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Jennings MR, Parks RJ. Human Adenovirus Gene Expression and Replication Is Regulated through Dynamic Changes in Nucleoprotein Structure throughout Infection. Viruses 2023; 15:161. [PMID: 36680201 PMCID: PMC9863843 DOI: 10.3390/v15010161] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 12/31/2022] [Accepted: 01/03/2023] [Indexed: 01/07/2023] Open
Abstract
Human adenovirus (HAdV) is extremely common and can rapidly spread in confined populations such as daycare centers, hospitals, and retirement homes. Although HAdV usually causes only minor illness in otherwise healthy patients, HAdV can cause significant morbidity and mortality in certain populations, such as the very young, very old, or immunocompromised individuals. During infection, the viral DNA undergoes dramatic changes in nucleoprotein structure that promote the rapid expression of viral genes, replication of the DNA, and generation of thousands of new infectious virions-each process requiring a distinct complement of virus and host-encoded proteins. In this review, we summarize our current understanding of the nucleoprotein structure of HAdV DNA during the various phases of infection, the cellular proteins implicated in mediating these changes, and the role of epigenetics in HAdV gene expression and replication.
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Affiliation(s)
- Morgan R. Jennings
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Robin J. Parks
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Centre for Neuromuscular Disease, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Medicine, The Ottawa Hospital, Ottawa, ON K1H 8L6, Canada
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Price AM, Steinbock RT, Lauman R, Charman M, Hayer KE, Kumar N, Halko E, Lum KK, Wei M, Wilson AC, Garcia BA, Depledge DP, Weitzman MD. Novel viral splicing events and open reading frames revealed by long-read direct RNA sequencing of adenovirus transcripts. PLoS Pathog 2022; 18:e1010797. [PMID: 36095031 PMCID: PMC9499273 DOI: 10.1371/journal.ppat.1010797] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 09/22/2022] [Accepted: 08/05/2022] [Indexed: 01/07/2023] Open
Abstract
Adenovirus is a common human pathogen that relies on host cell processes for transcription and processing of viral RNA and protein production. Although adenoviral promoters, splice junctions, and polyadenylation sites have been characterized using low-throughput biochemical techniques or short read cDNA-based sequencing, these technologies do not fully capture the complexity of the adenoviral transcriptome. By combining Illumina short-read and nanopore long-read direct RNA sequencing approaches, we mapped transcription start sites and RNA cleavage and polyadenylation sites across the adenovirus genome. In addition to confirming the known canonical viral early and late RNA cassettes, our analysis of splice junctions within long RNA reads revealed an additional 35 novel viral transcripts that meet stringent criteria for expression. These RNAs include fourteen new splice junctions which lead to expression of canonical open reading frames (ORFs), six novel ORF-containing transcripts, and 15 transcripts encoding for messages that could alter protein functions through truncation or fusion of canonical ORFs. In addition, we detect RNAs that bypass canonical cleavage sites and generate potential chimeric proteins by linking distinct gene transcription units. Among these chimeric proteins we detected an evolutionarily conserved protein containing the N-terminus of E4orf6 fused to the downstream DBP/E2A ORF. Loss of this novel protein, E4orf6/DBP, was associated with aberrant viral replication center morphology and poor viral spread. Our work highlights how long-read sequencing technologies combined with mass spectrometry can reveal further complexity within viral transcriptomes and resulting proteomes.
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Affiliation(s)
- Alexander M. Price
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Robert T. Steinbock
- Cell & Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Richard Lauman
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Matthew Charman
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Katharina E. Hayer
- Department of Biomedical and Health Informatics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Namrata Kumar
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Edwin Halko
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Krystal K. Lum
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Monica Wei
- Cell & Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Angus C. Wilson
- Department of Microbiology, New York University School of Medicine, New York city, New York, United States of America
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Daniel P. Depledge
- Department of Microbiology, New York University School of Medicine, New York city, New York, United States of America
- Institute of Virology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Hannover, Germany
| | - Matthew D. Weitzman
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
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Saha B, Parks RJ. Recent Advances in Novel Antiviral Therapies against Human Adenovirus. Microorganisms 2020; 8:E1284. [PMID: 32842697 PMCID: PMC7563841 DOI: 10.3390/microorganisms8091284] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/15/2020] [Accepted: 08/19/2020] [Indexed: 12/27/2022] Open
Abstract
Human adenovirus (HAdV) is a very common pathogen that typically causes minor disease in most patients. However, the virus can cause significant morbidity and mortality in certain populations, including young children, the elderly, and those with compromised immune systems. Currently, there are no approved therapeutics to treat HAdV infections, and the standard treatment relies on drugs approved to combat other viral infections. Such treatments often show inconsistent efficacy, and therefore, more effective antiviral therapies are necessary. In this review, we discuss recent developments in the search for new chemical and biological anti-HAdV therapeutics, including drugs that are currently undergoing preclinical/clinical testing, and small molecule screens for the identification of novel compounds that abrogate HAdV replication and disease.
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Affiliation(s)
- Bratati Saha
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada;
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Robin J. Parks
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada;
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Centre for Neuromuscular Disease, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Department of Medicine, The Ottawa Hospital, Ottawa, ON K1H 8L6, Canada
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Human adenovirus type 5 vectors deleted of early region 1 (E1) undergo limited expression of early replicative E2 proteins and DNA replication in non-permissive cells. PLoS One 2017; 12:e0181012. [PMID: 28700677 PMCID: PMC5507307 DOI: 10.1371/journal.pone.0181012] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/23/2017] [Indexed: 11/23/2022] Open
Abstract
Adenovirus (Ad) vectors deleted of the early region 1 (E1) are widely used for transgene delivery in preclinical and clinical gene therapy studies. Although proteins encoded within the E1 region are required for efficient virus replication, previous studies have suggested that certain viral or cellular proteins can functionally compensate for E1, leading to expression of the early region 2 (E2)-encoded replicative proteins and subsequent virus replication. We have generated a series of E1-encoding and E1-deficient Ad vectors containing a FLAG-epitope tag on each of the E2-encoded proteins: DNA-binding protein (DBP), terminal protein (TP) and DNA polymerase (Pol). Using these constructs, we show that for the replication-competent virus, the expression level of each E2-encoded protein declines with increasing distance from the E2 promoter, with E2A-encoded DBP expression being ~800-fold higher than E2B-encoded TP. Pol was expressed at extremely low levels in infected cells, and immunoprecipitation from cell lysates was required prior to its detection by immunoblot. We further show that DBP was expressed 200- to 400-fold less efficiently from an E1-deficient virus compared to a replication-competent virus in A549 and HepG2 cells, which was accompanied by a very small increase in genome copy number. For the E1-deficient virus, late gene expression (a marker of virus replication) was only observed at very high multiplicities of infection. These data show that E1-deleted Ad gives rise to limited expression of the E2-encoded genes and replication in infected cells, but highlight the importance of considering viral dose-dependent effects in gene therapy studies.
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El-Mogy MA, Abdalla MA, Misic V, Haj-Ahmad Y. Effect of adenovirus infection on transgene expression under the adenoviral MLP/TPL and the CMVie promoter/enhancer in CHO cells. J Genet Eng Biotechnol 2017; 15:211-217. [PMID: 30647657 PMCID: PMC6296590 DOI: 10.1016/j.jgeb.2017.04.003] [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: 02/26/2015] [Revised: 02/27/2017] [Accepted: 04/05/2017] [Indexed: 11/19/2022]
Abstract
The adenovirus major late promoter (MLP) and its translational regulator - the tripartite leader (TPL) sequence - can actively drive efficient gene expression during adenoviral infection. However, both elements have not been widely tested in transgene expression outside of the adenovirus genome context. In this study, we tested whether the combination of MLP and TPL would enhance transgene expression beyond that of the most widely used promoter in transgene expression in mammalian cells, the cytomegalovirus immediate early (CMVie) promoter/enhancer. The activity of these two regulatory elements was compared in Chinese hamster ovary (CHO) cells. Although transient expression was significantly higher under the control of the CMVie promoter/enhance compared to the MLP/TPL, this difference was greater at the level of transcription (30 folds) than translation (11 folds). Even with adenovirus infection to provide additional elements (in trans), CMVie promoter/enhancer exhibited significantly higher activity relative to MLP/TPL. Interestingly, the CMVie promoter/enhancer was 1.9 folds more active in adenovirus-infected cells than in non-infected cells. Our study shows that the MLP-TPL drives lower transgene expression than the CMVie promoter/enhancer particularly at the transcription level. The data also highlight the utility of the TPL sequence at the translation level and/or possible overwhelming of the cellular translational machinery by the high transcription activity of the CMVie promoter/enhancer. In addition, here we present data that show stimulation of the CMVie promoter/enhancer by adenovirus infection, which may prove interesting in future work to test the combination of CMVie/TPL sequence, and additional adenovirus elements, for transgene expression.
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Key Words
- Adenovirus
- CHO, Chinese hamster ovary
- CMVie promoter/enhancer
- CMVie, cytomegalovirus immediate early
- GFP, green fluorescence proteins
- IRES, internal ribosome entry site
- MLP
- MLP, major late promoter
- MOI, multiplicity of infection
- PFU, plaque forming unit
- RFU, relative fluorescence units
- TPL
- TPL, tripartite leader
- Transgene expression
- qPCR, Quantitative PCR
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Affiliation(s)
- Mohamed A. El-Mogy
- Molecular Biology Department, National Research Centre, Dokki, Giza, Egypt
- Department of Biological Sciences, Brock University, St. Catharines, ON, Canada
- Corresponding author at: Molecular Biology Department, National Research Centre, Dokki, Giza, Egypt.
| | - Moemen A.K. Abdalla
- Department of Biochemistry, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Vanja Misic
- Department of Biological Sciences, Brock University, St. Catharines, ON, Canada
| | - Yousef Haj-Ahmad
- Department of Biological Sciences, Brock University, St. Catharines, ON, Canada
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Comparison of the Life Cycles of Genetically Distant Species C and Species D Human Adenoviruses Ad6 and Ad26 in Human Cells. J Virol 2015; 89:12401-17. [PMID: 26423951 DOI: 10.1128/jvi.01534-15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 09/25/2015] [Indexed: 01/01/2023] Open
Abstract
UNLABELLED Our understanding of adenovirus (Ad) biology is largely extrapolated from human species C Ad5. Most humans are immune to Ad5, so lower-seroprevalence viruses like human Ad6 and Ad26 are being tested as therapeutic vectors. Ad6 and Ad26 differ at the DNA level by 34%. To better understand how this might impact their biology, we examined the life cycle of the two viruses in human lung cells in vitro. Both viruses infected A549 cells with similar efficiencies, executed DNA replication with identical kinetics within 12 h, and began killing cells within 72 h. While Ad6-infected cells remained adherent until death, Ad26-infected cells detached within 12 h of infection but remained viable. Next-generation sequencing (NGS) of mRNA from infected cells demonstrated that viral transcripts constituted 1% of cellular mRNAs within 6 h and 8 to 16% within 12 h. Quantitative PCR and NGS revealed the activation of key early genes at 6 h and transition to late gene activation by 12 h by both viruses. There were marked differences in the balance of E1A and E1B activation by the two viruses and in the expression of E3 immune evasion mRNAs. Ad6 was markedly more effective at suppressing major histocompatibility complex class I (MHC I) display on the cell surface and in evading TRAIL-mediated apoptosis than was Ad26. These data demonstrate shared as well as divergent life cycles in these genetically distant human adenoviruses. An understanding of these differences expands the knowledge of alternative Ad species and may inform the selection of related Ads for therapeutic development. IMPORTANCE A burgeoning number of adenoviruses (Ads) are being harnessed as therapeutics, yet the biology of these viruses is generally extrapolated from Ad2 and Ad5. Here, we are the first to compare the transcriptional programs of two genetically distant Ads by mRNA next-generation sequencing (NGS). Species C Ad6 and Ad26 are being pursued as lower-seroprevalence Ad vectors but differ at the DNA level by 34%. Head-to-head comparison in human lung cells by NGS revealed that the two viruses generally conform to our general understanding of the Ad transcriptional program. However, fine mapping revealed subtle and strong differences in how these two viruses execute these programs, including differences in the balance of E1A and E1B mRNAs and in E3 immune evasion genes. This suggests that not all adenoviruses behave like Ad2 and Ad5 and that they may have unique strategies to infect cells and evade the immune system.
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The adenovirus genome contributes to the structural stability of the virion. Viruses 2014; 6:3563-83. [PMID: 25254384 PMCID: PMC4189039 DOI: 10.3390/v6093563] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/15/2014] [Accepted: 09/17/2014] [Indexed: 11/17/2022] Open
Abstract
Adenovirus (Ad) vectors are currently the most commonly used platform for therapeutic gene delivery in human gene therapy clinical trials. Although these vectors are effective, many researchers seek to further improve the safety and efficacy of Ad-based vectors through detailed characterization of basic Ad biology relevant to its function as a vector system. Most Ad vectors are deleted of key, or all, viral protein coding sequences, which functions to not only prevent virus replication but also increase the cloning capacity of the vector for foreign DNA. However, radical modifications to the genome size significantly decreases virion stability, suggesting that the virus genome plays a role in maintaining the physical stability of the Ad virion. Indeed, a similar relationship between genome size and virion stability has been noted for many viruses. This review discusses the impact of the genome size on Ad virion stability and emphasizes the need to consider this aspect of virus biology in Ad-based vector design.
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Henriques AM, Fevereiro M, Fagulha T, Ramos F, Barros SC, Luís T, Duarte M. U exon variability as a discriminatory tool for Bayesian analysis of adenoviruses. INFECTION GENETICS AND EVOLUTION 2014; 25:117-21. [PMID: 24788000 DOI: 10.1016/j.meegid.2014.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 04/15/2014] [Accepted: 04/18/2014] [Indexed: 10/25/2022]
Abstract
Members of the family Adenoviridae are divided into five genera and infect a wide variety of vertebrates with a narrow host range, usually restricted to one species. Due to the high genetic diversity and distinct genomic organization, classification of adenoviruses is difficult to achieve and often performed by phylogenetic analysis. The most commonly used region for phylogenetic inference of adenoviruses is the DNA polymerase (AdPol) gene carried out at amino acid level. In this paper we investigated the suitability of the U exon to discriminate adenoviruses. The tree based on this genus-common feature, obtained with 23 short amino acid sequences, offered a clearest discrimination of the members of the adenovirus family (Adenoviridae) than the trees generated with the complete or partial polymerase protein sequences. Therefore, our results demonstrate that the U exon is an effective tool for a refined phylogenetic inference and genus classification of the Adenoviridae family.
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Affiliation(s)
- Ana M Henriques
- Instituto Nacional de Investigação Agrária e Veterinária, Laboratório de Virologia, Lisboa, Portugal
| | - Miguel Fevereiro
- Instituto Nacional de Investigação Agrária e Veterinária, Laboratório de Virologia, Lisboa, Portugal
| | - Teresa Fagulha
- Instituto Nacional de Investigação Agrária e Veterinária, Laboratório de Virologia, Lisboa, Portugal
| | - Fernanda Ramos
- Instituto Nacional de Investigação Agrária e Veterinária, Laboratório de Virologia, Lisboa, Portugal
| | - Sílvia C Barros
- Instituto Nacional de Investigação Agrária e Veterinária, Laboratório de Virologia, Lisboa, Portugal
| | - Tiago Luís
- Instituto Nacional de Investigação Agrária e Veterinária, Laboratório de Virologia, Lisboa, Portugal
| | - Margarida Duarte
- Instituto Nacional de Investigação Agrária e Veterinária, Laboratório de Virologia, Lisboa, Portugal.
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Zhao H, Chen M, Pettersson U. A new look at adenovirus splicing. Virology 2014; 456-457:329-41. [DOI: 10.1016/j.virol.2014.04.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 01/23/2014] [Accepted: 04/03/2014] [Indexed: 10/25/2022]
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