Structural genomics of the Epstein–Barr virus

Tarbouriech, Nicolas; Buisson, Marlyse; Géoui, Thibault; Daenke, Susan; Cusack, Stephen; Burmeister, W.P.

doi:10.1107/s0907444906030034

Cited by 39 publications

(42 citation statements)

References 73 publications

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“…3A), as defined by Tarbouriech et al (36). HKNPC2, -3, 4, -5, -8, and -9 had 105 to 111 nonsynonymous mutations located in the latent genes, whereas HKNPC6 and -7 had higher numbers of 145 and 137 mutations, respectively.…”

Section: Resultsmentioning

confidence: 99%

Genomic Diversity of Epstein-Barr Virus Genomes Isolated from Primary Nasopharyngeal Carcinoma Biopsy Samples

Kwok

Palser

et al. 2014

J Virol

101

111

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Undifferentiated nasopharyngeal carcinoma (NPC) has a 100% association with Epstein-Barr virus (EBV). However, only three EBV genomes isolated from NPC patients have been sequenced to date, and the role of EBV genomic variations in the pathogenesis of NPC is unclear. We sought to obtain the sequences of EBV genomes in multiple NPC biopsy specimens in the same geographic location in order to reveal their sequence diversity. Three published EBV (B95-8, C666-1, and HKNPC1) genomes were first resequenced using the sequencing workflow of target enrichment of EBV DNA by hybridization, followed by next-generation sequencing, de novo assembly, and joining of contigs by Sanger sequencing. The sequences of eight NPC biopsy specimenderived EBV (NPC-EBV) genomes, designated HKNPC2 to HKNPC9, were then determined. They harbored 1,736 variations in total, including 1,601 substitutions, 64 insertions, and 71 deletions, compared to the reference EBV. Furthermore, genes encoding latent, early lytic, and tegument proteins and glycoproteins were found to contain nonsynonymous mutations of potential biological significance. Phylogenetic analysis showed that the HKNPC6 and -7 genomes, which were isolated from tumor biopsy specimens of advanced metastatic NPC cases, were distinct from the other six NPC-EBV genomes, suggesting the presence of at least two parental lineages of EBV among the NPC-EBV genomes. In conclusion, much greater sequence diversity among EBV isolates derived from NPC biopsy specimens is demonstrated on a whole-genome level through a complete sequencing workflow. Large-scale sequencing and comparison of EBV genomes isolated from NPC and normal subjects should be performed to assess whether EBV genomic variations contribute to NPC pathogenesis. IMPORTANCEThis study established a sequencing workflow from EBV DNA capture and sequencing to de novo assembly and contig joining. We reported eight newly sequenced EBV genomes isolated from primary NPC biopsy specimens and revealed the sequence diversity on a whole-genome level among these EBV isolates. At least two lineages of EBV strains are observed, and recombination among these lineages is inferred. Our study has demonstrated the value of, and provided a platform for, genome sequencing of EBV.T he incidence rate of undifferentiated nasopharyngeal carcinoma (NPC) is exceptionally high in the southern part of China, and this type of carcinoma is 100% associated with Epstein-Barr virus (EBV) (1). To investigate the role of EBV genomic variation in the pathogenesis of NPC, EBV strains had been characterized in NPC by genotyping polymorphic markers in the EBER1 and -2, LMP1, BHRF1, BZLF1, and EBNA1 gene loci in tumor samples obtained from China, southern Asia, and northern Africa (2-7). Association of LMP1 deletion variant Asp335 with NPC in Hong Kong was reported (8). Specific EBNA1 (V-val) and LMP1 subtypes (China 1) also showed preferential occurrence in NPC biopsy specimens (9, 10). However, genetic variations in the small subsets of genes investigated were not ...

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Section: Resultsmentioning

confidence: 99%

Genomic Diversity of Epstein-Barr Virus Genomes Isolated from Primary Nasopharyngeal Carcinoma Biopsy Samples

Kwok

Palser

et al. 2014

J Virol

101

111

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“…structures from viral proteins, which are, in general, more flexible and unstable (46)(47)(48). We particularly faced these challenges when overexpressing and purifying the flexible N-terminal domain of ICP27, between residues 1 to 210.…”

Section: Figmentioning

confidence: 99%

Structure of the C-Terminal Domain of the Multifunctional ICP27 Protein from Herpes Simplex Virus 1

Patel

Dahlroth

Rajakannan

et al. 2015

J Virol

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Herpesviruses are nuclear-replicating viruses that have successfully evolved to evade the immune system of humans, establishing lifelong infections. ICP27 from herpes simplex virus is a multifunctional regulatory protein that is functionally conserved in all known human herpesviruses. It has the potential to interact with an array of cellular proteins, as well as intronless viral RNAs. ICP27 plays an essential role in viral transcription, nuclear export of intronless RNAs, translation of viral transcripts, and virion host shutoff function. It has also been implicated in several signaling pathways and the prevention of apoptosis. Although much is known about its central role in viral replication and infection, very little is known about the structure and mechanistic properties of ICP27 and its homologs. We present the first crystal structure of ICP27 C-terminal domain at a resolution of 2.0 Å. The structure reveals the C-terminal half of ICP27 to have a novel fold consisting of ␣-helices and long loops, along with a unique CHCC-type of zinc-binding motif. The two termini of this domain extend from the central core and hint to possibilities of making interactions. ICP27 essential domain is capable of forming self-dimers as seen in the structure, which is confirmed by analytical ultracentrifugation study. Preliminary in vitro phosphorylation assays reveal that this domain may be regulated by cellular kinases. IMPORTANCE ICP27 is a key regulatory protein of the herpes simplex virus and has functional homologs in all known human herpesviruses.Understanding the structure of this protein is a step ahead in deciphering the mechanism by which the virus thrives. In this study, we present the first structure of the C-terminal domain of ICP27 and describe its novel features. We critically analyze the structure and compare our results to the information available form earlier studies. This structure can act as a guide in future experimental designs and can add to a better understanding of mechanism of ICP27, as well as that of its homologs. Herpes simplex virus (HSV) and other human herpesviruses (HHVs; e.g., Epstein-Barr virus and varicella-zoster virus) have evolved a unique strategy of virion host shutoff, in which they efficiently suppress the host protein synthesis. At the onset of the lytic phase, viral immediate-early (IE) genes are expressed first. These IE proteins are responsible for inducing the expression of viral early and late genes. The key IE protein of HSV, infectious cell protein 27 (ICP27), helps in the host shutoff function (1, 2). This 63-kDa protein consists of 512 amino acids and is involved in multiple functions, such as stalling host pre-RNA processing, exporting intronless viral mRNAs out of the nucleus, shuttling between host nucleus and cytoplasm facilitated by its nuclear export signal (NES) and nuclear localization signal (NLS), and interacting with RNA via its RGG box (3, 4). Most of these functions are conserved across the Herpesviridae family, and ICP27 homologs are present in all kno...

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“…EBV is also associated with the development of certain malignancies, including African Burkitt lymphomas, B-cell lymphomas of immunocompromised patients, nasopharyngeal carcinomas, Hodgkin's disease, and occasionally with T-cell lymphomas and gastric cancers [2]. The EBV genome is composed of linear double-stranded DNA, with approximately 172 kilobase pairs in length [3], which encodes about 86 proteins [4]. According to their localization in the virions, the proteins could be divided into five groups: envelope, tegument, capsid, and unclassified and nonstructural proteins.…”

Section: Introductionmentioning

confidence: 99%

Characterization of the Nucleocytoplasmic Transport Mechanisms of Epstein-Barr Virus BFLF2

Chen

Zou

et al. 2018

Cell Physiol Biochem

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Background/Aims: Epstein-Barr virus (EBV) BFLF2, the homologue of herpes simplex virus 1 (HSV-1) UL31, is crucial for the efficient viral DNA packaging and primary egress across the nuclear membrane. However, we still do not know its subcellular transport mechanisms. Methods: Interspecies heterokaryon assays were utilized to detect the nucleocytoplasmic shuttling of BFLF2, and mutation analysis, plasmid transfection and fluorescence microscopy assays were performed to identify the functional nuclear localization sequence (NLS) and nuclear export sequence (NES) of BFLF2 in live cells. Furthermore, the nuclear import and export of BFLF2 were assessed by confocal microscopy, co-immunoprecipitation and immunoblot assays. Results: BFLF2 was confirmed to shuttle between the nucleus and cytoplasm. Two predicted NESs were shown to be nonfunctional, yet we proved that the nuclear export of BFLF2 was mediated through transporter associated with antigen processing (TAP), but not chromosomal region maintenance 1 (CRM1) dependent pathway. Furthermore, one functional NLS, ²²RRLMHPHHRNYTASKASAH⁴⁰, was identified, and the aa22-23, aa22-25, aa28-30 and aa37-40 had an important role in the nuclear localization of BFLF2. Besides, the nuclear import of BFLF2 was demonstrated through Ran-, importin α7-, importin β1- and transportin-1-dependent mechanism that does not require importin α1, α3 and α5. Conclusion: These works are of significance for the further study of the functions of BFLF2 during EBV infection, as well as for further insights into the design of new antiviral drug target and vaccine development against EBV.

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Structural genomics of the Epstein–Barr virus

Cited by 39 publications

References 73 publications

Genomic Diversity of Epstein-Barr Virus Genomes Isolated from Primary Nasopharyngeal Carcinoma Biopsy Samples

Genomic Diversity of Epstein-Barr Virus Genomes Isolated from Primary Nasopharyngeal Carcinoma Biopsy Samples

Structure of the C-Terminal Domain of the Multifunctional ICP27 Protein from Herpes Simplex Virus 1

Characterization of the Nucleocytoplasmic Transport Mechanisms of Epstein-Barr Virus BFLF2

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