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Castellano LA, McNamara RJ, Pallarés HM, Gamarnik AV, Alvarez DE, Bazzini AA. Dengue virus preferentially uses human and mosquito non-optimal codons. Mol Syst Biol 2024:10.1038/s44320-024-00052-7. [PMID: 39039212 DOI: 10.1038/s44320-024-00052-7] [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: 01/29/2024] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 07/24/2024] Open
Abstract
Codon optimality refers to the effect that codon composition has on messenger RNA (mRNA) stability and translation level and implies that synonymous codons are not silent from a regulatory point of view. Here, we investigated the adaptation of virus genomes to the host optimality code using mosquito-borne dengue virus (DENV) as a model. We demonstrated that codon optimality exists in mosquito cells and showed that DENV preferentially uses nonoptimal (destabilizing) codons and avoids codons that are defined as optimal (stabilizing) in either human or mosquito cells. Human genes enriched in the codons preferentially and frequently used by DENV are upregulated during infection, and so is the tRNA decoding the nonoptimal and DENV preferentially used codon for arginine. We found that adaptation during single-host passaging in human or mosquito cells results in the selection of synonymous mutations towards DENV's preferred nonoptimal codons that increase virus fitness. Finally, our analyses revealed that hundreds of viruses preferentially use nonoptimal codons, with those infecting a single host displaying an even stronger bias, suggesting that host-pathogen interaction shapes virus-synonymous codon choice.
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Affiliation(s)
- Luciana A Castellano
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO, 64110, USA
| | - Ryan J McNamara
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO, 64110, USA
| | - Horacio M Pallarés
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO, 64110, USA
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires IIBBA-CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| | - Andrea V Gamarnik
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires IIBBA-CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| | - Diego E Alvarez
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín-CONICET, San Martín B1650, Argentina
| | - Ariel A Bazzini
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO, 64110, USA.
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS, 66160, USA.
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2
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Sulkowski A, Bouton C, Swanson C. Syn-CpG-Spacer: A Panel web app for synonymous recoding of viral genomes with CpG dinucleotides. JOURNAL OF OPEN SOURCE SOFTWARE 2024; 9:6332. [PMID: 38650605 PMCID: PMC7615850 DOI: 10.21105/joss.06332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Vertebrate genomes contain lower than expected frequencies of the CpG dinucleotide. Consequently, many vertebrate viruses have evolved to mimic this composition, possibly in order to evade host antiviral defences (Greenbaum et al., 2008). For example, the antiviral protein ZAP binds CpGs in viral single stranded RNA with specific spacing requirements (Gonçalves-Carneiro et al., 2022), though CpGs are also likely depleted in viral genomes due to other selective pressures (Forni et al., 2023). Increasing CpG abundance by synonymous recoding could facilitate attenuation of viruses without compromising their epitope antigenicity by changing non-CpG codons to alternatives containing CpG without changing the overall amino acid sequence (Gonçalves-Carneiro et al., 2022; Le Nouën et al., 2019; Sharp et al., 2023). There are three ways CpGs can be synonymously introduced in codons: at positions 1-2 for arginine (e.g. AGA → CGA), 2-3 for several amino acids (e.g. ACA → ACG), or in a 3-1 split configuration, if a subsequent codon begins with a G (e.g. ATA-GCA → ATC-GCA). Syn-CpG-Spacer is a Python progressive web app (PWA) (MDN Web Docs, 2023) made with the Panel library (Panel Development Team, 2024) that allows for consistent recoding of viral sequences and applying biologically relevant constraints. These include setting a minimum gap between CpG's, optimising for an average CpG gap, protecting cis-acting regulatory signals from modification, and modulating the A-content in the overall sequence. The app features a sequence viewer made with the Bokeh library (Bokeh Development Team, 2024) that highlights CpG dinucleotides, allowing for efficient analysis of the resulting distribution of CpGs. This is complemented by a statistical data table. Utilising Biopython (Cock et al., 2009) modules, the user can load their sequence as a FASTA file and download the outputs as an alignment in the same format. As a PWA running on Pyodide (The Pyodide development team, 2023), the code is only executed in the user's browser and they can install the app onto their machine for offline use.
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Affiliation(s)
- Aleksander Sulkowski
- Department of Infectious Diseases, King's College London, London, United Kingdom
| | - Clément Bouton
- Department of Infectious Diseases, King's College London, London, United Kingdom
| | - Chad Swanson
- Department of Infectious Diseases, King's College London, London, United Kingdom
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3
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de Andrade KQ, Cirne-Santos CC. Antiviral Activity of Zinc Finger Antiviral Protein (ZAP) in Different Virus Families. Pathogens 2023; 12:1461. [PMID: 38133344 PMCID: PMC10747524 DOI: 10.3390/pathogens12121461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023] Open
Abstract
The CCCH-type zinc finger antiviral protein (ZAP) in humans, specifically isoforms ZAP-L and ZAP-S, is a crucial component of the cell's intrinsic immune response. ZAP acts as a post-transcriptional RNA restriction factor, exhibiting its activity during infections caused by retroviruses and alphaviruses. Its function involves binding to CpG (cytosine-phosphate-guanine) dinucleotide sequences present in viral RNA, thereby directing it towards degradation. Since vertebrate cells have a suppressed frequency of CpG dinucleotides, ZAP is capable of distinguishing foreign genetic elements. The expression of ZAP leads to the reduction of viral replication and impedes the assembly of new virus particles. However, the specific mechanisms underlying these effects have yet to be fully understood. Several questions regarding ZAP's mechanism of action remain unanswered, including the impact of CpG dinucleotide quantity on ZAP's activity, whether this sequence is solely required for the binding between ZAP and viral RNA, and whether the recruitment of cofactors is dependent on cell type, among others. This review aims to integrate the findings from studies that elucidate ZAP's antiviral role in various viral infections, discuss gaps that need to be filled through further studies, and shed light on new potential targets for therapeutic intervention.
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Affiliation(s)
- Kívia Queiroz de Andrade
- Laboratory of Immunology of Infectious Disease, Immunology Department, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, SP, Brazil
| | - Claudio Cesar Cirne-Santos
- Laboratory of Molecular Virology and Marine Biotechnology, Department of Cellular and Molecular Biology, Institute of Biology, Federal Fluminense University, Niterói 24020-150, RJ, Brazil
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4
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Forni D, Pozzoli U, Cagliani R, Clerici M, Sironi M. Dinucleotide biases in RNA viruses that infect vertebrates or invertebrates. Microbiol Spectr 2023; 11:e0252923. [PMID: 37800906 PMCID: PMC10714974 DOI: 10.1128/spectrum.02529-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/12/2023] [Indexed: 10/07/2023] Open
Abstract
IMPORTANCE Akin to a molecular signature, dinucleotide composition can be exploited by the zinc-finger antiviral protein (ZAP) to restrict CpG-rich (and UpA-rich) RNA viruses. ZAP evolved in tetrapods, and it is not encoded by invertebrates and fish. Because a systematic analysis is missing, we analyzed the genomes of RNA viruses that infect vertebrates or invertebrates. We show that vertebrate single-stranded (ss) RNA(+) viruses and, to a lesser extent, double-stranded RNA viruses tend to have stronger CpG bias than invertebrate viruses. Conversely, ssRNA(-) viruses have similar dinucleotide composition whether they infect vertebrates or invertebrates. Analysis of ssRNA(+) viruses that infect mammals, reptiles, and fish indicated that ZAP is unlikely to be a major driver of CpG depletion. We also show that, compared to other coronaviruses, the genome of SARS-CoV-2 is not homogeneously CpG-depleted. Our study provides new insights into virus evolution and strategies for recoding RNA virus genomes.
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Affiliation(s)
- Diego Forni
- Bioinformatics Lab, Scientific Institute IRCCS E. MEDEA, Bosisio Parini, Italy
| | - Uberto Pozzoli
- Bioinformatics Lab, Scientific Institute IRCCS E. MEDEA, Bosisio Parini, Italy
| | - Rachele Cagliani
- Bioinformatics Lab, Scientific Institute IRCCS E. MEDEA, Bosisio Parini, Italy
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, Milan, Italy
- Don C. Gnocchi Foundation ONLUS, IRCCS, Milan, Italy
| | - Manuela Sironi
- Bioinformatics Lab, Scientific Institute IRCCS E. MEDEA, Bosisio Parini, Italy
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5
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Hegelmeyer NK, Parkin LA, Previti ML, Andrade J, Utama R, Sejour RJ, Gardin J, Muller S, Ketchum S, Yurovsky A, Futcher B, Goodwin S, Ueberheide B, Seeliger JC. Gene recoding by synonymous mutations creates promiscuous intragenic transcription initiation in mycobacteria. mBio 2023; 14:e0084123. [PMID: 37787543 PMCID: PMC10653884 DOI: 10.1128/mbio.00841-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 08/16/2023] [Indexed: 10/04/2023] Open
Abstract
IMPORTANCE Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis, one of the deadliest infectious diseases worldwide. Previous studies have established that synonymous recoding to introduce rare codon pairings can attenuate viral pathogens. We hypothesized that non-optimal codon pairing could be an effective strategy for attenuating gene expression to create a live vaccine for Mtb. We instead discovered that these synonymous changes enabled the transcription of functional mRNA that initiated in the middle of the open reading frame and from which many smaller protein products were expressed. To our knowledge, this is one of the first reports that synonymous recoding of a gene in any organism can create or induce intragenic transcription start sites.
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Affiliation(s)
- Nuri K. Hegelmeyer
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA
| | - Lia A. Parkin
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Mary L. Previti
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA
| | - Joshua Andrade
- Proteomics Laboratory, New York University Grossman School of Medicine, New York, New York, USA
| | - Raditya Utama
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Richard J. Sejour
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Justin Gardin
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Stephanie Muller
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Steven Ketchum
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Alisa Yurovsky
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Bruce Futcher
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Beatrix Ueberheide
- Proteomics Laboratory, New York University Grossman School of Medicine, New York, New York, USA
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York, USA
| | - Jessica C. Seeliger
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA
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6
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Takizawa N, Kawaguchi RK. Comprehensive in virio structure probing analysis of the influenza A virus identifies functional RNA structures involved in viral genome replication. Comput Struct Biotechnol J 2023; 21:5259-5272. [PMID: 37954152 PMCID: PMC10632597 DOI: 10.1016/j.csbj.2023.10.036] [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: 08/03/2023] [Revised: 10/17/2023] [Accepted: 10/17/2023] [Indexed: 11/14/2023] Open
Abstract
The influenza A virus genome is segmented into eight viral RNAs (vRNA). Secondary structures of vRNA are known to be involved in the viral proliferation process. Comprehensive vRNA structures in vitro, in virio, and in cellulo have been analyzed. However, the resolution of the structure map can be improved by comparative analysis and statistical modeling. Construction of a more high-resolution and reliable RNA structure map can identify uncharacterized functional structure motifs on vRNA in virion. Here, we establish the global map of the vRNA secondary structure in virion using the combination of dimethyl sulfate (DMS)-seq and selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE)-seq with a robust statistical analysis. Our high-resolution analysis identified a stem-loop structure at nucleotide positions 39 - 60 of segment 6 and further validated the structure at nucleotide positions 87 - 130 of segment 5 that was previously predicted to form a pseudoknot structure in silico. Notably, when the cells were infected with recombinant viruses which possess the mutations to disrupt the structure, the replication and packaging of the viral genome were drastically decreased. Our results provide comprehensive and high-resolution information on the influenza A virus genome structures in virion and evidence that the functional RNA structure motifs on the influenza A virus genome are associated with appropriate replication and packaging of the viral genome.
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Affiliation(s)
- Naoki Takizawa
- Laboratory of Virology, Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan
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7
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Molteni C, Forni D, Cagliani R, Bravo IG, Sironi M. Evolution and diversity of nucleotide and dinucleotide composition in poxviruses. J Gen Virol 2023; 104. [PMID: 37792576 DOI: 10.1099/jgv.0.001897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023] Open
Abstract
Poxviruses (family Poxviridae) have long dsDNA genomes and infect a wide range of hosts, including insects, birds, reptiles and mammals. These viruses have substantial incidence, prevalence and disease burden in humans and in other animals. Nucleotide and dinucleotide composition, mostly CpG and TpA, have been largely studied in viral genomes because of their evolutionary and functional implications. We analysed here the nucleotide and dinucleotide composition, as well as codon usage bias, of a set of representative poxvirus genomes, with a very diverse host spectrum. After correcting for overall nucleotide composition, entomopoxviruses displayed low overall GC content, no enrichment in TpA and large variation in CpG enrichment, while chordopoxviruses showed large variation in nucleotide composition, no obvious depletion in CpG and a weak trend for TpA depletion in GC-rich genomes. Overall, intergenome variation in dinucleotide composition in poxviruses is largely accounted for by variation in overall genomic GC levels. Nonetheless, using vaccinia virus as a model, we found that genes expressed at the earliest times in infection are more CpG-depleted than genes expressed at later stages. This observation has parallels in betahepesviruses (also large dsDNA viruses) and suggests an antiviral role for the innate immune system (e.g. via the zinc-finger antiviral protein ZAP) in the early phases of poxvirus infection. We also analysed codon usage bias in poxviruses and we observed that it is mostly determined by genomic GC content, and that stratification after host taxonomy does not contribute to explaining codon usage bias diversity. By analysis of within-species diversity, we show that genomic GC content is the result of mutational biases. Poxvirus genomes that encode a DNA ligase are significantly AT-richer than those that do not, suggesting that DNA repair systems shape mutation biases. Our data shed light on the evolution of poxviruses and inform strategies for their genetic manipulation for therapeutic purposes.
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Affiliation(s)
- Cristian Molteni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Diego Forni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Rachele Cagliani
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Ignacio G Bravo
- Laboratoire MIVEGEC (Univ Montpellier CNRS, IRD), Centre National de la Recherche Scientifique, Montpellier, France
| | - Manuela Sironi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
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8
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Chin WX, Kong HY, Zhu IXY, Teo ZY, Faruk R, Lee RCH, Ho SX, Aw ZQ, Yi B, Hou XJ, Tan AKY, Yogarajah T, Huber RG, Cai Y, Wan Y, Chu JJH. Flavivirus genome recoding by codon optimisation confers genetically stable in vivo attenuation in both mice and mosquitoes. PLoS Pathog 2023; 19:e1011753. [PMID: 37883598 PMCID: PMC10629665 DOI: 10.1371/journal.ppat.1011753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 11/07/2023] [Accepted: 10/14/2023] [Indexed: 10/28/2023] Open
Abstract
Virus genome recoding is an attenuation method that confers genetically stable attenuation by rewriting a virus genome with numerous silent mutations. Prior flavivirus genome recoding attempts utilised codon deoptimisation approaches. However, these codon deoptimisation approaches act in a species dependent manner and were unable to confer flavivirus attenuation in mosquito cells or in mosquito animal models. To overcome these limitations, we performed flavivirus genome recoding using the contrary approach of codon optimisation. The genomes of flaviviruses such as dengue virus type 2 (DENV2) and Zika virus (ZIKV) contain functional RNA elements that regulate viral replication. We hypothesised that flavivirus genome recoding by codon optimisation would introduce silent mutations that disrupt these RNA elements, leading to decreased replication efficiency and attenuation. We chose DENV2 and ZIKV as representative flaviviruses and recoded them by codon optimising their genomes for human expression. Our study confirms that this recoding approach of codon optimisation does translate into reduced replication efficiency in mammalian, human, and mosquito cells as well as in vivo attenuation in both mice and mosquitoes. In silico modelling and RNA SHAPE analysis confirmed that DENV2 recoding resulted in the extensive disruption of genomic structural elements. Serial passaging of recoded DENV2 resulted in the emergence of rescue or adaptation mutations, but no reversion mutations. These rescue mutations were unable to rescue the delayed replication kinetics and in vivo attenuation of recoded DENV2, demonstrating that recoding confers genetically stable attenuation. Therefore, our recoding approach is a reliable attenuation method with potential applications for developing flavivirus vaccines.
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Affiliation(s)
- Wei-Xin Chin
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology and Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore
| | - Hao Yuin Kong
- NUSMed Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Isabelle Xin Yu Zhu
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology and Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore
| | - Zi Yun Teo
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology and Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore
| | - Regina Faruk
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology and Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore
| | - Regina Ching Hua Lee
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology and Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore
| | - Si Xian Ho
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology and Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore
| | - Zhen Qin Aw
- NUSMed Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Bowen Yi
- NUSMed Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Xin Jun Hou
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Antson Kiat Yee Tan
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Thinesshwary Yogarajah
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology and Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore
| | - Roland G. Huber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Yu Cai
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Yue Wan
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Justin Jang Hann Chu
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology and Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore
- NUSMed Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
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9
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Megremis S, Constantinides B, Xepapadaki P, Yap CF, Sotiropoulos AG, Bachert C, Finotto S, Jartti T, Tapinos A, Vuorinen T, Andreakos E, Robertson DL, Papadopoulos NG. Respiratory eukaryotic virome expansion and bacteriophage deficiency characterize childhood asthma. Sci Rep 2023; 13:8319. [PMID: 37221274 PMCID: PMC10205716 DOI: 10.1038/s41598-023-34730-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 05/06/2023] [Indexed: 05/25/2023] Open
Abstract
Asthma development and exacerbation is linked to respiratory virus infections. There is limited information regarding the presence of viruses during non-exacerbation/infection periods. We investigated the nasopharyngeal/nasal virome during a period of asymptomatic state, in a subset of 21 healthy and 35 asthmatic preschool children from the Predicta cohort. Using metagenomics, we described the virome ecology and the cross-species interactions within the microbiome. The virome was dominated by eukaryotic viruses, while prokaryotic viruses (bacteriophages) were independently observed with low abundance. Rhinovirus B species consistently dominated the virome in asthma. Anelloviridae were the most abundant and rich family in both health and asthma. However, their richness and alpha diversity were increased in asthma, along with the co-occurrence of different Anellovirus genera. Bacteriophages were richer and more diverse in healthy individuals. Unsupervised clustering identified three virome profiles that were correlated to asthma severity and control and were independent of treatment, suggesting a link between the respiratory virome and asthma. Finally, we observed different cross-species ecological associations in the healthy versus the asthmatic virus-bacterial interactome, and an expanded interactome of eukaryotic viruses in asthma. Upper respiratory virome "dysbiosis" appears to be a novel feature of pre-school asthma during asymptomatic/non-infectious states and merits further investigation.
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Affiliation(s)
- Spyridon Megremis
- University of Manchester, Manchester, UK.
- University of Leicester, Leicester, UK.
| | | | | | | | | | | | - Susetta Finotto
- Friedrich Alexander University Erlangen-Nurnberg, Erlangen, Germany
| | - Tuomas Jartti
- University of Turku, Turku, Finland
- University of Oulu, Oulu, Finland
| | | | | | | | | | - Nikolaos G Papadopoulos
- University of Manchester, Manchester, UK.
- National and Kapodistrian University of Athens, Athens, Greece.
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10
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Sharp CP, Thompson BH, Nash TJ, Diebold O, Pinto RM, Thorley L, Lin YT, Sives S, Wise H, Clohisey Hendry S, Grey F, Vervelde L, Simmonds P, Digard P, Gaunt ER. CpG dinucleotide enrichment in the influenza A virus genome as a live attenuated vaccine development strategy. PLoS Pathog 2023; 19:e1011357. [PMID: 37146066 PMCID: PMC10191365 DOI: 10.1371/journal.ppat.1011357] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 05/17/2023] [Accepted: 04/12/2023] [Indexed: 05/07/2023] Open
Abstract
Synonymous recoding of RNA virus genomes is a promising approach for generating attenuated viruses to use as vaccines. Problematically, recoding typically hinders virus growth, but this may be rectified using CpG dinucleotide enrichment. CpGs are recognised by cellular zinc-finger antiviral protein (ZAP), and so in principle, removing ZAP sensing from a virus propagation system will reverse attenuation of a CpG-enriched virus, enabling high titre yield of a vaccine virus. We tested this using a vaccine strain of influenza A virus (IAV) engineered for increased CpG content in genome segment 1. Virus attenuation was mediated by the short isoform of ZAP, correlated with the number of CpGs added, and was enacted via turnover of viral transcripts. The CpG-enriched virus was strongly attenuated in mice, yet conveyed protection from a potentially lethal challenge dose of wildtype virus. Importantly for vaccine development, CpG-enriched viruses were genetically stable during serial passage. Unexpectedly, in both MDCK cells and embryonated hens' eggs that are used to propagate live attenuated influenza vaccines, the ZAP-sensitive virus was fully replication competent. Thus, ZAP-sensitive CpG enriched viruses that are defective in human systems can yield high titre in vaccine propagation systems, providing a realistic, economically viable platform to augment existing live attenuated vaccines.
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Affiliation(s)
- Colin P. Sharp
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Beth H. Thompson
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Tessa J. Nash
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Ola Diebold
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Rute M. Pinto
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Luke Thorley
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Yao-Tang Lin
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Samantha Sives
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Helen Wise
- Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, United Kingdom
| | - Sara Clohisey Hendry
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Finn Grey
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Lonneke Vervelde
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - Paul Digard
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Eleanor R. Gaunt
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
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11
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Hegelmeyer NK, Previti ML, Andrade J, Utama R, Sejour RJ, Gardin J, Muller S, Ketchum S, Yurovsky A, Futcher B, Goodwin S, Ueberheide B, Seeliger JC. Gene recoding by synonymous mutations creates promiscuous intragenic transcription initiation in mycobacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.17.532606. [PMID: 36993691 PMCID: PMC10055193 DOI: 10.1101/2023.03.17.532606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Each genome encodes some codons more frequently than their synonyms (codon usage bias), but codons are also arranged more frequently into specific pairs (codon pair bias). Recoding viral genomes and yeast or bacterial genes with non-optimal codon pairs has been shown to decrease gene expression. Gene expression is thus importantly regulated not only by the use of particular codons but by their proper juxtaposition. We therefore hypothesized that non-optimal codon pairing could likewise attenuate Mtb genes. We explored the role of codon pair bias by recoding Mtb genes ( rpoB, mmpL3, ndh ) and assessing their expression in the closely related and tractable model organism M. smegmatis . To our surprise, recoding caused the expression of multiple smaller protein isoforms from all three genes. We confirmed that these smaller proteins were not due to protein degradation, but instead issued from new transcription initiation sites positioned within the open reading frame. New transcripts gave rise to intragenic translation initiation sites, which in turn led to the expression of smaller proteins. We next identified the nucleotide changes associated with these new sites of transcription and translation. Our results demonstrated that apparently benign, synonymous changes can drastically alter gene expression in mycobacteria. More generally, our work expands our understanding of the codon-level parameters that control translation and transcription initiation. IMPORTANCE Mycobacterium tuberculosis ( Mtb ) is the causative agent of tuberculosis, one of the deadliest infectious diseases worldwide. Previous studies have established that synonymous recoding to introduce rare codon pairings can attenuate viral pathogens. We hypothesized that non-optimal codon pairing could be an effective strategy for attenuating gene expression to create a live vaccine for Mtb . We instead discovered that these synonymous changes enabled the transcription of functional mRNA that initiated in the middle of the open reading frame and from which many smaller protein products were expressed. To our knowledge, this is the first report that synonymous recoding of a gene in any organism can create or induce intragenic transcription start sites.
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Affiliation(s)
- Nuri K. Hegelmeyer
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA
| | - Mary L. Previti
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA
| | - Joshua Andrade
- Proteomics Laboratory, New York University Grossman School of Medicine, New York, New York, USA
| | - Raditya Utama
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Richard J. Sejour
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Justin Gardin
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Stephanie Muller
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Steven Ketchum
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Alisa Yurovsky
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Bruce Futcher
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Beatrix Ueberheide
- Proteomics Laboratory, New York University Grossman School of Medicine, New York, New York, USA
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York, USA
| | - Jessica C. Seeliger
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA
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12
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Characterization of Live-Attenuated Powassan Virus Vaccine Candidates Identifies an Efficacious Prime-Boost Strategy for Mitigating Powassan Virus Disease in a Murine Model. Vaccines (Basel) 2023; 11:vaccines11030612. [PMID: 36992196 PMCID: PMC10058527 DOI: 10.3390/vaccines11030612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/10/2023] Open
Abstract
Powassan virus (POWV) is an emerging tick-borne virus and cause of lethal encephalitis in humans. The lack of treatment or prevention strategies for POWV disease underscores the need for an effective POWV vaccine. Here, we took two independent approaches to develop vaccine candidates. First, we recoded the POWV genome to increase the dinucleotide frequencies of CpG and UpA to potentially attenuate the virus by raising its susceptibility to host innate immune factors, such as the zinc-finger antiviral protein (ZAP). Secondly, we took advantage of the live-attenuated yellow fever virus vaccine 17D strain (YFV-17D) as a vector to express the structural genes pre-membrane (prM) and envelope (E) of POWV. The chimeric YFV-17D-POWV vaccine candidate was further attenuated for in vivo application by removing an N-linked glycosylation site within the nonstructural protein (NS)1 of YFV-17D. This live-attenuated chimeric vaccine candidate significantly protected mice from POWV disease, conferring a 70% survival rate after lethal challenge when administered in a homologous two-dose regimen. Importantly, when given in a heterologous prime-boost vaccination scheme, in which vaccination with the initial chimeric virus was followed by a protein boost with the envelope protein domain III (EDIII), 100% of the mice were protected without showing any signs of morbidity. Combinations of this live-attenuated chimeric YFV-17D-POWV vaccine candidate with an EDIII protein boost warrant further studies for the development of an effective vaccine strategy for the prevention of POWV disease.
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13
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Gurjar P, Karuvantevida N, Rzhepakovsky IV, Khan AA, Khandia R. A Synthetic Biology Approach for Vaccine Candidate Design against Delta Strain of SARS-CoV-2 Revealed Disruption of Favored Codon Pair as a Better Strategy over Using Rare Codons. Vaccines (Basel) 2023; 11:vaccines11020487. [PMID: 36851364 PMCID: PMC9967482 DOI: 10.3390/vaccines11020487] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 02/13/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
The SARS-CoV-2 delta variant (B.1.617.2) appeared for the first time in December 2020 and later spread worldwide. Currently available vaccines are not so efficacious in curbing the viral pathogenesis of the delta strain of COVID; therefore, the development of a safe and effective vaccine is required. In the present study, we envisaged molecular patterns in the structural genes' spike, nucleoprotein, membrane, and envelope of the SARS-CoV-2 delta variant. The study was based on determining compositional features, dinucleotide odds ratio, synonymous codon usage, positive and negative codon contexts, rare codons, and insight into relatedness between the human host isoacceptor tRNA and preferred codons from the structural genes. We found specific patterns, including a significant abundance of T nucleotide over all other three nucleotides. The underrepresentation of GpA, GpG, CpC, and CpG dinucleotides and the overrepresentation of TpT, ApA, CpT, and TpG were observed. A preference towards ACT- (Thr), AAT- (Asn), TTT- (Phe), and TTG- (Leu) initiated codons and aversion towards CGG (Arg), CCG (Pro), and CAC (His) was present in the structural genes of the delta strain. The interaction between the host tRNA pool and preferred codons of the envisaged structural genes revealed that the virus preferred the codons for those suboptimal numbers of isoacceptor tRNA were present. We see this as a strategy adapted by the virus to keep the translation rate low to facilitate the correct folding of viral proteins. The information generated in the study helps design the attenuated vaccine candidate against the SARS-CoV-2 delta variant using a synthetic biology approach. Three strategies were tested: changing TpT to TpA, introducing rare codons, and disrupting favored codons. It found that disrupting favored codons is a better approach to reducing virus fitness and attenuating SARS-CoV-2 delta strain using structural genes.
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Affiliation(s)
- Pankaj Gurjar
- Department of Science and Engineering, Novel Global Community Educational Foundation, Hebersham, NSW 2770, Australia
| | - Noushad Karuvantevida
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai P.O. Box 505055, United Arab Emirates
| | | | - Azmat Ali Khan
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
- Correspondence: (A.A.K.); or (R.K.)
| | - Rekha Khandia
- Department of Biochemistry and Genetics, Barkatullah Universty, Bhopal 462026, India
- Correspondence: (A.A.K.); or (R.K.)
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14
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Morris KM, Mishra A, Raut AA, Gaunt ER, Borowska D, Kuo RI, Wang B, Vijayakumar P, Chingtham S, Dutta R, Baillie K, Digard P, Vervelde L, Burt DW, Smith J. The molecular basis of differential host responses to avian influenza viruses in avian species with differing susceptibility. Front Cell Infect Microbiol 2023; 13:1067993. [PMID: 36926515 PMCID: PMC10011077 DOI: 10.3389/fcimb.2023.1067993] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 02/09/2023] [Indexed: 03/04/2023] Open
Abstract
Introduction Highly pathogenic avian influenza (HPAI) viruses, such as H5N1, continue to pose a serious threat to animal agriculture, wildlife and to public health. Controlling and mitigating this disease in domestic birds requires a better understanding of what makes some species highly susceptible (such as turkey and chicken) while others are highly resistant (such as pigeon and goose). Susceptibility to H5N1 varies both with species and strain; for example, species that are tolerant of most H5N1 strains, such as crows and ducks, have shown high mortality to emerging strains in recent years. Therefore, in this study we aimed to examine and compare the response of these six species, to low pathogenic avian influenza (H9N2) and two strains of H5N1 with differing virulence (clade 2.2 and clade 2.3.2.1) to determine how susceptible and tolerant species respond to HPAI challenge. Methods Birds were challenged in infection trials and samples (brain, ileum and lung) were collected at three time points post infection. The transcriptomic response of birds was examined using a comparative approach, revealing several important discoveries. Results We found that susceptible birds had high viral loads and strong neuro-inflammatory response in the brain, which may explain the neurological symptoms and high mortality rates exhibited following H5N1 infection. We discovered differential regulation of genes associated with nerve function in the lung and ileum, with stronger differential regulation in resistant species. This has intriguing implications for the transmission of the virus to the central nervous system (CNS) and may also indicate neuro-immune involvement at the mucosal surfaces. Additionally, we identified delayed timing of the immune response in ducks and crows following infection with the more deadly H5N1 strain, which may account for the higher mortality in these species caused by this strain. Lastly, we identified candidate genes with potential roles in susceptibility/resistance which provide excellent targets for future research. Discussion This study has helped elucidate the responses underlying susceptibility to H5N1 influenza in avian species, which will be critical in developing sustainable strategies for future control of HPAI in domestic poultry.
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Affiliation(s)
- Katrina M. Morris
- The Roslin Institute and R(D)SVS, The University of Edinburgh, Edinburgh, United Kingdom
- *Correspondence: Katrina M. Morris, ;
| | - Anamika Mishra
- National Institute of High Security Animal Diseases, Indian Council of Agricultural Research, Bhopal, India
| | - Ashwin A. Raut
- National Institute of High Security Animal Diseases, Indian Council of Agricultural Research, Bhopal, India
| | - Eleanor R. Gaunt
- The Roslin Institute and R(D)SVS, The University of Edinburgh, Edinburgh, United Kingdom
| | - Dominika Borowska
- The Roslin Institute and R(D)SVS, The University of Edinburgh, Edinburgh, United Kingdom
| | - Richard I. Kuo
- The Roslin Institute and R(D)SVS, The University of Edinburgh, Edinburgh, United Kingdom
| | - Bo Wang
- The Roslin Institute and R(D)SVS, The University of Edinburgh, Edinburgh, United Kingdom
| | - Periyasamy Vijayakumar
- National Institute of High Security Animal Diseases, Indian Council of Agricultural Research, Bhopal, India
| | - Santhalembi Chingtham
- National Institute of High Security Animal Diseases, Indian Council of Agricultural Research, Bhopal, India
| | - Rupam Dutta
- National Institute of High Security Animal Diseases, Indian Council of Agricultural Research, Bhopal, India
| | - Kenneth Baillie
- The Roslin Institute and R(D)SVS, The University of Edinburgh, Edinburgh, United Kingdom
| | - Paul Digard
- The Roslin Institute and R(D)SVS, The University of Edinburgh, Edinburgh, United Kingdom
| | - Lonneke Vervelde
- The Roslin Institute and R(D)SVS, The University of Edinburgh, Edinburgh, United Kingdom
| | - David W. Burt
- The Roslin Institute and R(D)SVS, The University of Edinburgh, Edinburgh, United Kingdom
| | - Jacqueline Smith
- The Roslin Institute and R(D)SVS, The University of Edinburgh, Edinburgh, United Kingdom
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15
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Gonçalves-Carneiro D, Mastrocola E, Lei X, DaSilva J, Chan YF, Bieniasz PD. Rational attenuation of RNA viruses with zinc finger antiviral protein. Nat Microbiol 2022; 7:1558-1567. [PMID: 36075961 PMCID: PMC9519448 DOI: 10.1038/s41564-022-01223-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 08/03/2022] [Indexed: 01/28/2023]
Abstract
Attenuation of a virulent virus is a proven approach for generating vaccines but can be unpredictable. For example, synonymous recoding of viral genomes can attenuate replication but sometimes results in pleiotropic effects that confound rational vaccine design. To enable specific, conditional attenuation of viruses, we examined target RNA features that enable zinc finger antiviral protein (ZAP) function. ZAP recognized CpG dinucleotides and targeted CpG-rich RNAs for depletion, but RNA features such as CpG numbers, spacing and surrounding nucleotide composition that enable specific modulation by ZAP were undefined. Using synonymously mutated HIV-1 genomes, we defined several sequence features that govern ZAP sensitivity and enable stable attenuation. We applied rules derived from experiments with HIV-1 to engineer a mutant enterovirus A71 genome whose attenuation was stable and strictly ZAP-dependent, both in cell culture and in mice. The conditionally attenuated enterovirus A71 mutant elicited neutralizing antibodies that were protective against wild-type enterovirus A71 infection and disease in mice. ZAP sensitivity can thus be readily applied for the rational design of conditionally attenuated viral vaccines.
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Affiliation(s)
| | - Emily Mastrocola
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Xiao Lei
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Justin DaSilva
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Yoke Fun Chan
- Department of Medical Microbiology, University of Malaya, Kuala Lumpur, Malaysia
| | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
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16
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Udenze D, Trus I, Berube N, Karniychuk U. CpG content in the Zika virus genome affects infection phenotypes in the adult brain and fetal lymph nodes. Front Immunol 2022; 13:943481. [PMID: 35983032 PMCID: PMC9379343 DOI: 10.3389/fimmu.2022.943481] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
Increasing the number of CpG dinucleotides in RNA viral genomes, while preserving the original amino acid composition, leads to impaired infection which does not cause disease. Beneficially, impaired infection evokes antiviral host immune responses providing a cutting-edge vaccine approach. For example, we previously showed that CpG-enriched Zika virus variants cause attenuated infection phenotypes and protect against lethal challenge in mice. While CpG recoding is an emerging and promising vaccine approach, little is known about infection phenotypes caused by recoded viruses in vivo, particularly in non-rodent species. Here, we used well-established mouse and porcine models to study infection phenotypes of the CpG-enriched neurotropic and congenital virus—Zika virus, directly in the target tissues—the brain and placenta. Specifically, we used the uttermost challenge and directly injected mice intracerebrally to compare infection phenotypes caused by wild-type and two CpG-recoded Zika variants and model the scenario where vaccine strains breach the blood-brain barrier. Also, we directly injected porcine fetuses to compare in utero infection phenotypes and model the scenario where recoded vaccine strains breach the placental barrier. While overall infection kinetics were comparable between wild-type and recoded virus variants, we found convergent phenotypical differences characterized by reduced pathology in the mouse brain and reduced replication of CpG-enriched variants in fetal lymph nodes. Next, using next-generation sequencing for the whole virus genome, we compared the stability of de novo introduced CpG dinucleotides during prolonged virus infection in the brain and placenta. Most de novo introduced CpG dinucleotides were preserved in sequences of recoded Zika viruses showing the stability of vaccine variants. Altogether, our study emphasized further directions to fine-tune the CpG recoding vaccine approach for better safety and can inform future immunization strategies.
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Affiliation(s)
- Daniel Udenze
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
- School of Public Health, University of Saskatchewan, Saskatoon, SK, Canada
| | - Ivan Trus
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
- Dioscuri Centre for RNA-Protein Interactions in Human Health and Disease, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Nathalie Berube
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
| | - Uladzimir Karniychuk
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
- School of Public Health, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
- *Correspondence: Uladzimir Karniychuk,
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17
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Jaglan A, Satija S, Singh D, Phartyal R, Verma M. Intra-genomic heterogeneity in CpG dinucleotide composition in dengue virus. Acta Trop 2022; 232:106501. [PMID: 35513073 DOI: 10.1016/j.actatropica.2022.106501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/29/2022] [Accepted: 05/01/2022] [Indexed: 11/01/2022]
Abstract
PURPOSE Dengue virus is a life-threatening virus and cases of dengue infection have been increasing steadily in the past decades causing millions of deaths every year. So far, there is no vaccine that works effectively on all serotypes. Recently, CpG-recoded vaccines have proved to be effective against few viruses. METHODS In this study, evaluation and interpretation of more than 4547 Dengue virus genome sequences were included for analyzing novel CpG dinucleotides rich regions which are shared amid all serotypes. Genomic regions of DENV were synonymously CpG recoded using in silico methods and analyzed for adaptation in both human and Aedes spp. hosts based on CAI scores. RESULTS The analysis mirrored that serotypes 1, 3, and 4 shared CpG islands present in common regions. DENV-2 CpG islands showed no similarity with any of the CpG islands present in other serotypes. While DENV-3 sequences were found to possess the maximum number of conserved CpG islands stretches; DENV-2 was found to possess the lowest number. We found that all serotypes (with an exception of serotype 2) have CpG island in their 3' UTR. In silico CpG recoding of DENV genomic regions resulted in ∼ 3 fold increase of CpG dinucleotide frequency and comparative analysis based on CAI scores showed decreased adaptive fitness of CpG recoded DENV inside human host. CONCLUSION These CG-dinucleotide-enriched RNA sequences can be targeted by ZAP (zinc-finger antiviral protein) which can differentiate between host mRNA and viral mRNA. Our in silico findings can further be exploited for CpG-recoding of DENV genomes which can evoke cellular and humoral immune responses by recruiting ZAP-induced RNA degradation machinery and hence providing a promising approach for vaccine development.
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18
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Tisthammer KH, Solis C, Orcales F, Nzerem M, Winstead R, Dong W, Joy JB, Pennings PS. Assessing in vivo mutation frequencies and creating a high-resolution genome-wide map of fitness costs of Hepatitis C virus. PLoS Genet 2022; 18:e1010179. [PMID: 35500034 PMCID: PMC9113599 DOI: 10.1371/journal.pgen.1010179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 05/17/2022] [Accepted: 03/30/2022] [Indexed: 11/18/2022] Open
Abstract
Like many viruses, Hepatitis C Virus (HCV) has a high mutation rate, which helps the virus adapt quickly, but mutations come with fitness costs. Fitness costs can be studied by different approaches, such as experimental or frequency-based approaches. The frequency-based approach is particularly useful to estimate in vivo fitness costs, but this approach works best with deep sequencing data from many hosts are. In this study, we applied the frequency-based approach to a large dataset of 195 patients and estimated the fitness costs of mutations at 7957 sites along the HCV genome. We used beta regression and random forest models to better understand how different factors influenced fitness costs. Our results revealed that costs of nonsynonymous mutations were three times higher than those of synonymous mutations, and mutations at nucleotides A or T had higher costs than those at C or G. Genome location had a modest effect, with lower costs for mutations in HVR1 and higher costs for mutations in Core and NS5B. Resistance mutations were, on average, costlier than other mutations. Our results show that in vivo fitness costs of mutations can be site and virus specific, reinforcing the utility of constructing in vivo fitness cost maps of viral genomes.
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Affiliation(s)
- Kaho H. Tisthammer
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
- * E-mail:
| | - Caroline Solis
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Faye Orcales
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Madu Nzerem
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Ryan Winstead
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Weiyan Dong
- BC Centre for Excellence in HIV/AIDS, Vancouver, British Colombia, Canada
| | - Jeffrey B. Joy
- BC Centre for Excellence in HIV/AIDS, Vancouver, British Colombia, Canada
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Bioinformatics Programme, University of British Columbia, Vancouver, British Colombia, Canada
| | - Pleuni S. Pennings
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
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19
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Gaunt ER, Digard P. Compositional biases in RNA viruses: Causes, consequences and applications. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1679. [PMID: 34155814 PMCID: PMC8420353 DOI: 10.1002/wrna.1679] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/29/2021] [Accepted: 05/31/2021] [Indexed: 01/05/2023]
Abstract
If each of the four nucleotides were represented equally in the genomes of viruses and the hosts they infect, each base would occur at a frequency of 25%. However, this is not observed in nature. Similarly, the order of nucleotides is not random (e.g., in the human genome, guanine follows cytosine at a frequency of ~0.0125, or a quarter the number of times predicted by random representation). Codon usage and codon order are also nonrandom. Furthermore, nucleotide and codon biases vary between species. Such biases have various drivers, including cellular proteins that recognize specific patterns in nucleic acids, that once triggered, induce mutations or invoke intrinsic or innate immune responses. In this review we examine the types of compositional biases identified in viral genomes and current understanding of the evolutionary mechanisms underpinning these trends. Finally, we consider the potential for large scale synonymous recoding strategies to engineer RNA virus vaccines, including those with pandemic potential, such as influenza A virus and Severe Acute Respiratory Syndrome Coronavirus Virus 2. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Evolution and Genomics > Computational Analyses of RNA RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition.
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Affiliation(s)
- Eleanor R. Gaunt
- Department of Infection and ImmunityThe Roslin Institute, The University of EdinburghEdinburghUK
| | - Paul Digard
- Department of Infection and ImmunityThe Roslin Institute, The University of EdinburghEdinburghUK
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20
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Trus I, Udenze D, Karniychuk U. Generation of CpG-Recoded Zika Virus Vaccine Candidates. Methods Mol Biol 2022; 2410:289-302. [PMID: 34914053 DOI: 10.1007/978-1-0716-1884-4_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Experimental increase of cytosine-phosphate-guanine (CpG) dinucleotides in an RNA virus genome impairs infection. Beneficially, this weak infection may lead to robust antiviral host immunity providing a cutting-edge approach for vaccines. For example, we have recently demonstrated that recoded Zika virus variants with the increased CpG content showed considerable attenuated infection phenotypes and protection against lethal challenge in mice. Here, we describe the workflow for the design and generation of CpG-recoded Zika virus vaccine candidates. The workflow can be adapted for other viruses.
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Affiliation(s)
- Ivan Trus
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK, Canada
| | - Daniel Udenze
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK, Canada
| | - Uladzimir Karniychuk
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK, Canada.
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21
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Kmiec D, Lista MJ, Ficarelli M, Swanson CM, Neil SJD. S-farnesylation is essential for antiviral activity of the long ZAP isoform against RNA viruses with diverse replication strategies. PLoS Pathog 2021; 17:e1009726. [PMID: 34695163 PMCID: PMC8568172 DOI: 10.1371/journal.ppat.1009726] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 11/04/2021] [Accepted: 10/07/2021] [Indexed: 11/18/2022] Open
Abstract
The zinc finger antiviral protein (ZAP) is a broad inhibitor of virus replication. Its best-characterized function is to bind CpG dinucleotides present in viral RNAs and, through the recruitment of TRIM25, KHNYN and other cofactors, target them for degradation or prevent their translation. The long and short isoforms of ZAP (ZAP-L and ZAP-S) have different intracellular localization and it is unclear how this regulates their antiviral activity against viruses with different sites of replication. Using ZAP-sensitive and ZAP-insensitive human immunodeficiency virus type I (HIV-1), which transcribe the viral RNA in the nucleus and assemble virions at the plasma membrane, we show that the catalytically inactive poly-ADP-ribose polymerase (PARP) domain in ZAP-L is essential for CpG-specific viral restriction. Mutation of a crucial cysteine in the C-terminal CaaX box that mediates S-farnesylation and, to a lesser extent, the residues in place of the catalytic site triad within the PARP domain, disrupted the activity of ZAP-L. Addition of the CaaX box to ZAP-S partly restored antiviral activity, explaining why ZAP-S lacks antiviral activity for CpG-enriched HIV-1 despite conservation of the RNA-binding domain. Confocal microscopy confirmed the CaaX motif mediated localization of ZAP-L to vesicular structures and enhanced physical association with intracellular membranes. Importantly, the PARP domain and CaaX box together jointly modulate the interaction between ZAP-L and its cofactors TRIM25 and KHNYN, implying that its proper subcellular localisation is required to establish an antiviral complex. The essential contribution of the PARP domain and CaaX box to ZAP-L antiviral activity was further confirmed by inhibition of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication, which replicates in double-membrane vesicles derived from the endoplasmic reticulum. Thus, compartmentalization of ZAP-L on intracellular membranes provides an essential effector function in ZAP-L-mediated antiviral activity against divergent viruses with different subcellular replication sites.
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Affiliation(s)
- Dorota Kmiec
- Department of Infectious Diseases, King’s College London, London, United Kingdom
| | - María José Lista
- Department of Infectious Diseases, King’s College London, London, United Kingdom
| | - Mattia Ficarelli
- Department of Infectious Diseases, King’s College London, London, United Kingdom
| | - Chad M. Swanson
- Department of Infectious Diseases, King’s College London, London, United Kingdom
| | - Stuart J. D. Neil
- Department of Infectious Diseases, King’s College London, London, United Kingdom
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22
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Morales AC, Rice AM, Ho AT, Mordstein C, Mühlhausen S, Watson S, Cano L, Young B, Kudla G, Hurst LD. Causes and Consequences of Purifying Selection on SARS-CoV-2. Genome Biol Evol 2021; 13:evab196. [PMID: 34427640 PMCID: PMC8504154 DOI: 10.1093/gbe/evab196] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2021] [Indexed: 02/06/2023] Open
Abstract
Owing to a lag between a deleterious mutation's appearance and its selective removal, gold-standard methods for mutation rate estimation assume no meaningful loss of mutations between parents and offspring. Indeed, from analysis of closely related lineages, in SARS-CoV-2, the Ka/Ks ratio was previously estimated as 1.008, suggesting no within-host selection. By contrast, we find a higher number of observed SNPs at 4-fold degenerate sites than elsewhere and, allowing for the virus's complex mutational and compositional biases, estimate that the mutation rate is at least 49-67% higher than would be estimated based on the rate of appearance of variants in sampled genomes. Given the high Ka/Ks one might assume that the majority of such intrahost selection is the purging of nonsense mutations. However, we estimate that selection against nonsense mutations accounts for only ∼10% of all the "missing" mutations. Instead, classical protein-level selective filters (against chemically disparate amino acids and those predicted to disrupt protein functionality) account for many missing mutations. It is less obvious why for an intracellular parasite, amino acid cost parameters, notably amino acid decay rate, is also significant. Perhaps most surprisingly, we also find evidence for real-time selection against synonymous mutations that move codon usage away from that of humans. We conclude that there is common intrahost selection on SARS-CoV-2 that acts on nonsense, missense, and possibly synonymous mutations. This has implications for methods of mutation rate estimation, for determining times to common ancestry and the potential for intrahost evolution including vaccine escape.
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Affiliation(s)
- Atahualpa Castillo Morales
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, United Kingdom
| | - Alan M Rice
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, United Kingdom
| | - Alexander T Ho
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, United Kingdom
| | - Christine Mordstein
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, United Kingdom
- MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, The University of Edinburgh, United Kingdom
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Stefanie Mühlhausen
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, United Kingdom
| | - Samir Watson
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Laura Cano
- MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, The University of Edinburgh, United Kingdom
| | - Bethan Young
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, United Kingdom
- MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, The University of Edinburgh, United Kingdom
| | - Grzegorz Kudla
- MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, The University of Edinburgh, United Kingdom
| | - Laurence D Hurst
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, United Kingdom
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23
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Lin YT, Chau LF, Coutts H, Mahmoudi M, Drampa V, Lee CH, Brown A, Hughes DJ, Grey F. Does the Zinc Finger Antiviral Protein (ZAP) Shape the Evolution of Herpesvirus Genomes? Viruses 2021; 13:1857. [PMID: 34578438 PMCID: PMC8473364 DOI: 10.3390/v13091857] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/12/2021] [Accepted: 09/13/2021] [Indexed: 01/02/2023] Open
Abstract
An evolutionary arms race occurs between viruses and hosts. Hosts have developed an array of antiviral mechanisms aimed at inhibiting replication and spread of viruses, reducing their fitness, and ultimately minimising pathogenic effects. In turn, viruses have evolved sophisticated counter-measures that mediate evasion of host defence mechanisms. A key aspect of host defences is the ability to differentiate between self and non-self. Previous studies have demonstrated significant suppression of CpG and UpA dinucleotide frequencies in the coding regions of RNA and small DNA viruses. Artificially increasing these dinucleotide frequencies results in a substantial attenuation of virus replication, suggesting dinucleotide bias could facilitate recognition of non-self RNA. The interferon-inducible gene, zinc finger antiviral protein (ZAP) is the host factor responsible for sensing CpG dinucleotides in viral RNA and restricting RNA viruses through direct binding and degradation of the target RNA. Herpesviruses are large DNA viruses that comprise three subfamilies, alpha, beta and gamma, which display divergent CpG dinucleotide patterns within their genomes. ZAP has recently been shown to act as a host restriction factor against human cytomegalovirus (HCMV), a beta-herpesvirus, which in turn evades ZAP detection by suppressing CpG levels in the major immediate-early transcript IE1, one of the first genes expressed by the virus. While suppression of CpG dinucleotides allows evasion of ZAP targeting, synonymous changes in nucleotide composition that cause genome biases, such as low GC content, can cause inefficient gene expression, especially in unspliced transcripts. To maintain compact genomes, the majority of herpesvirus transcripts are unspliced. Here we discuss how the conflicting pressures of ZAP evasion, the need to maintain compact genomes through the use of unspliced transcripts and maintaining efficient gene expression may have shaped the evolution of herpesvirus genomes, leading to characteristic CpG dinucleotide patterns.
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Affiliation(s)
- Yao-Tang Lin
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK; (Y.-T.L.); (L.-F.C.); (H.C.); (M.M.); (V.D.); (C.-H.L.); (A.B.)
| | - Long-Fung Chau
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK; (Y.-T.L.); (L.-F.C.); (H.C.); (M.M.); (V.D.); (C.-H.L.); (A.B.)
| | - Hannah Coutts
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK; (Y.-T.L.); (L.-F.C.); (H.C.); (M.M.); (V.D.); (C.-H.L.); (A.B.)
| | - Matin Mahmoudi
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK; (Y.-T.L.); (L.-F.C.); (H.C.); (M.M.); (V.D.); (C.-H.L.); (A.B.)
| | - Vayalena Drampa
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK; (Y.-T.L.); (L.-F.C.); (H.C.); (M.M.); (V.D.); (C.-H.L.); (A.B.)
| | - Chen-Hsuin Lee
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK; (Y.-T.L.); (L.-F.C.); (H.C.); (M.M.); (V.D.); (C.-H.L.); (A.B.)
| | - Alex Brown
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK; (Y.-T.L.); (L.-F.C.); (H.C.); (M.M.); (V.D.); (C.-H.L.); (A.B.)
| | - David J. Hughes
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY16 9ST, UK;
| | - Finn Grey
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK; (Y.-T.L.); (L.-F.C.); (H.C.); (M.M.); (V.D.); (C.-H.L.); (A.B.)
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24
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Daron J, Bravo IG. Variability in Codon Usage in Coronaviruses Is Mainly Driven by Mutational Bias and Selective Constraints on CpG Dinucleotide. Viruses 2021; 13:v13091800. [PMID: 34578381 PMCID: PMC8473333 DOI: 10.3390/v13091800] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 12/18/2022] Open
Abstract
The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the third human-emerged virus of the 21st century from the Coronaviridae family, causing the ongoing coronavirus disease 2019 (COVID-19) pandemic. Due to the high zoonotic potential of coronaviruses, it is critical to unravel their evolutionary history of host species breadth, host-switch potential, adaptation and emergence, to identify viruses posing a pandemic risk in humans. We present here a comprehensive analysis of the composition and codon usage bias of the 82 Orthocoronavirinae members, infecting 47 different avian and mammalian hosts. Our results clearly establish that synonymous codon usage varies widely among viruses, is only weakly dependent on their primary host, and is dominated by mutational bias towards AU-enrichment and by CpG avoidance. Indeed, variation in GC3 explains around 34%, while variation in CpG frequency explains around 14% of total variation in codon usage bias. Further insight on the mutational equilibrium within Orthocoronavirinae revealed that most coronavirus genomes are close to their neutral equilibrium, the exception being the three recently infecting human coronaviruses, which lie further away from the mutational equilibrium than their endemic human coronavirus counterparts. Finally, our results suggest that, while replicating in humans, SARS-CoV-2 is slowly becoming AU-richer, likely until attaining a new mutational equilibrium.
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Affiliation(s)
- Josquin Daron
- Laboratoire MIVEGEC (CNRS, IRD, Université de Montpellier), 34394 Montpellier, France;
- Correspondence:
| | - Ignacio G. Bravo
- Laboratoire MIVEGEC (CNRS, IRD, Université de Montpellier), 34394 Montpellier, France;
- Center for Research on the Ecology and Evolution of Diseases (CREES), 34394 Montpellier, France
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25
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Shaw AE, Rihn SJ, Mollentze N, Wickenhagen A, Stewart DG, Orton RJ, Kuchi S, Bakshi S, Collados MR, Turnbull ML, Busby J, Gu Q, Smollett K, Bamford CGG, Sugrue E, Johnson PCD, Da Silva AF, Castello A, Streicker DG, Robertson DL, Palmarini M, Wilson SJ. The antiviral state has shaped the CpG composition of the vertebrate interferome to avoid self-targeting. PLoS Biol 2021; 19:e3001352. [PMID: 34491982 PMCID: PMC8423302 DOI: 10.1371/journal.pbio.3001352] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 07/07/2021] [Indexed: 12/24/2022] Open
Abstract
Antiviral defenses can sense viral RNAs and mediate their destruction. This presents a challenge for host cells since they must destroy viral RNAs while sparing the host mRNAs that encode antiviral effectors. Here, we show that highly upregulated interferon-stimulated genes (ISGs), which encode antiviral proteins, have distinctive nucleotide compositions. We propose that self-targeting by antiviral effectors has selected for ISG transcripts that occupy a less self-targeted sequence space. Following interferon (IFN) stimulation, the CpG-targeting antiviral effector zinc-finger antiviral protein (ZAP) reduces the mRNA abundance of multiple host transcripts, providing a mechanistic explanation for the repression of many (but not all) interferon-repressed genes (IRGs). Notably, IRGs tend to be relatively CpG rich. In contrast, highly upregulated ISGs tend to be strongly CpG suppressed. Thus, ZAP is an example of an effector that has not only selected compositional biases in viral genomes but also appears to have notably shaped the composition of host transcripts in the vertebrate interferome. Our cells are poised to combat viral infection through antiviral effectors. This study proposes that as well as targeting viral RNAs, antiviral effectors sometimes target host mRNAs too; over millions of years, this has selected for compositional biases in the host’s transcriptional response to virus infection.
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Affiliation(s)
- Andrew E. Shaw
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
- The Pirbright Institute, Woking, United Kingdom
| | - Suzannah J. Rihn
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Nardus Mollentze
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Arthur Wickenhagen
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Douglas G. Stewart
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Richard J. Orton
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Srikeerthana Kuchi
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Siddharth Bakshi
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | | | - Matthew L. Turnbull
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Joseph Busby
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Quan Gu
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Katherine Smollett
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Connor G. G. Bamford
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Elena Sugrue
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Paul C. D. Johnson
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Ana Filipe Da Silva
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Alfredo Castello
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Daniel G. Streicker
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - David L. Robertson
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Massimo Palmarini
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Sam J. Wilson
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
- * E-mail:
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26
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Jia F, Li L, Liu H, Lv P, Shi X, Wu Y, Ling C, Xu F. Development of a rabies virus-based retrograde tracer with high trans-monosynaptic efficiency by reshuffling glycoprotein. Mol Brain 2021; 14:109. [PMID: 34238335 PMCID: PMC8265122 DOI: 10.1186/s13041-021-00821-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 07/04/2021] [Indexed: 11/12/2022] Open
Abstract
Rabies virus (RV) is the most widely used vector for mapping neural circuits. Previous studies have shown that the RV glycoprotein can be a target to improve the retrograde transsynaptic tracing efficiency. However, the current versions still label only a small portion of all presynaptic neurons. Here, we reshuffled the oG sequence, a chimeric glycoprotein, with positive codon pair bias score (CPBS) based on bioinformatic analysis of mouse codon pair bias, generating ooG, a further optimized glycoprotein. Our experimental data reveal that the ooG has a higher expression level than the oG in vivo, which significantly increases the tracing efficiency by up to 12.6 and 62.1-fold compared to oG and B19G, respectively. The new tool can be used for labeling neural circuits Therefore, the approach reported here provides a convenient, efficient and universal strategy to improve protein expression for various application scenarios such as trans-synaptic tracing efficiency, cell engineering, and vaccine and oncolytic virus designs.
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Affiliation(s)
- Fan Jia
- Guangdong Provincial Key Laboratory of Brain Connectome and Behavior, CAS Key Laboratory of Brain Connectome and Manipulation, The Brain Cognition and Brain Disease Institute (BCBDI), Translational Research Center for the Nervous System (TRCNS), Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, 518055, China.
- NMPA Key Laboratory for Research and Evaluation of Viral Vector Technology in Cell and Gene Therapy Medicinal Products, Key Laboratory of Quality Control Technology for Virus-Based Therapeutics, Guangdong Provincial Medical Products Administration, Shenzhen Key Laboratory of Viral Vectors for Biomedicine, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Li Li
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems,, Wuhan Center for Magnetic Resonance, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Haizhou Liu
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Pei Lv
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems,, Wuhan Center for Magnetic Resonance, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Xiangwei Shi
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems,, Wuhan Center for Magnetic Resonance, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Wu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems,, Wuhan Center for Magnetic Resonance, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Chen Ling
- Division of Molecular and Cellular Therapy, Department of Pediatrics, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Fuqiang Xu
- Guangdong Provincial Key Laboratory of Brain Connectome and Behavior, CAS Key Laboratory of Brain Connectome and Manipulation, The Brain Cognition and Brain Disease Institute (BCBDI), Translational Research Center for the Nervous System (TRCNS), Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, 518055, China.
- NMPA Key Laboratory for Research and Evaluation of Viral Vector Technology in Cell and Gene Therapy Medicinal Products, Key Laboratory of Quality Control Technology for Virus-Based Therapeutics, Guangdong Provincial Medical Products Administration, Shenzhen Key Laboratory of Viral Vectors for Biomedicine, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems,, Wuhan Center for Magnetic Resonance, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China.
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China.
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
- Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China.
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27
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Pereira-Gómez M, Carrau L, Fajardo Á, Moreno P, Moratorio G. Altering Compositional Properties of Viral Genomes to Design Live-Attenuated Vaccines. Front Microbiol 2021; 12:676582. [PMID: 34276608 PMCID: PMC8278477 DOI: 10.3389/fmicb.2021.676582] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 06/01/2021] [Indexed: 12/11/2022] Open
Abstract
Live-attenuated vaccines have been historically used to successfully prevent numerous diseases caused by a broad variety of RNA viruses due to their ability to elicit strong and perdurable immune-protective responses. In recent years, various strategies have been explored to achieve viral attenuation by rational genetic design rather than using classic and empirical approaches, based on successive passages in cell culture. A deeper understanding of evolutionary implications of distinct viral genomic compositional aspects, as well as substantial advances in synthetic biology technologies, have provided a framework to achieve new viral attenuation strategies. Herein, we will discuss different approaches that are currently applied to modify compositional features of viruses in order to develop novel live-attenuated vaccines.
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Affiliation(s)
- Marianoel Pereira-Gómez
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Lucía Carrau
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Álvaro Fajardo
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Pilar Moreno
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Gonzalo Moratorio
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Montevideo, Uruguay
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28
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Ficarelli M, Neil SJD, Swanson CM. Targeted Restriction of Viral Gene Expression and Replication by the ZAP Antiviral System. Annu Rev Virol 2021; 8:265-283. [PMID: 34129371 DOI: 10.1146/annurev-virology-091919-104213] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The zinc finger antiviral protein (ZAP) restricts the replication of a broad range of RNA and DNA viruses. ZAP directly binds viral RNA, targeting it for degradation and inhibiting its translation. While the full scope of RNA determinants involved in mediating selective ZAP activity are unclear, ZAP binds CpG dinucleotides, dictating at least part of its target specificity. ZAP interacts with many cellular proteins, although only a few have been demonstrated to be essential for its antiviral activity, including the 3'-5' exoribonuclease exosome complex, TRIM25, and KHNYN. In addition to inhibiting viral gene expression, ZAP also directly and indirectly targets a subset of cellular messenger RNAs to regulate the innate immune response. Overall, ZAP protects a cell from viral infection by restricting viral replication and regulating cellular gene expression. Further understanding of the ZAP antiviral system may allow for novel viral vaccine and anticancer therapy development. Expected final online publication date for the Annual Review of Virology, Volume 8 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Mattia Ficarelli
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London SE1 9RT, United Kingdom;
| | - Stuart J D Neil
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London SE1 9RT, United Kingdom;
| | - Chad M Swanson
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London SE1 9RT, United Kingdom;
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29
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The Evolution of Severe Acute Respiratory Syndrome Coronavirus-2 during Pandemic and Adaptation to the Host. J Mol Evol 2021; 89:341-356. [PMID: 33993372 PMCID: PMC8123100 DOI: 10.1007/s00239-021-10008-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 03/25/2021] [Indexed: 12/02/2022]
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 is a zoonotic virus with a possible origin in bats and potential transmission to humans through an intermediate host. When zoonotic viruses jump to a new host, they undergo both mutational and natural selective pressures that result in non-synonymous and synonymous adaptive changes, necessary for efficient replication and rapid spread of diseases in new host species. The nucleotide composition and codon usage pattern of SARS-CoV-2 indicate the presence of a highly conserved, gene-specific codon usage bias. The codon usage pattern of SARS-CoV-2 is mostly antagonistic to human and bat codon usage. SARS-CoV-2 codon usage bias is mainly shaped by the natural selection, while mutational pressure plays a minor role. The time-series analysis of SARS-CoV-2 genome indicates that the virus is slowly evolving. Virus isolates from later stages of the outbreak have more biased codon usage and nucleotide composition than virus isolates from early stages of the outbreak.
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30
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Wang G, Zheng C. Zinc finger proteins in the host-virus interplay: multifaceted functions based on their nucleic acid-binding property. FEMS Microbiol Rev 2021; 45:fuaa059. [PMID: 33175962 DOI: 10.1093/femsre/fuaa059] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/07/2020] [Indexed: 12/14/2022] Open
Abstract
Zinc finger proteins (ZFPs) are a huge family comprised of massive, structurally diverse proteins characterized by zinc ion coordinating. They engage in the host-virus interplay in-depth and occupy a significant portion of the host antiviral arsenal. Nucleic acid-binding is the basic property of certain ZFPs, which draws increasing attention due to their immense influence on viral infections. ZFPs exert multiple roles on the viral replications and host cell transcription profiles by recognizing viral genomes and host mRNAs. Their roles could be either antiviral or proviral and were separately discussed. Our review covers the recent research progress and provides a comprehensive understanding of ZFPs in antiviral immunity based on their DNA/RNA binding property.
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Affiliation(s)
- Guanming Wang
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, No.1 Xue Yuan Road, University Town, FuZhou Fujian, 350108, China
| | - Chunfu Zheng
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, No.1 Xue Yuan Road, University Town, FuZhou Fujian, 350108, China
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Dr NW, Calgary, Alberta, Canada, AB T2N 4N1
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31
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Callens M, Pradier L, Finnegan M, Rose C, Bedhomme S. Read between the lines: Diversity of non-translational selection pressures on local codon usage. Genome Biol Evol 2021; 13:6263832. [PMID: 33944930 PMCID: PMC8410138 DOI: 10.1093/gbe/evab097] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2021] [Indexed: 12/14/2022] Open
Abstract
Protein coding genes can contain specific motifs within their nucleotide sequence that function as a signal for various biological pathways. The presence of such sequence motifs within a gene can have beneficial or detrimental effects on the phenotype and fitness of an organism, and this can lead to the enrichment or avoidance of this sequence motif. The degeneracy of the genetic code allows for the existence of alternative synonymous sequences that exclude or include these motifs, while keeping the encoded amino acid sequence intact. This implies that locally, there can be a selective pressure for preferentially using a codon over its synonymous alternative in order to avoid or enrich a specific sequence motif. This selective pressure could -in addition to mutation, drift and selection for translation efficiency and accuracy- contribute to shape the codon usage bias. In this review, we discuss patterns of avoidance of (or enrichment for) the various biological signals contained in specific nucleotide sequence motifs: transcription and translation initiation and termination signals, mRNA maturation signals, and antiviral immune system targets. Experimental data on the phenotypic or fitness effects of synonymous mutations in these sequence motifs confirm that they can be targets of local selection pressures on codon usage. We also formulate the hypothesis that transposable elements could have a similar impact on codon usage through their preferred integration sequences. Overall, selection on codon usage appears to be a combination of a global selection pressure imposed by the translation machinery, and a patchwork of local selection pressures related to biological signals contained in specific sequence motifs.
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Affiliation(s)
- Martijn Callens
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS, Université de Montpellier, Université Paul Valéry Montpellier 3, Ecole Pratique des Hautes Etudes, Institut de Recherche pour le Développement, 34000 Montpellier, France
| | - Léa Pradier
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS, Université de Montpellier, Université Paul Valéry Montpellier 3, Ecole Pratique des Hautes Etudes, Institut de Recherche pour le Développement, 34000 Montpellier, France
| | - Michael Finnegan
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS, Université de Montpellier, Université Paul Valéry Montpellier 3, Ecole Pratique des Hautes Etudes, Institut de Recherche pour le Développement, 34000 Montpellier, France
| | - Caroline Rose
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS, Université de Montpellier, Université Paul Valéry Montpellier 3, Ecole Pratique des Hautes Etudes, Institut de Recherche pour le Développement, 34000 Montpellier, France
| | - Stéphanie Bedhomme
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS, Université de Montpellier, Université Paul Valéry Montpellier 3, Ecole Pratique des Hautes Etudes, Institut de Recherche pour le Développement, 34000 Montpellier, France
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Fros JJ, Visser I, Tang B, Yan K, Nakayama E, Visser TM, Koenraadt CJM, van Oers MM, Pijlman GP, Suhrbier A, Simmonds P. The dinucleotide composition of the Zika virus genome is shaped by conflicting evolutionary pressures in mammalian hosts and mosquito vectors. PLoS Biol 2021; 19:e3001201. [PMID: 33872300 PMCID: PMC8084339 DOI: 10.1371/journal.pbio.3001201] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 04/29/2021] [Accepted: 03/23/2021] [Indexed: 12/29/2022] Open
Abstract
Most vertebrate RNA viruses show pervasive suppression of CpG and UpA dinucleotides, closely resembling the dinucleotide composition of host cell transcriptomes. In contrast, CpG suppression is absent in both invertebrate mRNA and RNA viruses that exclusively infect arthropods. Arthropod-borne (arbo) viruses are transmitted between vertebrate hosts by invertebrate vectors and thus encounter potentially conflicting evolutionary pressures in the different cytoplasmic environments. Using a newly developed Zika virus (ZIKV) model, we have investigated how demands for CpG suppression in vertebrate cells can be reconciled with potentially quite different compositional requirements in invertebrates and how this affects ZIKV replication and transmission. Mutant viruses with synonymously elevated CpG or UpA dinucleotide frequencies showed attenuated replication in vertebrate cell lines, which was rescued by knockout of the zinc-finger antiviral protein (ZAP). Conversely, in mosquito cells, ZIKV mutants with elevated CpG dinucleotide frequencies showed substantially enhanced replication compared to wild type. Host-driven effects on virus replication attenuation and enhancement were even more apparent in mouse and mosquito models. Infections with CpG- or UpA-high ZIKV mutants in mice did not cause typical ZIKV-induced tissue damage and completely protected mice during subsequent challenge with wild-type virus, which demonstrates their potential as live-attenuated vaccines. In contrast, the CpG-high mutants displayed enhanced replication in Aedes aegypti mosquitoes and a larger proportion of mosquitoes carried infectious virus in their saliva. These findings show that mosquito cells are also capable of discriminating RNA based on dinucleotide composition. However, the evolutionary pressure on the CpG dinucleotides of viral genomes in arthropod vectors directly opposes the pressure present in vertebrate host cells, which provides evidence that an adaptive compromise is required for arbovirus transmission. This suggests that the genome composition of arbo flaviviruses is crucial to maintain the balance between high-level replication in the vertebrate host and persistent replication in the mosquito vector. The genome of the flavivirus Zika virus is stuck in a tug-of-war between two directly opposing evolutionary pressures that are present in the cells of mammalian host organisms and mosquito vectors; this results in an adaptive compromise, as manifested in the virus’s genome dinucleotide composition.
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Affiliation(s)
- Jelke J. Fros
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
- Laboratory of Virology, Wageningen University and Research, Wageningen, the Netherlands
- * E-mail:
| | - Imke Visser
- Laboratory of Virology, Wageningen University and Research, Wageningen, the Netherlands
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Bing Tang
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Kexin Yan
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Eri Nakayama
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Department of Virology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tessa M. Visser
- Laboratory of Entomology, Wageningen University and Research, Wageningen, the Netherlands
| | | | - Monique M. van Oers
- Laboratory of Virology, Wageningen University and Research, Wageningen, the Netherlands
| | - Gorben P. Pijlman
- Laboratory of Virology, Wageningen University and Research, Wageningen, the Netherlands
| | - Andreas Suhrbier
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Peter Simmonds
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
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Insect-Specific Flavivirus Replication in Mammalian Cells Is Inhibited by Physiological Temperature and the Zinc-Finger Antiviral Protein. Viruses 2021; 13:v13040573. [PMID: 33805437 PMCID: PMC8066048 DOI: 10.3390/v13040573] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/23/2021] [Accepted: 03/25/2021] [Indexed: 12/16/2022] Open
Abstract
The genus Flavivirus contains pathogenic vertebrate-infecting flaviviruses (VIFs) and insect-specific flaviviruses (ISF). ISF transmission to vertebrates is inhibited at multiple stages of the cellular infection cycle, via yet to be elucidated specific antiviral responses. The zinc-finger antiviral protein (ZAP) in vertebrate cells can bind CpG dinucleotides in viral RNA, limiting virus replication. Interestingly, the genomes of ISFs contain more CpG dinucleotides compared to VIFs. In this study, we investigated whether ZAP prevents two recently discovered lineage II ISFs, Binjari (BinJV) and Hidden Valley viruses (HVV) from replicating in vertebrate cells. BinJV protein and dsRNA replication intermediates were readily observed in human ZAP knockout cells when cultured at 34 °C. In ZAP-expressing cells, inhibition of the interferon response via interferon response factors 3/7 did not improve BinJV protein expression, whereas treatment with kinase inhibitor C16, known to reduce ZAP’s antiviral function, did. Importantly, at 34 °C, both BinJV and HVV successfully completed the infection cycle in human ZAP knockout cells evident from infectious progeny virus in the cell culture supernatant. Therefore, we identify vertebrate ZAP as an important barrier that protects vertebrate cells from ISF infection. This provides new insights into flavivirus evolution and the mechanisms associated with host switching.
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Jordan-Paiz A, Franco S, Martínez MA. Impact of Synonymous Genome Recoding on the HIV Life Cycle. Front Microbiol 2021; 12:606087. [PMID: 33796084 PMCID: PMC8007914 DOI: 10.3389/fmicb.2021.606087] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 02/25/2021] [Indexed: 12/19/2022] Open
Abstract
Synonymous mutations within protein coding regions introduce changes in DNA or messenger (m) RNA, without mutating the encoded proteins. Synonymous recoding of virus genomes has facilitated the identification of previously unknown virus biological features. Moreover, large-scale synonymous recoding of the genome of human immunodeficiency virus type 1 (HIV-1) has elucidated new antiviral mechanisms within the innate immune response, and has improved our knowledge of new functional virus genome structures, the relevance of codon usage for the temporal regulation of viral gene expression, and HIV-1 mutational robustness and adaptability. Continuous improvements in our understanding of the impacts of synonymous substitutions on virus phenotype - coupled with the decreased cost of chemically synthesizing DNA and improved methods for assembling DNA fragments - have enhanced our ability to identify potential HIV-1 and host factors and other aspects involved in the infection process. In this review, we address how silent mutagenesis impacts HIV-1 phenotype and replication capacity. We also discuss the general potential of synonymous recoding of the HIV-1 genome to elucidate unknown aspects of the virus life cycle, and to identify new therapeutic targets.
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Affiliation(s)
- Ana Jordan-Paiz
- IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona (UAB), Badalona, Spain
| | - Sandra Franco
- IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona (UAB), Badalona, Spain
| | - Miguel Angel Martínez
- IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona (UAB), Badalona, Spain
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Comparative Genomics and Integrated Network Approach Unveiled Undirected Phylogeny Patterns, Co-mutational Hot Spots, Functional Cross Talk, and Regulatory Interactions in SARS-CoV-2. mSystems 2021; 6:6/1/e00030-21. [PMID: 33622851 PMCID: PMC8573956 DOI: 10.1128/msystems.00030-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has resulted in 92 million cases in a span of 1 year. The study focuses on understanding population-specific variations attributing its high rate of infections in specific geographical regions particularly in the United States. Rigorous phylogenomic network analysis of complete SARS-CoV-2 genomes (245) inferred five central clades named a (ancestral), b, c, d, and e (subtypes e1 and e2). Clade d and subclade e2 were found exclusively comprised of U.S. strains. Clades were distinguished by 10 co-mutational combinations in Nsp3, ORF8, Nsp13, S, Nsp12, Nsp2, and Nsp6. Our analysis revealed that only 67.46% of single nucleotide polymorphism (SNP) mutations were at the amino acid level. T1103P mutation in Nsp3 was predicted to increase protein stability in 238 strains except for 6 strains which were marked as ancestral type, whereas co-mutation (P409L and Y446C) in Nsp13 were found in 64 genomes from the United States highlighting its 100% co-occurrence. Docking highlighted mutation (D614G) caused reduction in binding of spike proteins with angiotensin-converting enzyme 2 (ACE2), but it also showed better interaction with the TMPRSS2 receptor contributing to high transmissibility among U.S. strains. We also found host proteins, MYO5A, MYO5B, and MYO5C, that had maximum interaction with viral proteins (nucleocapsid [N], spike [S], and membrane [M] proteins). Thus, blocking the internalization pathway by inhibiting MYO5 proteins which could be an effective target for coronavirus disease 2019 (COVID-19) treatment. The functional annotations of the host-pathogen interaction (HPI) network were found to be closely associated with hypoxia and thrombotic conditions, confirming the vulnerability and severity of infection. We also screened CpG islands in Nsp1 and N conferring the ability of SARS-CoV-2 to enter and trigger zinc antiviral protein (ZAP) activity inside the host cell. IMPORTANCE In the current study, we presented a global view of mutational pattern observed in SARS-CoV-2 virus transmission. This provided a who-infect-whom geographical model since the early pandemic. This is hitherto the most comprehensive comparative genomics analysis of full-length genomes for co-mutations at different geographical regions especially in U.S. strains. Compositional structural biology results suggested that mutations have a balance of opposing forces affecting pathogenicity suggesting that only a few mutations are effective at the translation level. Novel HPI analysis and CpG predictions elucidate the proof of concept of hypoxia and thrombotic conditions in several patients. Thus, the current study focuses the understanding of population-specific variations attributing a high rate of SARS-CoV-2 infections in specific geographical regions which may eventually be vital for the most severely affected countries and regions for sharp development of custom-made vindication strategies.
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Intrinsic Immune Mechanisms Restricting Human Cytomegalovirus Replication. Viruses 2021; 13:v13020179. [PMID: 33530304 PMCID: PMC7911179 DOI: 10.3390/v13020179] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 12/14/2022] Open
Abstract
Cellular restriction factors (RFs) act as important constitutive innate immune barriers against viruses. In 2006, the promyelocytic leukemia protein was described as the first RF against human cytomegalovirus (HCMV) infection which is antagonized by the viral immediate early protein IE1. Since then, at least 15 additional RFs against HCMV have been identified, including the chromatin regulatory protein SPOC1, the cytidine deaminase APOBEC3A and the dNTP triphosphohydrolase SAMHD1. These RFs affect distinct steps of the viral replication cycle such as viral entry, gene expression, the synthesis of progeny DNA or egress. This review summarizes our current knowledge on intrinsic immune mechanisms restricting HCMV replication as well as on the viral strategies to counteract the inhibitory effects of RFs. Detailed knowledge on the interplay between host RFs and antagonizing viral factors will be fundamental to develop new approaches to combat HCMV infection.
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Abstract
The development of safe and effective vaccines against viruses is central to disease control. With advancements in DNA synthesis technology, the production of synthetic viral genomes has fueled many research efforts that aim to generate attenuated viruses by introducing synonymous mutations. Elucidation of the mechanisms underlying virus attenuation through synonymous mutagenesis is revealing interesting new biology that can be exploited for vaccine development. Here, we review recent advancements in this field of synthetic virology and focus on the molecular mechanisms of attenuation by genetic recoding of viruses. We highlight the action of the zinc finger antiviral protein (ZAP) and RNase L, two proteins involved in the inhibition of viruses enriched for CpG and UpA dinucleotides, that are often the products of virus recoding algorithms. Additionally, we discuss current challenges in the field as well as studies that may illuminate how other host functions, such as translation, are potentially involved in the attenuation of recoded viruses.
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Rice AM, Castillo Morales A, Ho AT, Mordstein C, Mühlhausen S, Watson S, Cano L, Young B, Kudla G, Hurst LD. Evidence for Strong Mutation Bias toward, and Selection against, U Content in SARS-CoV-2: Implications for Vaccine Design. Mol Biol Evol 2021; 38:67-83. [PMID: 32687176 PMCID: PMC7454790 DOI: 10.1093/molbev/msaa188] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Large-scale re-engineering of synonymous sites is a promising strategy to generate vaccines either through synthesis of attenuated viruses or via codon-optimized genes in DNA vaccines. Attenuation typically relies on deoptimization of codon pairs and maximization of CpG dinucleotide frequencies. So as to formulate evolutionarily informed attenuation strategies that aim to force nucleotide usage against the direction favored by selection, here, we examine available whole-genome sequences of SARS-CoV-2 to infer patterns of mutation and selection on synonymous sites. Analysis of mutational profiles indicates a strong mutation bias toward U. In turn, analysis of observed synonymous site composition implicates selection against U. Accounting for dinucleotide effects reinforces this conclusion, observed UU content being a quarter of that expected under neutrality. Possible mechanisms of selection against U mutations include selection for higher expression, for high mRNA stability or lower immunogenicity of viral genes. Consistent with gene-specific selection against CpG dinucleotides, we observe systematic differences of CpG content between SARS-CoV-2 genes. We propose an evolutionarily informed approach to attenuation that, unusually, seeks to increase usage of the already most common synonymous codons. Comparable analysis of H1N1 and Ebola finds that GC3 deviated from neutral equilibrium is not a universal feature, cautioning against generalization of results.
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Affiliation(s)
- Alan M Rice
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Atahualpa Castillo Morales
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Alexander T Ho
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Christine Mordstein
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
- MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Stefanie Mühlhausen
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Samir Watson
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Laura Cano
- MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Bethan Young
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
- MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Grzegorz Kudla
- MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Laurence D Hurst
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
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Loew L, Goonawardane N, Ratcliff J, Nguyen D, Simmonds P. Use of a small DNA virus model to investigate mechanisms of CpG dinucleotide-induced attenuation of virus replication. J Gen Virol 2020; 101:1202-1218. [PMID: 32783803 PMCID: PMC7879557 DOI: 10.1099/jgv.0.001477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 07/10/2020] [Indexed: 01/19/2023] Open
Abstract
Suppression of the CpG dinucleotide is widespread in RNA viruses infecting vertebrates and plants, and in the genomes of retroviruses and small mammalian DNA viruses. The functional basis for CpG suppression in the latter was investigated through the construction of mutants of the parvovirus, minute virus of mice (MVM) with increased CpG or TpA dinucleotides in the VP gene. CpG-high mutants displayed extraordinary attenuation in A9 cells compared to wild-type MVM (>six logs), while TpA elevation showed no replication effect. Attenuation was independent of Toll-like receptor 9 and STING-mediated DNA recognition pathways and unrelated to effects on translation efficiency. While translation from codon-optimized VP RNA was enhanced in a cell-free assay, MVM containing this sequence was highly attenuated. Further mutational analysis indicated that this arose through its increased numbers of CpG dinucleotides (7→70) and separately from its increased G+C content (42.3→57.4 %), which independently attenuated replication. CpG-high viruses showed impaired NS mRNA expression by qPCR and reduced NS and particularly VP protein expression detected by immunofluorescence and replication in A549 cells, effects reversed in zinc antiviral protein (ZAP) knockout cells, even though nuclear relocalization of VP remained defective. The demonstrated functional basis for CpG suppression in MVM and potentially other small DNA viruses and the observed intolerance of CpGs in coding sequences, even after codon optimization, has implications for the use of small DNA virus vectors in gene therapy and immunization.
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Affiliation(s)
- Lisa Loew
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK
- Present address: Clinical Biomanufacturing Facility, University of Oxford, Old Road, Headington, Oxford OX3 7BN, UK
| | - Niluka Goonawardane
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK
| | - Jeremy Ratcliff
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK
| | - Dung Nguyen
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK
| | - Peter Simmonds
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK
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Van Leuven JT, Ederer MM, Burleigh K, Scott L, Hughes RA, Codrea V, Ellington AD, Wichman HA, Miller CR. ΦX174 Attenuation by Whole-Genome Codon Deoptimization. Genome Biol Evol 2020; 13:5921183. [PMID: 33045052 PMCID: PMC7881332 DOI: 10.1093/gbe/evaa214] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2020] [Indexed: 12/11/2022] Open
Abstract
Natural selection acting on synonymous mutations in protein-coding genes influences genome composition and evolution. In viruses, introducing synonymous mutations in genes encoding structural proteins can drastically reduce viral growth, providing a means to generate potent, live-attenuated vaccine candidates. However, an improved understanding of what compositional features are under selection and how combinations of synonymous mutations affect viral growth is needed to predictably attenuate viruses and make them resistant to reversion. We systematically recoded all nonoverlapping genes of the bacteriophage ΦX174 with codons rarely used in its Escherichia coli host. The fitness of recombinant viruses decreases as additional deoptimizing mutations are made to the genome, although not always linearly, and not consistently across genes. Combining deoptimizing mutations may reduce viral fitness more or less than expected from the effect size of the constituent mutations and we point out difficulties in untangling correlated compositional features. We test our model by optimizing the same genes and find that the relationship between codon usage and fitness does not hold for optimization, suggesting that wild-type ΦX174 is at a fitness optimum. This work highlights the need to better understand how selection acts on patterns of synonymous codon usage across the genome and provides a convenient system to investigate the genetic determinants of virulence.
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Affiliation(s)
- James T Van Leuven
- Department of Biological Science, University of Idaho.,Institute for Modeling Collaboration and Innovation, University of Idaho
| | | | - Katelyn Burleigh
- Department of Biological Science, University of Idaho.,Present address: Seattle Children's Research Institute, Seattle, WA
| | - LuAnn Scott
- Department of Biological Science, University of Idaho
| | - Randall A Hughes
- Applied Research Laboratories, University of Texas, Austin.,Present address: Biotechnology Branch, CCDC US Army Research Laboratory, Adelphi, MD
| | - Vlad Codrea
- Institute for Cellular and Molecular Biology, University of Texas, Austin
| | - Andrew D Ellington
- Applied Research Laboratories, University of Texas, Austin.,Institute for Cellular and Molecular Biology, University of Texas, Austin
| | - Holly A Wichman
- Department of Biological Science, University of Idaho.,Institute for Modeling Collaboration and Innovation, University of Idaho
| | - Craig R Miller
- Department of Biological Science, University of Idaho.,Institute for Modeling Collaboration and Innovation, University of Idaho
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41
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Lin YT, Chiweshe S, McCormick D, Raper A, Wickenhagen A, DeFillipis V, Gaunt E, Simmonds P, Wilson SJ, Grey F. Human cytomegalovirus evades ZAP detection by suppressing CpG dinucleotides in the major immediate early 1 gene. PLoS Pathog 2020; 16:e1008844. [PMID: 32886716 PMCID: PMC7498042 DOI: 10.1371/journal.ppat.1008844] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 09/17/2020] [Accepted: 07/28/2020] [Indexed: 12/12/2022] Open
Abstract
The genomes of RNA and small DNA viruses of vertebrates display significant suppression of CpG dinucleotide frequencies. Artificially increasing dinucleotide frequencies results in substantial attenuation of virus replication, suggesting that these compositional changes may facilitate recognition of non-self RNA sequences. Recently, the interferon inducible protein ZAP, was identified as the host factor responsible for sensing CpG in viral RNA, through direct binding and possibly downstream targeting for degradation. Using an arrayed interferon stimulated gene expression library screen, we identified ZAPS, and its associated factor TRIM25, as inhibitors of human cytomegalovirus (HCMV) replication. Exogenous expression of ZAPS and TRIM25 significantly reduced virus replication while knockdown resulted in increased virus replication. HCMV displays a strikingly heterogeneous pattern of CpG representation with specific suppression of CpG motifs within the IE1 major immediate early transcript which is absent in subsequently expressed genes. We demonstrated that suppression of CpG dinucleotides in the IE1 gene allows evasion of inhibitory effects of ZAP. We show that acute virus replication is mutually exclusive with high levels of cellular ZAP, potentially explaining the higher levels of CpG in viral genes expressed subsequent to IE1 due to the loss of pressure from ZAP in infected cells. Finally, we show that TRIM25 regulates alternative splicing between the ZAP short and long isoforms during HCMV infection and interferon induction, with knockdown of TRIM25 resulting in decreased ZAPS and corresponding increased ZAPL expression. These results demonstrate for the first time that ZAP is a potent host restriction factor against large DNA viruses and that HCMV evades ZAP detection through suppression of CpG dinucleotides within the major immediate early 1 transcript. Furthermore, TRIM25 is required for efficient upregulation of the interferon inducible short isoform of ZAP through regulation of alternative splicing.
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Affiliation(s)
- Yao-Tang Lin
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Stephen Chiweshe
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Dominique McCormick
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Anna Raper
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Arthur Wickenhagen
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Victor DeFillipis
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Eleanor Gaunt
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Peter Simmonds
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Sam J. Wilson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Finn Grey
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
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42
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Digard P, Lee HM, Sharp C, Grey F, Gaunt E. Intra-genome variability in the dinucleotide composition of SARS-CoV-2. Virus Evol 2020; 6:veaa057. [PMID: 33029383 PMCID: PMC7454914 DOI: 10.1093/ve/veaa057] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
CpG dinucleotides are under-represented in the genomes of single-stranded RNA viruses, and SARS-CoV-2 is no exception to this. Artificial modification of CpG frequency is a valid approach for live attenuated vaccine development; if this is to be applied to SARS-CoV-2, we must first understand the role CpG motifs play in regulating SARS-CoV-2 replication. Accordingly, the CpG composition of the SARS-CoV-2 genome was characterised. CpG suppression among coronaviruses does not differ between virus genera but does vary with host species and primary replication site (a proxy for tissue tropism), supporting the hypothesis that viral CpG content may influence cross-species transmission. Although SARS-CoV-2 exhibits overall strong CpG suppression, this varies considerably across the genome, and the Envelope (E) open reading frame (ORF) and ORF10 demonstrate an absence of CpG suppression. Across the Coronaviridae, E genes display remarkably high variation in CpG composition, with those of SARS and SARS-CoV-2 having much higher CpG content than other coronaviruses isolated from humans. This is an ancestrally derived trait reflecting their bat origins. Conservation of CpG motifs in these regions suggests that they have a functionality which over-rides the need to suppress CpG; an observation relevant to future strategies towards a rationally attenuated SARS-CoV-2 vaccine.
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Affiliation(s)
- Paul Digard
- Department of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Hui Min Lee
- Department of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Colin Sharp
- Department of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Finn Grey
- Department of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Eleanor Gaunt
- Department of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
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Trus I, Berube N, Jiang P, Rak J, Gerdts V, Karniychuk U. Zika Virus with Increased CpG Dinucleotide Frequencies Shows Oncolytic Activity in Glioblastoma Stem Cells. Viruses 2020; 12:v12050579. [PMID: 32466170 PMCID: PMC7290362 DOI: 10.3390/v12050579] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/14/2020] [Accepted: 05/15/2020] [Indexed: 12/31/2022] Open
Abstract
We studied whether cytosine phosphate–guanine (CpG) recoding in a viral genome may provide oncolytic candidates with reduced infection kinetics in nonmalignant brain cells, but with high virulence in glioblastoma stem cells (GSCs). As a model, we used well-characterized CpG-recoded Zika virus vaccine candidates that previously showed genetic stability and safety in animal models. In vitro, one of the CpG-recoded Zika virus variants had reduced infection kinetics in nonmalignant brain cells but high infectivity and oncolytic activity in GSCs as represented by reduced cell proliferation. The recoded virus also efficiently replicated in GSC-derived tumors in ovo with a significant reduction of tumor growth. We also showed that some GSCs may be resistant to Zika virus oncolytic activity, emphasizing the need for personalized oncolytic therapy or a strategy to overcome resistance in GSCs. Collectively, we demonstrated the potential of the CpG recoding approach for oncolytic virus development that encourages further research towards a better understanding of host–tumor–CpG-recoded virus interactions.
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Affiliation(s)
- Ivan Trus
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; (I.T.); (N.B.); (V.G.)
| | - Nathalie Berube
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; (I.T.); (N.B.); (V.G.)
| | - Peng Jiang
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854-8082, USA;
| | - Janusz Rak
- The Research Institute of the McGill University Health Centre, Montreal, QC H3H 2R9, Canada;
| | - Volker Gerdts
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; (I.T.); (N.B.); (V.G.)
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Uladzimir Karniychuk
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; (I.T.); (N.B.); (V.G.)
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
- School of Public Health, University of Saskatchewan, Saskatoon, SK S7N 2Z4, Canada
- Correspondence:
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44
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Martínez MA, Jordan-Paiz A, Franco S, Nevot M. Synonymous genome recoding: a tool to explore microbial biology and new therapeutic strategies. Nucleic Acids Res 2020; 47:10506-10519. [PMID: 31584076 PMCID: PMC6846928 DOI: 10.1093/nar/gkz831] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/12/2019] [Accepted: 09/30/2019] [Indexed: 12/18/2022] Open
Abstract
Synthetic genome recoding is a new means of generating designed organisms with altered phenotypes. Synonymous mutations introduced into the protein coding region tolerate modifications in DNA or mRNA without modifying the encoded proteins. Synonymous genome-wide recoding has allowed the synthetic generation of different small-genome viruses with modified phenotypes and biological properties. Recently, a decreased cost of chemically synthesizing DNA and improved methods for assembling DNA fragments (e.g. lambda red recombination and CRISPR-based editing) have enabled the construction of an Escherichia coli variant with a 4-Mb synthetic synonymously recoded genome with a reduced number of sense codons (n = 59) encoding the 20 canonical amino acids. Synonymous genome recoding is increasing our knowledge of microbial interactions with innate immune responses, identifying functional genome structures, and strategically ameliorating cis-inhibitory signaling sequences related to splicing, replication (in eukaryotes), and complex microbe functions, unraveling the relevance of codon usage for the temporal regulation of gene expression and the microbe mutant spectrum and adaptability. New biotechnological and therapeutic applications of this methodology can easily be envisaged. In this review, we discuss how synonymous genome recoding may impact our knowledge of microbial biology and the development of new and better therapeutic methodologies.
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Affiliation(s)
- Miguel Angel Martínez
- IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona (UAB), Badalona, Spain
| | - Ana Jordan-Paiz
- IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona (UAB), Badalona, Spain
| | - Sandra Franco
- IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona (UAB), Badalona, Spain
| | - Maria Nevot
- IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona (UAB), Badalona, Spain
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45
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Nchioua R, Bosso M, Kmiec D, Kirchhoff F. Cellular Factors Targeting HIV-1 Transcription and Viral RNA Transcripts. Viruses 2020; 12:v12050495. [PMID: 32365692 PMCID: PMC7290996 DOI: 10.3390/v12050495] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/24/2020] [Accepted: 04/27/2020] [Indexed: 02/06/2023] Open
Abstract
Restriction factors are structurally and functionally diverse cellular proteins that constitute a first line of defense against viral pathogens. Exceptions exist, but typically these proteins are upregulated by interferons (IFNs), target viral components, and are rapidly evolving due to the continuous virus–host arms race. Restriction factors may target HIV replication at essentially each step of the retroviral replication cycle, and the suppression of viral transcription and the degradation of viral RNA transcripts are emerging as major innate immune defense mechanisms. Recent data show that some antiviral factors, such as the tripartite motif-containing protein 22 (TRIM22) and the γ-IFN-inducible protein 16 (IFI16), do not target HIV-1 itself but limit the availability of the cellular transcription factor specificity protein 1 (Sp1), which is critical for effective viral gene expression. In addition, several RNA-interacting cellular factors including RNAse L, the NEDD4-binding protein 1 (N4BP1), and the zinc finger antiviral protein (ZAP) have been identified as important immune effectors against HIV-1 that may be involved in the maintenance of the latent viral reservoirs, representing the major obstacle against viral elimination and cure. Here, we review recent findings on specific cellular antiviral factors targeting HIV-1 transcription or viral RNA transcripts and discuss their potential role in viral latency.
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Affiliation(s)
- Rayhane Nchioua
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany; (R.N.); (M.B.)
| | - Matteo Bosso
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany; (R.N.); (M.B.)
| | - Dorota Kmiec
- Department of Infectious Diseases, King’s College London, Guy’s Hospital, London SE1 9RT, UK;
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany; (R.N.); (M.B.)
- Correspondence: ; Tel.: +49-731-5006-5150
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46
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Lytras S, Hughes J. Synonymous Dinucleotide Usage: A Codon-Aware Metric for Quantifying Dinucleotide Representation in Viruses. Viruses 2020; 12:E462. [PMID: 32325924 PMCID: PMC7232450 DOI: 10.3390/v12040462] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/30/2020] [Accepted: 04/17/2020] [Indexed: 12/29/2022] Open
Abstract
Distinct patterns of dinucleotide representation, such as CpG and UpA suppression, are characteristic of certain viral genomes. Recent research has uncovered vertebrate immune mechanisms that select against specific dinucleotides in targeted viruses. This evidence highlights the importance of systematically examining the dinucleotide composition of viral genomes. We have developed a novel metric, called synonymous dinucleotide usage (SDU), for quantifying dinucleotide representation in coding sequences. Our method compares the abundance of a given dinucleotide to the null hypothesis of equal synonymous codon usage in the sequence. We present a Python3 package, DinuQ, for calculating SDU and other relevant metrics. We have applied this method on two sets of invertebrate- and vertebrate-specific flaviviruses and rhabdoviruses. The SDU shows that the vertebrate viruses exhibit consistently greater under-representation of CpG dinucleotides in all three codon positions in both datasets. In comparison to existing metrics for dinucleotide quantification, the SDU allows for a statistical interpretation of its values by comparing it to a null expectation based on the codon table. Here we apply the method to viruses, but coding sequences of other living organisms can be analysed in the same way.
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Affiliation(s)
- Spyros Lytras
- MRC—University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
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47
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Groenke N, Trimpert J, Merz S, Conradie AM, Wyler E, Zhang H, Hazapis OG, Rausch S, Landthaler M, Osterrieder N, Kunec D. Mechanism of Virus Attenuation by Codon Pair Deoptimization. Cell Rep 2020; 31:107586. [DOI: 10.1016/j.celrep.2020.107586] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 03/06/2020] [Accepted: 04/08/2020] [Indexed: 12/17/2022] Open
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Ficarelli M, Antzin-Anduetza I, Hugh-White R, Firth AE, Sertkaya H, Wilson H, Neil SJD, Schulz R, Swanson CM. CpG Dinucleotides Inhibit HIV-1 Replication through Zinc Finger Antiviral Protein (ZAP)-Dependent and -Independent Mechanisms. J Virol 2020; 94:e01337-19. [PMID: 31748389 PMCID: PMC7158733 DOI: 10.1128/jvi.01337-19] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 11/06/2019] [Indexed: 02/07/2023] Open
Abstract
CpG dinucleotides are suppressed in the genomes of many vertebrate RNA viruses, including HIV-1. The cellular antiviral protein ZAP (zinc finger antiviral protein) binds CpGs and inhibits HIV-1 replication when CpGs are introduced into the viral genome. However, it is not known if ZAP-mediated restriction is the only mechanism driving CpG suppression. To determine how CpG dinucleotides affect HIV-1 replication, we increased their abundance in multiple regions of the viral genome and analyzed the effect on RNA expression, protein abundance, and infectious-virus production. We found that the antiviral effect of CpGs was not correlated with their abundance. Interestingly, CpGs inserted into some regions of the genome sensitize the virus to ZAP antiviral activity more efficiently than insertions into other regions, and this sensitivity can be modulated by interferon treatment or ZAP overexpression. Furthermore, the sensitivity of the virus to endogenous ZAP was correlated with its sensitivity to the ZAP cofactor KHNYN. Finally, we show that CpGs in some contexts can also inhibit HIV-1 replication by ZAP-independent mechanisms, and one of these is the activation of a cryptic splice site at the expense of a canonical splice site. Overall, we show that the location and sequence context of the CpG in the viral genome determines its antiviral activity.IMPORTANCE Some RNA virus genomes are suppressed in the nucleotide combination of a cytosine followed by a guanosine (CpG), indicating that they are detrimental to the virus. The antiviral protein ZAP binds viral RNA containing CpGs and prevents the virus from multiplying. However, it remains unknown how the number and position of CpGs in viral genomes affect restriction by ZAP and whether CpGs have other antiviral mechanisms. Importantly, manipulating the CpG content in viral genomes could help create new vaccines. HIV-1 shows marked CpG suppression, and by introducing CpGs into its genome, we show that ZAP efficiently targets a specific region of the viral genome, that the number of CpGs does not predict the magnitude of antiviral activity, and that CpGs can inhibit HIV-1 gene expression through a ZAP-independent mechanism. Overall, the position of CpGs in the HIV-1 genome determines the magnitude and mechanism through which they inhibit the virus.
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Affiliation(s)
- Mattia Ficarelli
- Department of Infectious Diseases, King's College London, London, United Kingdom
| | | | - Rupert Hugh-White
- Department of Medical and Molecular Genetics, King's College London, London, United Kingdom
| | - Andrew E Firth
- Division of Virology, University of Cambridge, Cambridge, United Kingdom
| | - Helin Sertkaya
- Department of Infectious Diseases, King's College London, London, United Kingdom
| | - Harry Wilson
- Department of Infectious Diseases, King's College London, London, United Kingdom
| | - Stuart J D Neil
- Department of Infectious Diseases, King's College London, London, United Kingdom
| | - Reiner Schulz
- Department of Medical and Molecular Genetics, King's College London, London, United Kingdom
| | - Chad M Swanson
- Department of Infectious Diseases, King's College London, London, United Kingdom
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49
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Trus I, Udenze D, Berube N, Wheler C, Martel MJ, Gerdts V, Karniychuk U. CpG-Recoding in Zika Virus Genome Causes Host-Age-Dependent Attenuation of Infection With Protection Against Lethal Heterologous Challenge in Mice. Front Immunol 2020; 10:3077. [PMID: 32038625 PMCID: PMC6993062 DOI: 10.3389/fimmu.2019.03077] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 12/17/2019] [Indexed: 12/12/2022] Open
Abstract
Experimental increase of CpG dinucleotides in an RNA virus genome impairs infection providing a promising approach for vaccine development. While CpG recoding is an emerging and promising vaccine approach, little is known about infection phenotypes caused by recoded viruses in vivo. For example, infection phenotypes, immunogenicity, and protective efficacy induced by CpG-recoded viruses in different age groups were not studied yet. This is important, because attenuation of infection phenotypes caused by recoded viruses may depend on the population-based expression of cellular components targeting viral CpG dinucleotides. In the present study, we generated several Zika virus (ZIKV) variants with the increasing CpG content and compared infection in neonatal and adult mice. Increasing the CpG content caused host-age-dependent attenuation of infection with considerable attenuation in neonates and high attenuation in adults. Expression of the zinc-finger antiviral protein (ZAP)—the host protein targeting viral CpG dinucleotides—was also age-dependent. Similar to the wild-type virus, ZIKV variants with the increased CpG content evoked robust cellular and humoral immune responses and protection against lethal challenge. Collectively, the host age should be accounted for in future studies on mechanisms targeting viral CpG dinucleotides, development of safe dinucleotide recoding strategies, and applications of CpG-recoded vaccines.
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Affiliation(s)
- Ivan Trus
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK, Canada
| | - Daniel Udenze
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK, Canada.,School of Public Health, University of Saskatchewan, Saskatoon, SK, Canada
| | - Nathalie Berube
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK, Canada
| | - Colette Wheler
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK, Canada
| | - Marie-Jocelyne Martel
- Department of Obstetrics and Gynecology, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Volker Gerdts
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK, Canada.,Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Uladzimir Karniychuk
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK, Canada.,School of Public Health, University of Saskatchewan, Saskatoon, SK, Canada.,Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
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50
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Kmiec D, Nchioua R, Sherrill-Mix S, Stürzel CM, Heusinger E, Braun E, Gondim MVP, Hotter D, Sparrer KMJ, Hahn BH, Sauter D, Kirchhoff F. CpG Frequency in the 5' Third of the env Gene Determines Sensitivity of Primary HIV-1 Strains to the Zinc-Finger Antiviral Protein. mBio 2020; 11:e02903-19. [PMID: 31937644 PMCID: PMC6960287 DOI: 10.1128/mbio.02903-19] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 11/27/2019] [Indexed: 02/07/2023] Open
Abstract
CpG dinucleotide suppression has been reported to allow HIV-1 to evade inhibition by the zinc-finger antiviral protein (ZAP). Here, we show that primate lentiviruses display marked differences in CpG frequencies across their genome, ranging from 0.44% in simian immunodeficiency virus SIVwrc from Western red colobus to 2.3% in SIVmon infecting mona monkeys. Moreover, functional analyses of a large panel of human and simian immunodeficiency viruses revealed that the magnitude of CpG suppression does not correlate with their susceptibility to ZAP. However, we found that the number of CpG dinucleotides within a region of ∼700 bases at the 5' end of the env gene determines ZAP sensitivity of primary HIV-1 strains but not of HIV-2. Increased numbers of CpGs in this region were associated with reduced env mRNA expression and viral protein production. ZAP sensitivity profiles of chimeric simian-human immunodeficiency viruses (SHIVs) expressing different HIV-1 env genes were highly similar to those of the corresponding HIV-1 strains. The frequency of CpGs in the identified env region correlated with differences in clinical progression rates. Thus, the CpG frequency in a specific part of env, rather than the overall genomic CpG content, governs the susceptibility of HIV-1 to ZAP and might affect viral pathogenicity in vivoIMPORTANCE Evasion of the zinc-finger antiviral protein (ZAP) may drive CpG dinucleotide suppression in HIV-1 and many other viral pathogens but the viral determinants of ZAP sensitivity are poorly defined. Here, we examined CpG suppression and ZAP sensitivity in a large number of primate lentiviruses and demonstrate that their genomic frequency of CpGs varies substantially and does not correlate with ZAP sensitivity. We further show that the number of CpG residues in a defined region at the 5' end of the env gene together with structural features plays a key role in HIV-1 susceptibility to ZAP and correlates with differences in clinical progression rates in HIV-1-infected individuals. Our identification of a specific part of env as a major determinant of HIV-1 susceptibility to ZAP restriction provides a basis for future studies of the underlying inhibitory mechanisms and their potential relevance in the pathogenesis of AIDS.
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Affiliation(s)
- Dorota Kmiec
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Rayhane Nchioua
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Scott Sherrill-Mix
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Christina M Stürzel
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Elena Heusinger
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Elisabeth Braun
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Marcos V P Gondim
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Dominik Hotter
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | | | - Beatrice H Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Daniel Sauter
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
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