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Kulanayake S, Dar F, Tikoo SK. Regions of Bovine Adenovirus-3 Protein VII Involved in Interactions with Viral and Cellular Proteins. Viruses 2024; 16:732. [PMID: 38793614 PMCID: PMC11125828 DOI: 10.3390/v16050732] [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: 03/21/2024] [Revised: 04/30/2024] [Accepted: 04/30/2024] [Indexed: 05/26/2024] Open
Abstract
The L 1 region of bovine adenovirus (BAdV)-3 encodes a multifunctional protein named protein VII. Anti-protein VII sera detected a protein of 26 kDa in transfected or BAdV-3-infected cells, which localizes to nucleus and nucleolus of infected/transfected cells. Analysis of mutant protein VII identified four redundant overlapping nuclear/nucleolar localization signals as deletion of all four potential nuclear/nucleolar localization signals localizes protein VII predominantly to the cytoplasm. The nuclear import of protein VII appears to use importin α (α-1), importin-β (β-1) and transportin-3 nuclear transport receptors. In addition, different nuclear transport receptors also require part of protein VII outside nuclear localization sequences for efficient interaction. Proteomic analysis of protein complexes purified from recombinant BAdV-3 expressing protein VII containing Strep Tag II identified potential viral and cellular proteins interacting with protein VII. Here, we confirm that protein VII interacts with IVa2 and protein VIII in BAdV-3-infected cells. Moreover, amino acids 91-101 and 126-137, parts of non-conserved region of protein VII, are required for interaction with IVa2 and protein VIII, respectively.
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Affiliation(s)
- Shermila Kulanayake
- Vaccinology & Immunotherapeutics Program, School of Public Health, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada; (S.K.); (F.D.)
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Faryal Dar
- Vaccinology & Immunotherapeutics Program, School of Public Health, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada; (S.K.); (F.D.)
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Suresh K. Tikoo
- Vaccinology & Immunotherapeutics Program, School of Public Health, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada; (S.K.); (F.D.)
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
- Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
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2
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Mazboudi R, Mulhall Maasz H, Resch MD, Wen K, Gottlieb P, Alimova A, Khayat R, Collins ND, Kuschner RA, Galarza JM. A recombinant virus-like particle vaccine against adenovirus-7 induces a potent humoral response. NPJ Vaccines 2023; 8:155. [PMID: 37821505 PMCID: PMC10567840 DOI: 10.1038/s41541-023-00754-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 10/02/2023] [Indexed: 10/13/2023] Open
Abstract
Adenoviruses (AdVs) cause infections in humans that range from mild to severe, and can cause outbreaks particularly in close contact settings. Several human AdV types have been identified, which can cause a wide array of clinical manifestations. AdV types 4 and 7 (AdV-4 and AdV-7), which are among the most commonly circulating types in the United States, are known to cause acute respiratory disease that can result in hospitalization and rarely, death. Currently, the only vaccines approved for use in humans are live virus vaccines against AdV-4 and AdV-7, though these vaccines are only authorized for use in U.S. military personnel. While they are efficacious, use of these live virus vaccines carries considerable risks of vaccine-associated viral shedding and recombination. Here, we present an alternative vaccination strategy against AdV-7 using the virus-like particle platform (AdVLP-7). We describe the production of stable recombinant AdVLP-7, and demonstrate that AdVLP-7 is structurally analogous to wild-type AdV-7 virions (WT AdV-7). Preclinical immunogenicity studies in mice show that AdVLP-7 elicits a potent humoral immune response, comparable to that observed in mice immunized with WT AdV-7. Specifically, AdVLP-7 induces high titers of antibodies against AdV-7-specific antigens that can effectively neutralize AdV-7.
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Affiliation(s)
- Ryan Mazboudi
- TechnoVax, Inc., 6 Westchester Plaza, Elmsford, NY, 10523, USA
| | | | - Matthew D Resch
- TechnoVax, Inc., 6 Westchester Plaza, Elmsford, NY, 10523, USA
| | - Ke Wen
- TechnoVax, Inc., 6 Westchester Plaza, Elmsford, NY, 10523, USA
| | - Paul Gottlieb
- CUNY School of Medicine, The City College of New York, New York, NY, 10031, USA
| | - Aleksandra Alimova
- CUNY School of Medicine, The City College of New York, New York, NY, 10031, USA
| | - Reza Khayat
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY, 10031, USA
| | - Natalie D Collins
- Viral Diseases Branch, Walter Reed Army Institute for Research, Silver Spring, MD, 20910, USA
| | - Robert A Kuschner
- Viral Diseases Branch, Walter Reed Army Institute for Research, Silver Spring, MD, 20910, USA
| | - Jose M Galarza
- TechnoVax, Inc., 6 Westchester Plaza, Elmsford, NY, 10523, USA.
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3
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Benhaghnazar RL, Medina-Kauwe L. Adenovirus-Derived Nano-Capsid Platforms for Targeted Delivery and Penetration of Macromolecules into Resistant and Metastatic Tumors. Cancers (Basel) 2023; 15:3240. [PMID: 37370850 PMCID: PMC10296971 DOI: 10.3390/cancers15123240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/31/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Macromolecular therapeutics such as nucleic acids, peptides, and proteins have the potential to overcome treatment barriers for cancer. For example, nucleic acid or peptide biologics may offer an alternative strategy for attacking otherwise undruggable therapeutic targets such as transcription factors and similar oncologic drivers. Delivery of biological therapeutics into tumor cells requires a robust system of cell penetration to access therapeutic targets within the cell interior. A highly effective means of accomplishing this may be borrowed from cell-penetrating pathogens such as viruses. In particular, the cell entry function of the adenovirus penton base capsid protein has been effective at penetrating tumor cells for the intracellular deposition of macromolecular therapies and membrane-impermeable drugs. Here, we provide an overview describing the evolution of tumor-targeted penton-base-derived nano-capsids as a framework for discussing the requirements for overcoming key barriers to macromolecular delivery. The development and pre-clinical testing of these proteins for therapeutic delivery has begun to also uncover the elusive mechanism underlying the membrane-penetrating function of the penton base. An understanding of this mechanism may unlock the potential for macromolecular therapeutics to be effectively delivered into cancer cells and to provide a treatment option for tumors resisting current clinical therapies.
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Affiliation(s)
| | - Lali Medina-Kauwe
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA;
- Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
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4
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Wang WC, Sayedahmed EE, Mittal SK. Significance of Preexisting Vector Immunity and Activation of Innate Responses for Adenoviral Vector-Based Therapy. Viruses 2022; 14:v14122727. [PMID: 36560730 PMCID: PMC9787786 DOI: 10.3390/v14122727] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
An adenoviral (AdV)-based vector system is a promising platform for vaccine development and gene therapy applications. Administration of an AdV vector elicits robust innate immunity, leading to the development of humoral and cellular immune responses against the vector and the transgene antigen, if applicable. The use of high doses (1011-1013 virus particles) of an AdV vector, especially for gene therapy applications, could lead to vector toxicity due to excessive levels of innate immune responses, vector interactions with blood factors, or high levels of vector transduction in the liver and spleen. Additionally, the high prevalence of AdV infections in humans or the first inoculation with the AdV vector result in the development of vector-specific immune responses, popularly known as preexisting vector immunity. It significantly reduces the vector efficiency following the use of an AdV vector that is prone to preexisting vector immunity. Several approaches have been developed to overcome this problem. The utilization of rare human AdV types or nonhuman AdVs is the primary strategy to evade preexisting vector immunity. The use of heterologous viral vectors, capsid modification, and vector encapsulation are alternative methods to evade vector immunity. The vectors can be optimized for clinical applications with comprehensive knowledge of AdV vector immunity, toxicity, and circumvention strategies.
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5
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Greber UF, Suomalainen M. Adenovirus entry: Stability, uncoating, and nuclear import. Mol Microbiol 2022; 118:309-320. [PMID: 35434852 PMCID: PMC9790413 DOI: 10.1111/mmi.14909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/09/2022] [Accepted: 04/12/2022] [Indexed: 12/30/2022]
Abstract
Adenoviruses (AdVs) are widespread in vertebrates. They infect the respiratory and gastrointestinal tracts, the eyes, heart, liver, and kidney, and are lethal to immunosuppressed people. Mastadenoviruses infecting mammals comprise several hundred different types, and many specifically infect humans. Human adenoviruses are the most widely used vectors in clinical applications, including cancer treatment and COVID-19 vaccination. AdV vectors are physically and genetically stable and generally safe in humans. The particles have an icosahedral coat and a nucleoprotein core with a DNA genome. We describe the concept of AdV cell entry and highlight recent advances in cytoplasmic transport, uncoating, and nuclear import of the viral DNA. We highlight a recently discovered "linchpin" function of the virion protein V ensuring cytoplasmic particle stability, which is relaxed at the nuclear pore complex by cues from the E3 ubiquitin ligase Mind bomb 1 (MIB1) and the proteasome triggering disruption. Capsid disruption by kinesin motor proteins and microtubules exposes the linchpin and renders protein V a target for MIB1 ubiquitination, which dissociates V from viral DNA and enhances DNA nuclear import. These advances uncover mechanisms controlling capsid stability and premature uncoating and provide insight into nuclear transport of nucleic acids.
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Affiliation(s)
- Urs F. Greber
- Department of Molecular Life SciencesUniversity of ZurichZurichSwitzerland
| | - Maarit Suomalainen
- Department of Molecular Life SciencesUniversity of ZurichZurichSwitzerland
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6
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Adenoviruses in Avian Hosts: Recent Discoveries Shed New Light on Adenovirus Diversity and Evolution. Viruses 2022; 14:v14081767. [PMID: 36016389 PMCID: PMC9416666 DOI: 10.3390/v14081767] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/09/2022] [Accepted: 08/11/2022] [Indexed: 11/16/2022] Open
Abstract
While adenoviruses cause infections in a wide range of vertebrates, members of the genus Atadenovirus, Siadenovirus, and Aviadenovirus predominantly infect avian hosts. Several recent studies on avian adenoviruses have encouraged us to re-visit previously proposed adenovirus evolutionary concepts. Complete genomes and partial DNA polymerase sequences of avian adenoviruses were extracted from NCBI and analysed using various software. Genomic analyses and constructed phylogenetic trees identified the atadenovirus origin from an Australian native passerine bird in contrast to the previously established reptilian origin. In addition, we demonstrated that the theories on higher AT content in atadenoviruses are no longer accurate and cannot be considered as a species demarcation criterion for the genus Atadenovirus. Phylogenetic reconstruction further emphasised the need to reconsider siadenovirus origin, and we recommend extended studies on avian adenoviruses in wild birds to provide finer evolutionary resolution.
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7
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Abstract
Charge detection mass spectrometry (CDMS) is a single-particle technique where the masses of individual ions are determined from simultaneous measurement of their mass-to-charge ratio (m/z) and charge. Masses are determined for thousands of individual ions, and then the results are binned to give a mass spectrum. Using this approach, accurate mass distributions can be measured for heterogeneous and high-molecular-weight samples that are usually not amenable to analysis by conventional mass spectrometry. Recent applications include heavily glycosylated proteins, protein complexes, protein aggregates such as amyloid fibers, infectious viruses, gene therapies, vaccines, and vesicles such as exosomes.
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Affiliation(s)
- Martin F Jarrold
- Chemistry Department, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47404, United States
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8
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Reddy VS, Yu X, Barry MA. Refined Capsid Structure of Human Adenovirus D26 at 3.4 Å Resolution. Viruses 2022; 14:v14020414. [PMID: 35216007 PMCID: PMC8878492 DOI: 10.3390/v14020414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 01/24/2022] [Accepted: 02/11/2022] [Indexed: 12/11/2022] Open
Abstract
Various adenoviruses are being used as viral vectors for the generation of vaccines against chronic and emerging diseases (e.g., AIDS, COVID-19). Here, we report the improved capsid structure for one of these vectors, human adenovirus D26 (HAdV-D26), at 3.4 Å resolution, by reprocessing the previous cryo-electron microscopy dataset and obtaining a refined model. In addition to overall improvements in the model, the highlights of the structure include (1) locating a segment of the processed peptide of VIII that was previously believed to be released from the mature virions, (2) reorientation of the helical appendage domain (APD) of IIIa situated underneath the vertex region relative to its counterpart observed in the cleavage defective (ts1) mutant of HAdV-C5 that resulted in the loss of interactions between the APD and hexon bases, and (3) the revised conformation of the cleaved N-terminal segments of pre-protein VI (pVIn), located in the hexon cavities, is highly conserved, with notable stacking interactions between the conserved His13 and Phe18 residues. Taken together, the improved model of HAdV-D26 capsid provides a better understanding of protein–protein interactions in HAdV capsids and facilitates the efforts to modify and/or design adenoviral vectors with altered properties. Last but not least, we provide some insights into clotting factors (e.g., FX and PF4) binding to AdV vectors.
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Affiliation(s)
- Vijay S Reddy
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xiaodi Yu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael A Barry
- Department of Internal Medicine, Mayo Clinic, Rochester, MN 55902, USA
- Division of Infectious Diseases, Mayo Clinic, Rochester, MN 55905, USA
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
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9
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Structure of a Cell Entry Defective Human Adenovirus Provides Insights into Precursor Proteins and Capsid Maturation. J Mol Biol 2022; 434:167350. [PMID: 34774568 PMCID: PMC8752480 DOI: 10.1016/j.jmb.2021.167350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 02/01/2023]
Abstract
Maturation of adenoviruses is distinguished by proteolytic processing of several interior minor capsid proteins and core proteins by the adenoviral protease and subsequent reorganization of adenovirus core. We report the results derived from the icosahedrally averaged cryo-EM structure of a cell entry defective form of adenovirus, designated ts1, at a resolution of 3.7 Å as well as of the localized reconstructions of unique hexons and penton base. The virion structure revealed the structures and organization of precursors of minor capsid proteins, pIIIa, pVI and pVIII, which are closely associated with the hexons on the capsid interior. In addition to a well-ordered helical domain (a.a. 310-397) of pIIIa, highlights of the structure include the precursors of VIII display significantly different structures near the cleavage sites. Moreover, we traced residues 4-96 of the membrane lytic protein (pVI) that includes an amphipathic helix occluded deep in the hexon cavity suggesting the possibility of co-assembly of hexons with the precursors of VI. In addition, we observe a second copy of pVI ordered up to residue L40 in the peripentonal hexons and a few fragments of density corresponding to 2nd and 3rd copies of pVI in other hexons. However, we see no evidence of precursors of VII binding in the hexon cavity. These findings suggest the possibility that differently bound pVI molecules undergo processing at the N-terminal cleavage sites at varying efficiencies, subsequently creating competition between the cleaved and uncleaved forms of VI, followed by reorganization, processing, and release of VI molecules from the hexon cavities.
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10
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Barnes LF, Draper BE, Jarrold MF. Analysis of Recombinant Adenovirus Vectors by Ion Trap Charge Detection Mass Spectrometry: Accurate Molecular Weight Measurements beyond 150 MDa. Anal Chem 2022; 94:1543-1551. [PMID: 35023731 DOI: 10.1021/acs.analchem.1c02439] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Adenovirus is one of the largest nonenveloped, double-stranded DNA viruses. It is widely used as a gene therapy vector and has recently received a lot of attention as a novel vaccine platform for SARS-CoV-2. Human adenovirus 5 (HAdV5) contains over 2500 protein molecules and has a 36 kbp genome. Adenovirus is well beyond the range of conventional mass spectrometry, and it was unclear how well such a large complex could be desolvated. Here, we report molecular weight (MW) distributions measured for HAdV5 and for 11 recombinant AdV vectors with genomes of varying lengths. The MW distributions were recorded using ion trap charge detection mass spectrometry (CDMS), a single-particle technique where m/z and charge are measured for individual ions. The results show that ions as large as 150 MDa can be effectively desolvated and accurate MW distributions obtained. The MW distribution for HAdV5 contains a narrow peak at 156.1 MDa, assigned to the infectious virus. A smaller peak at 129.6 MDa is attributed to incomplete particles that have not packaged a genome. The ions in the 129.6 MDa peak have a much lower average charge than those in the peak at 156.1 MDa. This is attributed to the empty particles missing some or all of the fibers that decorate the surface of the virion. The MW measured for the mature virus (156.1 MDa) is much larger than that predicted from sequence masses and copy numbers of the constituents (142.5 MDa). Measurements performed for recombinant AdV as a function of genome length show that for every 1 MDa increase in the genome MW, the MW of the mature virus increases by around 2.3 MDa. The additional 1.3 MDa is attributed to core proteins that are copackaged with the DNA. This observation suggests that the discrepancy between the measured and expected MWs for mature HAdV5 is due to an underestimate in the copy numbers of the core proteins.
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Affiliation(s)
- Lauren F Barnes
- Chemistry Department, Indiana University, 800 E Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Benjamin E Draper
- Megadalton Solutions, Inc., 3750 E Bluebird Lane, Bloomington, Indiana 47401, United States
| | - Martin F Jarrold
- Chemistry Department, Indiana University, 800 E Kirkwood Avenue, Bloomington, Indiana 47405, United States
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11
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Strack A, Deinzer A, Thirion C, Schrödel S, Dörrie J, Sauerer T, Steinkasserer A, Knippertz I. Breaking Entry-and Species Barriers: LentiBOOST ® Plus Polybrene Enhances Transduction Efficacy of Dendritic Cells and Monocytes by Adenovirus 5. Viruses 2022; 14:v14010092. [PMID: 35062296 PMCID: PMC8781300 DOI: 10.3390/v14010092] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 12/29/2021] [Indexed: 12/19/2022] Open
Abstract
Due to their ability to trigger strong immune responses, adenoviruses (HAdVs) in general and the serotype5 (HAdV-5) in particular are amongst the most popular viral vectors in research and clinical application. However, efficient transduction using HAdV-5 is predominantly achieved in coxsackie and adenovirus receptor (CAR)-positive cells. In the present study, we used the transduction enhancer LentiBOOST® comprising the polycationic Polybrene to overcome these limitations. Using LentiBOOST®/Polybrene, we yielded transduction rates higher than 50% in murine bone marrow-derived dendritic cells (BMDCs), while maintaining their cytokine expression profile and their capability to induce T-cell proliferation. In human dendritic cells (DCs), we increased the transduction rate from 22% in immature (i)DCs or 43% in mature (m)DCs to more than 80%, without inducing cytotoxicity. While expression of specific maturation markers was slightly upregulated using LentiBOOST®/Polybrene on iDCs, no effect on mDC phenotype or function was observed. Moreover, we achieved efficient HAdV5 transduction also in human monocytes and were able to subsequently differentiate them into proper iDCs and functional mDCs. In summary, we introduce LentiBOOST® comprising Polybrene as a highly potent adenoviral transduction agent for new in-vitro applications in a set of different immune cells in both mice and humans.
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Affiliation(s)
- Astrid Strack
- Department of Immune Modulation, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Hartmannstr. 14, 91052 Erlangen, Germany; (A.D.); (A.S.)
- Correspondence: (A.S.); (I.K.)
| | - Andrea Deinzer
- Department of Immune Modulation, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Hartmannstr. 14, 91052 Erlangen, Germany; (A.D.); (A.S.)
- Institute of Clinical Microbiology, Immunology and Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Wasserturmstraße 3/5, 91054 Erlangen, Germany
| | - Christian Thirion
- SIRION Biotech GmbH, Am Klopferspitz 19, 82152 Martinsried, Germany; (C.T.); (S.S.)
| | - Silke Schrödel
- SIRION Biotech GmbH, Am Klopferspitz 19, 82152 Martinsried, Germany; (C.T.); (S.S.)
| | - Jan Dörrie
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Hartmannstr. 14, 91052 Erlangen, Germany; (J.D.); (T.S.)
| | - Tatjana Sauerer
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Hartmannstr. 14, 91052 Erlangen, Germany; (J.D.); (T.S.)
| | - Alexander Steinkasserer
- Department of Immune Modulation, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Hartmannstr. 14, 91052 Erlangen, Germany; (A.D.); (A.S.)
| | - Ilka Knippertz
- Department of Immune Modulation, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Hartmannstr. 14, 91052 Erlangen, Germany; (A.D.); (A.S.)
- Correspondence: (A.S.); (I.K.)
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12
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Bauer M, Gomez-Gonzalez A, Suomalainen M, Schilling N, Hemmi S, Greber UF. A viral ubiquitination switch attenuates innate immunity and triggers nuclear import of virion DNA and infection. SCIENCE ADVANCES 2021; 7:eabl7150. [PMID: 34919430 PMCID: PMC8682987 DOI: 10.1126/sciadv.abl7150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Antiviral defense and virus exclusion from the cell nucleus restrict foreign nucleic acid influx and infection. How the genomes of DNA viruses evade cytosolic pattern recognition and cross the nuclear envelope is incompletely understood. Here, we show that the virion protein V of adenovirus functions as a linchpin between the genome and the capsid, thereby securing particle integrity. Absence of protein V destabilizes cytoplasmic particles and promotes premature genome release, raising cytokine levels through the DNA sensor cGAS. Non-ubiquitinable V yields stable virions, genome misdelivery to the cytoplasm, and increased cytokine levels. In contrast, normal protein V is ubiquitinated at the nuclear pore complex, dissociates from the virion depending on the E3 ubiquitin ligase Mib1 and the proteasome, and allows genome delivery into the nucleus for infection. Our data uncover previously unknown cellular and viral mechanisms of viral DNA nuclear import in pathogenesis, vaccination, gene therapy, and synthetic biology.
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Affiliation(s)
- Michael Bauer
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, Zurich CH8057, Switzerland
| | - Alfonso Gomez-Gonzalez
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, Zurich CH8057, Switzerland
- Life Science Zurich Graduate School, ETH and University of Zurich, Zurich 8057, Switzerland
| | - Maarit Suomalainen
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, Zurich CH8057, Switzerland
| | - Nicolas Schilling
- Center for Microscopy and Image Analysis, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Silvio Hemmi
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, Zurich CH8057, Switzerland
| | - Urs F. Greber
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, Zurich CH8057, Switzerland
- Corresponding author.
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13
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Core-Shell Imprinted Particles for Adenovirus Binding. MATERIALS 2021; 14:ma14247692. [PMID: 34947287 PMCID: PMC8703578 DOI: 10.3390/ma14247692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 11/28/2021] [Accepted: 12/10/2021] [Indexed: 11/17/2022]
Abstract
Virus-imprinted polymers were synthesized via surface imprinting strategies to produce core-shell imprinted particles selective for human adenovirus type 5. High binding affinity of the target virus towards the resulting imprinted layer was confirmed and unspecific binding was reduced in presence of blocking agents, i.e., via bovine serum albumin and skim milk in combination with Tween 20. In addition, the imprinted materials were applied for adenovirus extraction from cell culture supernatants. High levels of virus binding with negligible binding of matrix proteins confirmed the suitability of these materials for binding and extraction of the target virus from complex matrices.
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14
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Virus against virus: strategies for using adenovirus vectors in the treatment of HPV-induced cervical cancer. Acta Pharmacol Sin 2021; 42:1981-1990. [PMID: 33633364 PMCID: PMC8633276 DOI: 10.1038/s41401-021-00616-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 01/17/2021] [Indexed: 01/31/2023] Open
Abstract
Although most human papillomavirus (HPV) infections are harmless, persistent infection with high-risk types of HPV is known to be the leading cause of cervical cancer. Following the infection of the epithelium and integration into the host genome, the oncogenic proteins E6 and E7 disrupt cell cycle control by inducing p53 and retinoblastoma (Rb) degradation. Despite the FDA approval of prophylactic vaccines, there are still issues with cervical cancer treatment; thus, many therapeutic approaches have been developed to date. Due to strong immunogenicity, a high capacity for packaging foreign DNA, safety, and the ability to infect a myriad of cells, adenoviruses have drawn attention of researchers. Adenovirus vectors have been used for different purposes, including as oncolytic agents to kill cancer cells, carrier for RNA interference to block oncoproteins expression, vaccines for eliciting immune responses, especially in cytotoxic T lymphocytes (CTLs), and gene therapy vehicles for restoring p53 and Rb function.
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15
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Wang Y, Zhang Z, Shang L, Gao H, Du X, Li F, Gao Y, Qi G, Guo W, Qu Z, Dong T. Immunological Study of Reconstructed Common Ancestral Sequence of Adenovirus Hexon Protein. Front Microbiol 2021; 12:717047. [PMID: 34777273 PMCID: PMC8578728 DOI: 10.3389/fmicb.2021.717047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 10/08/2021] [Indexed: 11/16/2022] Open
Abstract
Aim: To reconstruct the ancestral sequence of human adenoviral hexon protein by combining sequence variations and structural information. And to provide a candidate hexon protein for developing new adenoviral vector capable of escaping the pre-existing immunity in healthy populations. Methods: The sequences of 74 adenovirus-type strains were used to predict the ancestral sequence of human adenovirus hexon protein using FastML and MEGA software. The three-dimensional structure model was built using homology modeling methods. The immunological features of ancestral loop 1 and loop 2 regions of sequences were tested using protein segments expressed in a prokaryotic expression system and polypeptides synthesized with human serum samples. Results: The tower region of the hexon protein had the highest sequence variability, while the neck and base regions remained constant among different types. The modern strains successfully predicted the common ancestral sequence of the human adenovirus hexon. The positive sera against neutralizing epitopes on the common ancestor of adenoviral hexon were relatively rare among healthy adults. Conclusion: The existing strains inferred the common ancestor of human adenoviruses, with epitopes never observed in the current human strains. The predicted common ancestor hexon is a good prospect in the improvement of adenovirus vectors.
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Affiliation(s)
- Yingchen Wang
- Department of Microbiology, Public Health College, Harbin Medical University, Harbin, China
| | - Zhe Zhang
- Department of Microbiology, Public Health College, Harbin Medical University, Harbin, China
| | - Lei Shang
- Department of Microbiology, Public Health College, Harbin Medical University, Harbin, China
| | - Hong Gao
- Department of Microbiology, Public Health College, Harbin Medical University, Harbin, China
| | - Xiqiao Du
- Department of Microbiology, Public Health College, Harbin Medical University, Harbin, China.,Harbin Center for Disease Control and Prevention, Harbin, China
| | - Falong Li
- Department of Microbiology, Public Health College, Harbin Medical University, Harbin, China
| | - Ya Gao
- Department of Microbiology, Public Health College, Harbin Medical University, Harbin, China
| | - Guiyun Qi
- The Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Weiyuan Guo
- The Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Zhangyi Qu
- Department of Microbiology, Public Health College, Harbin Medical University, Harbin, China.,Department of Natural Focus Disease Control, Institute of Environment-Associated Disease, Sino-Russia Joint Medical Research Center, Harbin Medical University, Harbin, China
| | - Tuo Dong
- Department of Microbiology, Public Health College, Harbin Medical University, Harbin, China
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16
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Adenovirus Structure: What Is New? Int J Mol Sci 2021; 22:ijms22105240. [PMID: 34063479 PMCID: PMC8156859 DOI: 10.3390/ijms22105240] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 02/06/2023] Open
Abstract
Adenoviruses are large (~950 Å) and complex non-enveloped, dsDNA icosahedral viruses. They have a pseudo-T = 25 triangulation number with at least 12 different proteins composing the virion. These include the major and minor capsid proteins, core proteins, maturation protease, terminal protein, and packaging machinery. Although adenoviruses have been studied for more than 60 years, deciphering their architecture has presented a challenge for structural biology techniques. An outstanding event was the first near-atomic resolution structure of human adenovirus type 5 (HAdV-C5), solved by cryo-electron microscopy (cryo-EM) in 2010. Discovery of new adenovirus types, together with methodological advances in structural biology techniques, in particular cryo-EM, has lately produced a considerable amount of new, high-resolution data on the organization of adenoviruses belonging to different species. In spite of these advances, the organization of the non-icosahedral core is still a great unknown. Nevertheless, alternative techniques such as atomic force microscopy (AFM) are providing interesting glimpses on the role of the core proteins in genome condensation and virion stability. Here we summarize the current knowledge on adenovirus structure, with an emphasis on high-resolution structures obtained since 2010.
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17
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Almuqrin A, Davidson AD, Williamson MK, Lewis PA, Heesom KJ, Morris S, Gilbert SC, Matthews DA. SARS-CoV-2 vaccine ChAdOx1 nCoV-19 infection of human cell lines reveals low levels of viral backbone gene transcription alongside very high levels of SARS-CoV-2 S glycoprotein gene transcription. Genome Med 2021; 13:43. [PMID: 33722288 PMCID: PMC7958140 DOI: 10.1186/s13073-021-00859-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 02/23/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND ChAdOx1 nCoV-19 is a recombinant adenovirus vaccine against SARS-CoV-2 that has passed phase III clinical trials and is now in use across the globe. Although replication-defective in normal cells, 28 kbp of adenovirus genes is delivered to the cell nucleus alongside the SARS-CoV-2 S glycoprotein gene. METHODS We used direct RNA sequencing to analyse transcript expression from the ChAdOx1 nCoV-19 genome in human MRC-5 and A549 cell lines that are non-permissive for vector replication alongside the replication permissive cell line, HEK293. In addition, we used quantitative proteomics to study over time the proteome and phosphoproteome of A549 and MRC5 cells infected with the ChAdOx1 nCoV-19 vaccine. RESULTS The expected SARS-CoV-2 S coding transcript dominated in all cell lines. We also detected rare S transcripts with aberrant splice patterns or polyadenylation site usage. Adenovirus vector transcripts were almost absent in MRC-5 cells, but in A549 cells, there was a broader repertoire of adenoviral gene expression at very low levels. Proteomically, in addition to S glycoprotein, we detected multiple adenovirus proteins in A549 cells compared to just one in MRC5 cells. CONCLUSIONS Overall, the ChAdOx1 nCoV-19 vaccine's transcriptomic and proteomic repertoire in cell culture is as expected. The combined transcriptomic and proteomics approaches provide a detailed insight into the behaviour of this important class of vaccine using state-of-the-art techniques and illustrate the potential of this technique to inform future viral vaccine vector design.
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Affiliation(s)
- Abdulaziz Almuqrin
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University Walk, University of Bristol, Bristol, BS8 1TD, UK
- Department of Clinical Laboratory Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Andrew D Davidson
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University Walk, University of Bristol, Bristol, BS8 1TD, UK
| | - Maia Kavanagh Williamson
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University Walk, University of Bristol, Bristol, BS8 1TD, UK
| | - Philip A Lewis
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University Walk, University of Bristol, Bristol, BS8 1TD, UK
| | - Kate J Heesom
- Proteomics Facility, Faculty of Life Sciences, University Walk, University of Bristol, Bristol, BS8 1TD, UK
| | - Susan Morris
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Sarah C Gilbert
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - David A Matthews
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University Walk, University of Bristol, Bristol, BS8 1TD, UK.
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18
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Kulanayake S, Tikoo SK. Adenovirus Core Proteins: Structure and Function. Viruses 2021; 13:v13030388. [PMID: 33671079 PMCID: PMC7998265 DOI: 10.3390/v13030388] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 02/19/2021] [Accepted: 02/24/2021] [Indexed: 01/04/2023] Open
Abstract
Adenoviruses have served as a model for investigating viral-cell interactions and discovering different cellular processes, such as RNA splicing and DNA replication. In addition, the development and evaluation of adenoviruses as the viral vectors for vaccination and gene therapy has led to detailed investigations about adenovirus biology, including the structure and function of the adenovirus encoded proteins. While the determination of the structure and function of the viral capsid proteins in adenovirus biology has been the subject of numerous reports, the last few years have seen increased interest in elucidating the structure and function of the adenovirus core proteins. Here, we provide a review of research about the structure and function of the adenovirus core proteins in adenovirus biology.
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Affiliation(s)
- Shermila Kulanayake
- Vaccine and Infectious Disease Organization-International Vaccine Center (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK S7N5E3, Canada;
- Vaccinology & Immunotherapeutics Program, School of Public Health, University of Saskatchewan, Saskatoon, SK S7N5E3, Canada
| | - Suresh K. Tikoo
- Vaccine and Infectious Disease Organization-International Vaccine Center (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK S7N5E3, Canada;
- Vaccinology & Immunotherapeutics Program, School of Public Health, University of Saskatchewan, Saskatoon, SK S7N5E3, Canada
- Correspondence:
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19
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Zhao X, Tikoo SK. Nuclear and Nucleolar Localization of Bovine Adenovirus-3 Protein V. Front Microbiol 2021; 11:579593. [PMID: 33488533 PMCID: PMC7815533 DOI: 10.3389/fmicb.2020.579593] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 12/03/2020] [Indexed: 02/01/2023] Open
Abstract
The L2 region of bovine adenovirus-3 (BAdV-3) encodes a Mastadenovirus genus-specific protein, designated as pV, which is important for the production of progeny viruses. Here, we demonstrate that BAdV-3 pV, expressed as 55 kDa protein, localizes to the nucleus and specifically targets nucleolus of the infected cells. Analysis of deletion mutants of pV suggested that amino acids 81–120, 190–210, and 380–389 act as multiple nuclear localization signals (NLS), which also appear to serve as the binding sites for importin α-3 protein, a member of the importin α/β nuclear import receptor pathway. Moreover, pV amino acids 21–50 and 380–389 appear to act as nucleolar localization signals (NoLs). Interestingly, amino acids 380–389 appear to act both as NLS and as NoLS. The presence of NoLS is essential for the production of infectious progeny virions, as deletion of both NoLs are lethal for the production of infectious BAdV-3. Analysis of mutant BAV.pVd1d3 (isolated in pV completing CRL cells) containing deletion/mutation of both NoLS in non-complementing CRL cells not only revealed the altered intracellular localization of mutant pV but also reduced the expression of some late proteins. However, it does not appear to affect the incorporation of viral proteins, including mutant pV, in BAV.pVd1d3 virions. Further analysis of CsCl purified BAV.pVd1d3 suggested the presence of thermo-labile virions with disrupted capsids, which appear to affect the infectivity of the progeny virions. Our results suggest that pV contains overlapping and non-overlapping NoLS/NLS. Moreover, the presence of both NoLS appear essential for the production of stable and infectious progeny BAV.pVd1d3 virions.
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Affiliation(s)
- Xin Zhao
- VIDO-InterVac, University of Saskatchewan, Saskatoon, SK, Canada.,Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Suresh K Tikoo
- VIDO-InterVac, University of Saskatchewan, Saskatoon, SK, Canada.,Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK, Canada.,Vaccinology and Imuunothepapeutics Program, School of Public Health, University of Saskatchewan, Saskatoon, SK, Canada
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20
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Reddy VS, Barry MA. Structural Organization and Protein-Protein Interactions in Human Adenovirus Capsid. Subcell Biochem 2021; 96:503-518. [PMID: 33252742 DOI: 10.1007/978-3-030-58971-4_16] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Human adenoviruses (HAdVs) are large (150 MDa), complex, nonenveloped dsDNA viruses that cause self-limiting respiratory, ocular and enteric infections. They are significant health hazard in young, elderly and immuno-compromised populations. Moreover, various adenoviruses (AdVs) of mammalian origin are being used as vectors in gene, vaccine and cancer therapies. Multiple copies of at least 13 different proteins, all in all ~2800 protein molecules, come together to form an adenovirus virion packaging the ~36 Kbp geome. The details of structural organization of the adenovirus capsid and underlying network of protein-protein interactions provide clues into designing the modified and novel adenovirus vectors with desired functionalities and/or targeting specificities. The advancements in 3D structure determination by cryo-electron microscopy (cryo-EM) in the past decade have enabled unveiling of the complex organization of adenovirus architecture at near atomic resolution. Specifically, these studies revealed the structures and the network of interactions involving cement/minor proteins in stabilizing the AdV icosahedral architecture, which appear to be mostly conserved among human adenoviruses. In this chapter, we describe the current state of knowledge on the structure and organization of human adenoviruses.
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Affiliation(s)
- Vijay S Reddy
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA.
| | - Michael A Barry
- Department of Internal Medicine, Division of Infectious Diseases, Mayo Clinic, Rochester, MN, 55902, USA
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21
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Dedeo CL, Teschke CM, Alexandrescu AT. Keeping It Together: Structures, Functions, and Applications of Viral Decoration Proteins. Viruses 2020; 12:v12101163. [PMID: 33066635 PMCID: PMC7602432 DOI: 10.3390/v12101163] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/09/2020] [Accepted: 10/11/2020] [Indexed: 12/14/2022] Open
Abstract
Decoration proteins are viral accessory gene products that adorn the surfaces of some phages and viral capsids, particularly tailed dsDNA phages. These proteins often play a "cementing" role, reinforcing capsids against accumulating internal pressure due to genome packaging, or environmental insults such as extremes of temperature or pH. Many decoration proteins serve alternative functions, including target cell recognition, participation in viral assembly, capsid size determination, or modulation of host gene expression. Examples that currently have structures characterized to high-resolution fall into five main folding motifs: β-tulip, β-tadpole, OB-fold, Ig-like, and a rare knotted α-helical fold. Most of these folding motifs have structure homologs in virus and target cell proteins, suggesting horizontal gene transfer was important in their evolution. Oligomerization states of decoration proteins range from monomers to trimers, with the latter most typical. Decoration proteins bind to a variety of loci on capsids that include icosahedral 2-, 3-, and 5-fold symmetry axes, as well as pseudo-symmetry sites. These binding sites often correspond to "weak points" on the capsid lattice. Because of their unique abilities to bind virus surfaces noncovalently, decoration proteins are increasingly exploited for technology, with uses including phage display, viral functionalization, vaccination, and improved nanoparticle design for imaging and drug delivery. These applications will undoubtedly benefit from further advances in our understanding of these versatile augmenters of viral functions.
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22
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Kleinberger T. En Guard! The Interactions between Adenoviruses and the DNA Damage Response. Viruses 2020; 12:v12090996. [PMID: 32906746 PMCID: PMC7552057 DOI: 10.3390/v12090996] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/01/2020] [Accepted: 09/01/2020] [Indexed: 02/07/2023] Open
Abstract
Virus–host cell interactions include several skirmishes between the virus and its host, and the DNA damage response (DDR) network is one of their important battlegrounds. Although some aspects of the DDR are exploited by adenovirus (Ad) to improve virus replication, especially at the early phase of infection, a large body of evidence demonstrates that Ad devotes many of its proteins, including E1B-55K, E4orf3, E4orf4, E4orf6, and core protein VII, and utilizes varied mechanisms to inhibit the DDR. These findings indicate that the DDR would strongly restrict Ad replication if allowed to function efficiently. Various Ad serotypes inactivate DNA damage sensors, including the Mre11-Rad50-Nbs1 (MRN) complex, DNA-dependent protein kinase (DNA-PK), and Poly (ADP-ribose) polymerase 1 (PARP-1). As a result, these viruses inhibit signaling via DDR transducers, such as the ataxia-telangiectasia mutated (ATM) and ATM- and Rad3-related (ATR) kinases, to downstream effectors. The different Ad serotypes utilize both shared and distinct mechanisms to inhibit various branches of the DDR. The aim of this review is to understand the interactions between Ad proteins and the DDR and to appreciate how these interactions contribute to viral replication.
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Affiliation(s)
- Tamar Kleinberger
- Department of Molecular Microbiology, Faculty of Medicine, Technion-Israel Institute of Technology, 1 Efron St., Bat Galim, Haifa 31096, Israel
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23
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Goradel NH, Negahdari B, Ghorghanlu S, Jahangiri S, Arashkia A. Strategies for enhancing intratumoral spread of oncolytic adenoviruses. Pharmacol Ther 2020; 213:107586. [PMID: 32479843 DOI: 10.1016/j.pharmthera.2020.107586] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 05/11/2020] [Indexed: 02/06/2023]
Abstract
Oncolytic viruses, effectively replicate viruses within malignant cells to lyse them without affecting normal ones, have recently shown great promise in developing therapeutic options for cancer. Adenoviruses (Ads) are one of the candidates in oncolytic virotheraoy due to its easily manipulated genomic DNA and expression of wide rane of its receptors on the various cancers. Although systematic delivery of oncolytic adenoviruses can target both primary and metastatic tumors, there are some drawbacks in the effective systematic delivery of oncolytic adenoviruses, including pre-existing antibodies and liver tropism. To overcome these limitations, intratumural (IT) administration of oncolytic viruses have been proposed. However, IT injection of Ads leaves much of the tumor mass unaffected and Ads are not able to disperse more in the tumor microenvironment (TME). To this end, various strategies have been developed to enhance the IT spread of oncolytic adenoviruses, such as using extracellular matrix degradation enzymes, junction opening peptides, and fusogenic proteins. In the present paper, we reviewed different oncolytic adenoviruses, their application in the clinical trials, and strategies for enhancing their IT spread.
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Affiliation(s)
- Nasser Hashemi Goradel
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Babak Negahdari
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran.
| | - Sajjad Ghorghanlu
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Samira Jahangiri
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Arash Arashkia
- Department of Molecular Virology, Pasteur Institute of Iran, Tehran, Iran.
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24
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Regions of bovine adenovirus-3 IVa2 involved in nuclear/nucleolar localization and interaction with pV. Virology 2020; 546:25-37. [PMID: 32452415 DOI: 10.1016/j.virol.2020.04.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/18/2020] [Accepted: 04/06/2020] [Indexed: 12/15/2022]
Abstract
Bovine adenovirus-3 (BAdV-3) is a non enveloped, icosahedral DNA virus containing a genome of 34446 bps. The intermediate region of BAdV-3 encodes pIX and IVa2 proteins. Here, we report the characterization of BAdV-3 IVa2. Anti-IVa2 serum detected a 50 kDa protein at 24-48 h post infection in BAdV-3 infected cells. The IVa2 localizes to nucleus and nucleolus of BAdV-3 infected cells. Analysis of mutant IVa2 demonstrated that amino acids 1-25 and 373-448 are required for nuclear and nucleolar localization of IVa2, respectively. The nuclear import of IVa2 utilize importin α -1 of importin nuclear import pathway. Although deletion/substitution of amino acids 4-18 is sufficient to abrogate the nuclear localization of IVa2, amino acids 1-25 are required for nuclear localization of a cytoplasmic protein. Furthermore, we demonstrate that amino acids 1-25 and 120-140 of IVa2 interact with importin α-1 and pV proteins, respectively in BAdV-3 infected cells.
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25
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Abstract
Viruses are obligatory parasites that take advantage of intracellular niches to replicate. During infection, their genomes are carried in capsids across the membranes of host cells to sites of virion production by exploiting cellular behaviour and resources to guide and achieve all aspects of delivery and the downstream virus manufacturing process. Successful entry hinges on execution of a precisely tuned viral uncoating program where incoming capsids disassemble in consecutive steps to ensure that genomes are released at the right time, and in the right place for replication to occur. Each step of disassembly is cell-assisted, involving individual pathways that transmit signals to regulate discrete functions, but at the same time, these signalling pathways are organized into larger networks, which communicate back and forth in complex ways in response to the presence of virus. In this review, we consider the elegant strategy by which adenoviruses (AdVs) target and navigate cellular networks to initiate the production of progeny virions. There are many remarkable aspects about the AdV entry program; for example, the virus gains targeted control of a large well-defined local network neighbourhood by coupling several interacting processes (including endocytosis, autophagy and microtubule trafficking) around a collective reference state centred on the interactional topology and multifunctional nature of protein VI. Understanding the network targeting activity of protein VI, as well as other built-in mechanisms that allow AdV particles to be efficient at navigating the subsystems of the cell, can be used to improve viral vectors, but also has potential to be incorporated for use in entirely novel delivery systems.
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Affiliation(s)
- Justin W Flatt
- Faculty of Biological and Environmental Sciences and HiLIFE-Institute of Biotechnology, University of Helsinki , 00790 Helsinki , Finland
| | - Sarah J Butcher
- Faculty of Biological and Environmental Sciences and HiLIFE-Institute of Biotechnology, University of Helsinki , 00790 Helsinki , Finland
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26
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Ni R, Chau Y. Nanoassembly of Oligopeptides and DNA Mimics the Sequential Disassembly of a Spherical Virus. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201913611] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Rong Ni
- Department of Chemical and Biological EngineeringThe Hong Kong University of Science and Technology Clearwater Bay Kowloon, Hong Kong China
| | - Ying Chau
- Department of Chemical and Biological EngineeringThe Hong Kong University of Science and Technology Clearwater Bay Kowloon, Hong Kong China
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27
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Ni R, Chau Y. Nanoassembly of Oligopeptides and DNA Mimics the Sequential Disassembly of a Spherical Virus. Angew Chem Int Ed Engl 2019; 59:3578-3584. [DOI: 10.1002/anie.201913611] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Indexed: 11/05/2022]
Affiliation(s)
- Rong Ni
- Department of Chemical and Biological EngineeringThe Hong Kong University of Science and Technology Clearwater Bay Kowloon, Hong Kong China
| | - Ying Chau
- Department of Chemical and Biological EngineeringThe Hong Kong University of Science and Technology Clearwater Bay Kowloon, Hong Kong China
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28
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Ismail AM, Zhou X, Dyer DW, Seto D, Rajaiya J, Chodosh J. Genomic foundations of evolution and ocular pathogenesis in human adenovirus species D. FEBS Lett 2019; 593:3583-3608. [PMID: 31769017 PMCID: PMC7185199 DOI: 10.1002/1873-3468.13693] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/16/2019] [Accepted: 11/20/2019] [Indexed: 12/27/2022]
Abstract
Human adenovirus commonly causes infections of respiratory, gastrointestinal, genitourinary, and ocular surface mucosae. Although most adenovirus eye infections are mild and self-limited, specific viruses within human adenovirus species D are associated with epidemic keratoconjunctivitis (EKC), a severe and highly contagious ocular surface infection, which can lead to chronic and/or recurrent, visually disabling keratitis. In this review, we discuss the links between adenovirus ontogeny, genomics, immune responses, and corneal pathogenesis, for those viruses that cause EKC.
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Affiliation(s)
- Ashrafali M. Ismail
- Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - Xiaohong Zhou
- Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - David W. Dyer
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Donald Seto
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, Virginia, USA
| | - Jaya Rajaiya
- Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - James Chodosh
- Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
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29
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Wang N, Zhao D, Wang J, Zhang Y, Wang M, Gao Y, Li F, Wang J, Bu Z, Rao Z, Wang X. Architecture of African swine fever virus and implications for viral assembly. Science 2019; 366:640-644. [PMID: 31624094 DOI: 10.1126/science.aaz1439] [Citation(s) in RCA: 207] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 10/09/2019] [Indexed: 01/27/2023]
Abstract
African swine fever virus (ASFV) is a giant and complex DNA virus that causes a highly contagious and often lethal swine disease for which no vaccine is available. Using an optimized image reconstruction strategy, we solved the ASFV capsid structure up to 4.1 angstroms, which is built from 17,280 proteins, including one major (p72) and four minor (M1249L, p17, p49, and H240R) capsid proteins organized into pentasymmetrons and trisymmetrons. The atomic structure of the p72 protein informs putative conformational epitopes, distinguishing ASFV from other nucleocytoplasmic large DNA viruses. The minor capsid proteins form a complicated network below the outer capsid shell, stabilizing the capsid by holding adjacent capsomers together. Acting as core organizers, 100-nanometer-long M1249L proteins run along each edge of the trisymmetrons that bridge two neighboring pentasymmetrons and form extensive intermolecular networks with other capsid proteins, driving the formation of the capsid framework. These structural details unveil the basis of capsid stability and assembly, opening up new avenues for African swine fever vaccine development.
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Affiliation(s)
- Nan Wang
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dongming Zhao
- State Key Laboratory of Veterinary Biotechnology and National High Containment Laboratory for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Jialing Wang
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yangling Zhang
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ming Wang
- State Key Laboratory of Veterinary Biotechnology and National High Containment Laboratory for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Yan Gao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,Laboratory of Structural Biology, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Fang Li
- State Key Laboratory of Veterinary Biotechnology and National High Containment Laboratory for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Jingfei Wang
- State Key Laboratory of Veterinary Biotechnology and National High Containment Laboratory for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Zhigao Bu
- State Key Laboratory of Veterinary Biotechnology and National High Containment Laboratory for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China.
| | - Zihe Rao
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China. .,Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,Laboratory of Structural Biology, School of Medicine, Tsinghua University, Beijing 100084, China.,State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300353, China
| | - Xiangxi Wang
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China. .,University of Chinese Academy of Sciences, Beijing 100049, China
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Pennington MR, Saha A, Painter DF, Gavazzi C, Ismail AM, Zhou X, Chodosh J, Rajaiya J. Disparate Entry of Adenoviruses Dictates Differential Innate Immune Responses on the Ocular Surface. Microorganisms 2019; 7:E351. [PMID: 31540200 PMCID: PMC6780103 DOI: 10.3390/microorganisms7090351] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 09/08/2019] [Accepted: 09/11/2019] [Indexed: 12/31/2022] Open
Abstract
Human adenovirus infection of the ocular surface is associated with severe keratoconjunctivitis and the formation of subepithelial corneal infiltrates, which may persist and impair vision for months to years following infection. Long term pathology persists well beyond the resolution of viral replication, indicating that the prolonged immune response is not virus-mediated. However, it is not clear how these responses are sustained or even initiated following infection. This review discusses recent work from our laboratory and others which demonstrates different entry pathways specific to both adenovirus and cell type. These findings suggest that adenoviruses may stimulate specific pattern recognition receptors in an entry/trafficking-dependent manner, leading to distinct immune responses dependent on the virus/cell type combination. Additional work is needed to understand the specific connections between adenoviral entry and the stimulation of innate immune responses by the various cell types present on the ocular surface.
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Affiliation(s)
- Matthew R Pennington
- Howe Laboratory, Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA.
| | - Amrita Saha
- Howe Laboratory, Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA.
| | - David F Painter
- Howe Laboratory, Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA.
| | - Christina Gavazzi
- Howe Laboratory, Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA.
| | - Ashrafali M Ismail
- Howe Laboratory, Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA.
| | - Xiaohong Zhou
- Howe Laboratory, Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA.
| | - James Chodosh
- Howe Laboratory, Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA.
| | - Jaya Rajaiya
- Howe Laboratory, Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA.
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31
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Abstract
Viruses must navigate the complex endomembranous network of the host cell to cause infection. In the case of a non-enveloped virus that lacks a surrounding lipid bilayer, endocytic uptake from the plasma membrane is not sufficient to cause infection. Instead, the virus must travel within organelle membranes to reach a specific cellular destination that supports exposure or arrival of the virus to the cytosol. This is achieved by viral penetration across a host endomembrane, ultimately enabling entry of the virus into the nucleus to initiate infection. In this review, we discuss the entry mechanisms of three distinct non-enveloped DNA viruses-adenovirus (AdV), human papillomavirus (HPV), and polyomavirus (PyV)-highlighting how each exploit different intracellular transport machineries and membrane penetration apparatus associated with the endosome, Golgi, and endoplasmic reticulum (ER) membrane systems to infect a host cell. These processes not only illuminate a highly-coordinated interplay between non-enveloped viruses and their host, but may provide new strategies to combat non-enveloped virus-induced diseases.
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Affiliation(s)
- Chelsey C Spriggs
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Mara C Harwood
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, United States; Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Billy Tsai
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, United States; Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI, United States.
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32
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Biphasic Functional Interaction between the Adenovirus E4orf4 Protein and DNA-PK. J Virol 2019; 93:JVI.01365-18. [PMID: 30842317 DOI: 10.1128/jvi.01365-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 02/22/2019] [Indexed: 02/06/2023] Open
Abstract
The adenovirus (Ad) E4orf4 protein contributes to virus-induced inhibition of the DNA damage response (DDR) by reducing ATM and ATR signaling. Consequently, E4orf4 inhibits DNA repair and sensitizes transformed cells to killing by DNA-damaging drugs. Inhibition of ATM and ATR signaling contributes to the efficiency of virus replication and may provide one explanation for the cancer selectivity of cell death induced by the expression of E4orf4 alone. In this report, we investigate a direct interaction of E4orf4 with the DDR. We show that E4orf4 physically associates with the DNA-dependent protein kinase (DNA-PK), and we demonstrate a biphasic functional interaction between these proteins, wherein DNA-PK is required for ATM and ATR inhibition by E4orf4 earlier during infection but is inhibited by E4orf4 as infection progresses. This biphasic process is accompanied by initial augmentation and a later inhibition of DNA-PK autophosphorylation as well as by colocalization of DNA-PK with early Ad replication centers and distancing of DNA-PK from late replication centers. Moreover, inhibition of DNA-PK improves Ad replication more effectively when a DNA-PK inhibitor is added later rather than earlier during infection. When expressed alone, E4orf4 is recruited to DNA damage sites in a DNA-PK-dependent manner. DNA-PK inhibition reduces the ability of E4orf4 to induce cancer cell death, likely because E4orf4 is prevented from arriving at the damage sites and from inhibiting the DDR. Our results support an important role for the E4orf4-DNA-PK interaction in Ad replication and in facilitation of E4orf4-induced cancer-selective cell death.IMPORTANCE Several DNA viruses evolved mechanisms to inhibit the cellular DNA damage response (DDR), which acts as an antiviral defense system. We present a novel mechanism by which the adenovirus (Ad) E4orf4 protein inhibits the DDR. E4orf4 interacts with the DNA damage sensor DNA-PK in a biphasic manner. Early during infection, E4orf4 requires DNA-PK activity to inhibit various branches of the DDR, whereas it later inhibits DNA-PK itself. Furthermore, although both E4orf4 and DNA-PK are recruited to virus replication centers (RCs), DNA-PK is later distanced from late-phase RCs. Delayed DNA-PK inhibition greatly contributes to Ad replication efficiency. When E4orf4 is expressed alone, it is recruited to DNA damage sites. Inhibition of DNA-PK prevents both recruitment and the previously reported ability of E4orf4 to kill cancer cells. Our results support an important role for the E4orf4-DNA-PK interaction in Ad replication and in facilitation of E4orf4-induced cancer-selective cell death.
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Santos-Pérez I, Charro D, Gil-Carton D, Azkargorta M, Elortza F, Bamford DH, Oksanen HM, Abrescia NGA. Structural basis for assembly of vertical single β-barrel viruses. Nat Commun 2019; 10:1184. [PMID: 30862777 PMCID: PMC6414509 DOI: 10.1038/s41467-019-08927-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 02/08/2019] [Indexed: 11/10/2022] Open
Abstract
The vertical double β-barrel major capsid protein (MCP) fold, fingerprint of the PRD1-adeno viral lineage, is widespread in many viruses infecting organisms across the three domains of life. The discovery of PRD1-like viruses with two MCPs challenged the known assembly principles. Here, we present the cryo-electron microscopy (cryo-EM) structures of the archaeal, halophilic, internal membrane-containing Haloarcula californiae icosahedral virus 1 (HCIV-1) and Haloarcula hispanica icosahedral virus 2 (HHIV-2) at 3.7 and 3.8 Å resolution, respectively. Our structures reveal proteins located beneath the morphologically distinct two- and three-tower capsomers and homopentameric membrane proteins at the vertices that orchestrate the positioning of pre-formed vertical single β-barrel MCP heterodimers. The cryo-EM based structures together with the proteomics data provide insights into the assembly mechanism of this type of viruses and into those with membrane-less double β-barrel MCPs. Here, the authors present the cryo-EM structures of two archaeal, halophilic, internal membrane-containing icosahedral viruses at 3.7 and 3.8 Å resolution, providing insights into the assembly process of these and related PRD1-adeno lineage viruses.
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Affiliation(s)
- Isaac Santos-Pérez
- Molecular Recognition and Host-pathogen Interactions Programme, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, 48160, Derio, Spain
| | - Diego Charro
- Molecular Recognition and Host-pathogen Interactions Programme, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, 48160, Derio, Spain
| | - David Gil-Carton
- Molecular Recognition and Host-pathogen Interactions Programme, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, 48160, Derio, Spain
| | - Mikel Azkargorta
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Bizkaia Technology Park, 48160, Derio, Spain
| | - Felix Elortza
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Bizkaia Technology Park, 48160, Derio, Spain
| | - Dennis H Bamford
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, Viikki Biocenter, University of Helsinki, P.O. Box 56, Viikinkaari 9, 00014, Helsinki, Finland
| | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, Viikki Biocenter, University of Helsinki, P.O. Box 56, Viikinkaari 9, 00014, Helsinki, Finland
| | - Nicola G A Abrescia
- Molecular Recognition and Host-pathogen Interactions Programme, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, 48160, Derio, Spain. .,IKERBASQUE, Basque Foundation for Science, 48013, Bilbao, Spain.
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Denning D, Bennett S, Mullen T, Moyer C, Vorselen D, Wuite GJL, Nemerow G, Roos WH. Maturation of adenovirus primes the protein nano-shell for successful endosomal escape. NANOSCALE 2019; 11:4015-4024. [PMID: 30768112 DOI: 10.1039/c8nr10182e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The ability of adenoviruses to infect a broad range of species has spurred a growing interest in nanomedicine to use adenovirus as a cargo delivery vehicle. While successful maturation of adenovirus and controlled disassembly are critical for efficient infection, the underlying mechanisms regulating these processes are not well understood. Here, we present Atomic Force Microscopy nanoindentation and fatigue studies of adenovirus capsids at different maturation stages to scrutinize their dynamic uncoating properties. Surprisingly, we find that the early intermediate immature (lacking DNA) capsid is mechanically indistinguishable in both break force and spring constant from the mature (containing DNA) capsid. However, mature and immature capsids do display distinct disassembly pathways, as revealed by our mechanically-induced fatigue analysis. The mature capsid first loses the pentons, followed by either long-term capsid stability or abrupt and complete disassembly. However, the immature capsid has a stable penton region and undergoes a stochastic disassembly mechanism, thought to be due to the absence of genomic pressure. Strikingly, the addition of the genome alone is not sufficient to achieve penton destabilization as indicated by the penton stability of the maturation-intermediate mutant, G33A. Full penton destabilization was achieved only when the genome was present in addition to the successful maturation-linked proteolytic cleavage of preprotein VI. Therefore these findings strongly indicate that maturation of adenovirus in concert with genomic pressure induces penton destabilization and thus, primes the capsid for controlled disassembly. This latter aspect is critical for efficient infection and successful cargo delivery.
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Affiliation(s)
- D Denning
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, The Netherlands and Natuur- en Sterrenkunde and LaserLaB, Vrije Universiteit Amsterdam, The Netherlands.
| | - S Bennett
- Department of Immunology and Microbiology, the Scripps Research Institute, La Jolla, CA 92037, USA.
| | - T Mullen
- Department of Immunology and Microbiology, the Scripps Research Institute, La Jolla, CA 92037, USA.
| | - C Moyer
- Department of Immunology and Microbiology, the Scripps Research Institute, La Jolla, CA 92037, USA.
| | - D Vorselen
- Natuur- en Sterrenkunde and LaserLaB, Vrije Universiteit Amsterdam, The Netherlands.
| | - G J L Wuite
- Natuur- en Sterrenkunde and LaserLaB, Vrije Universiteit Amsterdam, The Netherlands.
| | - G Nemerow
- Department of Immunology and Microbiology, the Scripps Research Institute, La Jolla, CA 92037, USA.
| | - W H Roos
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, The Netherlands
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35
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San Martín C. Virus Maturation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1215:129-158. [DOI: 10.1007/978-3-030-14741-9_7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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36
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Shao C, Liu Z, Yang H, Wang S, Burley SK. Outlier analyses of the Protein Data Bank archive using a probability-density-ranking approach. Sci Data 2018; 5:180293. [PMID: 30532050 PMCID: PMC6289109 DOI: 10.1038/sdata.2018.293] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 11/12/2018] [Indexed: 02/02/2023] Open
Abstract
Outlier analyses are central to scientific data assessments. Conventional outlier identification methods do not work effectively for Protein Data Bank (PDB) data, which are characterized by heavy skewness and the presence of bounds and/or long tails. We have developed a data-driven nonparametric method to identify outliers in PDB data based on kernel probability density estimation. Unlike conventional outlier analyses based on location and scale, Probability Density Ranking can be used for robust assessments of distance from other observations. Analyzing PDB data from the vantage points of probability and frequency enables proper outlier identification, which is important for quality control during deposition-validation-biocuration of new three-dimensional structure data. Ranking of Probability Density also permits use of Most Probable Range as a robust measure of data dispersion that is more compact than Interquartile Range. The Probability-Density-Ranking approach can be employed to analyze outliers and data-spread on any large data set with continuous distribution.
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Affiliation(s)
- Chenghua Shao
- RCSB Protein Data Bank, Rutgers, The State University of New
Jersey, Piscataway,
NJ
08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State
University of New Jersey, Piscataway, NJ
08854, USA
| | - Zonghong Liu
- Department of Statistics and Biostatistics, Rutgers, The State
University of New Jersey, New
Brunswick, NJ,
08903, USA
| | - Huanwang Yang
- RCSB Protein Data Bank, Rutgers, The State University of New
Jersey, Piscataway,
NJ
08854, USA
| | - Sijian Wang
- Institute for Quantitative Biomedicine, Rutgers, The State
University of New Jersey, Piscataway, NJ
08854, USA
- Department of Statistics and Biostatistics, Rutgers, The State
University of New Jersey, New
Brunswick, NJ,
08903, USA
| | - Stephen K. Burley
- RCSB Protein Data Bank, Rutgers, The State University of New
Jersey, Piscataway,
NJ
08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State
University of New Jersey, Piscataway, NJ
08854, USA
- Rutgers Cancer Institute of New Jersey, Rutgers, The State
University of New Jersey, New
Brunswick, NJ,
08903, USA
- RCSB Protein Data Bank, San Diego Supercomputer Center and
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California
San Diego, La Jolla,
CA
92093, USA
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37
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Song G. A time and memory efficient recipe for fast normal mode computations of complexes with icosahedral symmetry. J Mol Graph Model 2018; 87:30-40. [PMID: 30476733 DOI: 10.1016/j.jmgm.2018.10.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 10/22/2018] [Accepted: 10/24/2018] [Indexed: 11/26/2022]
Abstract
With the recent breakthroughs in experimental technologies, structure determination of extremely large assemblies, many with icosahedral symmetry, has been rapidly accelerating. Computational studies of their dynamics are important to deciphering their functions as well as to structural refinement but are challenged by their extremely large size, which ranges from hundreds of thousands to even millions of atoms. Group theory can be used to significantly speed up the normal mode computations of these symmetric complexes, but the derivation is often obscured by the complexity of group theory and consequently is not widely accessible. To address this problem, this work presents an easy recipe for normal mode computations of complexes with icosahedral symmetry. The recipe details how the Hessian matrix in symmetry coordinates can be constructed in a few easy steps of matrix multiplications, without going through the complexity of group theory. All the "ingredient" matrices required in the recipe are fully provided in the Supplemental Information for easy reproduction. The work is timely considering the expected large in-flux of many more icosahedral assemblies in the near future. The recipe uses a minimum amount of memory and solves the normal modes in a significantly reduced amount of time, making it feasible to perform normal mode computations of these assemblies on most computer systems.
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Affiliation(s)
- Guang Song
- Department of Computer Science, Program of Bioinformatics and Computational Biology, Iowa State University, Ames, IA, 50011, USA.
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38
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Porcine Adenovirus Type 3 E3 Encodes a Structural Protein Essential for Capsid Stability and Production of Infectious Progeny Virions. J Virol 2018; 92:JVI.00680-18. [PMID: 30068639 DOI: 10.1128/jvi.00680-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 07/16/2018] [Indexed: 11/20/2022] Open
Abstract
The adenovirus E3 region encodes proteins that are not essential for viral replication in vitro The porcine adenovirus type 3 (PAdV-3) E3 region encodes three proteins, including 13.7K. Here, we report that 13.7K is expressed as an early protein, which localizes to the nucleus of infected cells. The 13.7K protein is a structural protein, as it is incorporated in CsCl-purified virions. The 13.7K protein appears to be essential for PAdV-3 replication, as mutant PAV13.73A expressing a mutated 13.7K could be isolated only in VIDO AS2 cells expressing the 13.7K protein. Analysis of PAV13.73A suggested that even in the presence of reduced levels of some late viral proteins, there appeared to be no effect on virus assembly and production of mature virions. Further analysis of CsCl-purified PAV13.73A by transmission electron microscopy revealed the presence of disrupted/broken capsids, suggesting that inactivation of 13.7K protein expression may produce fragile capsids. Our results suggest that the PAdV-3 E3 region-encoded 13.7K protein is a capsid protein, which appears to be essential for the formation of stable capsids and production of infectious progeny virions.IMPORTANCE Although E3 region-encoded proteins are involved in the modulation of leukocyte functions (N. Arnberg, Proc Natl Acad Sci U S A 110:19976-19977, 2013) and inducing a lytic infection of lymphocytes (V. K. Murali, D. A. Ornelles, L. R. Gooding, H. T. Wilms, W. Huang, A. E. Tollefson, W. S. Wold, and C. Garnett-Benson, J Virol 88:903-912, 2014), none of the E3 proteins appear to be a component of virion capsid or required for replication of adenovirus. Here, we demonstrate that the 13.7K protein encoded by the E3 region of porcine adenovirus type 3 is a component of progeny virion capsids and appears to be essential for maintaining the integrity of virion capsid and production of infectious progeny virions. To our knowledge, this is the first report to suggest that an adenovirus E3-encoded protein is an essential structural protein.
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Revised Crystal Structure of Human Adenovirus Reveals the Limits on Protein IX Quasi-Equivalence and on Analyzing Large Macromolecular Complexes. J Mol Biol 2018; 430:4132-4141. [PMID: 30121295 DOI: 10.1016/j.jmb.2018.08.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 07/19/2018] [Accepted: 08/04/2018] [Indexed: 11/23/2022]
Abstract
We report the revised crystal structure of a pseudo-typed human adenovirus at 3.8-Å resolution that is consistent with the atomic models of minor proteins determined by cryo-electron microscopy. The diffraction data from multiple crystals were rescaled and merged to increase the data completeness. The densities for the minor proteins were initially identified in the phase-refined omit maps that were further improved by the phases from docked poly-alanine models to build atomic structures. While the trimeric fiber molecules are disordered due to flexibility and imposition of 5-fold symmetry, the remaining major capsid proteins hexon and penton base are clearly ordered, with the exception of hypervariable region 1 of hexons, the RGD containing loop, and the N-termini of the penton base. The exterior minor protein IX together with the interior minor proteins IIIa and VIII stabilizes the adenovirus virion. A segment of N-terminal pro-peptide of VI is found in the interior cavities of peripentonal hexons, and the rest of VI is disordered. While the triskelion substructures formed by the N-termini of IX conform to excellent quasi 3-fold symmetry, the tetrameric coiled-coils formed by the C-termini and organized in parallel and anti-parallel arrangement do not exhibit any quasi-symmetry. This observation also conveys the pitfalls of using the quasi-equivalence as validation criteria for the structural analysis of extended (non-modular) capsid proteins such as IX. Together, these results remedy certain discrepancies in the previous X-ray model in agreement with the cryo-electron microscopy models.
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Progress in Adenoviral Capsid-Display Vaccines. Biomedicines 2018; 6:biomedicines6030081. [PMID: 30049954 PMCID: PMC6165093 DOI: 10.3390/biomedicines6030081] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 07/20/2018] [Accepted: 07/23/2018] [Indexed: 12/31/2022] Open
Abstract
Adenoviral vectored vaccines against infectious diseases are currently in clinical trials due to their capacity to induce potent antigen-specific B- and T-cell immune responses. Heterologous prime-boost vaccination with adenoviral vector and, for example, adjuvanted protein-based vaccines can further enhance antigen-specific immune responses. Although leading to potent immune responses, these heterologous prime-boost regimens may be complex and impact manufacturing costs limiting efficient implementation. Typically, adenoviral vectors are engineered to genetically encode a transgene in the E1 region and utilize the host cell machinery to express the encoded antigen and thereby induce immune responses. Similarly, adenoviral vectors can be engineered to display foreign immunogenic peptides on the capsid-surface by insertion of antigens in capsid proteins hexon, fiber and protein IX. The ability to use adenoviral vectors as antigen-display particles, with or without using the genetic vaccine function, greatly increases the versatility of the adenoviral vector for vaccine development. This review describes the application of adenoviral capsid antigen-display vaccine vectors by focusing on their distinct advantages and possible limitations in vaccine development.
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Capsid protein structure, self-assembly, and processing reveal morphogenesis of the marine virophage mavirus. Proc Natl Acad Sci U S A 2018; 115:7332-7337. [PMID: 29941605 PMCID: PMC6048507 DOI: 10.1073/pnas.1805376115] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Virophages have the unique property of parasitizing giant viruses within unicellular hosts. Little is understood about how they form infectious virions in this tripartite interplay. We provide mechanistic insights into assembly and maturation of mavirus, a marine virophage, by combining structural and stability studies on capsomers, virus-like particles (VLPs), and native virions. We found that the mavirus protease processes the double jelly-roll (DJR) major capsid protein (MCP) at multiple C-terminal sites and that these sites are conserved among virophages. Mavirus MCP assembled in Escherichia coli in the absence and presence of penton protein, forming VLPs with defined size and shape. While quantifying VLPs in E. coli lysates, we found that full-length rather than processed MCP is the competent state for capsid assembly. Full-length MCP was thermally more labile than truncated MCP, and crystal structures of both states indicate that full-length MCP has an expanded DJR core. Thus, we propose that the MCP C-terminal domain serves as a scaffolding domain by adding strain on MCP to confer assembly competence. Mavirus protease processed MCP more efficiently after capsid assembly, which provides a regulation mechanism for timing capsid maturation. By analogy to Sputnik and adenovirus, we propose that MCP processing renders mavirus particles infection competent by loosening interactions between genome and capsid shell and destabilizing pentons for genome release into host cells. The high structural similarity of mavirus and Sputnik capsid proteins together with conservation of protease and MCP processing suggest that assembly and maturation mechanisms described here are universal for virophages.
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Abstract
AbstractPrions are proteins that can self-propagate, leading to the misfolding of proteins. In addition to the previously demonstrated pathogenic roles of prions during the development of different mammalian diseases, including neurodegenerative diseases, they have recently been shown to represent an important functional component in many prokaryotic and eukaryotic organisms and bacteriophages, confirming the previously unexplored important regulatory and functional roles. However, an in-depth analysis of these domains in eukaryotic viruses has not been performed. Here, we examined the presence of prion-like proteins in eukaryotic viruses that play a primary role in different ecosystems and that are associated with emerging diseases in humans. We identified relevant functional associations in different viral processes and regularities in their presence at different taxonomic levels. Using the prion-like amino-acid composition computational algorithm, we detected 2679 unique putative prion-like domains within 2,742,160 publicly available viral protein sequences. Our findings indicate that viral prion-like proteins can be found in different viruses of insects, plants, mammals, and humans. The analysis performed here demonstrated common patterns in the distribution of prion-like domains across viral orders and families, and revealed probable functional associations with different steps of viral replication and interaction with host cells. These data allow the identification of the viral prion-like proteins as potential novel regulators of viral infections.
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Abstract
Prions are proteins that can self-propagate, leading to the misfolding of proteins. In addition to the previously demonstrated pathogenic roles of prions during the development of different mammalian diseases, including neurodegenerative diseases, they have recently been shown to represent an important functional component in many prokaryotic and eukaryotic organisms and bacteriophages, confirming the previously unexplored important regulatory and functional roles. However, an in-depth analysis of these domains in eukaryotic viruses has not been performed. Here, we examined the presence of prion-like proteins in eukaryotic viruses that play a primary role in different ecosystems and that are associated with emerging diseases in humans. We identified relevant functional associations in different viral processes and regularities in their presence at different taxonomic levels. Using the prion-like amino-acid composition computational algorithm, we detected 2679 unique putative prion-like domains within 2,742,160 publicly available viral protein sequences. Our findings indicate that viral prion-like proteins can be found in different viruses of insects, plants, mammals, and humans. The analysis performed here demonstrated common patterns in the distribution of prion-like domains across viral orders and families, and revealed probable functional associations with different steps of viral replication and interaction with host cells. These data allow the identification of the viral prion-like proteins as potential novel regulators of viral infections.
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Affiliation(s)
- George Tetz
- Human Microbiology Institute, New York, NY, 10027, USA.
| | - Victor Tetz
- Human Microbiology Institute, New York, NY, 10027, USA
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Lasswitz L, Chandra N, Arnberg N, Gerold G. Glycomics and Proteomics Approaches to Investigate Early Adenovirus-Host Cell Interactions. J Mol Biol 2018; 430:1863-1882. [PMID: 29746851 PMCID: PMC7094377 DOI: 10.1016/j.jmb.2018.04.039] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 04/24/2018] [Accepted: 04/30/2018] [Indexed: 12/14/2022]
Abstract
Adenoviruses as most viruses rely on glycan and protein interactions to attach to and enter susceptible host cells. The Adenoviridae family comprises more than 80 human types and they differ in their attachment factor and receptor usage, which likely contributes to the diverse tropism of the different types. In the past years, methods to systematically identify glycan and protein interactions have advanced. In particular sensitivity, speed and coverage of mass spectrometric analyses allow for high-throughput identification of glycans and peptides separated by liquid chromatography. Also, developments in glycan microarray technologies have led to targeted, high-throughput screening and identification of glycan-based receptors. The mapping of cell surface interactions of the diverse adenovirus types has implications for cell, tissue, and species tropism as well as drug development. Here we review known adenovirus interactions with glycan- and protein-based receptors, as well as glycomics and proteomics strategies to identify yet elusive virus receptors and attachment factors. We finally discuss challenges, bottlenecks, and future research directions in the field of non-enveloped virus entry into host cells. Adenovirus entry into cells is guided by specific glycan and protein interactions. Glycan arrays and shotgun glycomics methods are valuable technologies to identify virus–glycan interactions. Shotgun proteomics and ligand-based receptor capture are powerful methods for proteinaceous receptor discovery. A combination of shotgun glycomics and proteomics with CRISPR/Cas9 and RNAi validation holds the promise of generating a systems biology view of virus entry processes.
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Affiliation(s)
- Lisa Lasswitz
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Medical School Hannover and the Helmholtz Centre for Infection Research, 30625 Hannover, Germany
| | - Naresh Chandra
- Department of Clinical Microbiology, Virology, Umeå University, SE-90185 Umeå, Sweden; Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-90185 Umea, Sweden
| | - Niklas Arnberg
- Department of Clinical Microbiology, Virology, Umeå University, SE-90185 Umeå, Sweden; Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-90185 Umea, Sweden.
| | - Gisa Gerold
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Medical School Hannover and the Helmholtz Centre for Infection Research, 30625 Hannover, Germany; Department of Clinical Microbiology, Virology, Umeå University, SE-90185 Umeå, Sweden; Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, SE-90185 Umea, Sweden.
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Azinas S, Bano F, Torca I, Bamford DH, Schwartz GA, Esnaola J, Oksanen HM, Richter RP, Abrescia NG. Membrane-containing virus particles exhibit the mechanics of a composite material for genome protection. NANOSCALE 2018; 10:7769-7779. [PMID: 29658555 PMCID: PMC5944389 DOI: 10.1039/c8nr00196k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 03/02/2018] [Indexed: 06/08/2023]
Abstract
The protection of the viral genome during extracellular transport is an absolute requirement for virus survival and replication. In addition to the almost universal proteinaceous capsids, certain viruses add a membrane layer that encloses their double-stranded (ds) DNA genome within the protein shell. Using the membrane-containing enterobacterial virus PRD1 as a prototype, and a combination of nanoindentation assays by atomic force microscopy and finite element modelling, we show that PRD1 provides a greater stability against mechanical stress than that achieved by the majority of dsDNA icosahedral viruses that lack a membrane. We propose that the combination of a stiff and brittle proteinaceous shell coupled with a soft and compliant membrane vesicle yields a tough composite nanomaterial well-suited to protect the viral DNA during extracellular transport.
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Affiliation(s)
- S. Azinas
- Molecular recognition and host–pathogen interactions programme , CIC bioGUNE , CIBERehd , Derio , Spain
- Biosurfaces Lab , CIC biomaGUNE , San Sebastian , Spain
| | - F. Bano
- Biosurfaces Lab , CIC biomaGUNE , San Sebastian , Spain
| | - I. Torca
- Mechanical and Industrial Production Department , Mondragon University , Arrasate-Mondragón , Spain
| | - D. H. Bamford
- Molecular and Integrative Biosciences Research Programme , Faculty of Biological and Environmental Sciences , Viikki Biocenter , University of Helsinki , Finland
| | - G. A. Schwartz
- Centro de Física de Materiales , (CSIC-UPV/EHU) & Donostia International Physics Center , San Sebastian , Spain
| | - J. Esnaola
- Mechanical and Industrial Production Department , Mondragon University , Arrasate-Mondragón , Spain
| | - H. M. Oksanen
- Molecular and Integrative Biosciences Research Programme , Faculty of Biological and Environmental Sciences , Viikki Biocenter , University of Helsinki , Finland
| | - R. P. Richter
- Biosurfaces Lab , CIC biomaGUNE , San Sebastian , Spain
- School of Biomedical Sciences , Faculty of Biological Sciences , School of Physics and Astronomy , Faculty of Mathematics and Physical Sciences , and Astbury Centre for Structural Molecular Biology University of Leeds , Leeds , UK . ; Tel: +44 113 3431969
| | - N. G. Abrescia
- Molecular recognition and host–pathogen interactions programme , CIC bioGUNE , CIBERehd , Derio , Spain
- IKERBASQUE , Basque Foundation for Science , Bilbao , Spain . ; Fax: +34 946572502 ; Tel: +34 946572523
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Gaba A, Ayalew LE, Patel A, Kumar P, Tikoo SK. Bovine adenovirus‐3 protein VIII associates with eukaryotic initiation factor‐6 during infection. Cell Microbiol 2018. [DOI: 10.1111/cmi.12842] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Amit Gaba
- VIDO‐InterVacUniversity of Saskatchewan Saskatoon Saskatchewan Canada
- Veterinary MicrobiologyUniversity of Saskatchewan Saskatoon Saskatchewan Canada
| | - Lisanework E. Ayalew
- VIDO‐InterVacUniversity of Saskatchewan Saskatoon Saskatchewan Canada
- Veterinary MicrobiologyUniversity of Saskatchewan Saskatoon Saskatchewan Canada
| | - Amrutlal Patel
- VIDO‐InterVacUniversity of Saskatchewan Saskatoon Saskatchewan Canada
- Veterinary MicrobiologyUniversity of Saskatchewan Saskatoon Saskatchewan Canada
| | - Pankaj Kumar
- VIDO‐InterVacUniversity of Saskatchewan Saskatoon Saskatchewan Canada
| | - Suresh K. Tikoo
- VIDO‐InterVacUniversity of Saskatchewan Saskatoon Saskatchewan Canada
- Veterinary MicrobiologyUniversity of Saskatchewan Saskatoon Saskatchewan Canada
- Vaccinology & Immunotherapeutics Program, School of Public HealthUniversity of Saskatchewan Saskatoon Saskatchewan Canada
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Abstract
Increasingly more and larger structural complexes are being determined
experimentally. The sizes of these systems pose a formidable computational challenge
to the study of their vibrational dynamics by normal mode analysis. To overcome this challenge, this work presents a novel resonance-inspired approach. Tests on large shell structures
of protein capsids demonstrate there is a strong
resonance between the vibrations of a whole capsid and those of individual capsomeres.
We then show how this resonance can be taken advantage of to significantly speed up normal
mode computations.
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Affiliation(s)
- Hyuntae Na
- Computer Science, Penn State Harrisburg, Middletown, Pennsylvania, UNITED STATES
| | - Guang Song
- Computer Science, Iowa State University, 226 Atanasoff Hall, AMES, Iowa, 50010-4844, UNITED STATES
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A single point mutation in precursor protein VI doubles the mechanical strength of human adenovirus. J Biol Phys 2017; 44:119-132. [PMID: 29243050 PMCID: PMC5928017 DOI: 10.1007/s10867-017-9479-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 11/10/2017] [Indexed: 12/23/2022] Open
Abstract
Viruses are extensively studied as vectors for vaccine applications and gene therapies. For these applications, understanding the material properties of viruses is crucial for creating optimal functionality. Using atomic force microscopy (AFM) nanoindentation, we studied the mechanical properties of human adenovirus type 5 with the fiber of type 35 (Ad5F35) and compared it to viral capsids with a single point mutation in the protein VI precursor protein (pVI-S28C). Surprisingly, the pVI-S28C mutant turned out to be twice as stiff as the Ad5F35 capsids. We suggest that this major increase in strength is the result of the DNA crosslinking activity of precursor protein VII, as this protein was detected in the pVI-S28C mutant capsids. The infectivity was similar for both capsids, indicating that mutation did not affect the ability of protein VI to lyse the endosomal membrane. This study highlights that it is possible to increase the mechanical stability of a capsid even with a single point mutation while not affecting the viral life cycle. Such insight can help enable the development of more stable vectors for therapeutic applications.
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Atomic Structures of Minor Proteins VI and VII in Human Adenovirus. J Virol 2017; 91:JVI.00850-17. [PMID: 28978703 DOI: 10.1128/jvi.00850-17] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 09/15/2017] [Indexed: 12/31/2022] Open
Abstract
Human adenoviruses (Ad) are double-stranded DNA (dsDNA) viruses associated with infectious diseases, but they are better known as tools for gene delivery and oncolytic anticancer therapy. Atomic structures of Ad provide the basis for the development of antivirals and for engineering efforts toward more effective applications. Since 2010, atomic models of human Ad5 have been derived independently from photographic film cryo-electron microscopy (cryo-EM) and X-ray crystallography studies, but discrepancies exist concerning the assignment of cement proteins IIIa, VIII, and IX. To clarify these discrepancies, we employed the technology of direct electron counting to obtain a cryo-EM structure of human Ad5 at 3.2-Å resolution. Our improved structure unambiguously confirms our previous cryo-EM models of proteins IIIa, VIII, and IX and explains the likely cause of conflict in the crystallography models. The improved structure also allows the identification of three new components in the cavity of hexon-the cleaved N terminus of precursor protein VI (pVIn), the cleaved N terminus of precursor protein VII (pVIIn2), and mature protein VI. The binding of pVIIn2-and, by extension, that of genome-condensing pVII-to hexons is consistent with the previously proposed dsDNA genome-capsid coassembly for adenoviruses, which resembles that of single-stranded RNA (ssRNA) viruses but differs from the well-established mechanism of pumping dsDNA into a preformed protein capsid exemplified by tailed bacteriophages and herpesviruses.IMPORTANCE Adenovirus is a double-edged sword to humans: it is a widespread pathogen but can be used as a bioengineering tool for anticancer and gene therapies. The atomic structure of the virus provides the basis for antiviral and application developments, but conflicting atomic models for the important cement proteins IIIa, VIII, and IX from conventional/film cryo-EM and X-ray crystallography studies have caused confusion. Using cutting-edge cryo-EM technology with electron counting, we improved the structure of human adenovirus type 5 and confirmed our previous models of cement proteins IIIa, VIII, and IX, thus clarifying the inconsistent structures. The improved structure also reveals atomic details of membrane-lytic protein VI and genome-condensing protein VII and supports the previously proposed genome-capsid coassembly mechanism for adenoviruses.
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Isolation and Characterization of Metallosphaera Turreted Icosahedral Virus, a Founding Member of a New Family of Archaeal Viruses. J Virol 2017; 91:JVI.00925-17. [PMID: 28768871 DOI: 10.1128/jvi.00925-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 07/25/2017] [Indexed: 11/20/2022] Open
Abstract
Our understanding of archaeal virus diversity and structure is just beginning to emerge. Here we describe a new archaeal virus, tentatively named Metallosphaera turreted icosahedral virus (MTIV), that was isolated from an acidic hot spring in Yellowstone National Park, USA. Two strains of the virus were identified and were found to replicate in an archaeal host species closely related to Metallosphaera yellowstonensis Each strain encodes a 9.8- to 9.9-kb linear double-stranded DNA (dsDNA) genome with large inverted terminal repeats. Each genome encodes 21 open reading frames (ORFs). The ORFs display high homology between the strains, but they are quite distinct from other known viral genes. The 70-nm-diameter virion is built on a T=28 icosahedral lattice. Both single particle cryo-electron microscopy and cryotomography reconstructions reveal an unusual structure that has 42 turret-like projections: 12 pentameric turrets positioned on the icosahedral 5-fold axes and 30 turrets with apparent hexameric symmetry positioned on the icosahedral 2-fold axes. Both the virion structural properties and the genome content support MTIV as the founding member of a new family of archaeal viruses.IMPORTANCE Many archaeal viruses are quite different from viruses infecting bacteria and eukaryotes. Initial characterization of MTIV reveals a virus distinct from other known bacterial, eukaryotic, and archaeal viruses; this finding suggests that viruses infecting Archaea are still an understudied group. As the first known virus infecting a Metallosphaera sp., MTIV provides a new system for exploring archaeal virology by examining host-virus interactions and the unique features of MTIV structure-function relationships. These studies will likely expand our understanding of virus ecology and evolution.
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