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Journal articleTaylor MRG, Spirek M, Chaurasiya KR, et al., 2015,
Rad51 Paralogs Remodel Pre-synaptic Rad51 Filaments to Stimulate Homologous Recombination
, Cell, Vol: 162, Pages: 271-286, ISSN: 0092-8674Repair of DNA double strand breaks by homologous recombination (HR) is initiated by Rad51 filament nucleation on single-stranded DNA (ssDNA), which catalyzes strand exchange with homologous duplex DNA. BRCA2 and the Rad51 paralogs are tumor suppressors and critical mediators of Rad51. To gain insight into Rad51 paralog function, we investigated a heterodimeric Rad51 paralog complex, RFS-1/RIP-1, and uncovered the molecular basis by which Rad51 paralogs promote HR. Unlike BRCA2, which nucleates RAD-51-ssDNA filaments, RFS-1/RIP-1 binds and remodels pre-synaptic filaments to a stabilized, “open,” and flexible conformation, in which the ssDNA is more accessible to nuclease digestion and RAD-51 dissociation rate is reduced. Walker box mutations in RFS-1, which abolish filament remodeling, fail to stimulate RAD-51 strand exchange activity, demonstrating that remodeling is essential for RFS-1/RIP-1 function. We propose that Rad51 paralogs stimulate HR by remodeling the Rad51 filament, priming it for strand exchange with the template duplex.
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Journal articleBazot Q, Paschos K, Skalska L, et al., 2015,
Epstein-Barr virus proteins EBNA3A and EBNA3C together induce expression of the oncogenic microRNA cluster miR-221/miR-222 and ablate expression of its target p57KIP2.
, PLOS Pathogens, Vol: 11, ISSN: 1553-7366We show that two host-encoded primary RNAs (pri-miRs) and the corresponding microRNA (miR) clusters - widely reported to have cell transformation-associated activity - are regulated by EBNA3A and EBNA3C. Utilising a variety of EBV-transformed lymphoblastoid cell lines (LCLs) carrying knockout-, revertant- or conditional-EBV recombinants, it was possible to demonstrate unambiguously that EBNA3A and EBNA3C are both required for transactivation of the oncogenic miR-221/miR-222 cluster that is expressed at high levels in multiple human tumours - including lymphoma/leukemia. ChIP, ChIP-seq, and chromosome conformation capture analyses indicate that this activation results from direct targeting of both EBV proteins to chromatin at the miR-221/miR-222 genomic locus and activation via a long-range interaction between enhancer elements and the transcription start site of a long non-coding pri-miR located 28kb upstream of the miR sequences. Reduced levels of miR-221/miR-222 produced by inactivation or deletion of EBNA3A or EBNA3C resulted in increased expression of the cyclin-dependent kinase inhibitor p57KIP2, a well-established target of miR-221/miR-222. MiR blocking experiments confirmed that miR-221/miR-222 target p57KIP2 expression in LCLs. In contrast, EBNA3A and EBNA3C are necessary to silence the tumour suppressor cluster miR-143/miR-145, but here ChIP-seq suggests that repression is probably indirect. This miR cluster is frequently down-regulated or deleted in human cancer, however, the targets in B cells are unknown. Together these data indicate that EBNA3A and EBNA3C contribute to B cell transformation by inhibiting multiple tumour suppressor proteins, not only by direct repression of protein-encoding genes, but also by the manipulation of host long non-coding pri-miRs and miRs.
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Journal articleBamford A, Crowe BHA, Hacohen Y, et al., 2015,
Pediatric Herpes Simplex Virus Encephalitis Complicated by <i>N</i>-Methyl-<i>D</i>-aspartate Receptor Antibody Encephalitis
, JOURNAL OF THE PEDIATRIC INFECTIOUS DISEASES SOCIETY, Vol: 4, Pages: E17-E21, ISSN: 2048-7193- Cite
- Citations: 25
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Journal articlePalser AL, Grayson NE, White RE, et al., 2015,
Genome Diversity of Epstein-Barr Virus from Multiple Tumor Types and Normal Infection
, Journal of Virology, Vol: 89, Pages: 5222-5237, ISSN: 1098-5514Epstein-Barr virus (EBV) infects most of the world’s population and is causally associated with several human cancers, but littleis known about how EBV genetic variation might influence infection or EBV-associated disease. There are currently no publishedwild-type EBV genome sequences from a healthy individual and very few genomes from EBV-associated diseases. We havesequenced 71 geographically distinct EBV strains from cell lines, multiple types of primary tumor, and blood samples and thefirst EBV genome from the saliva of a healthy carrier. We show that the established genome map of EBV accurately represents allstrains sequenced, but novel deletions are present in a few isolates. We have increased the number of type 2 EBV genomes sequencedfrom one to 12 and establish that the type 1/type 2 classification is a major feature of EBV genome variation, definedalmost exclusively by variation of EBNA2 and EBNA3 genes, but geographic variation is also present. Single nucleotide polymorphism(SNP) density varies substantially across all known open reading frames and is highest in latency-associated genes. SomeT-cell epitope sequences in EBNA3 genes show extensive variation across strains, and we identify codons under positive selection,both important considerations for the development of vaccines and T-cell therapy. We also provide new evidence for recombinationbetween strains, which provides a further mechanism for the generation of diversity. Our results provide the firstglobal view of EBV sequence variation and demonstrate an effective method for sequencing large numbers of genomes to furtherunderstand the genetics of EBV infection.
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Journal articleSerrao E, Ballandras-Colas A, Cherepanov P, et al., 2015,
Key determinants of target DNA recognition by retroviral intasomes
, Retrovirology, Vol: 12, ISSN: 1742-4690Background: Retroviral integration favors weakly conserved palindrome sequences at the sites of viral DNA joiningand generates a short (4–6 bp) duplication of host DNA flanking the provirus. We previously determined two keyparameters that underlie the target DNA preference for prototype foamy virus (PFV) and human immunodeficiencyvirus type 1 (HIV-1) integration: flexible pyrimidine (Y)/purine (R) dinucleotide steps at the centers of the integrationsites, and base contacts with specific integrase residues, such as Ala188 in PFV integrase and Ser119 in HIV-1 integrase.Here we examined the dinucleotide preference profiles of a range of retroviruses and correlated these findings withrespect to length of target site duplication (TSD).Results: Integration datasets covering six viral genera and the three lengths of TSD were accessed from the literatureor generated in this work. All viruses exhibited significant enrichments of flexible YR and/or selection against rigid RYdinucleotide steps at the centers of integration sites, and the magnitude of this enrichment inversely correlated withTSD length. The DNA sequence environments of in vivo-generated HIV-1 and PFV sites were consistent with integrationinto nucleosomes, however, the local sequence preferences were largely independent of target DNA chromatinization.Integration sites derived from cells infected with the gammaretrovirus reticuloendotheliosis virus strain A (Rev-A),which yields a 5 bp TSD, revealed the targeting of global chromatin features most similar to those of Moloneymurine leukemia virus, which yields a 4 bp duplication. In vitro assays revealed that Rev-A integrase interacts withand is catalytically stimulated by cellular bromodomain containing 4 protein.Conclusions: Retroviral integrases have likely evolved to bend target DNA to fit scissile phosphodiester bondsinto two active sites for integration, and viruses that cut target DNA with a 6 bp stagger may not need to bendDNA as sharply as viruses tha
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Journal articleFoerster A, Maertens GN, Farrell PJ, et al., 2015,
Dimerization of Matrix Protein Is Required for Budding of Respiratory Syncytial Virus
, Journal of Virology, Vol: 89, Pages: 4624-4635, ISSN: 1098-5514Respiratory syncytial virus (RSV) infects epithelial cells of the respiratory tract and is a major cause of bronchiolitis and pneumonia in children and the elderly. The virus assembles and buds through the plasma membrane, forming elongated membrane filaments, but details of how this happens remain obscure. Oligomerization of the matrix protein (M) is a key step in the process of assembly and infectious virus production. In addition, it was suggested to affect the conformation of the fusion protein, the major current target for RSV antivirals, in the mature virus. The structure and assembly of M are thus key parameters in the RSV antiviral development strategy. The structure of RSV M was previously published as a monomer. Other paramyxovirus M proteins have been shown to dimerize, and biochemical data suggest that RSV M also dimerizes. Here, using size exclusion chromatography-multiangle laser light scattering, we show that the protein is dimeric in solution. We also crystallized M in two crystal forms and show that it assembles into equivalent dimers in both lattices. Dimerization interface mutations destabilize the M dimer in vitro. To assess the biological relevance of dimerization, we used confocal imaging to show that dimerization interface mutants of M fail to assemble into viral filaments on the plasma membrane. Additionally, budding and release of virus-like particles are prevented in M mutants that fail to form filaments. Importantly, we show that M is biologically active as a dimer and that the switch from M dimers to higher-order oligomers triggers viral filament assembly and virus production.
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Journal articleAllday MJ, Bazot Q, White RE, 2015,
The EBNA3 Family: Two Oncoproteins and a Tumour Suppressor that Are Central to the Biology of EBV in B Cells
, EPSTEIN BARR VIRUS, VOL 2: ONE HERPES VIRUS: MANY DISEASES, Vol: 391, Pages: 61-117, ISSN: 0070-217X- Author Web Link
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- Citations: 61
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Journal articleFarrell PJ, 2015,
Epstein-Barr Virus Strain Variation
, EPSTEIN BARR VIRUS, VOL 1: ONE HERPES VIRUS: MANY DISEASES, Vol: 390, Pages: 45-69, ISSN: 0070-217X- Author Web Link
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- Citations: 41
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Journal articleLong JS, Benfield CT, Barclay WS, 2014,
One-way trip: Influenza virus' adaptation to gallinaceous poultry may limit its pandemic potential
, Bioessays, Vol: 37, Pages: 204-212, ISSN: 1521-1878We hypothesise that some influenza virus adaptations to poultry may explain why the barrier for human-to-human transmission is not easily overcome once the virus has crossed from wild birds to chickens. Since the cluster of human infections with H5N1 influenza in Hong Kong in 1997, chickens have been recognized as the major source of avian influenza virus infection in humans. Although often severe, these infections have been limited in their subsequent human-to-human transmission, and the feared H5N1 pandemic has not yet occurred. Here we examine virus adaptations selected for during replication in chickens and other gallinaceous poultry. These include altered receptor binding and increased pH of fusion of the haemagglutinin as well as stalk deletions of the neuraminidase protein. This knowledge could aid the delivery of vaccines and increase our ability to prioritize research efforts on those viruses from the diverse array of avian influenza viruses that have greatest human pandemic potential.
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Journal articlePekkonen P, Jarviluoma A, Zinovkina N, et al., 2014,
KSHV viral cyclin interferes with T-cell development and induces lymphoma through Cdk6 and Notch activation in vivo
, CELL CYCLE, Vol: 13, Pages: 3670-3684, ISSN: 1538-4101- Author Web Link
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- Citations: 18
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