scholarly journals A Global Analysis of Evolutionary Conservation among Known and Predicted Gammaherpesvirus MicroRNAs

2009 ◽  
Vol 84 (2) ◽  
pp. 716-728 ◽  
Author(s):  
Nicole Walz ◽  
Thomas Christalla ◽  
Uwe Tessmer ◽  
Adam Grundhoff
Keyword(s):  
Global Analysis ◽  
Japanese Macaque ◽  
Computational Prediction ◽  
Evolutionary Conservation ◽  
Viral Genomes ◽  
Small Noncoding Rnas ◽  
Barr Virus ◽  
Large Numbers ◽  
Evolutionarily Conserved ◽  
Epstein Barr

ABSTRACT MicroRNAs (miRNAs) are small, noncoding RNAs which posttranscriptionally regulate gene expression. The current release of the miRNA registry lists 16 viruses which encode a total of 146 miRNA hairpins. Strikingly, 139 of these are encoded by members of the herpesvirus family, suggesting an important role for miRNAs in the herpesvirus life cycle. However, with the exception of 7 miRNA hairpins known to be shared by Epstein-Barr virus (EBV) and the closely related rhesus lymphocryptovirus (rLCV), the known herpesvirus miRNAs show little evidence of evolutionary conservation. We have performed a global analysis of miRNA conservation among gammaherpesviruses which is not limited to family members known to encode miRNAs but includes also those which have not been previously analyzed. For this purpose, we have performed a computational prediction of miRNA candidates of all fully sequenced gammaherpesvirus genomes, followed by sequence/structure alignments. Our results indicate that gammaherpesvirus miRNA conservation is limited to two pairs of viral genomes. One is the already-known case of EBV and rLCV. These viruses, however, share significantly more miRNAs than previously thought, as we identified and experimentally verified 10 novel conserved as well as 7 novel nonconserved rLCV pre-miRNA hairpins. The second case consists of rhesus rhadinovirus (RRV), which is predicted to share at least 9 pre-miRNAs with the closely related Japanese macaque herpesvirus (JMHV). Although several other gammaherpesviruses are predicted to encode large numbers of clustered miRNAs at conserved genomic loci, no further examples of evolutionarily conserved miRNA sequences were found.

scholarly journals Histone Loaders CAF1 and HIRA Restrict Epstein-Barr Virus B-Cell Lytic Reactivation

mBio ◽  
2020 ◽  
Vol 11 (5) ◽  
Author(s):  
Yuchen Zhang ◽  
Chang Jiang ◽  
Stephen J. Trudeau ◽  
Yohei Narita ◽  
Bo Zhao ◽  
...  
Keyword(s):  
B Cells ◽  
Burkitt Lymphoma ◽  
Epstein Barr Virus ◽  
Chromatin Assembly ◽  
Lytic Cycle ◽  
Histone Chaperones ◽  
Viral Genomes ◽  
Barr Virus ◽  
Lytic Reactivation ◽  
Epstein Barr

ABSTRACT Epstein-Barr virus (EBV) infects 95% of adults worldwide and causes infectious mononucleosis. EBV is associated with endemic Burkitt lymphoma, Hodgkin lymphoma, posttransplant lymphomas, nasopharyngeal and gastric carcinomas. In these cancers and in most infected B-cells, EBV maintains a state of latency, where nearly 80 lytic cycle antigens are epigenetically suppressed. To gain insights into host epigenetic factors necessary for EBV latency, we recently performed a human genome-wide CRISPR screen that identified the chromatin assembly factor CAF1 as a putative Burkitt latency maintenance factor. CAF1 loads histones H3 and H4 onto newly synthesized host DNA, though its roles in EBV genome chromatin assembly are uncharacterized. Here, we found that CAF1 depletion triggered lytic reactivation and virion secretion from Burkitt cells, despite also strongly inducing interferon-stimulated genes. CAF1 perturbation diminished occupancy of histones 3.1 and 3.3 and of repressive histone 3 lysine 9 and 27 trimethyl (H3K9me3 and H3K27me3) marks at multiple viral genome lytic cycle regulatory elements. Suggestive of an early role in establishment of latency, EBV strongly upregulated CAF1 expression in newly infected primary human B-cells prior to the first mitosis, and histone 3.1 and 3.3 were loaded on the EBV genome by this time point. Knockout of CAF1 subunit CHAF1B impaired establishment of latency in newly EBV-infected Burkitt cells. A nonredundant latency maintenance role was also identified for the DNA synthesis-independent histone 3.3 loader histone regulatory homologue A (HIRA). Since EBV latency also requires histone chaperones alpha thalassemia/mental retardation syndrome X-linked chromatin remodeler (ATRX) and death domain-associated protein (DAXX), EBV coopts multiple host histone pathways to maintain latency, and these are potential targets for lytic induction therapeutic approaches. IMPORTANCE Epstein-Barr virus (EBV) was discovered as the first human tumor virus in endemic Burkitt lymphoma, the most common childhood cancer in sub-Saharan Africa. In Burkitt lymphoma and in 200,000 EBV-associated cancers per year, epigenetic mechanisms maintain viral latency, during which lytic cycle factors are silenced. This property complicated EBV’s discovery and facilitates tumor immunoevasion. DNA methylation and chromatin-based mechanisms contribute to lytic gene silencing. Here, we identified histone chaperones CAF1 and HIRA, which have key roles in host DNA replication-dependent and replication-independent pathways, respectively, as important for EBV latency. EBV strongly upregulates CAF1 in newly infected B-cells, where viral genomes acquire histone 3.1 and 3.3 variants prior to the first mitosis. Since histone chaperones ATRX and DAXX also function in maintenance of EBV latency, our results suggest that EBV coopts multiple histone pathways to reprogram viral genomes and highlight targets for lytic induction therapeutic strategies.

scholarly journals Hitchhiking of Viral Genomes on Cellular Chromosomes

2019 ◽  
Vol 6 (1) ◽  
pp. 275-296 ◽  
Author(s):  
Tami L. Coursey ◽  
Alison A. McBride
Keyword(s):  
Viral Genome ◽  
Viral Infections ◽  
Genome Replication ◽  
Mitotic Chromosomes ◽  
Dna Viruses ◽  
Viral Genomes ◽  
Barr Virus ◽  
Dividing Cells ◽  
Viral Genome Replication ◽  
Epstein Barr

Persistent viral infections require a host cell reservoir that maintains functional copies of the viral genome. To this end, several DNA viruses maintain their genomes as extrachromosomal DNA minichromosomes in actively dividing cells. These viruses typically encode a viral protein that binds specifically to viral DNA genomes and tethers them to host mitotic chromosomes, thus enabling the viral genomes to hitchhike or piggyback into daughter cells. Viruses that use this tethering mechanism include papillomaviruses and the gammaherpesviruses Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus. This review describes the advantages and consequences of persistent extrachromosomal viral genome replication.

scholarly journals Demonstration of monoclonal EBV genomes in Hodgkin's disease and Ki-1- positive anaplastic large cell lymphoma by combined Southern blot and in situ hybridization [see comments]

Blood ◽  
1989 ◽  
Vol 74 (2) ◽  
pp. 810-816 ◽  
Author(s):  
I Anagnostopoulos ◽  
H Herbst ◽  
G Niedobitek ◽  
H Stein
Keyword(s):  
In Situ Hybridization ◽  
Hodgkin's Disease ◽  
Hodgkin’S Disease ◽  
Large Cell ◽  
Viral Genomes ◽  
Barr Virus ◽  
Infected Cells ◽  
Epstein Barr ◽  
Distinct Morphology

Abstract Forty-two cases of Hodgkin's disease (HD) and 22 cases of Ki-1-positive anaplastic large cell (Ki-1 + ALC) lymphoma were examined by Southern blotting for the presence of Epstein-Barr virus (EBV) DNA. Seven cases of HD and one case of Ki-1 + ALC lymphoma scored positive with a probe specific for the internal repetitive region of the EBV genome. Subsequently, these viral genomes could be demonstrated to be monoclonal in origin using an EBV terminal region DNA probe. In situ hybridization revealed that in two HD cases, the EBV infected cells had the distinct morphology of Hodgkin and Reed-Sternberg cells, thus suggesting a direct pathoetiological relationship between EBV and some cases of HD.

scholarly journals 5-hydroxymethylation of the EBV genome regulates the latent to lytic switch

2015 ◽  
Vol 112 (52) ◽  
pp. E7257-E7265 ◽  
Author(s):  
Coral K. Wille ◽  
Dhananjay M. Nawandar ◽  
Amanda N. Henning ◽  
Shidong Ma ◽  
Kayla M. Oetting ◽  
...  
Keyword(s):  
Viral Reactivation ◽  
Viral Genomes ◽  
Barr Virus ◽  
Ebv Infection ◽  
Differentiated Cells ◽  
Modified Dna ◽  
Lytic Reactivation ◽  
Viral Promoters ◽  
Immediate Early Proteins ◽  
Epstein Barr

Latent Epstein–Barr virus (EBV) infection and cellular hypermethylation are hallmarks of undifferentiated nasopharyngeal carcinoma (NPC). However, EBV infection of normal oral epithelial cells is confined to differentiated cells and is lytic. Here we demonstrate that the EBV genome can become 5-hydroxymethylated and that this DNA modification affects EBV lytic reactivation. We show that global 5-hydroxymethylcytosine (5hmC)-modified DNA accumulates during normal epithelial-cell differentiation, whereas EBV+ NPCs have little if any 5hmC-modified DNA. Furthermore, we find that increasing cellular ten–eleven translocation (TET) activity [which converts methylated cytosine (5mC) to 5hmC] decreases methylation, and increases 5hmC modification, of lytic EBV promoters in EBV-infected cell lines containing highly methylated viral genomes. Conversely, inhibition of endogenous TET activity increases lytic EBV promoter methylation in an EBV-infected telomerase-immortalized normal oral keratinocyte (NOKs) cell line where lytic viral promoters are largely unmethylated. We demonstrate that these cytosine modifications differentially affect the ability of the two EBV immediate-early proteins, BZLF1 (Z) and BRLF1 (R), to induce the lytic form of viral infection. Although methylation of lytic EBV promoters increases Z-mediated and inhibits R-mediated lytic reactivation, 5hmC modification of lytic EBV promoters has the opposite effect. We also identify a specific CpG-containing Z-binding site on the BRLF1 promoter that must be methylated for Z-mediated viral reactivation and show that TET-mediated 5hmC modification of this site in NOKs prevents Z-mediated viral reactivation. Decreased 5-hydroxymethylation of cellular and viral genes may contribute to NPC formation.

scholarly journals Sequence and Functional Analysis of EBNA-LP and EBNA2 Proteins from Nonhuman Primate Lymphocryptoviruses

2000 ◽  
Vol 74 (1) ◽  
pp. 379-389 ◽  
Author(s):  
RongSheng Peng ◽  
Alexey V. Gordadze ◽  
Ezequiel M. Fuentes Pananá ◽  
Fred Wang ◽  
Jianchao Zong ◽  
...  
Keyword(s):  
B Lymphocytes ◽  
Molecular Mechanisms ◽  
Repeat Sequence ◽  
Amino Acid Sequences ◽  
Serine Phosphorylation ◽  
Comparative Approach ◽  
Functional Conservation ◽  
Barr Virus ◽  
Evolutionarily Conserved ◽  
Epstein Barr

ABSTRACT The Epstein-Barr virus (EBV) EBNA-LP and EBNA2 proteins are the first to be synthesized during establishment of latent infection in B lymphocytes. EBNA2 is a key transcriptional regulator of both viral and cellular gene expression and is essential for EBV-induced immortalization of B lymphocytes. EBNA-LP is also important for EBV-induced immortalization of B lymphocytes, but far less is known about the functional domains and cellular cofactors that mediate EBNA-LP function. While recent studies suggest that serine phosphorylation of EBNA-LP and coactivation of EBNA2-mediated transactivation are important, more detailed mutational and genetic studies are complicated by the repeat regions that comprise the majority of the EBNA-LP sequence. Therefore, we have used a comparative approach by studying the EBNA-LP homologues from baboon and rhesus macaque lymphocryptoviruses (LCVs) (baboon LCV and rhesus LCV). The predicted baboon and rhesus LCV EBNA-LP amino acid sequences are 61 and 64% identical to the EBV EBNA-LP W1 and W2 exons and 51% identical to the EBV EBNA-LP Y1 and Y2 exons. Five evolutionarily conserved regions can be defined, and four of eight potential serine residues are conserved among all three EBNA-LPs. The major internal repeat sequence also revealed a highly conserved Wp EBNA promoter with strong conservation of upstream activating sequences important for Wp transcriptional regulation. To test whether transcriptional coactivating properties were common to the rhesus LCV EBNA-LP, a rhesus LCV EBNA2 homologue was cloned and expressed. The rhesus LCV EBNA2 transcriptionally transactivates EBNA2-responsive promoters through a CBF1-dependent mechanism. The rhesus LCV EBNA-LP was able to further enhance rhesus LCV or EBV EBNA2 transactivation 5- to 12-fold. Thus, there is strong structural and functional conservation among the simian EBNA-LP homologues. Identification of evolutionarily conserved serine residues and regions in EBNA-LP homologues provides important clues for identifying the cellular cofactors and molecular mechanisms mediating these conserved viral functions.

scholarly journals A pentameric protein ring with novel architecture is required for herpesviral packaging

2020 ◽  
Author(s):  
Allison L. Didychuk ◽  
Stephanie N. Gates ◽  
Matthew R. Gardner ◽  
Lisa M. Strong ◽  
Andreas Martin ◽  
...  
Keyword(s):  
Viral Genome ◽  
Molecular Motor ◽  
Dna Viruses ◽  
Dna Mutation ◽  
Viral Genomes ◽  
Barr Virus ◽  
Double Stranded Dna ◽  
Accessory Factor ◽  
Epstein Barr ◽  
Positively Charged

Genome packaging in large double-stranded DNA viruses requires a powerful molecular motor to force the viral genome into nascent capsids. This process appears mechanistically similar in two evolutionarily distant viruses, the herpesviruses and the tailed bacteriophages, which infect different kingdoms of life. While the motor and mechanism as a whole are thought to be conserved, accessory factors that influence packaging are divergent and poorly understood, despite their essential roles. An accessory factor required for herpesviral packaging is encoded by ORF68 in the oncogenic virus Kaposi’s sarcoma-associated herpesvirus (KSHV), whose homolog in Epstein Barr Virus (EBV) is BFLF1. Here, we present structures of both KSHV ORF68 and EBV BFLF1, revealing that these proteins form a highly similar homopentameric ring. The central channel of this ring is positively charged, and we demonstrate that this region of KSHV ORF68 binds double-stranded DNA. Mutation of individual positively charged residues within but not outside the channel ablates DNA binding, and in the context of KSHV infection these mutants fail to package the viral genome or produce progeny virions. Thus, we propose a model in which ORF68 facilitates the transfer of newly replicated viral genomes to the packaging motor.

scholarly journals The Epstein-Barr Virus EBNA1 Protein

Scientifica ◽  
2012 ◽  
Vol 2012 ◽  
pp. 1-15 ◽  
Author(s):  
Lori Frappier
Keyword(s):  
Dna Sequences ◽  
Epstein Barr Virus ◽  
Latent Infection ◽  
Multiple Roles ◽  
Human Herpes ◽  
Viral Genomes ◽  
Barr Virus ◽  
Human Herpes Virus ◽  
The Subject ◽  
Epstein Barr

Epstein-Barr virus (EBV) is a widespread human herpes virus that immortalizes cells as part of its latent infection and is a causative agent in the development of several types of lymphomas and carcinomas. Replication and stable persistence of the EBV genomes in latent infection require the viral EBNA1 protein, which binds specific DNA sequences in the viral DNA. While the roles of EBNA1 were initially thought to be limited to effects on the viral genomes, more recently EBNA1 has been found to have multiple effects on cellular proteins and pathways that may also be important for viral persistence. In addition, a role for EBNA1 in lytic infection has been recently identified. The multiple roles of EBNA1 in EBV infection are the subject of this paper.

scholarly journals Epstein-Barr Virus Nuclear Antigen 2 (EBNA2) Gene Deletion Is Consistently Linked with EBNA3A, -3B, and -3C Expression in Burkitt's Lymphoma Cells and with Increased Resistance to Apoptosis

2005 ◽  
Vol 79 (16) ◽  
pp. 10709-10717 ◽  
Author(s):  
Gemma L. Kelly ◽  
Anne E. Milner ◽  
Rosemary J. Tierney ◽  
Debbie S. G. Croom-Carter ◽  
Markus Altmann ◽  
...  
Keyword(s):  
Epstein Barr Virus ◽  
Nuclear Antigen ◽  
Cell Phenotype ◽  
Parent Cell ◽  
Wild Type ◽  
Apoptosis Resistance ◽  
Viral Genomes ◽  
Barr Virus ◽  
Restricted Form ◽  
Epstein Barr

ABSTRACT Most Epstein-Barr virus (EBV)-positive Burkitt's lymphomas (BLs) carry a wild-type EBV genome and express EBV nuclear antigen 1 (EBNA1) selectively from the BamHI Q promoter (latency I). Recently we identified a distinct subset of BLs carrying both wild-type and EBNA2 gene-deleted (transformation-defective) viral genomes. The cells displayed an atypical “BamHI W promoter (Wp)-restricted” form of latency where Wp (rather than Qp) was active and EBNA1, -3A, -3B, -3C, and -LP were expressed in the absence of EBNA2 or latent membrane proteins 1 and 2. Here we present data strongly supporting the view that the EBNA2-deleted genome is transcriptionally active in these cells and the wild-type genome is silent. Single-cell cloning of three parental Wp-restricted BL lines generated clones carrying either both viral genomes or the EBNA2-deleted genome only, never clones with the wild-type genome only. All rescued clones displayed the Wp-restricted form of latency characteristic of the parent line and retained the original parent cell phenotype. Interestingly, Wp-restricted parent lines and derived clones were markedly more resistant to inducers of apoptosis than standard latency I BL lines. Furthermore, in vitro infection of EBV-negative BL lines with an EBNA2 gene-deleted virus generated EBV-positive converts with Wp-restricted latency and a similarly marked apoptosis resistance. We postulate that, in the subset of BLs displaying Wp-restricted latency, infection of a tumor progenitor cell with an EBNA2 gene-deleted virus has provided that cell with a survival advantage through broadening antigen expression to include the EBNA3 proteins.

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