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Galkin AP, Sysoev EI, Valina AA. Amyloids and prions in the light of evolution. Curr Genet 2023; 69:189-202. [PMID: 37165144 DOI: 10.1007/s00294-023-01270-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/02/2023] [Accepted: 05/04/2023] [Indexed: 05/12/2023]
Abstract
Functional amyloids have been identified in a wide variety of organisms including bacteria, fungi, plants, and vertebrates. Intracellular and extracellular amyloid fibrils of different proteins perform storage, protective, structural, and regulatory functions. The structural organization of amyloid fibrils determines their unique physical and biochemical properties. The formation of these fibrillar structures can provide adaptive advantages that are picked up by natural selection. Despite the great interest in functional and pathological amyloids, questions about the conservatism of the amyloid properties of proteins and the regularities in the appearance of these fibrillar structures in evolution remain almost unexplored. Using bioinformatics approaches and summarizing the data published previously, we have shown that amyloid fibrils performing similar functions in different organisms have been arising repeatedly and independently in the course of evolution. On the other hand, we show that the amyloid properties of a number of bacterial and eukaryotic proteins are evolutionarily conserved. We also discuss the role of protein-based inheritance in the evolution of microorganisms. Considering that missense mutations and the emergence of prions cause the same consequences, we propose the concept that the formation of prions, similarly to mutations, generally causes a negative effect, although it can also lead to adaptations in rare cases. In general, our analysis revealed certain patterns in the emergence and spread of amyloid fibrillar structures in the course of evolution.
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Affiliation(s)
- Alexey P Galkin
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, St. Petersburg, Russian Federation, 199034.
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russian Federation, 199034.
| | - Evgeniy I Sysoev
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, St. Petersburg, Russian Federation, 199034
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russian Federation, 199034
| | - Anna A Valina
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russian Federation, 199034
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2
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Danilov LG, Sukhanova XV, Rogoza TM, Antonova EY, Trubitsina NP, Zhouravleva GA, Bondarev SA. Identification of New FG-Repeat Nucleoporins with Amyloid Properties. Int J Mol Sci 2023; 24:ijms24108571. [PMID: 37239918 DOI: 10.3390/ijms24108571] [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: 03/31/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
Amyloids are fibrillar protein aggregates with a cross-β structure. More than two hundred different proteins with amyloid or amyloid-like properties are already known. Functional amyloids with conservative amyloidogenic regions were found in different organisms. Protein aggregation appears to be beneficial for the organism in these cases. Therefore, this property might be conservative for orthologous proteins. The amyloid aggregates of the CPEB protein were suggested to play an important role in the long-term memory formation in Aplysia californica, Drosophila melanogaster, and Mus musculus. Moreover, the FXR1 protein demonstrates amyloid properties among the Vertebrates. A few nucleoporins (e.g., yeast Nup49, Nup100, Nup116, and human Nup153 and Nup58), are supposed or proved to form amyloid fibrils. In this study, we performed wide-scale bioinformatic analysis of nucleoporins with FG-repeats (phenylalanine-glycine repeats). We demonstrated that most of the barrier nucleoporins possess potential amyloidogenic properties. Furthermore, the aggregation-prone properties of several Nsp1 and Nup100 orthologs in bacteria and yeast cells were analyzed. Only two new nucleoporins, Drosophila melanogaster Nup98 and Schizosaccharomyces pombe Nup98, aggregated in different experiments. At the same time, Taeniopygia guttata Nup58 only formed amyloids in bacterial cells. These results rather contradict the hypothesis about the functional aggregation of nucleoporins.
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Affiliation(s)
- Lavrentii G Danilov
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Xenia V Sukhanova
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Tatiana M Rogoza
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
- St. Petersburg Branch, Vavilov Institute of General Genetics, Russian Academy of Sciences, 194064 St. Petersburg, Russia
| | - Ekaterina Y Antonova
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Nina P Trubitsina
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Stanislav A Bondarev
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
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Kawasaki T, Yamaguchi Y, Kitahara H, Irizawa A, Tani M. Exploring Biomolecular Self-Assembly with Far-Infrared Radiation. Biomolecules 2022; 12:biom12091326. [PMID: 36139165 PMCID: PMC9496551 DOI: 10.3390/biom12091326] [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: 08/23/2022] [Revised: 09/13/2022] [Accepted: 09/17/2022] [Indexed: 11/29/2022] Open
Abstract
Physical engineering technology using far-infrared radiation has been gathering attention in chemical, biological, and material research fields. In particular, the high-power radiation at the terahertz region can give remarkable effects on biological materials distinct from a simple thermal treatment. Self-assembly of biological molecules such as amyloid proteins and cellulose fiber plays various roles in medical and biomaterials fields. A common characteristic of those biomolecular aggregates is a sheet-like fibrous structure that is rigid and insoluble in water, and it is often hard to manipulate the stacking conformation without heating, organic solvents, or chemical reagents. We discovered that those fibrous formats can be conformationally regulated by means of intense far-infrared radiations from a free-electron laser and gyrotron. In this review, we would like to show the latest and the past studies on the effects of far-infrared radiation on the fibrous biomaterials and to suggest the potential use of the far-infrared radiation for regulation of the biomolecular self-assembly.
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Affiliation(s)
- Takayasu Kawasaki
- Accelerator Laboratory, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba 305-0801, Ibaraki, Japan
- Correspondence:
| | - Yuusuke Yamaguchi
- Research Center for Development of Far-Infrared Region, University of Fukui, 3-9-1 Bunkyo, Fukui 910-8507, Fukui, Japan
| | - Hideaki Kitahara
- Research Center for Development of Far-Infrared Region, University of Fukui, 3-9-1 Bunkyo, Fukui 910-8507, Fukui, Japan
| | - Akinori Irizawa
- SR Center, Research Organization of Science and Technology, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu 525-8577, Shiga, Japan
| | - Masahiko Tani
- Research Center for Development of Far-Infrared Region, University of Fukui, 3-9-1 Bunkyo, Fukui 910-8507, Fukui, Japan
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Amyloid Properties of the FXR1 Protein Are Conserved in Evolution of Vertebrates. Int J Mol Sci 2022; 23:ijms23147997. [PMID: 35887344 PMCID: PMC9319111 DOI: 10.3390/ijms23147997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/16/2022] [Accepted: 07/18/2022] [Indexed: 12/10/2022] Open
Abstract
Functional amyloids are fibrillary proteins with a cross-β structure that play a structural or regulatory role in pro- and eukaryotes. Previously, we have demonstrated that the RNA-binding FXR1 protein functions in an amyloid form in the rat brain. This RNA-binding protein plays an important role in the regulation of long-term memory, emotions, and cancer. Here, we evaluate the amyloid properties of FXR1 in organisms representing various classes of vertebrates. We show the colocalization of FXR1 with amyloid-specific dyes in the neurons of amphibians, reptiles, and birds. Moreover, FXR1, as with other amyloids, forms detergent-resistant insoluble aggregates in all studied animals. The FXR1 protein isolated by immunoprecipitation from the brains of different vertebrate species forms fibrils, which show yellow-green birefringence after staining with Congo red. Our data indicate that in the evolution of vertebrates, FXR1 acquired amyloid properties at least 365 million years ago. Based on the obtained data, we discuss the possible role of FXR1 amyloid fibrils in the regulation of vital processes in the brain of vertebrates.
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Fassler JS, Skuodas S, Weeks DL, Phillips BT. Protein Aggregation and Disaggregation in Cells and Development. J Mol Biol 2021; 433:167215. [PMID: 34450138 PMCID: PMC8530975 DOI: 10.1016/j.jmb.2021.167215] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 08/01/2021] [Accepted: 08/18/2021] [Indexed: 12/12/2022]
Abstract
Protein aggregation is a feature of numerous neurodegenerative diseases. However, regulated, often reversible, formation of protein aggregates, also known as condensates, helps control a wide range of cellular activities including stress response, gene expression, memory, cell development and differentiation. This review presents examples of aggregates found in biological systems, how they are used, and cellular strategies that control aggregation and disaggregation. We include features of the aggregating proteins themselves, environmental factors, co-aggregates, post-translational modifications and well-known aggregation-directed activities that influence their formation, material state, stability and dissolution. We highlight the emerging roles of biomolecular condensates in early animal development, and disaggregation processing proteins that have recently been shown to play key roles in gametogenesis and embryogenesis.
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Affiliation(s)
- Jan S Fassler
- Department of Biology, University of Iowa, Iowa City, IA 52242, United States.
| | - Sydney Skuodas
- Department of Biology, University of Iowa, Iowa City, IA 52242, United States. https://twitter.com/@sskuodas
| | - Daniel L Weeks
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, United States
| | - Bryan T Phillips
- Department of Biology, University of Iowa, Iowa City, IA 52242, United States. https://twitter.com/@bt4phillips
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Elovsson G, Bergkvist L, Brorsson AC. Exploring Aβ Proteotoxicity and Therapeutic Candidates Using Drosophila melanogaster. Int J Mol Sci 2021; 22:ijms221910448. [PMID: 34638786 PMCID: PMC8508956 DOI: 10.3390/ijms221910448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/24/2021] [Accepted: 09/25/2021] [Indexed: 11/30/2022] Open
Abstract
Alzheimer’s disease is a widespread and devastating neurological disorder associated with proteotoxic events caused by the misfolding and aggregation of the amyloid-β peptide. To find therapeutic strategies to combat this disease, Drosophila melanogaster has proved to be an excellent model organism that is able to uncover anti-proteotoxic candidates due to its outstanding genetic toolbox and resemblance to human disease genes. In this review, we highlight the use of Drosophila melanogaster to both study the proteotoxicity of the amyloid-β peptide and to screen for drug candidates. Expanding the knowledge of how the etiology of Alzheimer’s disease is related to proteotoxicity and how drugs can be used to block disease progression will hopefully shed further light on the field in the search for disease-modifying treatments.
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Affiliation(s)
- Greta Elovsson
- Division of Molecular Biotechnology, Department of Physics, Chemistry and Biology, Linköping University, 58183 Linköping, Sweden;
| | - Liza Bergkvist
- Department of Neurobiology, Care Sciences and Society, Karolinska Institute, 17164 Solna, Sweden;
| | - Ann-Christin Brorsson
- Division of Molecular Biotechnology, Department of Physics, Chemistry and Biology, Linköping University, 58183 Linköping, Sweden;
- Correspondence:
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Sergeeva AV, Belashova TA, Bondarev SA, Velizhanina ME, Barbitoff YA, Matveenko AG, Valina AA, Simanova AL, Zhouravleva GA, Galkin AP. Direct proof of the amyloid nature of yeast prions [PSI+] and [PIN+] by the method of immunoprecipitation of native fibrils. FEMS Yeast Res 2021; 21:6360323. [PMID: 34463335 DOI: 10.1093/femsyr/foab046] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 08/28/2021] [Indexed: 12/12/2022] Open
Abstract
Prions are proteins that can exist in several structurally and functionally distinct states, one or more of which is transmissible. Yeast proteins Sup35 and Rnq1 in prion state ([PSI+] and [PIN+], respectively) form oligomers and aggregates, which are transmitted from parents to offspring in a series of generations. Several pieces of indirect evidence indicate that these aggregates also possess amyloid properties, but their binding to amyloid-specific dyes has not been shown in vivo. Meanwhile, it is the specific binding to the Congo Red dye and birefringence in polarized light after such staining that is considered the gold standard for proving the amyloid properties of a protein. Here, we used immunoprecipitation to extract native fibrils of the Sup35 and Rnq1 proteins from yeast strains with different prion status. These fibrils are detected by electron microscopy, stained with Congo Red and exhibit yellow-green birefringence after such staining. All these data show that the Sup35 and Rnq1 proteins in prion state form amyloid fibrils in vivo. The technology of fibrils extraction in combination with standard cytological methods can be used to identify new pathological and functional amyloids in any organism and to analyze the structural features of native amyloid fibrils.
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Affiliation(s)
- Aleksandra V Sergeeva
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, Universitetskaya emb. 7/9, St. Petersburg, 199034, Russian Federation
| | - Tatyana A Belashova
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, Universitetskaya emb. 7/9, St. Petersburg, 199034, Russian Federation.,Laboratory of Amyloid Biology, St. Petersburg State University, Universitetskaya emb. 7/9, St. Petersburg, 199034, Russian Federation
| | - Stanislav A Bondarev
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, Universitetskaya emb. 7/9, St. Petersburg, 199034, Russian Federation
| | - Marya E Velizhanina
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, Universitetskaya emb. 7/9, St. Petersburg, 199034, Russian Federation.,Laboratory of Signal Regulation, All-Russia Research Institute for Agricultural Microbiology, Podbelsky Chaussee, 3 , Pushkin, St. Petersburg, Russian Federation
| | - Yury A Barbitoff
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, Universitetskaya emb. 7/9, St. Petersburg, 199034, Russian Federation
| | - Andrew G Matveenko
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, Universitetskaya emb. 7/9, St. Petersburg, 199034, Russian Federation
| | - Anna A Valina
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, Universitetskaya emb. 7/9, St. Petersburg, 199034, Russian Federation
| | - Angelina L Simanova
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, Universitetskaya emb. 7/9, St. Petersburg, 199034, Russian Federation
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, Universitetskaya emb. 7/9, St. Petersburg, 199034, Russian Federation
| | - Alexey P Galkin
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, Universitetskaya emb. 7/9, St. Petersburg, 199034, Russian Federation.,Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, Universitetskaya emb. 7/9, St. Petersburg, 199034, Russian Federation
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