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Ciminski K, Flore V, Jakob C, Mues H, Smedegaard Frederiksen A, Schwemmle M, Bolte H, Giese S. Functionality of IAV packaging signals depends on site-specific charges within the viral nucleoprotein. J Virol 2024; 98:e0197223. [PMID: 38470155 PMCID: PMC11019843 DOI: 10.1128/jvi.01972-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/20/2024] [Indexed: 03/13/2024] Open
Abstract
The coordinated packaging of the segmented genome of the influenza A virus (IAV) into virions is an essential step of the viral life cycle. This process is controlled by the interaction of packaging signals present in all eight viral RNA (vRNA) segments and the viral nucleoprotein (NP), which binds vRNA via a positively charged binding groove. However, mechanistic models of how the packaging signals and NP work together to coordinate genome packaging are missing. Here, we studied genome packaging in influenza A/SC35M virus mutants that carry mutated packaging signals as well as specific amino acid substitutions at the highly conserved lysine (K) residues 184 and 229 in the RNA-binding groove of NP. Because these lysines are acetylated and thus neutrally charged in infected host cells, we replaced them with glutamine to mimic the acetylated, neutrally charged state or arginine to mimic the non-acetylated, positively charged state. Our analysis shows that the coordinated packaging of eight vRNAs is influenced by (i) the charge state of the replacing amino acid and (ii) its location within the RNA-binding groove. Accordingly, we propose that lysine acetylation induces different charge states within the RNA-binding groove of NP, thereby supporting the activity of specific packaging signals during coordinated genome packaging. IMPORTANCE Influenza A viruses (IAVs) have a segmented viral RNA (vRNA) genome encapsidated by multiple copies of the viral nucleoprotein (NP) and organized into eight distinct viral ribonucleoprotein complexes. Although genome segmentation contributes significantly to viral evolution and adaptation, it requires a highly sophisticated genome-packaging mechanism. How eight distinct genome complexes are incorporated into the virion is poorly understood, but previous research suggests an essential role for both vRNA packaging signals and highly conserved NP amino acids. By demonstrating that the packaging process is controlled by charge-dependent interactions of highly conserved lysine residues in NP and vRNA packaging signals, our study provides new insights into the sophisticated packaging mechanism of IAVs.
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Affiliation(s)
- Kevin Ciminski
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Viktoria Flore
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Celia Jakob
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Helen Mues
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Anne Smedegaard Frederiksen
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Martin Schwemmle
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Hardin Bolte
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sebastian Giese
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
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Das S, Parray HA, Chiranjivi AK, Kumar P, Goswami A, Bansal M, Rathore DK, Kumar R, Samal S. Kennedy Epitope (KE)-dependent Retrograde Transport of Efficiently Cleaved HIV-1 Envelopes (Envs) and its Effect on Env Cell Surface Expression and Viral Particle Formation. Protein J 2024; 43:375-386. [PMID: 37794304 DOI: 10.1007/s10930-023-10161-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2023] [Indexed: 10/06/2023]
Abstract
Efficiently cleaved HIV-1 Envs are the closest mimics of functional Envs as they specifically expose only bNAb (broadly neutralizing antibody) epitopes and not non-neutralizing ones, making them suitable for developing vaccine immunogens. We have previously identified several efficiently cleaved Envs from clades A, B, C and B/C. We also described that truncation of the CT (C-terminal tail) of a subset of these Envs, but not others, impairs their ectodomain conformation/antigenicity on the cell surface in a CT conserved hydrophilic domain (CHD) or Kennedy epitope (KE)-dependent manner. Here, we report that those Envs (4 - 2.J41 and JRCSF), whose native-like ectodomain conformation/antigenicity on the cell surface is disrupted upon CT truncation, but not other Envs like JRFL, whose CT truncation does not have an effect on ectodomain integrity on the cell surface, are also defective in retrograde transport from early to late endosomes. Restoration of the CHD/KE in the CT of these Envs restores wild-type levels of distribution between early and late endosomes. In the presence of retrograde transport inhibitor Retro 2, cell surface expression of 4 - 2.J41 and JRCSF Envs increases [as does in the presence of Rab7a DN and Rab7b DN (DN: dominant negative)] but particle formation decreases for 4 - 2.J41 and JRCSF Env pseudotyped viruses. Our results show for the first time a correlation between CT-dependent, CHD/KE regulated retrograde transport and cell surface expression/viral particle formation of these efficiently cleaved Envs. Based on our results we hypothesize that a subset of these efficiently cleaved Envs use a CT-dependent, CHD/KE-mediated mechanism for assembly and release from late endosomes.
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Affiliation(s)
- Supratik Das
- Infection and Immunology, Translational Research Program, 3rd Milestone, Faridabad-Gurgaon Expressway, PO box #04, Faridabad, 121001, Haryana, India.
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, PO box #04, Faridabad, 121001, Haryana, India.
| | - Hilal Ahmad Parray
- Infection and Immunology, Translational Research Program, 3rd Milestone, Faridabad-Gurgaon Expressway, PO box #04, Faridabad, 121001, Haryana, India
| | - Adarsh Kumar Chiranjivi
- Infection and Immunology, Translational Research Program, 3rd Milestone, Faridabad-Gurgaon Expressway, PO box #04, Faridabad, 121001, Haryana, India
| | - Prince Kumar
- Infection and Immunology, Translational Research Program, 3rd Milestone, Faridabad-Gurgaon Expressway, PO box #04, Faridabad, 121001, Haryana, India
| | - Abhishek Goswami
- Infection and Immunology, Translational Research Program, 3rd Milestone, Faridabad-Gurgaon Expressway, PO box #04, Faridabad, 121001, Haryana, India
| | - Manish Bansal
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, PO box #04, Faridabad, 121001, Haryana, India
| | - Deepak Kumar Rathore
- Infection and Immunology, Translational Research Program, 3rd Milestone, Faridabad-Gurgaon Expressway, PO box #04, Faridabad, 121001, Haryana, India
| | - Rajesh Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology - Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Sweety Samal
- Infection and Immunology, Translational Research Program, 3rd Milestone, Faridabad-Gurgaon Expressway, PO box #04, Faridabad, 121001, Haryana, India
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3
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Coshic K, Maffeo C, Winogradoff D, Aksimentiev A. The structure and physical properties of a packaged bacteriophage particle. Nature 2024; 627:905-914. [PMID: 38448589 DOI: 10.1038/s41586-024-07150-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 02/01/2024] [Indexed: 03/08/2024]
Abstract
A string of nucleotides confined within a protein capsid contains all the instructions necessary to make a functional virus particle, a virion. Although the structure of the protein capsid is known for many virus species1,2, the three-dimensional organization of viral genomes has mostly eluded experimental probes3,4. Here we report all-atom structural models of an HK97 virion5, including its entire 39,732 base pair genome, obtained through multiresolution simulations. Mimicking the action of a packaging motor6, the genome was gradually loaded into the capsid. The structure of the packaged capsid was then refined through simulations of increasing resolution, which produced a 26 million atom model of the complete virion, including water and ions confined within the capsid. DNA packaging occurs through a loop extrusion mechanism7 that produces globally different configurations of the packaged genome and gives each viral particle individual traits. Multiple microsecond-long all-atom simulations characterized the effect of the packaged genome on capsid structure, internal pressure, electrostatics and diffusion of water, ions and DNA, and revealed the structural imprints of the capsid onto the genome. Our approach can be generalized to obtain complete all-atom structural models of other virus species, thereby potentially revealing new drug targets at the genome-capsid interface.
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Affiliation(s)
- Kush Coshic
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Christopher Maffeo
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - David Winogradoff
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Aleksei Aksimentiev
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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4
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Jih J, Liu YT, Liu W, Zhou ZH. The incredible bulk: Human cytomegalovirus tegument architectures uncovered by AI-empowered cryo-EM. Sci Adv 2024; 10:eadj1640. [PMID: 38394211 PMCID: PMC10889378 DOI: 10.1126/sciadv.adj1640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 01/22/2024] [Indexed: 02/25/2024]
Abstract
The compartmentalization of eukaryotic cells presents considerable challenges to the herpesvirus life cycle. The herpesvirus tegument, a bulky proteinaceous aggregate sandwiched between herpesviruses' capsid and envelope, is uniquely evolved to address these challenges, yet tegument structure and organization remain poorly characterized. We use deep-learning-enhanced cryogenic electron microscopy to investigate the tegument of human cytomegalovirus virions and noninfectious enveloped particles (NIEPs; a genome packaging-aborted state), revealing a portal-biased tegumentation scheme. We resolve atomic structures of portal vertex-associated tegument (PVAT) and identify multiple configurations of PVAT arising from layered reorganization of pUL77, pUL48 (large tegument protein), and pUL47 (inner tegument protein) assemblies. Analyses show that pUL77 seals the last-packaged viral genome end through electrostatic interactions, pUL77 and pUL48 harbor a head-linker-capsid-binding motif conducive to PVAT reconfiguration, and pUL47/48 dimers form 45-nm-long filaments extending from the portal vertex. These results provide a structural framework for understanding how herpesvirus tegument facilitates and evolves during processes spanning viral genome packaging to delivery.
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Affiliation(s)
- Jonathan Jih
- Molecular Biology Institute, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Yun-Tao Liu
- California NanoSystems Institute, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Wei Liu
- California NanoSystems Institute, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Z. Hong Zhou
- Molecular Biology Institute, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
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5
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Dai YC, Yeh SY, Cheng YY, Huang WH, Liou GG, Yang TY, Chang CY, Fang TF, Chang CW, Su MT, Lee CP, Chen MR. BGLF4 kinase regulates the formation of the EBV cytoplasmic assembly compartment and the recruitment of cellular IQGAP1 for virion release. J Virol 2024; 98:e0189923. [PMID: 38294245 PMCID: PMC10878254 DOI: 10.1128/jvi.01899-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 12/26/2023] [Indexed: 02/01/2024] Open
Abstract
After Epstein-Barr virus (EBV) genome replication and encapsidation in the nucleus, nucleocapsids are translocated into the cytoplasm for subsequent tegumentation and maturation. The EBV BGLF4 kinase, which induces partial disassembly of the nuclear lamina, and the nuclear egress complex BFRF1/BFLF2 coordinately facilitate the nuclear egress of nucleocapsids. Here, we demonstrate that within EBV reactivated epithelial cells, viral capsids, tegument proteins, and glycoproteins are clustered in the juxtanuclear concave region, accompanied by redistributed cytoplasmic organelles and the cytoskeleton regulator IQ-domain GTPase-activation protein 1 (IQGAP1), close to the microtubule-organizing center (MTOC). The assembly compartment (AC) structure was diminished in BGLF4-knockdown TW01-EBV cells and BGLF4-knockout bacmid-carrying TW01 cells, suggesting that the formation of AC structure is BGLF4-dependent. Notably, glycoprotein gp350/220 was observed by confocal imaging to be distributed in the perinuclear concave region and surrounded by the endoplasmic reticulum (ER) membrane marker calnexin, indicating that the AC may be located within a globular structure derived from ER membranes, adjacent to the outer nuclear membrane. Moreover, the viral capsid protein BcLF1 and tegument protein BBLF1 were co-localized with IQGAP1 near the cytoplasmic membrane in the late stage of replication. Knockdown of IQGAP1 did not affect the AC formation but decreased virion release from both TW01-EBV and Akata+ cells, suggesting IQGAP1-mediated trafficking regulates EBV virion release. The data presented here show that BGLF4 is required for cytoskeletal rearrangement, coordination with the redistribution of cytoplasmic organelles and IQGAP1 for virus maturation, and subsequent IQGAP1-dependent virion release.IMPORTANCEEBV genome is replicated and encapsidated in the nucleus, and the resultant nucleocapsids are translocated to the cytoplasm for subsequent virion maturation. We show that a cytoplasmic AC, containing viral proteins, markers of the endoplasmic reticulum, Golgi, and endosomes, is formed in the juxtanuclear region of epithelial and B cells during EBV reactivation. The viral BGLF4 kinase contributes to the formation of the AC. The cellular protein IQGAP1 is also recruited to the AC and partially co-localizes with the virus capsid protein BcLF1 and tegument protein BBLF1 in EBV-reactivated cells, dependent on the BGLF4-induced cytoskeletal rearrangement. In addition, virion release was attenuated in IQGAP1-knockdown epithelial and B cells after reactivation, suggesting that IQGAP1-mediated trafficking may regulate the efficiency of virus maturation and release.
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Affiliation(s)
- Yu-Ching Dai
- Graduate Institute and Department of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Szu-Yun Yeh
- Graduate Institute and Department of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yi-Ying Cheng
- Graduate Institute and Department of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Wei-Han Huang
- Graduate Institute and Department of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Gunn-Guang Liou
- Office of Research and Development, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Tsung-Yu Yang
- Graduate Institute and Department of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chao-Yuan Chang
- Graduate Institute and Department of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Tien-Fang Fang
- Graduate Institute and Department of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chou-Wei Chang
- Graduate Institute and Department of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Mei-Tzu Su
- Graduate Institute and Department of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chung-Pei Lee
- School of Nursing, National Taipei University of Nursing and Health Sciences, Taipei, Taiwan
| | - Mei-Ru Chen
- Graduate Institute and Department of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
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6
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De Castro E, Hulo C, Masson P, Auchincloss A, Bridge A, Le Mercier P. ViralZone 2024 provides higher-resolution images and advanced virus-specific resources. Nucleic Acids Res 2024; 52:D817-D821. [PMID: 37897348 PMCID: PMC10767872 DOI: 10.1093/nar/gkad946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/09/2023] [Accepted: 10/12/2023] [Indexed: 10/30/2023] Open
Abstract
ViralZone (http://viralzone.expasy.org) is a knowledge repository for viruses that links biological knowledge and databases. It contains data on virion structure, genome, proteome, replication cycle and host-virus interactions. The new update provides better access to the data through contextual popups and higher resolution images in Scalable Vector Graphics (SVG) format. These images are designed to be dynamic and interactive with human viruses to give users better access to the data. In addition, a new coronavirus-specific resource provides regularly updated data on variants and molecular biology of SARS-CoV-2. Other virus-specific resources have been added to the database, particularly for HIV, herpesviruses and poxviruses.
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Affiliation(s)
- Edouard De Castro
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, CMU, 1 Michel Servet, 1211 Geneva 4, Switzerland
| | - Chantal Hulo
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, CMU, 1 Michel Servet, 1211 Geneva 4, Switzerland
| | - Patrick Masson
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, CMU, 1 Michel Servet, 1211 Geneva 4, Switzerland
| | - Andrea Auchincloss
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, CMU, 1 Michel Servet, 1211 Geneva 4, Switzerland
| | - Alan Bridge
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, CMU, 1 Michel Servet, 1211 Geneva 4, Switzerland
| | - Philippe Le Mercier
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, CMU, 1 Michel Servet, 1211 Geneva 4, Switzerland
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7
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Lorenzi A, Arvin MJ, Burke GR, Strand MR. Functional characterization of Microplitis demolitor bracovirus genes that encode nucleocapsid components. J Virol 2023; 97:e0081723. [PMID: 37877717 PMCID: PMC10688341 DOI: 10.1128/jvi.00817-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 09/19/2023] [Indexed: 10/26/2023] Open
Abstract
IMPORTANCE Understanding how bracoviruses (BVs) function in wasps is of broad interest in the study of virus evolution. This study characterizes most of the Microplitis demolitor bracovirus (MdBV) genes whose products are nucleocapsid components. Results indicate several genes unknown outside of nudiviruses and BVs are essential for normal capsid assembly. Results also indicate most MdBV tyrosine recombinase family members and the DNA binding protein p6.9-1 are required for DNA processing and packaging into nucleocapsids.
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Affiliation(s)
- Ange Lorenzi
- Department of Entomology, University of Georgia, Athens, Georgia, USA
| | - Michael J. Arvin
- Department of Entomology, University of Georgia, Athens, Georgia, USA
| | - Gaelen R. Burke
- Department of Entomology, University of Georgia, Athens, Georgia, USA
| | - Michael R. Strand
- Department of Entomology, University of Georgia, Athens, Georgia, USA
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8
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Rochal SB, Konevtsova OV, Golushko IY, Podgornik R. Close packings of identical proteins in small spherical capsids and similar proteinaceous shells. Soft Matter 2023; 19:8649-8658. [PMID: 37921635 DOI: 10.1039/d3sm01106b] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
Understanding the principles governing protein arrangement in viral capsids and structurally similar protein shells can enable the development of new antiviral strategies and the design of artificial protein cages for various applications. We study these principles within the context of the close packing problem, by analyzing dozens of small spherical shells assembled from a single type of protein. First, we use icosahedral spherical close packings containing 60T identical disks, where T ≤ 4, to rationalize the protein arrangement in twenty real icosahedral shells both satisfying and violating the paradigmatic Caspar-Klug model. We uncover a striking correspondence between the protein mass centers in the considered shells and the centers of disks in the close packings. To generalize the packing model, we consider proteins with a weak shape anisotropy and propose an interaction energy, minimization of which allows us to obtain spherical dense packings of slightly anisotropic structural units. In the case of strong anisotropy, we model the proteins as sequences of overlapping discs of different sizes, with minimum energy configuration not only resulting in packings, accurately reproducing locations and orientations of individual proteins, but also revealing that icosahedral packings that display the handedness of real capsids are energetically more favorable. Finally, by introducing effective disc charges, we rationalize the formation of inter-protein bonds in protein shells.
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Affiliation(s)
- Sergei B Rochal
- Physics Faculty, Southern Federal University, Rostov-on-Don, Russia.
| | - Olga V Konevtsova
- Physics Faculty, Southern Federal University, Rostov-on-Don, Russia.
| | - Ivan Yu Golushko
- Physics Faculty, Southern Federal University, Rostov-on-Don, Russia.
| | - Rudolf Podgornik
- School of Physical Sciences and Kavli Institute for Theoretical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
- CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- Wenzhou Institute of the University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
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9
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Farafonov VS, Stich M, Nerukh DA. Complete Virion Simulated: All-Atom Model of an MS2 Bacteriophage with Native Genome. J Chem Theory Comput 2023; 19:7924-7933. [PMID: 37856311 DOI: 10.1021/acs.jctc.3c00846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
For the first time, a complete all-atom molecular dynamics (MD) model of a virus, bacteriophage MS2, in its entirety, including a protein outer shell, native genomic RNA with necessary divalent ions, and surrounding explicit aqueous solution with ions at physiological concentration, was built. The model is based on an experimentally measured cryo-EM structure, which was substantially augmented by reconstructing missing or low-resolution parts of the measured density (where the atomistic structure cannot be fit unambiguously). The model was tested by a quarter of a microsecond MD run, and various biophysical characteristics are obtained and analyzed. The developed methodology of building the model can be used for reconstructing other large biomolecular structures when experimental data are fragmented and/or of varying resolution, while the model itself can be used for studying the biology of MS2, including the dynamics of its interaction with the host bacteria.
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Affiliation(s)
- Vladimir S Farafonov
- Department of Physical Chemistry, V. N. Karazin Kharkiv National University, Kharkiv 61022, Ukraine
- Department of Mathematics, Aston University, Birmingham B4 7ET, U.K
| | - Michael Stich
- Department of Mathematics, Aston University, Birmingham B4 7ET, U.K
- Área de Matemática Aplicada, Departamento de Matemática Aplicada, Ciencia e Ingeniería de Materiales y Tecnología Electrónica, Universidad Rey Juan Carlos, C. Tulipán s/n, Móstoles, Madrid 28933, Spain
| | - Dmitry A Nerukh
- Department of Mathematics, Aston University, Birmingham B4 7ET, U.K
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Lao Z, Li Y, Mi X, Tang Q, Li J, Chen Y, Yang Y. Synthetic pentatrideca-valent triazolylsialoside inhibits influenza virus hemagglutinin/neuraminidase and aggregates virion particles. Eur J Med Chem 2023; 259:115578. [PMID: 37467617 DOI: 10.1016/j.ejmech.2023.115578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 07/21/2023]
Abstract
A synthetic multivalent hemagglutinin and neuraminidase inhibitor was developed by the conjugation of a septa-valent triazolylsialoside to bovine serum albumin using di-(N-succinimidyl) adipate. Matrixassisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) confirmed the attachment of five septa-valent sialyl lactosides to the protein backbone, resulting in a pentatrideca-valent sialyl conjugate. This pseudo-glycoprotein demonstrated a high affinity for hemagglutinin/neuraminidase as well as for the drug-resistant NA mutation on the influenza virus surface due to the cluster effect. The conjugate also exhibited potent antiviral activity against a wide range of virus strains without cytotoxicity at high concentrations. Mechanistic studies revealed that the pentatrideca-valent sialyl conjugate bound strongly to the influenza virion particles through interactions with HA/NA on the virion surfaces. The KD of the interaction was approximately 1 μM, as determined by isothermal calorimetric titration, allowing the capture and trapping of the influenza virions and preventing their further infection of host cells. These findings provide insight into the development of new antiviral agents using multivalent sialic acid clusters.
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Affiliation(s)
- Zhiqi Lao
- Department of Medical Laboratory, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong, 518020, China; Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, 510632, China
| | - Yang Li
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, No. 29, 13th Avenue, TEDA, Tianjin, 300457, China
| | - Xue Mi
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, No. 29, 13th Avenue, TEDA, Tianjin, 300457, China
| | - Qi Tang
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, No. 29, 13th Avenue, TEDA, Tianjin, 300457, China
| | - Jie Li
- Department of Plastic and Reconstructive Surgery, Ninth People's Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200011, China.
| | - Yue Chen
- Department of Medical Laboratory, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong, 518020, China.
| | - Yang Yang
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, No. 29, 13th Avenue, TEDA, Tianjin, 300457, China.
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11
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Li W, Qin Z, Nand E, Grunst MW, Grover JR, Bess JW, Lifson JD, Zwick MB, Tagare HD, Uchil PD, Mothes W. HIV-1 Env trimers asymmetrically engage CD4 receptors in membranes. Nature 2023; 623:1026-1033. [PMID: 37993716 PMCID: PMC10686830 DOI: 10.1038/s41586-023-06762-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 10/19/2023] [Indexed: 11/24/2023]
Abstract
Human immunodeficiency virus 1 (HIV-1) infection is initiated by binding of the viral envelope glycoprotein (Env) to the cell-surface receptor CD41-4. Although high-resolution structures of Env in a complex with the soluble domains of CD4 have been determined, the binding process is less understood in native membranes5-13. Here we used cryo-electron tomography to monitor Env-CD4 interactions at the membrane-membrane interfaces formed between HIV-1 and CD4-presenting virus-like particles. Env-CD4 complexes organized into clusters and rings, bringing the opposing membranes closer together. Env-CD4 clustering was dependent on capsid maturation. Subtomogram averaging and classification revealed that Env bound to one, two and finally three CD4 molecules, after which Env adopted an open state. Our data indicate that asymmetric HIV-1 Env trimers bound to one and two CD4 molecules are detectable intermediates during virus binding to host cell membranes, which probably has consequences for antibody-mediated immune responses and vaccine immunogen design.
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Affiliation(s)
- Wenwei Li
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA.
| | - Zhuan Qin
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Elizabeth Nand
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Michael W Grunst
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Jonathan R Grover
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Julian W Bess
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Michael B Zwick
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Hemant D Tagare
- Department of Radiology and Biomedical Imaging, Yale University, New Haven, CT, USA
| | - Pradeep D Uchil
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA.
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12
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Hou YN, Jin YQ, Zhang XF, Tang F, Hou JW, Liu ZM, Han ZB, Zhang H, Du LF, Shao S, Su JG, Liang Y, Zhang J, Li QM. Chimeric virus-like particles of human norovirus constructed by structure-guided epitope grafting elicit cross-reactive immunity against both GI.1 and GII.4 genotypes. J Virol 2023; 97:e0093823. [PMID: 37792003 PMCID: PMC10617407 DOI: 10.1128/jvi.00938-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 08/14/2023] [Indexed: 10/05/2023] Open
Abstract
IMPORTANCE Human norovirus (HuNoV) is highly infectious and can result in severe illnesses in the elderly and children. So far, there is no effective antiviral drug to treat HuNoV infection, and thus, the development of HuNoV vaccines is urgent. However, NoV evolves rapidly, and currently, at least 10 genogroups with numerous genotypes have been found. The genetic diversity of NoV and the lack of cross-protection between different genotypes pose challenges to the development of broadly protective vaccines. In this study, guided by structural alignment between GI.1 and GII.4 HuNoV VP1 proteins, several chimeric-type virus-like particles (VLPs) were designed through surface-exposed loop grafting. Mouse immunization studies show that two of the designed chimeric VLPs induced cross-immunity against both GI.1 and GII.4 HuNoVs. To our knowledge, this is the first designed chimeric VLPs that can induce cross-immune activities across different genogroups of HuNoV, which provides valuable strategies for the development of cross-reactive HuNoV vaccines.
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Affiliation(s)
- Ya Nan Hou
- The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China
- National Engineering Center for New Vaccine Research, Beijing, China
| | - Yu Qin Jin
- The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China
- National Engineering Center for New Vaccine Research, Beijing, China
| | - Xue Feng Zhang
- The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China
- National Engineering Center for New Vaccine Research, Beijing, China
| | - Fang Tang
- The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China
- National Engineering Center for New Vaccine Research, Beijing, China
| | - Jun Wei Hou
- The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China
- National Engineering Center for New Vaccine Research, Beijing, China
| | - Zhao Ming Liu
- The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China
- National Engineering Center for New Vaccine Research, Beijing, China
| | - Zi Bo Han
- The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China
- National Engineering Center for New Vaccine Research, Beijing, China
| | - Hao Zhang
- The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China
- National Engineering Center for New Vaccine Research, Beijing, China
| | - Li Fang Du
- The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China
- National Engineering Center for New Vaccine Research, Beijing, China
| | - Shuai Shao
- The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China
- National Engineering Center for New Vaccine Research, Beijing, China
| | - Ji Guo Su
- National Engineering Center for New Vaccine Research, Beijing, China
- High Performance Computing Center, National Vaccine and Serum Institute (NVSI), Beijing, China
| | - Yu Liang
- The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China
- National Engineering Center for New Vaccine Research, Beijing, China
| | - Jing Zhang
- The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China
- National Engineering Center for New Vaccine Research, Beijing, China
| | - Qi Ming Li
- The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China
- National Engineering Center for New Vaccine Research, Beijing, China
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13
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Rao PG, Lambert GS, Upadhyay C. Broadly neutralizing antibody epitopes on HIV-1 particles are exposed after virus interaction with host cells. J Virol 2023; 97:e0071023. [PMID: 37681958 PMCID: PMC10537810 DOI: 10.1128/jvi.00710-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/07/2023] [Indexed: 09/09/2023] Open
Abstract
The envelope (Env) glycoproteins on HIV-1 virions are the sole target of broadly neutralizing antibodies (bNAbs) and the focus of vaccines. However, many cross-reactive conserved epitopes are often occluded on virus particles, contributing to the evasion of humoral immunity. This study aimed to identify the Env epitopes that are exposed/occluded on HIV-1 particles and to investigate the mechanisms contributing to their masking. Using a flow cytometry-based assay, three HIV-1 isolates, and a panel of antibodies, we show that only select epitopes, including V2i, the gp120-g41 interface, and gp41-MPER, are accessible on HIV-1 particles, while V3, V2q, and select CD4bs epitopes are masked. These epitopes become accessible after allosteric conformational changes are induced by the pre-binding of select Abs, prompting us to test if similar conformational changes are required for these Abs to exhibit their neutralization capability. We tested HIV-1 neutralization where the virus-mAb mix was pre-incubated/not pre-incubated for 1 hour prior to adding the target cells. Similar levels of neutralization were observed under both assay conditions, suggesting that the interaction between virus and target cells sensitizes the virions for neutralization via bNAbs. We further show that lectin-glycan interactions can also expose these epitopes. However, this effect is dependent on the lectin specificity. Given that, bNAbs are ideal for providing sterilizing immunity and are the goal of current HIV-1 vaccine efforts, these data offer insight on how HIV-1 may occlude these vulnerable epitopes from the host immune response. In addition, the findings can guide the formulation of effective antibody combinations for therapeutic use. IMPORTANCE The human immunodeficiency virus (HIV-1) envelope (Env) glycoprotein mediates viral entry and is the sole target of neutralizing antibodies. Our data suggest that antibody epitopes including V2q (e.g., PG9, PGT145), CD4bs (e.g., VRC01, 3BNC117), and V3 (2219, 2557) are masked on HIV-1 particles. The PG9 and 2219 epitopes became accessible for binding after conformational unmasking was induced by the pre-binding of select mAbs. Attempts to understand the masking mechanism led to the revelation that interaction between virus and host cells is needed to sensitize the virions for neutralization by broadly neutralizing antibodies (bNAbs). These data provide insight on how bNAbs may gain access to these occluded epitopes to exert their neutralization effects and block HIV-1 infection. These findings have important implications for the way we evaluate the neutralizing efficacy of antibodies and can potentially guide vaccine design.
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Affiliation(s)
- Priyanka Gadam Rao
- Division of Infectious Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Gregory S. Lambert
- Division of Infectious Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Chitra Upadhyay
- Division of Infectious Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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14
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Wallace S, Kartau M, Kakkar T, Davis C, Szemiel A, Samardzhieva I, Vijayakrishnan S, Cole S, De Lorenzo G, Maillart E, Gautier K, Lapthorn AJ, Patel AH, Gadegaard N, Kadodwala M, Hutchinson E, Karimullah AS. Multiplexed Biosensing of Proteins and Virions with Disposable Plasmonic Assays. ACS Sens 2023; 8:3338-3348. [PMID: 37610841 PMCID: PMC10521139 DOI: 10.1021/acssensors.2c02238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 08/08/2023] [Indexed: 08/25/2023]
Abstract
Our growing ability to tailor healthcare to the needs of individuals has the potential to transform clinical treatment. However, the measurement of multiple biomarkers to inform clinical decisions requires rapid, effective, and affordable diagnostics. Chronic diseases and rapidly evolving pathogens in a larger population have also escalated the need for improved diagnostic capabilities. Current chemical diagnostics are often performed in centralized facilities and are still dependent on multiple steps, molecular labeling, and detailed analysis, causing the result turnaround time to be over hours and days. Rapid diagnostic kits based on lateral flow devices can return results quickly but are only capable of detecting a handful of pathogens or markers. Herein, we present the use of disposable plasmonics with chiroptical nanostructures as a platform for low-cost, label-free optical biosensing with multiplexing and without the need for flow systems often required in current optical biosensors. We showcase the detection of SARS-CoV-2 in complex media as well as an assay for the Norovirus and Zika virus as an early developmental milestone toward high-throughput, single-step diagnostic kits for differential diagnosis of multiple respiratory viruses and any other emerging diagnostic needs. Diagnostics based on this platform, which we term "disposable plasmonics assays," would be suitable for low-cost screening of multiple pathogens or biomarkers in a near-point-of-care setting.
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Affiliation(s)
- Stephanie Wallace
- School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, G12 8QQ Glasgow, U.K
| | - Martin Kartau
- School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, G12 8QQ Glasgow, U.K
| | - Tarun Kakkar
- School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, G12 8QQ Glasgow, U.K
| | - Chris Davis
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, G61 1QH Glasgow, U.K
| | - Agnieszka Szemiel
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, G61 1QH Glasgow, U.K
| | - Iliyana Samardzhieva
- School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, G12 8QQ Glasgow, U.K
| | - Swetha Vijayakrishnan
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, G61 1QH Glasgow, U.K
| | - Sarah Cole
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, G61 1QH Glasgow, U.K
| | - Giuditta De Lorenzo
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, G61 1QH Glasgow, U.K
| | - Emmanuel Maillart
- HORIBA France SAS, 14, Boulevard Thomas Gobert-Passage Jobin Yvon, CS 45002, 91120 Palaiseau, France
| | - Kevin Gautier
- School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, G12 8QQ Glasgow, U.K
| | - Adrian J Lapthorn
- School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, G12 8QQ Glasgow, U.K
| | - Arvind H Patel
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, G61 1QH Glasgow, U.K
| | - Nikolaj Gadegaard
- James Watt School of Engineering, University of Glasgow, Rankine Building, Oakfield Avenue, G12 8LT Glasgow, U.K
| | - Malcolm Kadodwala
- School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, G12 8QQ Glasgow, U.K
| | - Edward Hutchinson
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, G61 1QH Glasgow, U.K
| | - Affar S Karimullah
- School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, G12 8QQ Glasgow, U.K
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15
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Talledge N, Yang H, Shi K, Coray R, Yu G, Arndt WG, Meng S, Baxter GC, Mendonça LM, Castaño-Díez D, Aihara H, Mansky LM, Zhang W. HIV-2 Immature Particle Morphology Provides Insights into Gag Lattice Stability and Virus Maturation. J Mol Biol 2023; 435:168143. [PMID: 37150290 PMCID: PMC10524356 DOI: 10.1016/j.jmb.2023.168143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 05/01/2023] [Accepted: 05/01/2023] [Indexed: 05/09/2023]
Abstract
Retrovirus immature particle morphology consists of a membrane enclosed, pleomorphic, spherical and incomplete lattice of Gag hexamers. Previously, we demonstrated that human immunodeficiency virus type 2 (HIV-2) immature particles possess a distinct and extensive Gag lattice morphology. To better understand the nature of the continuously curved hexagonal Gag lattice, we have used the single particle cryo-electron microscopy method to determine the HIV-2 Gag lattice structure for immature virions. The reconstruction map at 5.5 Å resolution revealed a stable, wineglass-shaped Gag hexamer structure with structural features consistent with other lentiviral immature Gag lattice structures. Cryo-electron tomography provided evidence for nearly complete ordered Gag lattice structures in HIV-2 immature particles. We also solved a 1.98 Å resolution crystal structure of the carboxyl-terminal domain (CTD) of the HIV-2 capsid (CA) protein that identified a structured helix 12 supported via an interaction of helix 10 in the absence of the SP1 region of Gag. Residues at the helix 10-12 interface proved critical in maintaining HIV-2 particle release and infectivity. Taken together, our findings provide the first 3D organization of HIV-2 immature Gag lattice and important insights into both HIV Gag lattice stabilization and virus maturation.
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Affiliation(s)
- Nathaniel Talledge
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA. https://twitter.com/BioChemTalledge
| | - Huixin Yang
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Comparative Molecular Biosciences Graduate Program, University of Minnesota - Twin Cities, St. Paul, MN 55108, USA
| | - Ke Shi
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA
| | - Raffaele Coray
- BioEM Lab, Biozentrum, University of Basel - Basel, Switzerland
| | - Guichuan Yu
- Minnesota Supercomputing Institute, Office of the Vice President for Research, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Characterization Facility, College of Sciences and Engineering, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA
| | - William G Arndt
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Biochemistry, Molecular Biology and Biophysics Graduate Program, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA
| | - Shuyu Meng
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Molecular Pharmacology and Therapeutics Graduate Program, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA
| | - Gloria C Baxter
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Molecular, Cellular, Developmental Biology, and Genetics Graduate Program, University of Minnesota - Twin Cities, USA
| | - Luiza M Mendonça
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Biochemistry, Molecular Biology and Biophysics Graduate Program, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA
| | | | - Hideki Aihara
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Biochemistry, Molecular Biology and Biophysics Graduate Program, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA
| | - Louis M Mansky
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Comparative Molecular Biosciences Graduate Program, University of Minnesota - Twin Cities, St. Paul, MN 55108, USA; Biochemistry, Molecular Biology and Biophysics Graduate Program, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Molecular Pharmacology and Therapeutics Graduate Program, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA.
| | - Wei Zhang
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Characterization Facility, College of Sciences and Engineering, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA.
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16
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Bayfield OW, Shkoporov AN, Yutin N, Khokhlova EV, Smith JLR, Hawkins DEDP, Koonin EV, Hill C, Antson AA. Structural atlas of a human gut crassvirus. Nature 2023; 617:409-416. [PMID: 37138077 PMCID: PMC10172136 DOI: 10.1038/s41586-023-06019-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 03/27/2023] [Indexed: 05/05/2023]
Abstract
CrAssphage and related viruses of the order Crassvirales (hereafter referred to as crassviruses) were originally discovered by cross-assembly of metagenomic sequences. They are the most abundant viruses in the human gut, are found in the majority of individual gut viromes, and account for up to 95% of the viral sequences in some individuals1-4. Crassviruses are likely to have major roles in shaping the composition and functionality of the human microbiome, but the structures and roles of most of the virally encoded proteins are unknown, with only generic predictions resulting from bioinformatic analyses4,5. Here we present a cryo-electron microscopy reconstruction of Bacteroides intestinalis virus ΦcrAss0016, providing the structural basis for the functional assignment of most of its virion proteins. The muzzle protein forms an assembly about 1 MDa in size at the end of the tail and exhibits a previously unknown fold that we designate the 'crass fold', that is likely to serve as a gatekeeper that controls the ejection of cargos. In addition to packing the approximately 103 kb of virus DNA, the ΦcrAss001 virion has extensive storage space for virally encoded cargo proteins in the capsid and, unusually, within the tail. One of the cargo proteins is present in both the capsid and the tail, suggesting a general mechanism for protein ejection, which involves partial unfolding of proteins during their extrusion through the tail. These findings provide a structural basis for understanding the mechanisms of assembly and infection of these highly abundant crassviruses.
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Affiliation(s)
- Oliver W Bayfield
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK.
| | - Andrey N Shkoporov
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork, Ireland
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Ekaterina V Khokhlova
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork, Ireland
| | - Jake L R Smith
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Dorothy E D P Hawkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Colin Hill
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork, Ireland
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK.
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17
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Fang Q, Tang WC, Fokine A, Mahalingam M, Shao Q, Rossmann MG, Rao VB. Structures of a large prolate virus capsid in unexpanded and expanded states generate insights into the icosahedral virus assembly. Proc Natl Acad Sci U S A 2022; 119:e2203272119. [PMID: 36161892 PMCID: PMC9546572 DOI: 10.1073/pnas.2203272119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 08/31/2022] [Indexed: 11/18/2022] Open
Abstract
Many icosahedral viruses assemble proteinaceous precursors called proheads or procapsids. Proheads are metastable structures that undergo a profound structural transition known as expansion that transforms an immature unexpanded head into a mature genome-packaging head. Bacteriophage T4 is a model virus, well studied genetically and biochemically, but its structure determination has been challenging because of its large size and unusually prolate-shaped, ∼1,200-Å-long and ∼860-Å-wide capsid. Here, we report the cryogenic electron microscopy (cryo-EM) structures of T4 capsid in both of its major conformational states: unexpanded at a resolution of 5.1 Å and expanded at a resolution of 3.4 Å. These are among the largest structures deposited in Protein Data Bank to date and provide insights into virus assembly, head length determination, and shell expansion. First, the structures illustrate major domain movements and ∼70% additional gain in inner capsid volume, an essential transformation to contain the entire viral genome. Second, intricate intracapsomer interactions involving a unique insertion domain dramatically change, allowing the capsid subunits to rotate and twist while the capsomers remain fastened at quasi-threefold axes. Third, high-affinity binding sites emerge for a capsid decoration protein that clamps adjacent capsomers, imparting extraordinary structural stability. Fourth, subtle conformational changes at capsomers' periphery modulate intercapsomer angles between capsomer planes that control capsid length. Finally, conformational changes were observed at the symmetry-mismatched portal vertex, which might be involved in triggering head expansion. These analyses illustrate how small changes in local capsid subunit interactions lead to profound shifts in viral capsid morphology, stability, and volume.
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Affiliation(s)
- Qianglin Fang
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Wei-Chun Tang
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of America, Washington, DC 20064
| | - Andrei Fokine
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907
| | - Marthandan Mahalingam
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of America, Washington, DC 20064
| | - Qianqian Shao
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Michael G. Rossmann
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907
| | - Venigalla B. Rao
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of America, Washington, DC 20064
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18
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Morozova OV, Manuvera VA, Grishchechkin AE, Barinov NA, Shevlyagina NV, Zhukhovitsky VG, Lazarev VN, Klinov DV. Targeting of Silver Cations, Silver-Cystine Complexes, Ag Nanoclusters, and Nanoparticles towards SARS-CoV-2 RNA and Recombinant Virion Proteins. Viruses 2022; 14:v14050902. [PMID: 35632644 PMCID: PMC9144282 DOI: 10.3390/v14050902] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 04/20/2022] [Accepted: 04/22/2022] [Indexed: 11/28/2022] Open
Abstract
Background: Nanosilver possesses antiviral, antibacterial, anti-inflammatory, anti-angiogenesis, antiplatelet, and anticancer properties. The development of disinfectants, inactivated vaccines, and combined etiotropic and immunomodulation therapy against respiratory viral infections, including COVID-19, remains urgent. Aim: Our goal was to determine the SARS-CoV-2 molecular targets (genomic RNA and the structural virion proteins S and N) for silver-containing nanomaterials. Methods: SARS-CoV-2 gene cloning, purification of S2 and N recombinant proteins, viral RNA isolation from patients’ blood samples, reverse transcription with quantitative real-time PCR ((RT)2-PCR), ELISA, and multiplex immunofluorescent analysis with magnetic beads (xMAP) for detection of 17 inflammation markers. Results: Fluorescent Ag nanoclusters (NCs) less than 2 nm with a few recovered silver atoms, citrate coated Ag nanoparticles (NPs) with diameters of 20–120 nm, and nanoconjugates of 50–150 nm consisting of Ag NPs with different protein envelopes were constructed from AgNO3 and analyzed by means of transmission electron microscopy (TEM), atomic force microscopy (AFM), ultraviolet-visible light absorption, and fluorescent spectroscopy. SARS-CoV-2 RNA isolated from COVID-19 patients’ blood samples was completely cleaved with the artificial RNase complex compound Li+[Ag+2Cys2−(OH−)2(NH3)2] (Ag-2S), whereas other Ag-containing materials provided partial RNA degradation only. Treatment of the SARS-CoV-2 S2 and N recombinant antigens with AgNO3 and Ag NPs inhibited their binding with specific polyclonal antibodies, as shown by ELISA. Fluorescent Ag NCs with albumin or immunoglobulins, Ag-2S complex, and nanoconjugates of Ag NPs with protein shells had no effect on the interaction between coronavirus recombinant antigens and antibodies. Reduced production of a majority of the 17 inflammation biomarkers after treatment of three human cell lines with nanosilver was demonstrated by xMAP. Conclusion: The antiviral properties of the silver nanomaterials against SARS-CoV-2 coronavirus differed. The small-molecular-weight artificial RNase Ag-2S provided exhaustive RNA destruction but could not bind with the SARS-CoV-2 recombinant antigens. On the contrary, Ag+ ions and Ag NPs interacted with the SARS-CoV-2 recombinant antigens N and S but were less efficient at performing viral RNA cleavage. One should note that SARS-CoV-2 RNA was more stable than MS2 phage RNA. The isolated RNA of both the MS2 phage and SARS-CoV-2 were more degradable than the MS2 phage and coronavirus particles in patients’ blood, due to the protection with structural proteins. To reduce the risk of the virus resistance, a combined treatment with Ag-2S and Ag NPs could be used. To prevent cytokine storm during the early stages of respiratory infections with RNA-containing viruses, nanoconjugates of Ag NPs with surface proteins could be recommended.
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Affiliation(s)
- Olga V. Morozova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1A Malaya Pirogovskaya St., 119435 Moscow, Russia; (V.A.M.); (N.A.B.); (V.N.L.); (D.V.K.)
- D.I. Ivanovsky Institute of Virology of the National Research Center of Epidemiology and Microbiology of N.F. Gamaleya of the Russian Ministry of Health, 16 Gamaleya St., 123098 Moscow, Russia; (A.E.G.); (N.V.S.); (V.G.Z.)
- Sirius University of Science and Technology, 1 Olympic Ave., 354349 Sochi, Russia
- Correspondence:
| | - Valentin A. Manuvera
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1A Malaya Pirogovskaya St., 119435 Moscow, Russia; (V.A.M.); (N.A.B.); (V.N.L.); (D.V.K.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine of Federal Medical Biological Agency, 1A Malaya Pirogovskaya St., 119435 Moscow, Russia
- Moscow Institute of Physics and Technology, 9 Institutsky Per., 141700 Dolgoprudny, Russia
| | - Alexander E. Grishchechkin
- D.I. Ivanovsky Institute of Virology of the National Research Center of Epidemiology and Microbiology of N.F. Gamaleya of the Russian Ministry of Health, 16 Gamaleya St., 123098 Moscow, Russia; (A.E.G.); (N.V.S.); (V.G.Z.)
| | - Nikolay A. Barinov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1A Malaya Pirogovskaya St., 119435 Moscow, Russia; (V.A.M.); (N.A.B.); (V.N.L.); (D.V.K.)
- Sirius University of Science and Technology, 1 Olympic Ave., 354349 Sochi, Russia
| | - Nataliya V. Shevlyagina
- D.I. Ivanovsky Institute of Virology of the National Research Center of Epidemiology and Microbiology of N.F. Gamaleya of the Russian Ministry of Health, 16 Gamaleya St., 123098 Moscow, Russia; (A.E.G.); (N.V.S.); (V.G.Z.)
| | - Vladimir G. Zhukhovitsky
- D.I. Ivanovsky Institute of Virology of the National Research Center of Epidemiology and Microbiology of N.F. Gamaleya of the Russian Ministry of Health, 16 Gamaleya St., 123098 Moscow, Russia; (A.E.G.); (N.V.S.); (V.G.Z.)
| | - Vassili N. Lazarev
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1A Malaya Pirogovskaya St., 119435 Moscow, Russia; (V.A.M.); (N.A.B.); (V.N.L.); (D.V.K.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine of Federal Medical Biological Agency, 1A Malaya Pirogovskaya St., 119435 Moscow, Russia
- Moscow Institute of Physics and Technology, 9 Institutsky Per., 141700 Dolgoprudny, Russia
| | - Dmitry V. Klinov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1A Malaya Pirogovskaya St., 119435 Moscow, Russia; (V.A.M.); (N.A.B.); (V.N.L.); (D.V.K.)
- Sirius University of Science and Technology, 1 Olympic Ave., 354349 Sochi, Russia
- Moscow Institute of Physics and Technology, 9 Institutsky Per., 141700 Dolgoprudny, Russia
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19
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Ruszkowski M, Strugala A, Indyka P, Tresset G, Figlerowicz M, Urbanowicz A. Cryo-EM reconstructions of BMV-derived virus-like particles reveal assembly defects in the icosahedral lattice structure. Nanoscale 2022; 14:3224-3233. [PMID: 35156989 DOI: 10.1039/d1nr05650f] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The increasing interest in virus-like particles (VLPs) has been reflected by the growing number of studies on their assembly and application. However, the formation of complete VLPs is a complex phenomenon, making it difficult to rationally design VLPs with desired features de novo. In this paper, we describe VLPs assembled in vitro from the recombinant capsid protein of brome mosaic virus (BMV). The analysis of VLPs was performed by Cryo-EM reconstructions and allowed us to visualize a few classes of VLPs, giving insight into the VLP self-assembly process. Apart from the mature icosahedral VLP practically identical with native virions, we describe putative VLP intermediates displaying non-icosahedral arrangements of capsomers, proposed to occur before the final disorder-order transition stage of icosahedral VLP assembly. Some of the described VLP classes show a lack of protein shell continuity, possibly resulting from too strong interaction with the cargo (in this case tRNA) with the capsid protein. We believe that our results are a useful prerequisite for the rational design of VLPs in the future and lead the way to the effective production of modified VLPs.
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Affiliation(s)
- Milosz Ruszkowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Aleksander Strugala
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Paulina Indyka
- Jagiellonian University, Solaris National Synchrotron Radiation Centre, Czerwone Maki 98, 30-392 Cracow, Poland
- Jagiellonian University, Malopolska Centre of Biotechnology (MCB), 30-387 Cracow, Poland
| | - Guillaume Tresset
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, 91405 Orsay, France
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Anna Urbanowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
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20
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Rudy MJ, Coughlan C, Hixon AM, Clarke P, Tyler KL. Density Analysis of Enterovirus D68 Shows Viral Particles Can Associate with Exosomes. Microbiol Spectr 2022; 10:e0245221. [PMID: 35170992 PMCID: PMC8849102 DOI: 10.1128/spectrum.02452-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 01/27/2022] [Indexed: 11/25/2022] Open
Abstract
Enterovirus D68 (EV-D68) is an emerging pathogen which causes respiratory disease and is associated with an acute flaccid myelitis that predominately affects children. EV-D68 can infect motor neurons, causing cell death and a loss of motor control leading to flaccid paralysis. However, it remains unknown how viral particles gain entry into the central nervous system (CNS). Here, we show that three distinct densities of EV-D68 particle can be isolated from infected muscle and neural cell lines (RD and SH-SY5Y) using high-speed density centrifugation to separate cell supernatant. The lowest-density peak is composed of viral particles, which have adhered to the exterior surface of a small extracellular vesicle called an exosome. Analysis of prototypic (historic) and contemporary EV-D68 strains suggests that binding to exosomes is a ubiquitous characteristic of EV-D68. We further show that interaction with exosomes increases viral infectivity in a neural cell line. Analysis of the two higher-density peaks, which are not associated with exosomes, revealed that a significant amount of viral titer in the modern (2014) EV-D68 strains is found at 1.20 g/cm3, whereas this density has a very low viral titer in the prototypic Fermon strain. IMPORTANCE Despite the strong causal link between enterovirus D68 (EV-D68) and acute flaccid myelitis (AFM), it remains unclear how EV-D68 gains entry into the central nervous system and what receptors enable it to infect motor neurons. We show that EV-D68 particles can adhere to exosomes, placing EV-D68 among a handful of other picornaviruses which are known to interact with extracellular vesicles. Uptake and infection of permissive cells by virally contaminated exosomes would have major implications in the search for the EV-D68 receptor, as well as providing a possible route for viral entry into motor neurons. This work identifies a novel cellular entry route for EV-D68 and may facilitate the identification of genetic risk factors for development of AFM.
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Affiliation(s)
- Michael J. Rudy
- Department of Neurology, University of Colorado, Aurora, Colorado, USA
| | - Christina Coughlan
- Department of Neurology, University of Colorado, Aurora, Colorado, USA
- University of Colorado Alzheimer’s and Cognition Center, Aurora, Colorado, USA
- Linda Crnic Institute for Down Syndrome, Aurora, Colorado, USA
| | - Alison M. Hixon
- Medical Scientist Training Program, University of Colorado, Aurora, Colorado, USA
| | - Penny Clarke
- Department of Neurology, University of Colorado, Aurora, Colorado, USA
| | - Kenneth L. Tyler
- Department of Neurology, University of Colorado, Aurora, Colorado, USA
- Department of Immunology and Microbiology, University of Colorado, Aurora, Colorado, USA
- Division of Infectious Disease, Department of Medicine, University of Colorado, Aurora, Colorado, USA
- VA Medical Center, Aurora, Colorado, USA
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21
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Murer L, Petkidis A, Vallet T, Vignuzzi M, Greber UF. Chemical Evolution of Rhinovirus Identifies Capsid-Destabilizing Mutations Driving Low-pH-Independent Genome Uncoating. J Virol 2022; 96:e0106021. [PMID: 34705560 PMCID: PMC8791267 DOI: 10.1128/jvi.01060-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 10/20/2021] [Indexed: 12/24/2022] Open
Abstract
Rhinoviruses (RVs) cause recurrent infections of the nasal and pulmonary tracts, life-threatening conditions in chronic respiratory illness patients, predisposition of children to asthmatic exacerbation, and large economic cost. RVs are difficult to treat. They rapidly evolve resistance and are genetically diverse. Here, we provide insight into RV drug resistance mechanisms against chemical compounds neutralizing low pH in endolysosomes. Serial passaging of RV-A16 in the presence of the vacuolar proton ATPase inhibitor bafilomycin A1 (BafA1) or the endolysosomotropic agent ammonium chloride (NH4Cl) promoted the emergence of resistant virus populations. We found two reproducible point mutations in viral proteins 1 and 3 (VP1 and VP3), A2526G (serine 66 to asparagine [S66N]), and G2274U (cysteine 220 to phenylalanine [C220F]), respectively. Both mutations conferred cross-resistance to BafA1, NH4Cl, and the protonophore niclosamide, as identified by massive parallel sequencing and reverse genetics, but not the double mutation, which we could not rescue. Both VP1-S66 and VP3-C220 locate at the interprotomeric face, and their mutations increase the sensitivity of virions to low pH, elevated temperature, and soluble intercellular adhesion molecule 1 receptor. These results indicate that the ability of RV to uncoat at low endosomal pH confers virion resistance to extracellular stress. The data endorse endosomal acidification inhibitors as a viable strategy against RVs, especially if inhibitors are directly applied to the airways. IMPORTANCE Rhinoviruses (RVs) are the predominant agents causing the common cold. Anti-RV drugs and vaccines are not available, largely due to rapid evolutionary adaptation of RVs giving rise to resistant mutants and an immense diversity of antigens in more than 160 different RV types. In this study, we obtained insight into the cell biology of RVs by harnessing the ability of RVs to evolve resistance against host-targeting small chemical compounds neutralizing endosomal pH, an important cue for uncoating of normal RVs. We show that RVs grown in cells treated with inhibitors of endolysosomal acidification evolved capsid mutations yielding reduced virion stability against elevated temperature, low pH, and incubation with recombinant soluble receptor fragments. This fitness cost makes it unlikely that RV mutants adapted to neutral pH become prevalent in nature. The data support the concept of host-directed drug development against respiratory viruses in general, notably at low risk of gain-of-function mutations.
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Affiliation(s)
- Luca Murer
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Anthony Petkidis
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Thomas Vallet
- Institut Pasteur, Viral Populations and Pathogenesis Unit, Department of Virology, CNRS UMR 3569, Paris, France
| | - Marco Vignuzzi
- Institut Pasteur, Viral Populations and Pathogenesis Unit, Department of Virology, CNRS UMR 3569, Paris, France
| | - Urs F. Greber
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
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22
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Chang JY, Gorzelnik KV, Thongchol J, Zhang J. Structural Assembly of Qβ Virion and Its Diverse Forms of Virus-like Particles. Viruses 2022; 14:225. [PMID: 35215818 PMCID: PMC8880383 DOI: 10.3390/v14020225] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 01/18/2022] [Accepted: 01/21/2022] [Indexed: 02/04/2023] Open
Abstract
The coat proteins (CPs) of single-stranded RNA bacteriophages (ssRNA phages) directly assemble around the genomic RNA (gRNA) to form a near-icosahedral capsid with a single maturation protein (Mat) that binds the gRNA and interacts with the retractile pilus during infection of the host. Understanding the assembly of ssRNA phages is essential for their use in biotechnology, such as RNA protection and delivery. Here, we present the complete gRNA model of the ssRNA phage Qβ, revealing that the 3' untranslated region binds to the Mat and the 4127 nucleotides fold domain-by-domain, and is connected through long-range RNA-RNA interactions, such as kissing loops. Thirty-three operator-like RNA stem-loops are located and primarily interact with the asymmetric A/B CP-dimers, suggesting a pathway for the assembly of the virions. Additionally, we have discovered various forms of the virus-like particles (VLPs), including the canonical T = 3 icosahedral, larger T = 4 icosahedral, prolate, oblate forms, and a small prolate form elongated along the 3-fold axis. These particles are all produced during a normal infection, as well as when overexpressing the CPs. When overexpressing the shorter RNA fragments encoding only the CPs, we observed an increased percentage of the smaller VLPs, which may be sufficient to encapsidate a shorter RNA.
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Affiliation(s)
| | | | | | - Junjie Zhang
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; (J.-Y.C.); (K.V.G.); (J.T.)
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23
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Havranek KE, Reyes Ballista JM, Hines KM, Brindley MA. Untargeted Lipidomics of Vesicular Stomatitis Virus-Infected Cells and Viral Particles. Viruses 2021; 14:v14010003. [PMID: 35062207 PMCID: PMC8778780 DOI: 10.3390/v14010003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/03/2021] [Accepted: 12/05/2021] [Indexed: 11/16/2022] Open
Abstract
The viral lifecycle is critically dependent upon host lipids. Enveloped viral entry requires fusion between viral and cellular membranes. Once an infection has occurred, viruses may rely on host lipids for replication and egress. Upon exit, enveloped viruses derive their lipid bilayer from host membranes during the budding process. Furthermore, host lipid metabolism and signaling are often hijacked to facilitate viral replication. We employed an untargeted HILIC-IM-MS lipidomics approach and identified host lipid species that were significantly altered during vesicular stomatitis virus (VSV) infection. Many glycerophospholipid and sphingolipid species were modified, and ontological enrichment analysis suggested that the alterations to the lipid profile change host membrane properties. Lysophosphatidylcholine (LPC), which can contribute to membrane curvature and serve as a signaling molecule, was depleted during infection, while several ceramide sphingolipids were augmented during infection. Ceramide and sphingomyelin lipids were also enriched in viral particles, indicating that sphingolipid metabolism is important during VSV infection.
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Affiliation(s)
- Katherine E. Havranek
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA; (K.E.H.); (J.M.R.B.)
| | - Judith Mary Reyes Ballista
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA; (K.E.H.); (J.M.R.B.)
| | - Kelly Marie Hines
- Department of Chemistry, Franklin College of Arts and Sciences, University of Georgia, Athens, GA 30602, USA
- Correspondence: (K.M.H.); (M.A.B.); Tel.: +1-706-542-1966 (K.M.H.); +1-706-542-5796 (M.A.B.)
| | - Melinda Ann Brindley
- Department of Infectious Diseases, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
- Correspondence: (K.M.H.); (M.A.B.); Tel.: +1-706-542-1966 (K.M.H.); +1-706-542-5796 (M.A.B.)
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24
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Fatehi F, Bingham RJ, Dechant PP, Stockley PG, Twarock R. Therapeutic interfering particles exploiting viral replication and assembly mechanisms show promising performance: a modelling study. Sci Rep 2021; 11:23847. [PMID: 34903795 PMCID: PMC8668974 DOI: 10.1038/s41598-021-03168-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/22/2021] [Indexed: 11/09/2022] Open
Abstract
Defective interfering particles arise spontaneously during a viral infection as mutants lacking essential parts of the viral genome. Their ability to replicate in the presence of the wild-type (WT) virus (at the expense of viable viral particles) is mimicked and exploited by therapeutic interfering particles. We propose a strategy for the design of therapeutic interfering RNAs (tiRNAs) against positive-sense single-stranded RNA viruses that assemble via packaging signal-mediated assembly. These tiRNAs contain both an optimised version of the virus assembly manual that is encoded by multiple dispersed RNA packaging signals and a replication signal for viral polymerase, but lack any protein coding information. We use an intracellular model for hepatitis C viral (HCV) infection that captures key aspects of the competition dynamics between tiRNAs and viral genomes for virally produced capsid protein and polymerase. We show that only a small increase in the assembly and replication efficiency of the tiRNAs compared with WT virus is required in order to achieve a treatment efficacy greater than 99%. This demonstrates that the proposed tiRNA design could be a promising treatment option for RNA viral infections.
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Affiliation(s)
- Farzad Fatehi
- York Cross-disciplinary Centre for Systems Analysis, University of York, York, YO10 5GE, UK
- Department of Mathematics, University of York, York, YO10 5DD, UK
| | - Richard J Bingham
- York Cross-disciplinary Centre for Systems Analysis, University of York, York, YO10 5GE, UK
- Department of Mathematics, University of York, York, YO10 5DD, UK
- Department of Biology, University of York, York, YO10 5DD, UK
| | - Pierre-Philippe Dechant
- York Cross-disciplinary Centre for Systems Analysis, University of York, York, YO10 5GE, UK
- Department of Mathematics, University of York, York, YO10 5DD, UK
- School of Science, Technology and Health, York St John University, York, YO31 7EX, UK
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - Reidun Twarock
- York Cross-disciplinary Centre for Systems Analysis, University of York, York, YO10 5GE, UK.
- Department of Mathematics, University of York, York, YO10 5DD, UK.
- Department of Biology, University of York, York, YO10 5DD, UK.
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25
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Ahammad T, Khan RH, Sahu ID, Drew DL, Faul E, Li T, McCarrick RM, Lorigan GA. Pinholin S 21 mutations induce structural topology and conformational changes. Biochim Biophys Acta Biomembr 2021; 1863:183771. [PMID: 34499883 DOI: 10.1016/j.bbamem.2021.183771] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 08/30/2021] [Accepted: 09/01/2021] [Indexed: 12/23/2022]
Abstract
The bacteriophage infection cycle is terminated at a predefined time to release the progeny virions via a robust lytic system composed of holin, endolysin, and spanin proteins. Holin is the timekeeper of this process. Pinholin S21 is a prototype holin of phage Φ21, which determines the timing of host cell lysis through the coordinated efforts of pinholin and antipinholin. However, mutations in pinholin and antipinholin play a significant role in modulating the timing of lysis depending on adverse or favorable growth conditions. Earlier studies have shown that single point mutations of pinholin S21 alter the cell lysis timing, a proxy for pinholin function as lysis is also dependent on other lytic proteins. In this study, continuous wave electron paramagnetic resonance (CW-EPR) power saturation and double electron-electron resonance (DEER) spectroscopic techniques were used to directly probe the effects of mutations on the structure and conformational changes of pinholin S21 that correlate with pinholin function. DEER and CW-EPR power saturation data clearly demonstrate that increased hydrophilicity induced by residue mutations accelerate the externalization of antipinholin transmembrane domain 1 (TMD1), while increased hydrophobicity prevents the externalization of TMD1. This altered hydrophobicity is potentially accelerating or delaying the activation of pinholin S21. It was also found that mutations can influence intra- or intermolecular interactions in this system, which contribute to the activation of pinholin and modulate the cell lysis timing. This could be a novel approach to analyze the mutational effects on other holin systems, as well as any other membrane protein in which mutation directly leads to structural and conformational changes.
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Affiliation(s)
- Tanbir Ahammad
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Rasal H Khan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA; Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Daniel L Drew
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Emily Faul
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Tianyan Li
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Robert M McCarrick
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA.
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26
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Saha I, Preece B, Peterson A, Durden H, MacArthur B, Lowe J, Belnap D, Vershinin M, Saffarian S. Gag-Gag Interactions Are Insufficient to Fully Stabilize and Order the Immature HIV Gag Lattice. Viruses 2021; 13:1946. [PMID: 34696376 PMCID: PMC8540168 DOI: 10.3390/v13101946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/24/2021] [Accepted: 09/24/2021] [Indexed: 11/16/2022] Open
Abstract
Immature HIV virions harbor a lattice of Gag molecules with significant ordering in CA-NTD, CA-CTD and SP1 regions. This ordering plays a major role during HIV maturation. To test the condition in which the Gag lattice forms in vivo, we assembled virus like particles (VLPs) by expressing only HIV Gag in mammalian cells. Here we show that these VLPs incorporate a similar number of Gag molecules compared to immature HIV virions. However, within these VLPs, Gag molecules diffuse with a pseudo-diffusion rate of 10 nm2/s, this pseudo-diffusion is abrogated in the presence of melittin and is sensitive to mutations within the SP1 region. Using cryotomography, we show that unlike immature HIV virions, in the Gag lattice of VLPs the CA-CTD and SP1 regions are significantly less ordered. Our observations suggest that within immature HIV virions, other viral factors in addition to Gag, contribute to ordering in the CA-CTD and SP1 regions.
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Affiliation(s)
- Ipsita Saha
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA;
| | - Benjamin Preece
- Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112, USA; (B.P.); (A.P.); (H.D.); (B.M.); (M.V.)
- Department of Physics and Astronomy, University of Utah, Salt Lake City, UT 84112, USA
| | - Abby Peterson
- Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112, USA; (B.P.); (A.P.); (H.D.); (B.M.); (M.V.)
- Department of Physics and Astronomy, University of Utah, Salt Lake City, UT 84112, USA
| | - Haley Durden
- Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112, USA; (B.P.); (A.P.); (H.D.); (B.M.); (M.V.)
- Department of Physics and Astronomy, University of Utah, Salt Lake City, UT 84112, USA
| | - Brian MacArthur
- Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112, USA; (B.P.); (A.P.); (H.D.); (B.M.); (M.V.)
- Department of Physics and Astronomy, University of Utah, Salt Lake City, UT 84112, USA
| | - Jake Lowe
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA; (J.L.); (D.B.)
| | - David Belnap
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA; (J.L.); (D.B.)
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Michael Vershinin
- Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112, USA; (B.P.); (A.P.); (H.D.); (B.M.); (M.V.)
- Department of Physics and Astronomy, University of Utah, Salt Lake City, UT 84112, USA
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA; (J.L.); (D.B.)
| | - Saveez Saffarian
- Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112, USA; (B.P.); (A.P.); (H.D.); (B.M.); (M.V.)
- Department of Physics and Astronomy, University of Utah, Salt Lake City, UT 84112, USA
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA; (J.L.); (D.B.)
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27
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Manukhova TI, Evtushenko EA, Ksenofontov AL, Arutyunyan AM, Kovalenko AO, Nikitin NA, Karpova OV. Thermal remodelling of Alternanthera mosaic virus virions and virus-like particles into protein spherical particles. PLoS One 2021; 16:e0255378. [PMID: 34320024 PMCID: PMC8318239 DOI: 10.1371/journal.pone.0255378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 07/15/2021] [Indexed: 11/24/2022] Open
Abstract
The present work addresses the thermal remodelling of flexible plant viruses with a helical structure and virus-like particles (VLPs). Here, for the first time, the possibility of filamentous Alternanthera mosaic virus (AltMV) virions' thermal transition into structurally modified spherical particles (SP) has been demonstrated. The work has established differences in formation conditions of SP from virions (SPV) and VLPs (SPVLP) that are in accordance with structural data (on AltMV virions and VLPs). SP originate from AltMV virions through an intermediate stage. However, the same intermediate stage was not detected during AltMV VLPs' structural remodelling. According to the biochemical analysis, AltMV SPV consist of protein and do not include RNA. The structural characterisation of AltMV SPV/VLP by circular dichroism, intrinsic fluorescence spectroscopy and thioflavin T fluorescence assay has been performed. AltMV SPV/VLP adsorption properties and the availability of chemically reactive surface amino acids have been analysed. The revealed characteristics of AltMV SPV/VLP indicate that they could be applied as protein platforms for target molecules presentation and for the design of functionally active complexes.
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Affiliation(s)
- Tatiana I. Manukhova
- Faculty of Biology, Department of Virology, Lomonosov Moscow State University, Moscow, Russia
| | - Ekaterina A. Evtushenko
- Faculty of Biology, Department of Virology, Lomonosov Moscow State University, Moscow, Russia
| | - Alexander L. Ksenofontov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Alexander M. Arutyunyan
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Angelina O. Kovalenko
- Faculty of Biology, Department of Virology, Lomonosov Moscow State University, Moscow, Russia
| | - Nikolai A. Nikitin
- Faculty of Biology, Department of Virology, Lomonosov Moscow State University, Moscow, Russia
| | - Olga V. Karpova
- Faculty of Biology, Department of Virology, Lomonosov Moscow State University, Moscow, Russia
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28
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Takemura K. Surface Plasmon Resonance (SPR)- and Localized SPR (LSPR)-Based Virus Sensing Systems: Optical Vibration of Nano- and Micro-Metallic Materials for the Development of Next-Generation Virus Detection Technology. Biosensors (Basel) 2021; 11:250. [PMID: 34436053 PMCID: PMC8391291 DOI: 10.3390/bios11080250] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/13/2021] [Accepted: 07/23/2021] [Indexed: 01/04/2023]
Abstract
The global damage that a widespread viral infection can cause is evident from the ongoing COVID-19 pandemic. The importance of virus detection to prevent the spread of viruses has been reaffirmed by the pandemic and the associated social and economic damage. Surface plasmon resonance (SPR) in microscale and localized SPR (LSPR) in nanoscale virus sensing systems are thought to be useful as next-generation detection methods. Many studies have been conducted on ultra-sensitive technologies, especially those based on signal amplification. In some cases, it has been reported that even a low viral load can be measured, indicating that the virus can be detected in patients even in the early stages of the viral infection. These findings corroborate that SPR and LSPR are effective in minimizing false-positives and false-negatives that are prevalent in the existing virus detection techniques. In this review, the methods and signal responses of SPR and LSPR-based virus detection technologies are summarized. Furthermore, this review surveys some of the recent developments reported and discusses the limitations of SPR and LSPR-based virus detection as the next-generation detection technologies.
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Affiliation(s)
- Kenshin Takemura
- Sensing System Research Center, The National Institute of Advanced Industrial Science and Technology, 07-1 Shuku-Machi, Tosu 841-0052, Japan
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29
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Cao C, Cai Z, Xiao X, Rao J, Chen J, Hu N, Yang M, Xing X, Wang Y, Li M, Zhou B, Wang X, Wang J, Xue Y. The architecture of the SARS-CoV-2 RNA genome inside virion. Nat Commun 2021; 12:3917. [PMID: 34168138 PMCID: PMC8225788 DOI: 10.1038/s41467-021-22785-x] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 03/30/2021] [Indexed: 02/08/2023] Open
Abstract
SARS-CoV-2 carries the largest single-stranded RNA genome and is the causal pathogen of the ongoing COVID-19 pandemic. How the SARS-CoV-2 RNA genome is folded in the virion remains unknown. To fill the knowledge gap and facilitate structure-based drug development, we develop a virion RNA in situ conformation sequencing technology, named vRIC-seq, for probing viral RNA genome structure unbiasedly. Using vRIC-seq data, we reconstruct the tertiary structure of the SARS-CoV-2 genome and reveal a surprisingly "unentangled globule" conformation. We uncover many long-range duplexes and higher-order junctions, both of which are under purifying selections and contribute to the sequential package of the SARS-CoV-2 genome. Unexpectedly, the D614G and the other two accompanying mutations may remodel duplexes into more stable forms. Lastly, the structure-guided design of potent small interfering RNAs can obliterate the SARS-CoV-2 in Vero cells. Overall, our work provides a framework for studying the genome structure, function, and dynamics of emerging deadly RNA viruses.
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Affiliation(s)
- Changchang Cao
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Zhaokui Cai
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xia Xiao
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jian Rao
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Juan Chen
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Naijing Hu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Minnan Yang
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xiaorui Xing
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yongle Wang
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Manman Li
- School of Life Sciences, Henan Normal University, Xinxiang, China
| | - Bing Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Xiangxi Wang
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jianwei Wang
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Yuanchao Xue
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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30
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Abstract
Portogloboviridae is a family of viruses with circular, double-stranded DNA genomes of about 20 kbp. Their icosahedral virions have a diameter of 87 nm, and consist of an outer protein shell, an inner lipid layer and a nucleoprotein core wound up into a spherical coil. Portogloboviruses infect hyperthermophilic archaea of the genus Saccharolobus, order Sulfolobales and are presumably nonlytic. Portogloboviruses encode mini-CRISPR arrays which they use to compete against other co-infecting viruses. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Portogloboviridae, which is available at ictv.global/report/portogloboviridae.
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Affiliation(s)
- David Prangishvili
- Institut Pasteur, 25, Rue du Dr Roux, 75015 Paris, France
- Ivane Javakhishvili Tbilisi State University, Tbilisi 1079, Georgia
| | - Ying Liu
- Archaeal Virology Unit, Institut Pasteur, 75015 Paris, France
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, 75015 Paris, France
| | - ICTV Report Consortium
- Institut Pasteur, 25, Rue du Dr Roux, 75015 Paris, France
- Ivane Javakhishvili Tbilisi State University, Tbilisi 1079, Georgia
- Archaeal Virology Unit, Institut Pasteur, 75015 Paris, France
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31
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Kobayashi R, Inaba H, Matsuura K. Fluorescence Correlation Spectroscopy Analysis of Effect of Molecular Crowding on Self-Assembly of β-Annulus Peptide into Artificial Viral Capsid. Int J Mol Sci 2021; 22:ijms22094754. [PMID: 33946174 PMCID: PMC8125178 DOI: 10.3390/ijms22094754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 04/26/2021] [Accepted: 04/29/2021] [Indexed: 12/11/2022] Open
Abstract
Recent progress in the de novo design of self-assembling peptides has enabled the construction of peptide-based viral capsids. Previously, we demonstrated that 24-mer β-annulus peptides from tomato bushy stunt virus spontaneously self-assemble into an artificial viral capsid. Here we propose to use the artificial viral capsid through the self-assembly of β-annulus peptide as a simple model to analyze the effect of molecular crowding environment on the formation process of viral capsid. Artificial viral capsids formed by co-assembly of fluorescent-labelled and unmodified β-annulus peptides in dilute aqueous solutions and under molecular crowding conditions were analyzed using fluorescence correlation spectroscopy (FCS). The apparent particle size and the dissociation constant (Kd) of the assemblies decreased with increasing concentration of the molecular crowding agent, i.e., polyethylene glycol (PEG). This is the first successful in situ analysis of self-assembling process of artificial viral capsid under molecular crowding conditions.
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Affiliation(s)
- Risako Kobayashi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan; (R.K.); (H.I.)
| | - Hiroshi Inaba
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan; (R.K.); (H.I.)
- Centre for Research on Green Sustainable Chemistry, Tottori University, Tottori 680-8552, Japan
| | - Kazunori Matsuura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan; (R.K.); (H.I.)
- Centre for Research on Green Sustainable Chemistry, Tottori University, Tottori 680-8552, Japan
- Correspondence: ; Tel.: +81-857-31-5262
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32
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Plante JA, Liu Y, Liu J, Xia H, Johnson BA, Lokugamage KG, Zhang X, Muruato AE, Zou J, Fontes-Garfias CR, Mirchandani D, Scharton D, Bilello JP, Ku Z, An Z, Kalveram B, Freiberg AN, Menachery VD, Xie X, Plante KS, Weaver SC, Shi PY. Spike mutation D614G alters SARS-CoV-2 fitness. Nature 2021; 592:116-121. [PMID: 33106671 PMCID: PMC8158177 DOI: 10.1038/s41586-020-2895-3] [Citation(s) in RCA: 1056] [Impact Index Per Article: 352.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/20/2020] [Indexed: 11/09/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein substitution D614G became dominant during the coronavirus disease 2019 (COVID-19) pandemic1,2. However, the effect of this variant on viral spread and vaccine efficacy remains to be defined. Here we engineered the spike D614G substitution in the USA-WA1/2020 SARS-CoV-2 strain, and found that it enhances viral replication in human lung epithelial cells and primary human airway tissues by increasing the infectivity and stability of virions. Hamsters infected with SARS-CoV-2 expressing spike(D614G) (G614 virus) produced higher infectious titres in nasal washes and the trachea, but not in the lungs, supporting clinical evidence showing that the mutation enhances viral loads in the upper respiratory tract of COVID-19 patients and may increase transmission. Sera from hamsters infected with D614 virus exhibit modestly higher neutralization titres against G614 virus than against D614 virus, suggesting that the mutation is unlikely to reduce the ability of vaccines in clinical trials to protect against COVID-19, and that therapeutic antibodies should be tested against the circulating G614 virus. Together with clinical findings, our work underscores the importance of this variant in viral spread and its implications for vaccine efficacy and antibody therapy.
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Affiliation(s)
- Jessica A Plante
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Yang Liu
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jianying Liu
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Hongjie Xia
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Bryan A Johnson
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Kumari G Lokugamage
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Xianwen Zhang
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Antonio E Muruato
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jing Zou
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Camila R Fontes-Garfias
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Divya Mirchandani
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Dionna Scharton
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | | | - Zhiqiang Ku
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Zhiqiang An
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Birte Kalveram
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Alexander N Freiberg
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, USA
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA
| | - Vineet D Menachery
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
| | - Kenneth S Plante
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA.
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA.
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA.
| | - Scott C Weaver
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA.
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA.
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA.
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, USA.
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA.
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, USA.
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.
| | - Pei-Yong Shi
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA.
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, USA.
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA.
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, USA.
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.
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33
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Loveday EK, Hain KS, Kochetkova I, Hedges JF, Robison A, Snyder DT, Brumfield SK, Young MJ, Jutila MA, Chang CB, Taylor MP. Effect of Inactivation Methods on SARS-CoV-2 Virion Protein and Structure. Viruses 2021; 13:562. [PMID: 33810401 PMCID: PMC8066162 DOI: 10.3390/v13040562] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 03/22/2021] [Indexed: 12/31/2022] Open
Abstract
The risk posed by Severe Acute Respiratory Syndrome Coronavirus -2 (SARS-CoV-2) dictates that live-virus research is conducted in a biosafety level 3 (BSL3) facility. Working with SARS-CoV-2 at lower biosafety levels can expedite research yet requires the virus to be fully inactivated. In this study, we validated and compared two protocols for inactivating SARS-CoV-2: heat treatment and ultraviolet irradiation. The two methods were optimized to render the virus completely incapable of infection while limiting the destructive effects of inactivation. We observed that 15 min of incubation at 65 °C completely inactivates high titer viral stocks. Complete inactivation was also achieved with minimal amounts of UV power (70,000 µJ/cm2), which is 100-fold less power than comparable studies. Once validated, the two methods were then compared for viral RNA quantification, virion purification, and antibody detection assays. We observed that UV irradiation resulted in a 2-log reduction of detectable genomes compared to heat inactivation. Protein yield following virion enrichment was equivalent for all inactivation conditions, but the quality of resulting viral proteins and virions were differentially impacted depending on inactivation method and time. Here, we outline the strengths and weaknesses of each method so that investigators might choose the one which best meets their research goals.
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Affiliation(s)
- Emma K. Loveday
- Department of Chemical & Biological Engineering, Montana State University, Bozeman, MT 59717, USA; (E.K.L.); (C.B.C.)
| | - Kyle S. Hain
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT 59717, USA; (K.S.H.); (I.K.); (J.F.H.); (A.R.); (D.T.S.); (M.A.J.)
| | - Irina Kochetkova
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT 59717, USA; (K.S.H.); (I.K.); (J.F.H.); (A.R.); (D.T.S.); (M.A.J.)
| | - Jodi F. Hedges
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT 59717, USA; (K.S.H.); (I.K.); (J.F.H.); (A.R.); (D.T.S.); (M.A.J.)
| | - Amanda Robison
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT 59717, USA; (K.S.H.); (I.K.); (J.F.H.); (A.R.); (D.T.S.); (M.A.J.)
| | - Deann T. Snyder
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT 59717, USA; (K.S.H.); (I.K.); (J.F.H.); (A.R.); (D.T.S.); (M.A.J.)
| | - Susan K. Brumfield
- Department of Plant Science and Plant Pathology, Montana State University; Bozeman, MT 59717, USA; (S.K.B.); (M.J.Y.)
| | - Mark J. Young
- Department of Plant Science and Plant Pathology, Montana State University; Bozeman, MT 59717, USA; (S.K.B.); (M.J.Y.)
| | - Mark A. Jutila
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT 59717, USA; (K.S.H.); (I.K.); (J.F.H.); (A.R.); (D.T.S.); (M.A.J.)
| | - Connie B. Chang
- Department of Chemical & Biological Engineering, Montana State University, Bozeman, MT 59717, USA; (E.K.L.); (C.B.C.)
| | - Matthew P. Taylor
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT 59717, USA; (K.S.H.); (I.K.); (J.F.H.); (A.R.); (D.T.S.); (M.A.J.)
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34
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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.
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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
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35
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Yu A, Pak AJ, He P, Monje-Galvan V, Casalino L, Gaieb Z, Dommer AC, Amaro RE, Voth GA. A multiscale coarse-grained model of the SARS-CoV-2 virion. Biophys J 2021; 120:1097-1104. [PMID: 33253634 PMCID: PMC7695975 DOI: 10.1016/j.bpj.2020.10.048] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/27/2020] [Accepted: 10/30/2020] [Indexed: 01/01/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the COVID-19 pandemic. Computer simulations of complete viral particles can provide theoretical insights into large-scale viral processes including assembly, budding, egress, entry, and fusion. Detailed atomistic simulations are constrained to shorter timescales and require billion-atom simulations for these processes. Here, we report the current status and ongoing development of a largely "bottom-up" coarse-grained (CG) model of the SARS-CoV-2 virion. Data from a combination of cryo-electron microscopy (cryo-EM), x-ray crystallography, and computational predictions were used to build molecular models of structural SARS-CoV-2 proteins, which were then assembled into a complete virion model. We describe how CG molecular interactions can be derived from all-atom simulations, how viral behavior difficult to capture in atomistic simulations can be incorporated into the CG models, and how the CG models can be iteratively improved as new data become publicly available. Our initial CG model and the detailed methods presented are intended to serve as a resource for researchers working on COVID-19 who are interested in performing multiscale simulations of the SARS-CoV-2 virion.
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Affiliation(s)
- Alvin Yu
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics and James Franck Institute, The University of Chicago, Chicago, Illinois
| | - Alexander J Pak
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics and James Franck Institute, The University of Chicago, Chicago, Illinois
| | - Peng He
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics and James Franck Institute, The University of Chicago, Chicago, Illinois
| | - Viviana Monje-Galvan
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics and James Franck Institute, The University of Chicago, Chicago, Illinois
| | - Lorenzo Casalino
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
| | - Zied Gaieb
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
| | - Abigail C Dommer
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics and James Franck Institute, The University of Chicago, Chicago, Illinois.
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36
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Barauna VG, Singh MN, Barbosa LL, Marcarini WD, Vassallo PF, Mill JG, Ribeiro-Rodrigues R, Campos LCG, Warnke PH, Martin FL. Ultrarapid On-Site Detection of SARS-CoV-2 Infection Using Simple ATR-FTIR Spectroscopy and an Analysis Algorithm: High Sensitivity and Specificity. Anal Chem 2021; 93:2950-2958. [PMID: 33481583 PMCID: PMC7857139 DOI: 10.1021/acs.analchem.0c04608] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 01/12/2021] [Indexed: 12/15/2022]
Abstract
There is an urgent need for ultrarapid testing regimens to detect the severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2] infections in real-time within seconds to stop its spread. Current testing approaches for this RNA virus focus primarily on diagnosis by RT-qPCR, which is time-consuming, costly, often inaccurate, and impractical for general population rollout due to the need for laboratory processing. The latency until the test result arrives with the patient has led to further virus spread. Furthermore, latest antigen rapid tests still require 15-30 min processing time and are challenging to handle. Despite increased polymerase chain reaction (PCR)-test and antigen-test efforts, the pandemic continues to evolve worldwide. Herein, we developed a superfast, reagent-free, and nondestructive approach of attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy with subsequent chemometric analysis toward the prescreening of virus-infected samples. Contrived saliva samples spiked with inactivated γ-irradiated COVID-19 virus particles at levels down to 1582 copies/mL generated infrared (IR) spectra with a good signal-to-noise ratio. Predominant virus spectral peaks are tentatively associated with nucleic acid bands, including RNA. At low copy numbers, the presence of a virus particle was found to be capable of modifying the IR spectral signature of saliva, again with discriminating wavenumbers primarily associated with RNA. Discrimination was also achievable following ATR-FTIR spectral analysis of swabs immersed in saliva variously spiked with virus. Next, we nested our test system in a clinical setting wherein participants were recruited to provide demographic details, symptoms, parallel RT-qPCR testing, and the acquisition of pharyngeal swabs for ATR-FTIR spectral analysis. Initial categorization of swab samples into negative versus positive COVID-19 infection was based on symptoms and PCR results (n = 111 negatives and 70 positives). Following training and validation (using n = 61 negatives and 20 positives) of a genetic algorithm-linear discriminant analysis (GA-LDA) algorithm, a blind sensitivity of 95% and specificity of 89% was achieved. This prompt approach generates results within 2 min and is applicable in areas with increased people traffic that require sudden test results such as airports, events, or gate controls.
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Affiliation(s)
- Valério G. Barauna
- Department
of Physiological Sciences, Federal University
of Espírito Santo, 29075-910 Vitoria, Brazil
| | - Maneesh N. Singh
- Biocel
UK Ltd., 15 Riplingham
Road, West Ella, Hull HU10
6TS, U.K.
| | - Leonardo Leal Barbosa
- Department
of Physiological Sciences, Federal University
of Espírito Santo, 29075-910 Vitoria, Brazil
| | - Wena Dantas Marcarini
- Department
of Physiological Sciences, Federal University
of Espírito Santo, 29075-910 Vitoria, Brazil
| | - Paula Frizera Vassallo
- Department
of Physiological Sciences, Federal University
of Espírito Santo, 29075-910 Vitoria, Brazil
- Clinical
Hospital, Federal University of Minas Gerais, 31270-901 Belo
Horizonte, Brazil
| | - Jose Geraldo Mill
- Department
of Physiological Sciences, Federal University
of Espírito Santo, 29075-910 Vitoria, Brazil
| | | | - Luciene C. G. Campos
- Department
of Biological Science, Santa Cruz State
University, 45662-900 Bahia, Brazil
| | - Patrick H. Warnke
- Praxisklinik
am Ballastkai, Ballastkai
5, 24937 Flensburg, Germany
- Department
of OMF-Surgery, Christian-Albrechts-University
of Kiel, 24118 Kiel, Germany
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Gatault P, Jones IKA, Meyer C, Kreklywich C, Alexander T, Smith PP, Denton M, Powell J, Orloff SL, Streblow DN. Rat and human cytomegalovirus ORF116 encodes a virion envelope glycoprotein required for infectivity. Virology 2021; 557:23-33. [PMID: 33601113 DOI: 10.1016/j.virol.2020.12.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/22/2020] [Accepted: 12/23/2020] [Indexed: 11/17/2022]
Abstract
Herpesviruses encode multiple glycoproteins required for different stages of viral attachment, fusion, and envelopment. The protein encoded by the human cytomegalovirus (HCMV) open reading frame UL116 forms a stable complex with glycoprotein H that is incorporated into virions. However, the function of this complex remains unknown. Herein, we characterize R116, the rat CMV (RCMV) putative homolog of UL116. Two R116 transcripts were identified in fibroblasts with three proteins expressed with molecular weights of 42, 58, and 82 kDa. R116 is N-glycosylated, expressed with late viral gene kinetics, and is incorporated into the virion envelope. RCMV lacking R116 failed to result in productive infection of fibroblasts and siRNA knockdown of R116 substantially reduced RCMV infectivity. Complementation in trans of an R116-deficient virus restored ability of the virus to infect fibroblasts. Finally, UL116 knockdown also decreased HCMV infectivity indicating that R116 and UL116 both contribute to viral infectivity.
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Affiliation(s)
- Philippe Gatault
- Renal Transplant Unit, 10 Boulevard Tonnellé, University Hospital of Tours, France
| | - Iris K A Jones
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Christine Meyer
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Craig Kreklywich
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Timothy Alexander
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Patricia P Smith
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Michael Denton
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Josh Powell
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Susan L Orloff
- Department of Surgery, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Daniel N Streblow
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Portland, OR, 97239, USA.
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Nguyen N, Strnad O, Klein T, Luo D, Alharbi R, Wonka P, Maritan M, Mindek P, Autin L, Goodsell DS, Viola I. Modeling in the Time of COVID-19: Statistical and Rule-based Mesoscale Models. IEEE Trans Vis Comput Graph 2021; 27:722-732. [PMID: 33055034 PMCID: PMC8642830 DOI: 10.1109/tvcg.2020.3030415] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/31/2020] [Accepted: 08/14/2020] [Indexed: 06/11/2023]
Abstract
We present a new technique for the rapid modeling and construction of scientifically accurate mesoscale biological models. The resulting 3D models are based on a few 2D microscopy scans and the latest knowledge available about the biological entity, represented as a set of geometric relationships. Our new visual-programming technique is based on statistical and rule-based modeling approaches that are rapid to author, fast to construct, and easy to revise. From a few 2D microscopy scans, we determine the statistical properties of various structural aspects, such as the outer membrane shape, the spatial properties, and the distribution characteristics of the macromolecular elements on the membrane. This information is utilized in the construction of the 3D model. Once all the imaging evidence is incorporated into the model, additional information can be incorporated by interactively defining the rules that spatially characterize the rest of the biological entity, such as mutual interactions among macromolecules, and their distances and orientations relative to other structures. These rules are defined through an intuitive 3D interactive visualization as a visual-programming feedback loop. We demonstrate the applicability of our approach on a use case of the modeling procedure of the SARS-CoV-2 virion ultrastructure. This atomistic model, which we present here, can steer biological research to new promising directions in our efforts to fight the spread of the virus.
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Affiliation(s)
- Ngan Nguyen
- King Abdullah University of Science and Technology (KAUST)Saudi Arabia
| | - Ondřej Strnad
- King Abdullah University of Science and Technology (KAUST)Saudi Arabia
| | | | - Deng Luo
- King Abdullah University of Science and Technology (KAUST)Saudi Arabia
| | - Ruwayda Alharbi
- King Abdullah University of Science and Technology (KAUST)Saudi Arabia
| | - Peter Wonka
- King Abdullah University of Science and Technology (KAUST)Saudi Arabia
| | | | | | | | | | - Ivan Viola
- King Abdullah University of Science and Technology (KAUST)Saudi Arabia
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Chakravarty A, Rao AL. The interplay between capsid dynamics and pathogenesis in tripartite bromoviruses. Curr Opin Virol 2021; 47:45-51. [PMID: 33517133 DOI: 10.1016/j.coviro.2020.12.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/17/2020] [Accepted: 12/24/2020] [Indexed: 11/18/2022]
Abstract
Infectious virus capsids or virions are considered static structures and undergo various conformational transitions to replicate and infect a wide range of eukaryotic cells. Therefore, virus capsids must be stable enough to overcome the physicochemical environment and flexible enough to reorganize their biologically relevant surface peptides for optimal interaction with the host machinery. Although viral capsid fluctuations, referred to as dynamics or breathing, have been well studied in RNA viruses pathogenic to animals, such information is limited among plant viruses. However, more recent attempts have been made in characterizing the capsid dynamics in the plant virus genus bromovirus characterized by having a tripartite, positive-sense RNA genome. Using the available research data on the genus bromovirus members, this review is focused on updating the readers on the interrelationships between the viral capsid dynamics and host-pathogen interactions.
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Affiliation(s)
- Antara Chakravarty
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521-0122, United States
| | - Ayala Ln Rao
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521-0122, United States.
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Sharma A, Preece B, Swann H, Fan X, McKenney RJ, Ori-McKenney KM, Saffarian S, Vershinin MD. Structural stability of SARS-CoV-2 virus like particles degrades with temperature. Biochem Biophys Res Commun 2021; 534:343-346. [PMID: 33272571 PMCID: PMC7699159 DOI: 10.1016/j.bbrc.2020.11.080] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 11/18/2020] [Indexed: 12/15/2022]
Abstract
SARS-CoV-2 is a novel coronavirus which has caused the COVID-19 pandemic. Other known coronaviruses show a strong pattern of seasonality, with the infection cases in humans being more prominent in winter. Although several plausible origins of such seasonal variability have been proposed, its mechanism is unclear. SARS-CoV-2 is transmitted via airborne droplets ejected from the upper respiratory tract of the infected individuals. It has been reported that SARS-CoV-2 can remain infectious for hours on surfaces. As such, the stability of viral particles both in liquid droplets as well as dried on surfaces is essential for infectivity. Here we have used atomic force microscopy to examine the structural stability of individual SARS-CoV-2 virus like particles at different temperatures. We demonstrate that even a mild temperature increase, commensurate with what is common for summer warming, leads to dramatic disruption of viral structural stability, especially when the heat is applied in the dry state. This is consistent with other existing non-mechanistic studies of viral infectivity, provides a single particle perspective on viral seasonality, and strengthens the case for a resurgence of COVID-19 in winter.
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Affiliation(s)
- A Sharma
- Department of Physics and Astronomy, University of Utah, Salt Lake City, UT, USA
| | - B Preece
- Department of Physics and Astronomy, University of Utah, Salt Lake City, UT, USA
| | - H Swann
- Department of Physics and Astronomy, University of Utah, Salt Lake City, UT, USA
| | - X Fan
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, USA
| | - R J McKenney
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, USA
| | - K M Ori-McKenney
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, USA
| | - S Saffarian
- Department of Physics and Astronomy, University of Utah, Salt Lake City, UT, USA; Center for Cell and Genome Science, University of Utah, Salt Lake City, UT, USA; Department of Biology, University of Utah, Salt Lake City, UT, USA.
| | - M D Vershinin
- Department of Physics and Astronomy, University of Utah, Salt Lake City, UT, USA; Center for Cell and Genome Science, University of Utah, Salt Lake City, UT, USA; Department of Biology, University of Utah, Salt Lake City, UT, USA.
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41
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Abstract
A common characteristic of virus capsids is icosahedral symmetry, yet these highly symmetric structures can display asymmetric features within their virions and undergo asymmetric dynamics. The fields of structural and computational biology have entered a new realm in the investigation of virus infection mechanisms, with the ability to observe symmetry-breaking features. This review will cover important studies on icosahedral virus structure and dynamics, covering both symmetric and asymmetric conformational changes. However, the main emphasis of the review will be towards recent studies employing cryo-electron microscopy or molecular dynamics simulations, which can uncover asymmetric aspects of these systems relevant to understanding viral physical-chemical properties and their biological impact.
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Affiliation(s)
- Asis K Jana
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Eric R May
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA.
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Croft S, Wong YC, Smith SA, Flesch IEA, Tscharke DC. Surprisingly Effective Priming of CD8 + T Cells by Heat-Inactivated Vaccinia Virus Virions. J Virol 2020; 94:e01486-20. [PMID: 32759313 PMCID: PMC7527048 DOI: 10.1128/jvi.01486-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 07/27/2020] [Indexed: 12/29/2022] Open
Abstract
Robust priming of CD8+ T cells by viruses is considered to require infection and de novo expression of viral antigens. A corollary of this is that inactivated viruses are thought of as being inevitably poor vaccines for eliciting these responses. In contrast to this dogma, we found that some antigens present in vaccinia virus (VACV) virions prime strong CD8+ T cell responses when the virus was rendered noninfectious by heat. More surprisingly, in some cases these responses were similar in magnitude to those primed by infectious virus administered at an equivalent dose. Next, we tested whether this was a special property of particular antigens and their epitopes and found that foreign epitopes tagged onto three different VACV virion proteins were able to elicit CD8+ T cell responses irrespective of whether the virus was viable or heat killed. Further, the polyfunctionality and cytotoxic ability of the CD8+ T cells primed by these VACVs was equivalent irrespective of whether they were administered to mice as inactivated or live viruses. Finally, we used these VACVs in prime-boost combinations of inactivated and live virus and found that priming with dead virus before a live booster was the most immunogenic regime. We conclude that VACV virions can be efficient vectors for targeting antigens to dendritic cells for effective priming of CD8+ T cells, even when rendered noninfectious and speculate that this might also be the case for other viruses.IMPORTANCE The design of viral vectored vaccines is often considered to require a trade-off between efficacy and safety. This is especially the case for vaccines that aim to induce killer (CD8+) T cells, where there is a well-established dogma that links infection in vaccinated individuals with effective induction of immunity. However, we found that some proteins of vaccinia virus generate strong CD8+ T cell responses even when the virus preparation was inactivated by heat prior to administration as a vaccine. We took advantage of this finding by engineering a new vaccine vector virus that could be used as an inactivated vaccine. These results suggest that vaccinia virus may be a more versatile vaccine vector than previously appreciated and that in some instances safety can be prioritized by the complete elimination of viral replication without a proportional loss of immunogenicity.
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Affiliation(s)
- Sarah Croft
- John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Yik Chun Wong
- John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Stewart A Smith
- John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Inge E A Flesch
- John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - David C Tscharke
- John Curtin School of Medical Research, The Australian National University, Canberra, Australia
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43
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Mäntynen S, Laanto E, Sundberg LR, Poranen MM, Oksanen HM, Report Consortium ICTV. ICTV Virus Taxonomy Profile: Finnlakeviridae. J Gen Virol 2020; 101:894-895. [PMID: 32840474 PMCID: PMC7654751 DOI: 10.1099/jgv.0.001488] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 08/05/2020] [Indexed: 01/21/2023] Open
Abstract
Finnlakeviridae is a family of icosahedral, internal membrane-containing bacterial viruses with circular, single-stranded DNA genomes. The family includes the genus, Finnlakevirus, with the species, Flavobacterium virus FLiP. Flavobacterium phage FLiP was isolated with its Gram-negative host bacterium from a boreal freshwater habitat in Central Finland in 2010. It is the first described single-stranded DNA virus with an internal membrane and shares minimal sequence similarity with other known viruses. The virion organization (pseudo T=21 dextro) and major capsid protein fold (double-β-barrel) resemble those of Pseudoalteromonas phage PM2 (family Corticoviridae), which has a double-stranded DNA genome. A similar major capsid protein fold is also found in other double-stranded DNA viruses in the kingdom Bamfordvirae. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) report on the family Finnlakeviridae, which is available at ictv.global/report/finnlakeviridae.
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Affiliation(s)
- Sari Mäntynen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, 00014 University of Helsinki, Finland
- Department of Microbiology and Molecular Genetics, University of California, Davis, One Shields Avenue, Davis, California 95616, USA
| | - Elina Laanto
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, 00014 University of Helsinki, Finland
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, Survontie 9, 40014 University of Jyväskylä, Finland
| | - Lotta-Riina Sundberg
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, Survontie 9, 40014 University of Jyväskylä, Finland
| | - Minna M. Poranen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, 00014 University of Helsinki, Finland
| | - Hanna M. Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, 00014 University of Helsinki, Finland
| | - ICTV Report Consortium
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, 00014 University of Helsinki, Finland
- Department of Microbiology and Molecular Genetics, University of California, Davis, One Shields Avenue, Davis, California 95616, USA
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, Survontie 9, 40014 University of Jyväskylä, Finland
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44
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Riedel C, Hennrich AA, Conzelmann KK. Components and Architecture of the Rhabdovirus Ribonucleoprotein Complex. Viruses 2020; 12:v12090959. [PMID: 32872471 PMCID: PMC7552012 DOI: 10.3390/v12090959] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/27/2020] [Accepted: 08/27/2020] [Indexed: 12/14/2022] Open
Abstract
Rhabdoviruses, as single-stranded, negative-sense RNA viruses within the order Mononegavirales, are characterised by bullet-shaped or bacteroid particles that contain a helical ribonucleoprotein complex (RNP). Here, we review the components of the RNP and its higher-order structural assembly.
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Affiliation(s)
- Christiane Riedel
- Institute of Virology, Department of Pathobiology, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
- Correspondence:
| | - Alexandru A. Hennrich
- Max von Pettenkofer-Institute Virology, Faculty of Medicine, and Gene Center, LMU Munich, 81377 Munich, Germany; (A.A.H.); (K.-K.C.)
| | - Karl-Klaus Conzelmann
- Max von Pettenkofer-Institute Virology, Faculty of Medicine, and Gene Center, LMU Munich, 81377 Munich, Germany; (A.A.H.); (K.-K.C.)
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45
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Li Z, Li W, Lu M, Bess J, Chao CW, Gorman J, Terry DS, Zhang B, Zhou T, Blanchard SC, Kwong PD, Lifson JD, Mothes W, Liu J. Subnanometer structures of HIV-1 envelope trimers on aldrithiol-2-inactivated virus particles. Nat Struct Mol Biol 2020; 27:726-734. [PMID: 32601441 PMCID: PMC8138683 DOI: 10.1038/s41594-020-0452-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 05/18/2020] [Indexed: 12/12/2022]
Abstract
The HIV-1 envelope glycoprotein (Env) trimer, composed of gp120 and gp41 subunits, mediates viral entry into cells. Recombinant Env trimers have been studied structurally, but characterization of Env embedded in intact virus membranes has been limited to low resolution. Here, we deploy cryo-electron tomography and subtomogram averaging to determine the structures of Env trimers on aldrithiol-2 (AT-2)-inactivated virions in ligand-free, antibody-bound and CD4-bound forms at subnanometer resolution. Tomographic reconstructions document molecular features consistent with high-resolution structures of engineered soluble and detergent-solubilized Env trimers. One of three conformational states previously predicted by smFRET was not observed by cryo-ET, potentially owing to AT-2 inactivation. We did observe Env trimers to open in situ in response to CD4 binding, with an outward movement of gp120-variable loops and an extension of a critical gp41 helix. Overall features of Env trimer embedded in AT-2-treated virions appear well-represented by current engineered trimers.
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Affiliation(s)
- Ze Li
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Fudan University Shanghai Cancer Center, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wenwei Li
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
| | - Maolin Lu
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Julian Bess
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Cara W Chao
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Daniel S Terry
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Scott C Blanchard
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA.
| | - Jun Liu
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA.
- Microbial Sciences Institute, Yale University, West Haven, CT, USA.
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Wagemans J, Tsonos J, Holtappels D, Fortuna K, Hernalsteens JP, De Greve H, Estrozi LF, Bacia-Verloop M, Moriscot C, Noben JP, Schoehn G, Lavigne R. Structural Analysis of Jumbo Coliphage phAPEC6. Int J Mol Sci 2020; 21:ijms21093119. [PMID: 32354127 PMCID: PMC7247149 DOI: 10.3390/ijms21093119] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 04/27/2020] [Accepted: 04/27/2020] [Indexed: 01/24/2023] Open
Abstract
The phAPEC6 genome encodes 551 predicted gene products, with the vast majority (83%) of unknown function. Of these, 62 have been identified as virion-associated proteins by mass spectrometry (ESI-MS/MS), including the major capsid protein (Gp225; present in 1620 copies), which shows a HK97 capsid protein-based fold. Cryo-electron microscopy experiments showed that the 350-kbp DNA molecule of Escherichia coli virus phAPEC6 is packaged in at least 15 concentric layers in the phage capsid. A capsid inner body rod is also present, measuring about 91 nm by 18 nm and oriented along the portal axis. In the phAPEC6 contractile tail, 25 hexameric stacked rings can be distinguished, built of the identified tail sheath protein (Gp277). Cryo-EM reconstruction reveals the base of the unique hairy fibers observed during an initial transmission electron microscopy (TEM) analysis. These very unusual filaments are ordered at three annular positions along the contractile sheath, as well as around the capsid, and may be involved in host interaction.
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Affiliation(s)
- Jeroen Wagemans
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21—box 2462, 3001 Leuven, Belgium; (J.W.); (J.T.); (D.H.); (K.F.)
| | - Jessica Tsonos
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21—box 2462, 3001 Leuven, Belgium; (J.W.); (J.T.); (D.H.); (K.F.)
- Department of Biology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium;
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium;
| | - Dominique Holtappels
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21—box 2462, 3001 Leuven, Belgium; (J.W.); (J.T.); (D.H.); (K.F.)
| | - Kiandro Fortuna
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21—box 2462, 3001 Leuven, Belgium; (J.W.); (J.T.); (D.H.); (K.F.)
| | | | - Henri De Greve
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium;
- VIB Center for Structural Biology, Pleinlaan 2, 1050 Brussels, Belgium
| | - Leandro F. Estrozi
- Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France; (L.F.E.); (M.B.-V.)
| | - Maria Bacia-Verloop
- Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France; (L.F.E.); (M.B.-V.)
| | - Christine Moriscot
- Univ. Grenoble Alpes, CNRS, CEA, EMBL, Integrated Structural Biology Grenoble (ISBG), F-38042 Grenoble, France;
| | - Jean-Paul Noben
- Biomedical Research Institute and Transnational University Limburg, Hasselt University, Agoralaan D, 3590 Hasselt, Belgium;
| | - Guy Schoehn
- Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France; (L.F.E.); (M.B.-V.)
- Correspondence: (G.S.); (R.L.); Tel.: +33-4-5742-8568 (G.S.); +32-16-3795-24 (R.L.)
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21—box 2462, 3001 Leuven, Belgium; (J.W.); (J.T.); (D.H.); (K.F.)
- Correspondence: (G.S.); (R.L.); Tel.: +33-4-5742-8568 (G.S.); +32-16-3795-24 (R.L.)
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Martín-Bravo M, Gomez Llorente JM, Hernández-Rojas J. A minimal coarse-grained model for the low-frequency normal mode analysis of icosahedral viral capsids. Soft Matter 2020; 16:3443-3455. [PMID: 32196061 DOI: 10.1039/d0sm00299b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The main goal of this work is the design of a coarse-grained theoretical model of minimal resolution for the study of the physical properties of icosahedral virus capsids within the linear-response regime. In this model the capsid is represented as an interacting many-body system whose composing elements are capsid subunits (capsomers), which are treated as three-dimensional rigid bodies. The total interaction potential energy is written as a sum of pairwise capsomer-capsomer interactions. Based on previous work [Gomez Llorente et al., Soft Matter, 2014, 10, 3560], a minimal and complete anisotropic binary interaction that includes a full Hessian matrix of independent force constants is proposed. In this interaction model, capsomers have rotational symmetry around an axis of order n > 2. The full coarse-grained model is applied to analyse the low-frequency normal-mode spectrum of icosahedral T = 1 capsids. The model performance is evaluated by fitting its predicted spectrum to the full-atom results for the Satellite Tobacco Necrosis Virus (STNV) capsid [Dykeman and Sankey, Phys. Rev. Lett., 2008, 100, 028101]. Two capsomer choices that are compatible with the capsid icosahedral symmetry are checked, namely pentamers (n = 5) and trimers (n = 3). Both subunit types provide fair fits, from which the magnitude of the coarse-grained force constants for a real virus is obtained. The model is able to uncover latent instabilities whose analysis is fully consistent with the current knowledge about the STNV capsid, which does not self-assemble in the absence of RNA and is thermally unstable. The straightforward generalisability of the model beyond the linear regime and its completeness make it a promising tool to theoretically interpret many experimental data such as those provided by the atomic force microscopy or even to better understand processes far from equilibrium such as the capsid self-assembly.
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Affiliation(s)
- M Martín-Bravo
- Departamento de Física and IUdEA, Universidad de La Laguna, 38200 Tenerife, Spain.
| | - J M Gomez Llorente
- Departamento de Física and IUdEA, Universidad de La Laguna, 38200 Tenerife, Spain.
| | - J Hernández-Rojas
- Departamento de Física and IUdEA, Universidad de La Laguna, 38200 Tenerife, Spain.
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48
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Zhou Y, Routh A. Mapping RNA-capsid interactions and RNA secondary structure within virus particles using next-generation sequencing. Nucleic Acids Res 2020; 48:e12. [PMID: 31799606 PMCID: PMC6954446 DOI: 10.1093/nar/gkz1124] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/31/2019] [Accepted: 11/16/2019] [Indexed: 01/24/2023] Open
Abstract
To characterize RNA-capsid binding sites genome-wide within mature RNA virus particles, we have developed a Next-Generation Sequencing (NGS) platform: viral Photo-Activatable Ribonucleoside CrossLinking (vPAR-CL). In vPAR-CL, 4-thiouridine is incorporated into the encapsidated genomes of virus particles and subsequently UV-crosslinked to adjacent capsid proteins. We demonstrate that vPAR-CL can readily and reliably identify capsid binding sites in genomic viral RNA by detecting crosslink-specific uridine to cytidine transitions in NGS data. Using Flock House virus (FHV) as a model system, we identified highly consistent and significant vPAR-CL signals across virus RNA genome, indicating a clear tropism of the encapsidated RNA genome. Certain interaction sites coincide with previously identified functional RNA motifs. We additionally performed dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) to generate a high-resolution profile of single-stranded genomic RNA inside viral particles. Combining vPAR-CL and DMS-MaPseq reveals that the predominant RNA-capsid interaction sites favored double-stranded RNA regions. We disrupted secondary structures associated with vPAR-CL sites using synonymous mutations, resulting in varied effects to virus replication, propagation and packaging. Certain mutations showed substantial deficiency in virus replication, suggesting these RNA-capsid sites are multifunctional. These provide further evidence to support that FHV packaging and replication are highly coordinated and inter-dependent events.
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Affiliation(s)
- Yiyang Zhou
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
| | - Andrew Routh
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
- To whom correspondence should be address. Tel: +1 409 772 3663;
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49
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Watts S, Julian TR, Maniura-Weber K, Graule T, Salentinig S. Colloidal Transformations in MS2 Virus Particles: Driven by pH, Influenced by Natural Organic Matter. ACS Nano 2020; 14:1879-1887. [PMID: 32027487 DOI: 10.1021/acsnano.9b08112] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Enteric viruses, such as enterovirus, norovirus, and rotavirus, are among the leading causes of disease outbreaks due to contaminated drinking and recreational water. Viruses are difficult to remove from water through filtration based on physical size exclusion-for example by gravity-driven filters-due to their nanoscale size. To understand virus removal in drinking water treatment systems, the colloidal nanostructure of a model virus, the MS2 bacteriophage, has been investigated in relation to the effect of pH and natural organic matter in water. Dynamic light scattering, small-angle X-ray scattering, and cryogenic transmission electron microscopy demonstrated that the water pH has a major influence on the colloidal structure of the virus: The bacteriophage MS2's structure in water in the range pH = 7.0 to 9.0 was found to be spherical with core-shell-type structure with a total diameter of 27 nm and a core radius of around 8 nm. Reversible transformations from 27 nm particles at pH = 7.0 to micrometer-sized aggregates at pH = 3.0 were observed. In addition, the presence of natural organic matter that simulates the organic components present in surface water was found to enhance repulsion between virus particles, reduce the size of aggregates, and promote disaggregation upon pH increase. These findings allow a better understanding of virus interactions in water and have implications for water treatment using filtration processes and coagulation. The results will further guide the comprehensive design of advanced virus filter materials.
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Affiliation(s)
- Samuel Watts
- Biointerfaces Lab , Empa, Swiss Federal Laboratories for Material Science and Technology , Lerchenfeldstrasse 5 , 9014 St. Gallen , Switzerland
| | - Timothy R Julian
- Eawag , Swiss Federal Institute of Aquatic Science , Überlandstrasse 133 , 8600 Dübendorf , Switzerland
- Swiss Tropical and Public Health Institute , 4002 Basel , Switzerland
- University of Basel , 4003 Basel , Switzerland
| | - Katharina Maniura-Weber
- Biointerfaces Lab , Empa, Swiss Federal Laboratories for Material Science and Technology , Lerchenfeldstrasse 5 , 9014 St. Gallen , Switzerland
| | - Thomas Graule
- High Performance Ceramics Lab , Empa, Swiss Federal Laboratories for Materials Science and Technology , Überlandstrasse 129 , 8600 Dübendorf , Switzerland
| | - Stefan Salentinig
- Biointerfaces Lab , Empa, Swiss Federal Laboratories for Material Science and Technology , Lerchenfeldstrasse 5 , 9014 St. Gallen , Switzerland
- Department of Chemistry , University of Fribourg , Chemin du Musée 9 , 1700 Fribourg , Switzerland
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50
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Yoshimura M, Chen NC, Guan HH, Chuankhayan P, Lin CC, Nakagawa A, Chen CJ. Noncrystallographic symmetry-constrained map obtained by direct density optimization. Acta Crystallogr D Struct Biol 2020; 76:147-154. [PMID: 32038045 PMCID: PMC7008515 DOI: 10.1107/s2059798319017297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 12/27/2019] [Indexed: 11/11/2022] Open
Abstract
Noncrystallographic symmetry (NCS) averaging following molecular-replacement phasing is generally the major technique used to solve a structure with several molecules in one asymmetric unit, such as a spherical icosahedral viral particle. As an alternative method to NCS averaging, a new approach to optimize or to refine the electron density directly under NCS constraints is proposed. This method has the same effect as the conventional NCS-averaging method but does not include the process of Fourier synthesis to generate the electron density from amplitudes and the corresponding phases. It has great merit for the solution of structures with limited data that are either twinned or incomplete at low resolution. This method was applied to the case of the T = 1 shell-domain subviral particle of Penaeus vannamei nodavirus with data affected by twinning using the REFMAC5 refinement software.
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Affiliation(s)
- Masato Yoshimura
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu 30076, Taiwan
| | - Nai-Chi Chen
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu 30076, Taiwan
| | - Hong-Hsiang Guan
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu 30076, Taiwan
| | - Phimonphan Chuankhayan
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu 30076, Taiwan
| | - Chien-Chih Lin
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu 30076, Taiwan
| | - Atsushi Nakagawa
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Chun-Jung Chen
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu 30076, Taiwan
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan 701, Taiwan
- Department of Physics, National Tsing Hua University, Hsinchu 30043, Taiwan
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