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Sae-Ueng U, Bunsuwansakul C, Showpanish K, Phironrit N, Thadajarassiri J, Nehls C. Nanomechanical resilience and thermal stability of RSJ2 phage. Sci Rep 2024; 14:19389. [PMID: 39169068 DOI: 10.1038/s41598-024-70056-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 08/12/2024] [Indexed: 08/23/2024] Open
Abstract
As the world moves toward a green economy and sustainable agriculture, bacterial viruses or bacteriophages (phages) become attractive biocontrol agents for controlling crop diseases. Effective utilization of phages in farms requires integrated knowledge of crops, pathogens, phages, and surroundings. Phages must encounter environmental fluctuations, including temperature, and must remain infectious for successful bacteria lysis. This work studied a soilborne RSJ2 phage discovered in Thailand, which can eliminate Ralstonia solanacearum, causing bacterial wilt disease in chili. We investigated how phage infectivity and nanomechanics responded to thermal changes. The plaque-based assay showed that the infectivity of the RSJ2 phage was stable within 24-40 °C, an average temperature fluctuation in tropical regions. The structural examination also showed that the phage remained intact. The nanomechanical property of the phage was inspected by the atomic force microscopy-based nanoindentation. The result revealed that the phage stiffness within 24-40 °C was statistically similar (0.05-0.06 N/m). Upon heating at 40 °C for 1, 5, and 10 h and resting at 25 °C, the stiffness of the phage particles increased to 0.09-0.11 N/m (54-83% increase). The stiffness results suggest structural adaptation of the protein subunits as a response to thermal alteration. The study exhibits that the phage structure is highly dynamic and can nanomechanically respond to varying temperatures. The phage stiffness may reveal insight into phage adaptation to environmental factors. Equipped with the knowledge of phage infectivity, structure, and nanomechanics, we can design practical guidelines for effective phage usage in farming and propelling green and safe agriculture.
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Affiliation(s)
- Udom Sae-Ueng
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand.
| | - Chooseel Bunsuwansakul
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Kittiya Showpanish
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Namthip Phironrit
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Jidapa Thadajarassiri
- Department of Mathematics, Faculty of Science, Srinakharinwirot University, Bangkok, 10110, Thailand
| | - Christians Nehls
- Research Center Borstel - Leibniz Lung Center (FZB), Borstel, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
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Fernandez de la Mora J, Almazán F, Rodríguez JM. Spontaneous Interconversion between Different Narrowly Defined Shapes of Rotavirus Double-Layered Particles Studied in Real Time by High-Resolution Mobility Analysis. Anal Chem 2023; 95:11483-11490. [PMID: 37463035 DOI: 10.1021/acs.analchem.3c01994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Rotavirus double-layered particles (DLPs) are studied in the gas phase with a high-resolution differential mobility analyzer (DMA). DLPs were transferred to 10 mM aqueous ammonium acetate, electrosprayed into the gas phase, converted into primarily singly charged particles, and DMA-analyzed. Up to seven slightly different conformations were resolved, whose apparently random, fast (minutes), and reversible interconversions were followed in real time. They sometimes evolved into just two distinct structures, with periods of one dominating over the other and vice versa. Differences between the DLP structures in solution and in the gas phase are clearly revealed by the smaller DLP diameter found here (60 versus 70 nm). Nevertheless, we argue that the multiple gas-phase conformers observed originate in as many conformations pre-existing in solution. We further hypothesize that these conformers correspond to incomplete DLPs having lost some of the VP6 trimer quintets surrounding each of the 12 5-fold axes. Instances of this peculiar loss have been previously documented by cryoelectron microscopy for the rotavirus Wa strain, as well as via charge detection mass spectrometry for five other rotavirus strains included in the RotaTec vaccine. Evidence of this loss systematically found for all 7 rotavirus types so far studied in aqueous ammonium acetate may be a special feature of this electrolyte.
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Affiliation(s)
- Juan Fernandez de la Mora
- Department of Mechanical Engineering and Materials Science, Yale University, 9 Hillhouse Avenue, New Haven, Connecticut 06520-8286, United States
| | - Fernando Almazán
- Department of Cellular and Molecular Biology, Centro Nacional de Biotecnología (CNB), CSIC, Darwin 3, 28049 Madrid, Spain
| | - Javier M Rodríguez
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB), CSIC, Darwin 3, 28049 Madrid, Spain
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Sae-Ueng U, Bhunchoth A, Phironrit N, Treetong A, Sapcharoenkun C, Chatchawankanphanich O, Leartsakulpanich U, Chitnumsub P. Thermoresponsive C22 phage stiffness modulates the phage infectivity. Sci Rep 2022; 12:13001. [PMID: 35906255 PMCID: PMC9338302 DOI: 10.1038/s41598-022-16795-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 07/15/2022] [Indexed: 12/01/2022] Open
Abstract
Bacteriophages offer a sustainable alternative for controlling crop disease. However, the lack of knowledge on phage infection mechanisms makes phage-based biological control varying and ineffective. In this work, we interrogated the temperature dependence of the infection and thermo-responsive behavior of the C22 phage. This soilborne podovirus is capable of lysing Ralstonia solanacearum, causing bacterial wilt disease. We revealed that the C22 phage could better infect the pathogenic host cell when incubated at low temperatures (25, 30 °C) than at high temperatures (35, 40 °C). Measurement of the C22 phage stiffness revealed that the phage stiffness at low temperatures was 2–3 times larger than at high temperatures. In addition, the imaging results showed that more C22 phage particles were attached to the cell surface at low temperatures than at high temperatures, associating the phage stiffness and the phage attachment. The result suggests that the structure and stiffness modulation in response to temperature change improve infection, providing mechanistic insight into the C22 phage lytic cycle. Our study signifies the need to understand phage responses to the fluctuating environment for effective phage-based biocontrol implementation.
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Affiliation(s)
- Udom Sae-Ueng
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand.
| | - Anjana Bhunchoth
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Namthip Phironrit
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Alongkot Treetong
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Chaweewan Sapcharoenkun
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Orawan Chatchawankanphanich
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Ubolsree Leartsakulpanich
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Penchit Chitnumsub
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
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4
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Dechant PP, He YH. Machine-learning a virus assembly fitness landscape. PLoS One 2021; 16:e0250227. [PMID: 33951035 PMCID: PMC8099058 DOI: 10.1371/journal.pone.0250227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 04/01/2021] [Indexed: 02/05/2023] Open
Abstract
Realistic evolutionary fitness landscapes are notoriously difficult to construct. A recent cutting-edge model of virus assembly consists of a dodecahedral capsid with 12 corresponding packaging signals in three affinity bands. This whole genome/phenotype space consisting of 312 genomes has been explored via computationally expensive stochastic assembly models, giving a fitness landscape in terms of the assembly efficiency. Using latest machine-learning techniques by establishing a neural network, we show that the intensive computation can be short-circuited in a matter of minutes to astounding accuracy.
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Affiliation(s)
- Pierre-Philippe Dechant
- School of Science, Technology & Health, York St John University, York, United Kingdom
- York Cross-disciplinary Centre for Systems Analysis, University of York, Heslington, United Kingdom
- Department of Mathematics, University of York, Heslington, United Kingdom
| | - Yang-Hui He
- Department of Mathematics, City, University of London, London, United Kingdom
- Merton College, University of Oxford, Oxford, United Kingdom
- School of Physics, NanKai University, Tianjin, P.R. China
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Emanuel MD, Cherstvy AG, Metzler R, Gompper G. Buckling transitions and soft-phase invasion of two-component icosahedral shells. Phys Rev E 2021; 102:062104. [PMID: 33465945 DOI: 10.1103/physreve.102.062104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 11/11/2020] [Indexed: 12/18/2022]
Abstract
What is the optimal distribution of two types of crystalline phases on the surface of icosahedral shells, such as of many viral capsids? We here investigate the distribution of a thin layer of soft material on a crystalline convex icosahedral shell. We demonstrate how the shapes of spherical viruses can be understood from the perspective of elasticity theory of thin two-component shells. We develop a theory of shape transformations of an icosahedral shell upon addition of a softer, but still crystalline, material onto its surface. We show how the soft component "invades" the regions with the highest elastic energy and stress imposed by the 12 topological defects on the surface. We explore the phase diagram as a function of the surface fraction of the soft material, the shell size, and the incommensurability of the elastic moduli of the rigid and soft phases. We find that, as expected, progressive filling of the rigid shell by the soft phase starts from the most deformed regions of the icosahedron. With a progressively increasing soft-phase coverage, the spherical segments of domes are filled first (12 vertices of the shell), then the cylindrical segments connecting the domes (30 edges) are invaded, and, ultimately, the 20 flat faces of the icosahedral shell tend to be occupied by the soft material. We present a detailed theoretical investigation of the first two stages of this invasion process and develop a model of morphological changes of the cone structure that permits noncircular cross sections. In conclusion, we discuss the biological relevance of some structures predicted from our calculations, in particular for the shape of viral capsids.
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Affiliation(s)
- Marc D Emanuel
- Theoretical Physics of Living Matter, Institute of Biological Information Processing, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.,Kavli Institute for Nanoscience, Technical University Delft, 2628 CJ Delft, Netherlands
| | - Andrey G Cherstvy
- Theoretical Physics of Living Matter, Institute of Biological Information Processing, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.,Institute for Physics & Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
| | - Ralf Metzler
- Institute for Physics & Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
| | - Gerhard Gompper
- Theoretical Physics of Living Matter, Institute of Biological Information Processing, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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Kernes J, Levine AJ. Effects of curvature on the propagation of undulatory waves in lower dimensional elastic materials. Phys Rev E 2021; 103:013002. [PMID: 33601515 DOI: 10.1103/physreve.103.013002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 12/16/2020] [Indexed: 06/12/2023]
Abstract
The mechanics of lower dimensional elastic structures depends strongly on the geometry of their stress-free state. Elastic deformations separate into in-plane stretching and lower energy out-of-plane bending deformations. For elastic structures with a curved stress-free state, these two elastic modes are coupled within linear elasticity. We investigate the effect of that curvature-induced coupling on wave propagation in lower dimensional elastic structures, focusing on the simplest example-a curved elastic rod in two dimensions. We focus only on the geometry-induced coupling between bending and longitudinal (in-plane) strain that is common to both rods in two dimensions and to elastic shells. We find that the dispersion relation of the waves becomes gapped in the presence of finite curvature; bending modes are absent below a frequency proportional to the curvature of the rod. By studying the scattering of undulatory waves off regions of uniform curvature, we find that undulatory waves with frequencies in the gap associated with the curved region tunnel through that curved region via conversion into compression waves. These results should be directly applicable to the spectrum and spatial distribution of phonon modes in a number of curved rod-like elastic solids, including carbon nanotubes and biopolymer filaments.
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Affiliation(s)
- Jonathan Kernes
- Department of Physics and Astronomy, UCLA, Los Angeles, California 90095-1596, USA
| | - Alex J Levine
- Department of Physics and Astronomy, UCLA, Los Angeles, California 90095-1596, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095-1596, USA
- Department of Computational Medicine, UCLA, Los Angeles, California 90095-1596, USA
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Bruinsma RF, Wuite GJL, Roos WH. Physics of viral dynamics. NATURE REVIEWS. PHYSICS 2021; 3:76-91. [PMID: 33728406 PMCID: PMC7802615 DOI: 10.1038/s42254-020-00267-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/20/2020] [Indexed: 05/12/2023]
Abstract
Viral capsids are often regarded as inert structural units, but in actuality they display fascinating dynamics during different stages of their life cycle. With the advent of single-particle approaches and high-resolution techniques, it is now possible to scrutinize viral dynamics during and after their assembly and during the subsequent development pathway into infectious viruses. In this Review, the focus is on the dynamical properties of viruses, the different physical virology techniques that are being used to study them, and the physical concepts that have been developed to describe viral dynamics.
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Affiliation(s)
- Robijn F. Bruinsma
- Department of Physics and Astronomy, University of California, Los Angeles, California, USA
| | - Gijs J. L. Wuite
- Fysica van levende systemen, Vrije Universiteit, Amsterdam, the Netherlands
| | - Wouter H. Roos
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, the Netherlands
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Singh AR, Košmrlj A, Bruinsma R. Finite Temperature Phase Behavior of Viral Capsids as Oriented Particle Shells. PHYSICAL REVIEW LETTERS 2020; 124:158101. [PMID: 32357054 PMCID: PMC7219451 DOI: 10.1103/physrevlett.124.158101] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 03/16/2020] [Indexed: 05/02/2023]
Abstract
A general phase plot is proposed for discrete particle shells that allows for thermal fluctuations of the shell geometry and of the inter-particle connectivities. The phase plot contains a first-order melting transition, a buckling transition, and a collapse transition and is used to interpret the thermodynamics of microbiological shells.
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Affiliation(s)
- Amit R Singh
- Department of Physics and Astronomy, Johns Hopkins University, Baltimore, Maryland 21218, USA
- Currently at Department of Mechanical Engineering, Birla Institute of Technology and Science, Pilani, Rajasthan 333031, India
| | - Andrej Košmrlj
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey 08540, USA
- Princeton Institute for the Science and Technology of Materials (PRISM), Princeton University, Princeton, New Jersey 08544, USA
| | - Robijn Bruinsma
- Departments of Physics and Astronomy, and Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
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