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Lin G, Zhang Y. Mutations in the non-structural protein coding region regulate gene expression from replicon RNAs derived from Venezuelan equine encephalitis virus. Biotechnol Lett 2023:10.1007/s10529-023-03379-7. [PMID: 37266878 DOI: 10.1007/s10529-023-03379-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 02/14/2023] [Accepted: 04/11/2023] [Indexed: 06/03/2023]
Abstract
Self-replicating RNA (repRNA) derived from Venezuelan equine encephalitis (VEE) virus is a promising platform for gene therapy and confers prolonged gene expression due to its self-replicating capability, but repRNA suffers from a suboptimal transgene expression level due to its induction of intracellular innate response which may result in inhibition of translation. To improve transgene expression of repRNA, we introduced point mutations in the non-structural protein 1-4 (nsP1-4) coding region of VEE replicon vectors. As a proof of concept, inflammatory cytokines served as genes of interest and were cloned in their wild type and several mutant replicon vectors, followed by transfection in mammalian cells. Our data show that VEE replicons bearing nsP1GGAC-nsP2T or nsP1GGAC-nsP2AT mutations in the nsP1-4 coding region could significantly reduce the recognition by innate immunity as evidenced by the decreased production of type I interferon, and enhance transgene expression in host cells. Thus, the newly discovered mutant VEE replicon vectors could serve as promising gene expression platforms to advance VEE-derived repRNA-based gene therapies.
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Affiliation(s)
- Guibin Lin
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou, 511442, Guangdong, China
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, 510006, Guangdong, China
- Guangdong Provincial Key Laboratory of Biomedical Engineering, South China University of Technology, Guangzhou, 510006, Guangdong, China
- Key Laboratory of Biomedical Materials and Engineering of the Ministry of Education, South China University of Technology, Guangzhou, 510006, Guangdong, China
| | - Yuan Zhang
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou, 511442, Guangdong, China.
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, 510006, Guangdong, China.
- Guangdong Provincial Key Laboratory of Biomedical Engineering, South China University of Technology, Guangzhou, 510006, Guangdong, China.
- Key Laboratory of Biomedical Materials and Engineering of the Ministry of Education, South China University of Technology, Guangzhou, 510006, Guangdong, China.
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Skidmore AM, Bradfute SB. The life cycle of the alphaviruses: From an antiviral perspective. Antiviral Res 2023; 209:105476. [PMID: 36436722 PMCID: PMC9840710 DOI: 10.1016/j.antiviral.2022.105476] [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: 06/20/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022]
Abstract
The alphaviruses are a widely distributed group of positive-sense, single stranded, RNA viruses. These viruses are largely arthropod-borne and can be found on all populated continents. These viruses cause significant human disease, and recently have begun to spread into new populations, such as the expansion of Chikungunya virus into southern Europe and the Caribbean, where it has established itself as endemic. The study of alphaviruses is an active and expanding field, due to their impacts on human health, their effects on agriculture, and the threat that some pose as potential agents of biological warfare and terrorism. In this systematic review we will summarize both historic knowledge in the field as well as recently published data that has potential to shift current theories in how alphaviruses are able to function. This review is comprehensive, covering all parts of the alphaviral life cycle as well as a brief overview of their pathology and the current state of research in regards to vaccines and therapeutics for alphaviral disease.
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Affiliation(s)
- Andrew M Skidmore
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, 915 Camino de Salud, IDTC Room 3245, Albuquerque, NM, 87131, USA.
| | - Steven B Bradfute
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, 915 Camino de Salud, IDTC Room 3330A, Albuquerque, NM, 87131, USA.
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An "Uncharacterized" Australian Virus Is the Earliest Known Example of Ross River Virus with Changes in the nsP3 Protein Associated with the Explosive Outbreak of Ross River Virus Infection in the Pacific Region from 1979 to 1980. Microbiol Resour Announc 2021; 10:e0083821. [PMID: 34792379 PMCID: PMC8601134 DOI: 10.1128/mra.00838-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ross River virus recovered from a South Australian patient during an outbreak of epidemic polyarthritis in 1971 is the earliest known genome sequence with the duplicated 12-amino-acid motif in the nsP3 protein that was found in strains responsible for the outbreak of epidemic polyarthritis in the Pacific region from 1979 to 1980.
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Abdullah N, Ahemad N, Aliazis K, Khairat JE, Lee TC, Abdul Ahmad SA, Adnan NAA, Macha NO, Hassan SS. The Putative Roles and Functions of Indel, Repetition and Duplication Events in Alphavirus Non-Structural Protein 3 Hypervariable Domain (nsP3 HVD) in Evolution, Viability and Re-Emergence. Viruses 2021; 13:v13061021. [PMID: 34071712 PMCID: PMC8228767 DOI: 10.3390/v13061021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 11/23/2022] Open
Abstract
Alphavirus non-structural proteins 1–4 (nsP1, nsP2, nsP3, and nsP4) are known to be crucial for alphavirus RNA replication and translation. To date, nsP3 has been demonstrated to mediate many virus–host protein–protein interactions in several fundamental alphavirus mechanisms, particularly during the early stages of replication. However, the molecular pathways and proteins networks underlying these mechanisms remain poorly described. This is due to the low genetic sequence homology of the nsP3 protein among the alphavirus species, especially at its 3′ C-terminal domain, the hypervariable domain (HVD). Moreover, the nsP3 HVD is almost or completely intrinsically disordered and has a poor ability to form secondary structures. Evolution in the nsP3 HVD region allows the alphavirus to adapt to vertebrate and insect hosts. This review focuses on the putative roles and functions of indel, repetition, and duplication events that have occurred in the alphavirus nsP3 HVD, including characterization of the differences and their implications for specificity in the context of virus–host interactions in fundamental alphavirus mechanisms, which have thus directly facilitated the evolution, adaptation, viability, and re-emergence of these viruses.
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Affiliation(s)
- Nurshariza Abdullah
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Selangor, Malaysia; (N.A.); (N.A.A.A.); (N.O.M.)
| | - Nafees Ahemad
- School of Pharmacy, Monash University Malaysia, Bandar Sunway 47500, Selangor, Malaysia;
- Infectious Diseases and Health Cluster, Tropical Medicine and Biology Platform, Monash University Malaysia, Bandar Sunway 47500, Selangor, Malaysia
| | - Konstantinos Aliazis
- Institute of Immunology and Immunotherapy, Centre for Liver and Gastrointestinal Research, University of Birmingham, Birmingham B15 2TT, UK;
| | - Jasmine Elanie Khairat
- Institute of Biological Sciences, Faculty of Science, University Malaya, Kuala Lumpur 50603, Malaysia;
| | - Thong Chuan Lee
- Faculty of Industrial Sciences & Technology, University Malaysia Pahang, Lebuhraya Tun Razak, Gambang, Kuantan 26300, Pahang, Malaysia;
| | - Siti Aisyah Abdul Ahmad
- Immunogenetic Unit, Allergy and Immunology Research Center, Institute for Medical Research, Ministry of Health Malaysia, Shah Alam 40170, Selangor, Malaysia;
| | - Nur Amelia Azreen Adnan
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Selangor, Malaysia; (N.A.); (N.A.A.A.); (N.O.M.)
| | - Nur Omar Macha
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Selangor, Malaysia; (N.A.); (N.A.A.A.); (N.O.M.)
| | - Sharifah Syed Hassan
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Selangor, Malaysia; (N.A.); (N.A.A.A.); (N.O.M.)
- Infectious Diseases and Health Cluster, Tropical Medicine and Biology Platform, Monash University Malaysia, Bandar Sunway 47500, Selangor, Malaysia
- Correspondence: ; Tel.: +60-3-5514-6340
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Liu W, Kizu JR, Matley DR, Grant R, McCallum FJ, Moller CG, Carthew TL, Hang J, Gubala AJ, Aaskov JG. Circulation of 2 Barmah Forest Virus Lineages in Military Training Areas, Australia. Emerg Infect Dis 2020; 26:3061-3065. [PMID: 33219791 PMCID: PMC7706964 DOI: 10.3201/eid2612.191747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
During 2017–2018, Barmah Forest virus was recovered from mosquitoes trapped in military training areas in Australia and from a soldier infected at 1 of these areas. Phylogenies of the nucleotide sequences of the envelope glycoprotein gene E2 and the 3′ untranslated region suggest that 2 lineages are circulating in eastern Australia.
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Michie A, Ernst T, Chua ILJ, Lindsay MDA, Neville PJ, Nicholson J, Jardine A, Mackenzie JS, Smith DW, Imrie A. Phylogenetic and Timescale Analysis of Barmah Forest Virus as Inferred from Genome Sequence Analysis. Viruses 2020; 12:E732. [PMID: 32640629 PMCID: PMC7412159 DOI: 10.3390/v12070732] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/24/2020] [Accepted: 07/04/2020] [Indexed: 11/17/2022] Open
Abstract
Barmah Forest virus (BFV) is a medically important mosquito-borne alphavirus endemic to Australia. Symptomatic disease can be a major cause of morbidity, associated with fever, rash, and debilitating arthralgia. BFV disease is similar to that caused by Ross River virus (RRV), the other major Australian alphavirus. Currently, just four BFV whole-genome sequences are available with no genome-scale phylogeny in existence to robustly characterise genetic diversity. Thirty novel genome sequences were derived for this study, for a final 34-taxon dataset sampled over a 44 year period. Three distinct BFV genotypes were characterised (G1-3) that have circulated in Australia and Papua New Guinea (PNG). Evidence of spatio-temporal co-circulation of G2 and G3 within regions of Australia was noted, including in the South West region of Western Australia (WA) during the first reported disease outbreaks in the state's history. Compared with RRV, the BFV population appeared more stable with less frequent emergence of novel lineages. Preliminary in vitro assessment of RRV and BFV replication kinetics found that RRV replicates at a significantly faster rate and to a higher, more persistent titre compared with BFV, perhaps indicating mosquitoes may be infectious with RRV for longer than with BFV. This investigation resolved a greater diversity of BFV, and a greater understanding of the evolutionary dynamics and history was attained.
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Affiliation(s)
- Alice Michie
- School of Biomedical Sciences, University of Western Australia, Nedlands, WA 6009, Australia; (A.M.); (T.E.)
| | - Timo Ernst
- School of Biomedical Sciences, University of Western Australia, Nedlands, WA 6009, Australia; (A.M.); (T.E.)
| | - I-Ly Joanna Chua
- PathWest Laboratory Medicine Western Australia, Perth, WA 6000, Australia; (I-L.J.C.); (J.S.M.); (D.W.S.)
| | - Michael D. A. Lindsay
- Environmental Health Hazards, Department of Health, Perth, WA 6000, Australia; (M.D.A.L.); (P.J.N.); (J.N.); (A.J.)
| | - Peter J. Neville
- Environmental Health Hazards, Department of Health, Perth, WA 6000, Australia; (M.D.A.L.); (P.J.N.); (J.N.); (A.J.)
| | - Jay Nicholson
- Environmental Health Hazards, Department of Health, Perth, WA 6000, Australia; (M.D.A.L.); (P.J.N.); (J.N.); (A.J.)
| | - Andrew Jardine
- Environmental Health Hazards, Department of Health, Perth, WA 6000, Australia; (M.D.A.L.); (P.J.N.); (J.N.); (A.J.)
| | - John S. Mackenzie
- PathWest Laboratory Medicine Western Australia, Perth, WA 6000, Australia; (I-L.J.C.); (J.S.M.); (D.W.S.)
- Faculty of Health Sciences, Curtin University, Bentley WA 6102, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia 4067, Australia
| | - David W. Smith
- PathWest Laboratory Medicine Western Australia, Perth, WA 6000, Australia; (I-L.J.C.); (J.S.M.); (D.W.S.)
| | - Allison Imrie
- School of Biomedical Sciences, University of Western Australia, Nedlands, WA 6009, Australia; (A.M.); (T.E.)
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Genome-Scale Phylogeny and Evolutionary Analysis of Ross River Virus Reveals Periodic Sweeps of Lineage Dominance in Western Australia, 1977-2014. J Virol 2020; 94:JVI.01234-19. [PMID: 31666378 PMCID: PMC6955267 DOI: 10.1128/jvi.01234-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 10/11/2019] [Indexed: 11/20/2022] Open
Abstract
Ross River virus (RRV) causes the most common mosquito-borne infection in Australia and causes a significant burden of suffering to infected individuals as well as being a large burden to the Australian economy. The genetic diversity of RRV and its evolutionary history have so far only been studied using partial E2 gene analysis with a limited number of isolates. Robust whole-genome analysis has not yet been conducted. This study generated 94 novel near-whole-genome sequences to investigate the evolutionary history of RRV to better understand its genetic diversity through comprehensive whole-genome phylogeny. A better understanding of RRV genetic diversity will enable better diagnostics, surveillance, and potential future vaccine design. Ross River virus (RRV), an alphavirus of the Togaviridae family, is the most medically significant mosquito-borne virus of Australia. Past RRV phylogenetic and evolutionary analyses have been based on partial genome analyses only. Three geographically distinct RRV lineages, the Eastern, the Western, and the supposedly extinct North-Eastern lineage, were classified previously. We sought to expand on past phylogenies through robust genome-scale phylogeny to better understand RRV genetic diversity and evolutionary dynamics. We analyzed 106 RRV complete coding sequences, which included 13 genomes available on NCBI and 94 novel sequences derived for this study, sampled throughout Western Australia (1977–2014) and during the substantial Pacific Islands RRV epidemic (1979–1980). Our final data set comprised isolates sampled over 59 years (1959–2018) from a range of locations. Four distinct genotypes were defined, with the newly described genotype 4 (G4) found to be the contemporary lineage circulating in Western Australia. The prior geographical classification of RRV lineages was not supported by our findings, with evidence of geographical and temporal cocirculation of distinct genetic groups. Bayesian Markov chain Monte Carlo (MCMC) analysis revealed that RRV lineages diverged from a common ancestor approximately 94 years ago, with distinct lineages emerging roughly every 10 years over the past 50 years in periodic bursts of genetic diversity. Our study has enabled a more robust analysis of RRV evolutionary history and resolved greater genetic diversity that had been previously defined by partial E2 gene analysis. IMPORTANCE Ross River virus (RRV) causes the most common mosquito-borne infection in Australia and causes a significant burden of suffering to infected individuals as well as being a large burden to the Australian economy. The genetic diversity of RRV and its evolutionary history have so far only been studied using partial E2 gene analysis with a limited number of isolates. Robust whole-genome analysis has not yet been conducted. This study generated 94 novel near-whole-genome sequences to investigate the evolutionary history of RRV to better understand its genetic diversity through comprehensive whole-genome phylogeny. A better understanding of RRV genetic diversity will enable better diagnostics, surveillance, and potential future vaccine design.
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Complete Genomic Sequence of an Australian Sindbis Virus Isolated 44 Years Ago Reveals Unique Indels in the E2 and nsP3 Proteins. Microbiol Resour Announc 2019; 8:8/20/e00246-19. [PMID: 31097499 PMCID: PMC6522784 DOI: 10.1128/mra.00246-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The complete genome sequence of a Sindbis virus (SINV) strain (SINV_AUS_1975_18953) isolated in Australia in 1975 from Culex annulirostris mosquitoes revealed unique deletions in amino acid positions 182 to 184 and 201 to 228 of the E2 envelope protein and multiple indels in the nonstructural protein 3 (nsP3). The complete genome sequence of a Sindbis virus (SINV) strain (SINV_AUS_1975_18953) isolated in Australia in 1975 from Culex annulirostris mosquitoes revealed unique deletions in amino acid positions 182 to 184 and 201 to 228 of the E2 envelope protein and multiple indels in the nonstructural protein 3 (nsP3).
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Genome Sequences of Three Ross River Virus Isolates Obtained from the Australian Defence Force. Microbiol Resour Announc 2019; 8:8/14/e00064-19. [PMID: 30948463 PMCID: PMC6449554 DOI: 10.1128/mra.00064-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The complete genome sequences of three Ross River virus (RRV) isolates from infected Australian Defence Force (ADF) personnel and from mosquitoes collected in ADF training areas were determined. Phylogenetic analysis in comparison with all available complete RRV nucleotide sequences from GenBank split these three RRV isolates into two distinct sublineages. The complete genome sequences of three Ross River virus (RRV) isolates from infected Australian Defence Force (ADF) personnel and from mosquitoes collected in ADF training areas were determined. Phylogenetic analysis in comparison with all available complete RRV nucleotide sequences from GenBank split these three RRV isolates into two distinct sublineages.
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Mosimann ALP, de Siqueira MK, Ceole LF, Nunes Duarte Dos Santos C. A new Aura virus isolate in Brazil shows segment duplication in the variable region of the nsP3 gene. Parasit Vectors 2018; 11:321. [PMID: 29843810 PMCID: PMC5975265 DOI: 10.1186/s13071-018-2907-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 05/20/2018] [Indexed: 12/03/2022] Open
Abstract
Background A new isolate of Aura virus serendipitously discovered as a cell culture contaminant is reported in this manuscript. Aura virus belongs to the family Togaviridae and is classified in the genus Alphavirus. There are only two reports of Aura virus isolation from mosquitoes in the scientific literature, and the existence of a vertebrate host is still unknown. The discovery of this new isolate was based on transmission electron microscopy and nucleic acid amplification through a non-specific RT-PCR amplification protocol followed by sequencing. Results Genetic analysis has shown that the new virus shares a high degree of identity with the previously described isolate (GenBank: AF126284.1). A major difference was observed in the nsP3 gene in which a 234-nucleotide duplication has been identified. Furthermore, a pronounced difference was observed in cell cultures compared to the data available for the previously described isolate. Cell permissiveness and phenotypic characteristics in C6/36, Vero and BHK-21 cells were found to differ from previous reports. This may be due to the genetic differences that have been observed. Conclusions The genetic and biological characteristics of the new Aura virus isolate are suggestive of viral adaptation to the cell substrate. The development of a cDNA clone will lend a perspective and better understanding of these results as well as open avenues for its use as a biotechnological tool, as seen for other alphaviruses. Electronic supplementary material The online version of this article (10.1186/s13071-018-2907-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ana Luiza Pamplona Mosimann
- Laboratory of Molecular Virology, Instituto Carlos Chagas, FIOCRUZ, Rua Prof. Algacyr Munhoz Mader 3775, Cidade Industrial, Curitiba, PR, 81350-010, Brazil
| | - Mirian Krystel de Siqueira
- Laboratory of Molecular Virology, Instituto Carlos Chagas, FIOCRUZ, Rua Prof. Algacyr Munhoz Mader 3775, Cidade Industrial, Curitiba, PR, 81350-010, Brazil.,Present Address: Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, 13083-970, Brazil
| | - Ligia Fernanda Ceole
- Laboratory of Cell Biology, Instituto Carlos Chagas, FIOCRUZ, Rua Prof. Algacyr Munhoz Mader 3775, Cidade Industrial, Curitiba, PR, 81350-010, Brazil
| | - Claudia Nunes Duarte Dos Santos
- Laboratory of Molecular Virology, Instituto Carlos Chagas, FIOCRUZ, Rua Prof. Algacyr Munhoz Mader 3775, Cidade Industrial, Curitiba, PR, 81350-010, Brazil.
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The Enigmatic Alphavirus Non-Structural Protein 3 (nsP3) Revealing Its Secrets at Last. Viruses 2018; 10:v10030105. [PMID: 29495654 PMCID: PMC5869498 DOI: 10.3390/v10030105] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 02/20/2018] [Accepted: 02/22/2018] [Indexed: 12/21/2022] Open
Abstract
Alphaviruses encode 4 non-structural proteins (nsPs), most of which have well-understood functions in capping and membrane association (nsP1), polyprotein processing and RNA helicase activity (nsP2) and as RNA-dependent RNA polymerase (nsP4). The function of nsP3 has been more difficult to pin down and it has long been referred to as the more enigmatic of the nsPs. The protein comprises three domains, an N-terminal macro domain, a central zinc-binding domain and a C-terminal hypervariable domain (HVD). In this article, we review old and new literature about the functions of the three domains. Much progress in recent years has contributed to a picture of nsP3, particularly through its HVD as a hub for interactions with host cell molecules, with multiple effects on the biology of the host cell at early points in infection. These and many future discoveries will provide targets for anti-viral therapies as well as strategies for modification of vectors for vaccine and oncolytic interventions.
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Lim EXY, Lee WS, Madzokere ET, Herrero LJ. Mosquitoes as Suitable Vectors for Alphaviruses. Viruses 2018; 10:v10020084. [PMID: 29443908 PMCID: PMC5850391 DOI: 10.3390/v10020084] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 02/07/2018] [Accepted: 02/08/2018] [Indexed: 12/28/2022] Open
Abstract
Alphaviruses are arthropod-borne viruses and are predominantly transmitted via mosquito vectors. This vector preference by alphaviruses raises the important question of the determinants that contribute to vector competence. There are several tissue barriers of the mosquito that the virus must overcome in order to establish a productive infection. Of importance are the midgut, basal lamina and the salivary glands. Infection of the salivary glands is crucial for virus transmission during the mosquito’s subsequent bloodfeed. Other factors that may contribute to vector competence include the microflora and parasites present in the mosquito, environmental conditions, the molecular determinants of the virus to adapt to the vector, as well as the effect of co-infection with other viruses. Though mosquito innate immunity is a contributing factor to vector competence, it will not be discussed in this review. Detailed understanding of these factors will be instrumental in minimising transmission of alphaviral diseases.
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Affiliation(s)
- Elisa X Y Lim
- Institute for Glycomics, Griffith University, Gold Coast Campus, Southport, QLD 4215, Australia.
| | - Wai Suet Lee
- Institute for Glycomics, Griffith University, Gold Coast Campus, Southport, QLD 4215, Australia.
| | - Eugene T Madzokere
- Institute for Glycomics, Griffith University, Gold Coast Campus, Southport, QLD 4215, Australia.
| | - Lara J Herrero
- Institute for Glycomics, Griffith University, Gold Coast Campus, Southport, QLD 4215, Australia.
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Kim DY, Reynaud JM, Rasalouskaya A, Akhrymuk I, Mobley JA, Frolov I, Frolova EI. New World and Old World Alphaviruses Have Evolved to Exploit Different Components of Stress Granules, FXR and G3BP Proteins, for Assembly of Viral Replication Complexes. PLoS Pathog 2016; 12:e1005810. [PMID: 27509095 PMCID: PMC4980055 DOI: 10.1371/journal.ppat.1005810] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 07/13/2016] [Indexed: 11/18/2022] Open
Abstract
The positive-strand RNA viruses initiate their amplification in the cell from a single genome delivered by virion. This single RNA molecule needs to become involved in replication process before it is recognized and degraded by cellular machinery. In this study, we show that distantly related New World and Old World alphaviruses have independently evolved to utilize different cellular stress granule-related proteins for assembly of complexes, which recruit viral genomic RNA and facilitate formation of viral replication complexes (vRCs). Venezuelan equine encephalitis virus (VEEV) utilizes all members of the Fragile X syndrome (FXR) family, while chikungunya and Sindbis viruses exploit both members of the G3BP family. Despite being in different families, these proteins share common characteristics, which determine their role in alphavirus replication, namely, the abilities for RNA-binding and for self-assembly into large structures. Both FXR and G3BP proteins interact with virus-specific, repeating amino acid sequences located in the C-termini of hypervariable, intrinsically disordered domains (HVDs) of viral nonstructural protein nsP3. We demonstrate that these host factors orchestrate assembly of vRCs and play key roles in RNA and virus replication. Only knockout of all of the homologs results in either pronounced or complete inhibition of replication of different alphaviruses. The use of multiple homologous proteins with redundant functions mediates highly efficient recruitment of viral RNA into the replication process. This independently evolved acquisition of different families of cellular proteins by the disordered protein fragment to support alphavirus replication suggests that other RNA viruses may utilize a similar mechanism of host factor recruitment for vRC assembly. The use of different host factors by alphavirus species may be one of the important determinants of their pathogenesis. Many viruses encode proteins containing intrinsically disordered domains, whose functions are as yet unknown. Here we show that such a domain (HVD) in the alphavirus nsP3 protein orchestrates assembly of viral replication complexes through interaction with RNA-binding cellular factors. Surprisingly, geographically isolated viruses have evolved to utilize different cellular proteins: the nsP3 HVD of Venezuelan equine encephalitis virus (VEEV) binds all members of the FXR family, while nsP3 HVDs of Sindbis and chikungunya viruses interact with G3BP proteins. Despite being in different families, G3BPs and FXRs have similar domain organization, and assemble into higher order complexes, such as stress granules. Alphaviruses exploit their abilities for complex self-assembly and RNA binding to build RNA-containing pre-replication complexes. Using CRISPR/Cas9 mediated knockouts, we show that deletion of all homologs strongly affects virus replication, while knockout of a single FXR or G3BP homolog has no or mild effect. Our data suggest that an alphavirus HVD serves as a hub to recruit host factors for replication complex assembly and may determine virus adaptation to distinct cellular environments. Notably, the improved understanding of HVD interactions allows alphavirus replication to be switched from an FXR- to G3BP-dependent mode and opens new possibilities for development of antiviral therapeutics.
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Affiliation(s)
- Dal Young Kim
- Department of Microbiology, University of Alabama at Birmingham, Alabama, United States of America
| | - Josephine M. Reynaud
- Department of Microbiology, University of Alabama at Birmingham, Alabama, United States of America
| | - Aliaksandra Rasalouskaya
- Department of Microbiology, University of Alabama at Birmingham, Alabama, United States of America
| | - Ivan Akhrymuk
- Department of Microbiology, University of Alabama at Birmingham, Alabama, United States of America
| | - James A. Mobley
- Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Surgery, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Ilya Frolov
- Department of Microbiology, University of Alabama at Birmingham, Alabama, United States of America
| | - Elena I. Frolova
- Department of Microbiology, University of Alabama at Birmingham, Alabama, United States of America
- * E-mail:
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14
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Fros JJ, Geertsema C, Zouache K, Baggen J, Domeradzka N, van Leeuwen DM, Flipse J, Vlak JM, Failloux AB, Pijlman GP. Mosquito Rasputin interacts with chikungunya virus nsP3 and determines the infection rate in Aedes albopictus. Parasit Vectors 2015; 8:464. [PMID: 26384002 PMCID: PMC4573678 DOI: 10.1186/s13071-015-1070-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 09/03/2015] [Indexed: 01/22/2023] Open
Abstract
Background Chikungunya virus (CHIKV) is an arthritogenic alphavirus (family Togaviridae), transmitted by Aedes species mosquitoes. CHIKV re-emerged in 2004 with multiple outbreaks worldwide and recently reached the Americas where it has infected over a million individuals in a rapidly expanding epidemic. While alphavirus replication is well understood in general, the specific function (s) of non-structural protein nsP3 remain elusive. CHIKV nsP3 modulates the mammalian stress response by preventing stress granule formation through sequestration of G3BP. In mosquitoes, nsP3 is a determinant of vector specificity, but its functional interaction with mosquito proteins is unclear. Methods In this research we studied the domains required for localization of CHIKV nsP3 in insect cells and demonstrated its molecular interaction with Rasputin (Rin), the mosquito homologue of G3BP. The biological involvement of Rin in CHIKV infection was investigated in live Ae. albopictus mosquitoes. Results In insect cells, nsP3 localized as cytoplasmic granules, which was dependent on the central domain and the C-terminal variable region but independent of the N-terminal macrodomain. Ae. albopictus Rin displayed a diffuse, cytoplasmic localization, but was effectively sequestered into nsP3-granules upon nsP3 co-expression. Site-directed mutagenesis showed that the Rin-nsP3 interaction involved the NTF2-like domain of Rin and two conserved TFGD repeats in the C-terminal variable domain of nsP3. Although in vitro silencing of Rin did not impact nsP3 localization or CHIKV replication in cell culture, Rin depletion in vivo significantly decreased the CHIKV infection rate and transmissibility in Ae.albopictus. Conclusions We identified the nsP3 hypervariable C-terminal domain as a critical factor for granular localization and sequestration of mosquito Rin. Our study offers novel insight into a conserved virus-mosquito interaction at the molecular level, and reveals a strong proviral role for G3BP homologue Rin in live mosquitoes, making the nsP3-Rin interaction a putative target to interfere with the CHIKV transmission cycle.
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Affiliation(s)
- Jelke J Fros
- Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
| | - Corinne Geertsema
- Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
| | - Karima Zouache
- Institut Pasteur, Department of Virology, Arboviruses and Insect Vectors, 25-28 rue du Docteur Roux, 75724, Paris, cedex 15, France.
| | - Jim Baggen
- Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
| | - Natalia Domeradzka
- Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
| | - Daniël M van Leeuwen
- Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
| | - Jacky Flipse
- Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
| | - Just M Vlak
- Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
| | - Anna-Bella Failloux
- Institut Pasteur, Department of Virology, Arboviruses and Insect Vectors, 25-28 rue du Docteur Roux, 75724, Paris, cedex 15, France.
| | - Gorben P Pijlman
- Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
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15
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Rupp JC, Sokoloski KJ, Gebhart NN, Hardy RW. Alphavirus RNA synthesis and non-structural protein functions. J Gen Virol 2015. [PMID: 26219641 DOI: 10.1099/jgv.0.000249] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The members of the genus Alphavirus are positive-sense RNA viruses, which are predominantly transmitted to vertebrates by a mosquito vector. Alphavirus disease in humans can be severely debilitating, and depending on the particular viral species, infection may result in encephalitis and possibly death. In recent years, alphaviruses have received significant attention from public health authorities as a consequence of the dramatic emergence of chikungunya virus in the Indian Ocean islands and the Caribbean. Currently, no safe, approved or effective vaccine or antiviral intervention exists for human alphavirus infection. The molecular biology of alphavirus RNA synthesis has been well studied in a few species of the genus and represents a general target for antiviral drug development. This review describes what is currently understood about the regulation of alphavirus RNA synthesis, the roles of the viral non-structural proteins in this process and the functions of cis-acting RNA elements in replication, and points to open questions within the field.
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Affiliation(s)
- Jonathan C Rupp
- Department of Biology, Indiana University, 212 South Hawthorne Drive, Bloomington, IN 47405, USA
| | - Kevin J Sokoloski
- Department of Biology, Indiana University, 212 South Hawthorne Drive, Bloomington, IN 47405, USA
| | - Natasha N Gebhart
- Department of Biology, Indiana University, 212 South Hawthorne Drive, Bloomington, IN 47405, USA
| | - Richard W Hardy
- Department of Biology, Indiana University, 212 South Hawthorne Drive, Bloomington, IN 47405, USA
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16
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Hypervariable domain of nonstructural protein nsP3 of Venezuelan equine encephalitis virus determines cell-specific mode of virus replication. J Virol 2013; 87:7569-84. [PMID: 23637407 DOI: 10.1128/jvi.00720-13] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Venezuelan equine encephalitis virus (VEEV) is one of the most pathogenic members of the Alphavirus genus in the Togaviridae family. This genus is divided into the Old World and New World alphaviruses, which demonstrate profound differences in pathogenesis, replication, and virus-host interactions. VEEV is a representative member of the New World alphaviruses. The biology of this virus is still insufficiently understood, particularly the function of its nonstructural proteins in RNA replication and modification of the intracellular environment. One of these nonstructural proteins, nsP3, contains a hypervariable domain (HVD), which demonstrates very low overall similarity between different alphaviruses, suggesting the possibility of its function in virus adaptation to different hosts and vectors. The results of our study demonstrate the following. (i) Phosphorylation of the VEEV nsP3-specific HVD does not play a critical role in virus replication in cells of vertebrate origin but is important for virus replication in mosquito cells. (ii) The VEEV HVD is not required for viral RNA replication in the highly permissive BHK-21 cell line. In fact, it can be either completely deleted or replaced by a heterologous protein sequence. These variants require only one or two additional adaptive mutations in nsP3 and/or nsP2 proteins to achieve an efficiently replicating phenotype. (iii) However, the carboxy-terminal repeat in the VEEV HVD is indispensable for VEEV replication in the cell lines other than BHK-21 and plays a critical role in formation of VEEV-specific cytoplasmic protein complexes. Natural VEEV variants retain at least one of the repeated elements in their nsP3 HVDs.
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17
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Saxton-Shaw KD, Ledermann JP, Borland EM, Stovall JL, Mossel EC, Singh AJ, Wilusz J, Powers AM. O'nyong nyong virus molecular determinants of unique vector specificity reside in non-structural protein 3. PLoS Negl Trop Dis 2013; 7:e1931. [PMID: 23359824 PMCID: PMC3554527 DOI: 10.1371/journal.pntd.0001931] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 10/16/2012] [Indexed: 11/18/2022] Open
Abstract
O'nyong nyong virus (ONNV) and Chikungunya virus (CHIKV) are two closely related alphaviruses with very different infection patterns in the mosquito, Anopheles gambiae. ONNV is the only alphavirus transmitted by anopheline mosquitoes, but specific molecular determinants of infection of this unique vector specificity remain unidentified. Fifteen distinct chimeric viruses were constructed to evaluate both structural and non-structural regions of the genome and infection patterns were determined through artificial infectious feeds in An. gambiae with each of these chimeras. Only one region, non-structural protein 3 (nsP3), was sufficient to up-regulate infection to rates similar to those seen with parental ONNV. When ONNV non-structural protein 3 (nsP3) replaced nsP3 from CHIKV virus in one of the chimeric viruses, infection rates in An. gambiae went from 0% to 63.5%. No other single gene or viral region addition was able to restore infection rates. Thus, we have shown that a non-structural genome element involved in viral replication is a major element involved in ONNV's unique vector specificity.
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Affiliation(s)
- Kali D. Saxton-Shaw
- Division of Vector Borne Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
| | - Jeremy P. Ledermann
- Division of Vector Borne Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
| | - Erin M. Borland
- Division of Vector Borne Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
| | - Janae L. Stovall
- Division of Vector Borne Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
| | - Eric C. Mossel
- Division of Vector Borne Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Amber J. Singh
- Division of Vector Borne Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Ann M. Powers
- Division of Vector Borne Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
- * E-mail:
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18
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Liu WJ, Rourke MF, Holmes EC, Aaskov JG. Persistence of multiple genetic lineages within intrahost populations of Ross River virus. J Virol 2011; 85:5674-8. [PMID: 21430052 PMCID: PMC3094999 DOI: 10.1128/jvi.02622-10] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 03/14/2011] [Indexed: 11/20/2022] Open
Abstract
We examined the structure and extent of genetic diversity in intrahost populations of Ross River virus (RRV) in samples from six human patients, focusing on the nonstructural (nsP3) and structural (E2) protein genes. Strikingly, although the samples were collected from contrasting ecological settings 3,000 kilometers apart in Australia, we observed multiple viral lineages in four of the six individuals, which is indicative of widespread mixed infections. In addition, a comparison with previously published RRV sequences revealed that these distinct lineages have been in circulation for at least 5 years, and we were able to document their long-term persistence over extensive geographical distances.
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Affiliation(s)
- Wen J. Liu
- Australian Army Malaria Institute, Brisbane, Australia
| | | | - Edward C. Holmes
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, Mueller Laboratory, University Park, Pennsylvania 16802
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland 20892
| | - John G. Aaskov
- Australian Army Malaria Institute, Brisbane, Australia
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
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