1
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Spechenkova N, Samarskaya VO, Kalinina NO, Zavriev SK, MacFarlane S, Love AJ, Taliansky M. Plant Poly(ADP-Ribose) Polymerase 1 Is a Potential Mediator of Cross-Talk between the Cajal Body Protein Coilin and Salicylic Acid-Mediated Antiviral Defence. Viruses 2023; 15:1282. [PMID: 37376582 DOI: 10.3390/v15061282] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/28/2023] [Accepted: 05/28/2023] [Indexed: 06/29/2023] Open
Abstract
The nucleolus and Cajal bodies (CBs) are sub-nuclear domains with well-known roles in RNA metabolism and RNA-protein assembly. However, they also participate in other important aspects of cell functioning. This study uncovers a previously unrecognised mechanism by which these bodies and their components regulate host defences against pathogen attack. We show that the CB protein coilin interacts with poly(ADP-ribose) polymerase 1 (PARP1), redistributes it to the nucleolus and modifies its function, and that these events are accompanied by substantial increases in endogenous concentrations of salicylic acid (SA), activation of SA-responsive gene expression and callose deposition leading to the restriction of tobacco rattle virus (TRV) systemic infection. Consistent with this, we also find that treatment with SA subverts the negative effect of the pharmacological PARP inhibitor 3-aminobenzamide (3AB) on plant recovery from TRV infection. Our results suggest that PARP1 could act as a key molecular actuator in the regulatory network which integrates coilin activities as a stress sensor for virus infection and SA-mediated antivirus defence.
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Affiliation(s)
- Nadezhda Spechenkova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia
| | - Viktoriya O Samarskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia
| | - Natalya O Kalinina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Sergey K Zavriev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia
| | - S MacFarlane
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Andrew J Love
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Michael Taliansky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
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2
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Popovic M. The SARS-CoV-2 Hydra, a tiny monster from the 21st century: Thermodynamics of the BA.5.2 and BF.7 variants. MICROBIAL RISK ANALYSIS 2023; 23:100249. [PMID: 36777924 PMCID: PMC9898946 DOI: 10.1016/j.mran.2023.100249] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 02/01/2023] [Accepted: 02/01/2023] [Indexed: 06/01/2023]
Abstract
SARS-CoV-2 resembles the ancient mythical creature Hydra. Just like with the Hydra, when one head is cut, it is followed by appearance of two more heads, suppression of one SARS-CoV-2 variant causes appearance of newer variants. Unlike Hydra that grows identical heads, newer SARS-CoV-2 variants are usually more infective, which can be observed as time evolution of the virus at hand, which occurs through acquisition of mutations during time. The appearance of new variants is followed by appearance of new COVID-19 pandemic waves. With the appearance of new pandemic waves and determining of sequences, in the scientific community and general public the question is always raised of whether the new variant will be more virulent and more pathogenic. The two variants characterized in this paper, BA.5.2 and BF.7, have caused a pandemic wave during the late 2022. This paper gives full chemical and thermodynamic characterization of the BA.5.2 and BF.7 variants of SARS-CoV-2. Having in mind that Gibbs energy of binding and biosynthesis represent the driving forces for the viral life cycle, based on the calculated thermodynamic properties we can conclude that the newer variants are more infective than earlier ones, but that their pathogenicity has not changed.
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Affiliation(s)
- Marko Popovic
- School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
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3
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Biothermodynamics of Viruses from Absolute Zero (1950) to Virothermodynamics (2022). Vaccines (Basel) 2022; 10:vaccines10122112. [PMID: 36560522 PMCID: PMC9784531 DOI: 10.3390/vaccines10122112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
Biothermodynamics of viruses is among the youngest but most rapidly developing scientific disciplines. During the COVID-19 pandemic, it closely followed the results published by molecular biologists. Empirical formulas were published for 50 viruses and thermodynamic properties for multiple viruses and virus variants, including all variants of concern of SARS-CoV-2, SARS-CoV, MERS-CoV, Ebola virus, Vaccinia and Monkeypox virus. A review of the development of biothermodynamics of viruses during the last several decades and intense development during the last 3 years is described in this paper.
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4
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Chan SK, Steinmetz NF. Isolation of Tobacco Mosaic Virus-Binding Peptides for Biotechnology Applications. Chembiochem 2022; 23:e202200040. [PMID: 35320626 PMCID: PMC9262120 DOI: 10.1002/cbic.202200040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/17/2022] [Indexed: 11/09/2022]
Abstract
Tobacco mosaic virus (TMV) was the first virus to be discovered and it is now widely used as a tool for biological research and biotechnology applications. TMV particles can be decorated with functional molecules by genetic engineering or bioconjugation. However, this can destabilize the nanoparticles, and/or multiple rounds of modification may be necessary, reducing product yields and preventing the display of certain cargo molecules. To overcome these challenges, we used phage display technology and biopanning to isolate a TMV-binding peptide (TBPT25 ) with strong binding properties (IC50 =0.73 μM, KD =0.16 μM), allowing the display of model cargos via a single mixing step. The TMV-binding peptide is specific for TMV but does not recognize free coat proteins and can therefore be used to decorate intact TMV or detect intact TMV particles in crude plant sap.
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Affiliation(s)
- Soo Khim Chan
- Department of Nanoengineering, University of California San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Nicole F Steinmetz
- Department of NanoEngineering, Department of Bioengineering, Department of Radiology, Center for Nano-ImmunoEngineering, Moores Cancer Center, Institute for Materials Discovery and Design, University of California San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
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5
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Lee KZ, Basnayake Pussepitiyalage V, Lee YH, Loesch-Fries LS, Harris MT, Hemmati S, Solomon KV. Engineering Tobacco Mosaic Virus and Its Virus-Like-Particles for Synthesis of Biotemplated Nanomaterials. Biotechnol J 2021; 16:e2000311. [PMID: 33135368 DOI: 10.1002/biot.202000311] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/27/2020] [Indexed: 12/12/2022]
Abstract
Biomolecules are increasingly attractive templates for the synthesis of functional nanomaterials. Chief among them is the plant tobacco mosaic virus (TMV) due to its high aspect ratio, narrow size distribution, diverse biochemical functionalities presented on the surface, and compatibility with a number of chemical conjugations. These properties are also easily manipulated by genetic modification to enable the synthesis of a range of metallic and non-metallic nanomaterials for diverse applications. This article reviews the characteristics of TMV and related viruses, and their virus-like particle (VLP) derivatives, and how these may be manipulated to extend their use and function. A focus of recent efforts has been on greater understanding and control of the self-assembly processes that drive biotemplate formation. How these features have been exploited in engineering applications such as, sensing, catalysis, and energy storage are briefly outlined. While control of VLP surface features is well-established, fewer tools exist to control VLP self-assembly, which limits efforts to control template uniformity and synthesis of certain templated nanomaterials. However, emerging advances in synthetic biology, machine learning, and other fields promise to accelerate efforts to control template uniformity and nanomaterial synthesis enabling more widescale industrial use of VLP-based biotemplates.
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Affiliation(s)
- Kok Zhi Lee
- Agricultural & Biological Engineering, Purdue University, 225 S University St, West Lafayette, IN, 47907, USA
| | | | - Yu-Hsuan Lee
- School of Chemical Engineering, Purdue University, 480 W Stadium Ave, West Lafayette, IN, 47907, USA
| | - L Sue Loesch-Fries
- Department of Botany and Plant Pathology, Purdue University, 915 W State St, West Lafayette, IN, 47907, USA
| | - Michael T Harris
- School of Chemical Engineering, Purdue University, 480 W Stadium Ave, West Lafayette, IN, 47907, USA
| | - Shohreh Hemmati
- School of Chemical Engineering, Oklahoma State University, 420 Engineering North, Stillwater, OK, 74078, USA
| | - Kevin V Solomon
- Agricultural & Biological Engineering, Purdue University, 225 S University St, West Lafayette, IN, 47907, USA
- Laboratory of Renewable Resources Engineering (LORRE), Purdue University, 500 Central Drive, West Lafayette, IN, 47907, USA
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6
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Metavarayuth K, Maturavongsadit P, Chen X, Sitasuwan P, Lu L, Su J, Wang Q. Nanotopographical Cues Mediate Osteogenesis of Stem Cells on Virus Substrates through BMP-2 Intermediate. NANO LETTERS 2019; 19:8372-8380. [PMID: 31296009 DOI: 10.1021/acs.nanolett.9b02001] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Recent studies have demonstrated rapid osteogenic differentiation of bone marrow-derived mesenchymal stem cells (BMSCs) on substrates with plant virus modified nanotopographical cues as a promising strategy for bone repair; however, the mechanisms remain unclear. We hypothesized that the highly structurally ordered virus coat proteins, responsible for targeting specific cellular components, are critical for the osteogenesis promotion. In this study, hybrid viral gold nanorods were prepared to explore the effects of highly ordered arranged virus coat proteins on osteogenic differentiation of BMSCs. The results herein indicate that it is the nanotopographical cues modified by structurally ordered virus nanoparticles, not the chemical properties of virus surface, that mediate osteogenesis. Bone morphogenetic protein 2 (BMP-2) expression is significantly increased and serves as a modulator that mediates the osteogenic differentiation in response to the viral particle coatings. After BMP-2 is inhibited by Noggin, the osteogenesis promoting effects are significantly compromised, demonstrated by lower alkaline phosphatase activity and calcium sequestration. This study reveals that plant virus modified nanotopographical substrates promote osteogenic differentiation of BMSCs through increasing BMP-2 autocrine. It provides key insights to engineering functional materials for rapid bone repair.
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Affiliation(s)
- Kamolrat Metavarayuth
- Department of Chemistry and Biochemistry , University of South Carolina , 631 Sumter Street , Columbia , South Carolina 29208 , United States
| | - Panita Maturavongsadit
- Joint Department of Biomedical Engineering , University of North Carolina at Chapel Hill and North Carolina State University , Chapel Hill , North Carolina 27599 , United States
| | - Xiao Chen
- Department of Orthopedics Trauma , Changhai Hospital, Second Military Medical University , Shanghai 200433 , China
| | - Pongkwan Sitasuwan
- Department of Chemistry and Biochemistry , University of South Carolina , 631 Sumter Street , Columbia , South Carolina 29208 , United States
| | - Lin Lu
- Department of Chemistry and Biochemistry , University of South Carolina , 631 Sumter Street , Columbia , South Carolina 29208 , United States
| | - Jiacan Su
- Department of Orthopedics Trauma , Changhai Hospital, Second Military Medical University , Shanghai 200433 , China
| | - Qian Wang
- Department of Chemistry and Biochemistry , University of South Carolina , 631 Sumter Street , Columbia , South Carolina 29208 , United States
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7
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Shaw J, Yu C, Makhotenko AV, Makarova SS, Love AJ, Kalinina NO, MacFarlane S, Chen J, Taliansky ME. Interaction of a plant virus protein with the signature Cajal body protein coilin facilitates salicylic acid-mediated plant defence responses. THE NEW PHYTOLOGIST 2019; 224:439-453. [PMID: 31215645 DOI: 10.1111/nph.15994] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 06/06/2019] [Indexed: 05/22/2023]
Abstract
In addition to well-known roles in RNA metabolism, the nucleolus and Cajal bodies (CBs), both located within the nucleus, are involved in plant responses to biotic and abiotic stress. Previously we showed that plants in which expression of the CB protein coilin is downregulated are more susceptible to certain viruses including tobacco rattle virus (TRV), suggesting a role of coilin in antiviral defence. Experiments with coilin-deficient plants and the deletion mutant of the TRV 16K protein showed that both 16K and coilin are required for restriction of systemic TRV infection. The potential mechanisms of coilin-mediated antiviral defence were elucidated via experiments involving co-immunoprecipitation, use of NahG transgenic plants deficient in salicylic acid (SA) accumulation, measurement of endogenous SA concentrations and assessment of SA-responsive gene expression. Here we show that TRV 16K interacts with and relocalizes coilin to the nucleolus. In wild-type plants these events are accompanied by activation of SA-responsive gene expression and restriction of TRV systemic infection. By contrast, viral systemic spread was enhanced in NahG plants, implicating SA in these processes. Our findings suggest that coilin is involved in plant defence, responding to TRV infection by recognition of the TRV-encoded 16K protein and activating SA-dependent defence pathways.
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Affiliation(s)
- Jane Shaw
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Chulang Yu
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, 117997, China
| | - Antonida V Makhotenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the RAS, Moscow, 117997, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow, 119991, Russia
| | - Svetlana S Makarova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the RAS, Moscow, 117997, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow, 119991, Russia
| | - Andrew J Love
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Natalia O Kalinina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the RAS, Moscow, 117997, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow, 119991, Russia
| | - Stuart MacFarlane
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Jianping Chen
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, 117997, China
| | - Michael E Taliansky
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the RAS, Moscow, 117997, Russia
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8
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Makarova SS, Makhotenko AV, Khromov AV, Skurat EV, Solovyev AG, Makarov VV, Kalinina NO. Non-structural Functions of Hordeivirus Capsid Protein Identified in Plants Infected by a Chimeric Tobamovirus. BIOCHEMISTRY. BIOKHIMIIA 2018; 83:1543-1551. [PMID: 30878029 DOI: 10.1134/s000629791812012x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 09/12/2018] [Indexed: 11/23/2022]
Abstract
Capsid proteins (CPs) of (+)RNA-containing plant viruses are multifunctional proteins involved in many stages of viral infection cycle, in addition to their main function of virus capsid formation. For example, the tobamoviral CP ensures virus systemic transport in plants and defines the virus-host interactions, thereby influencing the virus host range, virus infectivity, pathogenicity, and manifestation of infection symptoms. Hordeiviruses and tobamoviruses belong to the Virgaviridae family and have rod-shaped virions with a helical symmetry; their CPs are similar in structure. However, no non-structural functions of hordeiviral CPs have been described so far. In this study, we assayed possible non-structural functions of CP from the barley stripe mosaic virus (BSMV) (hordeivirus). To do this, the genome of turnip vein clearing virus (TVCV) (tobamovirus) was modified by substituting the TVCV CP gene with the BSMV CP gene or its mutants. We found that BSMV CP efficiently replaced TVCV CP at all stages of viral infection. In particular, BSMV CP performed the role of tobamoviral CP in the long-distance transport of the chimeric virus, acted as a hypersensitive response elicitor, and served as a pathogenicity determinant that influenced the symptoms of the viral infection. The chimeric tobamovirus coding for the C-terminally truncated BSMV CP displayed an increased infectivity and was transported in plants in a form of atypical virions (ribonucleoprotein complexes).
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Affiliation(s)
- S S Makarova
- Lomonosov Moscow State University, Biological Faculty, Moscow, 119991, Russia
| | - A V Makhotenko
- Lomonosov Moscow State University, Biological Faculty, Moscow, 119991, Russia
| | - A V Khromov
- Lomonosov Moscow State University, Biological Faculty, Moscow, 119991, Russia
| | - E V Skurat
- Lomonosov Moscow State University, Biological Faculty, Moscow, 119991, Russia
| | - A G Solovyev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, 127550, Russia
| | - V V Makarov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - N O Kalinina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
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9
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Riekel C, Burghammer M, Snigirev I, Rosenthal M. Microstructural metrology of tobacco mosaic virus nanorods during radial compression and heating. SOFT MATTER 2018; 14:194-204. [PMID: 29138785 DOI: 10.1039/c7sm01332a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We determined stress-induced deformations and the thermal stability of nanorod-shaped tobacco mosaic virus (TMV) capsids in coffee-ring structures by X-ray nanodiffraction. The hexagonal capsids lattice transforms under compression in the outer boundary zone of the coffee-ring into a tetragonal lattice. The helical pitch of the nanorods increases by about 2.5% across the outer boundary zone while the lateral distance between nanorods decreases continuously across the whole coffee-ring structure by about 2% due to compressive forces. The diffraction patterns show a mixture of helical scattering and Bragg peaks attributed to a lattice of nanorods interlocked by their helical grooves. Thermo-nanodiffraction reveals water loss up to about 100 °C resulting in a reduction of the helical pitch by about 6% with respect to its maximum value and a reduction of the nanorods separation by about 0.5 nm. Up to about 200 °C the pitch is increasing again by about 2%. Secondary crystallization in the bulk reaches a maximum at 150-160 °C. At higher temperatures the crystallinity is continuously decreasing up to about 220 °C. Above about 200 °C and depending on the heating history, the nanorods start disintegrating into small, randomly oriented aggregates.
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Affiliation(s)
- C Riekel
- The European Synchrotron, ESRF, CS40220, F-38043 Grenoble Cedex 9, France.
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10
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Adigun OO, Retzlaff-Roberts EL, Novikova G, Wang L, Kim BS, Ilavsky J, Miller JT, Loesch-Fries LS, Harris MT. BSMV as a Biotemplate for Palladium Nanomaterial Synthesis. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:1716-1724. [PMID: 28118012 DOI: 10.1021/acs.langmuir.6b03341] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The vast unexplored virus biodiversity makes the application of virus templates to nanomaterial synthesis especially promising. Here, a new biotemplate, Barley stripe mosaic virus (BSMV) was successfully used to synthesize organic-metal nanorods of similarly high quality to those produced with Tobacco mosaic virus (TMV). The mineralization behavior was characterized in terms of the reduction and adsorption of precursor and nanocrystal formation processes. The BSMV surface-mediated reduction of Pd(2+) proceeded via first-order kinetics in both Pd(2+) and BSMV. The adsorption equilibrium relationship of PdCl3H2O- on the BSMV surface was described by a multistep Langmuir isotherm suggesting alternative adsorbate-adsorbent interactions when compared to those on TMV. It was deduced that the first local isotherm is governed by electrostatically driven adsorption, which is then followed by sorption driven by covalent affinity of metal precursor molecules for amino acid residues. Furthermore, the total adsorption capacity of palladium species on BSMV is more than double of that on TMV. Finally, study of the BSMV-Pd particles by combining USAXS and SAXS enabled the characterization of all length scales in the synthesized nanomaterials. Results confirm the presence of core-shell cylindrical particles with 1-2 nm grains. The nanorods were uniform and monodisperse, with controllable diameters and therefore, of similar quality to those synthesized with TMV. Overall, BSMV has been confirmed as a viable alternate biotemplate with unique biomineralization behavior. With these results, the biotemplate toolbox has been expanded for the synthesis of new materials and comparative study of biomineralization processes.
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Affiliation(s)
- Oluwamayowa O Adigun
- School of Chemical Engineering, Purdue University , 480 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Erin Lynn Retzlaff-Roberts
- School of Chemical Engineering, Purdue University , 480 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Gloria Novikova
- School of Chemical Engineering, Purdue University , 480 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Longfei Wang
- Department of Botany and Plant Pathology, Purdue University , 915 West State Street, West Lafayette, Indiana 47907, United States
| | | | - Jan Ilavsky
- X-ray Science Division, APS Argonne National Laboratory , 9700S Cass Avenue, Lemont, Illinois 60439, United States
| | - Jeffrey T Miller
- School of Chemical Engineering, Purdue University , 480 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - L Sue Loesch-Fries
- Department of Botany and Plant Pathology, Purdue University , 915 West State Street, West Lafayette, Indiana 47907, United States
| | - Michael T Harris
- School of Chemical Engineering, Purdue University , 480 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
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11
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Makarov VV, Kalinina NO. Structure and Noncanonical Activities of Coat Proteins of Helical Plant Viruses. BIOCHEMISTRY (MOSCOW) 2016; 81:1-18. [PMID: 26885578 DOI: 10.1134/s0006297916010016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The main function of virus coat protein is formation of the capsid that protects the virus genome against degradation. However, besides the structural function, coat proteins have many additional important activities in the infection cycle of the virus and in the defense response of host plants to viral infection. This review focuses on noncanonical functions of coat proteins of helical RNA-containing plant viruses with positive genome polarity. Analysis of data on the structural organization of coat proteins of helical viruses has demonstrated that the presence of intrinsically disordered regions within the protein structure plays an important role in implementation of nonstructural functions and largely determines the multifunctionality of coat proteins.
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Affiliation(s)
- V V Makarov
- Lomonosov Moscow State University, Belozersky Institute of Physico-Chemical Biology, Moscow, 119991, Russia.
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12
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Solovyev AG, Makarov VV. Helical capsids of plant viruses: architecture with structural lability. J Gen Virol 2016; 97:1739-1754. [DOI: 10.1099/jgv.0.000524] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- A. G. Solovyev
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - V. V. Makarov
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
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13
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Love AJ, Makarov VV, Sinitsyna OV, Shaw J, Yaminsky IV, Kalinina NO, Taliansky ME. A Genetically Modified Tobacco Mosaic Virus that can Produce Gold Nanoparticles from a Metal Salt Precursor. FRONTIERS IN PLANT SCIENCE 2015; 6:984. [PMID: 26617624 PMCID: PMC4639705 DOI: 10.3389/fpls.2015.00984] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 10/26/2015] [Indexed: 05/26/2023]
Abstract
We genetically modified tobacco mosaic virus (TMV) to surface display a characterized peptide with potent metal ion binding and reducing capacity (MBP TMV), and demonstrate that unlike wild type TMV, this construct can lead to the formation of discrete 10-40 nm gold nanoparticles when mixed with 3 mM potassium tetrachloroaurate. Using a variety of analytical physicochemical approaches it was found that these nanoparticles were crystalline in nature and stable. Given that the MBP TMV can produce metal nanomaterials in the absence of chemical reductants, it may have utility in the green production of metal nanomaterials.
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Affiliation(s)
- Andrew J. Love
- Cell and Molecular Sciences, The James Hutton InstituteDundee, UK
| | - Valentine V. Makarov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State UniversityMoscow, Russia
| | | | - Jane Shaw
- Cell and Molecular Sciences, The James Hutton InstituteDundee, UK
| | - Igor V. Yaminsky
- Physical Faculty, Lomonosov Moscow State UniversityMoscow, Russia
| | - Natalia O. Kalinina
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State UniversityMoscow, Russia
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14
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Study of rabies virus by Differential Scanning Calorimetry. Biochem Biophys Rep 2015; 4:329-336. [PMID: 29124221 PMCID: PMC5669403 DOI: 10.1016/j.bbrep.2015.10.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 10/22/2015] [Accepted: 10/23/2015] [Indexed: 12/25/2022] Open
Abstract
Differential Scanning Calorimetry (DSC) has been used in the past to study the thermal unfolding of many different viruses. Here we present the first DSC analysis of rabies virus. We show that non-inactivated, purified rabies virus unfolds cooperatively in two events centered at approximately 62 and 73 °C. Beta-propiolactone (BPL) treatment does not alter significantly viral unfolding behavior, indicating that viral inactivation does not alter protein structure significantly. The first unfolding event was absent in bromelain treated samples, causing an elimination of the G-protein ectodomain, suggesting that this event corresponds to G-protein unfolding. This hypothesis was confirmed by the observation that this first event was shifted to higher temperatures in the presence of three monoclonal, G-protein specific antibodies. We show that dithiothreitol treatment of the virus abolishes the first unfolding event, indicating that the reduction of G-protein disulfide bonds causes dramatic alterations to protein structure. Inactivated virus samples heated up to 70 °C also showed abolished recognition of conformational G-protein specific antibodies by Surface Plasmon Resonance analysis. The sharpness of unfolding transitions and the low standard deviations of the Tm values as derived from multiple analysis offers the possibility of using this analytical tool for efficient monitoring of the vaccine production process and lot to lot consistency. Differential Scanning Calorimetry analysis of rabies virus. Rabies virus unfolds in two thermal events. The first event corresponds to G-protein.
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15
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Clare DK, Pechnikova EV, Skurat EV, Makarov VV, Sokolova OS, Solovyev AG, Orlova EV. Novel Inter-Subunit Contacts in Barley Stripe Mosaic Virus Revealed by Cryo-Electron Microscopy. Structure 2015; 23:1815-1826. [PMID: 26278173 PMCID: PMC4597109 DOI: 10.1016/j.str.2015.06.028] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 05/27/2015] [Accepted: 06/21/2015] [Indexed: 11/30/2022]
Abstract
Barley stripe mosaic virus (BSMV, genus Hordeivirus) is a rod-shaped single-stranded RNA virus similar to viruses of the structurally characterized and well-studied genus Tobamovirus. Here we report the first high-resolution structure of BSMV at 4.1 Å obtained by cryo-electron microscopy. We discovered that BSMV forms two types of virion that differ in the number of coat protein (CP) subunits per turn and interactions between the CP subunits. While BSMV and tobacco mosaic virus CP subunits have a similar fold and interact with RNA using conserved residues, the axial contacts between the CP of these two viral groups are considerably different. BSMV CP subunits lack substantial axial contacts and are held together by a previously unobserved lateral contact formed at the virion surface via an interacting loop, which protrudes from the CP hydrophobic core to the adjacent CP subunit. These data provide an insight into diversity in structural organization of helical viruses.
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Affiliation(s)
- Daniel Kofi Clare
- Institute of Structural and Molecular Biology, UCL and Birkbeck, Malet Street, London WC1E 7HX, UK
| | - Eugenia V Pechnikova
- A.V. Shubnikov Institute of Crystallography RAS, 59 Leninsky Avenue, 119333 Moscow, Russia
| | - Eugene V Skurat
- Department of Biology, Moscow State University, 1 Leninskie Gory, Building 12, 119991 Moscow, Russia
| | - Valentin V Makarov
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Russia
| | - Olga S Sokolova
- A.V. Shubnikov Institute of Crystallography RAS, 59 Leninsky Avenue, 119333 Moscow, Russia; Department of Biology, Moscow State University, 1 Leninskie Gory, Building 12, 119991 Moscow, Russia
| | - Andrey G Solovyev
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Russia
| | - Elena V Orlova
- Institute of Structural and Molecular Biology, UCL and Birkbeck, Malet Street, London WC1E 7HX, UK.
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16
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Ksenofontov AL, Parshina EY, Fedorova NV, Arutyunyan AM, Rumvolt R, Paalme V, Baratova LA, Järvekülg L, Dobrov EN. Heating-induced transition of Potyvirus Potato Virus A coat protein into β-structure. J Biomol Struct Dyn 2015; 34:250-8. [PMID: 25851284 DOI: 10.1080/07391102.2015.1022604] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In our previous communication, we have reported that virions of plant Potyvirus Potato Virus A (PVA) have a peculiar structure characterized by high content of disordered regions in intravirus coat protein (CP). In this report, we describe unusual properties of the PVA CP. With the help of a number of physicochemical methods, we have observed that the PVA CP just released from the virions by heating at 60-70 °C undergoes association into oligomers and transition to β- (and even cross-β-) conformation. Transition to β-structure on heating has been recently reported for a number of viral and non-viral proteins. The PVA CP isolated by LiCl method was also transformed into cross-β-structure on heating to 60 °C. Using the algorithms for protein aggregation prediction, we found that the aggregation-prone segments should be located in the central region of a PVA CP molecule. Possibly this transition mimics some functions of PVA CP in the virus life cycle in infected plants.
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Affiliation(s)
- Alexander L Ksenofontov
- a A.N. Belozersky Institute of Physico-Chemical Biology , Lomonosov Moscow State University , 1/40 Leninskie gory, Moscow 119991 , Russia
| | - Evgenia Yu Parshina
- b Department of Biophysics , Moscow State University , Moscow 119991 , Russia
| | - Natalia V Fedorova
- a A.N. Belozersky Institute of Physico-Chemical Biology , Lomonosov Moscow State University , 1/40 Leninskie gory, Moscow 119991 , Russia
| | - Alexander M Arutyunyan
- a A.N. Belozersky Institute of Physico-Chemical Biology , Lomonosov Moscow State University , 1/40 Leninskie gory, Moscow 119991 , Russia
| | - Reet Rumvolt
- c Department of Gene Technology , Tallinn University of Technology , Akadeemia tee 15, Tallinn 12618 , Estonia
| | - Viiu Paalme
- c Department of Gene Technology , Tallinn University of Technology , Akadeemia tee 15, Tallinn 12618 , Estonia
| | - Ludmila A Baratova
- a A.N. Belozersky Institute of Physico-Chemical Biology , Lomonosov Moscow State University , 1/40 Leninskie gory, Moscow 119991 , Russia
| | - Lilian Järvekülg
- c Department of Gene Technology , Tallinn University of Technology , Akadeemia tee 15, Tallinn 12618 , Estonia
| | - Eugeny N Dobrov
- a A.N. Belozersky Institute of Physico-Chemical Biology , Lomonosov Moscow State University , 1/40 Leninskie gory, Moscow 119991 , Russia
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17
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Kendall A, Williams D, Bian W, Stewart PL, Stubbs G. Barley stripe mosaic virus: structure and relationship to the tobamoviruses. Virology 2013; 443:265-70. [PMID: 23725818 DOI: 10.1016/j.virol.2013.05.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 04/27/2013] [Accepted: 05/06/2013] [Indexed: 11/18/2022]
Abstract
Barley stripe mosaic virus (BSMV) is the type member of the genus Hordeivirus, rigid, rod-shaped viruses in the family Virgaviridae. We have used fiber diffraction and cryo-electron microscopy to determine the helical symmetry of BSMV to be 23.2 subunits per turn of the viral helix, and to obtain a low-resolution model of the virus by helical reconstruction methods. Features in the model support a structural relationship between the coat proteins of the hordeiviruses and the tobamoviruses.
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Affiliation(s)
- Amy Kendall
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
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18
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Ksenofontov AL, Paalme V, Arutyunyan AM, Semenyuk PI, Fedorova NV, Rumvolt R, Baratova LA, Järvekülg L, Dobrov EN. Partially disordered structure in intravirus coat protein of potyvirus potato virus A. PLoS One 2013; 8:e67830. [PMID: 23844104 PMCID: PMC3700898 DOI: 10.1371/journal.pone.0067830] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 05/21/2013] [Indexed: 11/25/2022] Open
Abstract
Potyviruses represent the most biologically successful group of plant viruses, but to our knowledge, this work is the first detailed study of physicochemical characteristics of potyvirus virions. We measured the UV absorption, far and near UV circular dichroism spectra, intrinsic fluorescence spectra, and differential scanning calorimetry (DSC) melting curves of intact particles of a potato virus A (PVA). PVA virions proved to have a peculiar combination of physicochemical properties. The intravirus coat protein (CP) subunits were shown to contain an unusually high fraction of disordered structures, whereas PVA virions had an almost normal thermal stability. Upon heating from 20 °C to 55 °C, the fraction of disordered structures in the intravirus CP further increased, while PVA virions remained intact at up to 55 °C, after which their disruption (and DSC melting) started. We suggest that the structure of PVA virions below 55 °C is stabilized by interactions between the remaining structured segments of intravirus CP. It is not improbable that the biological efficiency of PVA relies on the disordered structure of intravirus CP.
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Affiliation(s)
- Alexander L. Ksenofontov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Viiu Paalme
- Institute of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
- Competence Center for Cancer Research, Tallinn, Estonia
| | - Alexander M. Arutyunyan
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Pavel I. Semenyuk
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Natalia V. Fedorova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Reet Rumvolt
- Institute of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
- Competence Center for Cancer Research, Tallinn, Estonia
| | - Ludmila A. Baratova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Lilian Järvekülg
- Institute of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
- Competence Center for Cancer Research, Tallinn, Estonia
| | - Eugeny N. Dobrov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
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