1
|
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.
Collapse
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
| |
Collapse
|
2
|
Antonets KS, Belousov MV, Sulatskaya AI, Belousova ME, Kosolapova AO, Sulatsky MI, Andreeva EA, Zykin PA, Malovichko YV, Shtark OY, Lykholay AN, Volkov KV, Kuznetsova IM, Turoverov KK, Kochetkova EY, Bobylev AG, Usachev KS, Demidov ON, Tikhonovich IA, Nizhnikov AA. Accumulation of storage proteins in plant seeds is mediated by amyloid formation. PLoS Biol 2020; 18:e3000564. [PMID: 32701952 PMCID: PMC7377382 DOI: 10.1371/journal.pbio.3000564] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 06/19/2020] [Indexed: 02/04/2023] Open
Abstract
Amyloids are protein aggregates with a highly ordered spatial structure giving them unique physicochemical properties. Different amyloids not only participate in the development of numerous incurable diseases but control vital functions in archaea, bacteria and eukarya. Plants are a poorly studied systematic group in the field of amyloid biology. Amyloid properties have not yet been demonstrated for plant proteins under native conditions in vivo. Here we show that seeds of garden pea Pisum sativum L. contain amyloid-like aggregates of storage proteins, the most abundant one, 7S globulin Vicilin, forms bona fide amyloids in vivo and in vitro. Full-length Vicilin contains 2 evolutionary conserved β-barrel domains, Cupin-1.1 and Cupin-1.2, that self-assemble in vitro into amyloid fibrils with similar physicochemical properties. However, Cupin-1.2 fibrils unlike Cupin-1.1 can seed Vicilin fibrillation. In vivo, Vicilin forms amyloids in the cotyledon cells that bind amyloid-specific dyes and possess resistance to detergents and proteases. The Vicilin amyloid accumulation increases during seed maturation and wanes at germination. Amyloids of Vicilin resist digestion by gastrointestinal enzymes, persist in canned peas, and exhibit toxicity for yeast and mammalian cells. Our finding for the first time reveals involvement of amyloid formation in the accumulation of storage proteins in plant seeds.
Collapse
Affiliation(s)
- Kirill S. Antonets
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), St. Petersburg, Russia
- St. Petersburg State University, St. Petersburg, Russia
| | - Mikhail V. Belousov
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), St. Petersburg, Russia
- St. Petersburg State University, St. Petersburg, Russia
| | - Anna I. Sulatskaya
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Maria E. Belousova
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), St. Petersburg, Russia
| | - Anastasiia O. Kosolapova
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), St. Petersburg, Russia
- St. Petersburg State University, St. Petersburg, Russia
| | - Maksim I. Sulatsky
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | | | | | - Yury V. Malovichko
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), St. Petersburg, Russia
- St. Petersburg State University, St. Petersburg, Russia
| | - Oksana Y. Shtark
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), St. Petersburg, Russia
| | | | | | | | | | | | - Alexander G. Bobylev
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Konstantin S. Usachev
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Oleg. N. Demidov
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
- INSERM UMR1231, UBFC, Dijon, France
| | - Igor A. Tikhonovich
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), St. Petersburg, Russia
- St. Petersburg State University, St. Petersburg, Russia
| | - Anton A. Nizhnikov
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), St. Petersburg, Russia
- St. Petersburg State University, St. Petersburg, Russia
| |
Collapse
|
3
|
Kosolapova AO, Belousov MV, Sulatskaya AI, Belousova ME, Sulatsky MI, Antonets KS, Volkov KV, Lykholay AN, Shtark OY, Vasileva EN, Zhukov VA, Ivanova AN, Zykin PA, Kuznetsova IM, Turoverov KK, Tikhonovich IA, Nizhnikov AA. Two Novel Amyloid Proteins, RopA and RopB, from the Root Nodule Bacterium Rhizobium leguminosarum. Biomolecules 2019; 9:biom9110694. [PMID: 31690032 PMCID: PMC6920782 DOI: 10.3390/biom9110694] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 10/29/2019] [Accepted: 10/31/2019] [Indexed: 12/14/2022] Open
Abstract
Amyloids represent protein fibrils with a highly ordered spatial structure, which not only cause dozens of incurable human and animal diseases but also play vital biological roles in Archaea, Bacteria, and Eukarya. Despite the fact that association of bacterial amyloids with microbial pathogenesis and infectious diseases is well known, there is a lack of information concerning the amyloids of symbiotic bacteria. In this study, using the previously developed proteomic method for screening and identification of amyloids (PSIA), we identified amyloidogenic proteins in the proteome of the root nodule bacterium Rhizobium leguminosarum. Among 54 proteins identified, we selected two proteins, RopA and RopB, which are predicted to have β-barrel structure and are likely to be involved in the control of plant-microbial symbiosis. We demonstrated that the full-length RopA and RopB form bona fide amyloid fibrils in vitro. In particular, these fibrils are β-sheet-rich, bind Thioflavin T (ThT), exhibit green birefringence upon staining with Congo Red (CR), and resist treatment with ionic detergents and proteases. The heterologously expressed RopA and RopB intracellularly aggregate in yeast and assemble into amyloid fibrils at the surface of Escherichia coli. The capsules of the R. leguminosarum cells bind CR, exhibit green birefringence, and contain fibrils of RopA and RopB in vivo.
Collapse
Affiliation(s)
- Anastasiia O Kosolapova
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia.
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia.
| | - Mikhail V Belousov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia.
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia.
| | - Anna I Sulatskaya
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, 194064 St. Petersburg, Russia.
| | - Maria E Belousova
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia.
| | - Maksim I Sulatsky
- Laboratory of Cell Morphology, Institute of Cytology of the Russian Academy of Sciences, 194064 St. Petersburg, Russia.
| | - Kirill S Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia.
- Faculty of Biology, St. Petersburg State University (SPbSU), 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.
| | - Anna N Lykholay
- Research Resource Center "Molecular and Cell Technologies", Research Park, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia.
| | - Oksana Y Shtark
- Department of Biotechnology, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), St. Petersburg, 196608, Russia.
| | - Ekaterina N Vasileva
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia.
- Department of Biotechnology, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), St. Petersburg, 196608, Russia.
| | - Vladimir A Zhukov
- Department of Biotechnology, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), St. Petersburg, 196608, Russia.
| | - Alexandra N Ivanova
- Research Resource Center "Molecular and Cell Technologies", Research Park, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia.
- Komarov Botanical Institute RAS, 197376 Komarov Botanical Institute RAS, Russia.
| | - Pavel A Zykin
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia.
| | - Irina M Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, 194064 St. Petersburg, Russia.
| | - Konstantin K Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, 194064 St. Petersburg, Russia.
- Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia.
| | - Igor A Tikhonovich
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia.
- Department of Biotechnology, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), St. Petersburg, 196608, Russia.
| | - Anton A Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia.
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia.
| |
Collapse
|