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Hall R, Guedán A, Yap MW, Young GR, Harvey R, Stoye JP, Bishop KN. SARS-CoV-2 ORF6 disrupts innate immune signalling by inhibiting cellular mRNA export. PLoS Pathog 2022; 18:e1010349. [PMID: 36007063 PMCID: PMC9451085 DOI: 10.1371/journal.ppat.1010349] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 09/07/2022] [Accepted: 07/21/2022] [Indexed: 11/18/2022] Open
Abstract
SARS-CoV-2 is a betacoronavirus and the etiological agent of COVID-19, a devastating infectious disease. Due to its far-reaching effect on human health, there is an urgent and growing need to understand the viral molecular biology of SARS-CoV-2 and its interaction with the host cell. SARS-CoV-2 encodes 9 predicted accessory proteins, which are presumed to be dispensable for in vitro replication, most likely having a role in modulating the host cell environment to aid viral replication. Here we show that the ORF6 accessory protein interacts with cellular Rae1 to inhibit cellular protein production by blocking mRNA export. We utilised cell fractionation coupled with mRNAseq to explore which cellular mRNA species are affected by ORF6 expression and show that ORF6 can inhibit the export of many mRNA including those encoding antiviral factors such as IRF1 and RIG-I. We also show that export of these mRNA is blocked in the context of SARS-CoV-2 infection. Together, our studies identify a novel mechanism by which SARS-CoV-2 can manipulate the host cell environment to supress antiviral responses, providing further understanding to the replication strategies of a virus that has caused an unprecedented global health crisis.
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Affiliation(s)
- Ross Hall
- Retroviral Replication Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Anabel Guedán
- Retroviral Replication Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Melvyn W. Yap
- Retroviral Replication Laboratory, The Francis Crick Institute, London, United Kingdom
| | - George R. Young
- Bioinformatics and Biostatistics STP, The Francis Crick Institute, London, United Kingdom
| | - Ruth Harvey
- World Influenza Centre, The Francis Crick Institute, London, United Kingdom
| | - Jonathan P. Stoye
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, London, United Kingdom
- Department of Infectious Disease, Imperial College London, United Kingdom
| | - Kate N. Bishop
- Retroviral Replication Laboratory, The Francis Crick Institute, London, United Kingdom
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Yap MW, Young GR, Varnaite R, Morand S, Stoye JP. Duplication and divergence of the retrovirus restriction gene Fv1 in Mus caroli allows protection from multiple retroviruses. PLoS Genet 2020; 16:e1008471. [PMID: 32525879 PMCID: PMC7313476 DOI: 10.1371/journal.pgen.1008471] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 06/23/2020] [Accepted: 05/13/2020] [Indexed: 12/29/2022] Open
Abstract
Viruses and their hosts are locked in an evolutionary race where resistance to infection is acquired by the hosts while viruses develop strategies to circumvent these host defenses. Forming one arm of the host defense armory are cell autonomous restriction factors like Fv1. Originally described as protecting laboratory mice from infection by murine leukemia virus (MLV), Fv1s from some wild mice have also been found to restrict non-MLV retroviruses, suggesting an important role in the protection against viruses in nature. We surveyed the Fv1 genes of wild mice trapped in Thailand and characterized their restriction activities against a panel of retroviruses. An extra copy of the Fv1 gene, named Fv7, was found on chromosome 6 of three closely related Asian species of mice: Mus caroli, M. cervicolor, and M. cookii. The presence of flanking repeats suggested it arose by LINE-mediated retroduplication within their most recent common ancestor. A high degree of natural variation was observed in both Fv1 and Fv7 and, on top of positive selection at certain residues, insertions and deletions were present that changed the length of the reading frames. These genes exhibited a range of restriction phenotypes, with activities directed against gamma-, spuma-, and lentiviruses. It seems likely, at least in the case of M. caroli, that the observed gene duplication may expand the breadth of restriction beyond the capacity of Fv1 alone and that one or more such viruses have recently driven or continue to drive the evolution of the Fv1 and Fv7 genes.
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Affiliation(s)
| | | | | | - Serge Morand
- Centre National de la Recherche Scientifique-Centre de coopération
Internationale en Recherche Agronomique pour le Développement Animal et Gestion
Intégrée des Risques, Faculty of Veterinary Technology, Kasetsart University,
Bangkok, Thailand
| | - Jonathan P. Stoye
- The Francis Crick Institute, London, United Kingdom
- Faculty of Medicine, Imperial College London, London, United
Kingdom
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3
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Abstract
Both exogenous and endogenous retroviruses have long been studied in mice, and some of the earliest mouse studies focused on the heritability of genetic factors influencing permissivity and resistance to infection. The prototypic retroviral restriction factor, Fv1, is now understood to exhibit a degree of control across multiple retroviral genera and is highly diverse within Mus To better understand the age and evolutionary history of Fv1, a comprehensive survey of the Muroidea was conducted, allowing the progenitor integration to be dated to ∼45 million years. Intact coding potential is visible beyond Mus, and sequence analysis reveals strong signatures of positive selection also within field mice, ApodemusFv1's survival for such a period implies a recurring and shifting retroviral burden imparting the necessary selective pressures-an influence likely also common to analogous factors. Regions of Fv1 adapt cooperatively, highlighting its preference for repeated structures and suggesting that this functionally constrained aspect of the retroviral capsid lattice presents a common target in the evolution of intrinsic immunity.
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Affiliation(s)
- George R Young
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Melvyn W Yap
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Johan R Michaux
- Laboratoire de Génétique de la Conservation, Université de Liège, 4000 Liège, Belgium
- UMR Animal, Santé, Territoires, Risques et Ecosystèmes (ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Campus International de Baillarguet, Université de Montpellier, 34398 Montpellier, France
| | - Scott J Steppan
- Department of Biological Science, Florida State University, Tallahassee, FL 32304
| | - Jonathan P Stoye
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom;
- Department of Medicine, Imperial College London, London SW7 2AZ, United Kingdom
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Abstract
BACKGROUND The mouse protein Fv1 is a factor that can confer resistance to retroviral infection. The two major Fv1 alleles from laboratory mice, Fv1 (n) and Fv1 (b) , restrict infection by different murine leukaemia viruses (MLVs). Fv1(n) restricts B-tropic MLV, but not N-tropic MLV or NB-tropic MLV. In cells expressing Fv1(b) at natural levels, only N-MLV is restricted, however restriction of NB-MLV and partial restriction of B-MLV were observed when recombinant Fv1(b) was expressed from an MLV promoter in Fv1 null Mus dunni tail fibroblast cells. To investigate the relationship between expression level and restriction specificity we have developed new retroviral delivery vectors which allow inducible expression of Fv1, and yet allow sufficient production of fluorescent reporter proteins for analysis in our FACS-based restriction assay. RESULTS We demonstrated that at concentrations close to the endogenous expression level, Fv1(b) specifically restricts only N-MLV, but restriction of NB-MLV, and to a lesser extent B-MLV, could be gained by increasing the protein level of Fv1(b). By contrast, we found that even when Fv1(n) is expressed at very high levels, no significant inhibition of N-MLV or NB-MLV could be observed. Study of Fv1 mutants using this assay led to the identification of determinants for N/B tropism at an expression level close to that of endogenous Fv1(n) and Fv1(b). We also compared the recently described restriction activities of wild mice Fv1 proteins directed against non-MLV retroviruses when expressed at different levels. Fv1 from M. spretus restricted N-MLV, B-MLV and equine infectious anaemia virus equally even at low concentrations, while Fv1 from M. macedonicus showed even stronger restriction against equine infectious anaemia virus than to N-MLV. Restriction of feline foamy virus by Fv1 of M. caroli occurred at levels equivalent to MLV restriction. CONCLUSIONS Our data indicate that for some but not all Fv1 proteins, gain of restriction activities could be achieved by increasing the expression level of Fv1. However such a concentration dependent effect is not seen with most Fv1s and cannot explain the recently reported activities against non-MLVs. It will be interesting to examine whether overexpression of other capsid binding restriction factors such as TRIM5α or Mx2 result in novel restriction specificities.
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Affiliation(s)
- Wilson Li
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, NW7 1AA, UK
| | - Melvyn W Yap
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, NW7 1AA, UK
| | - Vicky Voss
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, NW7 1AA, UK
| | - Jonathan P Stoye
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, NW7 1AA, UK. .,Faculty of Medicine, Imperial College London, London, SW7 2AZ, UK.
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Yap MW, Colbeck E, Ellis SA, Stoye JP. Evolution of the retroviral restriction gene Fv1: inhibition of non-MLV retroviruses. PLoS Pathog 2014; 10:e1003968. [PMID: 24603659 PMCID: PMC3948346 DOI: 10.1371/journal.ppat.1003968] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 01/16/2014] [Indexed: 11/18/2022] Open
Abstract
Fv1 is the prototypic restriction factor that protects against infection by the murine leukemia virus (MLV). It was first identified in cells that were derived from laboratory mice and was found to be homologous to the gag gene of an endogenous retrovirus (ERV). To understand the evolution of the host restriction gene from its retroviral origins, Fv1s from wild mice were isolated and characterized. Most of these possess intact open reading frames but not all restricted N-, B-, NR-or NB-tropic MLVs, suggesting that other viruses could have played a role in the selection of the gene. The Fv1s from Mus spretus and Mus caroli were found to restrict equine infectious anemia virus (EIAV) and feline foamy virus (FFV) respectively, indicating that Fv1 could have a broader target range than previously thought, including activity against lentiviruses and spumaviruses. Analyses of the Fv1 sequences revealed a number of residues in the C-terminal region that had evolved under positive selection. Four of these selected residues were found to be involved in the novel restriction by mapping studies. These results strengthen the similarities between the two capsid binding restriction factors, Fv1 and TRIM5α, which support the hypothesis that Fv1 defended mice against waves of retroviral infection possibly including non-MLVs as well as MLVs. We have followed the evolution of the retroviral restriction gene, Fv1, by functional analysis. We show that Fv1 can recognize and restrict a wider range of retroviruses than previously thought including examples from the gammaretrovirus, lentivirus and foamy virus genera. Nearly every Fv1 tested showed a different pattern of restriction activity. We also identify several hypervariable regions in the coding sequence containing positively selected amino acids that we show to be directly involved in determining restriction specificity. Our results strengthen the analogy between Fv1 and another capsid-binding, retrovirus restriction factor, TRIM5α. Although they share no sequence identity they appear to share a similar design and appear likely to recognise different targets by a mechanism involving multiple weak interactions between a virus-binding domain containing several variable regions and the surface of the viral capsid. We also describe a pattern of constant genetic change, implying that different species of Mus have evolved in the face of ever-changing retroviral threats by viruses of different kinds.
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Affiliation(s)
- Melvyn W. Yap
- Division of Virology, National Institute for Medical Research, Mill Hill, London, United Kingdom
| | - Emily Colbeck
- Division of Virology, National Institute for Medical Research, Mill Hill, London, United Kingdom
| | - Scott A. Ellis
- Division of Virology, National Institute for Medical Research, Mill Hill, London, United Kingdom
| | - Jonathan P. Stoye
- Division of Virology, National Institute for Medical Research, Mill Hill, London, United Kingdom
- Faculty of Medicine, Imperial College London, London, United Kingdom
- * E-mail:
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Abstract
To test the hypothesis that rabbit endogenous lentivirus type K (RELIK) could play a role in shaping the evolution of TRIM5α, the susceptibility of viruses containing the RELIK capsid (CA) to TRIM5 restriction was evaluated. RELIK CA-containing viruses were susceptible to the TRIM5αs from Old World monkeys but were unaffected by most ape or New World monkey factors. TRIM5αs from various lagomorph species were also isolated and tested for anti-retroviral activity. The TRIM5αs from both cottontail rabbit and pika restrict a range of retroviruses, including HIV-1, HIV-2, FIV, EIAV and N-MLV. TRIM5αs from the European and cottontail rabbit, which have previously been found to contain RELIK, also restricted RELIK CA-containing viruses, whereas a weaker restriction was observed with chimeric TRIM5α containing the B30.2 domain from the pika, which lacks RELIK. Taken together, these results could suggest that the pika had not been exposed to exogenous RELIK and that endogenized RELIK might exert a selective pressure on lagomorph TRIM5α.
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Affiliation(s)
| | - Jonathan P. Stoye
- Division of Virology, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
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Goldstone DC, Flower TG, Ball NJ, Sanz-Ramos M, Yap MW, Ogrodowicz RW, Stanke N, Reh J, Lindemann D, Stoye JP, Taylor IA. A unique spumavirus Gag N-terminal domain with functional properties of orthoretroviral matrix and capsid. PLoS Pathog 2013; 9:e1003376. [PMID: 23675305 PMCID: PMC3649970 DOI: 10.1371/journal.ppat.1003376] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 04/04/2013] [Indexed: 11/19/2022] Open
Abstract
The Spumaretrovirinae, or foamyviruses (FVs) are complex retroviruses that infect many species of monkey and ape. Although FV infection is apparently benign, trans-species zoonosis is commonplace and has resulted in the isolation of the Prototypic Foamy Virus (PFV) from human sources and the potential for germ-line transmission. Despite little sequence homology, FV and orthoretroviral Gag proteins perform equivalent functions, including genome packaging, virion assembly, trafficking and membrane targeting. In addition, PFV Gag interacts with the FV Envelope (Env) protein to facilitate budding of infectious particles. Presently, there is a paucity of structural information with regards FVs and it is unclear how disparate FV and orthoretroviral Gag molecules share the same function. Therefore, in order to probe the functional overlap of FV and orthoretroviral Gag and learn more about FV egress and replication we have undertaken a structural, biophysical and virological study of PFV-Gag. We present the crystal structure of a dimeric amino terminal domain from PFV, Gag-NtD, both free and in complex with the leader peptide of PFV Env. The structure comprises a head domain together with a coiled coil that forms the dimer interface and despite the shared function it is entirely unrelated to either the capsid or matrix of Gag from other retroviruses. Furthermore, we present structural, biochemical and virological data that reveal the molecular details of the essential Gag-Env interaction and in addition we also examine the specificity of Trim5α restriction of PFV. These data provide the first information with regards to FV structural proteins and suggest a model for convergent evolution of gag genes where structurally unrelated molecules have become functionally equivalent.
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Affiliation(s)
- David C. Goldstone
- Division of Molecular Structure, MRC National Institute for Medical Research, the Ridgeway, Mill Hill, London, United Kingdom
| | - Thomas G. Flower
- Division of Molecular Structure, MRC National Institute for Medical Research, the Ridgeway, Mill Hill, London, United Kingdom
| | - Neil J. Ball
- Division of Molecular Structure, MRC National Institute for Medical Research, the Ridgeway, Mill Hill, London, United Kingdom
| | - Marta Sanz-Ramos
- Division of Virology, MRC National Institute for Medical Research, the Ridgeway, Mill Hill, London, United Kingdom
| | - Melvyn W. Yap
- Division of Virology, MRC National Institute for Medical Research, the Ridgeway, Mill Hill, London, United Kingdom
| | - Roksana W. Ogrodowicz
- Division of Molecular Structure, MRC National Institute for Medical Research, the Ridgeway, Mill Hill, London, United Kingdom
| | - Nicole Stanke
- Institute of Virology, Technische Universität Dresden, Dresden, Germany
| | - Juliane Reh
- Institute of Virology, Technische Universität Dresden, Dresden, Germany
| | - Dirk Lindemann
- Institute of Virology, Technische Universität Dresden, Dresden, Germany
| | - Jonathan P. Stoye
- Division of Virology, MRC National Institute for Medical Research, the Ridgeway, Mill Hill, London, United Kingdom
| | - Ian A. Taylor
- Division of Molecular Structure, MRC National Institute for Medical Research, the Ridgeway, Mill Hill, London, United Kingdom
- * E-mail:
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8
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Ohkura S, Goldstone DC, Yap MW, Holden-Dye K, Taylor IA, Stoye JP. Novel escape mutants suggest an extensive TRIM5α binding site spanning the entire outer surface of the murine leukemia virus capsid protein. PLoS Pathog 2011; 7:e1002011. [PMID: 21483490 PMCID: PMC3068999 DOI: 10.1371/journal.ppat.1002011] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Accepted: 01/28/2011] [Indexed: 12/18/2022] Open
Abstract
After entry into target cells, retroviruses encounter the host restriction
factors such as Fv1 and TRIM5α. While it is clear that these factors target
retrovirus capsid proteins (CA), recognition remains poorly defined in the
absence of structural information. To better understand the binding interaction
between TRIM5α and CA, we selected a panel of novel N-tropic murine
leukaemia virus (N-MLV) escape mutants by a serial passage of replication
competent N-MLV in rhesus macaque TRIM5α (rhTRIM5α)-positive cells using
a small percentage of unrestricted cells to allow multiple rounds of virus
replication. The newly identified mutations, many of which involve changes in
charge, are distributed over the outer ‘top’ surface of N-MLV CA,
including the N-terminal β-hairpin, and map up to 29 Ao apart.
Biological characterisation with a number of restriction factors revealed that
only one of the new mutations affects restriction by human TRIM5α,
indicating significant differences in the binding interaction between N-MLV and
the two TRIM5αs, whereas three of the mutations result in dual sensitivity
to Fv1n and Fv1b. Structural studies of two mutants show
that no major changes in the overall CA conformation are associated with escape
from restriction. We conclude that interactions involving much, if not all, of
the surface of CA are vital for TRIM5α binding. Host restriction factors such as TRIM5α are important for preventing cross
species transmission of a variety of retroviruses. They act to block viral
replication but their mode of virus recognition is poorly understood. To address
this question we have developed a procedure for isolating viruses that replicate
in the presence of restriction factors. Analysis of these viruses shows that
individual mutations across the entire surface of the viral capsid molecule can
relieve restriction. Escape from TRIM5α of one species does not necessarily
lead to escape from another. It seems likely that restriction factor recognition
involves extensive weak contacts between factor and virus. We suggest that this
represents an important design feature in a system that recognizes multiple
pathogens.
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Affiliation(s)
- Sadayuki Ohkura
- Division of Virology, MRC National Institute for Medical Research,
London, United Kingdom
| | - David C. Goldstone
- Division of Molecular Structure, MRC National Institute for Medical
Research, London, United Kingdom
| | - Melvyn W. Yap
- Division of Virology, MRC National Institute for Medical Research,
London, United Kingdom
| | - Kate Holden-Dye
- Division of Virology, MRC National Institute for Medical Research,
London, United Kingdom
| | - Ian A. Taylor
- Division of Molecular Structure, MRC National Institute for Medical
Research, London, United Kingdom
| | - Jonathan P. Stoye
- Division of Virology, MRC National Institute for Medical Research,
London, United Kingdom
- * E-mail:
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Goldstone DC, Yap MW, Robertson LE, Haire LF, Taylor WR, Katzourakis A, Stoye JP, Taylor IA. Structural and Functional Analysis of Prehistoric Lentiviruses Uncovers an Ancient Molecular Interface. Cell Host Microbe 2010; 8:248-59. [DOI: 10.1016/j.chom.2010.08.006] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Revised: 06/11/2010] [Accepted: 06/30/2010] [Indexed: 11/17/2022]
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Groom HCT, Yap MW, Galão RP, Neil SJD, Bishop KN. Susceptibility of xenotropic murine leukemia virus-related virus (XMRV) to retroviral restriction factors. Proc Natl Acad Sci U S A 2010; 107:5166-71. [PMID: 20194752 PMCID: PMC2841911 DOI: 10.1073/pnas.0913650107] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Xenotropic murine leukemia virus-related virus (XMRV) is a recently discovered gammaretrovirus that has been linked to prostate cancer and chronic fatigue syndrome. This virus is therefore an important potential human pathogen and, as such, it is essential to understand its host cell tropism. Intriguingly, infectious virus has been recovered from patient-derived peripheral blood mononuclear cells. These cells express several antiviral restriction factors that are capable of inhibiting the replication of a wide range of retroviruses, including other gamma retroviruses. This raises the possibility that, similar to HIV, XMRV may have acquired resistance to restriction. We therefore investigated the susceptibility of XMRV to a panel of different restriction factors. We found that both human APOBEC3 and tetherin proteins are able to block XMRV replication. Expression of human TRIM5alpha, however, had no effect on viral infectivity. There was no evidence that XMRV expressed countermeasures to overcome restriction. In addition, the virus was inhibited by factors from nonhuman species, including mouse Apobec3, tetherin, and Fv1 proteins. These results have important implications for predicting the natural target cells for XMRV replication, for relating infection to viral pathogenicity and pathology, and for the design of model systems with which to study XMRV-related diseases.
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Affiliation(s)
- Harriet C. T. Groom
- Division of Virology, MRC National Institute for Medical Research, London NW7 1AA, United Kingdom; and
| | - Melvyn W. Yap
- Division of Virology, MRC National Institute for Medical Research, London NW7 1AA, United Kingdom; and
| | - Rui Pedro Galão
- Department of Infectious Diseases, King's College London School of Medicine, Guy's Hospital, London SE1 9RT, United Kingdom
| | - Stuart J. D. Neil
- Department of Infectious Diseases, King's College London School of Medicine, Guy's Hospital, London SE1 9RT, United Kingdom
| | - Kate N. Bishop
- Division of Virology, MRC National Institute for Medical Research, London NW7 1AA, United Kingdom; and
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11
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Campbell EM, Dodding MP, Yap MW, Wu X, Gallois-Montbrun S, Malim MH, Stoye JP, Hope TJ. TRIM5 alpha cytoplasmic bodies are highly dynamic structures. Mol Biol Cell 2007; 18:2102-11. [PMID: 17392513 PMCID: PMC1877106 DOI: 10.1091/mbc.e06-12-1075] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2006] [Revised: 02/26/2007] [Accepted: 03/20/2007] [Indexed: 12/13/2022] Open
Abstract
Tripartite motif (TRIM)5 alpha has recently been identified as a host restriction factor that has the ability to block infection by certain retroviruses in a species-dependent manner. One interesting feature of this protein is that it is localized in distinct cytoplasmic clusters designated as cytoplasmic bodies. The potential role of these cytoplasmic bodies in TRIM5 alpha function remains to be defined. By using fluorescent fusion proteins and live cell microscopy, we studied the localization and dynamics of TRIM5 alpha cytoplasmic bodies. This analysis reveals that cytoplasmic bodies are highly mobile, exhibiting both short saltatory movements and unidirectional long-distance movements along the microtubule network. The morphology of the cytoplasmic bodies is also dynamic. Finally, photobleaching and photoactivation analysis reveals that the TRIM5 alpha protein present in the cytoplasmic bodies is very dynamic, rapidly exchanging between cytoplasmic bodies and a more diffuse cytoplasmic population. Therefore, TRIM5 alpha cytoplasmic bodies are dynamic structures more consistent with a role in function or regulation rather than protein aggregates or inclusion bodies that represent dead-end static structures.
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Affiliation(s)
- Edward M. Campbell
- *Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611-3008
| | - Mark P. Dodding
- Division of Virology, Medical Research Council National Institute for Medical Research, London, United Kingdom NW7 1AA; and
| | - Melvyn W. Yap
- Division of Virology, Medical Research Council National Institute for Medical Research, London, United Kingdom NW7 1AA; and
| | - Xiaolu Wu
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60612
| | - Sarah Gallois-Montbrun
- Department of Infectious Diseases, Guy's Hospital, King's College London School of Medicine, London, United Kingdom SE1 9RT
| | - Michael H. Malim
- Department of Infectious Diseases, Guy's Hospital, King's College London School of Medicine, London, United Kingdom SE1 9RT
| | - Jonathan P. Stoye
- Division of Virology, Medical Research Council National Institute for Medical Research, London, United Kingdom NW7 1AA; and
| | - Thomas J. Hope
- *Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611-3008
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12
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Yap MW, Mortuza GB, Taylor IA, Stoye JP. The design of artificial retroviral restriction factors. Virology 2007; 365:302-14. [PMID: 17493656 DOI: 10.1016/j.virol.2007.04.005] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2006] [Revised: 01/10/2007] [Accepted: 04/08/2007] [Indexed: 11/16/2022]
Abstract
In addition to the ability to bind the retroviral capsid protein, the retroviral restriction factors Fv1, Trim5alpha and Trim5-CypA share the common property of containing sequences that promote self-association. Otherwise Fv1 and Trim5alpha appear unrelated. Mutational analyses showed that restriction was invariably lost when changes designed to disrupt the sequences responsible for multimerization were introduced. A novel restriction protein could be obtained by substituting sequences from the self-associating domain of Fv1 for the Trim5 sequences in Trim5-CypA. Similarly, a fusion protein containing cyclophilin A joined to arfaptin2, a protein known to form extended dimers, was also shown to restrict HIV-1. Hence, multimerization of a capsid-binding domain could be the common minimum design feature for capsid-dependent retroviral restriction factors. However, not all domains that promote multimerization can substitute for the N-terminal domains of Fv1 and Trim5alpha. Moreover, only CypA can provide a capsid-binding site with different N-terminal domains. It is suggested that the spatial relationship between the multiple target binding sites may be important for restriction.
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Affiliation(s)
- Melvyn W Yap
- Division of Virology, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
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13
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Bishop KN, Mortuza GB, Howell S, Yap MW, Stoye JP, Taylor IA. Characterization of an amino-terminal dimerization domain from retroviral restriction factor Fv1. J Virol 2006; 80:8225-35. [PMID: 16873278 PMCID: PMC1563794 DOI: 10.1128/jvi.00395-06] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The Fv1 protein is an endogenous factor in mice that confers resistance to infection by certain classes of murine leukemia virus, a phenomenon referred to as restriction. The mechanism of restriction is not understood, and the low endogenous level of Fv1 in cells has prevented any biochemical or biophysical analysis of the protein. We have now purified recombinant Fv1(n) protein from a baculovirus system and demonstrate that Fv1 exists in a multimeric form. Furthermore, we have mapped the position of two domains within the protein using limited proteolysis. Biophysical characterization of the N-terminal domain reveals that it comprises a highly helical and extended dimeric structure. Based on these biochemical and biophysical data, we propose a model for the arrangement of domains in Fv1 and suggest that dimerization of the N-terminal domain is necessary for Fv1 function to allow the protein to interact with multiple capsid protomers in retroviral cores.
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Affiliation(s)
- Kate N. Bishop
- Divisions of Virology, Protein Structure, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, United Kingdom
| | - Gulnahar B. Mortuza
- Divisions of Virology, Protein Structure, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, United Kingdom
| | - Steven Howell
- Divisions of Virology, Protein Structure, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, United Kingdom
| | - Melvyn W. Yap
- Divisions of Virology, Protein Structure, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, United Kingdom
| | - Jonathan P. Stoye
- Divisions of Virology, Protein Structure, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, United Kingdom
| | - Ian A. Taylor
- Divisions of Virology, Protein Structure, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, United Kingdom
- Corresponding author. Mailing address: Division of Protein Structure, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, United Kingdom. Phone: 44 20 8816 2552. Fax: 44 20 8816 2580. E-mail:
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14
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Ohkura S, Yap MW, Sheldon T, Stoye JP. All three variable regions of the TRIM5alpha B30.2 domain can contribute to the specificity of retrovirus restriction. J Virol 2006; 80:8554-65. [PMID: 16912305 PMCID: PMC1563890 DOI: 10.1128/jvi.00688-06] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2006] [Accepted: 06/12/2006] [Indexed: 01/05/2023] Open
Abstract
Recent studies have revealed the contribution of TRIM5alpha to retrovirus restriction in cells from a variety of primate species. TRIM5alpha consists of a tripartite motif (the RBCC domain) followed by a B30.2 domain. The B30.2 domain is thought to be involved in determination of restriction specificity and contains three variable regions. To investigate the relationship between the phylogeny of primate TRIM5alpha and retrovirus restriction specificity, a series of chimeric TRIM5alpha consisting of the human RBCC domain followed by the B30.2 domain from various primates was constructed. These constructs showed restriction profiles largely consistent with the origin of the B30.2 domain. Restriction specificity was further investigated with a variety of TRIM5alphas containing mixed or mutated B30.2 domains. This study revealed the importance of all three variable regions for determining restriction specificity. Based on the molecular structures of other PRYSPRY domains solved recently, a model for the molecular structure of the B30.2 domain of TRIM5alpha was developed. The model revealed that the variable regions of the B30.2 domain are present as loops located on one side of the B30.2 core structure. It is hypothesized that these three loops form a binding surface for virus and that evolutionary changes in any one of the loops can alter restriction specificity.
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Affiliation(s)
- Sadayuki Ohkura
- Division of Virology, National Institute for Medical Research, Medical Research Council, London, UK
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15
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Yap MW, Dodding MP, Stoye JP. Trim-cyclophilin A fusion proteins can restrict human immunodeficiency virus type 1 infection at two distinct phases in the viral life cycle. J Virol 2006; 80:4061-7. [PMID: 16571822 PMCID: PMC1440439 DOI: 10.1128/jvi.80.8.4061-4067.2006] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2005] [Accepted: 01/25/2006] [Indexed: 11/20/2022] Open
Abstract
The Trim5alpha protein from several primates restricts retroviruses in a capsid (CA)-dependent manner. In owl monkeys, the B30.2 domain of Trim5 has been replaced by cyclophilin A (CypA) following a retrotransposition. Restriction of human immunodeficiency virus type 1 (HIV-1) by the resulting Trim5-CypA fusion protein depends on CA binding to CypA, suggesting both that the B30.2 domain might be involved in CA binding and that the tripartite RING motif, B-BOX, and coiled coil (RBCC) motif domain can function independently of the B30.2 domain in restriction. To investigate the potential of RBCCs from other Trims to participate in restricting HIV-1, CypA was fused to the RBCC of Trim1, Trim18, and Trim19 and tested for restriction. Despite low identity within the RBCC domain, all fusion proteins were found to restrict HIV-1 but not the nonbinding G89V mutant, indicating that the overall structure of RBCC and not its primary sequence was important for the restriction function. The critical interaction between CA and Trim-CypA appears to take place soon after viral entry. Quantitative PCR analysis of viral reverse transcriptase products revealed that the different fusion proteins block HIV-1 at two distinct stages of its life cycle, either prior to reverse transcription or just before integration. With Trim1 and Trim18, this timing is dependent on the length of the Trim component of the fusion protein. These observations suggest that restriction factor binding can have different mechanistic consequences.
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Affiliation(s)
- Melvyn W Yap
- Division of Virology, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, United Kingdom
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16
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Abstract
Murine leukemia virus is restricted in mouse cells lines by a host factor known as Fv1 and in human cell lines by Ref1. Genetic evidence indicates that these restriction factors target the virus capsid (CA) protein. Restriction can be overcome by adding virus at a high multiplicity of infection, indicating that the restriction factors can be saturated. Cells preexposed to restricted virus will allow infection by a second virus which would normally be restricted. This phenomenon is known as abrogation; it provides us with a tool with which to study the interaction of virus with restriction factors. We tested the abilities of several Gag processing mutants to abrogate restriction. Our results show that CA must be cleaved from both p12 and nucleocapsid in order for the incoming virion to interact with the restriction factor. Endogenous expression of properly processed CA, however, failed to abrogate restriction. These results suggest that as well as being processed, CA must also be properly assembled in the form of a condensed viral core in order to interact with Fv1 and Ref1. This polymeric structure may contain restriction factor binding sites not present in monomeric CA.
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Affiliation(s)
- Mark P Dodding
- Medical Research Council, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, United Kingdom
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17
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Yap MW, Nisole S, Stoye JP. A Single Amino Acid Change in the SPRY Domain of Human Trim5α Leads to HIV-1 Restriction. Curr Biol 2005; 15:73-8. [PMID: 15649369 DOI: 10.1016/j.cub.2004.12.042] [Citation(s) in RCA: 323] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2004] [Revised: 11/04/2004] [Accepted: 11/05/2004] [Indexed: 11/29/2022]
Abstract
Retroviral restriction factors are cellular proteins that interfere with retrovirus replication at a postpenetration, preintegration stage in the viral life cycle. The first restriction activity described was the mouse Fv1 gene. Three different alleles of Fv1, capable of restricting different murine leukaemia viruses (MLV), have been characterized at the molecular level. Two further activities, Ref1, which acts on MLV, and Lv1, which acts on lentiviruses, have been identified in other mammalian species. Recently, it has become clear that Ref1 and Lv1 are encoded by the same gene, Trim5alpha, which inhibits retrovirus replication in a species-specific manner. A series of chimeras between the human and rhesus monkey Trim5 genes were created to map and identify these specificity determinants. The Trim5alpha SPRY domain was found to be responsible for targeting HIV-1 restriction. By contrast, N-MLV restriction appears dependent on both the coiled-coil domain and the SPRY domain. A single amino acid substitution (R332P) in the human Trim5alpha can confer the ability to restrict HIV-1, suggesting that small changes during evolution may have profound effects on our susceptibility to cross-species infection.
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Affiliation(s)
- Melvyn W Yap
- Division of Virology, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, United Kingdom
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18
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Abstract
The specificity determinants for susceptibility to resistance by the Fv1 n and b alleles map to amino acid 110 of the murine leukemia virus CA protein. To study the interaction between Fv1 and CA, we examined changes in CA resulting in the loss of susceptibility to Fv1 resistance in naturally occurring NB- and NR-tropic viruses. A variety of amino acid changes affecting Fv1 tropism were identified, at CA positions 82, 92 to 95, 105, 114, and 117, and they all were mapped to the apparent exterior of virion-associated CA. These amino acids may form a binding surface for Fv1.
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Affiliation(s)
- Anthony Stevens
- Division of Virology, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, United Kingdom
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19
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Nisole S, Lynch C, Stoye JP, Yap MW. A Trim5-cyclophilin A fusion protein found in owl monkey kidney cells can restrict HIV-1. Proc Natl Acad Sci U S A 2004; 101:13324-8. [PMID: 15326303 PMCID: PMC516566 DOI: 10.1073/pnas.0404640101] [Citation(s) in RCA: 246] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2004] [Indexed: 11/18/2022] Open
Abstract
Lv1 restriction of HIV-1 in the cells of Old World monkeys is associated with the expression of the Trim5 gene. Uniquely, in owl monkey kidney cells, HIV-1 restriction is dependent on the ability of incoming viral capsid protein to bind cyclophilin A (CypA). Cloning of the owl monkey Trim5 gene now reveals the presence of an inserted CypA pseudogene within intron 7 of the Trim5 gene. This insertion results in the formation of a chimeric Trim5-CypA transcript. Transfer of a cDNA corresponding to this transcript into human cells confers cyclosporin A-sensitive resistance to HIV-1 infection. The restriction factor appears to be a chimeric protein created by retrotransposon-mediated exon shuffling.
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Affiliation(s)
- Sébastien Nisole
- Division of Virology, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, United Kingdom
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20
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Yap MW, Nisole S, Lynch C, Stoye JP. Trim5alpha protein restricts both HIV-1 and murine leukemia virus. Proc Natl Acad Sci U S A 2004; 101:10786-91. [PMID: 15249690 PMCID: PMC490012 DOI: 10.1073/pnas.0402876101] [Citation(s) in RCA: 376] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2004] [Accepted: 06/07/2004] [Indexed: 11/18/2022] Open
Abstract
Replication of HIV-1 and N-tropic murine leukemia virus (N-MLV) is restricted in a number of different primate cells. In some cell lines, cross-saturation experiments suggest that the two viruses are interacting with the same restriction factor. Recently, Trim5alpha protein from rhesus monkey was found to restrict HIV-1. We have confirmed this result and have shown that Trim5alpha from two African green monkey cell lines, Vero and CV-1, also restricts HIV-1. In addition, we show that human, rhesus, and African green monkey Trim5alpha can restrict N-MLV. By using a panel of MLV capsid mutants, subtle differences in the anti-MLV activity were identified among the different primate Trim5alpha cDNAs. Trim1 isolated from humans and green monkeys was also found to restrict N-MLV. We hypothesize that the Trim family of proteins plays a widespread role in innate immunity to viral infection.
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Affiliation(s)
- Melvyn W Yap
- Division of Virology, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, United Kingdom
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21
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Abstract
Budding through the host-cell membrane is a key step in the life cycle of many viruses. Recent studies of retrovirus replication implicate a large number of cellular proteins in this process.
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Affiliation(s)
- Melvyn W Yap
- Division of Virology, National Institute for Medical Research, The Ridgeway, London NW7 1AA, UK
| | - Jonathan P Stoye
- Division of Virology, National Institute for Medical Research, The Ridgeway, London NW7 1AA, UK
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22
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Abstract
Retroviral resistance mediated by the murine Fv1 gene is believed to result from a direct interaction between the Fv1 gene product and the viral capsid protein. To study the mechanism of Fv1 action, the expression and intracellular localisation of the Fv1 protein were examined. Only very low levels of protein expression seem necessary for virus restriction but the site of expression appears crucial. Active Fv1 was found in association with tubules of the trans-Golgi network, whereas an inactive form was localised in the endoplasmic reticulum. We hypothesize that Fv1 is compartmentalised in the cell on the pathway taken by virus en route to the nucleus, suggesting that incoming virus must pass the trans-Golgi network during its transit to the nucleus.
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Affiliation(s)
- Melvyn W Yap
- Division of Virology, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, United Kingdom
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23
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Abstract
A study was conducted to investigate the effects of increasing the amount of each retroviral component on vector production. It was found that, while the components of both amphotropic and ecotropic vectors were expressed independently of each other in a transient transfection system, increasing the amount of the gag/gag-pol component resulted in a decrease in virus titres for the amphotropic particles but not ecotropic particles. Analyses of the virus stocks produced indicated that the negative effect on titres was closely linked to the availability of envelope proteins for virion incorporation. The negative effect was not observed for ecotropic particle production in 293T cells, where the ecotropic receptor was absent, but was manifested when production was conducted in 293/12 cells expressing the ecotropic receptor. This suggested that the premature interaction between envelope and receptor in producer cells could limit the amount of envelope available for virion incorporation. In designing optimal vector production systems it is essential, therefore, to balance the concentration of the vector components and to ensure that there is never an excess of Gag/Gag-Pol.
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Affiliation(s)
- Melvyn W Yap
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK1
| | - Susan M Kingsman
- Oxford BioMedica (UK) Ltd, The Medawar Centre, The Oxford Science Park, Oxford OX4 4GA, UK2
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK1
| | - Alan J Kingsman
- Oxford BioMedica (UK) Ltd, The Medawar Centre, The Oxford Science Park, Oxford OX4 4GA, UK2
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK1
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Yap MW, Kara UA, ten Heggeler-Bordier B, Ting RC, Tan TM. Partial nucleotide sequence and organisation of extrachromosomal plastid-like DNA in Plasmodium berghei. Gene 1997; 200:91-8. [PMID: 9373142 DOI: 10.1016/s0378-1119(97)00385-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The murine malaria parasite Plasmodium berghei contains a plastid-like extrachromosomal genome. This genome is 30.7 kb in size and is transcriptionally active as shown by RT-PCR. DNA sequence analysis of the genome reveals 69.9-95.5% homology to sequences of the 35-kb extrachromosomal circle found in the human malaria species Plasmodium falciparum. Homologous sequences include regions of genes for the ssu-rRNA, lsu-rRNA, rpo B and clusters of t-RNAs. Sequence variation between the two Plasmodium species exists in the non-coding interspacing regions. A physical map has been constructed for the P. berghei circle, indicating the EcoRI and HindIII restriction sites as well as the arrangement of the rRNA, rpo B and tRNA genes. Arrangement of these genes is similar to that found on the P. falciparum 35-kb circle. The P. berghei circular element is distinct from the mitochondrial 6-kb DNA of both the murine and the human Plasmodium species. Preliminary results indicate that the circle may be a useful target for drug therapy.
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Affiliation(s)
- M W Yap
- Molecular Parasitology Laboratory, School of Biological Sciences, Singapore, Singapore
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