- Sampurna Garai
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Citu
- Computational Biology Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Sneh L. Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Sudhir K. Sopory
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Charanpreet Kaur
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Gitanjali Yadav
- Computational Biology Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
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21
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Zajkowski T, Lee MD, Mondal SS, Carbajal A, Dec R, Brennock PD, Piast RW, Snyder JE, Bense NB, Dzwolak W, Jarosz DF, Rothschild LJ. The Hunt for Ancient Prions: Archaeal Prion-Like Domains Form Amyloid-Based Epigenetic Elements. Mol Biol Evol 2021; 38:2088-2103. [PMID: 33480998 DOI: 10.1093/molbev/msab010] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Prions, proteins that can convert between structurally and functionally distinct states and serve as non-Mendelian mechanisms of inheritance, were initially discovered and only known in eukaryotes, and consequently considered to likely be a relatively late evolutionary acquisition. However, the recent discovery of prions in bacteria and viruses has intimated a potentially more ancient evolutionary origin. Here, we provide evidence that prion-forming domains exist in the domain archaea, the last domain of life left unexplored with regard to prions. We searched for archaeal candidate prion-forming protein sequences computationally, described their taxonomic distribution and phylogeny, and analyzed their associated functional annotations. Using biophysical in vitro assays, cell-based and microscopic approaches, and dye-binding analyses, we tested select candidate prion-forming domains for prionogenic characteristics. Out of the 16 tested, eight formed amyloids, and six acted as protein-based elements of information transfer driving non-Mendelian patterns of inheritance. We also identified short peptides from our archaeal prion candidates that can form amyloid fibrils independently. Lastly, candidates that tested positively in our assays had significantly higher tyrosine and phenylalanine content than candidates that tested negatively, an observation that may help future archaeal prion predictions. Taken together, our discovery of functional prion-forming domains in archaea provides evidence that multiple archaeal proteins are capable of acting as prions-thus expanding our knowledge of this epigenetic phenomenon to the third and final domain of life and bolstering the possibility that they were present at the time of the last universal common ancestor.
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Affiliation(s)
- Tomasz Zajkowski
- Centre of New Technologies, University of Warsaw, Warsaw, Poland.,University Space Research Association, Mountain View, CA, USA.,Blue Marble Space Institute of Science, Seattle, WA, USA
| | - Michael D Lee
- Blue Marble Space Institute of Science, Seattle, WA, USA
| | - Shamba S Mondal
- Laboratory of Bioinformatics, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Amanda Carbajal
- University Space Research Association, Mountain View, CA, USA.,University of California Santa Cruz, Santa Cruz, CA, USA
| | - Robert Dec
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | | | - Radoslaw W Piast
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | | | | | - Wojciech Dzwolak
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Daniel F Jarosz
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lynn J Rothschild
- Space Science and Astrobiology Division, NASA Ames Research Center, Moffett Field, CA, USA
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22
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Simon I, Delaleau M, Schwartz A, Boudvillain M. A Large Insertion Domain in the Rho Factor From a Low G + C, Gram-negative Bacterium is Critical for RNA Binding and Transcription Termination Activity. J Mol Biol 2021; 433:167060. [PMID: 34023400 DOI: 10.1016/j.jmb.2021.167060] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/30/2021] [Accepted: 05/16/2021] [Indexed: 10/21/2022]
Abstract
Rho-dependent termination of transcription (RDTT) is a critical regulatory mechanism specific to bacteria. In a subset of species including most Actinobacteria and Bacteroidetes, the Rho factor contains a large, poorly conserved N-terminal insertion domain (NID) of cryptic function. To date, only two NID-bearing Rho factors from high G + C Actinobacteria have been thoroughly characterized. Both can trigger RDTT at promoter-proximal sites or with structurally constrained transcripts that are unsuitable for the archetypal, NID-less Rho factor of Escherichia coli (EcRho). Here, we provide the first biochemical characterization of a NID-bearing Rho factor from a low G + C bacterium. We show that Bacteroides fragilis Rho (BfRho) is a bona fide RNA-dependent NTPase motor able to unwind long RNA:DNA duplexes and to disrupt transcription complexes. The large NID (~40% of total mass) strongly increases BfRho affinity for RNA, is strictly required for RDTT, but does not promote RDTT at promoter-proximal sites or with a structurally constrained transcript. Furthermore, the NID does not preclude modulation of RDTT by transcription factors NusA and NusG or by the Rho inhibitor bicyclomycin. Although the NID contains a prion-like Q/N-rich motif, it does not spontaneously trigger formation of β-amyloids. Thus, despite its unusually large RNA binding domain, BfRho behaves more like the NID-less EcRho than NID-bearing counterparts from high G + C Actinobacteria. Our data highlight the evolutionary plasticity of Rho's N-terminal region and illustrate how RDTT is adapted to distinct genomic contents.
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Affiliation(s)
- Isabelle Simon
- Centre de Biophysique Moléculaire, CNRS UPR4301, Rue Charles Sadron, 45071 Orléans cedex 2, France; ED 549, Santé, Sciences Biologiques & Chimie du Vivant, Université d'Orléans, France
| | - Mildred Delaleau
- Centre de Biophysique Moléculaire, CNRS UPR4301, Rue Charles Sadron, 45071 Orléans cedex 2, France
| | - Annie Schwartz
- Centre de Biophysique Moléculaire, CNRS UPR4301, Rue Charles Sadron, 45071 Orléans cedex 2, France
| | - Marc Boudvillain
- Centre de Biophysique Moléculaire, CNRS UPR4301, Rue Charles Sadron, 45071 Orléans cedex 2, France.
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23
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Dyrka W, Gąsior-Głogowska M, Szefczyk M, Szulc N. Searching for universal model of amyloid signaling motifs using probabilistic context-free grammars. BMC Bioinformatics 2021; 22:222. [PMID: 33926372 PMCID: PMC8086366 DOI: 10.1186/s12859-021-04139-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 04/19/2021] [Indexed: 11/16/2022] Open
Abstract
Background Amyloid signaling motifs are a class of protein motifs which share basic structural and functional features despite the lack of clear sequence homology. They are hard to detect in large sequence databases either with the alignment-based profile methods (due to short length and diversity) or with generic amyloid- and prion-finding tools (due to insufficient discriminative power). We propose to address the challenge with a machine learning grammatical model capable of generalizing over diverse collections of unaligned yet related motifs. Results First, we introduce and test improvements to our probabilistic context-free grammar framework for protein sequences that allow for inferring more sophisticated models achieving high sensitivity at low false positive rates. Then, we infer universal grammars for a collection of recently identified bacterial amyloid signaling motifs and demonstrate that the method is capable of generalizing by successfully searching for related motifs in fungi. The results are compared to available alternative methods. Finally, we conduct spectroscopy and staining analyses of selected peptides to verify their structural and functional relationship. Conclusions While the profile HMMs remain the method of choice for modeling homologous sets of sequences, PCFGs seem more suitable for building meta-family descriptors and extrapolating beyond the seed sample. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04139-y.
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Affiliation(s)
- Witold Dyrka
- Wydział Podstawowych Problemów Techniki, Katedra Inżynierii Biomedycznej, Politechnika Wrocławska, Wrocław, Poland.
| | - Marlena Gąsior-Głogowska
- Wydział Podstawowych Problemów Techniki, Katedra Inżynierii Biomedycznej, Politechnika Wrocławska, Wrocław, Poland
| | - Monika Szefczyk
- Wydział Chemiczny, Katedra Chemii Bioorganicznej, Politechnika Wrocławska, Wrocław, Poland
| | - Natalia Szulc
- Wydział Podstawowych Problemów Techniki, Katedra Inżynierii Biomedycznej, Politechnika Wrocławska, Wrocław, Poland
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24
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MED15 prion-like domain forms a coiled-coil responsible for its amyloid conversion and propagation. Commun Biol 2021; 4:414. [PMID: 33772081 PMCID: PMC7997880 DOI: 10.1038/s42003-021-01930-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 03/02/2021] [Indexed: 02/01/2023] Open
Abstract
A disordered to β-sheet transition was thought to drive the functional switch of Q/N-rich prions, similar to pathogenic amyloids. However, recent evidence indicates a critical role for coiled-coil (CC) regions within yeast prion domains in amyloid formation. We show that many human prion-like domains (PrLDs) contain CC regions that overlap with polyQ tracts. Most of the proteins bearing these domains are transcriptional coactivators, including the Mediator complex subunit 15 (MED15) involved in bridging enhancers and promoters. We demonstrate that the human MED15-PrLD forms homodimers in solution sustained by CC interactions and that it is this CC fold that mediates the transition towards a β-sheet amyloid state, its chemical or genetic disruption abolishing aggregation. As in functional yeast prions, a GFP globular domain adjacent to MED15-PrLD retains its structural integrity in the amyloid state. Expression of MED15-PrLD in human cells promotes the formation of cytoplasmic and perinuclear inclusions, kidnapping endogenous full-length MED15 to these aggregates in a prion-like manner. The prion-like properties of MED15 are conserved, suggesting novel mechanisms for the function and malfunction of this transcription coactivator.
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25
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Louka A, Zacco E, Temussi PA, Tartaglia GG, Pastore A. RNA as the stone guest of protein aggregation. Nucleic Acids Res 2020; 48:11880-11889. [PMID: 33068411 PMCID: PMC7708036 DOI: 10.1093/nar/gkaa822] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/12/2020] [Accepted: 10/14/2020] [Indexed: 12/13/2022] Open
Abstract
The study of prions as infectious aggregates dates several decades. From its original formulation, the definition of a prion has progressively changed to the point that many aggregation-prone proteins are now considered bona fide prions. RNA molecules, not included in the original 'protein-only hypothesis', are also being recognized as important factors contributing to the 'prion behaviour', that implies the transmissibility of an aberrant fold. In particular, an association has recently emerged between aggregation and the assembly of prion-like proteins in RNA-rich complexes, associated with both physiological and pathological events. Here, we discuss the historical rising of the concept of prion-like domains, their relation to RNA and their role in protein aggregation. As a paradigmatic example, we present the case study of TDP-43, an RNA-binding prion-like protein associated with amyotrophic lateral sclerosis. Through this example, we demonstrate how the current definition of prions has incorporated quite different concepts making the meaning of the term richer and more stimulating. An important message that emerges from our analysis is the dual role of RNA in protein aggregation, making RNA, that has been considered for many years a 'silent presence' or the 'stone guest' of protein aggregation, an important component of the process.
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Affiliation(s)
- Alexandra Louka
- UK Dementia Research Institute at the Maurice Wohl Institute of King's College London, London SE5 9RT, UK
| | - Elsa Zacco
- Center for Human Technologies, Central RNA laboratory, Istituto Italiano di Tecnologia, Genova 16152, Italy
| | - Piero Andrea Temussi
- UK Dementia Research Institute at the Maurice Wohl Institute of King's College London, London SE5 9RT, UK
- University “Federico II’’ Napoli, via Cynthia, Napoli 80100, Italy
| | - Gian Gaetano Tartaglia
- Center for Human Technologies, Central RNA laboratory, Istituto Italiano di Tecnologia, Genova 16152, Italy
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain and ICREA, 23 Passeig Lluıs Companys, Barcelona 08010, Spain
- Charles Darwin department of Biology and Biotechnology, Sapienza University of Rome, Piazzale A. Moro 5, Rome 00185, Italy
| | - Annalisa Pastore
- UK Dementia Research Institute at the Maurice Wohl Institute of King's College London, London SE5 9RT, UK
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26
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Wang W, Azizyan RA, Garro A, Kajava AV, Ventura S. Multifunctional Amyloid Oligomeric Nanoparticles for Specific Cell Targeting and Drug Delivery. Biomacromolecules 2020; 21:4302-4312. [PMID: 32885960 DOI: 10.1021/acs.biomac.0c01103] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Natural selection has endorsed proteins with amazing structures and functionalities that cannot be matched by synthetic means, explaining the exponential interest in developing protein-based materials. Protein self-assembly allows fabricating complex supramolecular structures from relatively simple building blocks, a bottom-up strategy naturally employed by amyloid fibrils. However, the design of amyloid-inspired materials with biological activity is inherently difficult. Here, we exploit a modular procedure to generate functional amyloid nanostructures with tight control of their mesoscopic properties. The soft amyloid core of a yeast prion was fused to dihydrofolate reductase through flexible linkers of different sizes. This enabled us to produce, for the first time, biocompatible protein-only amyloid-like oligomeric nanoparticles with defined dimensions in which the embedded enzyme remained highly active, as assessed by biophysical and enzymatic assays. The modular design allowed one to obtain multifunctional nanoparticles by incorporating the antibody-binding Z-domain to the protein fusion. We show how these assemblies can be exploited for antibody-directed targeting of specific cell types and the localized delivery of methotrexate, resulting in the intracellular uptake of the drug by cancer cells and their death. Overall, the novel protein particles we describe in this work might find applications in areas as diverse as biocatalysis, bioimaging, or targeted therapies.
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Affiliation(s)
- Weiqiang Wang
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Rafayel A Azizyan
- Centre de Recherche en Biologie cellulaire de Montpellier, UMR 5237 CNRS, Université Montpellier, Montpellier 34090, France.,Institut de Biologie Computationnelle, Université Montpellier, Montpellier 34090, France
| | - Adriana Garro
- Universidad Nacional de San Luis IMASL-CONICET, San Luis D5702, Argentina
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier, UMR 5237 CNRS, Université Montpellier, Montpellier 34090, France.,Institut de Biologie Computationnelle, Université Montpellier, Montpellier 34090, France
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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27
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Gotor NL, Armaos A, Calloni G, Torrent Burgas M, Vabulas R, De Groot NS, Tartaglia GG. RNA-binding and prion domains: the Yin and Yang of phase separation. Nucleic Acids Res 2020; 48:9491-9504. [PMID: 32857852 PMCID: PMC7515694 DOI: 10.1093/nar/gkaa681] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 07/08/2020] [Accepted: 08/05/2020] [Indexed: 12/17/2022] Open
Abstract
Proteins and RNAs assemble in membrane-less organelles that organize intracellular spaces and regulate biochemical reactions. The ability of proteins and RNAs to form condensates is encoded in their sequences, yet it is unknown which domains drive the phase separation (PS) process and what are their specific roles. Here, we systematically investigated the human and yeast proteomes to find regions promoting condensation. Using advanced computational methods to predict the PS propensity of proteins, we designed a set of experiments to investigate the contributions of Prion-Like Domains (PrLDs) and RNA-binding domains (RBDs). We found that one PrLD is sufficient to drive PS, whereas multiple RBDs are needed to modulate the dynamics of the assemblies. In the case of stress granule protein Pub1 we show that the PrLD promotes sequestration of protein partners and the RBD confers liquid-like behaviour to the condensate. Our work sheds light on the fine interplay between RBDs and PrLD to regulate formation of membrane-less organelles, opening up the avenue for their manipulation.
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Affiliation(s)
- Nieves Lorenzo Gotor
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Alexandros Armaos
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Center for Human Technologies, Istituto Italiano di Tecnologia, RNA System Biology Lab, Via Enrico Melen 83, 16152 Genoa, Italy
| | - Giulia Calloni
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, 60438, Germany
- Institute of Biophysical Chemistry, Goethe University Frankfurt, Frankfurt am Main,60438, Germany
| | - Marc Torrent Burgas
- Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - R Martin Vabulas
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, 60438, Germany
- Institute of Biophysical Chemistry, Goethe University Frankfurt, Frankfurt am Main,60438, Germany
- Charité – Universitätsmedizin Berlin, Institute of Biochemistry, 10117 Berlin, Germany
| | - Natalia Sanchez De Groot
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Gian Gaetano Tartaglia
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Center for Human Technologies, Istituto Italiano di Tecnologia, RNA System Biology Lab, Via Enrico Melen 83, 16152 Genoa, Italy
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), 23 Passeig Lluis Companys, 08010 Barcelona, Spain
- Department of Biology and Biotechnology, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
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Caballero AB, Gamez P. Nanochaperone-Based Strategies to Control Protein Aggregation Linked to Conformational Diseases. Angew Chem Int Ed Engl 2020; 60:41-52. [PMID: 32706460 DOI: 10.1002/anie.202007924] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Indexed: 12/14/2022]
Abstract
The generation of highly organized amyloid fibrils is associated with a wide range of conformational pathologies, including primarily neurodegenerative diseases. Such disorders are characterized by misfolded proteins that lose their normal physiological roles and acquire toxicity. Recent findings suggest that proteostasis network impairment may be one of the causes leading to the accumulation and spread of amyloids. These observations are certainly contributing to a new focus in anti-amyloid drug design, whose efforts are so far being centered on single-target approaches aimed at inhibiting amyloid aggregation. Chaperones, known to maintain proteostasis, hence represent interesting targets for the development of novel therapeutics owing to their potential protective role against protein misfolding diseases. In this minireview, research on nanoparticles that can either emulate or help molecular chaperones in recognizing and/or correcting protein misfolding is discussed. The nascent concept of "nanochaperone" may indeed set future directions towards the development of cost-effective, disease-modifying drugs to treat several currently fatal disorders.
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Affiliation(s)
- Ana B Caballero
- nanoBIC, Departament de Química Inorgànica i Orgànica, Universitat de Barcelona, Martí i Franquès, 1-11, 08028, Barcelona, Spain.,Institute of Nanoscience and Nanotechnology (IN2UB), Universitat de Barcelona, 08028, Barcelona, Spain
| | - Patrick Gamez
- nanoBIC, Departament de Química Inorgànica i Orgànica, Universitat de Barcelona, Martí i Franquès, 1-11, 08028, Barcelona, Spain.,Institute of Nanoscience and Nanotechnology (IN2UB), Universitat de Barcelona, 08028, Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010, Barcelona, Spain
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29
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Caballero AB, Gamez P. Nanochaperone‐Based Strategies to Control Protein Aggregation Linked to Conformational Diseases. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202007924] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Ana B. Caballero
- nanoBIC Departament de Química Inorgànica i Orgànica Universitat de Barcelona Martí i Franquès, 1–11 08028 Barcelona Spain
- Institute of Nanoscience and Nanotechnology (IN2UB) Universitat de Barcelona 08028 Barcelona Spain
| | - Patrick Gamez
- nanoBIC Departament de Química Inorgànica i Orgànica Universitat de Barcelona Martí i Franquès, 1–11 08028 Barcelona Spain
- Institute of Nanoscience and Nanotechnology (IN2UB) Universitat de Barcelona 08028 Barcelona Spain
- Catalan Institution for Research and Advanced Studies (ICREA) Passeig Lluís Companys 23 08010 Barcelona Spain
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30
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Abstract
Amyloids are protein polymers that were initially linked to human diseases. Across the whole Tree of Life, many disease-unrelated proteins are now emerging for which amyloids represent distinct functional states. Most bacterial amyloids described are extracellular, contributing to biofilm formation. However, only a few have been found in the bacterial cytosol. This paper reviews from the perspective of synthetic biology (SynBio) our understanding of the subtle line that separates functional from pathogenic and transmissible amyloids (prions). Amyloids are protein polymers that were initially linked to human diseases. Across the whole Tree of Life, many disease-unrelated proteins are now emerging for which amyloids represent distinct functional states. Most bacterial amyloids described are extracellular, contributing to biofilm formation. However, only a few have been found in the bacterial cytosol. This paper reviews from the perspective of synthetic biology (SynBio) our understanding of the subtle line that separates functional from pathogenic and transmissible amyloids (prions). In particular, it is focused on RepA-WH1, a functional albeit unconventional natural amyloidogenic protein domain that participates in controlling DNA replication of bacterial plasmids. SynBio approaches, including protein engineering and the design of allosteric effectors such as diverse ligands and an optogenetic module, have enabled the generation in RepA-WH1 of an intracellular cytotoxic prion-like agent in bacteria. The synthetic RepA-WH1 prion has the potential to develop into novel antimicrobials.
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31
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Detection of Protein Aggregation in Live Plasmodium Parasites. Antimicrob Agents Chemother 2020; 64:AAC.02135-19. [PMID: 32284383 DOI: 10.1128/aac.02135-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 04/06/2020] [Indexed: 02/08/2023] Open
Abstract
The rapid evolution of resistance in the malaria parasite to every single drug developed against it calls for the urgent identification of new molecular targets. Using a stain specific for the detection of intracellular amyloid deposits in live cells, we have detected the presence of abundant protein aggregates in Plasmodium falciparum blood stages and female gametes cultured in vitro, in the blood stages of mice infected by Plasmodium yoelii, and in the mosquito stages of the murine malaria species Plasmodium berghei Aggregated proteins could not be detected in early rings, the parasite form that starts the intraerythrocytic cycle. A proteomics approach was used to pinpoint actual aggregating polypeptides in functional P. falciparum blood stages, which resulted in the identification of 369 proteins, with roles particularly enriched in nuclear import-related processes. Five aggregation-prone short peptides selected from this protein pool exhibited different aggregation propensity according to Thioflavin-T fluorescence measurements, and were observed to form amorphous aggregates and amyloid fibrils in transmission electron microscope images. The results presented suggest that generalized protein aggregation might have a functional role in malaria parasites. Future antimalarial strategies based on the upsetting of the pathogen's proteostasis and therefore affecting multiple gene products could represent the entry to new therapeutic approaches.
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32
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Gavín R, Lidón L, Ferrer I, del Río JA. The Quest for Cellular Prion Protein Functions in the Aged and Neurodegenerating Brain. Cells 2020; 9:cells9030591. [PMID: 32131451 PMCID: PMC7140396 DOI: 10.3390/cells9030591] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/21/2020] [Accepted: 02/27/2020] [Indexed: 12/19/2022] Open
Abstract
Cellular (also termed ‘natural’) prion protein has been extensively studied for many years for its pathogenic role in prionopathies after misfolding. However, neuroprotective properties of the protein have been demonstrated under various scenarios. In this line, the involvement of the cellular prion protein in neurodegenerative diseases other than prionopathies continues to be widely debated by the scientific community. In fact, studies on knock-out mice show a vast range of physiological functions for the protein that can be supported by its ability as a cell surface scaffold protein. In this review, we first summarize the most commonly described roles of cellular prion protein in neuroprotection, including antioxidant and antiapoptotic activities and modulation of glutamate receptors. Second, in light of recently described interaction between cellular prion protein and some amyloid misfolded proteins, we will also discuss the molecular mechanisms potentially involved in protection against neurodegeneration in pathologies such as Alzheimer’s, Parkinson’s, and Huntington’s diseases.
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Affiliation(s)
- Rosalina Gavín
- Molecular and Cellular Neurobiotechnology, Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology (BIST), Science Park of Barcelona, 08028 Barcelona, Spain; (L.L.); (J.A.d.R.)
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
- Center for Networked Biomedical Research on Neurodegenerative Diseases (Ciberned), 28031 Barcelona, Spain;
- Institute of Neuroscience, University of Barcelona, 08028 Barcelona, Spain
- Correspondence: ; Tel.: +34-93-4031185
| | - Laia Lidón
- Molecular and Cellular Neurobiotechnology, Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology (BIST), Science Park of Barcelona, 08028 Barcelona, Spain; (L.L.); (J.A.d.R.)
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
- Center for Networked Biomedical Research on Neurodegenerative Diseases (Ciberned), 28031 Barcelona, Spain;
- Institute of Neuroscience, University of Barcelona, 08028 Barcelona, Spain
| | - Isidre Ferrer
- Center for Networked Biomedical Research on Neurodegenerative Diseases (Ciberned), 28031 Barcelona, Spain;
- Institute of Neuroscience, University of Barcelona, 08028 Barcelona, Spain
- Department of Pathology and Experimental Therapeutics, University of Barcelona, 08907 Barcelona, Spain
- Senior Consultant, Bellvitge University Hospital, Hospitalet de Llobregat, 08907 Barcelona, Spain
- Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - José Antonio del Río
- Molecular and Cellular Neurobiotechnology, Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology (BIST), Science Park of Barcelona, 08028 Barcelona, Spain; (L.L.); (J.A.d.R.)
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
- Center for Networked Biomedical Research on Neurodegenerative Diseases (Ciberned), 28031 Barcelona, Spain;
- Institute of Neuroscience, University of Barcelona, 08028 Barcelona, Spain
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33
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Ebo JS, Guthertz N, Radford SE, Brockwell DJ. Using protein engineering to understand and modulate aggregation. Curr Opin Struct Biol 2020; 60:157-166. [PMID: 32087409 PMCID: PMC7132541 DOI: 10.1016/j.sbi.2020.01.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 01/08/2020] [Accepted: 01/09/2020] [Indexed: 02/07/2023]
Abstract
Protein aggregation occurs through a variety of mechanisms, initiated by the unfolded, non-native, or even the native state itself. Understanding the molecular mechanisms of protein aggregation is challenging, given the array of competing interactions that control solubility, stability, cooperativity and aggregation propensity. An array of methods have been developed to interrogate protein aggregation, spanning computational algorithms able to identify aggregation-prone regions, to deep mutational scanning to define the entire mutational landscape of a protein's sequence. Here, we review recent advances in this exciting and emerging field, focussing on protein engineering approaches that, together with improved computational methods, hold promise to predict and control protein aggregation linked to human disease, as well as facilitating the manufacture of protein-based therapeutics.
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Affiliation(s)
- Jessica S Ebo
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK; School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Nicolas Guthertz
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK; School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK; School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK; School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
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34
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Lathe R, Darlix JL. Prion protein PrP nucleic acid binding and mobilization implicates retroelements as the replicative component of transmissible spongiform encephalopathy. Arch Virol 2020; 165:535-556. [PMID: 32025859 PMCID: PMC7024060 DOI: 10.1007/s00705-020-04529-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 12/13/2019] [Indexed: 12/21/2022]
Abstract
The existence of more than 30 strains of transmissible spongiform encephalopathy (TSE) and the paucity of infectivity of purified PrPSc, as well as considerations of PrP structure, are inconsistent with the protein-only (prion) theory of TSE. Nucleic acid is a strong contender as a second component. We juxtapose two key findings: (i) PrP is a nucleic-acid-binding antimicrobial protein that is similar to retroviral Gag proteins in its ability to trigger reverse transcription. (ii) Retroelement mobilization is widely seen in TSE disease. Given further evidence that PrP also mediates nucleic acid transport into and out of the cell, a strong case is to be made that a second element – retroelement nucleic acid – bound to PrP constitutes the second component necessary to explain the multiple strains of TSE.
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Affiliation(s)
- Richard Lathe
- Division of Infection Medicine, University of Edinburgh School of Medicine, Edinburgh, UK. .,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Moscow, Moscow Region, Russia.
| | - Jean-Luc Darlix
- Faculté de Pharmacie, Centre Nationale de la Recherche Scientifique (CNRS) Laboratory of Bioimaging and Pathologies (Unité Mixte de Recherche 7021), Université de Strasbourg, Illkirch, France.
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35
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Cascarina SM, Ross ED. Natural and pathogenic protein sequence variation affecting prion-like domains within and across human proteomes. BMC Genomics 2020; 21:23. [PMID: 31914925 PMCID: PMC6947906 DOI: 10.1186/s12864-019-6425-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 12/23/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Impaired proteostatic regulation of proteins with prion-like domains (PrLDs) is associated with a variety of human diseases including neurodegenerative disorders, myopathies, and certain forms of cancer. For many of these disorders, current models suggest a prion-like molecular mechanism of disease, whereby proteins aggregate and spread to neighboring cells in an infectious manner. The development of prion prediction algorithms has facilitated the large-scale identification of PrLDs among "reference" proteomes for various organisms. However, the degree to which intraspecies protein sequence diversity influences predicted prion propensity has not been systematically examined. RESULTS Here, we explore protein sequence variation introduced at genetic, post-transcriptional, and post-translational levels, and its influence on predicted aggregation propensity for human PrLDs. We find that sequence variation is relatively common among PrLDs and in some cases can result in relatively large differences in predicted prion propensity. Sequence variation introduced at the post-transcriptional level (via alternative splicing) also commonly affects predicted aggregation propensity, often by direct inclusion or exclusion of a PrLD. Finally, analysis of a database of sequence variants associated with human disease reveals a number of mutations within PrLDs that are predicted to increase prion propensity. CONCLUSIONS Our analyses expand the list of candidate human PrLDs, quantitatively estimate the effects of sequence variation on the aggregation propensity of PrLDs, and suggest the involvement of prion-like mechanisms in additional human diseases.
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Affiliation(s)
- Sean M Cascarina
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Eric D Ross
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA.
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36
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Pallarés I, Ventura S. Advances in the Prediction of Protein Aggregation Propensity. Curr Med Chem 2019; 26:3911-3920. [DOI: 10.2174/0929867324666170705121754] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 04/14/2017] [Accepted: 04/20/2017] [Indexed: 12/29/2022]
Abstract
Background:
Protein aggregation into β-sheet-enriched insoluble assemblies is being
found to be associated with an increasing number of debilitating human pathologies, such as Alzheimer’s
disease or type 2 diabetes, but also with premature aging. Furthermore, protein aggregation
represents a major bottleneck in the production and marketing of proteinbased therapeutics.
Thus, the development of methods to accurately forecast the aggregation propensity of a certain
protein is of much value.
Methods/Results:
A myriad of in vitro and in vivo aggregation studies have shown that the aggregation
propensity of a certain polypeptide sequence is highly dependent on its intrinsic properties
and, in most cases, driven by specific short regions of high aggregation propensity. These observations
have fostered the development of a first generation of algorithms aimed to predict protein
aggregation propensities from the protein sequence. A second generation of programs able to map
protein aggregation on protein structures is emerging. Herein, we review the most representative
online accessible predictive tools, emphasizing their main distinctive features and the range of
applications.
Conclusion:
In this review, we describe representative biocomputational approaches to evaluate
the aggregation properties of protein sequences and structures, while illustrating how they can
become very useful tools to target protein aggregation in biomedicine and biotechnology.
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Affiliation(s)
- Irantzu Pallarés
- Institut de Biotecnologia i Biomedicina, Universitat Autonoma de Barcelona, 08193-Bellaterra (Barcelona), Spain
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina, Universitat Autonoma de Barcelona, 08193-Bellaterra (Barcelona), Spain
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37
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Lévy E, El Banna N, Baïlle D, Heneman-Masurel A, Truchet S, Rezaei H, Huang ME, Béringue V, Martin D, Vernis L. Causative Links between Protein Aggregation and Oxidative Stress: A Review. Int J Mol Sci 2019; 20:ijms20163896. [PMID: 31405050 PMCID: PMC6719959 DOI: 10.3390/ijms20163896] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 07/30/2019] [Accepted: 08/01/2019] [Indexed: 01/17/2023] Open
Abstract
Compelling evidence supports a tight link between oxidative stress and protein aggregation processes, which are noticeably involved in the development of proteinopathies, such as Alzheimer’s disease, Parkinson’s disease, and prion disease. The literature is tremendously rich in studies that establish a functional link between both processes, revealing that oxidative stress can be either causative, or consecutive, to protein aggregation. Because oxidative stress monitoring is highly challenging and may often lead to artefactual results, cutting-edge technical tools have been developed recently in the redox field, improving the ability to measure oxidative perturbations in biological systems. This review aims at providing an update of the previously known functional links between oxidative stress and protein aggregation, thereby revisiting the long-established relationship between both processes.
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Affiliation(s)
- Elise Lévy
- Molecular Virology and Immunology Unit (VIM-UR892), INRA, Université Paris-Saclay, 78352 Jouy-en-Josas, France
- Institut Curie, PSL Research University, CNRS UMR3348, Université Paris-Sud, Université Paris-Saclay, 91400 Orsay, France
| | - Nadine El Banna
- Institut Curie, PSL Research University, CNRS UMR3348, Université Paris-Sud, Université Paris-Saclay, 91400 Orsay, France
| | - Dorothée Baïlle
- Institut Curie, PSL Research University, CNRS UMR3348, Université Paris-Sud, Université Paris-Saclay, 91400 Orsay, France
| | - Amélie Heneman-Masurel
- Institut Curie, PSL Research University, CNRS UMR3348, Université Paris-Sud, Université Paris-Saclay, 91400 Orsay, France
| | - Sandrine Truchet
- Molecular Virology and Immunology Unit (VIM-UR892), INRA, Université Paris-Saclay, 78352 Jouy-en-Josas, France
| | - Human Rezaei
- Molecular Virology and Immunology Unit (VIM-UR892), INRA, Université Paris-Saclay, 78352 Jouy-en-Josas, France
| | - Meng-Er Huang
- Institut Curie, PSL Research University, CNRS UMR3348, Université Paris-Sud, Université Paris-Saclay, 91400 Orsay, France
| | - Vincent Béringue
- Molecular Virology and Immunology Unit (VIM-UR892), INRA, Université Paris-Saclay, 78352 Jouy-en-Josas, France
| | - Davy Martin
- Molecular Virology and Immunology Unit (VIM-UR892), INRA, Université Paris-Saclay, 78352 Jouy-en-Josas, France.
| | - Laurence Vernis
- Institut Curie, PSL Research University, CNRS UMR3348, Université Paris-Sud, Université Paris-Saclay, 91400 Orsay, France.
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38
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Formation of Cross-Beta Supersecondary Structure by Soft-Amyloid Cores: Strategies for Their Prediction and Characterization. Methods Mol Biol 2019. [PMID: 30945222 DOI: 10.1007/978-1-4939-9161-7_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Proteins with prion-like behavior are attracting an increasing interest, since accumulating evidences indicate that they play relevant roles both in health and disease. The self-assembly of these proteins into insoluble aggregates is associated with severe neuropathological processes such as amyotrophic lateral sclerosis (ALS). However, in normal conditions, they are known to accomplish a wide range of functional roles. The conformational duality of prion-like proteins is often encoded in specific protein regions, named prion-like domains (PrLDs). PrLDs are usually long and disordered regions of low complexity. We have shown that PrLDs might contain soft-amyloid cores that contribute significantly to trigger their aggregation, as well as to support their propagation. Further exploration of the role of these sequences in the conformational conversion of prion-like proteins might provide novel insights into the mechanism of action and regulation of these polypeptides, enabling the future development of therapeutic strategies. Here, we describe a set of methodologies aimed to identify and characterize these short amyloid stretches in a protein or proteome of interest, ranging from in silico detection to in vitro and in vivo evaluation and validation.
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39
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Iglesias V, Paladin L, Juan-Blanco T, Pallarès I, Aloy P, Tosatto SCE, Ventura S. In silico Characterization of Human Prion-Like Proteins: Beyond Neurological Diseases. Front Physiol 2019; 10:314. [PMID: 30971948 PMCID: PMC6445884 DOI: 10.3389/fphys.2019.00314] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 03/07/2019] [Indexed: 12/18/2022] Open
Abstract
Prion-like behavior has been in the spotlight since it was first associated with the onset of mammalian neurodegenerative diseases. However, a growing body of evidence suggests that this mechanism could be behind the regulation of processes such as transcription and translation in multiple species. Here, we perform a stringent computational survey to identify prion-like proteins in the human proteome. We detected 242 candidate polypeptides and computationally assessed their function, protein–protein interaction networks, tissular expression, and their link to disease. Human prion-like proteins constitute a subset of modular polypeptides broadly expressed across different cell types and tissues, significantly associated with disease, embedded in highly connected interaction networks, and involved in the flow of genetic information in the cell. Our analysis suggests that these proteins might play a relevant role not only in neurological disorders, but also in different types of cancer and viral infections.
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Affiliation(s)
- Valentin Iglesias
- Institut de Biotecnologia i de Biomedicina, Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Lisanna Paladin
- Department of Biomedical Sciences, University of Padua, Padua, Italy
| | - Teresa Juan-Blanco
- Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Irantzu Pallarès
- Institut de Biotecnologia i de Biomedicina, Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Patrick Aloy
- Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Silvio C E Tosatto
- Department of Biomedical Sciences, University of Padua, Padua, Italy.,CNR Institute of Neuroscience, Padua, Italy
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina, Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
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40
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Espargaró A, Pont C, Gamez P, Muñoz-Torrero D, Sabate R. Amyloid Pan-inhibitors: One Family of Compounds To Cope with All Conformational Diseases. ACS Chem Neurosci 2019; 10:1311-1317. [PMID: 30380841 DOI: 10.1021/acschemneuro.8b00398] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Amyloids are ubiquitous protein aggregates sharing common internal structural features; they are present in all organisms, from prokaryotes to eukaryotes, where they play physiological or pathological roles. Importantly, amyloids, which are generated by aggregation of a range of distinct proteins, could be a key factor in a number of major human disorders, the so-called conformational diseases. Because all amyloids exhibit similar cross-β motifs, one may envisage that molecules capable of blocking the formation of β-sheet structures could abolish aggregation of all amyloid proteins, albeit with different efficacies. Herein, two different β-sheet blockers were tested against a selection of amyloidogenic proteins, encompassing all the major types of amyloid-based disorders. Analysis of their blocking efficiency, using a simple but contrasted cell-based screening procedure, unequivocally confirms that they indeed behave as aggregation pan-inhibitors. The significant inhibitory effects observed for these compounds against all tested amyloidogenic proteins could spur a broader biological evaluation of other known and new amyloid aggregation inhibitors to further determine the potential use of this class of compounds for the universal treatment of conformational diseases.
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Affiliation(s)
- Alba Espargaró
- Department of Pharmacy and Pharmaceutical Technology and Physical-Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, E-08028 Barcelona, Spain
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, E-08028 Barcelona, Spain
| | - Caterina Pont
- Laboratory of Pharmaceutical Chemistry (CSIC Associated Unit), Faculty of Pharmacy and Food Sciences, University of Barcelona, E-08028 Barcelona, Spain
| | - Patrick Gamez
- Department of Organic and Inorganic Chemistry, Faculty of Chemistry, University of Barcelona, E-08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), E-08010 Barcelona, Spain
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, E-08028 Barcelona, Spain
| | - Diego Muñoz-Torrero
- Laboratory of Pharmaceutical Chemistry (CSIC Associated Unit), Faculty of Pharmacy and Food Sciences, University of Barcelona, E-08028 Barcelona, Spain
- Institute of Biomedicine (IBUB), University of Barcelona, E-08028 Barcelona, Spain
| | - Raimon Sabate
- Department of Pharmacy and Pharmaceutical Technology and Physical-Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, E-08028 Barcelona, Spain
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, E-08028 Barcelona, Spain
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41
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Martinelli AHS, Lopes FC, John EBO, Carlini CR, Ligabue-Braun R. Modulation of Disordered Proteins with a Focus on Neurodegenerative Diseases and Other Pathologies. Int J Mol Sci 2019; 20:ijms20061322. [PMID: 30875980 PMCID: PMC6471803 DOI: 10.3390/ijms20061322] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/03/2019] [Accepted: 02/12/2019] [Indexed: 12/15/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) do not have rigid 3D structures, showing changes in their folding depending on the environment or ligands. Intrinsically disordered proteins are widely spread in eukaryotic genomes, and these proteins participate in many cell regulatory metabolism processes. Some IDPs, when aberrantly folded, can be the cause of some diseases such as Alzheimer′s, Parkinson′s, and prionic, among others. In these diseases, there are modifications in parts of the protein or in its entirety. A common conformational variation of these IDPs is misfolding and aggregation, forming, for instance, neurotoxic amyloid plaques. In this review, we discuss some IDPs that are involved in neurodegenerative diseases (such as beta amyloid, alpha synuclein, tau, and the “IDP-like” PrP), cancer (p53, c-Myc), and diabetes (amylin), focusing on the structural changes of these IDPs that are linked to such pathologies. We also present the IDP modulation mechanisms that can be explored in new strategies for drug design. Lastly, we show some candidate drugs that can be used in the future for the treatment of diseases caused by misfolded IDPs, considering that cancer therapy has more advanced research in comparison to other diseases, while also discussing recent and future developments in this area of research. Therefore, we aim to provide support to the study of IDPs and their modulation mechanisms as promising approaches to combat such severe diseases.
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Affiliation(s)
- Anne H S Martinelli
- Department of Molecular Biology and Biotechnology & Department of Biophysics, Biosciences Institute-IB, (UFRGS), Porto Alegre CEP 91501-970, RS, Brazil.
| | - Fernanda C Lopes
- Center for Biotechnology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre CEP 91501-970, RS, Brazil.
- Graduate Program in Cell and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre CEP 91501-970, RS, Brazil.
| | - Elisa B O John
- Center for Biotechnology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre CEP 91501-970, RS, Brazil.
- Graduate Program in Cell and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre CEP 91501-970, RS, Brazil.
| | - Célia R Carlini
- Graduate Program in Cell and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre CEP 91501-970, RS, Brazil.
- Graduate Program in Medicine and Health Sciences, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre CEP 91410-000, RS, Brazil.
- Brain Institute-InsCer, Laboratory of Neurotoxins, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre CEP 90610-000, RS, Brazil.
| | - Rodrigo Ligabue-Braun
- Department of Pharmaceutical Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre CEP 90050-170, RS, Brazil.
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42
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Iglesias V, Conchillo-Sole O, Batlle C, Ventura S. AMYCO: evaluation of mutational impact on prion-like proteins aggregation propensity. BMC Bioinformatics 2019; 20:24. [PMID: 30642249 PMCID: PMC6332698 DOI: 10.1186/s12859-019-2601-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 01/03/2019] [Indexed: 02/06/2023] Open
Abstract
Background Around 1% of human proteins are predicted to contain a disordered and low complexity prion-like domain (PrLD). Mutations in PrLDs have been shown promote a transition towards an aggregation-prone state in several diseases. Results Recently, we have shown that an algorithm that considers the effects of mutations on PrLDs composition, as well as on localized amyloid propensity can predict the impact of these amino acid changes on protein intracellular aggregation. In this application note, we implement this concept into the AMYCO web server, a refined algorithm that forecasts the influence of amino acid changes in prion-like proteins aggregation propensity better than state-of-the-art predictors. Conclusions The AMYCO web server allows for a fast and automated evaluation of the effect of mutations on the aggregation properties of prion-like proteins. This might uncover novel disease-linked amino acid changes in the sequences of human prion-like proteins. Additionally, it can find application in the in silico design of synthetic prion-like proteins with tuned aggregation propensities for different purposes. AMYCO does not require previous registration and is freely available to all users at: http://bioinf.uab.cat/amyco/. Electronic supplementary material The online version of this article (10.1186/s12859-019-2601-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Valentin Iglesias
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.,Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - Oscar Conchillo-Sole
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - Cristina Batlle
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.,Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain. .,Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.
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43
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Bantis LE, Nakas CT, Reiser B. Construction of confidence intervals for the maximum of the Youden index and the corresponding cutoff point of a continuous biomarker. Biom J 2018; 61:138-156. [DOI: 10.1002/bimj.201700107] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Revised: 07/20/2018] [Accepted: 07/24/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Leonidas E. Bantis
- Department of Biostatistics; University of Kansas Medical Center; Kansas City Kansas USA
| | - Christos T. Nakas
- Laboratory of Biometry, School of Agriculture; University of Thessaly; Nea Ionia Magnesia Greece
- University Institute of Clinical Chemistry, Inselspital, Bern University Hospital, University of Bern; Bern Switzerland
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Díaz-Caballero M, Fernández MR, Navarro S, Ventura S. Prion-based nanomaterials and their emerging applications. Prion 2018; 12:266-272. [PMID: 30196749 PMCID: PMC6277190 DOI: 10.1080/19336896.2018.1521235] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 08/22/2018] [Accepted: 08/23/2018] [Indexed: 12/12/2022] Open
Abstract
Protein misfolding and aggregation into highly ordered fibrillar structures have been traditionally associated with pathological processes. Nevertheless, nature has taken advantage of the particular properties of amyloids for functional purposes, like in the protection of organisms against environmental changing conditions. Over the last decades, these fibrillar structures have inspired the design of new nanomaterials with intriguing applications in biomedicine and nanotechnology such as tissue engineering, drug delivery, adhesive materials, biodegradable nanocomposites, nanowires or biosensors. Prion and prion-like proteins, which are considered a subclass of amyloids, are becoming ideal candidates for the design of new and tunable nanomaterials. In this review, we discuss the particular properties of this kind of proteins, and the current advances on the design of new materials based on prion sequences.
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Affiliation(s)
- Marta Díaz-Caballero
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autonoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Maria Rosario Fernández
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autonoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Susanna Navarro
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autonoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autonoma de Barcelona, Bellaterra (Barcelona), Spain
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45
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Pallarès I, de Groot NS, Iglesias V, Sant'Anna R, Biosca A, Fernàndez-Busquets X, Ventura S. Discovering Putative Prion-Like Proteins in Plasmodium falciparum: A Computational and Experimental Analysis. Front Microbiol 2018; 9:1737. [PMID: 30131778 PMCID: PMC6090025 DOI: 10.3389/fmicb.2018.01737] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 07/11/2018] [Indexed: 12/17/2022] Open
Abstract
Prions are a singular subset of proteins able to switch between a soluble conformation and a self-perpetuating amyloid state. Traditionally associated with neurodegenerative diseases, increasing evidence indicates that organisms exploit prion-like mechanisms for beneficial purposes. The ability to transit between conformations is encoded in the so-called prion domains, long disordered regions usually enriched in glutamine/asparagine residues. Interestingly, Plasmodium falciparum, the parasite that causes the most virulent form of malaria, is exceptionally rich in proteins bearing long Q/N-rich sequence stretches, accounting for roughly 30% of the proteome. This biased composition suggests that these protein regions might correspond to prion-like domains (PrLDs) and potentially form amyloid assemblies. To investigate this possibility, we performed a stringent computational survey for Q/N-rich PrLDs on P. falciparum. Our data indicate that ∼10% of P. falciparum protein sequences have prionic signatures, and that this subproteome is enriched in regulatory proteins, such as transcription factors and RNA-binding proteins. Furthermore, we experimentally demonstrate for several of the identified PrLDs that, despite their disordered nature, they contain inner short sequences able to spontaneously self-assemble into amyloid-like structures. Although the ability of these sequences to nucleate the conformational conversion of the respective full-length proteins should still be demonstrated, our analysis suggests that, as previously described for other organisms, prion-like proteins might also play a functional role in P. falciparum.
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Affiliation(s)
- Irantzu Pallarès
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain.,Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Natalia S de Groot
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Valentín Iglesias
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain.,Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Ricardo Sant'Anna
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain.,Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Arnau Biosca
- Nanomalaria Group, Institute for Bioengineering of Catalonia, The Barcelona Institute of Science and Technology, Barcelona, Spain.,Barcelona Institute for Global Health, Barcelona Centre for International Health Research (Hospital Clínic - Universitat de Barcelona), Barcelona, Spain.,Institute of Nanoscience and Nanotechnology, University of Barcelona, Barcelona, Spain
| | - Xavier Fernàndez-Busquets
- Nanomalaria Group, Institute for Bioengineering of Catalonia, The Barcelona Institute of Science and Technology, Barcelona, Spain.,Barcelona Institute for Global Health, Barcelona Centre for International Health Research (Hospital Clínic - Universitat de Barcelona), Barcelona, Spain.,Institute of Nanoscience and Nanotechnology, University of Barcelona, Barcelona, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain.,Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
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46
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Cereghetti G, Saad S, Dechant R, Peter M. Reversible, functional amyloids: towards an understanding of their regulation in yeast and humans. Cell Cycle 2018; 17:1545-1558. [PMID: 29963943 DOI: 10.1080/15384101.2018.1480220] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Protein aggregates, and in particular amyloids, are generally considered to be inherently irreversible aberrant clumps, and are often associated with pathologies, such as Alzheimer's disease, Parkinson's disease, or systemic amyloidosis. However, recent evidence demonstrates that some aggregates are not only fully reversible, but also perform essential physiological functions. Despite these new findings, very little is known about how these functional protein aggregates are regulated in a physiological context. Here, we take the yeast pyruvate kinase Cdc19 as an example of a protein forming functional, reversible, solid, amyloid-like aggregates in response to stress conditions. Cdc19 aggregation is regulated via an aggregation-prone low complexity region (LCR). In favorable growth conditions, this LCR is prevented from aggregating by phosphorylation or oligomerization, while upon glucose starvation it becomes exposed and allows aggregation. We suggest that LCR phosphorylation, oligomerization or partner-binding may be general and widespread mechanisms regulating LCR-mediated reversible protein aggregation. Moreover, we show that, as predicted by computational tools, Cdc19 forms amyloid-like aggregates in vitro. Interestingly, we also observe striking similarities between Cdc19 and its mammalian counterpart, PKM2. Indeed, also PKM2 harbors a LCR and contains several peptides with high amyloidogenic propensity, which coincide with known phosphorylation sites. Thus, we speculate that the formation of reversible, amyloid-like aggregates may be a general physiological mechanism for cells to adapt to stress conditions, and that the underlying regulatory mechanisms may be conserved from yeast to humans.
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Affiliation(s)
- Gea Cereghetti
- a Institute of Biochemistry, Department of Biology , ETH Zürich , Zürich , Switzerland.,b Life Science Zürich , Molecular Life Sciences , Zürich , Switzerland
| | - Shady Saad
- c Department of Chemical and Systems Biology , Stanford University , Stanford, CA , USA
| | - Reinhard Dechant
- a Institute of Biochemistry, Department of Biology , ETH Zürich , Zürich , Switzerland
| | - Matthias Peter
- a Institute of Biochemistry, Department of Biology , ETH Zürich , Zürich , Switzerland
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47
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Prion Replication in the Mammalian Cytosol: Functional Regions within a Prion Domain Driving Induction, Propagation, and Inheritance. Mol Cell Biol 2018; 38:MCB.00111-18. [PMID: 29784771 PMCID: PMC6048315 DOI: 10.1128/mcb.00111-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 05/14/2018] [Indexed: 12/19/2022] Open
Abstract
Prions of lower eukaryotes are transmissible protein particles that propagate by converting homotypic soluble proteins into growing protein assemblies. Prion activity is conferred by so-called prion domains, regions of low complexity that are often enriched in glutamines and asparagines (Q/N). Prions of lower eukaryotes are transmissible protein particles that propagate by converting homotypic soluble proteins into growing protein assemblies. Prion activity is conferred by so-called prion domains, regions of low complexity that are often enriched in glutamines and asparagines (Q/N). The compositional similarity of fungal prion domains with intrinsically disordered domains found in many mammalian proteins raises the question of whether similar sequence elements can drive prion-like phenomena in mammals. Here, we define sequence features of the prototype Saccharomyces cerevisiae Sup35 prion domain that govern prion activities in mammalian cells by testing the ability of deletion mutants to assemble into self-perpetuating particles. Interestingly, the amino-terminal Q/N-rich tract crucially important for prion induction in yeast was dispensable for the prion life cycle in mammalian cells. Spontaneous and template-assisted prion induction, growth, and maintenance were preferentially driven by the carboxy-terminal region of the prion domain that contains a putative soft amyloid stretch recently proposed to act as a nucleation site for prion assembly. Our data demonstrate that preferred prion nucleation domains can differ between lower and higher eukaryotes, resulting in the formation of prions with strikingly different amyloid cores.
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48
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Pujols J, Santos J, Pallarès I, Ventura S. The Disordered C-Terminus of Yeast Hsf1 Contains a Cryptic Low-Complexity Amyloidogenic Region. Int J Mol Sci 2018; 19:ijms19051384. [PMID: 29734798 PMCID: PMC5983738 DOI: 10.3390/ijms19051384] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 05/03/2018] [Accepted: 05/04/2018] [Indexed: 02/08/2023] Open
Abstract
Response mechanisms to external stress rely on networks of proteins able to activate specific signaling pathways to ensure the maintenance of cell proteostasis. Many of the proteins mediating this kind of response contain intrinsically disordered regions, which lack a defined structure, but still are able to interact with a wide range of clients that modulate the protein function. Some of these interactions are mediated by specific short sequences embedded in the longer disordered regions. Because the physicochemical properties that promote functional and abnormal interactions are similar, it has been shown that, in globular proteins, aggregation-prone and binding regions tend to overlap. It could be that the same principle applies for disordered protein regions. In this context, we show here that a predicted low-complexity interacting region in the disordered C-terminus of the stress response master regulator heat shock factor 1 (Hsf1) protein corresponds to a cryptic amyloid region able to self-assemble into fibrillary structures resembling those found in neurodegenerative disorders.
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Affiliation(s)
- Jordi Pujols
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, E-08193 Bellaterra (Barcelona), Spain.
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, E-08193 Bellaterra (Barcelona), Spain.
| | - Jaime Santos
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, E-08193 Bellaterra (Barcelona), Spain.
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, E-08193 Bellaterra (Barcelona), Spain.
| | - Irantzu Pallarès
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, E-08193 Bellaterra (Barcelona), Spain.
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, E-08193 Bellaterra (Barcelona), Spain.
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, E-08193 Bellaterra (Barcelona), Spain.
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, E-08193 Bellaterra (Barcelona), Spain.
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49
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Abstract
Prions are molecules characterized by self-propagation, which can undergo a conformational switch leading to the creation of new prions. Prion proteins have originally been associated with the development of mammalian pathologies; however, recently they have been shown to contribute to the environmental adaptation in a variety of prokaryotic and eukaryotic organisms. Bacteriophages are widespread and represent the important regulators of microbiota homeostasis and have been shown to be diverse across various bacterial families. Here, we examined whether bacteriophages contain prion-like proteins and whether these prion-like protein domains are involved in the regulation of homeostasis. We used a computational algorithm, prion-like amino acid composition, to detect prion-like domains in 370,617 publicly available bacteriophage protein sequences, which resulted in the identification of 5040 putative prions. We analyzed a set of these prion-like proteins, and observed regularities in their distribution across different phage families, associated with their interactions with the bacterial host cells. We found that prion-like domains could be found across all phages of various groups of bacteria and archaea. The results obtained in this study indicate that bacteriophage prion-like proteins are predominantly involved in the interactions between bacteriophages and bacterial cell, such as those associated with the attachment and penetration of bacteriophage in the cell, and the release of the phage progeny. These data allow the identification of phage prion-like proteins as novel regulators of the interactions between bacteriophages and bacterial cells.
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Affiliation(s)
- George Tetz
- Human Microbiology Institute, New York, NY, United States
| | - Victor Tetz
- Human Microbiology Institute, New York, NY, United States
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50
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Fernández MR, Batlle C, Gil-García M, Ventura S. Amyloid cores in prion domains: Key regulators for prion conformational conversion. Prion 2017; 11:31-39. [PMID: 28281928 DOI: 10.1080/19336896.2017.1282020] [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: 01/20/2023] Open
Abstract
Despite the significant efforts devoted to decipher the particular protein features that encode for a prion or prion-like behavior, they are still poorly understood. The well-characterized yeast prions constitute an ideal model system to address this question, because, in these proteins, the prion activity can be univocally assigned to a specific region of their sequence, known as the prion forming domain (PFD). These PFDs are intrinsically disordered, relatively long and, in many cases, of low complexity, being enriched in glutamine/asparagine residues. Computational analyses have identified a significant number of proteins having similar domains in the human proteome. The compositional bias of these regions plays an important role in the transition of the prions to the amyloid state. However, it is difficult to explain how composition alone can account for the formation of specific contacts that position correctly PFDs and provide the enthalpic force to compensate for the large entropic cost of immobilizing these domains in the initial assemblies. We have hypothesized that short, sequence-specific, amyloid cores embedded in PFDs can perform these functions and, accordingly, act as preferential nucleation centers in both spontaneous and seeded aggregation. We have shown that the implementation of this concept in a prediction algorithm allows to score the prion propensities of putative PFDs with high accuracy. Recently, we have provided experimental evidence for the existence of such amyloid cores in the PFDs of Sup35, Ure2, Swi1, and Mot3 yeast prions. The fibrils formed by these short stretches may recognize and promote the aggregation of the complete proteins inside cells, being thus a promising tool for targeted protein inactivation.
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Affiliation(s)
- María Rosario Fernández
- a Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular , Universitat Autonoma de Barcelona , Bellaterra (Barcelona) , Spain
| | - Cristina Batlle
- a Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular , Universitat Autonoma de Barcelona , Bellaterra (Barcelona) , Spain
| | - Marcos Gil-García
- a Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular , Universitat Autonoma de Barcelona , Bellaterra (Barcelona) , Spain
| | - Salvador Ventura
- a Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular , Universitat Autonoma de Barcelona , Bellaterra (Barcelona) , Spain
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