1
|
Trubitsina NP, Matiiv AB, Rogoza TM, Zudilova AA, Bezgina MD, Zhouravleva GA, Bondarev SA. Role of the Gut Microbiome and Bacterial Amyloids in the Development of Synucleinopathies. Biochemistry (Mosc) 2024; 89:523-542. [PMID: 38648770 DOI: 10.1134/s0006297924030118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/16/2024] [Accepted: 01/24/2024] [Indexed: 04/25/2024]
Abstract
Less than ten years ago, evidence began to accumulate about association between the changes in the composition of gut microbiota and development of human synucleinopathies, in particular sporadic form of Parkinson's disease. We collected data from more than one hundred and thirty experimental studies that reported similar results and summarized the frequencies of detection of different groups of bacteria in these studies. It is important to note that it is extremely rare that a unidirectional change in the population of one or another group of microorganisms (only an elevation or only a reduction) was detected in the patients with Parkinson's disease. However, we were able to identify several groups of bacteria that were overrepresented in the patients with Parkinson's disease in the analyzed studies. There are various hypotheses about the molecular mechanisms that explain such relationships. Usually, α-synuclein aggregation is associated with the development of inflammatory processes that occur in response to the changes in the microbiome. However, experimental evidence is accumulating on the influence of bacterial proteins, including amyloids (curli), as well as various metabolites, on the α-synuclein aggregation. In the review, we provided up-to-date information about such examples.
Collapse
Affiliation(s)
- Nina P Trubitsina
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Anton B Matiiv
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Tatyana M Rogoza
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
- St. Petersburg Branch of the Vavilov Institute of General Genetics, Saint Petersburg, 198504, Russia
| | - Anna A Zudilova
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Mariya D Bezgina
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
- Laboratory of Amyloid Biology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Stanislav A Bondarev
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia.
- Laboratory of Amyloid Biology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| |
Collapse
|
2
|
Bondarev SA, Uspenskaya MV, Leclercq J, Falgarone T, Zhouravleva GA, Kajava AV. AmyloComp: A Bioinformatic Tool for Prediction of Amyloid Co-aggregation. J Mol Biol 2024:168437. [PMID: 38185324 DOI: 10.1016/j.jmb.2024.168437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/13/2023] [Accepted: 01/03/2024] [Indexed: 01/09/2024]
Abstract
Typically, amyloid fibrils consist of multiple copies of the same protein. In these fibrils, each polypeptide chain adopts the same β-arc-containing conformation and these chains are stacked in a parallel and in-register manner. In the last few years, however, a considerable body of data has been accumulated about co-aggregation of different amyloid-forming proteins. Among known examples of the co-aggregation are heteroaggregates of different yeast prions and human proteins Rip1 and Rip3. Since the co-aggregation is linked to such important phenomena as infectivity of amyloids and molecular mechanisms of functional amyloids, we analyzed its structural aspects in more details. An axial stacking of different proteins within the same amyloid fibril is one of the most common type of co-aggregation. By using an approach based on structural similarity of the growing tips of amyloids, we developed a computational method to predict amyloidogenic β-arch structures that are able to interact with each other by the axial stacking. Furthermore, we compiled a dataset consisting of 26 experimentally known pairs of proteins capable or incapable to co-aggregate. We utilized this dataset to test and refine our algorithm. The developed method opens a way for a number of applications, including the identification of microbial proteins capable triggering amyloidosis in humans. AmyloComp is available on the website: https://bioinfo.crbm.cnrs.fr/index.php?route=tools&tool=30.
Collapse
Affiliation(s)
- Stanislav A Bondarev
- Department of Genetics and Biotechnology and Laboratory of Amyloid Biology, St. Petersburg State University, Saint Petersburg 199034, Russian Federation.
| | - Mayya V Uspenskaya
- Institute of Bioengineering, ITMO University, St. Petersburg 197101, Russian Federation
| | - Jérémy Leclercq
- Centre de Recherche en Biologie Cellulaire de Montpellier, CNRS, Université Montpellier, Montpellier 34293, France
| | - Théo Falgarone
- Centre de Recherche en Biologie Cellulaire de Montpellier, CNRS, Université Montpellier, Montpellier 34293, France
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology and Laboratory of Amyloid Biology, St. Petersburg State University, Saint Petersburg 199034, Russian Federation
| | - Andrey V Kajava
- Centre de Recherche en Biologie Cellulaire de Montpellier, CNRS, Université Montpellier, Montpellier 34293, France.
| |
Collapse
|
3
|
Zhouravleva GA, Bondarev SA, Trubitsina NP. How Big Is the Yeast Prion Universe? Int J Mol Sci 2023; 24:11651. [PMID: 37511408 PMCID: PMC10380529 DOI: 10.3390/ijms241411651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/14/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
The number of yeast prions and prion-like proteins described since 1994 has grown from two to nearly twenty. If in the early years most scientists working with the classic mammalian prion, PrPSc, were skeptical about the possibility of using the term prion to refer to yeast cytoplasmic elements with unusual properties, it is now clear that prion-like phenomena are widespread and that yeast can serve as a convenient model for studying them. Here we give a brief overview of the yeast prions discovered so far and focus our attention to the various approaches used to identify them. The prospects for the discovery of new yeast prions are also discussed.
Collapse
Affiliation(s)
- 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
| | - Nina P Trubitsina
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
| |
Collapse
|
4
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
5
|
Sokolov PA, Rolich VI, Vezo OS, Belousov MV, Bondarev SA, Zhouravleva GA, Kasyanenko NA. Amyloid fibril length distribution from dynamic light scattering data. Eur Biophys J 2022; 51:325-333. [PMID: 35546203 DOI: 10.1007/s00249-022-01600-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 03/19/2022] [Accepted: 04/24/2022] [Indexed: 06/15/2023]
Abstract
The study of the aggregation of amyloid proteins is challenging. A new approach to processing dynamic light scattering data was developed and tested using aggregates of the well-known model Sup35NM amyloid. After filtering and calculating the moving averages of autocorrelation functions to reduce impacts of noise, each averaged autocorrelation function is converted to the fibril length distribution via numerical modeling. The processing results were verified using atomic force and scanning electron microscopy data. Analysis of fibril length distribution changes over time gives valuable information about the aggregation process.
Collapse
Affiliation(s)
- Petr A Sokolov
- Department of Physics, St. Petersburg University, 7-9-11 Universitetskaya Emb, St. Petersburg, 199034, Russia.
| | - Valeriy I Rolich
- Department of Physics, St. Petersburg University, 7-9-11 Universitetskaya Emb, St. Petersburg, 199034, Russia
| | - Olga S Vezo
- Department of Physics, St. Petersburg University, 7-9-11 Universitetskaya Emb, St. Petersburg, 199034, Russia
| | - Mikhail V Belousov
- Department of Genetics and Biotechnology, St. Petersburg University, 7-9-11 Universitetskaya Emb, St. Petersburg, 199034, Russia
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 3 Podbelsky chausse, St. Petersburg, 196608, Russia
| | - Stanislav A Bondarev
- Department of Genetics and Biotechnology, St. Petersburg University, 7-9-11 Universitetskaya Emb, St. Petersburg, 199034, Russia
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology, St. Petersburg University, 7-9-11 Universitetskaya Emb, St. Petersburg, 199034, Russia
| | - Nina A Kasyanenko
- Department of Physics, St. Petersburg University, 7-9-11 Universitetskaya Emb, St. Petersburg, 199034, Russia
| |
Collapse
|
6
|
Matiiv AB, Trubitsina NP, Matveenko AG, Barbitoff YA, Zhouravleva GA, Bondarev SA. Structure and Polymorphism of Amyloid and Amyloid-Like Aggregates. Biochemistry (Mosc) 2022; 87:450-463. [PMID: 35790379 DOI: 10.1134/s0006297922050066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 04/08/2022] [Accepted: 04/09/2022] [Indexed: 06/15/2023]
Abstract
Amyloids are protein aggregates with the cross-β structure. The interest in amyloids is explained, on the one hand, by their role in the development of socially significant human neurodegenerative diseases, and on the other hand, by the discovery of functional amyloids, whose formation is an integral part of cellular processes. To date, more than a hundred proteins with the amyloid or amyloid-like properties have been identified. Studying the structure of amyloid aggregates has revealed a wide variety of protein conformations. In the review, we discuss the diversity of protein folds in the amyloid-like aggregates and the characteristic features of amyloid aggregates that determine their unusual properties, including stability and interaction with amyloid-specific dyes. The review also describes the diversity of amyloid aggregates and its significance for living organisms.
Collapse
Affiliation(s)
- Anton B Matiiv
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Nina P Trubitsina
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Andrew G Matveenko
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Yury A Barbitoff
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
- Bioinformatics Institute, Saint Petersburg, 197342, Russia
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
- Laboratory of Amyloid Biology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Stanislav A Bondarev
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia.
- Laboratory of Amyloid Biology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| |
Collapse
|
7
|
Zhouravleva GA, Bondarev SA, Zemlyanko OM, Moskalenko SE. [Role of Proteins Interacting with the eRF1 and eRF3 Release Factors in the Regulation of Translation and Prionization]. Mol Biol (Mosk) 2022; 56:206-226. [PMID: 35403616 DOI: 10.31857/s002689842201013x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 08/15/2021] [Indexed: 06/14/2023]
Abstract
The review discusses the role that proteins interacting with the translation termination factors eRF1 and eRF3 play in the control of protein synthesis and prionization. These proteins interact not only with each other, but also with many other proteins involved in controlling the efficiency of translation termination, and associate translation termination with other cell processes. The termination of translation is directly related not only to translation re-initiation and ribosome recycling, but also to mRNA stability and protein quality control. This connection is ensured by the interaction of eRF1 and eRF3 with proteins participating in various cell metabolic processes, such as mRNA transport from the nucleus into the cytoplasm (Dbp5/DDX19 and Gle1), ribosome recycling (Rli1/ABCE1), mRNA degradation (Upf proteins), and translation initiation (Pab1/PABP). In addition to genetic control, there is epigenetic control of translation termination. This mechanism is associated with prion polymerization of the Sup35 protein to form the [PSI^(+)] prion. The maintenance of the [PSI^(+)] prion, like other yeast prions, requires the operation of a system of molecular chaperones and protein sorting factors. The review considers in detail the interaction of the translation termination factors with proteins involved in various cellular processes.
Collapse
Affiliation(s)
- G A Zhouravleva
- Department of Genetics and Biotechnology, 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, St. Petersburg State University, St. Petersburg, 199034 Russia
- Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, 199034 Russia
| | - O M Zemlyanko
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, 199034 Russia
- Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, 199034 Russia
| | - S E Moskalenko
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, 199034 Russia
- St. Petersburg Branch, Vavilov Institute of General Genetics, Russian Academy of Sciences, St. Petersburg, 199034 Russia
| |
Collapse
|
8
|
Danilov LG, Moskalenko SE, Matveenko AG, Sukhanova XV, Belousov MV, Zhouravleva GA, Bondarev SA. The Human NUP58 Nucleoporin Can Form Amyloids In Vitro and In Vivo. Biomedicines 2021; 9:biomedicines9101451. [PMID: 34680573 PMCID: PMC8533070 DOI: 10.3390/biomedicines9101451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/05/2021] [Accepted: 10/08/2021] [Indexed: 12/20/2022] Open
Abstract
Amyloids are fibrillar protein aggregates with a cross-β structure and unusual features, including high resistance to detergent or protease treatment. More than two hundred different proteins with amyloid or amyloid-like properties are already known. Several examples of nucleoporins (e.g., yeast Nup49, Nup100, Nup116, and human NUP153) are supposed to form amyloid fibrils. In this study, we demonstrated an ability of the human NUP58 nucleoporin to form amyloid aggregates in vivo and in vitro. Moreover, we found two forms of NUP58 aggregates: oligomers and polymers stabilized by disulfide bonds. Bioinformatic analysis revealed that all known orthologs of this protein are potential amyloids which possess several regions with conserved ability to aggregation. The biological role of nucleoporin amyloid formation is debatable. We suggest that it is a rather abnormal process, which is characteristic for many proteins implicated in phase separation.
Collapse
Affiliation(s)
- Lavrentii G. Danilov
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (L.G.D.); (S.E.M.); (A.G.M.); (X.V.S.); (M.V.B.)
| | - Svetlana E. Moskalenko
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (L.G.D.); (S.E.M.); (A.G.M.); (X.V.S.); (M.V.B.)
- St. Petersburg Branch, Vavilov Institute of General Genetics, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Andrew G. Matveenko
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (L.G.D.); (S.E.M.); (A.G.M.); (X.V.S.); (M.V.B.)
| | - Xenia V. Sukhanova
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (L.G.D.); (S.E.M.); (A.G.M.); (X.V.S.); (M.V.B.)
| | - Mikhail V. Belousov
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (L.G.D.); (S.E.M.); (A.G.M.); (X.V.S.); (M.V.B.)
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia
| | - Galina A. Zhouravleva
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (L.G.D.); (S.E.M.); (A.G.M.); (X.V.S.); (M.V.B.)
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
- Correspondence: or (G.A.Z.); or (S.A.B.)
| | - Stanislav A. Bondarev
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (L.G.D.); (S.E.M.); (A.G.M.); (X.V.S.); (M.V.B.)
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
- Correspondence: or (G.A.Z.); or (S.A.B.)
| |
Collapse
|
9
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
10
|
Kharkov BB, Podkorytov IS, Bondarev SA, Belousov MV, Salikov VA, Zhouravleva GA, Skrynnikov NR. The Role of Rotational Motion in Diffusion NMR Experiments on Supramolecular Assemblies: Application to Sup35NM Fibrils. Angew Chem Int Ed Engl 2021; 60:15445-15451. [PMID: 33891789 DOI: 10.1002/anie.202102408] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/19/2021] [Indexed: 11/08/2022]
Abstract
Pulsed-field gradient (PFG) NMR is an important tool for characterization of biomolecules and supramolecular assemblies. However, for micrometer-sized objects, such as amyloid fibrils, these experiments become difficult to interpret because in addition to translational diffusion they are also sensitive to rotational diffusion. We have constructed a mathematical theory describing the outcome of PFG NMR experiments on rod-like fibrils. To test its validity, we have studied the fibrils formed by Sup35NM segment of the prion protein Sup35. The interpretation of the PFG NMR data in this system is fully consistent with the evidence from electron microscopy. Contrary to some previously expressed views, the signals originating from disordered regions in the fibrils can be readily differentiated from the similar signals representing small soluble species (e.g. proteolytic fragments). This paves the way for diffusion-sorted NMR experiments on complex amyloidogenic samples.
Collapse
Affiliation(s)
- Boris B Kharkov
- Laboratory of Biomolecular NMR, St. Petersburg State University, 199034, St. Petersburg, Russia
| | - Ivan S Podkorytov
- Laboratory of Biomolecular NMR, St. Petersburg State University, 199034, St. Petersburg, Russia
| | - Stanislav A Bondarev
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034, St. Petersburg, Russia
| | - Mikhail V Belousov
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034, St. Petersburg, Russia.,Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608, St. Petersburg, Russia
| | - Vladislav A Salikov
- Laboratory of Biomolecular NMR, St. Petersburg State University, 199034, St. Petersburg, Russia
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034, St. Petersburg, Russia
| | - Nikolai R Skrynnikov
- Laboratory of Biomolecular NMR, St. Petersburg State University, 199034, St. Petersburg, Russia.,Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| |
Collapse
|
11
|
Kharkov BB, Podkorytov IS, Bondarev SA, Belousov MV, Salikov VA, Zhouravleva GA, Skrynnikov NR. The Role of Rotational Motion in Diffusion NMR Experiments on Supramolecular Assemblies: Application to Sup35NM Fibrils. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Boris B. Kharkov
- Laboratory of Biomolecular NMR St. Petersburg State University 199034 St. Petersburg Russia
| | - Ivan S. Podkorytov
- Laboratory of Biomolecular NMR St. Petersburg State University 199034 St. Petersburg Russia
| | - Stanislav A. Bondarev
- Department of Genetics and Biotechnology St. Petersburg State University 199034 St. Petersburg Russia
| | - Mikhail V. Belousov
- Department of Genetics and Biotechnology St. Petersburg State University 199034 St. Petersburg Russia
- Laboratory for Proteomics of Supra-Organismal Systems All-Russia Research Institute for Agricultural Microbiology (ARRIAM) 196608 St. Petersburg Russia
| | - Vladislav A. Salikov
- Laboratory of Biomolecular NMR St. Petersburg State University 199034 St. Petersburg Russia
| | - Galina A. Zhouravleva
- Department of Genetics and Biotechnology St. Petersburg State University 199034 St. Petersburg Russia
| | - Nikolai R. Skrynnikov
- Laboratory of Biomolecular NMR St. Petersburg State University 199034 St. Petersburg Russia
- Department of Chemistry Purdue University West Lafayette IN 47907 USA
| |
Collapse
|
12
|
Barbitoff YA, Matveenko AG, Matiiv AB, Maksiutenko EM, Moskalenko SE, Drozdova PB, Polev DE, Beliavskaia AY, Danilov LG, Predeus AV, Zhouravleva GA. Chromosome-level genome assembly and structural variant analysis of two laboratory yeast strains from the Peterhof Genetic Collection lineage. G3 (Bethesda) 2021; 11:6129118. [PMID: 33677552 PMCID: PMC8759820 DOI: 10.1093/g3journal/jkab029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/22/2021] [Indexed: 01/23/2023]
Abstract
Thousands of yeast genomes have been sequenced with both traditional and long-read technologies, and multiple observations about modes of genome evolution for both wild and laboratory strains have been drawn from these sequences. In our study, we applied Oxford Nanopore and Illumina technologies to assemble complete genomes of two widely used members of a distinct laboratory yeast lineage, the Peterhof Genetic Collection (PGC), and investigate the structural features of these genomes including transposable element content, copy number alterations, and structural rearrangements. We identified numerous notable structural differences between genomes of PGC strains and the reference S288C strain. We discovered a substantial enrichment of mid-length insertions and deletions within repetitive coding sequences, such as in the SCH9 gene or the NUP100 gene, with possible impact of these variants on protein amyloidogenicity. High contiguity of the final assemblies allowed us to trace back the history of reciprocal unbalanced translocations between chromosomes I, VIII, IX, XI, and XVI of the PGC strains. We show that formation of hybrid alleles of the FLO genes during such chromosomal rearrangements is likely responsible for the lack of invasive growth of yeast strains. Taken together, our results highlight important features of laboratory yeast strain evolution using the power of long-read sequencing.
Collapse
Affiliation(s)
- Yury A Barbitoff
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia.,Bioinformatics Institute, St. Petersburg 197342, Russia
| | - Andrew G Matveenko
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia.,Bioinformatics Institute, St. Petersburg 197342, Russia
| | - Anton B Matiiv
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia.,Bioinformatics Institute, St. Petersburg 197342, Russia
| | - Evgeniia M Maksiutenko
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia.,St. Petersburg Branch, Vavilov Institute of General Genetics of the Russian Academy of Sciences, St. Petersburg 199034, Russia
| | - Svetlana E Moskalenko
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia.,St. Petersburg Branch, Vavilov Institute of General Genetics of the Russian Academy of Sciences, St. Petersburg 199034, Russia
| | | | | | - Alexandra Y Beliavskaia
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Lavrentii G Danilov
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Alexander V Predeus
- Bioinformatics Institute, St. Petersburg 197342, Russia.,University of Liverpool, Liverpool, UK, L7 3EA
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia
| |
Collapse
|
13
|
Matiiv AB, Trubitsina NP, Matveenko AG, Barbitoff YA, Zhouravleva GA, Bondarev SA. Amyloid and Amyloid-Like Aggregates: Diversity and the Term Crisis. Biochemistry (Mosc) 2021; 85:1011-1034. [PMID: 33050849 DOI: 10.1134/s0006297920090035] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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
|
14
|
Sulatskaya AI, Bondarev SA, Sulatsky MI, Trubitsina NP, Belousov MV, Zhouravleva GA, Llanos MA, Kajava AV, Kuznetsova IM, Turoverov KK. Point mutations affecting yeast prion propagation change the structure of its amyloid fibrils. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
15
|
Barbitoff YA, Matveenko AG, Bondarev SA, Maksiutenko EM, Kulikova AV, Zhouravleva GA. Quantitative assessment of chaperone binding to amyloid aggregates identifies specificity of Hsp40 interaction with yeast prion fibrils. FEMS Yeast Res 2020; 20:5831717. [PMID: 32379306 DOI: 10.1093/femsyr/foaa025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/05/2020] [Indexed: 12/18/2022] Open
Abstract
Yeast self-perpetuating protein aggregates (yeast prions) provide a framework to investigate the interaction of misfolded proteins with the protein quality control machinery. The major component of this system that facilitates propagation of all known yeast amyloid prions is the Hsp104 chaperone that catalyzes fibril fragmentation. Overproduction of Hsp104 cures some yeast prions via a fragmentation-independent mechanism. Importantly, major cytosolic chaperones of the Hsp40 group, Sis1 and Ydj1, oppositely affect yeast prion propagation, and are capable of stimulating different activities of Hsp104. In this work, we developed a quantitative method to investigate the Hsp40 binding to amyloid aggregates. We demonstrate that Sis1 binds fibrils formed by the Sup35NM protein with higher affinity compared to Ydj1. Moreover, the interaction of Sis1 with the fibrils formed by the other yeast prion protein, Rnq1, is orders of magnitude weaker. We show that the deletion of the dimerization domain of Sis1 (crucial for the curing of [PSI+] by excess Hsp104) decreases its affinity to both Sup35NM and Rnq1 fibrils. Taken together, these results suggest that tight binding of Hsp40 to the amyloid fibrils is likely to enhance aggregate malpartition instead of fibril fragmentation.
Collapse
Affiliation(s)
- Yury A Barbitoff
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab. 7/9, St. Petersburg, 199034 Russia
| | - Andrew G Matveenko
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab. 7/9, St. Petersburg, 199034 Russia
| | - Stanislav A Bondarev
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab. 7/9, St. Petersburg, 199034 Russia.,Laboratory of Amyloid Biology, St. Petersburg State University, Universitetskaya nab. 7/9, St. Petersburg, 199034 Russia
| | - Evgeniia M Maksiutenko
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab. 7/9, St. Petersburg, 199034 Russia.,St. Petersburg Branch, Vavilov Institute of General Genetics, Russian Academy of Sciences, Universitetskaya nab. 7/9, St. Petersburg, 199034 Russia
| | - Alexandra V Kulikova
- Peter the Great St. Petersburg Polytechnic University, Politekhnicheskaya ul. 29, St. Petersburg, 195251 Russia
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab. 7/9, St. Petersburg, 199034 Russia.,Laboratory of Amyloid Biology, St. Petersburg State University, Universitetskaya nab. 7/9, St. Petersburg, 199034 Russia
| |
Collapse
|
16
|
Drozdova PB, Barbitoff YA, Belousov MV, Skitchenko RK, Rogoza TM, Leclercq JY, Kajava AV, Matveenko AG, Zhouravleva GA, Bondarev SA. Estimation of amyloid aggregate sizes with semi-denaturing detergent agarose gel electrophoresis and its limitations. Prion 2020; 14:118-128. [PMID: 32306832 PMCID: PMC7199750 DOI: 10.1080/19336896.2020.1751574] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Semi-denaturing detergent agarose gel electrophoresis (SDD-AGE) was proposed by Vitaly V. Kushnirov in the Michael D. Ter-Avanesyan’s laboratory as a method to compare sizes of amyloid aggregates. Currently, this method is widely used for amyloid investigation, but mostly as a qualitative approach. In this work, we assessed the possibilities and limitations of the quantitative analysis of amyloid aggregate size distribution using SDD-AGE results. For this purpose, we used aggregates of two well-characterized yeast amyloid-forming proteins, Sup35 and Rnq1, and developed a protocol to standardize image analysis and process the result. A detailed investigation of factors that may affect the results of SDD-AGE revealed that both the cell lysis method and electrophoresis conditions can substantially affect the estimation of aggregate size. Despite this, quantitative analysis of SDD-AGE results is possible when one needs to estimate and compare the size of aggregates on the same gel, or even in different experiments, if the experimental conditions are tightly controlled and additional standards are used.
Collapse
Affiliation(s)
- Polina B Drozdova
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia.,Institute of Biology, Irkutsk State University, Irkutsk, Russia
| | - Yury A Barbitoff
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - Mikhail V Belousov
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia.,Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
| | - Rostislav K Skitchenko
- International Research Institute of Bioengineering, ITMO University, St. Petersburg, Russia
| | - Tatyana M Rogoza
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia.,Vavilov Institute of General Genetics Russian Academy of Sciences, St. Petersburg Branch, St. Petersburg, Russia
| | - Jeremy Y Leclercq
- Centre de Recherche En Biologie Cellulaire De Montpellier, UMR 5237 CNRS, Montpellier, France
| | - Andrey V Kajava
- International Research Institute of Bioengineering, ITMO University, St. Petersburg, Russia.,Centre de Recherche En Biologie Cellulaire De Montpellier, UMR 5237 CNRS, Montpellier, France
| | - Andrew G Matveenko
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia.,Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, Russia
| | - Stanislav A Bondarev
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia.,Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, Russia
| |
Collapse
|
17
|
Trubitsina NP, Zemlyanko OM, Bondarev SA, Zhouravleva GA. Nonsense Mutations in the Yeast SUP35 Gene Affect the [ PSI+] Prion Propagation. Int J Mol Sci 2020; 21:E1648. [PMID: 32121268 PMCID: PMC7084296 DOI: 10.3390/ijms21051648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/20/2020] [Accepted: 02/26/2020] [Indexed: 11/16/2022] Open
Abstract
The essential SUP35 gene encodes yeast translation termination factor eRF3. Previously, we isolated nonsense mutations sup35-n and proposed that the viability of such mutants can be explained by readthrough of the premature stop codon. Such mutations, as well as the prion [PSI+], can appear in natural yeast populations, and their combinations may have different effects on the cells. Here, we analyze the effects of the compatibility of sup35-n mutations with the [PSI+] prion in haploid and diploid cells. We demonstrated that sup35-n mutations are incompatible with the [PSI+] prion, leading to lethality of sup35-n [PSI+] haploid cells. In diploid cells the compatibility of [PSI+] with sup35-n depends on how the corresponding diploid was obtained. Nonsense mutations sup35-21, sup35-74, and sup35-218 are compatible with the [PSI+] prion in diploid strains, but affect [PSI+] properties and lead to the formation of new prion variant. The only mutation that could replace the SUP35 wild-type allele in both haploid and diploid [PSI+] strains, sup35-240, led to the prion loss. Possibly, short Sup351-55 protein, produced from the sup35-240 allele, is included in Sup35 aggregates and destabilize them. Alternatively, single molecules of Sup351-55 can stick to aggregate ends, and thus interrupt the fibril growth. Thus, we can conclude that sup35-240 mutation prevents [PSI+] propagation and can be considered as a new pnm mutation.
Collapse
Affiliation(s)
- Nina P. Trubitsina
- Department of Genetics and Biotechnology, Saint Petersburg State University, 199034 St. Petersburg, Russia; (N.P.T.); (O.M.Z.); (S.A.B.)
| | - Olga M. Zemlyanko
- Department of Genetics and Biotechnology, Saint Petersburg State University, 199034 St. Petersburg, Russia; (N.P.T.); (O.M.Z.); (S.A.B.)
- Laboratory of Amyloid Biology, Saint Petersburg State University, 199034 St. Petersburg, Russia
| | - Stanislav A. Bondarev
- Department of Genetics and Biotechnology, Saint Petersburg State University, 199034 St. Petersburg, Russia; (N.P.T.); (O.M.Z.); (S.A.B.)
- Laboratory of Amyloid Biology, Saint Petersburg State University, 199034 St. Petersburg, Russia
| | - Galina A. Zhouravleva
- Department of Genetics and Biotechnology, Saint Petersburg State University, 199034 St. Petersburg, Russia; (N.P.T.); (O.M.Z.); (S.A.B.)
- Laboratory of Amyloid Biology, Saint Petersburg State University, 199034 St. Petersburg, Russia
| |
Collapse
|
18
|
Danilov LG, Matveenko AG, Ryzhkova VE, Belousov MV, Poleshchuk OI, Likholetova DV, Sokolov PA, Kasyanenko NA, Kajava AV, Zhouravleva GA, Bondarev SA. Design of a New [ PSI +]-No-More Mutation in SUP35 With Strong Inhibitory Effect on the [ PSI +] Prion Propagation. Front Mol Neurosci 2019; 12:274. [PMID: 31803017 PMCID: PMC6877606 DOI: 10.3389/fnmol.2019.00274] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 10/28/2019] [Indexed: 12/04/2022] Open
Abstract
A number of [PSI+]-no-more (PNM) mutations, eliminating [PSI+] prion, were previously described in SUP35. In this study, we designed and analyzed a new PNM mutation based on the parallel in-register β-structure of Sup35 prion fibrils suggested by the known experimental data. In such an arrangement, substitution of non-charged residues by charged ones may destabilize the fibril structure. We introduced Q33K/A34K amino acid substitutions into the Sup35 protein, corresponding allele was called sup35-M0. The mutagenized residues were chosen based on ArchCandy in silico prediction of high inhibitory effect on the amyloidogenic potential of Sup35. The experiments confirmed that Sup35-M0 leads to the elimination of [PSI+] with high efficiency. Our data suggested that the elimination of the [PSI+] prion is associated with the decreased aggregation properties of the protein. The new mutation can induce the prion with very low efficiency and is able to propagate only weak [PSI+] prion variants. We also showed that Sup35-M0 protein co-aggregates with the wild-type Sup35 in vivo. Moreover, our data confirmed the utility of the strategy of substitution of non-charged residues by charged ones to design new mutations to inhibit a prion formation.
Collapse
Affiliation(s)
- Lavrentii G Danilov
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - Andrew G Matveenko
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - Varvara E Ryzhkova
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - Mikhail V Belousov
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia.,Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), St. Petersburg, Russia
| | - Olga I Poleshchuk
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - Daria V Likholetova
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - Petr A Sokolov
- Department of Molecular Biophysics and Polymer Physics, St. Petersburg State University, St. Petersburg, Russia
| | - Nina A Kasyanenko
- Department of Molecular Biophysics and Polymer Physics, St. Petersburg State University, St. Petersburg, Russia
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Université Montpellier, Montpellier, France.,Institut de Biologie Computationnelle (IBC), Universitè Montpellier, Montpellier, France
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia.,Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, Russia
| | - Stanislav A Bondarev
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia.,Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, Russia
| |
Collapse
|
19
|
Matveenko AG, Drozdova PB, Moskalenko SE, Tarasov OV, Zhouravleva GA. Whole genome sequencing data and analyses of the underlying SUP35 transcriptional regulation for a Saccharomyces cerevisiae nonsense suppressor mutant. Data Brief 2019; 23:103694. [PMID: 30788402 PMCID: PMC6369104 DOI: 10.1016/j.dib.2019.01.042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/06/2019] [Accepted: 01/18/2019] [Indexed: 11/18/2022] Open
Abstract
Termination of translation in eukaryotes is governed by two release factors encoded by the SUP45 and SUP35 genes in Saccharomyces cerevisiae. Previously, a set of mutations in these genes had been obtained. However, the exact sequence change associated with one mutation, sup35-222, was not identified by Sanger sequencing of the SUP35 region. Presented here are whole-genome sequencing data for the sup35-222 strain, data on copy number variation in its genome along with supporting pulse-field gel electrophoresis experiment data, and the list of single-nucleotide variations that differentiate this strain and its wild-type ancestor. One substitution upstream the SUP35 gene was located in a sequence corresponding to the Abf1-binding site. Data obtained from the introduction of this variation from sup35-222 strain into a different wild-type strain, specifically, detection of a nonsense-suppressor phenotype accompanied by a decrease in the Sup35 protein level, are also presented in this article.
Collapse
Affiliation(s)
- Andrew G. Matveenko
- Department of Genetics and Biotechnology, Saint Petersburg State University, St. Petersburg 199034, Russia
| | - Polina B. Drozdova
- Department of Genetics and Biotechnology, Saint Petersburg State University, St. Petersburg 199034, Russia
| | - Svetlana E. Moskalenko
- Department of Genetics and Biotechnology, Saint Petersburg State University, St. Petersburg 199034, Russia
- St. Petersburg Branch, Vavilov Institute of General Genetics, Russian Academy of Sciences, St. Petersburg 199034, Russia
| | - Oleg V. Tarasov
- Department of Genetics and Biotechnology, Saint Petersburg State University, St. Petersburg 199034, Russia
| | - Galina A. Zhouravleva
- Department of Genetics and Biotechnology, Saint Petersburg State University, St. Petersburg 199034, Russia
- Laboratory of Amyloid Biology, Saint Petersburg State University, St. Petersburg 199034, Russia
- Corresponding author at: Department of Genetics and Biotechnology, Saint-Petersburg State University, Universitetskaya emb., 7/9, St. Petersburg 199034, Russia.
| |
Collapse
|
20
|
Bondarev SA, Bondareva OV, Zhouravleva GA, Kajava AV. BetaSerpentine: a bioinformatics tool for reconstruction of amyloid structures. Bioinformatics 2018; 34:599-608. [PMID: 29444233 DOI: 10.1093/bioinformatics/btx629] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 10/03/2017] [Indexed: 11/12/2022] Open
Abstract
Motivation Numerous experimental studies have suggested that polypeptide chains of large amyloidogenic regions zig-zag in β-serpentine arrangements. These β-serpentines are stacked axially and form the superpleated β-structure. Despite this progress in the understanding of amyloid folds, the determination of their 3D structure at the atomic level is still a problem due to the polymorphism of these fibrils and incompleteness of experimental structural data. Today, the way to get insight into the atomic structure of amyloids is a combination of experimental studies with bioinformatics. Results We developed a computer program BetaSerpentine that reconstructs β-serpentine arrangements from individual β-arches predicted by ArchCandy program and ranks them in order of preference. It was shown that the BetaSerpentine program in combination with the experimental data can be used to gain insight into the detailed 3D structure of amyloids. It opens avenues to the structure-based interpretation and design of the experiments. Availability and implementation BetaSerpentine webserver can be accessed through website: http://bioinfo.montp.cnrs.fr/b-serpentine. Source code is available in git.hub repository (github.com/stanislavspbgu/BetaSerpentine). Contact stanislavspbgu@gmail.com or andrey.kajava@crbm.cnrs.fr. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Stanislav A Bondarev
- Laboratory of Amyloid Biology and Department of Genetics and Biotechnology, St. Petersburg State University, Saint Petersburg 199034, Russia
| | - Olga V Bondareva
- Laboratory of Molecular Systematics, Zoological Institute RAS, Saint Petersburg 199034, Russia
| | - Galina A Zhouravleva
- Laboratory of Amyloid Biology and Department of Genetics and Biotechnology, St. Petersburg State University, Saint Petersburg 199034, Russia
| | - Andrey V Kajava
- Structural Bioinformatics and Molecular Modeling, Centre de Recherche en Biologie Cellulaire de Montpellier, CNRS, Université Montpellier, Montpellier 34293, France.,Institut de Biologie Computationnelle, Montpellier 34095, France.,Bioengineering Department, University ITMO, Saint Petersburg, 197101, Russia
| |
Collapse
|
21
|
Bondarev SA, Antonets KS, Kajava AV, Nizhnikov AA, Zhouravleva GA. Protein Co-Aggregation Related to Amyloids: Methods of Investigation, Diversity, and Classification. Int J Mol Sci 2018; 19:ijms19082292. [PMID: 30081572 PMCID: PMC6121665 DOI: 10.3390/ijms19082292] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 07/29/2018] [Accepted: 08/02/2018] [Indexed: 01/04/2023] Open
Abstract
Amyloids are unbranched protein fibrils with a characteristic spatial structure. Although the amyloids were first described as protein deposits that are associated with the diseases, today it is becoming clear that these protein fibrils play multiple biological roles that are essential for different organisms, from archaea and bacteria to humans. The appearance of amyloid, first of all, causes changes in the intracellular quantity of the corresponding soluble protein(s), and at the same time the aggregate can include other proteins due to different molecular mechanisms. The co-aggregation may have different consequences even though usually this process leads to the depletion of a functional protein that may be associated with different diseases. The protein co-aggregation that is related to functional amyloids may mediate important biological processes and change of protein functions. In this review, we survey the known examples of the amyloid-related co-aggregation of proteins, discuss their pathogenic and functional roles, and analyze methods of their studies from bacteria and yeast to mammals. Such analysis allow for us to propose the following co-aggregation classes: (i) titration: deposition of soluble proteins on the amyloids formed by their functional partners, with such interactions mediated by a specific binding site; (ii) sequestration: interaction of amyloids with certain proteins lacking a specific binding site; (iii) axial co-aggregation of different proteins within the same amyloid fibril; and, (iv) lateral co-aggregation of amyloid fibrils, each formed by different proteins.
Collapse
Affiliation(s)
- Stanislav A Bondarev
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab., 7/9, St. Petersburg 199034, Russia.
- Laboratory of Amyloid Biology, St. Petersburg State University, Russia, Universitetskaya nab., 7/9, St. Petersburg 199034, Russia.
| | - Kirill S Antonets
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab., 7/9, St. Petersburg 199034, Russia.
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, Podbelskogo sh., 3, Pushkin, St. Petersburg 196608, Russia.
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Université Montpellier 1919 Route de Mende, CEDEX 5, 34293 Montpellier, France.
- Institut de Biologie Computationnelle (IBC), 34095 Montpellier, France.
- University ITMO, Institute of Bioengineering, Kronverksky Pr. 49, St. Petersburg 197101, Russia.
| | - Anton A Nizhnikov
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab., 7/9, St. Petersburg 199034, Russia.
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, Podbelskogo sh., 3, Pushkin, St. Petersburg 196608, Russia.
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab., 7/9, St. Petersburg 199034, Russia.
- Laboratory of Amyloid Biology, St. Petersburg State University, Russia, Universitetskaya nab., 7/9, St. Petersburg 199034, Russia.
| |
Collapse
|
22
|
Belousov MV, Bondarev SA, Kosolapova AO, Antonets KS, Sulatskaya AI, Sulatsky MI, Zhouravleva GA, Kuznetsova IM, Turoverov KK, Nizhnikov AA. M60-like metalloprotease domain of the Escherichia coli YghJ protein forms amyloid fibrils. PLoS One 2018; 13:e0191317. [PMID: 29381728 PMCID: PMC5790219 DOI: 10.1371/journal.pone.0191317] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 01/03/2018] [Indexed: 12/31/2022] Open
Abstract
Amyloids are protein fibrils with a characteristic spatial structure. Amyloids were long perceived as the pathogens involved in a set of lethal diseases in humans and animals. In recent decades, it has become clear that amyloids represent a quaternary protein structure that is not only pathological but also functionally important and is widely used by different organisms, ranging from archaea to animals, to implement diverse biological functions. The greatest biological variety of amyloids is found in prokaryotes, where they control the formation of biofilms and cell wall sheaths, facilitate the overcoming of surface tension, and regulate the metabolism of toxins. Several amyloid proteins were identified in the important model, biotechnological and pathogenic bacterium Escherichia coli. In previous studies, using a method for the proteomic screening and identification of amyloids, we identified 61 potentially amyloidogenic proteins in the proteome of E. coli. Among these proteins, YghJ was the most enriched with bioinformatically predicted amyloidogenic regions. YghJ is a lipoprotein with a zinc metalloprotease M60-like domain that is involved in mucin degradation in the intestine as well as in proinflammatory responses. In this study, we analyzed the amyloid properties of the YghJ M60-like domain and demonstrated that it forms amyloid-like fibrils in vitro and in vivo.
Collapse
Affiliation(s)
- Mikhail V. Belousov
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab., St. Petersburg, Russian Federation
| | - Stanislav A. Bondarev
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab., St. Petersburg, Russian Federation
- Laboratory of Amyloid Biology, St. Petersburg State University, Universitetskaya nab., St. Petersburg, Russian Federation
| | - Anastasiia O. Kosolapova
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab., St. Petersburg, Russian Federation
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Podbelskogo sh., Pushkin, St. Petersburg, Russian Federation
| | - Kirill S. Antonets
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab., St. Petersburg, Russian Federation
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Podbelskogo sh., Pushkin, St. Petersburg, Russian Federation
| | - Anna I. Sulatskaya
- Institute of Cytology, Russian Academy of Science, St. Petersburg, Russian Federation
| | - Maksim I. Sulatsky
- Institute of Cytology, Russian Academy of Science, St. Petersburg, Russian Federation
| | - Galina A. Zhouravleva
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab., St. Petersburg, Russian Federation
- Laboratory of Amyloid Biology, St. Petersburg State University, Universitetskaya nab., St. Petersburg, Russian Federation
| | - Irina M. Kuznetsova
- Institute of Cytology, Russian Academy of Science, St. Petersburg, Russian Federation
| | - Konstantin K. Turoverov
- Institute of Cytology, Russian Academy of Science, St. Petersburg, Russian Federation
- Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya, St. Petersburg, Russian Federation
| | - Anton A. Nizhnikov
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab., St. Petersburg, Russian Federation
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Podbelskogo sh., Pushkin, St. Petersburg, Russian Federation
- Vavilov Institute of General Genetics, Russian Academy of Sciences, St Petersburg Branch, Universitetskaya nab., St. Petersburg, Russian Federation
- * E-mail:
| |
Collapse
|
23
|
Sokolov PA, Bondarev SA, Belousov MV, Zhouravleva GA, Kasyanenko NA. Sup35NMp morphology evaluation on Au, Si, formvar and mica surfaces using AFM, SEM and TEM. J Struct Biol 2017; 201:5-14. [PMID: 29078994 DOI: 10.1016/j.jsb.2017.10.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 09/24/2017] [Accepted: 10/17/2017] [Indexed: 11/17/2022]
Abstract
Prion and some other incurable human neurodegenerative diseases are associated with misfolding of specific proteins, followed by the formation of amyloids. Despite the widespread usage of the transmission electron and of the atomic force microscopy for studing such amyloids, many related methodological issues still have not been studied until now. Here, we consider one of the first amyloids found in Saccharomyces cerevisiae yeast, i.e. Sup35NMp, to study the adsorption of monomeric protein and its fibrils on the surface of mica, silica, gold and on formvar film. Comparison of linear characteristics of these units calculated by processing of images obtained by the atomic force, transmission and scanning electron microscopy was carried out. The minimal number of measurements of fibril diameters to obtain the values in a given confidence interval were determined. We investigated the film formed by monomeric protein on mica surface, which veiled some morphology features of fibrils. Besides, we revealed that parts of the Sup35NMp excluded from the fibril core can form a wide "coat". The length of the protein forming the core of the fibrils was estimated.
Collapse
Affiliation(s)
- P A Sokolov
- Department of Physics, St. Petersburg State University, Russia.
| | - S A Bondarev
- Department of Genetics and Biotechnology, St. Petersburg State University, Russia; The Laboratory of Amyloid Biology, St. Petersburg State University, Russia
| | - M V Belousov
- Department of Genetics and Biotechnology, St. Petersburg State University, Russia
| | - G A Zhouravleva
- Department of Genetics and Biotechnology, St. Petersburg State University, Russia; The Laboratory of Amyloid Biology, St. Petersburg State University, Russia
| | - N A Kasyanenko
- Department of Physics, St. Petersburg State University, Russia
| |
Collapse
|
24
|
Bondarev SA, Likholetova DV, Belousov MV, Zhouravleva GA. [Rnq1 protein protects [PSI^(+)] prion from effect of the PNM mutation]. Mol Biol (Mosk) 2017; 51:367-371. [PMID: 28537243 DOI: 10.7868/s0026898417010050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 04/11/2016] [Indexed: 11/23/2022]
Abstract
The interaction of [PSI^(+)] and [PIN^(+)] factors in yeast Saccharomyces cerevisiae is known as the first evidence of prions networks. In [PIN^(+)] cells, Rnq1p prion aggregates work as a template for Sup35p aggregation, which is essential for [PSI^(+)] induction. No additional factors are required for subsequent Sup35p aggregation. Nevertheless, several recent reports provide data that indicate a more complex interplay between these prions. Our results show that the presence of Rnq1p in the cell significantly decreases the loss of [PSI^(+)] prion, which is caused by a double mutation in SUP35 (Q61K, Q62K substitutions in the Sup35 protein). These observations support the existence of interaction networks that converge on a strong linkage of prionogenic and prion-like proteins, and the participation of Rnq1 protein in the maintenance of prion [PSI^(+)].
Collapse
Affiliation(s)
- S A Bondarev
- Laboratory of Physiological Genetics, Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, 199034 Russia.,Laboratory of Amyloid BiologySt. Petersburg State University, St. Petersburg, 199034 Russia.,
| | - D V Likholetova
- Laboratory of Physiological Genetics, Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, 199034 Russia
| | - M V Belousov
- Laboratory of Physiological Genetics, Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, 199034 Russia
| | - G A Zhouravleva
- Laboratory of Physiological Genetics, Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, 199034 Russia.,Laboratory of Amyloid BiologySt. Petersburg State University, St. Petersburg, 199034 Russia
| |
Collapse
|
25
|
Barbitoff YA, Matveenko AG, Moskalenko SE, Zemlyanko OM, Newnam GP, Patel A, Chernova TA, Chernoff YO, Zhouravleva GA. To CURe or not to CURe? Differential effects of the chaperone sorting factor Cur1 on yeast prions are mediated by the chaperone Sis1. Mol Microbiol 2017; 105:242-257. [PMID: 28431189 DOI: 10.1111/mmi.13697] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2017] [Indexed: 02/06/2023]
Abstract
Yeast self-perpetuating protein aggregates (prions) provide a convenient model for studying various components of the cellular protein quality control system. Molecular chaperones and chaperone-sorting factors, such as yeast Cur1 protein, play key role in proteostasis via tight control of partitioning and recycling of misfolded proteins. In this study, we show that, despite the previously described ability of Cur1 to antagonize the yeast prion [URE3], it enhances propagation and phenotypic manifestation of another prion, [PSI+ ]. We demonstrate that both curing of [URE3] and enhancement of [PSI+ ] in the presence of excess Cur1 are counteracted by the cochaperone Hsp40-Sis1 in a dosage-dependent manner, and show that the effect of Cur1 on prions parallels effects of the attachment of nuclear localization signal to Sis1, indicating that Cur1 acts on prions via its previously reported ability to relocalize Sis1 from the cytoplasm to nucleus. This shows that the direction in which Cur1 influences a prion depends on how this specific prion responds to relocalization of Sis1.
Collapse
Affiliation(s)
- Yury A Barbitoff
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Andrew G Matveenko
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia.,Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg 199034, Russia.,St. Petersburg Branch, Vavilov Institute of General Genetics, Russian Academy of Sciences, St. Petersburg 199034, Russia
| | - Svetlana E Moskalenko
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia.,St. Petersburg Branch, Vavilov Institute of General Genetics, Russian Academy of Sciences, St. Petersburg 199034, Russia
| | - Olga M Zemlyanko
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia.,Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Gary P Newnam
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332-2000, USA
| | - Ayesha Patel
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332-2000, USA
| | - Tatiana A Chernova
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Yury O Chernoff
- Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg 199034, Russia.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332-2000, USA.,Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia
| |
Collapse
|
26
|
Matveenko AG, Belousov MV, Bondarev SA, Moskalenko SE, Zhouravleva GA. [Identification of new genes that affect [PSI^(+)] prion toxicity in Saccharomyces cerevisiae yeast]. Mol Biol (Mosk) 2017; 50:803-813. [PMID: 27830682 DOI: 10.7868/s0026898416050116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 03/09/2016] [Indexed: 11/23/2022]
Abstract
Translation termination is an important step in gene expression. Its correct processing is governed by eRF1 (Sup45) and eRF3 (Sup35) proteins. In Saccharomyces cerevisiae, mutations in the corresponding genes, as well as Sup35 aggregation in [PSI^(+)] cells that propagate the prion form of Sup35 lead to inaccurate stop codon recognition and, consequently, nonsense suppression. The presence of stronger prion variants results in the more efficient suppression of nonsense mutations. Previously, we proposed a synthetic lethality test that enables the identification of genes that may influence either translation termination factors or [PSI^(+)] manifestation. This is based on the fact that the combination of sup45 mutations with the strong [PSI^(+)] prion variant in diploids is lethal. In this work, a set of genes that were previously shown to enhance nonsense suppression was analyzed. It was found that ABF1, FKH2, and REB1 overexpression decreased the growth of strains in a prion-dependent manner and, thus, might influence [PSI^(+)] prion toxicity. It was also shown that the synthetic lethality of [PSI^(+)] and sup45 mutations increased with the overexpression of GLN3 and MOT3 that encode Q/N-rich transcription factors. An analysis of the effects of their expression on the transcription of the release factors genes revealed an increase in SUP35 transcription in both cases. Since SUP35 overexpression is known to be toxic in [PSI^(+)] strains, these genes apparently enhance [PSI^(+)] toxicity via the regulation of SUP35 transcription.
Collapse
Affiliation(s)
- A G Matveenko
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, 199034 Russia.,St. Petersburg Branch of Vavilov Institute of General Genetics, Russian Academy of Sciences, St. Petersburg, 199034 Russia
| | - M V Belousov
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, 199034 Russia
| | - S A Bondarev
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, 199034 Russia.,Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, 199034 Russia
| | - S E Moskalenko
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, 199034 Russia.,St. Petersburg Branch of Vavilov Institute of General Genetics, Russian Academy of Sciences, St. Petersburg, 199034 Russia
| | - G A Zhouravleva
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, 199034 Russia.,Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, 199034 Russia.,
| |
Collapse
|
27
|
Matveenko AG, Drozdova PB, Belousov MV, Moskalenko SE, Bondarev SA, Barbitoff YA, Nizhnikov AA, Zhouravleva GA. SFP1-mediated prion-dependent lethality is caused by increased Sup35 aggregation and alleviated by Sis1. Genes Cells 2016; 21:1290-1308. [DOI: 10.1111/gtc.12444] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 09/14/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Andrew G. Matveenko
- St Petersburg Branch; Vavilov Institute of General Genetics of the Russian Academy of Sciences; St Petersburg Russia
- Department of Genetics and Biotechnology; Saint Petersburg State University; St Petersburg Russia
- Laboratory of Amyloid Biology; Saint Petersburg State University; St Petersburg Russia
| | - Polina B. Drozdova
- Department of Genetics and Biotechnology; Saint Petersburg State University; St Petersburg Russia
- Laboratory of Amyloid Biology; Saint Petersburg State University; St Petersburg Russia
| | - Mikhail V. Belousov
- Department of Genetics and Biotechnology; Saint Petersburg State University; St Petersburg Russia
| | - Svetlana E. Moskalenko
- St Petersburg Branch; Vavilov Institute of General Genetics of the Russian Academy of Sciences; St Petersburg Russia
- Department of Genetics and Biotechnology; Saint Petersburg State University; St Petersburg Russia
| | - Stanislav A. Bondarev
- Department of Genetics and Biotechnology; Saint Petersburg State University; St Petersburg Russia
- Laboratory of Amyloid Biology; Saint Petersburg State University; St Petersburg Russia
| | - Yury A. Barbitoff
- Department of Genetics and Biotechnology; Saint Petersburg State University; St Petersburg Russia
| | - Anton A. Nizhnikov
- St Petersburg Branch; Vavilov Institute of General Genetics of the Russian Academy of Sciences; St Petersburg Russia
- Department of Genetics and Biotechnology; Saint Petersburg State University; St Petersburg Russia
- All-Russia Research Institute for Agricultural Microbiology; Pushkin St Petersburg Russia
| | - Galina A. Zhouravleva
- Department of Genetics and Biotechnology; Saint Petersburg State University; St Petersburg Russia
- Laboratory of Amyloid Biology; Saint Petersburg State University; St Petersburg Russia
| |
Collapse
|
28
|
Sulatskaya AI, Kuznetsova IM, Belousov MV, Bondarev SA, Zhouravleva GA, Turoverov KK. Stoichiometry and Affinity of Thioflavin T Binding to Sup35p Amyloid Fibrils. PLoS One 2016; 11:e0156314. [PMID: 27228180 PMCID: PMC4882037 DOI: 10.1371/journal.pone.0156314] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 05/12/2016] [Indexed: 11/25/2022] Open
Abstract
In this work two modes of binding of the fluorescent probe thioflavin T to yeast prion protein Sup35p amyloid fibrils were revealed by absorption spectrometry of solutions prepared by equilibrium microdialysis. These binding modes exhibited significant differences in binding affinity and stoichiometry. Moreover, the absorption spectrum and the molar extinction coefficient of the dye bound in each mode were determined. The fluorescence quantum yield of the dye bound in each mode was determined via a spectrofluorimetric study of the same solutions in which the recorded fluorescence intensity was corrected for the primary inner filter effect. As previously predicted, the existence of one of the detected binding modes may be due to the incorporation of the dye into the grooves along the fiber axis perpendicular to the β-sheets of the fibrils. It was assumed that the second type of binding with higher affinity may be due to the existence of ThT binding sites that are localized to areas where amyloid fibrils are clustered.
Collapse
Affiliation(s)
- Anna I. Sulatskaya
- Laboratory for Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Science, St. Petersburg, Tikhoretsky Ave. 4, 194064, Russia
| | - Irina M. Kuznetsova
- Laboratory for Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Science, St. Petersburg, Tikhoretsky Ave. 4, 194064, Russia
| | - Mikhail V. Belousov
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, Universitetskaya Emb. 7–9, 199034, Russia
| | - Stanislav A. Bondarev
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, Universitetskaya Emb. 7–9, 199034, Russia
- Laboratory of Amyloid Biology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Galina A. Zhouravleva
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, Universitetskaya Emb. 7–9, 199034, Russia
- Laboratory of Amyloid Biology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Konstantin K. Turoverov
- Laboratory for Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Science, St. Petersburg, Tikhoretsky Ave. 4, 194064, Russia
- Institute of Physics, Nanotechnology and Telecommunications, Peter the Great St.-Petersburg Polytechnic University, St. Petersburg, Polytechnicheskaya 29, 195251, Russia
- * E-mail:
| |
Collapse
|
29
|
Bondarev SA, Zhouravleva GA, Belousov MV, Kajava AV. Structure-based view on [PSI(+)] prion properties. Prion 2015; 9:190-9. [PMID: 26030475 PMCID: PMC4601339 DOI: 10.1080/19336896.2015.1044186] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 04/17/2015] [Accepted: 04/17/2015] [Indexed: 10/23/2022] Open
Abstract
Yeast [PSI(+)] prion is one of the most suitable and well characterized system for the investigation of the prion phenomenon. However, until recently, the lack of data on the 3D arrangement of Sup35p prion fibrils hindered progress in this area. The recent arrival in this field of new experimental techniques led to the parallel and in-register superpleated β-structure as a consensus model for Sup35p fibrils. Here, we analyzed the effect of amino acid substitutions of the Sup35 protein through the prism of this structural model. Application of a newly developed computational approach, called ArchCandy, gives us a better understanding of the effect caused by mutations on the fibril forming potential of Sup35 protein. This bioinformatics tool can be used for the design of new mutations with desired modification of prion properties. Thus, we provide examples of how today, having progress toward elucidation of the structural arrangement of Sup35p fibrils, researchers can advance more efficiently to a better understanding of prion [PSI(+)] stability and propagation.
Collapse
Key Words
- Asu mutations, antisupressor mutations
- EM, electron microscopy
- NMR, nuclear magnetic resonance
- PNM, [PSI+] no more
- STEM, scanning transmission electron microscopy
- amyloid, prion, protein misfolding, protein structure, Saccharomyces cerevisiae, superpleated β-structure, [PSI+]
Collapse
Affiliation(s)
- Stanislav A Bondarev
- Department of Genetics and Biotechnology; St. Petersburg State University; St. Petersburg, Russia
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology; St. Petersburg State University; St. Petersburg, Russia
| | - Mikhail V Belousov
- Department of Genetics and Biotechnology; St. Petersburg State University; St. Petersburg, Russia
| | - Andrey V Kajava
- Centre de Recherches de Biochimie Macromoléculaire; CNRS; Université Montpellier; Montpellier, Cedex 5, France
- University ITMO; St. Petersburg, Russia
- Institut de Biologie Computationnelle; Montpellier, Cedex 5, France
| |
Collapse
|
30
|
Bondarev SA, Shchepachev VV, Kajava AV, Zhouravleva GA. Effect of charged residues in the N-domain of Sup35 protein on prion [PSI+] stability and propagation. J Biol Chem 2013; 288:28503-13. [PMID: 23965990 DOI: 10.1074/jbc.m113.471805] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Recent studies have shown that Sup35p prion fibrils probably have a parallel in-register β-structure. However, the part(s) of the N-domain critical for fibril formation and maintenance of the [PSI(+)] phenotype remains unclear. Here we designed a set of five SUP35 mutant alleles (sup35(KK)) with lysine substitutions in each of five N-domain repeats, and investigated their effect on infectivity and ability of corresponding proteins to aggregate and coaggregate with wild type Sup35p in the [PSI(+)] strain. Alleles sup35-M1 (Y46K/Q47K) and sup35-M2 (Q61K/Q62K) led to prion loss, whereas sup35-M3 (Q70K/Q71K), sup35-M4 (Q80K/Q81K), and sup35-M5 (Q89K/Q90K) were able to maintain the [PSI(+)] prion. This suggests that the critical part of the parallel in-register β-structure for the studied [PSI(+)] prion variant lies in the first 63-69 residues. Our study also reveals an unexpected interplay between the wild type Sup35p and proteins expressed from the sup35(KK) alleles during prionization. Both Sup35-M1p and Sup35-M2p coaggregated with Sup35p, but only sup35-M2 led to prion loss in a dominant manner. We suggest that in the fibrils, Sup35p can bind to Sup35-M1p in the same conformation, whereas Sup35-M2p only allowed the Sup35p conformation that leads to the non-heritable fold. Mutations sup35-M4 and sup35-M5 influence the structure of the prion forming region to a lesser extent, and can lead to the formation of new prion variants.
Collapse
Affiliation(s)
- Stanislav A Bondarev
- From the Department of Genetics and Biotechnology, St. Petersburg State University, Saint Petersburg, Russia
| | | | | | | |
Collapse
|
31
|
Kiktev DA, Chernoff YO, Archipenko AV, Zhouravleva GA. Identification of genes influencing synthetic lethality of genetic and epigenetic alterations in translation termination factors in yeast. DOKL BIOCHEM BIOPHYS 2011; 438:117-9. [PMID: 21725886 DOI: 10.1134/s1607672911030021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Indexed: 11/23/2022]
Affiliation(s)
- D A Kiktev
- Department of Genetic and Breeding, St. Petersburg State University, St. Petersburg, 199034, Russia
| | | | | | | |
Collapse
|
32
|
Zhouravleva GA, Petrova AV. The role of translation termination factor eRF1 in the regulation of pseudohyphal growth in Saccharomyces cerevisiae cells. DOKL BIOCHEM BIOPHYS 2010; 433:209-11. [PMID: 20714858 DOI: 10.1134/s1607672910040162] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Indexed: 11/23/2022]
|
33
|
Abstract
In vivo amyloid formation is a widespread phenomenon in eukaryotes. Self-perpetuating amyloids provide a basis for the infectious or heritable protein isoforms (prions). At least for some proteins, amyloid-forming potential is conserved in evolution despite divergence of the amino acid (aa) sequences. In some cases, prion formation certainly represents a pathological process leading to a disease. However, there are several scenarios in which prions and other amyloids or amyloid-like aggregates are either shown or suspected to perform positive biological functions. Proven examples include self/nonself recognition, stress defense and scaffolding of other (functional) polymers. The role of prion-like phenomena in memory has been hypothesized. As an additional mechanism of heritable change, prion formation may in principle contribute to heritable variability at the population level. Moreover, it is possible that amyloid-based prions represent by-products of the transient feedback regulatory circuits, as normal cellular function of at least some prion proteins is decreased in the prion state.
Collapse
|
34
|
Moskalenko SE, Chabelskaya SV, Inge-Vechtomov SG, Philippe M, Zhouravleva GA. Viable nonsense mutants for the essential gene SUP45 of Saccharomyces cerevisiae. BMC Mol Biol 2003; 4:2. [PMID: 12589713 PMCID: PMC150568 DOI: 10.1186/1471-2199-4-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2002] [Accepted: 02/10/2003] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Termination of protein synthesis in eukaryotes involves at least two polypeptide release factors (eRFs) - eRF1 and eRF3. The highly conserved translation termination factor eRF1 in Saccharomyces cerevisiae is encoded by the essential gene SUP45. RESULTS We have isolated five sup45-n (n from nonsense) mutations that cause nonsense substitutions in the following amino acid positions of eRF1: Y53 --> UAA, E266 --> UAA, L283 --> UAA, L317 --> UGA, E385 --> UAA. We found that full-length eRF1 protein is present in all mutants, although in decreased amounts. All mutations are situated in a weak termination context. All these sup45-n mutations are viable in different genetic backgrounds, however their viability increases after growth in the absence of wild-type allele. Any of sup45-n mutations result in temperature sensitivity (37 degrees C). Most of the sup45-n mutations lead to decreased spore viability and spores bearing sup45-n mutations are characterized by limited budding after germination leading to formation of microcolonies of 4-20 cells. CONCLUSIONS Nonsense mutations in the essential gene SUP45 can be isolated in the absence of tRNA nonsense suppressors.
Collapse
Affiliation(s)
- Svetlana E Moskalenko
- Université de Rennes 1, CNRS UMR 6061, IFR 97, 2 av. Pr. Léon Bernard 35043 Rennes Cedex, France
- Department of Genetics, St Petersburg State University, Universitetskaya emb. 7/1, 199034, St Petersburg, Russia
| | - Svetlana V Chabelskaya
- Université de Rennes 1, CNRS UMR 6061, IFR 97, 2 av. Pr. Léon Bernard 35043 Rennes Cedex, France
- Department of Genetics, St Petersburg State University, Universitetskaya emb. 7/1, 199034, St Petersburg, Russia
| | - Sergei G Inge-Vechtomov
- Department of Genetics, St Petersburg State University, Universitetskaya emb. 7/1, 199034, St Petersburg, Russia
| | - Michel Philippe
- Université de Rennes 1, CNRS UMR 6061, IFR 97, 2 av. Pr. Léon Bernard 35043 Rennes Cedex, France
| | - Galina A Zhouravleva
- Université de Rennes 1, CNRS UMR 6061, IFR 97, 2 av. Pr. Léon Bernard 35043 Rennes Cedex, France
- Department of Genetics, St Petersburg State University, Universitetskaya emb. 7/1, 199034, St Petersburg, Russia
| |
Collapse
|
35
|
Mironova LN, Samsonova MG, Zhouravleva GA, Kulikov VN, Soom MJ. Reversions to respiratory competence of omnipotent sup45 suppressor mutants may be caused by secondary sup45 mutations. Curr Genet 1995; 27:195-200. [PMID: 7736601 DOI: 10.1007/bf00326148] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The molecular nature of the sup45 respiratory deficient omnipotent suppressor, and of three reversions to respiratory competence which removed the suppressor effect of the initial mutation, was examined. All reversions were caused by secondary sup45 mutations which indicates a direct connection between sup45 "respiratory" and "translational" functions. Computer analysis showed the local changes of Sup45 protein characteristics in the suppressor strain and revertants in comparison to the wild-type protein. The distribution of mutant sites in relation to evolutionary conserved, and tentatively functional, regions in the Sup45 protein is discussed.
Collapse
Affiliation(s)
- L N Mironova
- Department of Genetics, St. Petersburg St. University, Russia
| | | | | | | | | |
Collapse
|
36
|
Abstract
CL mutants with high instability of chromosome III were UV-induced in haploid strain disomic for chromosome III. The obtained CL mutants can be divided into two groups: (1) CL2, CL3, CL7, CL11-CL13 with elevated level of spontaneous inter- and intragenic recombination and (2) CL4, CL8 in which instability of chromosome III is not accompanied by elevation of mitotic recombination frequency. CL4 and CL8 mutants also show unstable maintenance of artificial minichromosomes with different chromosomal replicators and centromeric loci. The instability of chromosome III and minichromosomes in CL4 and CL8 is determined by two nonallelic genes designated ch14 and ch18. The role of ch14 and ch18 genes in mitotic chromosome transmission is discussed.
Collapse
Affiliation(s)
- V L Larionov
- Institute of Cytology, Academy of Sciences of the USSR, Leningrad
| | | | | | | | | | | |
Collapse
|