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Mirza Agha M, Tavili E, Dabirmanesh B. Functional amyloids. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 206:389-434. [PMID: 38811086 DOI: 10.1016/bs.pmbts.2024.03.009] [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
While amyloid has traditionally been viewed as a harmful formation, emerging evidence suggests that amyloids may also play a functional role in cell biology, contributing to normal physiological processes that have been conserved throughout evolution. Functional amyloids have been discovered in several creatures, spanning from bacteria to mammals. These amyloids serve a multitude of purposes, including but not limited to, forming biofilms, melanin synthesis, storage, information transfer, and memory. The functional role of amyloids has been consistently validated by the discovery of more functional amyloids, indicating a conceptual convergence. The biology of amyloids is well-represented by non-pathogenic amyloids, given the numerous ones already identified and the ongoing rate of new discoveries. In this chapter, functional amyloids in microorganisms, animals, and plants are described.
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Affiliation(s)
- Mansoureh Mirza Agha
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Elaheh Tavili
- 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.
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2
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Arakawa T, Niikura T, Kita Y, Akuta T. Sodium Dodecyl Sulfate Analogs as a Potential Molecular Biology Reagent. Curr Issues Mol Biol 2024; 46:621-633. [PMID: 38248342 PMCID: PMC10814491 DOI: 10.3390/cimb46010040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/03/2024] [Accepted: 01/05/2024] [Indexed: 01/23/2024] Open
Abstract
In this study, we review the properties of three anionic detergents, sodium dodecyl sulfate (SDS), Sarkosyl, and sodium lauroylglutamate (SLG), as they play a critical role in molecular biology research. SDS is widely used in electrophoresis and cell lysis for proteomics. Sarkosyl and, more frequently, SDS are used for the characterization of neuropathological protein fibrils and the solubilization of proteins. Many amyloid fibrils are resistant to SDS or Sarkosyl to different degrees and, thus, can be readily isolated from detergent-sensitive proteins. SLG is milder than the above two detergents and has been used in the solubilization and refolding of proteins isolated from inclusion bodies. Here, we show that both Sarkosyl and SLG have been used for protein refolding, that the effects of SLG on the native protein structure are weaker for SLG, and that SLG readily dissociates from the native proteins. We propose that SLG may be effective in cell lysis for functional proteomics due to no or weaker binding of SLG to the native proteins.
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Affiliation(s)
- Tsutomu Arakawa
- Alliance Protein Labs, 13380 Pantera Rd., San Diego, CA 92130, USA;
| | - Takako Niikura
- Department of Information and Communication Sciences, Faculty of Science and Technology, Sophia University, Tokyo 102-8554, Japan;
| | - Yoshiko Kita
- Alliance Protein Labs, 13380 Pantera Rd., San Diego, CA 92130, USA;
| | - Teruo Akuta
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna, Takahagi-shi 318-0004, Japan;
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3
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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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4
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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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5
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Search and Identification of Amyloid Proteins. Methods Protoc 2023; 6:mps6010016. [PMID: 36827503 PMCID: PMC9967629 DOI: 10.3390/mps6010016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 02/08/2023] Open
Abstract
Amyloids are fibrillar proteins with a cross-β structure. Pathological amyloids are associated with the development of a number of incurable diseases, while functional amyloids regulate vital processes. The detection of unknown amyloids in living objects is a difficult task, and therefore the question of the prevalence and biological significance of amyloids remains open. We present a description of two methods, the combination of which makes it possible to find and identify amyloid proteins in the proteome of various organisms. The method of proteomic screening for amyloids allows the detection of the proteins that form SDS-resistant aggregates. SDS resistance is a general feature of amyloid fibrils. Protein aggregates resistant to SDS treatment can be collected by ultracentrifugation and further identified by mass spectrometry. However, in addition to amyloids, SDS-resistant aggregates contain some non-amyloid proteins. To test the amyloid properties of proteins identified by proteomic screening, we developed the method of fibril immunoprecipitation followed by Congo red staining and birefringence analysis. The methods of proteomic screening and immunoprecipitation of fibrillar proteins have been successfully tested and applied for the identification of amyloid proteins in yeast and vertebrates.
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6
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Ivanov YD, Tatur VY, Shumov ID, Kozlov AF, Valueva AA, Ivanova IA, Ershova MO, Ivanova ND, Stepanov IN, Lukyanitsa AA, Ziborov VS. The Effect of a Rotating Cone on Horseradish Peroxidase Aggregation on Mica Revealed by Atomic Force Microscopy. MICROMACHINES 2022; 13:1947. [PMID: 36363968 PMCID: PMC9697547 DOI: 10.3390/mi13111947] [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] [Revised: 11/03/2022] [Accepted: 11/08/2022] [Indexed: 06/16/2023]
Abstract
Our study reported herein aims to determine whether an electromagnetic field, induced triboelectrically by a metallic cone, rotating at a frequency of 167 Hz, has an effect on the properties of the horseradish peroxidase (HRP) enzyme. Atomic force microscopy (AFM) was employed to detect even the most subtle effects on single enzyme molecules. In parallel, a macroscopic method (spectrophotometry) was used to reveal whether the enzymatic activity of HRP in solution was affected. An aqueous solution of the enzyme was incubated at a distance of 2 cm from the rotating cone. The experiments were performed at various incubation times. The control experiments were performed with a non-rotating cone. The incubation of the HRP solution was found to cause the disaggregation of the enzyme. At longer incubation times, this disaggregation was found to be accompanied by the formation of higher-order aggregates; however, no change in the HRP enzymatic activity was observed. The results of our experiments could be of interest in the development of enzyme-based biosensors with rotating elements such as stirrers. Additionally, the results obtained herein are important for the correct interpretation of data obtained with such biosensors.
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Affiliation(s)
- Yuri D. Ivanov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia
- Joint Institute for High Temperatures of the Russian Academy of Sciences, 125412 Moscow, Russia
| | - Vadim Y. Tatur
- Foundation of Perspective Technologies and Novations, 115682 Moscow, Russia
| | - Ivan D. Shumov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia
| | - Andrey F. Kozlov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia
| | - Anastasia A. Valueva
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia
| | - Irina A. Ivanova
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia
| | - Maria O. Ershova
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia
| | - Nina D. Ivanova
- Foundation of Perspective Technologies and Novations, 115682 Moscow, Russia
- Moscow State Academy of Veterinary Medicine and Biotechnology Named after Skryabin, 109472 Moscow, Russia
| | - Igor N. Stepanov
- Foundation of Perspective Technologies and Novations, 115682 Moscow, Russia
| | - Andrei A. Lukyanitsa
- Foundation of Perspective Technologies and Novations, 115682 Moscow, Russia
- Faculty of Computational Mathematics and Cybernetics, Moscow State University, 119991 Moscow, Russia
| | - Vadim S. Ziborov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia
- Joint Institute for High Temperatures of the Russian Academy of Sciences, 125412 Moscow, Russia
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7
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Kachkin DV, Volkov KV, Sopova JV, Bobylev AG, Fedotov SA, Inge-Vechtomov SG, Galzitskaya OV, Chernoff YO, Rubel AA, Aksenova AY. Human RAD51 Protein Forms Amyloid-like Aggregates In Vitro. Int J Mol Sci 2022; 23:ijms231911657. [PMID: 36232958 PMCID: PMC9570251 DOI: 10.3390/ijms231911657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/21/2022] [Accepted: 09/26/2022] [Indexed: 12/30/2022] Open
Abstract
RAD51 is a central protein of homologous recombination and DNA repair processes that maintains genome stability and ensures the accurate repair of double-stranded breaks (DSBs). In this work, we assessed amyloid properties of RAD51 in vitro and in the bacterial curli-dependent amyloid generator (C-DAG) system. Resistance to ionic detergents, staining with amyloid-specific dyes, polarized microscopy, transmission electron microscopy (TEM), X-ray diffraction and other methods were used to evaluate the properties and structure of RAD51 aggregates. The purified human RAD51 protein formed detergent-resistant aggregates in vitro that had an unbranched cross-β fibrillar structure, which is typical for amyloids, and were stained with amyloid-specific dyes. Congo-red-stained RAD51 aggregates demonstrated birefringence under polarized light. RAD51 fibrils produced sharp circular X-ray reflections at 4.7 Å and 10 Å, demonstrating that they had a cross-β structure. Cytoplasmic aggregates of RAD51 were observed in cell cultures overexpressing RAD51. We demonstrated that a key protein that maintains genome stability, RAD51, has amyloid properties in vitro and in the C-DAG system and discussed the possible biological relevance of this observation.
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Affiliation(s)
- Daniel V. Kachkin
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Kirill V. Volkov
- Research Resource Center “Molecular and Cell Technologies”, Research Park, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
| | - Julia V. Sopova
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
- Center of Transgenesis and Genome Editing, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Alexander G. Bobylev
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 3 Institutskaya St., 142290 Moscow, Russia
| | - Sergei A. Fedotov
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Sergei G. Inge-Vechtomov
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Oxana V. Galzitskaya
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 3 Institutskaya St., 142290 Moscow, Russia
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Yury O. Chernoff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332-2000, USA
| | - Aleksandr A. Rubel
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
- Correspondence: (A.A.R.); (A.Y.A.)
| | - Anna Y. Aksenova
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
- Correspondence: (A.A.R.); (A.Y.A.)
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8
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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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9
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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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10
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Brown A, Török M. Functional amyloids in the human body. Bioorg Med Chem Lett 2021; 40:127914. [PMID: 33691165 DOI: 10.1016/j.bmcl.2021.127914] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/20/2021] [Accepted: 02/23/2021] [Indexed: 11/18/2022]
Abstract
Amyloids have long been associated with a variety of human degenerative diseases. Discoveries indicate, however, that there are several amyloids that serve functional roles in the human body. These amyloids are involved in a variety of biological processes ranging from storage of peptide hormones to necroptosis of cells. Additionally, there are distinct differences between toxic amyloids and their functional counterparts including kinetics of assembly/disassembly and structural features. This digest article surveys the biological roles of functional amyloids found in the human body, key differences between functional and toxic amyloids, and potential therapeutic applications.
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Affiliation(s)
- Amy Brown
- Department of Chemistry, University of Massachusetts Boston, 100 Morrissey Blvd., Boston, MA 02125, USA
| | - Marianna Török
- Department of Chemistry, University of Massachusetts Boston, 100 Morrissey Blvd., Boston, MA 02125, USA.
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11
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Matiiv AB, Trubitsina NP, Matveenko AG, Barbitoff YA, Zhouravleva GA, Bondarev SA. Amyloid and Amyloid-Like Aggregates: Diversity and the Term Crisis. BIOCHEMISTRY (MOSCOW) 2021; 85:1011-1034. [PMID: 33050849 DOI: 10.1134/s0006297920090035] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Active accumulation of the data on new amyloids continuing nowadays dissolves boundaries of the term "amyloid". Currently, it is most often used to designate aggregates with cross-β structure. At the same time, amyloids also exhibit a number of other unusual properties, such as: detergent and protease resistance, interaction with specific dyes, and ability to induce transition of some proteins from a soluble form to an aggregated one. The same features have been also demonstrated for the aggregates lacking cross-β structure, which are commonly called "amyloid-like" and combined into one group, although they are very diverse. We have collected and systematized information on the properties of more than two hundred known amyloids and amyloid-like proteins with emphasis on conflicting examples. In particular, a number of proteins in membraneless organelles form aggregates with cross-β structure that are morphologically indistinguishable from the other amyloids, but they can be dissolved in the presence of detergents, which is not typical for amyloids. Such paradoxes signify the need to clarify the existing definition of the term amyloid. On the other hand, the demonstrated structural diversity of the amyloid-like aggregates shows the necessity of their classification.
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Affiliation(s)
- A B Matiiv
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - N P Trubitsina
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - A G Matveenko
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - Y A Barbitoff
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia.,Bioinformatics Institute, St. Petersburg, 197342, Russia
| | - G A Zhouravleva
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia.,Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - S A Bondarev
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia. .,Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, 199034, Russia
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12
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Chirinskaite AV, Siniukova VA, Velizhanina ME, Sopova JV, Belashova TA, Zadorsky SP. STXBP1 forms amyloid-like aggregates in rat brain and demonstrates amyloid properties in bacterial expression system. Prion 2021; 15:29-36. [PMID: 33590815 PMCID: PMC7894455 DOI: 10.1080/19336896.2021.1883980] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Amyloids are the fibrillar protein aggregates with cross-β structure. Traditionally amyloids were associated with pathology, however, nowadays more data is emerging about functional amyloids playing essential roles in cellular processes. We conducted screening for functional amyloids in rat brain. One of the identified proteins was STXBP1 taking part in vesicular transport and neurotransmitter secretion. Using SDD-AGE and protein fractionation we found out that STXBP1 forms small detergent-insoluble aggregates in rat brain. With immunoprecipitation analysis and C-DAG system, we showed that STXBP1 forms amyloid-like fibrils. Thus, STXBP1 demonstrates amyloid properties in rat brain and in bacterial expression system.
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Affiliation(s)
- A V Chirinskaite
- Department of Genetics and Biotechnology, St. Petersburg State University , St. Petersburg, Russian Federation.,Institute of Translational Biomedicine, St. Petersburg State University , St. Petersburg, Russian Federation
| | - V A Siniukova
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences , St. Petersburg, Russian Federation
| | - M E Velizhanina
- Department of Genetics and Biotechnology, St. Petersburg State University , St. Petersburg, Russian Federation.,Laboratory of Signal Regulation, All-Russia Research Institute for Agricultural Microbiology , Pushkin, St. Petersburg, Russian Federation
| | - J V Sopova
- Institute of Translational Biomedicine, St. Petersburg State University , St. Petersburg, Russian Federation.,Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences , St. Petersburg, Russian Federation.,Laboratory of Amyloid Biology, St. Petersburg State University , St. Petersburg, Russian Federation
| | - T A Belashova
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences , St. Petersburg, Russian Federation.,Laboratory of Amyloid Biology, St. Petersburg State University , St. Petersburg, Russian Federation
| | - S P Zadorsky
- Department of Genetics and Biotechnology, St. Petersburg State University , St. Petersburg, Russian Federation.,Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences , St. Petersburg, Russian Federation
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13
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Ivanov YD, Pleshakova TO, Shumov ID, Kozlov AF, Valueva AA, Ivanova IA, Ershova MO, Larionov DI, Repnikov VV, Ivanova ND, Tatur VY, Stepanov IN, Ziborov VS. AFM and FTIR Investigation of the Effect of Water Flow on Horseradish Peroxidase. Molecules 2021; 26:E306. [PMID: 33435278 PMCID: PMC7826892 DOI: 10.3390/molecules26020306] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 11/17/2022] Open
Abstract
Atomic force microscopy (AFM)-based fishing is a promising method for the detection of low-abundant proteins. This method is based on the capturing of the target proteins from the analyzed solution onto a solid substrate, with subsequent counting of the captured protein molecules on the substrate surface by AFM. Protein adsorption onto the substrate surface represents one of the key factors determining the capturing efficiency. Accordingly, studying the factors influencing the protein adsorbability onto the substrate surface represents an actual direction in biomedical research. Herein, the influence of water motion in a flow-based system on the protein adsorbability and on its enzymatic activity has been studied with an example of horseradish peroxidase (HRP) enzyme by AFM, attenuated total reflection Fourier-transform infrared spectroscopy (ATR-FTIR) and conventional spectrophotometry. In the experiments, HRP solution was incubated in a setup modeling the flow section of a biosensor communication. The measuring cell with the protein solution was placed near a coiled silicone pipe, through which water was pumped. The adsorbability of the protein onto the surface of the mica substrate has been studied by AFM. It has been demonstrated that incubation of the HRP solution near the coiled silicone pipe with flowing water leads to an increase in its adsorbability onto mica. This is accompanied by a change in the enzyme's secondary structure, as has been revealed by ATR-FTIR. At the same time, its enzymatic activity remains unchanged. The results reported herein can be useful in the development of models describing the influence of liquid flow on the properties of enzymes and other proteins. The latter is particularly important for the development of biosensors for biomedical applications-particularly for serological analysis, which is intended for the early diagnosis of various types of cancer and infectious diseases. Our results should also be taken into account in studies of the effects of protein aggregation on hemodynamics, which plays a key role in human body functioning.
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Affiliation(s)
- Yuri D. Ivanov
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (T.O.P.); (I.D.S.); (A.F.K.); (A.A.V.); (I.A.I.); (M.O.E.); (D.I.L.); (V.S.Z.)
| | - Tatyana O. Pleshakova
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (T.O.P.); (I.D.S.); (A.F.K.); (A.A.V.); (I.A.I.); (M.O.E.); (D.I.L.); (V.S.Z.)
| | - Ivan D. Shumov
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (T.O.P.); (I.D.S.); (A.F.K.); (A.A.V.); (I.A.I.); (M.O.E.); (D.I.L.); (V.S.Z.)
| | - Andrey F. Kozlov
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (T.O.P.); (I.D.S.); (A.F.K.); (A.A.V.); (I.A.I.); (M.O.E.); (D.I.L.); (V.S.Z.)
| | - Anastasia A. Valueva
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (T.O.P.); (I.D.S.); (A.F.K.); (A.A.V.); (I.A.I.); (M.O.E.); (D.I.L.); (V.S.Z.)
| | - Irina A. Ivanova
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (T.O.P.); (I.D.S.); (A.F.K.); (A.A.V.); (I.A.I.); (M.O.E.); (D.I.L.); (V.S.Z.)
| | - Maria O. Ershova
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (T.O.P.); (I.D.S.); (A.F.K.); (A.A.V.); (I.A.I.); (M.O.E.); (D.I.L.); (V.S.Z.)
| | - Dmitry I. Larionov
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (T.O.P.); (I.D.S.); (A.F.K.); (A.A.V.); (I.A.I.); (M.O.E.); (D.I.L.); (V.S.Z.)
| | | | - Nina D. Ivanova
- Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, Moscow 109472, Russia;
| | - Vadim Yu. Tatur
- Foundation of Perspective Technologies and Novations, Moscow 115682, Russia; (V.Y.T.); (I.N.S.)
| | - Igor N. Stepanov
- Foundation of Perspective Technologies and Novations, Moscow 115682, Russia; (V.Y.T.); (I.N.S.)
| | - Vadim S. Ziborov
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (T.O.P.); (I.D.S.); (A.F.K.); (A.A.V.); (I.A.I.); (M.O.E.); (D.I.L.); (V.S.Z.)
- Joint Institute for High Temperatures of the Russian Academy of Sciences, Moscow 125412, Russia
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14
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Siniukova VA, Sopova JV, Galkina SA, Galkin AP. Search for functional amyloid structures in chicken and fruit fly female reproductive cells. Prion 2020; 14:278-282. [PMID: 33300441 PMCID: PMC7734138 DOI: 10.1080/19336896.2020.1859439] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
We conducted a cytological search for amyloid structures in female reproductive cells of Gallus gallus domesticus and Drosophila melanogaster. We have shown that the amyloid-specific dye, Thioflavin S, but not Congo red, stains some cytoplasmic and even nuclear structures in chicken ovaries. In fruit fly eggs both Thioflavin S and Congo red specifically stain eggshell structures such as micropyle, dorsal appendages and pillars. Moreover, these structures, when stained with Congo red, demonstrate birefringence in polarized light, which is a characteristic feature of all classical amyloids. Our data show that female reproductive cells during evolution began to use amyloid fibrils to form various functional structures necessary for development under certain environmental conditions.
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Affiliation(s)
- V A Siniukova
- St. Petersburg Branch, Vavilov Institute of General Genetics , St. Petersburg, Russian Federation
| | - J V Sopova
- St. Petersburg Branch, Vavilov Institute of General Genetics , St. Petersburg, Russian Federation.,Laboratory of Amyloid Biology, St. Petersburg State University , St. Petersburg, Russian Federation
| | - S A Galkina
- Department of Genetics and Biotechnology, St. Petersburg State University , St. Petersburg, Russian Federation
| | - A P Galkin
- St. Petersburg Branch, Vavilov Institute of General Genetics , St. Petersburg, Russian Federation.,Department of Genetics and Biotechnology, St. Petersburg State University , St. Petersburg, Russian Federation
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15
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Andreychuk YV, Zadorsky SP, Zhuk AS, Stepchenkova EI, Inge-Vechtomov SG. Relationship between Type I and Type II Template Processes: Amyloids and Genome Stability. Mol Biol 2020. [DOI: 10.1134/s0026893320050027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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A simple procedure for bacterial expression and purification of the fragile X protein family. Sci Rep 2020; 10:15858. [PMID: 32985615 PMCID: PMC7522082 DOI: 10.1038/s41598-020-72984-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/07/2020] [Indexed: 11/23/2022] Open
Abstract
The fragile X protein family consists of three RNA-binding proteins involved in translational regulation. Fragile X mental retardation protein (FMRP) is well-studied, as its loss leads to fragile X syndrome, a neurodevelopmental disorder which is the most prevalent form of inherited mental retardation and the primary monogenetic cause of autism. Fragile X related proteins 1 and 2 (FXR1P and FXR2P) are autosomal paralogs of FMRP that are involved in promoting muscle development and neural development, respectively. There is great interest in studying this family of proteins, yet researchers have faced much difficulty in expressing and purifying the full-length versions of these proteins in sufficient quantities. We have developed a simple, rapid, and inexpensive procedure that allows for the recombinant expression and purification of full-length human FMRP, FXR1P, and FXR2P from Escherichia coli in high yields, free of protein and nucleic acid contamination. In order to assess the proteins’ function after purification, we confirmed their binding to pseudoknot and G-quadruplex forming RNAs as well as their ability to regulate translation in vitro.
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Functional Mammalian Amyloids and Amyloid-Like Proteins. Life (Basel) 2020; 10:life10090156. [PMID: 32825636 PMCID: PMC7555005 DOI: 10.3390/life10090156] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/12/2020] [Accepted: 08/19/2020] [Indexed: 02/06/2023] Open
Abstract
Amyloids are highly ordered fibrous cross-β protein aggregates that are notorious primarily because of association with a variety of incurable human and animal diseases (termed amyloidoses), including Alzheimer’s disease (AD), Parkinson’s disease (PD), type 2 diabetes (T2D), and prion diseases. Some amyloid-associated diseases, in particular T2D and AD, are widespread and affect hundreds of millions of people all over the world. However, recently it has become evident that many amyloids, termed “functional amyloids,” are involved in various activities that are beneficial to organisms. Functional amyloids were discovered in diverse taxa, ranging from bacteria to mammals. These amyloids are involved in vital biological functions such as long-term memory, storage of peptide hormones and scaffolding melanin polymerization in animals, substrate attachment, and biofilm formation in bacteria and fungi, etc. Thus, amyloids undoubtedly are playing important roles in biological and pathological processes. This review is focused on functional amyloids in mammals and summarizes approaches used for identifying new potentially amyloidogenic proteins and domains.
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18
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Functional amyloids of eukaryotes: criteria, classification, and biological significance. Curr Genet 2020; 66:849-866. [DOI: 10.1007/s00294-020-01079-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/16/2020] [Accepted: 04/20/2020] [Indexed: 11/26/2022]
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19
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Amyloidogenic Peptides in Human Neuro-Degenerative Diseases and in Microorganisms: A Sorrow Shared Is a Sorrow Halved? Molecules 2020; 25:molecules25040925. [PMID: 32093040 PMCID: PMC7070710 DOI: 10.3390/molecules25040925] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 02/17/2020] [Accepted: 02/17/2020] [Indexed: 01/06/2023] Open
Abstract
The term "amyloid" refers to proteinaceous deposits of peptides that might be generated from larger precursor proteins e.g., by proteolysis. Common to these peptides is a stable cross-β dominated secondary structure which allows self-assembly, leading to insoluble oligomers and lastly to fibrils. These highly ordered protein aggregates have been, for a long time, mainly associated with human neurodegenerative diseases such as Alzheimer's disease (Amyloid-β peptides). However, they also exert physiological functions such as in release of deposited hormones in human beings. In the light of the rediscovery of our microbial commensals as important companions in health and disease, the fact that microbes also possess amyloidogenic peptides is intriguing. Transmission of amyloids by iatrogenic means or by consumption of contaminated meat from diseased animals is a well-known fact. What if also our microbial commensals might drive human amyloidosis or suffer from our aggregated amyloids? Moreover, as the microbial amyloids are evolutionarily older, we might learn from these organisms how to cope with the sword of Damocles forged of endogenous, potentially toxic peptides. This review summarizes knowledge about the interplay between human amyloids involved in neurodegenerative diseases and microbial amyloids.
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