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Yemets A, Shadrina R, Blume R, Plokhovska S, Blume Y. Autophagy formation, microtubule disorientation, and alteration of ATG8 and tubulin gene expression under simulated microgravity in Arabidopsis thaliana. NPJ Microgravity 2024; 10:31. [PMID: 38499552 PMCID: PMC10948825 DOI: 10.1038/s41526-024-00381-9] [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: 08/14/2023] [Accepted: 03/08/2024] [Indexed: 03/20/2024] Open
Abstract
Autophagy plays an important role in plant growth and development, pathogen invasion and modulates plant response and adaptation to various abiotic stress stimuli. The biogenesis and trafficking of autophagosomes involve microtubules (MTs) as important actors in the autophagic process. However, initiation of autophagy in plants under microgravity has not been previously studied. Here we demonstrate how simulated microgravity induces autophagy development involving microtubular reorganization during period of autophagosome formation. It was shown that induction of autophagy with maximal autophagosome formation in root cells of Arabidopsis thaliana is observed after 6 days of clinostating, along with MT disorganization, which leads to visible changes in root morphology. Gradual decrease of autophagosome number was indicated on 9th and 12th days of the experiment as well as no significant re-orientation of MTs were identified. Respectively, analysis of α- and β-tubulins and ATG8 gene expression was carried out. In particular, the most pronounced increase of expression on both 6th and 9th days in response to simulated microgravity was detected for non-paralogous AtATG8b, AtATG8f, AtATG8i, and AtTUA2, AtTUA3 genes, as well as for the pair of β-tubulin duplicates, namely AtTUB2 and AtTUB3. Overall, the main autophagic response was observed after 6 and 9 days of exposure to simulated microgravity, followed by adaptive response after 12 days. These findings provide a key basis for further studies of cellular mechanisms of autophagy and involvement of cytoskeletal structures in autophagy biogenesis under microgravity, which would enable development of new approaches, aimed on enhancing plant adaptation to microgravity.
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Affiliation(s)
- Alla Yemets
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Baidy-Vyshnevetskoho St., 2a, Kyiv, 04123, Ukraine.
| | - Ruslana Shadrina
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Baidy-Vyshnevetskoho St., 2a, Kyiv, 04123, Ukraine
| | - Rostyslav Blume
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Baidy-Vyshnevetskoho St., 2a, Kyiv, 04123, Ukraine.
| | - Svitlana Plokhovska
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Baidy-Vyshnevetskoho St., 2a, Kyiv, 04123, Ukraine
| | - Yaroslav Blume
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Baidy-Vyshnevetskoho St., 2a, Kyiv, 04123, Ukraine.
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Kot K, Kot Y, Kurbanov R, Andriiash H, Tigunova O, Blume Y, Shulga S. The effect of human PBMCs immobilization on their Аβ42 aggregates-dependent proinflammatory state on a cellular model of Alzheimer's disease. Front Neurosci 2024; 18:1325287. [PMID: 38406587 PMCID: PMC10884286 DOI: 10.3389/fnins.2024.1325287] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/26/2024] [Indexed: 02/27/2024] Open
Abstract
The leading pathological mechanisms of Alzheimer's disease are amyloidosis and inflammation. The presented work was aimed to study the effect of human peripheral blood mononuclear cells (hPBMcs) cells-matrix adhesion on their pro-inflammatory state in vitro. Although direct interaction of Аβ42 to PBMC is not a cellular model of Alzheimer's disease, PBMCs may serve as test cells to detect Аβ42-dependent molecular effects in monitoring disease progression. Peripheral blood mononuclear cells (PBMCs) are used to assess changes in cytokines released in response to diseases or Alzheimer's disease-specific cytotoxic molecules such as Aβ42. The effect of recombinant amyloid β-peptide rАβ42 on the concentration of endogenous amyloid β-peptide Aβ40 and pro-inflammatory cytokines TNFα and IL-1β in human peripheral blood mononuclear cells that were cultured in suspension and immobilized in alginate microcarriers for 24 h were investigated. The localization and accumulation of Aβ40 and rAβ42 peptides in cells, as well as quantitative determination of the concentration of Aβ40 peptide, TNFα and IL-1β cytokines, was performed by intravital fluorescence imaging. The results were qualitatively similar for both cell models. It was determined that the content of TNFα and Aβ40 in the absence of rAβ42 in the incubation medium did not change for 24 h after incubation, and the content of IL-1β was lower compared to the cells that were not incubated. Incubation of cells in vitro with exogenous rAβ42 led to an increase in the intracellular content of TNFα and Aβ40, and no accumulation of IL-1β in cells was observed. The accumulation of Aβ40 in the cytoplasm was accompanied by the aggregation of rAβ42 on the outer surface of the cell plasma membrane. It was shown that the basic levels of indicators and the intensity of the response of immobilized cells to an exogenous stimulus were significantly greater than those of cells in suspension. To explore whether non-neuronal cells effects in alginate microcarriers were cell-matrix adhesion mediated, we tested the effect of blocking β1 integrins on proamyloidogenic and proinflammation cellular state. Immobilization within alginate hydrogels after incubation with the β1 integrins blocking antibodies showed a remarkable inhibition of TNFα and Aβ40 accumulation in rAβ42-treated cells. It can be concluded that activation of signal transduction and synthesizing activity of a portion of mononuclear cells of human peripheral blood is possible (can significantly increase) in the presence of cell-matrix adhesion.
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Affiliation(s)
- Kateryna Kot
- Biochemistry Department, V. N. Karazin Kharkiv National University of Ministry of Education and Science of Ukraine, Kharkiv, Ukraine
| | - Yurii Kot
- Biochemistry Department, V. N. Karazin Kharkiv National University of Ministry of Education and Science of Ukraine, Kharkiv, Ukraine
| | - Rustam Kurbanov
- Biochemistry Department, V. N. Karazin Kharkiv National University of Ministry of Education and Science of Ukraine, Kharkiv, Ukraine
| | - Hanna Andriiash
- Department of Genomics and Molecular Biotechnology, Institute of Food Biotechnology and Genomics National Academy of Science of Ukraine, Kyiv, Ukraine
| | - Olena Tigunova
- Department of Genomics and Molecular Biotechnology, Institute of Food Biotechnology and Genomics National Academy of Science of Ukraine, Kyiv, Ukraine
| | - Yaroslav Blume
- Department of Genomics and Molecular Biotechnology, Institute of Food Biotechnology and Genomics National Academy of Science of Ukraine, Kyiv, Ukraine
| | - Sergiy Shulga
- Department of Genomics and Molecular Biotechnology, Institute of Food Biotechnology and Genomics National Academy of Science of Ukraine, Kyiv, Ukraine
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Krupodorova T, Barshteyn V, Tsygankova V, Sevindik M, Blume Y. Strain-specific features of Pleurotus ostreatus growth in vitro and some of its biological activities. BMC Biotechnol 2024; 24:9. [PMID: 38331794 PMCID: PMC10851480 DOI: 10.1186/s12896-024-00834-9] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/29/2024] [Indexed: 02/10/2024] Open
Abstract
BACKGROUND The production of Pleurotus ostreatus mycelium as a promising object for use in food and other industries is hampered by a lack of information about the strain-specificity of this fungus mycelium growth and its acquisition of various biological activities. Therefore, this research aimed to investigate mycelial growth of different P. ostreatus strains on varies solid and liquid media as well as to evaluate strains antagonistic, antibacterial, antiradical scavenging activities, and total phenolic content. RESULTS Potato Dextrose Agar medium was suitable for all strains except P. ostreatus strain 2460. The best growth rate of P. ostreatus 2462 strain on solid culture media was 15.0 ± 0.8 mm/day, and mycelia best growth on liquid culture media-36.5 ± 0.2 g/l. P. ostreatus strains 551 and 1685 were more susceptible to positive effect of plant growth regulators Ivin, Methyur and Kamethur. Using of nutrient media based on combination of natural waste (amaranth flour cake and wheat germ, wheat bran, broken vermicelli and crumbs) has been increased the yield of P. ostreatus strains mycelium by 2.2-2.9 times compared to the control. All used P. ostreatus strains displayed strong antagonistic activity in co-cultivation with Aspergillus niger, Candida albicans, Issatchenkia orientalis, Fusarium poae, Microdochium nivale in dual-culture assay. P. ostreatus 2462 EtOAc mycelial extract good inhibited growth of Escherichia coli (17.0 ± 0.9 mm) while P. ostreatus 2460 suppressed Staphylococcus aureus growth (21.5 ± 0.5 mm) by agar well diffusion method. The highest radical scavenging effect displayed both mycelial extracts (EtOH and EtOAc) of P. ostreatus 1685 (61 and 56%) by DPPH assay as well as high phenolic content (7.17 and 6.73 mg GAE/g) by the Folin-Ciocalteu's method. The maximal total phenol content (7.52 mg GAE/g) demonstrated of P. ostreatus 2461 EtOH extract. CONCLUSIONS It is found that the growth, antibacterial, antiradical scavenging activity as well as total phenolic content were dependent on studied P. ostreatus strains in contrast to antagonistic activity. The proposed culture mediums of natural waste could be an alternative to commercial mediums for the production mycelial biomass of P. ostreatus strains.
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Affiliation(s)
- Tetiana Krupodorova
- Department of Plant Food Products and Biofortification, Institute of Food Biotechnology and Genomics of the National Academy of Sciences of Ukraine, Baidy-Vyshnevetskoho Str. 2a, Kyiv, 04123, Ukraine
| | - Victor Barshteyn
- Department of Plant Food Products and Biofortification, Institute of Food Biotechnology and Genomics of the National Academy of Sciences of Ukraine, Baidy-Vyshnevetskoho Str. 2a, Kyiv, 04123, Ukraine.
| | - Victoria Tsygankova
- Department of Chemistry of Bioactive Nitrogen-Containing Heterocyclic Bases, V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Sciences of Ukraine, Academician Kukhar Str. 1, Kyiv, 02094, Ukraine
| | - Mustafa Sevindik
- Department of Food Processing, Bahçe Vocational School, Osmaniye Korkut Ata University, İslam Ali Farsakoğlu Cad No:66, 80000, Bahçe/Osmaniye, Turkey
| | - Yaroslav Blume
- Department of Plant Food Products and Biofortification, Institute of Food Biotechnology and Genomics of the National Academy of Sciences of Ukraine, Baidy-Vyshnevetskoho Str. 2a, Kyiv, 04123, Ukraine
- Department of Genomics and Molecular Biotechnology, Institute of Food Biotechnology and Genomics of the National Academy of Sciences of Ukraine, Baidy-Vyshnevetskoho Str. 2a, 04123, Kyiv, Ukraine
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Kustovskiy Y, Karpov P, Blume Y, Yemets A. Ivermectin affects Arabidopsis thaliana microtubules through predicted binding site of β-tubulin. Plant Physiol Biochem 2024; 206:108296. [PMID: 38141401 DOI: 10.1016/j.plaphy.2023.108296] [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: 08/31/2023] [Revised: 12/05/2023] [Accepted: 12/18/2023] [Indexed: 12/25/2023]
Abstract
The ivermectin is a potent nematocide and insecticide, which has low toxicity for humans and domestic animals, but due to low biotransformation, it can be dangerous for non-target organisms. The recent determination of ivermectin absorption and accumulation in tissues of higher plants and multiple shreds of evidence of its negative impact on plant physiology provide a basis for the search for ivermectin's molecular targets and mechanisms of action in plant cells. In this research, for the first time, the ivermectin effect on microtubules of Arabidopsis thaliana cells was studied. It was revealed that ivermectin (250 μg mL-1) disrupts the microtubule network, induces the loss of microtubule orientation, leads to microtubule curvature and shrinkage, and their longitudinal and cross-linked bundling in various cells of A. thaliana primary roots. Further, the previously proposed binding of ivermectin to the β1-tubulin taxane site was developed and confirmed using molecular dynamics simulations of ivermectin complexes with Haemonchus contortus and A. thaliana β1-tubulins. It was predicted that similar to other microtubule stabilizing agents ivermectin binding causes M-loop stabilization in both H. contortus and A. thaliana β-tubulin, which leads to the enhancement of lateral contacts between subunits of adjacent protofilaments preventing microtubule depolymerization.
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Affiliation(s)
- Yevhen Kustovskiy
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Baidy-Vyshnevetskoho str., 2a, Kyiv, 04123, Ukraine; National University of Kyiv-Mohyla Academy, Skovorody str., 2, Kyiv, 04070, Ukraine.
| | - Pavel Karpov
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Baidy-Vyshnevetskoho str., 2a, Kyiv, 04123, Ukraine.
| | - Yaroslav Blume
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Baidy-Vyshnevetskoho str., 2a, Kyiv, 04123, Ukraine.
| | - Alla Yemets
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Baidy-Vyshnevetskoho str., 2a, Kyiv, 04123, Ukraine; National University of Kyiv-Mohyla Academy, Skovorody str., 2, Kyiv, 04070, Ukraine.
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Rayevsky A, Bulgakov E, Sharifi M, Samofalova D, Ozheredov D, Karpov P, Pantano S, Blume Y. In silico induced effect of N-ε-lysine acetylation on microtubule stability and subsequent interaction of microtubule-associated proteins. Cell Biol Int 2023. [PMID: 37272280 DOI: 10.1002/cbin.12052] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/23/2023] [Accepted: 05/21/2023] [Indexed: 06/06/2023]
Abstract
Plant systems have been considered valuable models for addressing fundamental questions of microtubule (MT) organization due to their considerable practical utility. Protein acetylation is a very common protein modification, and therate of acetylation can be modulated in cells in different biological states, and these changes can be detected at a molecular level. Here, we focused on K40, K112, and K394 residues as putative acetylation sites, which were shown to exist in both plants and mammals. Such residual effect of acetylation causes critical but unclear effect on MT stability. In turn, it was shown that acetylation indirectly affects the probability of interaction with different MAPs (Microtubule-associated proteins). In a multiscale study using an all-atom force field to reproduce several lattice-forming elements found on the surface the microtubule, we assembled a fragment of a plant microtubule composed of nine tubulins and used it as a model object along with the existing human complex. Triplets of tubulins assembled in a lattice cell were then simulated for both human and plant protein complexes, using a coarse-grained force field. We then analyzed the trajectories and identified some critical deformations of the MAP interaction surface. The initial coordinates were used to investigate the structural scenario in which autophagy-related protein 8 (ATG8) was able to interact with the MT fragment.
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Affiliation(s)
- Alexey Rayevsky
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Кyiv, Ukraine
- Department of Molecular Modeling, Enamine Ltd., Kyiv, Ukraine
| | - Elijah Bulgakov
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Кyiv, Ukraine
- Department of Molecular Modeling, Enamine Ltd., Kyiv, Ukraine
| | | | - Dariya Samofalova
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Кyiv, Ukraine
- R&D Department, Life Chemicals Inc., Niagara-on-the-Lake, Ontario, Canada
| | - Daniil Ozheredov
- Institute of High Technologies, Glushkova Ave, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| | - Pavel Karpov
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Кyiv, Ukraine
| | | | - Yaroslav Blume
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Кyiv, Ukraine
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Karelov A, Kozub N, Sozinova O, Pirko Y, Sozinov I, Yemets A, Blume Y. Wheat Genes Associated with Different Types of Resistance against Stem Rust ( Puccinia graminis Pers.). Pathogens 2022; 11:pathogens11101157. [PMID: 36297214 PMCID: PMC9608978 DOI: 10.3390/pathogens11101157] [Citation(s) in RCA: 2] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/25/2022] [Accepted: 10/05/2022] [Indexed: 11/13/2022] Open
Abstract
Stem rust is one wheat's most dangerous fungal diseases. Yield losses caused by stem rust have been significant enough to cause famine in the past. Some races of stem rust are considered to be a threat to food security even nowadays. Resistance genes are considered to be the most rational environment-friendly and widely used way to control the spread of stem rust and prevent yield losses. More than 60 genes conferring resistance against stem rust have been discovered so far (so-called Sr genes). The majority of the Sr genes discovered have lost their effectiveness due to the emergence of new races of stem rust. There are some known resistance genes that have been used for over 50 years and are still effective against most known races of stem rust. The goal of this article is to outline the different types of resistance against stem rust as well as the effective and noneffective genes, conferring each type of resistance with a brief overview of their origin and usage.
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Affiliation(s)
- Anatolii Karelov
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 04123 Kyiv, Ukraine
- Institute of Plant Protection, National Academy of Agrarian Sciences of Ukraine, 03022 Kyiv, Ukraine
- Correspondence: (A.K.); (Y.B.)
| | - Natalia Kozub
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 04123 Kyiv, Ukraine
- Institute of Plant Protection, National Academy of Agrarian Sciences of Ukraine, 03022 Kyiv, Ukraine
| | - Oksana Sozinova
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 04123 Kyiv, Ukraine
- Institute of Plant Protection, National Academy of Agrarian Sciences of Ukraine, 03022 Kyiv, Ukraine
| | - Yaroslav Pirko
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 04123 Kyiv, Ukraine
| | - Igor Sozinov
- Institute of Plant Protection, National Academy of Agrarian Sciences of Ukraine, 03022 Kyiv, Ukraine
| | - Alla Yemets
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 04123 Kyiv, Ukraine
| | - Yaroslav Blume
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 04123 Kyiv, Ukraine
- Correspondence: (A.K.); (Y.B.)
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Blume R, Yemets A, Korkhovyi V, Radchuk V, Rakhmetov D, Blume Y. Genome-wide identification and analysis of the cytokinin oxidase/dehydrogenase ( ckx) gene family in finger millet ( Eleusine coracana). Front Genet 2022; 13:963789. [PMID: 36299586 PMCID: PMC9589517 DOI: 10.3389/fgene.2022.963789] [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: 06/07/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
Cytokinin dehydrogenase/oxidase (CKX) enzymes play a key role in regulating cytokinin (CK) levels in plants by degrading the excess of this phytohormone. CKX genes have proven an attractive target for genetic engineering, as their silencing boosts cytokinin accumulation in various tissues, thereby contributing to a rapid increase in biomass and overall plant productivity. We previously reported a similar effect in finger millet (Eleusine coracana) somaclonal lines, caused by downregulation of EcCKX1 and EcCKX2. However, the CKX gene family has numerous representatives, especially in allopolyploid crop species, such as E. coracana. To date, the entire CKX gene family of E. coracana and its related species has not been characterized. We offer here, for the first time, a comprehensive genome-wide identification and analysis of a panel of CKX genes in finger millet. The functional genes identified in the E. coracana genome are compared with the previously-identified genes, EcCKX1 and EcCKX2. Exon-intron structural analysis and motif analysis of FAD- and CK-binding domains are performed. The phylogeny of the EcCKX genes suggests that CKX genes are divided into several distinct groups, corresponding to certain isotypes. Finally, the phenotypic effect of EcCKX1 and EcCKX2 in partially silencing the SE7 somaclonal line is investigated, showing that lines deficient in CKX-expression demonstrate increased grain yield and greater bushiness, enhanced biomass accumulation, and a shorter vegetation cycle.
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Affiliation(s)
- Rostyslav Blume
- Department of Population Genetics, Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Kyiv, Ukraine,*Correspondence: Rostyslav Blume,
| | - Alla Yemets
- Department of Cell Biology and Biotechnology, Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Vitaliy Korkhovyi
- Department of Cell Biology and Biotechnology, Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Volodymyr Radchuk
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Dzhamal Rakhmetov
- M. M. Gryshko National Botanic Garden of National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Yaroslav Blume
- Department of Genomics and Molecular Biotechnology, Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
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Yemets A, Plokhovska S, Pushkarova N, Blume Y. Quantum Dot-Antibody Conjugates for Immunofluorescence Studies of Biomolecules and Subcellular Structures. J Fluoresc 2022; 32:1713-1723. [PMID: 35670918 DOI: 10.1007/s10895-022-02968-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 01/24/2022] [Accepted: 05/05/2022] [Indexed: 01/14/2023]
Abstract
Quantum dots, or nanoscale semiconductors, are one of the most important materials for various research and development purposes. Due to their advantageous photoluminescence and electronic properties, namely, their unique photostability, high brightness, narrow emission spectra from visible to near-infrared wavelengths, convey them significant advantages over widely used fluorochromes, including organic dyes, fluorescent probes. Quantum dots are a unique instrument for a wide range of immunoassays with antibodies. The paper provides an overview of the developed and already applied methods of quantum dot surface modification, quantum dots conjugation to different antibodies (non-covalent, direct covalent linkage or with the use of special adapter molecules), as well as practical examples of recent quantum dot-antibody applications in the immunofluorescence microscopy for cell and cell structure imaging, fluorescent assays for biomolecules detection and in diagnostics of various diseases. The review presents advantages of quantum dot-antibody conjugation technology over the existing methods of immunofluorescence studies and a forward look into its potential prospects in biological and biomedical research.
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Affiliation(s)
- Alla Yemets
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Osypovskogo str., 2a, 04123, Kyiv, Ukraine.
| | - Svitlana Plokhovska
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Osypovskogo str., 2a, 04123, Kyiv, Ukraine
| | - Nadia Pushkarova
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Osypovskogo str., 2a, 04123, Kyiv, Ukraine
| | - Yaroslav Blume
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Osypovskogo str., 2a, 04123, Kyiv, Ukraine
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Borovaya M, Horiunova I, Plokhovska S, Pushkarova N, Blume Y, Yemets A. Synthesis, Properties and Bioimaging Applications of Silver-Based Quantum Dots. Int J Mol Sci 2021; 22:12202. [PMID: 34830084 PMCID: PMC8620749 DOI: 10.3390/ijms222212202] [Citation(s) in RCA: 13] [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: 08/30/2021] [Revised: 10/25/2021] [Accepted: 10/27/2021] [Indexed: 12/20/2022] Open
Abstract
Ag-based quantum dots (QDs) are semiconductor nanomaterials with exclusive electrooptical properties ideally adaptable for various biotechnological, chemical, and medical applications. Silver-based semiconductor nanocrystals have developed rapidly over the past decades. They have become a promising luminescent functional material for in vivo and in vitro fluorescent studies due to their ability to emit at the near-infrared (NIR) wavelength. In this review, we discuss the basic features of Ag-based QDs, the current status of classic (chemical) and novel methods ("green" synthesis) used to produce these QDs. Additionally, the advantages of using such organisms as bacteria, actinomycetes, fungi, algae, and plants for silver-based QDs biosynthesis have been discussed. The application of silver-based QDs as fluorophores for bioimaging application due to their fluorescence intensity, high quantum yield, fluorescent stability, and resistance to photobleaching has also been reviewed.
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Affiliation(s)
- Mariya Borovaya
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Osypovskoho Str. 2a, 04123 Kyiv, Ukraine; (I.H.); (S.P.); (N.P.); (Y.B.); (A.Y.)
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Vus K, Tarabara U, Danylenko I, Pirko Y, Krupodorova T, Yemets A, Blume Y, Turchenko V, Klymchuk D, Smertenko P, Zhytniakivska O, Trusova V, Petrushenko S, Bogatyrenko S, Gorbenko G. Silver nanoparticles as inhibitors of insulin amyloid formation: A fluorescence study. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117508] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Rayevsky A, Sharifi M, Samofalova D, Demchuk O, Karpov P, Blume Y. In silico mechanistic model of microtubule assembly inhibition by selective chromone derivatives. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Yamamoto S, Saito R, Nakamura S, Sogawa H, Karpov P, Shulga S, Blume Y, Kurita N. Proposal of Potent Inhibitors for a Bacterial Cell Division Protein FtsZ: Molecular Simulations Based on Molecular Docking and ab Initio Molecular Orbital Calculations. Antibiotics (Basel) 2020; 9:E846. [PMID: 33256135 PMCID: PMC7761175 DOI: 10.3390/antibiotics9120846] [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: 11/03/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 11/21/2022] Open
Abstract
The inhibition of a bacterial cell division protein, filamentous temperature-sensitive Z (FtsZ), prevents the reproduction of Mycobacteria. To propose potent inhibitors of FtsZ, the binding properties of FtsZ with various derivatives of Zantrin ZZ3 were investigated at an electronic level, using molecular simulations. We here employed protein-ligand docking, classical molecular mechanics (MM) optimizations, and ab initio fragment molecular orbital (FMO) calculations. Based on the specific interactions between FtsZ and the derivatives, as determined by FMO calculations, we proposed novel ligands, which can strongly bind to FtsZ and inhibit its aggregations. The introduction of a hydroxyl group into ZZ3 was found to enhance its binding affinity to FtsZ.
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Affiliation(s)
- Shohei Yamamoto
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan; (S.Y.); (R.S.); (S.N.); (H.S.)
| | - Ryosuke Saito
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan; (S.Y.); (R.S.); (S.N.); (H.S.)
| | - Shunya Nakamura
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan; (S.Y.); (R.S.); (S.N.); (H.S.)
| | - Haruki Sogawa
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan; (S.Y.); (R.S.); (S.N.); (H.S.)
| | - Pavel Karpov
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 2a, Osypovskogo str., Kyiv-123, 04123 Kyiv, Ukraine; (P.K.); (S.S.); (Y.B.)
| | - Sergey Shulga
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 2a, Osypovskogo str., Kyiv-123, 04123 Kyiv, Ukraine; (P.K.); (S.S.); (Y.B.)
| | - Yaroslav Blume
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 2a, Osypovskogo str., Kyiv-123, 04123 Kyiv, Ukraine; (P.K.); (S.S.); (Y.B.)
| | - Noriyuki Kurita
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan; (S.Y.); (R.S.); (S.N.); (H.S.)
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13
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Yemets A, Horiunova I, Blume Y. Cadmium, nickel, copper, and zinc influence on microfilament organization in Arabidopsis root cells. Cell Biol Int 2020; 45:211-226. [PMID: 33064326 DOI: 10.1002/cbin.11485] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 11/07/2019] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 01/01/2023]
Abstract
The plant cytoskeleton orchestrates such fundamental processes in cells as division, growth and development, polymer cross-linking, membrane anchorage, etc. Here, we describe the influence of Cd2+ , Ni2+ , Zn2+ , and Cu2+ on root development and vital organization of actin filaments into different cells of Arabidopsis thaliana line expressing GFP-FABD2. CdSO4 , NiSO4 , CuSO4 , and ZnSO4 were used in concentrations of 5-20 µM in this study. It was found that Cd, Ni, and Cu cause dose-dependent primary root growth inhibition and alteration of the root morphology, whereas Zn slightly stimulates root growth and does not affect the morphology of Arabidopsis roots. This growth inhibition/stimulation correlated with the various sensitivities of microfilaments to Cd, Ni, Cu, and Zn action. It was established that Cd, Ni, and Cu affected predominantly the actin filaments of meristematic cells. Cells of transition and elongation zones demonstrated strong actin filament sensitivity to Cd and Cu. Microfilaments of elongating root cells were more sensitive to Ni and Cu. Although Cd, Ni, and Cu stimulated root hair growth after long-term treatment, actin filaments were destroyed after 1 h exposure with these metals. Zn did not disrupt native actin filament organization in root cells. Thus, our investigation shows that microfilaments act as sensitive cellular targets for Cd, Ni, and Cu. More data on effects on native actin filaments organization would contribute to a better understanding of plant tolerance mechanisms to the action of these metals.
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Affiliation(s)
- Alla Yemets
- Department of Cell Biology and Biotechnology, Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Inna Horiunova
- Department of Cell Biology and Biotechnology, Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Yaroslav Blume
- Department of Genomics and Molecular Biotechnology, Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
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14
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Sato R, Vohra S, Yamamoto S, Suzuki K, Pavel K, Shulga S, Blume Y, Kurita N. Specific interactions between tau protein and curcumin derivatives: Molecular docking and ab initio molecular orbital simulations. J Mol Graph Model 2020; 98:107611. [PMID: 32276176 DOI: 10.1016/j.jmgm.2020.107611] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/27/2020] [Accepted: 03/27/2020] [Indexed: 10/24/2022]
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disorder in the world, and there is currently no potent medicine for the treatment of ADs. Curcumin, a primary chemical contained in the ancient Indian herb known as turmeric, has been extensively studied and shown to be effective in inhibiting the aggregations of amyloid-β and tau proteins, both of which are observed in the brains of AD patients. In the present study, we focused on the tau protein and investigated its specific interactions with curcumin derivatives, using molecular simulations based on molecular docking, molecular mechanics and ab initio fragment molecular orbital calculations. Based on the results, we attempted to propose novel potent inhibitors against the tau protein aggregation. Our molecular simulations provide useful information for developing novel medicines for the treatment of ADs.
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Affiliation(s)
- Riku Sato
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, 441-8580, Japan
| | - Shivani Vohra
- Chemical Engineering, Grove School of Engineering, The City College of New York, 160 Convent Avenue New York, NY, 10031, USA
| | - Shohei Yamamoto
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, 441-8580, Japan
| | - Katsumi Suzuki
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, 441-8580, Japan
| | - Karpov Pavel
- Institute for Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 2a. Osypovskogo Str., Kyiv-123, 04123, Ukraine
| | - Sergiy Shulga
- Institute for Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 2a. Osypovskogo Str., Kyiv-123, 04123, Ukraine
| | - Yaroslav Blume
- Institute for Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 2a. Osypovskogo Str., Kyiv-123, 04123, Ukraine
| | - Noriyuki Kurita
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, 441-8580, Japan.
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15
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Sogawa H, Sato R, Suzuki K, Tomioka S, Shinzato T, Karpov P, Shulga S, Blume Y, Kurita N. Binding sites of Zantrin inhibitors to the bacterial cell division protein FtsZ: Molecular docking and ab initio molecular orbital calculations. Chem Phys 2020. [DOI: 10.1016/j.chemphys.2019.110603] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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16
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Shinzato T, Sato R, Suzuki K, Tomioka S, Sogawa H, Shulga S, Blume Y, Kurita N. Proposal of therapeutic curcumin derivatives for Alzheimer’s disease based on ab initio molecular simulations. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2019.136883] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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17
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Sekan AS, Myronycheva OS, Karlsson O, Gryganskyi AP, Blume Y. Green potential of Pleurotus spp. in biotechnology. PeerJ 2019; 7:e6664. [PMID: 30967974 PMCID: PMC6446892 DOI: 10.7717/peerj.6664] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 02/22/2019] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND The genus Pleurotus is most exploitable xylotrophic fungi, with valuable biotechnological, medical, and nutritional properties. The relevant features of the representatives of this genus to provide attractive low-cost industrial tools have been reported in numerous studies to resolve the pressure of ecological issues. Additionally, a number of Pleurotus species are highly adaptive, do not require any special conditions for growth, and possess specific resistance to contaminating diseases and pests. The unique properties of Pleurotus species widely used in many environmental technologies, such as organic solid waste recycling, chemical pollutant degradation, and bioethanol production. METHODOLOGY The literature study encompasses peer-reviewed journals identified by systematic searches of electronic databases such as Google Scholar, NCBI, Springer, ResearchGate, ScienceDirect, and ISI Web of Knowledge. The search scheme was divided into several steps, as described below. RESULTS In this review, we describe studies examining the biotechnological feasibility of Pleurotus spp. to elucidate the importance of this genus for use in green technology. Here, we review areas of application of the genus Pleurotus as a prospective biotechnological tool. CONCLUSION The incomplete description of some fungal biochemical pathways emphasises the future research goals for this fungal culture.
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Affiliation(s)
- Alona S. Sekan
- Institute of Food Biotechnology and Genomics, National Academy of Science of Ukraine, Kyiv, Ukraine
| | - Olena S. Myronycheva
- Division of Wood Science and Engineering, Department of Engineering Sciences and Mathematics, Lulea University of Technology, Skelleftea, Sweden
| | - Olov Karlsson
- Division of Wood Science and Engineering, Department of Engineering Sciences and Mathematics, Lulea University of Technology, Skelleftea, Sweden
| | | | - Yaroslav Blume
- Institute of Food Biotechnology and Genomics, National Academy of Science of Ukraine, Kyiv, Ukraine
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18
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Morello L, Pydiura N, Galinousky D, Blume Y, Breviario D. Flax tubulin and CesA superfamilies represent attractive and challenging targets for a variety of genome- and base-editing applications. Funct Integr Genomics 2019; 20:163-176. [PMID: 30826923 DOI: 10.1007/s10142-019-00667-2] [Citation(s) in RCA: 5] [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: 02/22/2018] [Accepted: 02/07/2019] [Indexed: 02/07/2023]
Abstract
Flax is both a valuable resource and an interesting model crop. Despite a long history of flax genetic transformation only one transgenic linseed cultivar has been so far registered in Canada. Implementation and use of the genome-editing technologies that allow site-directed modification of endogenous genes without the introduction of foreign genes might improve this situation. Besides its potential for boosting crop yields, genome editing is now one of the best tools for carrying out reverse genetics and it is emerging as an especially versatile tool for studying basic biology. A complex interplay between the flax tubulin family (6 α-, 14 β-, and 2 γ-tubulin genes), the building block of microtubules, and the CesA (15-16 genes), the subunit of the multimeric cellulose-synthesizing complex devoted to the oriented deposition of the cellulose microfibrils is fundamental for the biosynthesis of the cell wall. The role of the different members of each family in providing specificities to the assembled complexes in terms of structure, dynamics, activity, and interaction remains substantially obscure. Genome-editing strategies, recently shown to be successful in flax, can therefore be useful to unravel the issue of functional redundancy and provide evidence for specific interactions between different members of the tubulin and CesA gene families, in relation to different phase and mode of cell wall biosynthesis.
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Affiliation(s)
- Laura Morello
- Istituto di Biologia e Biotecnologia Agraria IBBA-CNR, Via Alfonso Corti 12, 20133, Milan, Italy
| | - Nikolay Pydiura
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Osypovskoho St. 2a, Kyiv, 04123, Ukraine
| | - Dmitry Galinousky
- Institute of Genetics and Cytology, National Academy of Sciences of Belarus, Akademicheskaya St. 27, 220072, Minsk, Belarus
| | - Yaroslav Blume
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Osypovskoho St. 2a, Kyiv, 04123, Ukraine.
| | - Diego Breviario
- Istituto di Biologia e Biotecnologia Agraria IBBA-CNR, Via Alfonso Corti 12, 20133, Milan, Italy.
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19
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Tomioka S, Sogawa H, Shinzato T, Ishimura H, Okamoto A, Blume Y, Shulga S, Kurita N. Effect of Zn ion on the structure and electronic states of Aβ nonamer: molecular dynamics and ab initio molecular orbital calculations. Molecular Simulation 2019. [DOI: 10.1080/08927022.2019.1579328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Shogo Tomioka
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, Japan
| | - Haruki Sogawa
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, Japan
| | - Tomoki Shinzato
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, Japan
| | - Hiromi Ishimura
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, Japan
| | - Akisumi Okamoto
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, Japan
| | - Yaroslav Blume
- Institute for Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Kiev, Ukraine
| | - Sergiy Shulga
- Institute for Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Kiev, Ukraine
| | - Noriyuki Kurita
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, Japan
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20
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Pydiura N, Pirko Y, Galinousky D, Postovoitova A, Yemets A, Kilchevsky A, Blume Y. Genome‐wide identification, phylogenetic classification, and exon–intron structure characterization of the tubulin and actin genes in flax (Linum usitatissimum). Cell Biol Int 2018; 43:1010-1019. [DOI: 10.1002/cbin.11001] [Citation(s) in RCA: 11] [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: 06/20/2017] [Accepted: 05/31/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Nikolay Pydiura
- Institute of Food Biotechnology and GenomicsNational Academy of Sciences of UkraineKyiv Osipovskogo St. 2a04123 Ukraine
| | - Yaroslav Pirko
- Institute of Food Biotechnology and GenomicsNational Academy of Sciences of UkraineKyiv Osipovskogo St. 2a04123 Ukraine
| | - Dmitry Galinousky
- Institute of Genetics and CytologyNational Academy of Sciences of BelarusMinsk Akademicheskaya st., 27220072 Belarus
| | - Anastasiia Postovoitova
- Institute of Food Biotechnology and GenomicsNational Academy of Sciences of UkraineKyiv Osipovskogo St. 2a04123 Ukraine
| | - Alla Yemets
- Institute of Food Biotechnology and GenomicsNational Academy of Sciences of UkraineKyiv Osipovskogo St. 2a04123 Ukraine
| | - Aleksandr Kilchevsky
- Institute of Genetics and CytologyNational Academy of Sciences of BelarusMinsk Akademicheskaya st., 27220072 Belarus
| | - Yaroslav Blume
- Institute of Food Biotechnology and GenomicsNational Academy of Sciences of UkraineKyiv Osipovskogo St. 2a04123 Ukraine
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21
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Fujimori M, Sogawa H, Ota S, Karpov P, Shulga S, Blume Y, Kurita N. Specific interactions between mycobacterial FtsZ protein and curcumin derivatives: Molecular docking and ab initio molecular simulations. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2017.12.045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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22
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Ota S, Tomioka S, Sogawa H, Satou R, Fujimori M, Karpov P, Shulga S, Blume Y, Kurita N. Binding properties between curcumin and malarial tubulin: molecular-docking and ab initio fragment molecular orbital calculations. CBIJ 2018. [DOI: 10.1273/cbij.18.44] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Shintaro Ota
- Department of Computer Science and Engineering, Toyohashi University of Technology
| | - Shougo Tomioka
- Department of Computer Science and Engineering, Toyohashi University of Technology
| | - Haruki Sogawa
- Department of Computer Science and Engineering, Toyohashi University of Technology
| | - Riku Satou
- Department of Computer Science and Engineering, Toyohashi University of Technology
| | - Mitsuki Fujimori
- Department of Computer Science and Engineering, Toyohashi University of Technology
| | - Pavel Karpov
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine,
| | - Sergey Shulga
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine,
| | - Yaroslav Blume
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine,
| | - Noriyuki Kurita
- Department of Computer Science and Engineering, Toyohashi University of Technology
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23
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Rabokon A, Demkovych A, Sozinov A, Kozub N, Sozinov I, Pirko Y, Blume Y. Intron length polymorphism of β-tubulin genes of Aegilops biuncialis Vis. Cell Biol Int 2017; 43:1031-1039. [PMID: 29024189 DOI: 10.1002/cbin.10886] [Citation(s) in RCA: 10] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 10/08/2017] [Indexed: 12/13/2022]
Abstract
Intron-specific DNA polymorphism is present among plant β-tubulin gene family members and is considered to be one of the molecular markers based on the difference of tubulin introns length assayed both separately (TBP: 1st intron) or in combination (h-TBP: 1st and 2nd introns). These two approaches are possibly useful for wheat breeding programs, since TBP and h-TBP help to differentiate between the accessions of Aegilops biuncialis Vis., a wild relative of wheat. PCR-derived polymorphic fragments were resolved by PAGE electrophoresis. The length of amplicons varied significantly (395-3900 bp for TBP and 466-3440 bp for h-TBP), while the numbers of polymorphic bands were 21 for TBP and 23 for h-TBP, respectively. PIC mean value was circa 0.3. Dendrograms constructed on the basis of the Nei and Li coefficient with the high bootstrap support reveal a similar order of hierarchy for the samples analyzed using both methods. Thus, both techniques uncover DNA polymorphism level sufficiently high to distinguish different accessions of Ae. biuncialis Vis.
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Affiliation(s)
- Anastasiia Rabokon
- Institute of Food Biotechnology and Genomics, Osipovskogo St., 2a, Kyiv-123, 04123, Ukraine
| | - Andrii Demkovych
- Institute of Food Biotechnology and Genomics, Osipovskogo St., 2a, Kyiv-123, 04123, Ukraine
| | - Alexei Sozinov
- Institute of Food Biotechnology and Genomics, Osipovskogo St., 2a, Kyiv-123, 04123, Ukraine
| | - Natalia Kozub
- Institute of Food Biotechnology and Genomics, Osipovskogo St., 2a, Kyiv-123, 04123, Ukraine.,Institute of Plant Protection, Vasylkivska St., 33, Kyiv-022, 03022, Ukraine
| | - Igor Sozinov
- Institute of Plant Protection, Vasylkivska St., 33, Kyiv-022, 03022, Ukraine
| | - Yaroslav Pirko
- Institute of Food Biotechnology and Genomics, Osipovskogo St., 2a, Kyiv-123, 04123, Ukraine
| | - Yaroslav Blume
- Institute of Food Biotechnology and Genomics, Osipovskogo St., 2a, Kyiv-123, 04123, Ukraine
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24
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Galinousky D, Padvitski T, Bayer G, Pirko Y, Pydiura N, Anisimova N, Nikitinskaya T, Khotyleva L, Yemets A, Kilchevsky A, Blume Y. Expression analysis of cellulose synthase and main cytoskeletal protein genes in flax (
Linum usitatissimum
L.). Cell Biol Int 2017; 43:1065-1071. [DOI: 10.1002/cbin.10837] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 08/07/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Dmitry Galinousky
- Institute of Genetics and CytologyThe National Academy of Sciences of BelarusAkademicheskaya st., 27220072 Minsk Belarus
| | - Tsimafei Padvitski
- Institute of Genetics and CytologyThe National Academy of Sciences of BelarusAkademicheskaya st., 27220072 Minsk Belarus
| | - Galina Bayer
- Institute of Food Biotechnology and GenomicsThe National Academy of Sciences of UkraineОsipovskogo str., 2A04123 Kyiv Ukraine
| | - Yaroslav Pirko
- Institute of Food Biotechnology and GenomicsThe National Academy of Sciences of UkraineОsipovskogo str., 2A04123 Kyiv Ukraine
| | - Nikolay Pydiura
- Institute of Food Biotechnology and GenomicsThe National Academy of Sciences of UkraineОsipovskogo str., 2A04123 Kyiv Ukraine
| | - Natallia Anisimova
- Institute of Genetics and CytologyThe National Academy of Sciences of BelarusAkademicheskaya st., 27220072 Minsk Belarus
| | - Tatyana Nikitinskaya
- Institute of Genetics and CytologyThe National Academy of Sciences of BelarusAkademicheskaya st., 27220072 Minsk Belarus
| | - Liubov Khotyleva
- Institute of Genetics and CytologyThe National Academy of Sciences of BelarusAkademicheskaya st., 27220072 Minsk Belarus
| | - Alla Yemets
- Institute of Food Biotechnology and GenomicsThe National Academy of Sciences of UkraineОsipovskogo str., 2A04123 Kyiv Ukraine
| | - Aleksandr Kilchevsky
- Institute of Genetics and CytologyThe National Academy of Sciences of BelarusAkademicheskaya st., 27220072 Minsk Belarus
| | - Yaroslav Blume
- Institute of Food Biotechnology and GenomicsThe National Academy of Sciences of UkraineОsipovskogo str., 2A04123 Kyiv Ukraine
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25
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Olenieva V, Lytvyn D, Yemets A, Bergounioux C, Blume Y. Tubulin acetylation accompanies autophagy development induced by different abiotic stimuli in Arabidopsis thaliana. Cell Biol Int 2017; 43:1056-1064. [PMID: 28816419 DOI: 10.1002/cbin.10843] [Citation(s) in RCA: 12] [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] [Received: 05/16/2017] [Accepted: 08/12/2017] [Indexed: 12/31/2022]
Abstract
Microtubules (MTs) play an important role in the regulation of autophagy development in yeast and animal as well as in plant cells. MTs participate in maturation and traffic of autophagosomes through their dynamic state changes and post-translational modifications of tubulin, namely acetylation. We subjected Arabidopsis thaliana seedlings to metabolic-, salt-, osmotic stresses as well as irradiation of ultraviolet B and investigated the involvement of plant MTs in the development of stress-induced autophagy via tubulin acetylation. For this purpose Arabidopsis thaliana line expressing autophagy-related protein 8 h (atg8h)-GFP was generated to investigate autophagy, applying the level of free GFP as an indicator of autophagy development. Using autophagosome confocal imaging and Western blot analysis of Atg8 post-translational lipidation and synchronous GFP release it was shown that all examined stressful stimuli led to pronounced development of autophagy, particularly in different root tissues. Moreover, autophagy development was accompanied by α-tubulin acetylation under all stressful conditions. Presented data indicate the possible role of the post-translational acetylation of α-tubulin in the mediation of plant stress-induced autophagy.
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Affiliation(s)
- Vira Olenieva
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Dmytro Lytvyn
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Alla Yemets
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Catherine Bergounioux
- Laboratory of Cell Cycle Chromatin and Development, Institute of Plant Sciences Paris-Saclay IPS2, CNRS 9213, INRA 1403, Université Paris-Sud, Université Evry Val d'Essonne, Université Paris Diderot, Sorbonne Paris-Cite, Universite Paris-Saclay, Orsay, France
| | - Yaroslav Blume
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
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26
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Derevyanchuk M, Kretynin S, Iakovenko O, Litvinovskaya R, Zhabinskii V, Martinec J, Blume Y, Khripach V, Kravets V. Effect of 24-epibrassinolide on Brassica napus alternative respiratory pathway, guard cells movements and phospholipid signaling under salt stress. Steroids 2017; 117:16-24. [PMID: 27913097 DOI: 10.1016/j.steroids.2016.11.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 11/24/2016] [Accepted: 11/25/2016] [Indexed: 12/17/2022]
Abstract
Using Brassica napus roots we observed statistically significant increase in alternative respiratory pathway in response to exogenous 24-epibrassinolide (EBL) under optimal conditions and salinity. Also we observed activation of phospholipid signaling under the same conditions in response to EBL by measuring levels of lipid second messengers - diacylglycerol (DAG) and phosphatidic acid (PA). We found that brassinosteroids cause closure of stomata in isolated leaf disks while inhibitors of alternative oxidase cancelled these effects. This study demonstrates that BRs activate total respiration rate, alternative respiratory pathway, production of PA and DAG, stimulate stomata closure and growth under optimal conditions and salinity. Also, specific inhibitor of brassinosteroids biosynthesis decreased alternative respiratory pathway and production of lipid messengers in rape plants.
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Affiliation(s)
- Michael Derevyanchuk
- Department of the Molecular Mechanisms of Cell Metabolism Regulation, Institute of Bioorganic Chemistry and Petrochemistry, The National Academy of Sciences of Ukraine, 02660, Murmanska str., 1, Kyiv, Ukraine
| | - Sergii Kretynin
- Department of the Molecular Mechanisms of Cell Metabolism Regulation, Institute of Bioorganic Chemistry and Petrochemistry, The National Academy of Sciences of Ukraine, 02660, Murmanska str., 1, Kyiv, Ukraine
| | - Oksana Iakovenko
- Department of the Molecular Mechanisms of Cell Metabolism Regulation, Institute of Bioorganic Chemistry and Petrochemistry, The National Academy of Sciences of Ukraine, 02660, Murmanska str., 1, Kyiv, Ukraine
| | - Raisa Litvinovskaya
- Laboratory of Steroid Chemistry, Institute of Bioorganic Chemistry, The National Academy of Sciences of Belarus, 220141, Kuprevich str., 5, Minsk, Belarus
| | - Vladimir Zhabinskii
- Laboratory of Steroid Chemistry, Institute of Bioorganic Chemistry, The National Academy of Sciences of Belarus, 220141, Kuprevich str., 5, Minsk, Belarus
| | - Jan Martinec
- Department of Biology, Faculty of Sciences, Jan Evangelista Purkyne University, Usti nad Labem, Czech Republic
| | - Yaroslav Blume
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Osypovskogo 2a, Kyiv 04123, Ukraine
| | - Vladimir Khripach
- Laboratory of Steroid Chemistry, Institute of Bioorganic Chemistry, The National Academy of Sciences of Belarus, 220141, Kuprevich str., 5, Minsk, Belarus
| | - Volodymyr Kravets
- Department of the Molecular Mechanisms of Cell Metabolism Regulation, Institute of Bioorganic Chemistry and Petrochemistry, The National Academy of Sciences of Ukraine, 02660, Murmanska str., 1, Kyiv, Ukraine.
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Borovaya M, Pirko Y, Krupodorova T, Naumenko A, Blume Y, Yemets A. Biosynthesis of cadmium sulphide quantum dots by usingPleurotus ostreatus(Jacq.) P. Kumm. BIOTECHNOL BIOTEC EQ 2015. [DOI: 10.1080/13102818.2015.1064264] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Blume Y, Yemets A, Sheremet Y, Nyporko A, Sulimenko V, Sulimenko T, Dráber P. Exposure of beta-tubulin regions defined by antibodies on an Arabidopsis thaliana microtubule protofilament model and in the cells. BMC Plant Biol 2010; 10:29. [PMID: 20167106 PMCID: PMC2844066 DOI: 10.1186/1471-2229-10-29] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2009] [Accepted: 02/18/2010] [Indexed: 05/03/2023]
Abstract
BACKGROUND The function of the cortical microtubules, composed of alphabeta-tubulin heterodimers, is linked to their organizational state which is subject to spatial and temporal modulation by environmental cues. The role of tubulin posttranslational modifications in these processes is largely unknown. Although antibodies against small tubulin regions represent useful tool for studying molecular configuration of microtubules, data on the exposure of tubulin epitopes on plant microtubules are still limited. RESULTS Using homology modeling we have generated an Arabidopsis thaliana microtubule protofilament model that served for the prediction of surface exposure of five beta-tubulin epitopes as well as tyrosine residues. Peptide scans newly disclosed the position of epitopes detected by antibodies 18D6 (beta1-10), TUB2.1 (beta426-435) and TU-14 (beta436-445). Experimental verification of the results by immunofluorescence microscopy revealed that the exposure of epitopes depended on the mode of fixation. Moreover, homology modeling showed that only tyrosines in the C-terminal region of beta-tubulins (behind beta425) were exposed on the microtubule external side. Immunofluorescence microscopy revealed tyrosine phosphorylation of microtubules in plant cells, implying that beta-tubulins could be one of the targets for tyrosine kinases. CONCLUSIONS We predicted surface exposure of five beta-tubulin epitopes, as well as tyrosine residues, on the surface of A. thaliana microtubule protofilament model, and validated the obtained results by immunofluorescence microscopy on cortical microtubules in cells.The results suggest that prediction of epitope exposure on microtubules by means of homology modeling combined with site-directed antibodies can contribute to a better understanding of the interactions of plant microtubules with associated proteins.
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Affiliation(s)
- Yaroslav Blume
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Kiev 04123, Ukraine
| | - Alla Yemets
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Kiev 04123, Ukraine
| | - Yarina Sheremet
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Kiev 04123, Ukraine
| | - Alexey Nyporko
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Kiev 04123, Ukraine
| | - Vadym Sulimenko
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, 142 20 Prague, Czech Republic
| | - Tetyana Sulimenko
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, 142 20 Prague, Czech Republic
| | - Pavel Dráber
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, 142 20 Prague, Czech Republic
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Blume Y, Yemets A, Sulimenko V, Sulimenko T, Chan J, Lloyd C, Dráber P. Tyrosine phosphorylation of plant tubulin. Planta 2008; 229:143-50. [PMID: 18800224 DOI: 10.1007/s00425-008-0816-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2008] [Accepted: 08/15/2008] [Indexed: 05/03/2023]
Abstract
Phosphorylation of alphabeta-tubulins dimers by protein tyrosine kinases plays an important role in the regulation of cellular growth and differentiation in animal cells. In plants, however, the role of tubulin tyrosine phosphorylation is unknown and data on this tubulin modification are limited. In this study, we used an immunochemical approach to demonstrate that tubulin isolated by both immunoprecipitation and DEAE-chromatography is phosphorylated on tyrosine residues in cultured cells of Nicotiana tabacum. This opens up the possibility that tyrosine phosphorylation of tubulin could be involved in modulating the properties of plant microtubules.
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Affiliation(s)
- Yaroslav Blume
- Institute of Cell Biology and Genetic Engineering, National Academy of Sciences of Ukraine, Acad. Zabolotny Str., 148, 03680 Kiev, Ukraine.
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Abstract
Tubulins, as major components involved in the organization of microtubules, play an important role in plant development. We describe here the expression profiles of all known alpha-tubulin (TUA), beta-tubulin (TUB) and gamma-tubulin (TUG) genes of barley (Hordeum vulgare), involving eight newly identified TUB sequences, five established TUA genes and one TUG gene. Macroarray and Northern blot-based expression patterns in the pericarp, endosperm and embryo were obtained over the course of the development of the grain between anthesis and maturation. These revealed that the various tubulin genes differed in their levels of expression, and to some extent were tissue specific. Two expression peaks were detected in the developing endosperm. The first and more prominent peak, at 2 days after flowering, included expression of almost all the tubulin genes. These tubulins are thought to be involved in mitoses during the formation of the syncytial endosperm. The second, less pronounced but more extended, peak included only some of the tubulin genes (HvTUA3, HvTUB1 and HvTUG) and might be associated with the cell wall organization in aleurone and starchy endosperm. The HvTUA5 gene is expressed only in embryo of the developing grain and may be associated with shoot establishment. The expression profiles of the tubulin folding cofactors HvTFC A and HvTFC B as well as small G-protein HvArl2 genes were almost perfectly correlated with the global levels of tubulin mRNA, implying that they have a role in the control of the polymerization of alpha/beta-tubulin heterodimers.
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Affiliation(s)
- Volodymyr V Radchuk
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Corrensstrasse 3, D-06466 Gatersleben, Germany.
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Abstract
Tubulins are encoded by small gene families in plants. Based on the barley EST collection, cDNAs for alpha-, beta-, and gamma-tubulins were selected. Five genes for alpha-tubulin, eight newly identified beta-tubulin sequences and one gamma-tubulin gene were found to be expressed in barley. In silico analysis of relative abundance of the distinct tubulin sequences among ESTs derived from different libraries revealed that the various tubulin genes differed in their level of expression, and to some extent were tissue specific.
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Affiliation(s)
- Volodymyr Radchuk
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung, D-06466 Gatersleben, Germany. @ipk-gatersleben.de
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Smertenko A, Blume Y, Viklický V, Dráber P. Exposure of tubulin structural domains in Nicotiana tabacum microtubules probed by monoclonal antibodies. Eur J Cell Biol 1997; 72:104-12. [PMID: 9157006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
A panel of nine antibodies, specific to antigenic determinants located on N- or C-terminal structural domains of alpha and beta subunits of animal tubulin, and antibodies against acetylated, tyrosinated and polyglutamylated tubulins were utilized for probing the Nicotiana tabacum microtubules. The specificity of antibodies was confirmed by immunoblotting on whole cell lysates and on tubulin isoforms separated by high-resolution isoelectric focusing. Whereas antibodies TU-01 and TU-09 reacted with all alpha-tubulin isoforms and TU-06 reacted with all beta-tubulin isoforms, the other antibodies reacted with a limited number of tubulin isoforms. Antibody TU-14 reacted only with two beta-tubulin charge variants. In fixed cells, each of the antibodies stained microtubules of preprophase band, mitotic spindle and phragmoplast. Cortical microtubules were stained by all antibodies except TU-02 and TU-03, which did not decorate microtubules in interphase cells. Immunostaining of unfixed detergent-extracted cells revealed that antibodies against determinants on the C-terminal domains of both subunits decorated microtubules, but these were not stained with antibodies to determinants on the N-terminal domains. These data indicate that in plant microtubules at least several parts of the N-terminal domains of both subunits are either not exposed on the microtubule surface or are masked by the other proteins. In contrast, parts of the C-terminal domains are exposed on the exterior of microtubules. As for animal tubulins the majority of posttranslational modifications as well as binding sites for microtubule-associated proteins (MAPs) have been located to these regions, it is possible also in higher plants that the C-terminal structural domains of both tubulin subunits participate in the modulation of tubulin interactions with associated proteins.
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Affiliation(s)
- A Smertenko
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague/Czech Republic
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Smertenko A, Blume Y, Viklický V, Opatrný Z, Dráber P. Post-translational modifications and multiple tubulin isoforms in Nicotiana tabacum L. cells. Planta 1997; 201:349-58. [PMID: 9129339 DOI: 10.1007/s004250050077] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Distribution of post-translationally modified tubulins in cells of Nicotiana tabacum L. was analysed using a panel of specific antibodies. Polyglutamylated, tyrosinated, nontyrosinated, acetylated and delta 2-tubulin variants were detected on alpha-tubulin subunits; polyglutamylation was also found on beta-tubulin subunits. Modified tubulins were detected by immunofluorescence microscopy in interphase microtubules, preprophase bands, mitotic spindles as well as in phragmoplasts. They were, however, located differently in the various microtubule structures. The antibodies against tyrosinated, acetylated and polyglutamylated tubulins gave uniform staining along all microtubules, while antibodies against nontyrosinated and delta 2-tubulin provided dot-like staining of interphase microtubules. Additionally, immunoreactivity of antibodies against acetylated and delta 2-tubulins was strong in the pole regions of mitotic spindles. High-resolution isoelectric focusing revealed 22 tubulin charge variants in N. tabacum suspension cells. Immunoblotting with antibodies TU-01 and TU-06 against conserved antigenic determinants of alpha- and beta-tubulin molecules, respectively, revealed that 11 isoforms belonged to the alpha-subunit and 11 isoforms to the beta-subunit. Whereas antibodies against polyglutamylated, tyrosinated and acetylated tubulins reacted with several alpha-tubulin isoforms, antibodies against nontyrosinated and delta 2-tubulin reacted with only one. The combined data demonstrate that plant tubulin is extensively post-translationally modified and that these modifications participate in the generation of plant tubulin polymorphism.
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Affiliation(s)
- A Smertenko
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Czech Republic
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