1
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Liu J, Corroyer-Dulmont S, Pražák V, Khusainov I, Bahrami K, Welsch S, Vasishtan D, Obarska-Kosińska A, Thorkelsson SR, Grünewald K, Quemin ERJ, Turoňová B, Locker JK. The palisade layer of the poxvirus core is composed of flexible A10 trimers. Nat Struct Mol Biol 2024; 31:1105-1113. [PMID: 38316878 PMCID: PMC11257942 DOI: 10.1038/s41594-024-01218-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 01/05/2024] [Indexed: 02/07/2024]
Abstract
Due to its asymmetric shape, size and compactness, the structure of the infectious mature virus (MV) of vaccinia virus (VACV), the best-studied poxvirus, remains poorly understood. Instead, subviral particles, in particular membrane-free viral cores, have been studied with cryo-electron microscopy. Here, we compared viral cores obtained by detergent stripping of MVs with cores in the cellular cytoplasm, early in infection. We focused on the prominent palisade layer on the core surface, combining cryo-electron tomography, subtomogram averaging and AlphaFold2 structure prediction. We showed that the palisade is composed of densely packed trimers of the major core protein A10. Trimers display a random order and their classification indicates structural flexibility. A10 on cytoplasmic cores is organized in a similar manner, indicating that the structures obtained in vitro are physiologically relevant. We discuss our results in the context of the VACV replicative cycle, and the assembly and disassembly of the infectious MV.
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Affiliation(s)
- Jiasui Liu
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Simon Corroyer-Dulmont
- Centre for Structural Systems Biology, Leibniz Institute of Virology, Hamburg, Germany
- University of Hamburg, Hamburg, Germany
| | - Vojtěch Pražák
- Centre for Structural Systems Biology, Leibniz Institute of Virology, Hamburg, Germany
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Iskander Khusainov
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Karola Bahrami
- Electron Microscopy of Pathogens, Paul Ehrlich Institute, Langen, Germany
- University Clinic Frankfurt, Frankfurt am Main, Germany
| | - Sonja Welsch
- Max Planck Institute of Biophysics, Central Electron Microscopy Facility, Frankfurt am Main, Germany
| | - Daven Vasishtan
- Centre for Structural Systems Biology, Leibniz Institute of Virology, Hamburg, Germany
- Department of Biochemistry, University of Oxford, Oxford, UK
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Sigurdur R Thorkelsson
- Centre for Structural Systems Biology, Leibniz Institute of Virology, Hamburg, Germany
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Kay Grünewald
- Centre for Structural Systems Biology, Leibniz Institute of Virology, Hamburg, Germany.
- University of Hamburg, Hamburg, Germany.
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
| | - Emmanuelle R J Quemin
- Centre for Structural Systems Biology, Leibniz Institute of Virology, Hamburg, Germany.
- Department of Virology, Institute for Integrative Biology of the Cell (I2BC), CNRS UMR9198, Université Paris-Saclay, CEA, Gif-sur-Yvette, France.
| | - Beata Turoňová
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
| | - Jacomina Krijnse Locker
- Electron Microscopy of Pathogens, Paul Ehrlich Institute, Langen, Germany.
- Justus Liebig University of Giessen, Giessen, Germany.
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2
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Coulibaly F. Structure of the poxvirus core. Nat Struct Mol Biol 2024; 31:1001-1003. [PMID: 38890551 DOI: 10.1038/s41594-024-01331-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Affiliation(s)
- Fasséli Coulibaly
- Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia.
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, Australia.
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3
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Datler J, Hansen JM, Thader A, Schlögl A, Bauer LW, Hodirnau VV, Schur FKM. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nat Struct Mol Biol 2024; 31:1114-1123. [PMID: 38316877 PMCID: PMC11257981 DOI: 10.1038/s41594-023-01201-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 12/06/2023] [Indexed: 02/07/2024]
Abstract
Poxviruses are among the largest double-stranded DNA viruses, with members such as variola virus, monkeypox virus and the vaccination strain vaccinia virus (VACV). Knowledge about the structural proteins that form the viral core has remained sparse. While major core proteins have been annotated via indirect experimental evidence, their structures have remained elusive and they could not be assigned to individual core features. Hence, which proteins constitute which layers of the core, such as the palisade layer and the inner core wall, has remained enigmatic. Here we show, using a multi-modal cryo-electron microscopy (cryo-EM) approach in combination with AlphaFold molecular modeling, that trimers formed by the cleavage product of VACV protein A10 are the key component of the palisade layer. This allows us to place previously obtained descriptions of protein interactions within the core wall into perspective and to provide a detailed model of poxvirus core architecture. Importantly, we show that interactions within A10 trimers are likely generalizable over members of orthopox- and parapoxviruses.
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Affiliation(s)
- Julia Datler
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Jesse M Hansen
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Andreas Thader
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Alois Schlögl
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Lukas W Bauer
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | | | - Florian K M Schur
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria.
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4
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You T, Wang M, Zhang H, Wang X, Gao X, Yin X, Sun Y, Wang G, Chen HT, Ren S. Identification of the murine osteoblastic cell MC3T3-E1 as a permissive cell line in response to lumpy skin disease virus. J Virol Methods 2024; 326:114916. [PMID: 38479589 DOI: 10.1016/j.jviromet.2024.114916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 03/08/2024] [Accepted: 03/10/2024] [Indexed: 04/09/2024]
Abstract
Lumpy skin disease virus (LSDV) is a rapidly emerging pathogen in China. Screening suitable cells for LSDV replication is vital for future research on pathogenic mechanisms and vaccine development. Previous comparative studies have identified that the rodent-derived BHK21 is a highly susceptible cell model to LSDV infection. Using western blot, indirect immune-fluorescence assay, flow cytometry, and transmission electron microscopy methods, this study is the first to identify the murine osteoblastic cell line MC3T3-E1 as a novel permissive cell model for LSDV infection. The establishment of MC3T3-E1 as a suitable infectious cell model enhances our understanding of the species range and cell types of the permissive cells and nonpermissive that support LSDV replication. It is helpful to accelerate future research on the pathogenesis, clinical application, and vaccine development of LSDV.
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Affiliation(s)
- Ting You
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, PR China; Laboratory of Veterinary Microbiology, College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Meng Wang
- Laboratory of Veterinary Microbiology, College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Hongqiang Zhang
- Laboratory of Veterinary Microbiology, College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Xiangwei Wang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, PR China
| | - Xiaolong Gao
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, Qinghai 810016, PR China
| | - Xiangping Yin
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, PR China
| | - Yuefeng Sun
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, PR China
| | - Guirong Wang
- Laboratory of Veterinary Microbiology, College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, PR China.
| | - Hao-Tai Chen
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, PR China.
| | - Shanhui Ren
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, PR China.
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5
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Hernandez-Gonzalez M, Calcraft T, Nans A, Rosenthal PB, Way M. Palisade structure in intact vaccinia virions. mBio 2024; 15:e0313423. [PMID: 38171004 PMCID: PMC10865856 DOI: 10.1128/mbio.03134-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024] Open
Abstract
Vaccinia virus assembly in the cytoplasm of infected cells involves the formation of a biconcave viral core inside the maturing viral particle. The boundary of the core is defined by a pseudohexagonal palisade layer, composed of trimers projecting from an inner wall. To understand the assembly of this complex core architecture, we obtained a subnanometer structure of the palisade trimer by cryo-electron tomography and subtomogram averaging of purified intact virions. Using AlphaFold2 structure predictions, we determined that the palisade is formed from trimers of the proteolytically processed form of the viral protein A10. In addition, we found that each A10 protomer associates with an α-helix (residues 24-66) of A4. Cellular localization assays outside the context of infection demonstrate that the A4 N-terminus is necessary and sufficient to interact with A10. The interaction between A4 and A10 provides insights into how the palisade layer might become tightly associated with the viral membrane during virion maturation. Reconstruction of the palisade layer reveals that, despite local hexagonal ordering, the A10/A4 trimers are widely spaced, suggesting that additional components organize the lattice. This spacing would, however, allow the adoption of the characteristic biconcave shape of the viral core. Finally, we also found that the palisade incorporates multiple copies of a hexameric portal structure. We suggest that these portals are formed by E6, a viral protein that is essential for virion assembly and required to release viral mRNA from the core early in infection.IMPORTANCEPoxviruses such as variola virus (smallpox) and monkeypox cause diseases in humans. Other poxviruses, including vaccinia and modified vaccinia Ankara, are used as vaccine vectors. Given their importance, a greater structural understanding of poxvirus virions is needed. We now performed cryo-electron tomography of purified intact vaccinia virions to study the structure of the palisade, a protein lattice that defines the viral core boundary. We identified the main viral proteins that form the palisade and their interaction surfaces and provided new insights into the organization of the viral core.
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Affiliation(s)
- Miguel Hernandez-Gonzalez
- Cellular Signalling and Cytoskeletal Function Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Thomas Calcraft
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Andrea Nans
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Peter B. Rosenthal
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Michael Way
- Cellular Signalling and Cytoskeletal Function Laboratory, The Francis Crick Institute, London, United Kingdom
- Department of Infectious Disease, Imperial College, London, United Kingdom
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6
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Viral agents (2nd section). Transfusion 2024; 64 Suppl 1:S19-S207. [PMID: 38394038 DOI: 10.1111/trf.17630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 12/02/2023] [Indexed: 02/25/2024]
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7
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Aggarwal T, Kondabagil K. Assembly and Evolution of Poxviruses. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1451:35-54. [PMID: 38801570 DOI: 10.1007/978-3-031-57165-7_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Poxvirus assembly has been an intriguing area of research for several decades. While advancements in experimental techniques continue to yield fresh insights, many questions are still unresolved. Large genome sizes of up to 380 kbp, asymmetrical structure, an exterior lipid bilayer, and a cytoplasmic life cycle are some notable characteristics of these viruses. Inside the particle are two lateral bodies and a protein wall-bound-biconcave core containing the viral nucleocapsid. The assembly progresses through five major stages-endoplasmic reticulum (ER) membrane alteration and rupture, crescent formation, immature virion formation, genome encapsidation, virion maturation and in a subset of viruses, additional envelopment of the virion prior to its dissemination. Several large dsDNA viruses have been shown to follow a comparable sequence of events. In this chapter, we recapitulate our understanding of the poxvirus morphogenesis process while reviewing the most recent advances in the field. We also briefly discuss how virion assembly aids in our knowledge of the evolutionary links between poxviruses and other Nucleocytoplasmic Large DNA Viruses (NCLDVs).
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Affiliation(s)
- Tanvi Aggarwal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra, 400076, India
| | - Kiran Kondabagil
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra, 400076, India.
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8
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Riccardo V, Pablo GC. Neutralization Determinants on Poxviruses. Viruses 2023; 15:2396. [PMID: 38140637 PMCID: PMC10747254 DOI: 10.3390/v15122396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Smallpox was a highly contagious disease caused by the variola virus. The disease affected millions of people over thousands of years and variola virus ranked as one of the deadliest viruses in human history. The complete eradication of smallpox in 1980, a major triumph in medicine, was achieved through a global vaccination campaign using a less virulent poxvirus, vaccinia virus. Despite this success, the herd immunity established by this campaign has significantly waned, and concerns are rising about the potential reintroduction of variola virus as a biological weapon or the emergence of zoonotic poxviruses. These fears were further fueled in 2022 by a global outbreak of monkeypox virus (mpox), which spread to over 100 countries, thereby boosting interest in developing new vaccines using molecular approaches. However, poxviruses are complex and creating modern vaccines against them is challenging. This review focuses on the structural biology of the six major neutralization determinants on poxviruses (D8, H3, A27, L1, B5, and A33), the localization of epitopes targeted by neutralizing antibodies, and their application in the development of subunit vaccines.
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Affiliation(s)
| | - Guardado-Calvo Pablo
- Structural Biology of Infectious Diseases Unit, Institut Pasteur, Université Paris Cité, F-75015 Paris, France;
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9
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Mirzakhanyan Y, Jankevics A, Scheltema RA, Gershon PD. Combination of deep XLMS with deep learning reveals an ordered rearrangement and assembly of a major protein component of the vaccinia virion. mBio 2023; 14:e0113523. [PMID: 37646531 PMCID: PMC10653903 DOI: 10.1128/mbio.01135-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 07/11/2023] [Indexed: 09/01/2023] Open
Abstract
IMPORTANCE An outstanding problem in the understanding of poxvirus biology is the molecular structure of the mature virion. Via deep learning methods combined with chemical cross-linking mass spectrometry, we have addressed the structure and assembly pathway of P4a, a key poxvirus virion core component.
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Affiliation(s)
- Yeva Mirzakhanyan
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California, USA
| | - Andris Jankevics
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, the Netherlands
| | - Richard A. Scheltema
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, the Netherlands
| | - Paul David Gershon
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California, USA
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10
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Xia Q, Guo Z, Zong H, Seitz S, Yurdakul C, Ünlü MS, Wang L, Connor JH, Cheng JX. Single virus fingerprinting by widefield interferometric defocus-enhanced mid-infrared photothermal microscopy. Nat Commun 2023; 14:6655. [PMID: 37863905 PMCID: PMC10589364 DOI: 10.1038/s41467-023-42439-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 10/11/2023] [Indexed: 10/22/2023] Open
Abstract
Clinical identification and fundamental study of viruses rely on the detection of viral proteins or viral nucleic acids. Yet, amplification-based and antigen-based methods are not able to provide precise compositional information of individual virions due to small particle size and low-abundance chemical contents (e.g., ~ 5000 proteins in a vesicular stomatitis virus). Here, we report a widefield interferometric defocus-enhanced mid-infrared photothermal (WIDE-MIP) microscope for high-throughput fingerprinting of single viruses. With the identification of feature absorption peaks, WIDE-MIP reveals the contents of viral proteins and nucleic acids in single DNA vaccinia viruses and RNA vesicular stomatitis viruses. Different nucleic acid signatures of thymine and uracil residue vibrations are obtained to differentiate DNA and RNA viruses. WIDE-MIP imaging further reveals an enriched β sheet components in DNA varicella-zoster virus proteins. Together, these advances open a new avenue for compositional analysis of viral vectors and elucidating protein function in an assembled virion.
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Affiliation(s)
- Qing Xia
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, 02215, USA
| | - Zhongyue Guo
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Haonan Zong
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, 02215, USA
| | - Scott Seitz
- Department of Microbiology and National Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Celalettin Yurdakul
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, 02215, USA
| | - M Selim Ünlü
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, 02215, USA
| | - Le Wang
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, 02215, USA
| | - John H Connor
- Department of Microbiology and National Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, 02118, USA.
| | - Ji-Xin Cheng
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, 02215, USA.
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA.
- Photonics Center, Boston University, Boston, MA, 02215, USA.
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11
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Sanders S, Jensen Y, Reimer R, Bosse JB. From the beginnings to multidimensional light and electron microscopy of virus morphogenesis. Adv Virus Res 2023; 116:45-88. [PMID: 37524482 DOI: 10.1016/bs.aivir.2023.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Individual functional viral morphogenesis events are often dynamic, short, and infrequent and might be obscured by other pathways and dead-end products. Volumetric live cell imaging has become an essential tool for studying viral morphogenesis events. It allows following entire dynamic processes while providing functional evidence that the imaged process is involved in viral production. Moreover, it allows to capture many individual events and allows quantitative analysis. Finally, the correlation of volumetric live-cell data with volumetric electron microscopy (EM) can provide crucial insights into the ultrastructure and mechanisms of viral morphogenesis events. Here, we provide an overview and discussion of suitable imaging methods for volumetric correlative imaging of viral morphogenesis and frame them in a historical summary of their development.
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Affiliation(s)
- Saskia Sanders
- Department of Virology, Hannover Medical School, Hannover, Germany; Leibniz Institute of Virology (LIV), Hamburg, Germany; Centre for Structural Systems Biology, Hamburg, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Yannick Jensen
- Department of Virology, Hannover Medical School, Hannover, Germany; Leibniz Institute of Virology (LIV), Hamburg, Germany; Centre for Structural Systems Biology, Hamburg, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | | | - Jens B Bosse
- Department of Virology, Hannover Medical School, Hannover, Germany; Leibniz Institute of Virology (LIV), Hamburg, Germany; Centre for Structural Systems Biology, Hamburg, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany.
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12
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Jung JH, Chen X, Reese TS. Cryo-EM tomography and automatic segmentation delineate modular structures in the postsynaptic density. Front Synaptic Neurosci 2023; 15:1123564. [PMID: 37091879 PMCID: PMC10117989 DOI: 10.3389/fnsyn.2023.1123564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/02/2023] [Indexed: 04/08/2023] Open
Abstract
Postsynaptic densities (PSDs) are large protein complexes associated with the postsynaptic membrane of excitatory synapses important for synaptic function including plasticity. Conventional electron microscopy (EM) typically depicts PSDs as compact disk-like structures of hundreds of nanometers in size. Biochemically isolated PSDs were also similar in dimension revealing a predominance of proteins with the ability to polymerize into an extensive scaffold; several EM studies noted their irregular contours with often small granular structures (<30 nm) and holes. Super-resolution light microscopy studies observed clusters of PSD elements and their activity-induced lateral movement. Furthermore, our recent EM study on PSD fractions after sonication observed PSD fragments (40–90 nm in size) separate from intact PSDs; however, such structures within PSDs remained unidentified. Here we examined isolated PSDs by cryo-EM tomography with our new approach of automatic segmentation that enables delineation of substructures and their quantitative analysis. The delineated substructures broadly varied in size, falling behind 30 nm or exceeding 100 nm and showed that a considerable portion of the substructures (>38%) in isolated PSDs was in the same size range as those fragments. Furthermore, substructures spanning the entire thickness of the PSD were found, large enough to contain both membrane-associated and cytoplasmic proteins of the PSD; interestingly, they were similar to nanodomains in frequency. The structures detected here appear to constitute the isolated PSD as modules of various compositions, and this modular nature may facilitate remodeling of the PSD for proper synaptic function and plasticity.
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13
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Hernandez-Gonzalez M, Calcraft T, Nans A, Rosenthal PB, Way M. A succession of two viral lattices drives vaccinia virus assembly. PLoS Biol 2023; 21:e3002005. [PMID: 36862727 PMCID: PMC10013923 DOI: 10.1371/journal.pbio.3002005] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 03/14/2023] [Accepted: 01/19/2023] [Indexed: 03/03/2023] Open
Abstract
During its cytoplasmic replication, vaccinia virus assembles non-infectious spherical immature virions (IV) coated by a viral D13 lattice. Subsequently, IV mature into infectious brick-shaped intracellular mature virions (IMV) that lack D13. Here, we performed cryo-electron tomography (cryo-ET) of frozen-hydrated vaccinia-infected cells to structurally characterise the maturation process in situ. During IMV formation, a new viral core forms inside IV with a wall consisting of trimeric pillars arranged in a new pseudohexagonal lattice. This lattice appears as a palisade in cross-section. As maturation occurs, which involves a 50% reduction in particle volume, the viral membrane becomes corrugated as it adapts to the newly formed viral core in a process that does not appear to require membrane removal. Our study suggests that the length of this core is determined by the D13 lattice and that the consecutive D13 and palisade lattices control virion shape and dimensions during vaccinia assembly and maturation.
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Affiliation(s)
- Miguel Hernandez-Gonzalez
- Cellular signalling and cytoskeletal function laboratory, The Francis Crick Institute, London, United Kingdom
| | - Thomas Calcraft
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Andrea Nans
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Peter B Rosenthal
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Michael Way
- Cellular signalling and cytoskeletal function laboratory, The Francis Crick Institute, London, United Kingdom
- Department of Infectious Disease, Imperial College, London, United Kingdom
- * E-mail:
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14
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Lim CK, Roberts J, Moso M, Liew KC, Taouk ML, Williams E, Tran T, Steinig E, Caly L, Williamson DA. Mpox diagnostics: Review of current and emerging technologies. J Med Virol 2023; 95:e28429. [PMID: 36571266 PMCID: PMC10108241 DOI: 10.1002/jmv.28429] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/12/2022] [Accepted: 12/21/2022] [Indexed: 12/27/2022]
Abstract
Mpox is a zoonotic disease caused by monkeypox virus (MPXV) from the Orthopoxvirus genus. Unprecedented transmission events have led to more than 70 000 cases reported worldwide by October 2022. The change in mpox epidemiology has raised concerns of its ability to establish endemicity beyond its traditional geographical locations. In this review, we discuss the current understanding of mpox virology and viral dynamics that are relevant to mpox diagnostics. A synopsis of the traditional and emerging laboratory technologies useful for MPXV detection and in guiding "elimination" strategies is outlined in this review. Importantly, development in MPXV genomics has rapidly advanced our understanding of the role of viral evolution and adaptation in the current outbreak.
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Affiliation(s)
- Chuan Kok Lim
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,Department of Infectious Diseases, Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jason Roberts
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,Department of Infectious Diseases, Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Michael Moso
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,Department of Infectious Diseases, Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Kwee Chin Liew
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,Department of Infectious Diseases, Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Mona L Taouk
- Department of Infectious Diseases, Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Eloise Williams
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,Department of Infectious Diseases, Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Thomas Tran
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,Department of Infectious Diseases, Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Eike Steinig
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,Department of Infectious Diseases, Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Leon Caly
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,Department of Infectious Diseases, Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Deborah Ann Williamson
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,Department of Infectious Diseases, Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
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15
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Vijayakrishnan S. In Situ Imaging of Virus-Infected Cells by Cryo-Electron Tomography: An Overview. Subcell Biochem 2023; 106:3-36. [PMID: 38159222 DOI: 10.1007/978-3-031-40086-5_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Cryo-electron tomography (cryo-ET) has emerged as a powerful tool in structural biology to study viruses and is undergoing a resolution revolution. Enveloped viruses comprise several RNA and DNA pleomorphic viruses that are pathogens of clinical importance to humans and animals. Considerable efforts in cryogenic correlative light and electron microscopy (cryo-CLEM), cryogenic focused ion beam milling (cryo-FIB), and integrative structural techniques are helping to identify virus structures within cells leading to a rise of in situ discoveries shedding light on how viruses interact with their hosts during different stages of infection. This chapter reviews recent advances in the application of cryo-ET in imaging enveloped viruses and the structural and mechanistic insights revealed studying the viral infection cycle within their eukaryotic cellular hosts, with particular attention to viral entry, replication, assembly, and egress during infection.
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Affiliation(s)
- Swetha Vijayakrishnan
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Garscube Campus, Glasgow, Scotland, UK.
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16
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Hyun J. Poxvirus under the eyes of electron microscope. Appl Microsc 2022; 52:11. [DOI: 10.1186/s42649-022-00080-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/10/2022] [Indexed: 11/15/2022] Open
Abstract
AbstractZoonotic poxvirus infections pose significant threat to human health as we have witnessed recent spread of monkeypox. Therefore, insights into molecular mechanism behind poxvirus replication cycle are needed for the development of efficient antiviral strategies. Virion assembly is one of the key steps that determine the fate of replicating poxviruses. However, in-depth understanding of poxvirus assembly is challenging due to the complex nature of multi-step morphogenesis and heterogeneous virion structures. Despite these challenges, decades of research have revealed virion morphologies at various maturation stages, critical protein components and interactions with host cell compartments. Transmission electron microscopy has been employed as an indispensable tool for the examination of virion morphology, and more recently for the structure determination of protein complexes. In this review, we describe some of the major findings in poxvirus morphogenesis and the contributions of continuously advancing electron microscopy techniques.
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17
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Gupta T, He X, Uddin MR, Zeng X, Zhou A, Zhang J, Freyberg Z, Xu M. Self-supervised learning for macromolecular structure classification based on cryo-electron tomograms. Front Physiol 2022; 13:957484. [PMID: 36111160 PMCID: PMC9468634 DOI: 10.3389/fphys.2022.957484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/02/2022] [Indexed: 11/21/2022] Open
Abstract
Macromolecular structure classification from cryo-electron tomography (cryo-ET) data is important for understanding macro-molecular dynamics. It has a wide range of applications and is essential in enhancing our knowledge of the sub-cellular environment. However, a major limitation has been insufficient labelled cryo-ET data. In this work, we use Contrastive Self-supervised Learning (CSSL) to improve the previous approaches for macromolecular structure classification from cryo-ET data with limited labels. We first pretrain an encoder with unlabelled data using CSSL and then fine-tune the pretrained weights on the downstream classification task. To this end, we design a cryo-ET domain-specific data-augmentation pipeline. The benefit of augmenting cryo-ET datasets is most prominent when the original dataset is limited in size. Overall, extensive experiments performed on real and simulated cryo-ET data in the semi-supervised learning setting demonstrate the effectiveness of our approach in macromolecular labeling and classification.
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Affiliation(s)
- Tarun Gupta
- Department of Computer Science and Engineering, Indian Institute of Technology, Indore, India
| | - Xuehai He
- Department of Electrical and Computer Engineering, University of California, San Diego, San Diego, CA, United States
| | - Mostofa Rafid Uddin
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, United States
| | - Xiangrui Zeng
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, United States
| | - Andrew Zhou
- Irvington High School, Irvington, NY, United States
| | - Jing Zhang
- Department of Computer Science, University of California, Irvine, Irvine, CA, United States
| | - Zachary Freyberg
- Departments of Psychiatry and Cell Biology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Min Xu
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, United States
- *Correspondence: Min Xu,
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18
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Grimm C, Bartuli J, Fischer U. Cytoplasmic gene expression: lessons from poxviruses. Trends Biochem Sci 2022; 47:892-902. [DOI: 10.1016/j.tibs.2022.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 04/12/2022] [Accepted: 04/20/2022] [Indexed: 10/18/2022]
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19
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Cellular homologs of the double jelly-roll major capsid proteins clarify the origins of an ancient virus kingdom. Proc Natl Acad Sci U S A 2022; 119:2120620119. [PMID: 35078938 PMCID: PMC8812541 DOI: 10.1073/pnas.2120620119] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2021] [Indexed: 12/26/2022] Open
Abstract
Viruses are the most abundant biological entities on Earth and ubiquitous parasites of cellular life forms. The general scenario for the origin of viruses involves evolution from nonviral replicators, such as plasmids and transposons, via recruitment of host proteins for virion formation. One of the most common virion core components, the double jelly-roll major capsid protein of a broad variety of viruses with double-stranded DNA genomes, so far has been thought to represent a virus innovation. However, we present evidence, obtained by protein structure comparison, that this type of virus capsid protein also evolved from a cellular ancestor, a distinct family of carbohydrate-active enzymes. These findings reinforce the chimeric scenario of virus origin. Viruses are a distinct type of replicators that encode structural proteins encasing virus genomes in virions. For some of the widespread virus capsid proteins and other major components of virions, likely ancestors encoded by cellular life forms are identifiable. In particular, one of the most common capsid proteins, with the single jelly-roll (SJR) fold, appears to have evolved from a particular family of cellular carbohydrate-binding proteins. However, the double jelly-roll major capsid protein (DJR-MCP), the hallmark of the enormously diverse viruses of the kingdom Bamfordvirae within the realm Varidnaviria, which includes bacterial and archaeal icosahedral viruses as well as eukaryotic giant viruses, has been perceived as a virus innovation that evolved by duplication and fusion of the SJR capsid proteins. Here we employ protein structure comparison to show that the DJR fold is represented in several widespread families of cellular proteins, including several groups of carbohydrate-active enzymes. We show that DJR-MCPs share a common ancestry with a distinct family of bacterial DJR proteins (DUF2961) involved in carbohydrate metabolism. Based on this finding, we propose a scenario in which bamfordviruses evolved from nonviral replicators, in particular plasmids, by recruiting a host protein for capsid formation. This sequence of events appears to be the general route of virus origin. The results of this work indicate that virus kingdoms Bamfordvirae, with the DJR-MCPs, and Helvetiavirae that possess two SJR-MCPs, have distinct origins, suggesting a reappraisal of the realm Varidnaviria.
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20
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Seong D, Kingsak M, Lin Y, Wang Q, Hoque S. Fate and transport of enveloped viruses in indoor built spaces - through understanding vaccinia virus and surface interactions. BIOMATERIALS TRANSLATIONAL 2021; 2:50-60. [PMID: 35837253 PMCID: PMC9255826 DOI: 10.3877/cma.j.issn.2096-112x.2021.01.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 03/08/2021] [Accepted: 03/21/2021] [Indexed: 11/16/2022]
Abstract
The current coronavirus disease 2019 (COVID-19) pandemic has reinforced the necessity of understanding and establishing baseline information on the fate and transport mechanisms of viruses under indoor environmental conditions. Mechanisms governing virus interactions in built spaces have thus far been established based on our knowledge on the interaction of inorganic particles in indoor spaces and do not include characteristics specific to viruses. Studies have explored the biological and kinetic processes of microbes' attachments on surfaces in other fields but not in the built environment. There is also extensive literature on the influence of indoor architecture on air flow, temperature profiles, and forces influencing aerosol transport. Bridging the gap between these fields will lead to the generation of novel frameworks, methodologies and know-how that can identify undiscovered pathways taken by viruses and other microbes in the built environment. Our study summarizes the assessment of the influence of surface properties on the adhesion kinetics of vaccinia virus on gold, silica, glass, and stainless-steel surfaces. We found that on gold the virus layer was more viscoelastic compared to stainless-steel. There was negligible removal of the layer from the stainless-steel surface compared to the others. The results further highlight the importance of converging different fields of research to assess the fate and transport of microbes in indoor built spaces.
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21
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Quemin ERJ, Machala EA, Vollmer B, Pražák V, Vasishtan D, Rosch R, Grange M, Franken LE, Baker LA, Grünewald K. Cellular Electron Cryo-Tomography to Study Virus-Host Interactions. Annu Rev Virol 2020; 7:239-262. [PMID: 32631159 DOI: 10.1146/annurev-virology-021920-115935] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Viruses are obligatory intracellular parasites that reprogram host cells upon infection to produce viral progeny. Here, we review recent structural insights into virus-host interactions in bacteria, archaea, and eukaryotes unveiled by cellular electron cryo-tomography (cryoET). This advanced three-dimensional imaging technique of vitreous samples in near-native state has matured over the past two decades and proven powerful in revealing molecular mechanisms underlying viral replication. Initial studies were restricted to cell peripheries and typically focused on early infection steps, analyzing surface proteins and viral entry. Recent developments including cryo-thinning techniques, phase-plate imaging, and correlative approaches have been instrumental in also targeting rare events inside infected cells. When combined with advances in dedicated image analyses and processing methods, details of virus assembly and egress at (sub)nanometer resolution were uncovered. Altogether, we provide a historical and technical perspective and discuss future directions and impacts of cryoET for integrative structural cell biology analyses of viruses.
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Affiliation(s)
- Emmanuelle R J Quemin
- Centre for Structural Systems Biology, Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, University of Hamburg, D-22607 Hamburg, Germany;
| | - Emily A Machala
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Benjamin Vollmer
- Centre for Structural Systems Biology, Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, University of Hamburg, D-22607 Hamburg, Germany;
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Vojtěch Pražák
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Daven Vasishtan
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Rene Rosch
- Centre for Structural Systems Biology, Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, University of Hamburg, D-22607 Hamburg, Germany;
| | - Michael Grange
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Linda E Franken
- Centre for Structural Systems Biology, Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, University of Hamburg, D-22607 Hamburg, Germany;
| | - Lindsay A Baker
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Kay Grünewald
- Centre for Structural Systems Biology, Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, University of Hamburg, D-22607 Hamburg, Germany;
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
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22
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Huang A, Pressnall MM, Lu R, Huayamares SG, Griffin JD, Groer C, DeKosky BJ, Forrest ML, Berkland CJ. Human intratumoral therapy: Linking drug properties and tumor transport of drugs in clinical trials. J Control Release 2020; 326:203-221. [PMID: 32673633 DOI: 10.1016/j.jconrel.2020.06.029] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/23/2020] [Accepted: 06/25/2020] [Indexed: 01/08/2023]
Abstract
Cancer therapies aim to kill tumor cells directly or engage the immune system to fight malignancy. Checkpoint inhibitors, oncolytic viruses, cell-based immunotherapies, cytokines, and adjuvants have been applied to prompt the immune system to recognize and attack cancer cells. However, systemic exposure of cancer therapies can induce unwanted adverse events. Intratumoral administration of potent therapies utilizes small amounts of drugs, in an effort to minimize systemic exposure and off-target toxicities. Here, we discuss the properties of the tumor microenvironment and transport considerations for intratumoral drug delivery. Specifically, we consider various tumor tissue factors and physicochemical factors that can affect tumor retention after intratumoral injection. We also review approved and clinical-stage intratumoral therapies and consider how the molecular and biophysical properties (e.g. size and charge) of these therapies influences intratumoral transport (e.g. tumor retention and cellular uptake). Finally, we offer a critical review and highlight several emerging approaches to promote tumor retention and limit systemic exposure of potent intratumoral therapies.
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Affiliation(s)
- Aric Huang
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS, USA
| | - Melissa M Pressnall
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS, USA
| | - Ruolin Lu
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS, USA
| | | | - J Daniel Griffin
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS, USA; Bioengineering Graduate Program, University of Kansas, Lawrence, KS, USA
| | | | - Brandon J DeKosky
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS, USA; Department of Chemical and Petroleum Engineering, University of Kansas, Lawrence, KS, USA
| | - M Laird Forrest
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS, USA
| | - Cory J Berkland
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS, USA; Department of Chemical and Petroleum Engineering, University of Kansas, Lawrence, KS, USA; Bioengineering Graduate Program, University of Kansas, Lawrence, KS, USA.
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23
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Böhning J, Bharat TAM. Towards high-throughput in situ structural biology using electron cryotomography. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2020; 160:97-103. [PMID: 32579969 DOI: 10.1016/j.pbiomolbio.2020.05.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 05/21/2020] [Accepted: 05/27/2020] [Indexed: 01/11/2023]
Abstract
Electron cryotomography is a rapidly evolving method for imaging macromolecules directly within the native environment of cells and tissues. Combined with sub-tomogram averaging, it allows structural and cell biologists to obtain sub-nanometre resolution structures in situ. However, low throughput in cryo-ET sample preparation and data acquisition, as well as difficulties in target localisation and sub-tomogram averaging image processing, limit its widespread usability. In this review, we discuss new advances in the field that address these throughput and technical problems. We focus on recent efforts made to resolve issues in sample thinning, improvement in data collection speed at the microscope, strategies for localisation of macromolecules using correlated light and electron microscopy and advancements made to improve resolution in sub-tomogram averaging. These advances will considerably decrease the amount of time and effort required for cryo-ET and sub-tomogram averaging, ushering in a new era of structural biology where in situ macromolecular structure determination will be routine.
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Affiliation(s)
- Jan Böhning
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom; Central Oxford Structural Microscopy and Imaging Centre, South Parks Road, Oxford OX1 3RE, United Kingdom
| | - Tanmay A M Bharat
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom; Central Oxford Structural Microscopy and Imaging Centre, South Parks Road, Oxford OX1 3RE, United Kingdom.
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24
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Zhu H, Fohlerová Z, Pekárek J, Basova E, Neužil P. Recent advances in lab-on-a-chip technologies for viral diagnosis. Biosens Bioelectron 2020; 153:112041. [PMID: 31999560 PMCID: PMC7126858 DOI: 10.1016/j.bios.2020.112041] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 01/13/2020] [Accepted: 01/20/2020] [Indexed: 12/12/2022]
Abstract
The global risk of viral disease outbreaks emphasizes the need for rapid, accurate, and sensitive detection techniques to speed up diagnostics allowing early intervention. An emerging field of microfluidics also known as the lab-on-a-chip (LOC) or micro total analysis system includes a wide range of diagnostic devices. This review briefly covers both conventional and microfluidics-based techniques for rapid viral detection. We first describe conventional detection methods such as cell culturing, immunofluorescence or enzyme-linked immunosorbent assay (ELISA), or reverse transcription polymerase chain reaction (RT-PCR). These methods often have limited speed, sensitivity, or specificity and are performed with typically bulky equipment. Here, we discuss some of the LOC technologies that can overcome these demerits, highlighting the latest advances in LOC devices for viral disease diagnosis. We also discuss the fabrication of LOC systems to produce devices for performing either individual steps or virus detection in samples with the sample to answer method. The complete system consists of sample preparation, and ELISA and RT-PCR for viral-antibody and nucleic acid detection, respectively. Finally, we formulate our opinions on these areas for the future development of LOC systems for viral diagnostics.
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Affiliation(s)
- Hanliang Zhu
- Ministry of Education Key Laboratory of Micro/Nano Systems for Aerospace, Department of Microsystem Engineering, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China
| | - Zdenka Fohlerová
- Central European Institute of Technology, Brno University of Technology, 612 00, Brno, Czech Republic; Department of Microelectronics, Faculty of Electrical Engineering and Communication, Brno University of Technology, 616 00, Brno, Czech Republic
| | - Jan Pekárek
- Central European Institute of Technology, Brno University of Technology, 612 00, Brno, Czech Republic; Department of Microelectronics, Faculty of Electrical Engineering and Communication, Brno University of Technology, 616 00, Brno, Czech Republic
| | - Evgenia Basova
- Central European Institute of Technology, Brno University of Technology, 612 00, Brno, Czech Republic
| | - Pavel Neužil
- Ministry of Education Key Laboratory of Micro/Nano Systems for Aerospace, Department of Microsystem Engineering, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China; Central European Institute of Technology, Brno University of Technology, 612 00, Brno, Czech Republic; Department of Microelectronics, Faculty of Electrical Engineering and Communication, Brno University of Technology, 616 00, Brno, Czech Republic.
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25
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Obr M, Schur FKM. Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging. Adv Virus Res 2019; 105:117-159. [PMID: 31522703 DOI: 10.1016/bs.aivir.2019.07.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Describing the protein interactions that form pleomorphic and asymmetric viruses represents a considerable challenge to most structural biology techniques, including X-ray crystallography and single particle cryo-electron microscopy. Obtaining a detailed understanding of these interactions is nevertheless important, considering the number of relevant human pathogens that do not follow strict icosahedral or helical symmetry. Cryo-electron tomography and subtomogram averaging methods provide structural insights into complex biological environments and are well suited to go beyond structures of perfectly symmetric viruses. This chapter discusses recent developments showing that cryo-ET and subtomogram averaging can provide high-resolution insights into hitherto unknown structural features of pleomorphic and asymmetric virus particles. It also describes how these methods have significantly added to our understanding of retrovirus capsid assemblies in immature and mature viruses. Additional examples of irregular viruses and their associated proteins, whose structures have been studied via cryo-ET and subtomogram averaging, further support the versatility of these methods.
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Affiliation(s)
- Martin Obr
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Florian K M Schur
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria.
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26
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Stass R, Ng WM, Kim YC, Huiskonen JT. Structures of enveloped virions determined by cryogenic electron microscopy and tomography. Adv Virus Res 2019; 105:35-71. [PMID: 31522708 PMCID: PMC7112279 DOI: 10.1016/bs.aivir.2019.07.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Enveloped viruses enclose their genomes inside a lipid bilayer which is decorated by membrane proteins that mediate virus entry. These viruses display a wide range of sizes, morphologies and symmetries. Spherical viruses are often isometric and their envelope proteins follow icosahedral symmetry. Filamentous and pleomorphic viruses lack such global symmetry but their surface proteins may display locally ordered assemblies. Determining the structures of enveloped viruses, including the envelope proteins and their protein-protein interactions on the viral surface, is of paramount importance. These structures can reveal how the virions are assembled and released by budding from the infected host cell, how the progeny virions infect new cells by membrane fusion, and how antibodies bind surface epitopes to block infection. In this chapter, we discuss the uses of cryogenic electron microscopy (cryo-EM) in elucidating structures of enveloped virions. Starting from a detailed outline of data collection and processing strategies, we highlight how cryo-EM has been successfully utilized to provide unique insights into enveloped virus entry, assembly, and neutralization.
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Affiliation(s)
- Robert Stass
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Weng M Ng
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Young Chan Kim
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Juha T Huiskonen
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom; Helsinki Institute of Life Science HiLIFE and Research Programme in Molecular and Integrative Biosciences, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.
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27
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Li R, Zeng X, Sigmund SE, Lin R, Zhou B, Liu C, Wang K, Jiang R, Freyberg Z, Lv H, Xu M. Automatic localization and identification of mitochondria in cellular electron cryo-tomography using faster-RCNN. BMC Bioinformatics 2019; 20:132. [PMID: 30925860 PMCID: PMC6439989 DOI: 10.1186/s12859-019-2650-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Cryo-electron tomography (cryo-ET) enables the 3D visualization of cellular organization in near-native state which plays important roles in the field of structural cell biology. However, due to the low signal-to-noise ratio (SNR), large volume and high content complexity within cells, it remains difficult and time-consuming to localize and identify different components in cellular cryo-ET. To automatically localize and recognize in situ cellular structures of interest captured by cryo-ET, we proposed a simple yet effective automatic image analysis approach based on Faster-RCNN. RESULTS Our experimental results were validated using in situ cyro-ET-imaged mitochondria data. Our experimental results show that our algorithm can accurately localize and identify important cellular structures on both the 2D tilt images and the reconstructed 2D slices of cryo-ET. When ran on the mitochondria cryo-ET dataset, our algorithm achieved Average Precision >0.95. Moreover, our study demonstrated that our customized pre-processing steps can further improve the robustness of our model performance. CONCLUSIONS In this paper, we proposed an automatic Cryo-ET image analysis algorithm for localization and identification of different structure of interest in cells, which is the first Faster-RCNN based method for localizing an cellular organelle in Cryo-ET images and demonstrated the high accuracy and robustness of detection and classification tasks of intracellular mitochondria. Furthermore, our approach can be easily applied to detection tasks of other cellular structures as well.
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Affiliation(s)
- Ran Li
- Department of Automation, Tsinghua University, Beijing, China
| | - Xiangrui Zeng
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Stephanie E Sigmund
- Department of Cellular, Molecular and Biophysical Studies, Columbia University Medical Center, New York, NY, USA
| | - Ruogu Lin
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Bo Zhou
- Robotics Institute, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Chang Liu
- Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Kaiwen Wang
- Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Rui Jiang
- Department of Automation, Tsinghua University, Beijing, China
| | - Zachary Freyberg
- Departments of Psychiatry and Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Hairong Lv
- Department of Automation, Tsinghua University, Beijing, China.
| | - Min Xu
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA.
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28
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Abstract
Polymeric matrices inherently protect viral vectors from pre-existing immune conditions, limit dissemination to off-target sites, and can sustain vector release. Advancing methodologies in development of particulate based vehicles have led to improved encapsulation of viral vectors. Polymeric delivery systems have contributed to increasing cellular transduction, responsive release mechanisms, cellular infiltration, and cellular signaling. Synthetic polymers are easily customizable, and are capable of balancing matrix retention with cellular infiltration. Natural polymers contain inherent biorecognizable motifs adding therapeutic efficacy to the incorporated viral vector. Recombinant polymers use highly conserved motifs to carefully engineer matrices, allowing for precise design including elements of vector retention and responsive release mechanisms. Composite polymer systems provide opportunities to create matrices with unique properties. Carefully designed matrices can control spatiotemporal release patterns that synergize with approaches in regenerative medicine and antitumor therapies.
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Affiliation(s)
- Douglas Steinhauff
- Utah Center for Nanomedicine , Nano Institute of Utah , 36 South Wasatch Drive , Salt Lake City , Utah 84112 , United States
| | - Hamidreza Ghandehari
- Utah Center for Nanomedicine , Nano Institute of Utah , 36 South Wasatch Drive , Salt Lake City , Utah 84112 , United States
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29
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Abstract
Super-resolution microscopy enables the study of vaccinia architecture at subviral resolution with molecular specificity. Here, we outline how to use structured illumination microscopy (SIM) and stochastic optical reconstruction microscopy (STORM) to detect fluorescently tagged or immunolabeled viral proteins on purified virions. Tens to hundreds of individual virions can be imaged in a single field of view providing data for single-particle averaging or quantitative analysis of viral protein spatial organization.
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Affiliation(s)
- Robert Gray
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK.
| | - David Albrecht
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK.
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30
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Mirzakhanyan Y, Gershon P. The Vaccinia virion: Filling the gap between atomic and ultrastructure. PLoS Pathog 2019; 15:e1007508. [PMID: 30615658 PMCID: PMC6336343 DOI: 10.1371/journal.ppat.1007508] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 01/17/2019] [Accepted: 12/06/2018] [Indexed: 01/19/2023] Open
Abstract
We have investigated the molecular-level structure of the Vaccinia virion in situ by protein-protein chemical crosslinking, identifying 4609 unique-mass crosslink ions at an effective FDR of 0.33%, covering 2534 unique pairs of crosslinked protein positions, 625 of which were inter-protein. The data were statistically non-random and rational in the context of known structures, and showed biological rationality. Crosslink density strongly tracked the individual proteolytic maturation products of p4a and p4b, the two major virion structural proteins, and supported the prediction of transmembrane domains within membrane proteins. A clear sub-network of four virion structural proteins provided structural insights into the virion core wall, and proteins VP8 and A12 formed a strongly-detected crosslinked pair with an apparent structural role. A strongly-detected sub-network of membrane proteins A17, H3, A27 and A26 represented an apparent interface of the early-forming virion envelope with structures added later during virion morphogenesis. Protein H3 seemed to be the central hub not only for this sub-network but also for an 'attachment protein' sub-network comprising membrane proteins H3, ATI, CAHH(D8), A26, A27 and G9. Crosslinking data lent support to a number of known interactions and interactions within known complexes. Evidence is provided for the membrane targeting of genome telomeres. In covering several orders of magnitude in protein abundance, this study may have come close to the bottom of the protein-protein crosslinkome of an intact organism, namely a complex animal virus.
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Affiliation(s)
- Yeva Mirzakhanyan
- Department of Molecular Biology & Biochemistry, UC-Irvine, Irvine, California, United States of America
| | - Paul Gershon
- Department of Molecular Biology & Biochemistry, UC-Irvine, Irvine, California, United States of America
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31
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Neumüller J. Electron tomography-a tool for ultrastructural 3D visualization in cell biology and histology. Wien Med Wochenschr 2018; 168:322-329. [PMID: 30084092 PMCID: PMC6132546 DOI: 10.1007/s10354-018-0646-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 06/22/2018] [Indexed: 02/06/2023]
Abstract
Electron tomography (ET) was developed to overcome some of the problems associated reconstructing three-dimensional (3D) images from 2D election microscopy data from ultrathin slices. Virtual sections of semithin sample are obtained by incremental rotation of the target and this information is used to assemble a 3D image. Herein, we provide an instruction to ET including the physical principle, possibilities, and limitations. We review the development of innovative methods and highlight important investigations performed in our department and with our collaborators. ET has opened up the third dimension at the ultrastructural level and represents a milestone in structural molecular biology.
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Affiliation(s)
- Josef Neumüller
- Center of Anatomy and Cell Biology, Department of Cell and Developmental Biology, Medical University of Vienna, Schwarzspanierstraße 17, 1090, Vienna, Austria.
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32
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Witte R, Andriasyan V, Georgi F, Yakimovich A, Greber UF. Concepts in Light Microscopy of Viruses. Viruses 2018; 10:E202. [PMID: 29670029 PMCID: PMC5923496 DOI: 10.3390/v10040202] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 04/12/2018] [Accepted: 04/16/2018] [Indexed: 12/11/2022] Open
Abstract
Viruses threaten humans, livestock, and plants, and are difficult to combat. Imaging of viruses by light microscopy is key to uncover the nature of known and emerging viruses in the quest for finding new ways to treat viral disease and deepening the understanding of virus–host interactions. Here, we provide an overview of recent technology for imaging cells and viruses by light microscopy, in particular fluorescence microscopy in static and live-cell modes. The review lays out guidelines for how novel fluorescent chemical probes and proteins can be used in light microscopy to illuminate cells, and how they can be used to study virus infections. We discuss advantages and opportunities of confocal and multi-photon microscopy, selective plane illumination microscopy, and super-resolution microscopy. We emphasize the prevalent concepts in image processing and data analyses, and provide an outlook into label-free digital holographic microscopy for virus research.
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Affiliation(s)
- Robert Witte
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
| | - Vardan Andriasyan
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
| | - Fanny Georgi
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
| | - Artur Yakimovich
- MRC Laboratory for Molecular Cell Biology, University College London, Gower St., London WC1E 6BT, UK.
| | - Urs F Greber
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
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33
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Culley S, Albrecht D, Jacobs C, Pereira PM, Leterrier C, Mercer J, Henriques R. Quantitative mapping and minimization of super-resolution optical imaging artifacts. Nat Methods 2018; 15:263-266. [PMID: 29457791 PMCID: PMC5884429 DOI: 10.1038/nmeth.4605] [Citation(s) in RCA: 172] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 01/22/2018] [Indexed: 12/18/2022]
Abstract
Super-resolution microscopy depends on steps that can contribute to the formation of image artifacts, leading to misinterpretation of biological information. We present NanoJ-SQUIRREL, an ImageJ-based analytical approach that provides quantitative assessment of super-resolution image quality. By comparing diffraction-limited images and super-resolution equivalents of the same acquisition volume, this approach generates a quantitative map of super-resolution defects and can guide researchers in optimizing imaging parameters.
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Affiliation(s)
- Siân Culley
- MRC-Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
| | - David Albrecht
- MRC-Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Caron Jacobs
- MRC-Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Pedro Matos Pereira
- MRC-Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
| | | | - Jason Mercer
- MRC-Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Ricardo Henriques
- MRC-Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
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34
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Cyrklaff M, Frischknecht F, Kudryashev M. Functional insights into pathogen biology from 3D electron microscopy. FEMS Microbiol Rev 2018; 41:828-853. [PMID: 28962014 DOI: 10.1093/femsre/fux041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 07/25/2017] [Indexed: 01/10/2023] Open
Abstract
In recent years, novel imaging approaches revolutionised our understanding of the cellular and molecular biology of microorganisms. These include advances in fluorescent probes, dynamic live cell imaging, superresolution light and electron microscopy. Currently, a major transition in the experimental approach shifts electron microscopy studies from a complementary technique to a method of choice for structural and functional analysis. Here we review functional insights into the molecular architecture of viruses, bacteria and parasites as well as interactions with their respective host cells gained from studies using cryogenic electron tomography and related methodologies.
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Affiliation(s)
- Marek Cyrklaff
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Friedrich Frischknecht
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Mikhail Kudryashev
- Max Planck Institute of Biophysics, Max-von-Laue Strasse 3, 60438 Frankfurt, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe University of Frankfurt, Max-von-Laue Strasse 17, 60438 Frankfurt, Germany
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35
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The Dengue Virus Replication Complex: From RNA Replication to Protein-Protein Interactions to Evasion of Innate Immunity. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1062:115-129. [PMID: 29845529 DOI: 10.1007/978-981-10-8727-1_9] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Viruses from the Flavivirus family are the causative agents of dengue fever, Zika, Japanese encephalitis, West Nile encephalitis or Yellow fever and constitute major or emerging public health problems. A better understanding of the flavivirus replication cycle is likely to offer new opportunities for the design of antiviral therapies to treat severe conditions provoked by these viruses, but it should also help reveal fundamental biological mechanisms of the host cell. During virus replication, RNA synthesis is mediated by a dynamic and membrane-bound multi-protein assembly, named the replication complex (RC). The RC is composed of both viral and host-cell proteins that assemble within vesicles composed of the endoplasmic reticulum membrane, near the nucleus. At the heart of the flavivirus RC lies NS4B, a viral integral membrane protein that plays a role in virulence and in down-regulating the innate immune response. NS4B binds to the NS2B-NS3 protease-helicase, which itself interacts with the NS5 methyl-transferase polymerase. We present an overview of recent structural and functional data that augment our understanding of how viral RNA is replicated by dengue virus. We focus on structural data that illuminate the various roles played by proteins NS2B-NS3, NS4B and NS5. By participating in viral RNA cap methylation, the NS5 methyltransferase enables the virus to escape the host cell innate immune response. We present the molecular basis for this activity. We summarize what we know about the network of interactions established by NS2B-NS3, NS4B and NS5 (their "interactome"). This leads to a working model that is captured in the form of a rather naïve "cartoon", which we hope will be refined towards an atomic model in the near future.
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36
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Single-Particle Discrimination of Retroviruses from Extracellular Vesicles by Nanoscale Flow Cytometry. Sci Rep 2017; 7:17769. [PMID: 29259315 PMCID: PMC5736735 DOI: 10.1038/s41598-017-18227-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 12/07/2017] [Indexed: 12/12/2022] Open
Abstract
Retroviruses and small EVs overlap in size, buoyant densities, refractive indices and share many cell-derived surface markers making them virtually indistinguishable by standard biochemical methods. This poses a significant challenge when purifying retroviruses for downstream analyses or for phenotypic characterization studies of markers on individual virions given that EVs are a major contaminant of retroviral preparations. Nanoscale flow cytometry (NFC), also called flow virometry, is an adaptation of flow cytometry technology for the analysis of individual nanoparticles such as extracellular vesicles (EVs) and retroviruses. In this study we systematically optimized NFC parameters for the detection of retroviral particles in the range of 115–130 nm, including viral production, sample labeling, laser power and voltage settings. By using the retroviral envelope glycoprotein as a selection marker, and evaluating a number of fluorescent dyes and labeling methods, we demonstrate that it is possible to confidently distinguish retroviruses from small EVs by NFC. Our findings make it now possible to individually phenotype genetically modified retroviral particles that express a fluorescent envelope glycoprotein without removing EV contaminants from the sample.
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37
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Marion S, San Martín C, Šiber A. Role of Condensing Particles in Polymer Confinement: A Model for Virus-Packed "Minichromosomes". Biophys J 2017; 113:1643-1653. [PMID: 29045859 PMCID: PMC5647577 DOI: 10.1016/j.bpj.2017.08.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 07/18/2017] [Accepted: 08/14/2017] [Indexed: 12/22/2022] Open
Abstract
Confined mixtures of a polymer and nonspecifically binding particles (condensers) are studied as models for viruses containing double-stranded DNA (polymer) and condensing proteins (particles). We explore a model in which all interactions between the packed content (polymer and particles) and its confinement are purely repulsive, with only a short-range attraction between the condensers and polymer to simulate binding. In the range of physical parameters applicable to viruses, the model predicts reduction of pressure in the system effected by the condensers, despite the reduction in free volume. Condensers are found to be interspersed throughout the spherical confinement and only partially wrapped in the polymer, which acts as an effective medium for the condenser interactions. Crowding of the viral interior influences the DNA and protein organization, producing a picture inconsistent with a chromatin-like, beads-on-a-string structure. The model predicts an organization of the confined interior compatible with experimental data on unperturbed adenoviruses and polyomaviruses, at the same time providing insight into the role of condensing proteins in the viral infectious cycles of related viral families.
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Affiliation(s)
- Sanjin Marion
- Center of Excellence for Advanced Materials and Sensing Devices, Institute of Physics, Zagreb, Croatia; Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
| | - Carmen San Martín
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Antonio Šiber
- Center of Excellence for Advanced Materials and Sensing Devices, Institute of Physics, Zagreb, Croatia.
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38
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Inhibition of Poxvirus Gene Expression and Genome Replication by Bisbenzimide Derivatives. J Virol 2017; 91:JVI.00838-17. [PMID: 28659488 PMCID: PMC5571260 DOI: 10.1128/jvi.00838-17] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 06/22/2017] [Indexed: 12/19/2022] Open
Abstract
Virus infection of humans and livestock can be devastating for individuals and populations, sometimes resulting in large economic and societal impact. Prevention of virus disease by vaccination or antiviral agents is difficult to achieve. A notable exception was the eradication of human smallpox by vaccination over 30 years ago. Today, humans and animals remain susceptible to poxvirus infections, including zoonotic poxvirus transmission. Here we identified a small molecule, bisbenzimide (bisbenzimidazole), and its derivatives as potent agents against prototypic poxvirus infection in cell culture. We show that bisbenzimide derivatives, which preferentially bind the minor groove of double-stranded DNA, inhibit vaccinia virus infection by blocking viral DNA replication and abrogating postreplicative intermediate and late gene transcription. The bisbenzimide derivatives are potent against vaccinia virus and other poxviruses but ineffective against a range of other DNA and RNA viruses. The bisbenzimide derivatives are the first inhibitors of their class, which appear to directly target the viral genome without affecting cell viability. IMPORTANCE Smallpox was one of the most devastating diseases in human history until it was eradicated by a worldwide vaccination campaign. Due to discontinuation of routine vaccination more than 30 years ago, the majority of today's human population remains susceptible to infection with poxviruses. Here we present a family of bisbenzimide (bisbenzimidazole) derivatives, known as Hoechst nuclear stains, with high potency against poxvirus infection. Results from a variety of assays used to dissect the poxvirus life cycle demonstrate that bisbenzimides inhibit viral gene expression and genome replication. These findings can lead to the development of novel antiviral drugs that target viral genomes and block viral replication.
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39
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Daaboul GG, Freedman DS, Scherr SM, Carter E, Rosca A, Bernstein D, Mire CE, Agans KN, Hoenen T, Geisbert TW, Ünlü MS, Connor JH. Enhanced light microscopy visualization of virus particles from Zika virus to filamentous ebolaviruses. PLoS One 2017. [PMID: 28651016 PMCID: PMC5484481 DOI: 10.1371/journal.pone.0179728] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Light microscopy is a powerful tool in the detection and analysis of parasites, fungi, and prokaryotes, but has been challenging to use for the detection of individual virus particles. Unlabeled virus particles are too small to be visualized using standard visible light microscopy. Characterization of virus particles is typically performed using higher resolution approaches such as electron microscopy or atomic force microscopy. These approaches require purification of virions away from their normal millieu, requiring significant levels of expertise, and can only enumerate small numbers of particles per field of view. Here, we utilize a visible light imaging approach called Single Particle Interferometric Reflectance Imaging Sensor (SP-IRIS) that allows automated counting and sizing of thousands of individual virions. Virions are captured directly from complex solutions onto a silicon chip and then detected using a reflectance interference imaging modality. We show that the use of different imaging wavelengths allows the visualization of a multitude of virus particles. Using Violet/UV illumination, the SP-IRIS technique is able to detect individual flavivirus particles (~40 nm), while green light illumination is capable of identifying and discriminating between vesicular stomatitis virus and vaccinia virus (~360 nm). Strikingly, the technology allows the clear identification of filamentous infectious ebolavirus particles and virus-like particles. The ability to differentiate and quantify unlabeled virus particles extends the usefulness of traditional light microscopy and can be embodied in a straightforward benchtop approach allowing widespread applications ranging from rapid detection in biological fluids to analysis of virus-like particles for vaccine development and production.
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Affiliation(s)
| | | | - Steven M. Scherr
- Department of Mechanical Engineering, Boston University, Boston, MA, United States of America
| | - Erik Carter
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States of America
| | - Alexandru Rosca
- nanoView Diagnostics Inc., Boston, MA, United States of America
| | - David Bernstein
- nanoView Diagnostics Inc., Boston, MA, United States of America
| | - Chad E. Mire
- Galveston National Laboratory, Galveston, TX, United States of America
- Department of Microbiology, Galveston, TX, United States of America
- Immunology, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Krystle N. Agans
- Galveston National Laboratory, Galveston, TX, United States of America
- Department of Microbiology, Galveston, TX, United States of America
- Immunology, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Thomas Hoenen
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, MT, United States of America
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald–Isle of Riems, Germany
| | - Thomas W. Geisbert
- Galveston National Laboratory, Galveston, TX, United States of America
- Department of Microbiology, Galveston, TX, United States of America
- Immunology, University of Texas Medical Branch, Galveston, TX, United States of America
| | - M. Selim Ünlü
- Department of Electrical Engineering, Boston University, Boston, MA, United States of America
- Department of Biomedical Engineering, Boston University, Boston, MA, United States of America
- Physics Department, Boston University, Boston, MA, United States of America
| | - John H. Connor
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States of America
- Department of Biomedical Engineering, Boston University, Boston, MA, United States of America
- * E-mail:
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40
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Pham MD, Epperla CP, Hsieh CL, Chang W, Chang HC. Glycosaminoglycans-Specific Cell Targeting and Imaging Using Fluorescent Nanodiamonds Coated with Viral Envelope Proteins. Anal Chem 2017; 89:6527-6534. [PMID: 28548489 DOI: 10.1021/acs.analchem.7b00627] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Understanding virus-host interactions is crucial for vaccine development. This study investigates such interactions using fluorescent nanodiamonds (FNDs) coated with vaccinia envelope proteins as the model system. To achieve this goal, we noncovalently conjugated 100 nm FNDs with rA27(aa 21-84), a recombinant envelope protein of vaccinia virus, for glycosaminoglycans (GAGs)-specific targeting and imaging of living cells. Another recombinant protein rDA27(aa 33-84) that removes the GAGs-binding sequences was also used for comparison. Three types of A27-coated FNDs were generated, including rA27(aa 21-84)-FND, rDA27(aa 33-84)-FND, and hybrid rA27(aa 21-84)/rDA27(aa 33-84)-FND. The specificity of these viral protein-FND conjugates toward GAGs binding was examined by flow cytometry, fluorescence microscopy, and gel electrophoresis. Results obtained for normal and GAGs-deficient cells showed that the recombinant proteins maintain their GAG-targeting activities even after immobilization on the FND surface. Our studies provide a new nanoparticle-based platform not only to target specific cell types but also to track the fates of these immobilized viral proteins in targeted cells as well as to isolate and enrich GAGs-associated proteins on cell membrane.
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Affiliation(s)
- Minh D Pham
- Institute of Atomic and Molecular Sciences, Academia Sinica , Taipei 106, Taiwan.,Institute of Biotechnology, Vietnam Academy of Science and Technology , 18-Hoang Quoc Viet, Cau Giay, Ha noi, Vietnam
| | - Chandra Prakash Epperla
- Institute of Atomic and Molecular Sciences, Academia Sinica , Taipei 106, Taiwan.,Taiwan International Graduate Program-Molecular Science and Technology, Academia Sinica , Taipei 115, Taiwan.,Department of Chemistry, National Tsing Hua University , Hsinchu 300, Taiwan
| | - Chia-Lung Hsieh
- Institute of Atomic and Molecular Sciences, Academia Sinica , Taipei 106, Taiwan
| | - Wen Chang
- Institute of Molecular Biology, Academia Sinica , Taipei 115, Taiwan
| | - Huan-Cheng Chang
- Institute of Atomic and Molecular Sciences, Academia Sinica , Taipei 106, Taiwan.,Taiwan International Graduate Program-Molecular Science and Technology, Academia Sinica , Taipei 115, Taiwan.,Department of Chemical Engineering, National Taiwan University of Science and Technology , Taipei 106, Taiwan
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41
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Correlative super-resolution fluorescence and electron microscopy using conventional fluorescent proteins in vacuo. J Struct Biol 2017; 199:120-131. [PMID: 28576556 PMCID: PMC5531056 DOI: 10.1016/j.jsb.2017.05.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 04/27/2017] [Accepted: 05/29/2017] [Indexed: 12/12/2022]
Abstract
Super-resolution light microscopy, correlative light and electron microscopy, and volume electron microscopy are revolutionising the way in which biological samples are examined and understood. Here, we combine these approaches to deliver super-accurate correlation of fluorescent proteins to cellular structures. We show that YFP and GFP have enhanced blinking properties when embedded in acrylic resin and imaged under partial vacuum, enabling in vacuo single molecule localisation microscopy. In conventional section-based correlative microscopy experiments, the specimen must be moved between imaging systems and/or further manipulated for optimal viewing. These steps can introduce undesirable alterations in the specimen, and complicate correlation between imaging modalities. We avoided these issues by using a scanning electron microscope with integrated optical microscope to acquire both localisation and electron microscopy images, which could then be precisely correlated. Collecting data from ultrathin sections also improved the axial resolution and signal-to-noise ratio of the raw localisation microscopy data. Expanding data collection across an array of sections will allow 3-dimensional correlation over unprecedented volumes. The performance of this technique is demonstrated on vaccinia virus (with YFP) and diacylglycerol in cellular membranes (with GFP).
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42
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Baker JE, Sriram R, Miller BL. Recognition-mediated particle detection under microfluidic flow with waveguide-coupled 2D photonic crystals: towards integrated photonic virus detectors. LAB ON A CHIP 2017; 17:1570-1577. [PMID: 28357424 PMCID: PMC5482269 DOI: 10.1039/c7lc00221a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Label-free biodetection schemes compatible with standard CMOS fabrication methods constitute an important goal, as these are enabling tools for the mass production of high-sensitivity biosensors. Two-dimensional slab photonic crystal (2D slab-PhC) sensors have been posited as ultrahigh-sensitivity detection components, but to date recognition-mediated detection of viruses or simulants under flow has not been demonstrated. We report the design and optimization of a new W1 waveguide-coupled 2D slab-PhC sensor, with a geometry well suited to virus detection. Proof of concept experiments with fluorescent latex particles verified that the sensor could respond to infiltration of a single particle, both in air and under an aqueous cover layer. Subsequent experiments with antibody-functionalized sensors and virus simulants confirmed the ability of the device to detect virus-sized particles under flow via a recognition-mediated process. This work sets the stage for incorporation of 2D slab-PhC sensors into fully integrated photonic sensor systems.
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43
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Sagulenko E, Nouwens A, Webb RI, Green K, Yee B, Morgan G, Leis A, Lee KC, Butler MK, Chia N, Pham UTP, Lindgreen S, Catchpole R, Poole AM, Fuerst JA. Nuclear Pore-Like Structures in a Compartmentalized Bacterium. PLoS One 2017; 12:e0169432. [PMID: 28146565 PMCID: PMC5287468 DOI: 10.1371/journal.pone.0169432] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 12/02/2016] [Indexed: 01/02/2023] Open
Abstract
Planctomycetes are distinguished from other Bacteria by compartmentalization of cells via internal membranes, interpretation of which has been subject to recent debate regarding potential relations to Gram-negative cell structure. In our interpretation of the available data, the planctomycete Gemmata obscuriglobus contains a nuclear body compartment, and thus possesses a type of cell organization with parallels to the eukaryote nucleus. Here we show that pore-like structures occur in internal membranes of G.obscuriglobus and that they have elements structurally similar to eukaryote nuclear pores, including a basket, ring-spoke structure, and eight-fold rotational symmetry. Bioinformatic analysis of proteomic data reveals that some of the G. obscuriglobus proteins associated with pore-containing membranes possess structural domains found in eukaryote nuclear pore complexes. Moreover, immunogold labelling demonstrates localization of one such protein, containing a β-propeller domain, specifically to the G. obscuriglobus pore-like structures. Finding bacterial pores within internal cell membranes and with structural similarities to eukaryote nuclear pore complexes raises the dual possibilities of either hitherto undetected homology or stunning evolutionary convergence.
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Affiliation(s)
- Evgeny Sagulenko
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Amanda Nouwens
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Richard I. Webb
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland, Australia
| | - Kathryn Green
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland, Australia
| | - Benjamin Yee
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Garry Morgan
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland, Australia
| | - Andrew Leis
- CSIRO - Livestock Industries, Australian Animal Health Laboratory, Biosecurity Microscopy Facility (ABMF), Geelong, Victoria, Australia
| | - Kuo-Chang Lee
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Margaret K. Butler
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Nicholas Chia
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Uyen Thi Phuong Pham
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Stinus Lindgreen
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Ryan Catchpole
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
| | - Anthony M. Poole
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- Allan Wilson Centre, University of Canterbury, Christchurch, New Zealand
- Bioinformatics Institute, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - John A. Fuerst
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- * E-mail:
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Hughes L, Wilkins K, Goldsmith CS, Smith S, Hudson P, Patel N, Karem K, Damon I, Li Y, Olson VA, Satheshkumar PS. A rapid Orthopoxvirus purification protocol suitable for high-containment laboratories. J Virol Methods 2017; 243:68-73. [PMID: 28131867 PMCID: PMC9533856 DOI: 10.1016/j.jviromet.2017.01.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 01/19/2017] [Accepted: 01/20/2017] [Indexed: 11/07/2022]
Abstract
Virus purification in a high-containment setting provides unique challenges due to barrier precautions and operational safety approaches that are not necessary in lower biosafety level (BSL) 2 environments. The need for high risk group pathogen diagnostic assay development, anti-viral research, pathogenesis and vaccine efficacy research necessitates work in BSL-3 and BSL-4 labs with infectious agents. When this work is performed in accordance with BSL-4 practices, modifications are often required in standard protocols. Classical virus purification techniques are difficult to execute in a BSL-3 or BSL-4 laboratory because of the work practices used in these environments. Orthopoxviruses are a family of viruses that, in some cases, requires work in a high-containment laboratory and due to size do not lend themselves to simpler purification methods. Current CDC purification techniques of orthopoxviruses uses 1,1,2-trichlorotrifluoroethane, commonly known as Genetron®. Genetron® is a chlorofluorocarbon (CFC) that has been shown to be detrimental to the ozone and has been phased out and the limited amount of product makes it no longer a feasible option for poxvirus purification purposes. Here we demonstrate a new Orthopoxvirus purification method that is suitable for high-containment laboratories and produces virus that is not only comparable to previous purification methods, but improves on purity and yield.
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Affiliation(s)
- Laura Hughes
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA.
| | - Kimberly Wilkins
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Cynthia S Goldsmith
- Infectious Diseases Pathology Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Scott Smith
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Paul Hudson
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Nishi Patel
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Kevin Karem
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Inger Damon
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Yu Li
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Victoria A Olson
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - P S Satheshkumar
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
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Cheng W. The Density Code for the Development of a Vaccine? J Pharm Sci 2016; 105:3223-3232. [PMID: 27649885 PMCID: PMC5102155 DOI: 10.1016/j.xphs.2016.07.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 07/17/2016] [Accepted: 07/26/2016] [Indexed: 10/21/2022]
Abstract
The development of prophylactic vaccines remains largely empirical in nature and rarely have general rules been applied in the strategic decision and the formulation of a viral vaccine. Currently, there are a total of 15 virus agents from 12 unique virus families with vaccines licensed by the U.S. Food and Drug Administration. Extensive structural information on these viral particles and potential mechanisms of protection are available for the majority of these virus pathogens and their respective vaccines. Here I review the quantitative features of these viral surface antigens in relation to the molecular mechanisms of B-cell activation and point out a potential correlation between the density of immunogenic proteins displayed on the surface of the vaccine antigen carrier and the success of a vaccine. These features help us understand the humoral immunity induced by viral vaccines on a quantitative ground and re-emphasize the importance of antigen density on the activation of the immune system. Although the detailed mechanisms behind this phenomenon remain to be explored, it implies that both the size of antigen carriers and the density of immunogenic proteins displayed on these carriers are important parameters that may need to be optimized for the formulation of a vaccine.
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Affiliation(s)
- Wei Cheng
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109; Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109; Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109.
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46
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Lučić V, Fernández-Busnadiego R, Laugks U, Baumeister W. Hierarchical detection and analysis of macromolecular complexes in cryo-electron tomograms using Pyto software. J Struct Biol 2016; 196:503-514. [PMID: 27742578 DOI: 10.1016/j.jsb.2016.10.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 09/15/2016] [Accepted: 10/06/2016] [Indexed: 11/29/2022]
Abstract
Molecular complexes, arguably the basic units carrying cellular function, can be visualized directly in their native environment by cryo-electron tomography. Here we describe a procedure for the detection of small, pleomorphic membrane-bound molecular complexes in cryo-tomograms by a hierarchical connectivity segmentation. Validation on phantom and real data showed above 90% true positive rates. This segmentation procedure is implemented in the Pyto software package, together with methods for quantitative characterization and classification of complexes detected by our segmentation procedure and for statistical analysis between experimental conditions. Therefore, the methods presented provide a means for the detection and quantitative interpretation of structures captured in cryo-electron tomograms, as well as for the elucidation of their cellular function.
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Affiliation(s)
- Vladan Lučić
- Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
| | | | - Ulrike Laugks
- Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Wolfgang Baumeister
- Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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47
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Tang VA, Renner TM, Varette O, Le Boeuf F, Wang J, Diallo JS, Bell JC, Langlois MA. Single-particle characterization of oncolytic vaccinia virus by flow virometry. Vaccine 2016; 34:5082-5089. [PMID: 27614781 DOI: 10.1016/j.vaccine.2016.08.074] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 07/27/2016] [Accepted: 08/23/2016] [Indexed: 12/28/2022]
Abstract
Vaccinia virus (VV) is an oncolytic virus that is currently being evaluated as a promising cancer vaccine in several phase I, II and III clinical trials. Although several quality control tests are performed on each new batch of virus, these do not routinely include a systematic characterization of virus particle homogeneity, or relate the infectious titer to the total number of submicron sized particles (SSPs) present in the sample. SSPs are comprised of infectious virus and non-infectious viral particles, but also cell contaminants derived from the virus isolation procedures, such as cellular vesicles and debris. Here we have employed flow virometry (FV) analysis and sorting to isolate and characterize distinct SSP populations in therapeutic oncolytic VV preparations. We show that VV preparations contain SSPs heterogeneous in size and include large numbers of non-infectious VV particles. Furthermore, we used FV to illustrate how VV has a propensity to aggregate over time and under various handling and storage procedures. Accordingly, we find that together the infectious titer, the total number of SSPs, the number of viral genomes and the level of particle aggregation in a sample constitute useful parameters that greatly facilitate inter-sample assessment of physical quality, and also provides a means to monitor sample deterioration over time. Additionally, we have successfully employed FV sorting to further isolate virus from other particles by identifying a lipophilic dye that preferentially stains VV over other SSPs in the sample. Overall, we demonstrate that FV is a fast and effective tool that can be used to perform quality, and consistency control assessments of oncolytic VV vaccine preparations.
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Affiliation(s)
- Vera A Tang
- University of Ottawa Flow Cytometry and Virometry Core Facility, Canada
| | - Tyler M Renner
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Canada
| | - Oliver Varette
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Canada; Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Canada
| | - Fabrice Le Boeuf
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Canada
| | - Jiahu Wang
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Canada
| | - Jean-Simon Diallo
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Canada; Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Canada
| | - John C Bell
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Canada; Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Canada
| | - Marc-André Langlois
- University of Ottawa Flow Cytometry and Virometry Core Facility, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Canada.
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48
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Moss B. Membrane fusion during poxvirus entry. Semin Cell Dev Biol 2016; 60:89-96. [PMID: 27423915 DOI: 10.1016/j.semcdb.2016.07.015] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 07/11/2016] [Accepted: 07/12/2016] [Indexed: 12/23/2022]
Abstract
Poxviruses comprise a large family of enveloped DNA viruses that infect vertebrates and invertebrates. Poxviruses, unlike most DNA viruses, replicate in the cytoplasm and encode enzymes and other proteins that enable entry, gene expression, genome replication, virion assembly and resistance to host defenses. Entry of vaccinia virus, the prototype member of the family, can occur at the plasma membrane or following endocytosis. Whereas many viruses encode one or two proteins for attachment and membrane fusion, vaccinia virus encodes four proteins for attachment and eleven more for membrane fusion and core entry. The entry-fusion proteins are conserved in all poxviruses and form a complex, known as the Entry Fusion Complex (EFC), which is embedded in the membrane of the mature virion. An additional membrane that encloses the mature virion and is discarded prior to entry is present on an extracellular form of the virus. The EFC is held together by multiple interactions that depend on nine of the eleven proteins. The entry process can be divided into attachment, hemifusion and core entry. All eleven EFC proteins are required for core entry and at least eight for hemifusion. To mediate fusion the virus particle is activated by low pH, which removes one or more fusion repressors that interact with EFC components. Additional EFC-interacting fusion repressors insert into cell membranes and prevent secondary infection. The absence of detailed structural information, except for two attachment proteins and one EFC protein, is delaying efforts to determine the fusion mechanism.
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Affiliation(s)
- Bernard Moss
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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49
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VirusMapper: open-source nanoscale mapping of viral architecture through super-resolution microscopy. Sci Rep 2016; 6:29132. [PMID: 27374400 PMCID: PMC4931586 DOI: 10.1038/srep29132] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 06/15/2016] [Indexed: 11/15/2022] Open
Abstract
The nanoscale molecular assembly of mammalian viruses during their infectious life cycle remains poorly understood. Their small dimensions, generally bellow the 300nm diffraction limit of light microscopes, has limited most imaging studies to electron microscopy. The recent development of super-resolution (SR) light microscopy now allows the visualisation of viral structures at resolutions of tens of nanometers. In addition, these techniques provide the added benefit of molecular specific labelling and the capacity to investigate viral structural dynamics using live-cell microscopy. However, there is a lack of robust analytical tools that allow for precise mapping of viral structure within the setting of infection. Here we present an open-source analytical framework that combines super-resolution imaging and naïve single-particle analysis to generate unbiased molecular models. This tool, VirusMapper, is a high-throughput, user-friendly, ImageJ-based software package allowing for automatic statistical mapping of conserved multi-molecular structures, such as viral substructures or intact viruses. We demonstrate the usability of VirusMapper by applying it to SIM and STED images of vaccinia virus in isolation and when engaged with host cells. VirusMapper allows for the generation of accurate, high-content, molecular specific virion models and detection of nanoscale changes in viral architecture.
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50
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Dahiya SS, Kumar S, Mehta SC, Narnaware SD, Singh R, Tuteja FC. Camelpox: A brief review on its epidemiology, current status and challenges. Acta Trop 2016; 158:32-38. [PMID: 26902797 DOI: 10.1016/j.actatropica.2016.02.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 02/12/2016] [Accepted: 02/18/2016] [Indexed: 11/17/2022]
Abstract
Camelpox caused by a Camelpox virus (CMLV) is a very important host specific viral disease of camel. It is highly contagious in nature and causes serious impact on health even mortality of camels and economic losses to the camel owners. It manifests itself either in the local/mild or generalized/severe form. Various outbreaks of different pathogenicity have been reported from camel dwelling areas of the world. CMLV has been characterized in embryonated chicken eggs with the production of characteristic pock lesions and in various cell lines with the capacity to induce giant cells. Being of Poxviridae family, CMLV employs various strategies to impede host immune system and facilitates its own pathogenesis. Both live and attenuated vaccine has been found effective against CMLV infection. The present review gives a comprehensive overview of camelpox disease with respect to its transmission, epidemiology, virion characteristics, viral life cycle, host interaction and its immune modulation.
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Affiliation(s)
- Shyam Singh Dahiya
- National Research Center on Camel, Jorbeer, Bikaner, Rajasthan 334001, India.
| | - Sachin Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam 781039, India
| | | | - Shirish D Narnaware
- National Research Center on Camel, Jorbeer, Bikaner, Rajasthan 334001, India
| | - Raghvendar Singh
- National Research Center on Camel, Jorbeer, Bikaner, Rajasthan 334001, India
| | - Fateh Chand Tuteja
- National Research Center on Camel, Jorbeer, Bikaner, Rajasthan 334001, India
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