1
|
Imaging the Infection Cycle of T7 at the Single Virion Level. Int J Mol Sci 2022; 23:ijms231911252. [PMID: 36232552 PMCID: PMC9569847 DOI: 10.3390/ijms231911252] [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: 08/29/2022] [Revised: 09/17/2022] [Accepted: 09/21/2022] [Indexed: 11/17/2022] Open
Abstract
T7 phages are E. coli-infecting viruses that find and invade their target with high specificity and efficiency. The exact molecular mechanisms of the T7 infection cycle are yet unclear. As the infection involves mechanical events, single-particle methods are to be employed to alleviate the problems of ensemble averaging. Here we used TIRF microscopy to uncover the spatial dynamics of the target recognition and binding by individual T7 phage particles. In the initial phase, T7 virions bound reversibly to the bacterial membrane via two-dimensional diffusive exploration. Stable bacteriophage anchoring was achieved by tail-fiber complex to receptor binding which could be observed in detail by atomic force microscopy (AFM) under aqueous buffer conditions. The six anchored fibers of a given T7 phage-displayed isotropic spatial orientation. The viral infection led to the onset of an irreversible structural program in the host which occurred in three distinct steps. First, bacterial cell surface roughness, as monitored by AFM, increased progressively. Second, membrane blebs formed on the minute time scale (average ~5 min) as observed by phase-contrast microscopy. Finally, the host cell was lysed in a violent and explosive process that was followed by the quick release and dispersion of the phage progeny. DNA ejection from T7 could be evoked in vitro by photothermal excitation, which revealed that genome release is mechanically controlled to prevent premature delivery of host-lysis genes. The single-particle approach employed here thus provided an unprecedented insight into the details of the complete viral cycle.
Collapse
|
2
|
Delcanale P, Uriati E, Mariangeli M, Mussini A, Moreno A, Lelli D, Cavanna L, Bianchini P, Diaspro A, Abbruzzetti S, Viappiani C. The Interaction of Hypericin with SARS-CoV-2 Reveals a Multimodal Antiviral Activity. ACS APPLIED MATERIALS & INTERFACES 2022; 14:14025-14032. [PMID: 35302731 PMCID: PMC8972258 DOI: 10.1021/acsami.1c22439] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Hypericin is a photosensitizing drug that is active against membrane-enveloped viruses and therefore constitutes a promising candidate for the treatment of SARS-CoV-2 infections. The antiviral efficacy of hypericin is largely determined by its affinity toward viral components and by the number of active molecules loaded on single viruses. Here we use an experimental approach to follow the interaction of hypericin with SARS-CoV-2, and we evaluate its antiviral efficacy, both in the dark and upon photoactivation. Binding to viral particles is directly visualized with fluorescence microscopy, and a strong affinity for the viral particles, most likely for the viral envelope, is measured spectroscopically. The loading of a maximum of approximately 30 molecules per viral particle is estimated, despite with marked heterogeneity among particles. Because of this interaction, nanomolar concentrations of photoactivated hypericin substantially reduce virus infectivity on Vero E6 cells, but a partial effect is also observed in dark conditions, suggesting multiple mechanisms of action for this drug.
Collapse
Affiliation(s)
- Pietro Delcanale
- Dipartimento
di Scienze Matematiche, Fisiche e Informatiche, Università degli Studi di Parma, 43124 Parma, Italy
| | - Eleonora Uriati
- Dipartimento
di Scienze Matematiche, Fisiche e Informatiche, Università degli Studi di Parma, 43124 Parma, Italy
- Nanoscopy
@ Istituto Italiano di Tecnologia, 16152 Genova, Italy
| | - Matteo Mariangeli
- Dipartimento
di Scienze Matematiche, Fisiche e Informatiche, Università degli Studi di Parma, 43124 Parma, Italy
- Nanoscopy
@ Istituto Italiano di Tecnologia, 16152 Genova, Italy
| | - Andrea Mussini
- Dipartimento
di Scienze Matematiche, Fisiche e Informatiche, Università degli Studi di Parma, 43124 Parma, Italy
| | - Ana Moreno
- Istituto
Zooprofilattico Sperimentale della Lombardia e dell’Emilia
Romagna, 25124 Brescia, Italy
| | - Davide Lelli
- Istituto
Zooprofilattico Sperimentale della Lombardia e dell’Emilia
Romagna, 25124 Brescia, Italy
| | - Luigi Cavanna
- Dipartimento
di Oncologia-Ematologia, Azienda USL di
Piacenza, 29121 Piacenza, Italy
| | - Paolo Bianchini
- Nanoscopy
@ Istituto Italiano di Tecnologia, 16152 Genova, Italy
| | - Alberto Diaspro
- Nanoscopy
@ Istituto Italiano di Tecnologia, 16152 Genova, Italy
- DIFILAB,
Dipartimento di Fisica, Università
di Genova, 16146 Genova, Italy
| | - Stefania Abbruzzetti
- Dipartimento
di Scienze Matematiche, Fisiche e Informatiche, Università degli Studi di Parma, 43124 Parma, Italy
| | - Cristiano Viappiani
- Dipartimento
di Scienze Matematiche, Fisiche e Informatiche, Università degli Studi di Parma, 43124 Parma, Italy
| |
Collapse
|
3
|
Rousso I, Deshpande A. Applications of Atomic Force Microscopy in HIV-1 Research. Viruses 2022; 14:v14030648. [PMID: 35337055 PMCID: PMC8955997 DOI: 10.3390/v14030648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 12/10/2022] Open
Abstract
Obtaining an understanding of the mechanism underlying the interrelations between the structure and function of HIV-1 is of pivotal importance. In previous decades, this mechanism was addressed extensively in a variety of studies using conventional approaches. More recently, atomic force microscopy, which is a relatively new technique with unique capabilities, has been utilized to study HIV-1 biology. Atomic force microscopy can generate high-resolution images at the nanometer-scale and analyze the mechanical properties of individual HIV-1 virions, virus components (e.g., capsids), and infected live cells under near-physiological environments. This review describes the working principles and various imaging and analysis modes of atomic force microscopy, and elaborates on its distinctive contributions to HIV-1 research in areas such as mechanobiology and the physics of infection.
Collapse
|
4
|
Millar DP. Conformational Dynamics of DNA Polymerases Revealed at the Single-Molecule Level. Front Mol Biosci 2022; 9:826593. [PMID: 35281261 PMCID: PMC8913937 DOI: 10.3389/fmolb.2022.826593] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/20/2022] [Indexed: 12/25/2022] Open
Abstract
DNA polymerases are intrinsically dynamic macromolecular machines. The purpose of this review is to describe the single-molecule Förster resonance energy transfer (smFRET) methods that are used to probe the conformational dynamics of DNA polymerases, focusing on E. coli DNA polymerase I. The studies reviewed here reveal the conformational dynamics underpinning the nucleotide selection, proofreading and 5′ nuclease activities of Pol I. Moreover, the mechanisms revealed for Pol I are likely employed across the DNA polymerase family. smFRET methods have also been used to examine other aspects of DNA polymerase activity.
Collapse
|
5
|
Lyonnais S, Hénaut M, Neyret A, Merida P, Cazevieille C, Gros N, Chable-Bessia C, Muriaux D. Atomic force microscopy analysis of native infectious and inactivated SARS-CoV-2 virions. Sci Rep 2021; 11:11885. [PMID: 34088957 PMCID: PMC8178396 DOI: 10.1038/s41598-021-91371-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/26/2021] [Indexed: 12/14/2022] Open
Abstract
SARS-CoV-2 is an enveloped virus responsible for the Coronavirus Disease 2019 (COVID-19) pandemic. Here, single viruses were analyzed by atomic force microscopy (AFM) operating directly in a level 3 biosafety (BSL3) facility, which appeared as a fast and powerful method to assess at the nanoscale level and in 3D infectious virus morphology in its native conformation, or upon inactivation treatments. AFM imaging reveals structurally intact infectious and inactivated SARS-CoV-2 upon low concentration of formaldehyde treatment. This protocol combining AFM and plaque assays allows the preparation of intact inactivated SARS-CoV-2 particles for safe use of samples out of level 3 laboratory to accelerate researches against the COVID-19 pandemic. Overall, we illustrate how adapted BSL3-AFM is a remarkable toolbox for rapid and direct virus analysis based on nanoscale morphology.
Collapse
Affiliation(s)
| | - Mathilde Hénaut
- CEMIPAI, University of Montpellier, UAR3725 CNRS, Montpellier, France
| | - Aymeric Neyret
- CEMIPAI, University of Montpellier, UAR3725 CNRS, Montpellier, France
| | - Peggy Merida
- Institute of Research in Infectiology of Montpellier (IRIM), University of Montpellier, UMR9004 CNRS, Montpellier, France
| | - Chantal Cazevieille
- Institut des Neurosciences de Montpellier (INM), Université de Montpellier, Montpellier, France
| | - Nathalie Gros
- CEMIPAI, University of Montpellier, UAR3725 CNRS, Montpellier, France
| | | | - Delphine Muriaux
- CEMIPAI, University of Montpellier, UAR3725 CNRS, Montpellier, France.
- Institute of Research in Infectiology of Montpellier (IRIM), University of Montpellier, UMR9004 CNRS, Montpellier, France.
| |
Collapse
|
6
|
Arista-Romero M, Pujals S, Albertazzi L. Towards a Quantitative Single Particle Characterization by Super Resolution Microscopy: From Virus Structures to Antivirals Design. Front Bioeng Biotechnol 2021; 9:647874. [PMID: 33842446 PMCID: PMC8033170 DOI: 10.3389/fbioe.2021.647874] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/08/2021] [Indexed: 12/15/2022] Open
Abstract
In the last year the COVID19 pandemic clearly illustrated the potential threat that viruses pose to our society. The characterization of viral structures and the identification of key proteins involved in each step of the cycle of infection are crucial to develop treatments. However, the small size of viruses, invisible under conventional fluorescence microscopy, make it difficult to study the organization of protein clusters within the viral particle. The applications of super-resolution microscopy have skyrocketed in the last years, converting this group into one of the leading techniques to characterize viruses and study the viral infection in cells, breaking the diffraction limit by achieving resolutions up to 10 nm using conventional probes such as fluorescent dyes and proteins. There are several super-resolution methods available and the selection of the right one it is crucial to study in detail all the steps involved in the viral infection, quantifying and creating models of infection for relevant viruses such as HIV-1, Influenza, herpesvirus or SARS-CoV-1. Here we review the use of super-resolution microscopy (SRM) to study all steps involved in the viral infection and antiviral design. In light of the threat of new viruses, these studies could inspire future assays to unveil the viral mechanism of emerging viruses and further develop successful antivirals against them.
Collapse
Affiliation(s)
- Maria Arista-Romero
- Nanoscopy for Nanomedicine Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Silvia Pujals
- Nanoscopy for Nanomedicine Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Electronics and Biomedical Engineering, Faculty of Physics, Universitat de Barcelona, Barcelona, Spain
| | - Lorenzo Albertazzi
- Nanoscopy for Nanomedicine Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Biomedical Engineering, Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, Netherlands
| |
Collapse
|
7
|
Kiss B, Kis Z, Pályi B, Kellermayer MSZ. Topography, Spike Dynamics, and Nanomechanics of Individual Native SARS-CoV-2 Virions. NANO LETTERS 2021; 21:2675-2680. [PMID: 33474931 PMCID: PMC7839418 DOI: 10.1021/acs.nanolett.0c04465] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
SARS-CoV-2, the virus responsible for the current COVID-19 pandemic, displays a corona-shaped layer of spikes which play a fundamental role in the infection process. Recent structural data suggest that the spikes possess orientational freedom and the ribonucleoproteins segregate into basketlike structures. How these structural features regulate the dynamic and mechanical behavior of the native virion are yet unknown. By imaging and mechanically manipulating individual, native SARS-CoV-2 virions with atomic force microscopy, here, we show that their surface displays a dynamic brush owing to the flexibility and rapid motion of the spikes. The virions are highly compliant and able to recover from drastic mechanical perturbations. Their global structure is remarkably temperature resistant, but the virion surface becomes progressively denuded of spikes upon thermal exposure. The dynamics and the mechanics of SARS-CoV-2 are likely to affect its stability and interactions.
Collapse
Affiliation(s)
- Bálint Kiss
- Department
of Biophysics and Radiation Biology, Semmelweis
University, Tűzoltó str. 37-47, Budapest H-1094, Hungary
| | - Zoltán Kis
- National
Biosafety Laboratory, National Public Health
Center, Albert Flórián Rd 2-6, Budapest H-1097, Hungary
- Department
of Medical Microbiology, Semmelweis University, Nagyvárad Sq. 4, Budapest H-1089, Hungary
| | - Bernadett Pályi
- National
Biosafety Laboratory, National Public Health
Center, Albert Flórián Rd 2-6, Budapest H-1097, Hungary
| | - Miklós S. Z. Kellermayer
- Department
of Biophysics and Radiation Biology, Semmelweis
University, Tűzoltó str. 37-47, Budapest H-1094, Hungary
- Hungarian
Centre of Excellence for Molecular Medicine (HCEMM), In Vivo Imaging Advanced Core Facility, Budapest H-1094, Hungary
| |
Collapse
|
8
|
Abstract
After first describing the issue contents (Biophysical Reviews-Volume 12 Issue 6), this Editorial goes on to provide a short round-up of the activities of the journal in 2020. Directly following this Editorial are two obituaries marking the recent deaths of Prof. Fumio Oosawa (Japan) and Dr. Herbert Tabor (USA)-two major figures in Biophysical/Biochemical science from the last 100 years.
Collapse
Affiliation(s)
- Damien Hall
- Department of Life Sciences and Applied Chemistry, Nagoya Institute of Technology, Gokiso Showa, Nagoya, 466-8555 Japan
| |
Collapse
|
9
|
Hall D. Biophysical Reviews: a Q1 ranked journal in biophysics and structural biology. Biophys Rev 2020; 12:1085-1089. [PMID: 32996081 PMCID: PMC7523689 DOI: 10.1007/s12551-020-00764-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/18/2020] [Indexed: 02/08/2023] Open
Abstract
This Editorial for Biophysical Reviews (Volume 12, Issue 5) begins with a description of the two feature articles. The first being the latest in the "Meet the Editors Series" describing Rosangela Itri-the Biophysical Reviews Executive Editor responsible for the South American region. The second feature article is by Alexandra Zidovska, the inaugural winner of the 2020 "Michèle Auger Award for Young Scientists' Independent Research." Next highlighted are the Issue contents, which consist of five Commentaries/Letters and eleven Reviews. Finally, we conclude with a description of Biophysical Reviews' ascension within the world's major journal rankings index (Elsevier, Scimago)-becoming 12th overall (out of 156) within the biophysics category and receiving the coveted Q1 rating in both biophysics and structural biology sections.
Collapse
Affiliation(s)
- Damien Hall
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso Showa, Nagoya, Aichi, 466-8555, Japan.
| |
Collapse
|