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Zuev YF, Kusova AM, Sitnitsky AE. Protein translational diffusion as a way to detect intermolecular interactions. Biophys Rev 2023; 15:1111-1125. [PMID: 37975004 PMCID: PMC10643801 DOI: 10.1007/s12551-023-01108-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 07/26/2023] [Indexed: 11/19/2023] Open
Abstract
In this work, we analyze the information on the protein intermolecular interactions obtained from macromolecular diffusion. We have shown that the most hopeful results are given by our approach based on analysis of protein translational self-diffusion and collective diffusion obtained by dynamic light scattering and pulsed-field gradient NMR (PFG NMR) spectroscopy with the help of Vink's approach to analyze diffusion motion of particles by frictional formalism of non-equilibrium thermodynamics and the usage of the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory of colloid particles interactions in electrolyte solutions. Early we have shown that integration of Vink's theory with DLVO provides a reliable basis for uniform interpreting of PFG NMR and DLS experiments on concentration dependence of diffusion coefficients. Basic details of theoretical and mathematical procedures and a broad analysis of experimental attestation of proposed conception on proteins of various structural form, size, and shape are presented. In the present review, the main capabilities of our approach obtain the details of intermolecular interactions of proteins with different shapes, internal structures, and mass. The universality of Vink's approach is experimentally shown, which gives the appropriate description of experimental results for proteins of complicated structure and shape.
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Affiliation(s)
- Yuriy F. Zuev
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky St., 2/31, 420111 Kazan, Russia
| | - Aleksandra M. Kusova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky St., 2/31, 420111 Kazan, Russia
| | - Aleksandr E. Sitnitsky
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky St., 2/31, 420111 Kazan, Russia
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Manjunatha L, Rajashekara H, Uppala LS, Ambika DS, Patil B, Shankarappa KS, Nath VS, Kavitha TR, Mishra AK. Mechanisms of Microbial Plant Protection and Control of Plant Viruses. PLANTS (BASEL, SWITZERLAND) 2022; 11:3449. [PMID: 36559558 PMCID: PMC9785281 DOI: 10.3390/plants11243449] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/10/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Plant viral diseases are major constraints causing significant yield losses worldwide in agricultural and horticultural crops. The commonly used methods cannot eliminate viral load in infected plants. Many unconventional methods are presently being employed to prevent viral infection; however, every time, these methods are not found promising. As a result, it is critical to identify the most promising and sustainable management strategies for economically important plant viral diseases. The genetic makeup of 90 percent of viral diseases constitutes a single-stranded RNA; the most promising way for management of any RNA viruses is through use ribonucleases. The scope of involving beneficial microbial organisms in the integrated management of viral diseases is of the utmost importance and is highly imperative. This review highlights the importance of prokaryotic plant growth-promoting rhizobacteria/endophytic bacteria, actinomycetes, and fungal organisms, as well as their possible mechanisms for suppressing viral infection in plants via cross-protection, ISR, and the accumulation of defensive enzymes, phenolic compounds, lipopeptides, protease, and RNase activity against plant virus infection.
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Affiliation(s)
- Lakshmaiah Manjunatha
- Division of Crop Protection, ICAR-Indian Institute of Horticultural Research (IIHR), Bengaluru 560089, Karnataka, India
| | - Hosahatti Rajashekara
- Division of Crop Protection, ICAR-Directorate of Cashew Research (DCR), Dakshina Kannada 574202, Karnataka, India
| | - Leela Saisree Uppala
- Cranberry Station, East Wareham, University of Massachusetts, Amherst, MA 02538, USA
| | - Dasannanamalige Siddesh Ambika
- Department of Plant Pathology, College of Horticulture, University of Horticultural Sciences (Bagalkot), Bengaluru 560065, Karnataka, India
| | - Balanagouda Patil
- Department of Plant Pathology, University of Agricultural and Horticultural Sciences, Shivamogga 577255, Karnataka, India
| | - Kodegandlu Subbanna Shankarappa
- Department of Plant Pathology, College of Horticulture, University of Horticultural Sciences (Bagalkot), Bengaluru 560065, Karnataka, India
| | | | - Tiptur Rooplanaik Kavitha
- Department of Plant Pathology, University of Agricultural Sciences, GKVK, Bengaluru 560065, Karnataka, India
| | - Ajay Kumar Mishra
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
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Veselova SV, Sorokan AV, Burkhanova GF, Rumyantsev SD, Cherepanova EA, Alekseev VY, Sarvarova ER, Kasimova AR, Maksimov IV. By Modulating the Hormonal Balance and Ribonuclease Activity of Tomato Plants Bacillus subtilis Induces Defense Response against Potato Virus X and Potato Virus Y. Biomolecules 2022; 12:biom12020288. [PMID: 35204789 PMCID: PMC8961569 DOI: 10.3390/biom12020288] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/04/2022] [Accepted: 02/07/2022] [Indexed: 02/01/2023] Open
Abstract
Endophytic plant-growth-promoting microorganisms can protect plants against pathogens, but they have rarely been investigated as potential biocontrol agents and triggers of induced systemic resistance (ISR), regulated by phytohormones, against viruses. We studied the role of endophytic strains Bacillus subtilis 26D and B. subtilis Ttl2, which secrete ribonucleases and phytohormones, in the induction of tomato plant resistance against potato virus X and potato virus Y in a greenhouse condition. The endophytes reduced the accumulation of viruses in plants, increased the activity of plant ribonucleases and recovered the fruit yield of infected tomato plants. Both the 26D and Ttl2 strains induced ISR by activating the transcription of genes related to salicylate- and jasmonate-dependent responses. The 26D and Ttl2 strains increased the content of cytokinins and decreased the level of indolacetic acid in plants infected with PVX or PVY. PVY led to an increase of the abscisic acid (ABA) content in tomato plants, and PVX had the opposite effect. Both strains reduced the ABA content in plants infected with PVY and induced ABA accumulation in plants infected with PVX, which led to an increase in the resistance of plants. This is the first report of the protection of tomato plants against viral diseases by foliar application of endophytes.
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Ulyanova V, Nadyrova A, Dudkina E, Kuznetsova A, Ahmetgalieva A, Faizullin D, Surchenko Y, Novopashina D, Zuev Y, Kuznetsov N, Ilinskaya O. Structural and Functional Differences between Homologous Bacterial Ribonucleases. Int J Mol Sci 2022; 23:ijms23031867. [PMID: 35163789 PMCID: PMC8837141 DOI: 10.3390/ijms23031867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 01/28/2022] [Accepted: 02/04/2022] [Indexed: 02/04/2023] Open
Abstract
Small cationic guanyl-preferring ribonucleases (RNases) produced by the Bacillus species share a similar protein tertiary structure with a high degree of amino acid sequence conservation. However, they form dimers that differ in conformation and stability. Here, we have addressed the issues (1) whether the homologous RNases also have distinctions in catalytic activity towards different RNA substrates and interactions with the inhibitor protein barstar, and (2) whether these differences correlate with structural features of the proteins. Circular dichroism and dynamic light scattering assays revealed distinctions in the structures of homologous RNases. The activity levels of the RNases towards natural RNA substrates, as measured spectrometrically by acid-soluble hydrolysis products, were similar and decreased in the row high-polymeric RNA >>> transport RNA > double-stranded RNA. However, stopped flow kinetic studies on model RNA substrates containing the guanosine residue in a hairpin stem or a loop showed that the cleavage rates of these enzymes were different. Moreover, homologous RNases were inhibited by the barstar with diverse efficiency. Therefore, minor changes in structure elements of homologous proteins have a potential to significantly effect molecule stability and functional activities, such as catalysis or ligand binding.
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Affiliation(s)
- Vera Ulyanova
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia; (A.N.); (E.D.); (A.A.); (Y.S.); (O.I.)
- Correspondence:
| | - Alsu Nadyrova
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia; (A.N.); (E.D.); (A.A.); (Y.S.); (O.I.)
| | - Elena Dudkina
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia; (A.N.); (E.D.); (A.A.); (Y.S.); (O.I.)
| | - Aleksandra Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.K.); (D.N.); (N.K.)
| | - Albina Ahmetgalieva
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia; (A.N.); (E.D.); (A.A.); (Y.S.); (O.I.)
| | - Dzhigangir Faizullin
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, 420111 Kazan, Russia; (D.F.); (Y.Z.)
| | - Yulia Surchenko
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia; (A.N.); (E.D.); (A.A.); (Y.S.); (O.I.)
| | - Darya Novopashina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.K.); (D.N.); (N.K.)
| | - Yuriy Zuev
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, 420111 Kazan, Russia; (D.F.); (Y.Z.)
| | - Nikita Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.K.); (D.N.); (N.K.)
| | - Olga Ilinskaya
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia; (A.N.); (E.D.); (A.A.); (Y.S.); (O.I.)
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Makshakova ON, Safarova ER, Zuev YF. Structural insights in interactions between RNase from Bacillus Intermedius and rhamnogalacturonan I from potato. Carbohydr Polym 2021; 251:117038. [PMID: 33142596 DOI: 10.1016/j.carbpol.2020.117038] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/31/2020] [Accepted: 08/31/2020] [Indexed: 01/21/2023]
Abstract
Being biocompatible and biodegradable polymers, polysaccharides present a perspective material for drug delivery systems. This study aimed at unraveling the molecular details of interactions between rhamnogalacturonan I, brunched with galactan side chains, and RNase from Bacillus Intermedius, binase. FTIR- and NMR-spectroscopic analyses showed that binase interacts with side chains of the polysaccharide. In complexes with polysaccharide, the protein retains its native structure. The 2D-NMR techniques revealed eight protein residues responsive to polysaccharide binding. Further, computer simulations were carried out to provide the atomistic details of binase-polysaccharide complexes. Both blind and knowledge-based docking procedures elucidate the existence of epitopes on the binase surface with the preferential binding of galactan fragments. The refinement of these complexes by molecular dynamics simulations confirmed stable protein-polysaccharide interactions. The results of this study strengthen the knowledge on non-specific protein-carbohydrate interactions and outline the rhamnogalacturonan I as a possible matrix material for protein delivery systems.
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Affiliation(s)
- O N Makshakova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, 420111, Lobachevsky str. 2/31, Kazan, Russian Federation.
| | - E R Safarova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, 420111, Lobachevsky str. 2/31, Kazan, Russian Federation
| | - Y F Zuev
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, 420111, Lobachevsky str. 2/31, Kazan, Russian Federation
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Maksimov IV, Sorokan AV, Shein MY, Khairullin RM. Biological Methods of Plant Protection against Viruses: Problems and Prospects. APPL BIOCHEM MICRO+ 2020. [DOI: 10.1134/s0003683820060101] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Sorokan A, Cherepanova E, Burkhanova G, Veselova S, Rumyantsev S, Alekseev V, Mardanshin I, Sarvarova E, Khairullin R, Benkovskaya G, Maksimov I. Endophytic Bacillus spp. as a Prospective Biological Tool for Control of Viral Diseases and Non-vector Leptinotarsa decemlineata Say. in Solanum tuberosum L. Front Microbiol 2020; 11:569457. [PMID: 33178153 PMCID: PMC7593271 DOI: 10.3389/fmicb.2020.569457] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 09/10/2020] [Indexed: 12/19/2022] Open
Abstract
Viral diseases and their damage causing significant loss to economically important crops have increased by several folds during the last decade. All the conventional approaches are not able to eradicate the viral infection. Therefore, there is a need to look for efficient and eco-friendly viral disease-preventive measures. The genomic material of the majority of deleterious viruses of higher plants is RNA. One of the possible measures to control viruses is the use of ribonucleases (RNases), which can cleave RNA in the viral genome. Based on this, we investigated the RNase activity of endophytic Bacillus spp., which can enrich in 103–105 colony-forming units per gram of wet mass of aboveground part of potato plants. A high level of RNase activity was observed in the culture medium of Bacillus thuringiensis B-6066, Bacillus sp. STL-7, Bacillus sp. TS2, and Bacillus subtilis 26D. B. thuringiensis B-5351 had low RNase activity but high ability to colonize internal plant tissues, Bacillus sp. STL-7 with high RNase activity have relatively low number of cells in internal tissues of plants. B. thuringiensis B-6066, B. subtilis 26D, and Bacillus sp. TS stimulate RNase activity in potato plants for a long time after application. Strains with high ability to colonize internal plant tissues combined with high RNase activity reduced severity of viral diseases symptoms on plants and reduced the incidence of potato viruses M, S, and Y. It is worth noting that Bacillus spp. under investigation reduced the number of Leptinotarsa decemlineata Say. egg clusters and larvae on treated plants and showed antifeedant activity. This results in increase of potato productivity mainly in the fraction of major tubers. B. subtilis 26D and Bacillus sp. TS2 combining endophytic lifestyle, RNase, and antifeedant activity may become the basis for the development of biocontrol agents for plant protection.
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Affiliation(s)
- Antonina Sorokan
- Laboratory of Biochemistry of Plant Immunity, Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, Ufa, Russia
| | - Ekaterina Cherepanova
- Laboratory of Biochemistry of Plant Immunity, Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, Ufa, Russia
| | - Guzel Burkhanova
- Laboratory of Biochemistry of Plant Immunity, Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, Ufa, Russia
| | - Svetlana Veselova
- Laboratory of Biochemistry of Plant Immunity, Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, Ufa, Russia
| | - Sergey Rumyantsev
- Laboratory of Genomics of Plants, Ufa Federal Research Center, Institute of Biochemistry and Genetics, Russian Academy of Sciences, Ufa, Russia
| | - Valentin Alekseev
- Laboratory of Biochemistry of Plant Immunity, Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, Ufa, Russia
| | - Ildar Mardanshin
- Laboratory of Selection and Seed Production of Potato, Bashkir Research Institute of Agriculture, Ufa Federal Research Center, Russian Academy of Sciences, Ufa, Russia
| | - Elena Sarvarova
- Laboratory of Genomics of Plants, Ufa Federal Research Center, Institute of Biochemistry and Genetics, Russian Academy of Sciences, Ufa, Russia
| | - Ramil Khairullin
- Laboratory of Biochemistry of Plant Immunity, Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, Ufa, Russia
| | - Galina Benkovskaya
- Laboratory of Physiological Genetics, Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, Ufa, Russia
| | - Igor Maksimov
- Laboratory of Biochemistry of Plant Immunity, Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, Ufa, Russia
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9
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Mechanisms of Plant Tolerance to RNA Viruses Induced by Plant-Growth-Promoting Microorganisms. PLANTS 2019; 8:plants8120575. [PMID: 31817560 PMCID: PMC6963434 DOI: 10.3390/plants8120575] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/29/2019] [Accepted: 12/04/2019] [Indexed: 12/25/2022]
Abstract
Plant viruses are globally responsible for the significant crop losses of economically important plants. All common approaches are not able to eradicate viral infection. Many non-conventional strategies are currently used to control viral infection, but unfortunately, they are not always effective. Therefore, it is necessary to search for efficient and eco-friendly measures to prevent viral diseases. Since the genomic material of 90% higher plant viruses consists of single-stranded RNA, the best way to target the viral genome is to use ribonucleases (RNase), which can be effective against any viral disease of plants. Here, we show the importance of the search for endophytes with protease and RNase activity combined with the capacity to prime antiviral plant defense responses for their protection against viruses. This review discusses the possible mechanisms used to suppress a viral attack as well as the use of local endophytic bacteria for antiviral control in crops.
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Burkhanova GF, Sorokan AV, Cherepanova EA, Sarvarova ER, Khairullin RM, Maksimov IV. Endophytic Bacillus bacteria with RNase activity in the resistance of potato plants to viruses. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj19.561] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Viral diseases annually cause significant crop losses and significantly reduce the quality of products, including potatoes, some of the most important crops. Currently, viruses cannot be controlled with chemical pesticides, since known antiviral compounds are teratogenic and hazardous to people’s health. Biocontrol agents based on endophytic microorganisms may be an alternative to them. Many strains of Bacillus produce ribonucleases (RNases). Our laboratory possesses a collection of bacteria that produce various metabolites and have RNase activity. The results showed that the inoculation of potato with B. subtilis 26D and B. thuringiensis increased the grain yield by 32–43 %. In addition, the treatment of potato plants with Bacillus spp. significantly reduced the infection of potato plants with virus M. The prevalence of the disease in potato plants was significantly reduced from 60 % in the control to 18 % (B. subtillis 26D) and 25–33 % (B. thuringiensis) in the inoculated plants. Similarly, the infection index decreased from 14 in the control to 1 in the inoculated plants. The further study of molecular mechanisms related to bacterial induction of plant defense reactions in response to viral infections will lead to a better understanding of stress resistance problems. The endophytic microorganisms studied in this report may become the basis for the creation of biological agents for plant protection.
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Affiliation(s)
- G. F. Burkhanova
- Institute of Biochemistry and Genetics – Subdivision of the Ufa Federal Research Centre, RAS
| | - A. V. Sorokan
- Institute of Biochemistry and Genetics – Subdivision of the Ufa Federal Research Centre, RAS
| | - E. A. Cherepanova
- Institute of Biochemistry and Genetics – Subdivision of the Ufa Federal Research Centre, RAS
| | - E. R. Sarvarova
- Institute of Biochemistry and Genetics – Subdivision of the Ufa Federal Research Centre, RAS
| | - R. M. Khairullin
- Institute of Biochemistry and Genetics – Subdivision of the Ufa Federal Research Centre, RAS
| | - I. V. Maksimov
- Institute of Biochemistry and Genetics – Subdivision of the Ufa Federal Research Centre, RAS
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