scholarly journals The Unconventional Viruses of Ichneumonid Parasitoid Wasps

Viruses ◽  
2020 ◽  
Vol 12 (10) ◽  
pp. 1170 ◽  
Author(s):  
Anne-Nathalie Volkoff ◽  
Michel Cusson
Keyword(s):  
Viral Genome ◽  
Parasitoid Wasps ◽  
Genome Integration ◽  
Immature Development ◽  
Endogenous Viruses ◽  
Viral Genes

To ensure their own immature development as parasites, ichneumonid parasitoid wasps use endogenous viruses that they acquired through ancient events of viral genome integration. Thousands of species from the campoplegine and banchine wasp subfamilies rely, for their survival, on their association with these viruses, hijacked from a yet undetermined viral taxon. Here, we give an update of recent findings on the nature of the viral genes retained from the progenitor viruses and how they are organized in the wasp genome.

scholarly journals Bidirectional transcription from a solo long terminal repeat of the retrotransposon TED: symmetrical RNA start sites.

1986 ◽  
Vol 6 (5) ◽  
pp. 1599-1607 ◽  
Author(s):  
P D Friesen ◽  
W C Rice ◽  
D W Miller ◽  
L K Miller
Keyword(s):  
Long Terminal Repeat ◽  
Viral Genome ◽  
Nuclear Polyhedrosis Virus ◽  
Single Copy ◽  
Autographa Californica ◽  
Terminal Repeat ◽  
Viral Genes ◽  
Pair Sequence ◽  
Nuclear Polyhedrosis ◽  
Extension Analysis

A single copy of the retrotransposon TED was found integrated within the DNA genome of the insect baculovirus, Autographa californica nuclear polyhedrosis virus. After excision of the element from the viral genome, a single long terminal repeat (LTR) remained behind. We have examined the effect of this solo TED LTR on the local pattern of viral transcription. Most prominent was the transcription of two sets of abundant RNAs; both originated within the LTR but extended in opposite directions into flanking viral genes. By promoting symmetric transcription of adjacent genes, the solo LTR has the capacity to activate or repress gene expression in two directions. Primer extension analysis demonstrated that the divergent LTR transcripts were initiated near the same point within a 22-base-pair sequence having hyphenated twofold symmetry. Analogous symmetries at the initiation sites of other retrotransposon LTRs, including copia and Ty, suggested that these sequences serve to establish the precise start for transcription.

scholarly journals Chromosomal resolution reveals symbiotic virus colonization of parasitic wasp genomes

2020 ◽  
Author(s):  
Jérémy Gauthier ◽  
Hélène Boulain ◽  
Joke J.F.A. van Vugt ◽  
Lyam Baudry ◽  
Emma Persyn ◽  
...  
Keyword(s):  
Particle Production ◽  
Parasitic Wasp ◽  
Viral Gene Expression ◽  
Parasitoid Wasp ◽  
Viral Gene ◽  
Parasitoid Wasps ◽  
Genomic Comparison ◽  
Immune Genes ◽  
Endogenous Viruses ◽  
First Time

AbstractMost endogenous viruses, an important proportion of eukaryote genomes, are doomed to slowly decay. Little is known, however, on how they evolve when they confer a benefit to their host. Bracoviruses are essential for the parasitism success of parasitoid wasps, whose genomes they integrated ~103 million years ago. Here we show, from the assembly of a parasitoid wasp genome, for the first time at a chromosomal scale, that symbiotic bracovirus genes spread to and colonized all the chromosomes. Moreover, large viral clusters are stably maintained suggesting strong evolutionary constraints. Genomic comparison with another wasps revealed that this organization was already established ~53 mya. Transcriptomic analyses highlight temporal synchronization of viral gene expression, leading to particle production. Immune genes are not induced, however, indicating the virus is not perceived as foreign by the wasp. This recognition suggests that no conflicts remain between symbiotic partners when benefits to them converge.

scholarly journals KSHV ORF59 and PAN RNA Recruit Histone Demethylases to the Viral Chromatin during Lytic Reactivation

Viruses ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 420
Author(s):  
Kayla Hiura ◽  
Roxanne Strahan ◽  
Timsy Uppal ◽  
Brian Prince ◽  
Cyprian C. Rossetto ◽  
...  
Keyword(s):  
Viral Genome ◽  
Arginine Methylation ◽  
Histone Demethylases ◽  
Methyl Transferase ◽  
Lytic Reactivation ◽  
Viral Genes ◽  
Nuclear Rna ◽  
Processivity Factor ◽  
Epigenetic Gene Regulation ◽  
Histone Arginine Methylation

Kaposi’s sarcoma-associated herpesvirus (KSHV) causes multiple malignancies in immunocompromised individuals. KSHV primarily establishes a lifelong latency in infected humans during which only a subset of viral genes is expressed while most of the viral genome remains transcriptionally silent with condensed chromatin. However, during the lytic phase, the viral genome undergoes dramatic changes in chromatin landscape leading to a transcriptionally active state with the expression of most of the viral genes and production of progeny virions. Multiple cellular and viral factors influence the epigenetic gene regulation and transitioning of virus from latency to the lytic state. We have earlier shown that KSHV ORF59, viral processivity factor, binds to a protein arginine methyl transferase 5 (PRMT5) to alter the histone arginine methylation during reactivation. Additionally, ORF59 has been shown to interact with most abundantly expressed KSHV long noncoding polyadenylated nuclear RNA (PAN RNA), which associates with the viral epigenome during reactivation. Interestingly, PAN RNA interacts with UTX and JMJD3, cellular H3K27me3 demethylases, and removes the repressive marks on the chromatin. In this study, we report that the recruitment of histone demethylases to the viral chromatin is facilitated by the expression of ORF59 protein and PAN RNA. Using biochemical and localization assays including co-immunoprecipitation and immunofluorescence, we demonstate ORF59 localizes with UTX and JMJD3. Our results confirm that PAN RNA enhances the interaction of ORF59 with the chromatin modifying enzymes UTX and JMJD3.

scholarly journals CRISPR/Cas9-Mediated Knockout and In Situ Inversion of the ORF57 Gene from All Copies of the Kaposi's Sarcoma-Associated Herpesvirus Genome in BCBL-1 Cells

2019 ◽  
Vol 93 (21) ◽  
Author(s):  
Andrew BeltCappellino ◽  
Vladimir Majerciak ◽  
Alexei Lobanov ◽  
Justin Lack ◽  
Maggie Cam ◽  
...  
Keyword(s):  
Single Cell ◽  
Viral Genome ◽  
Expression Vector ◽  
Primary Effusion Lymphoma ◽  
Lytic Gene ◽  
Guide Rnas ◽  
Cell Clones ◽  
Single Cell Cloning ◽  
Viral Genes

ABSTRACT Kaposi’s sarcoma-associated herpesvirus (KSHV)-transformed primary effusion lymphoma cell lines contain ∼70 to 150 copies of episomal KSHV genomes per cell and have been widely used for studying the mechanisms of KSHV latency and lytic reactivation. Here, we report the first complete knockout (KO) of viral ORF57 gene from all ∼100 copies of KSHV genome per cell in BCBL-1 cells. This was achieved by a modified CRISPR/Cas9 technology to simultaneously express two guide RNAs (gRNAs) and Cas9 from a single expression vector in transfected cells in combination with multiple rounds of cell selection and single-cell cloning. CRISPR/Cas9-mediated genome engineering induces the targeted gene deletion and inversion in situ. We found the inverted ORF57 gene in the targeted site in the KSHV genome in one of two characterized single cell clones. Knockout of ORF57 from the KSHV genome led to viral genome instability, thereby reducing viral genome copies and expression of viral lytic genes in BCBL-1-derived single-cell clones. The modified CRISPR/Cas9 technology was very efficient in knocking out the ORF57 gene in iSLK/Bac16 and HEK293/Bac36 cells, where each cell contains only a few copies of the KSHV genome. The ORF57 KO genome was stable in iSLK/Bac16 cells, and, upon lytic induction, was partially rescued by ectopic ORF57 to express viral lytic gene ORF59 and produce infectious virions. Together, the technology developed in this study has paved the way to express two separate gRNAs and the Cas9 enzyme simultaneously in the same cell and could be efficiently applied to any genetic alterations from various genomes, including those in extreme high copy numbers. IMPORTANCE This study provides the first evidence that CRISPR/Cas9 technology can be applied to knock out the ORF57 gene from all ∼100 copies of the KSHV genome in primary effusion lymphoma (PEL) cells by coexpressing two guide RNAs (gRNAs) and Cas9 from a single expression vector in combination with single-cell cloning. The gene knockout efficiency in this system was evaluated rapidly using a direct cell PCR screening. The current CRISPR/Cas9 technology also mediated ORF57 inversion in situ in the targeted site of the KSHV genome. The successful rescue of viral lytic gene expression and infectious virion production from the ORF57 knockout (KO) genome further reiterates the essential role of ORF57 in KSHV infection and multiplication. This modified technology should be useful for knocking out any viral genes from a genome to dissect functions of individual viral genes in the context of the virus genome and to understand their contributions to viral genetics and the virus life cycle.

scholarly journals Phosphorylation by CK2 increases the SUMO-dependent activity of Cytomegalovirus transactivator IE2

2019 ◽  
Author(s):  
Vasvi Tripathi ◽  
Kiran Sankar Chatterjee ◽  
Ranabir Das
Keyword(s):  
Human Cytomegalovirus ◽  
Cross Talk ◽  
Viral Genome ◽  
Essential Gene ◽  
E3 Ligase ◽  
Host Protein ◽  
Genome Replication ◽  
Salt Bridges ◽  
Post Translational Modification ◽  
Viral Genes

AbstractViral factors manipulate the host post-translational modification (PTM) machinery for replication. Distinctly, phosphorylation and SUMOylation can regulate the activity of human cytomegalovirus (HCMV) protein IE2. However, the molecular mechanism of this process is unknown. Taking a structural, biochemical and cellular approach, we uncover a cross-talk of phosphorylation and SUMOylation exploited by IE2. A scan for the SUMO Interacting Motifs (SIMs) revealed two SIMs in IE2. A real-time SUMOylation assay indicated that the N-terminal SIM (IE2-SIM1) enhanced IE2 SUMOylation up to 4-fold. Kinetic analysis and structural studies proved that IE2 is a SUMO cis-E3 ligase. Two putative CK2 sites adjacent to IE2-SIM1 are phosphorylated in-vitro and in cellular conditions. Phosphorylation drastically increased the IE2/SUMO affinity, IE2-SUMOylation and cis-E3 activity of IE2. Additional salt-bridges between the phosphoserines and SUMO account for the higher IE2/SUMO affinity. Phosphorylation also enhances the SUMO-dependent transactivation activity and auto-repression activity of IE2. Together, our findings highlight a novel mechanism where SUMOylation and phosphorylation of the viral cis-E3 ligase and transactivator protein IE2, works in tandem to enable transcriptional regulation of viral genes.Author summaryThe host protein SUMO is a crucial regulator of cellular processes. Conjugation of other proteins to SUMO by a process called SUMOylation, can change the protein’s function or localization and regulate downstream cellular events. The SUMO pathway is exploited by viruses to transcribe viral genes and replicate the viral genome. IE2 is an essential gene of human Cytomegalovirus (HCMV), which acts as a transactivator and helps to transcribe other viral proteins required for viral genome replication and viral assembly. SUMOylation of IE2 is necessary for its function. Here, we have uncovered that IE2 functions as a cis-SUMO-E3 ligase, where a SUMO-Interacting Motif (SIM) in IE2 enhances its SUMOylation. Interestingly, phosphorylation of the SIM in IE2 augments its cis-E3 activity to further increase SUMOylation. Moreover, SIM phosphorylation also enhances the interaction between IE2 and SUMOylated binding partners. Thus, we uncover an exciting process, where phosphorylation enhances both covalent and non-covalent interaction of a protein (IE2) and SUMO. We also observe that the cross-talk of phosphorylation and SUMOylation has significant effects on the transactivation function of IE2. Overall, we discover how a viral protein IE2 exploits crosstalk between SUMOylation and Phosphorylation to enhance its activity and in turn, ensure efficient viral replication.

scholarly journals Reads Binning Improves the Assembly of Viral Genome Sequences From Metagenomic Samples

2021 ◽  
Vol 12 ◽  
Author(s):  
Kai Song
Keyword(s):  
Dna Sequences ◽  
Viral Genome ◽  
Metagenomic Data ◽  
Viral Sequence ◽  
Genome Sequences ◽  
Sequence Identification ◽  
Viral Genes ◽  
Eukaryotic Dna ◽  
Viral Sequences

Metagenomes can be considered as mixtures of viral, bacterial, and other eukaryotic DNA sequences. Mining viral sequences from metagenomes could shed insight into virus–host relationships and expand viral databases. Current alignment-based methods are unsuitable for identifying viral sequences from metagenome sequences because most assembled metagenomic contigs are short and possess few or no predicted genes, and most metagenomic viral genes are dissimilar to known viral genes. In this study, I developed a Markov model-based method, VirMC, to identify viral sequences from metagenomic data. VirMC uses Markov chains to model sequence signatures and construct a scoring model using a likelihood test to distinguish viral and bacterial sequences. Compared with the other two state-of-the-art viral sequence-prediction methods, VirFinder and PPR-Meta, my proposed method outperformed VirFinder and had similar performance with PPR-Meta for short contigs with length less than 400 bp. VirMC outperformed VirFinder and PPR-Meta for identifying viral sequences in contaminated metagenomic samples with eukaryotic sequences. VirMC showed better performance in assembling viral-genome sequences from metagenomic data (based on filtering potential bacterial reads). Applying VirMC to human gut metagenomes from healthy subjects and patients with type-2 diabetes (T2D) revealed that viral contigs could help classify healthy and diseased statuses. This alignment-free method complements gene-based alignment approaches and will significantly improve the precision of viral sequence identification.

scholarly journals CovProfile: profiling the viral genome and gene expressions of SARS-COV-2

2020 ◽  
Author(s):  
Yonghan Yu ◽  
Zhengtu Li ◽  
Yinhu Li ◽  
Le Yu ◽  
Wenlong Jia ◽  
...  
Keyword(s):  
Viral Genome ◽  
Terminally Ill ◽  
N Gene ◽  
Viral Gene ◽  
Computational Tool ◽  
M Gene ◽  
Gene Expressions ◽  
Genomic Variations ◽  
Viral Genes ◽  
Multiple Viral Strains

AbstractThe SARS-CoV-2 virus has infected more than one million people worldwide to date. Knowing its genome and gene expressions is essential to understand the virus’ mechanism. Here, we propose a computational tool CovProfile to detect the viral genomic variations as well as viral gene expressions from the sequences obtained from Nanopore devices. We applied CovProfile to 11 samples, each from a terminally ill patient, and discovered that all the patients are infected by multiple viral strains, which might affect the reliability of phylogenetic analysis. Moreover, the expression of viral genes ORF1ab gene, S gene, M gene, and N gene are high among most of the samples. While performing the tests, we noticed a consistent abundance of transcript segments of MUC5B, presumably from the host, across all the samples.

Bidirectional transcription from a solo long terminal repeat of the retrotransposon TED: symmetrical RNA start sites

1986 ◽  
Vol 6 (5) ◽  
pp. 1599-1607
Author(s):  
P D Friesen ◽  
W C Rice ◽  
D W Miller ◽  
L K Miller
Keyword(s):  
Long Terminal Repeat ◽  
Viral Genome ◽  
Nuclear Polyhedrosis Virus ◽  
Single Copy ◽  
Autographa Californica ◽  
Terminal Repeat ◽  
Viral Genes ◽  
Pair Sequence ◽  
Nuclear Polyhedrosis ◽  
Extension Analysis

A single copy of the retrotransposon TED was found integrated within the DNA genome of the insect baculovirus, Autographa californica nuclear polyhedrosis virus. After excision of the element from the viral genome, a single long terminal repeat (LTR) remained behind. We have examined the effect of this solo TED LTR on the local pattern of viral transcription. Most prominent was the transcription of two sets of abundant RNAs; both originated within the LTR but extended in opposite directions into flanking viral genes. By promoting symmetric transcription of adjacent genes, the solo LTR has the capacity to activate or repress gene expression in two directions. Primer extension analysis demonstrated that the divergent LTR transcripts were initiated near the same point within a 22-base-pair sequence having hyphenated twofold symmetry. Analogous symmetries at the initiation sites of other retrotransposon LTRs, including copia and Ty, suggested that these sequences serve to establish the precise start for transcription.

Viral gene expression during the establishment of human cytomegalovirus latent infection in myeloid progenitor cells

Blood ◽  
2006 ◽  
Vol 108 (12) ◽  
pp. 3691-3699 ◽  
Author(s):  
Allen K. L. Cheung ◽  
Allison Abendroth ◽  
Anthony L. Cunningham ◽  
Barry Slobedman
Keyword(s):  
Gene Expression ◽  
Viral Genome ◽  
Latent Infection ◽  
Viral Gene Expression ◽  
Viral Gene ◽  
Time Points ◽  
Myeloid Progenitor ◽  
Viral Genes ◽  
Myeloid Progenitor Cells ◽  
Establishment Phase

AbstractHuman cytomegalovirus (HCMV) establishes and maintains a latent infection in myeloid cells and can reactivate to cause serious disease in allograft recipients. To better understand the molecular events associated with the establishment of latency, we tracked the virus following infection of primary human myeloid progenitor cells at days 1, 2, 3, 5, and 11. At all time points, the viral genome was maintained in most cells at approximately 10 copies. Infectious virus was not detected, but virus could be reactivated by extended fibroblast coculture. In contrast to wild-type HCMV, the viral genome was rapidly lost from myeloid progenitors infected with ultraviolet (UV)–inactivated virus, suggesting viral gene expression was required for efficient establishment of latency. To identify viral genes associated with the establishment phase, RNA from each time point was interrogated using custom-made HCMV gene microarrays. Using this approach, we detected expression of viral RNAs at all time points. The pattern of expression differed from that which occurs during productive infection, and decreased over time. This study provides evidence that a molecular pathway into latency is associated with expression of a unique subset of viral transcripts. Viral genes expressed during the establishment phase may serve as targets for therapies to interrupt this process.

scholarly journals Resurrection of human endogenous retroviruses during aging reinforces senescence

2021 ◽  
Author(s):  
Xiaoqian Liu ◽  
Zunpeng Liu ◽  
Liang Sun ◽  
Jie Ren ◽  
Zeming Wu ◽  
...  
Keyword(s):  
Cellular Senescence ◽  
The Elderly ◽  
Endogenous Retrovirus ◽  
Endogenous Retroviruses ◽  
Epigenetic Alterations ◽  
Human Endogenous Retroviruses ◽  
Pathological Conditions ◽  
Endogenous Viruses ◽  
Viral Genes ◽  
Senescence Phenotype

ABSTRACTHuman endogenous retroviruses (HERVs) are under strict control by the host surveillance system but can become awakened under pathological conditions. Among them, the HERVK family, comprised of the evolutionarily youngest HERVs, is able to transcribe viral genes and producing retrovirus-like particles (RVLPs). However, whether HERVK is mobilized in the aging process and contributes to aging-related pathologies is largely unknown. Using diverse senescence models, we show that epigenetic alterations unlock HERVK expression, which leads to the formation of RVLPs. Derepression of HERVK promotes cellular senescence, while inhibiting HERVK prevents cellular senescence. HERVK RVLPs released from senescent cells or aged individuals are capable of conferring a senescence phenotype to young cells. Conversely, using antibodies to block the HERVK RVLPs abrogates their transmissible pro-senescence effect. Moreover, endogenous retrovirus expression is increased in aged human tissues and serum from the elderly. These findings indicate that the activation of endogenous viruses is part of the driving force of aging.

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