scholarly journals Cellular labeling of endogenous virus replication (CLEVR) reveals de novo insertions of the gypsy endogenous retrovirus in cell culture and in both neurons and glial cells of aging fruit flies

2018 ◽  
Author(s):  
Yung-Heng Chang ◽  
Richard M. Keegan ◽  
Lisa Prazak ◽  
Josh Dubnau
Keyword(s):  
Cell Culture ◽  
Glial Cells ◽  
De Novo ◽  
Endogenous Retrovirus ◽  
Endogenous Retroviruses ◽  
Ltr Retrotransposons ◽  
Endogenous Virus ◽  
Gypsy Element ◽  
Element Mobilization

AbstractEvidence is rapidly mounting that transposable element expression and replication may impact biology more widely than previously thought. This includes potential effects on normal physiology of somatic tissues and dysfunctional impacts in diseases associated with aging such as cancer and neurodegeneration. Investigation of the biological impact of mobile elements in somatic cells will be greatly facilitated by use of donor elements that are engineered to report de novo events in vivo. In multicellular organisms, successful reporters of LINE element mobilization have been in use for some time, but similar strategies have not been developed to report Long Terminal Repeat (LTR) retrotransposons and endogenous retroviruses. We describe Cellular Labeling of Endogenous Virus Replication (CLEVR), which reports replication of the gypsy element in Drosophila. The gypsy-CLEVR reporter reveals gypsy replication both in cell culture and in individual neurons and glial cells of the aging adult fly. We also demonstrate that the gypsy-CLEVR replication rate is increased when the short interfering RNA silencing system is genetically disrupted. This CLEVR strategy makes use of universally conserved features of retroviruses and should be widely applicable to other LTR-retrotransposons, endogenous retroviruses and exogenous retroviruses.

scholarly journals Characterization of Endogenous Retroviruses in Sheep

2003 ◽  
Vol 77 (20) ◽  
pp. 11268-11273 ◽  
Author(s):  
Nikolai Klymiuk ◽  
Mathias Müller ◽  
Gottfried Brem ◽  
Bernhard Aigner
Keyword(s):  
Endogenous Retrovirus ◽  
Ovis Aries ◽  
Endogenous Retroviruses ◽  
Open Reading Frames ◽  
In Vivo Experiments ◽  
Pregnant Sheep ◽  
Reading Frames

ABSTRACT Endogenous retrovirus (ERV) sequences have been found in all mammals. In vitro and in vivo experiments revealed ERV activation and cross-species infection in several species. Sheep (Ovis aries) are used for various biotechnological purposes; however, they have not yet been comprehensively screened for ERV sequences. Therefore, the aim of the study was to classify the ERV sequences in the ovine genome (OERV) by analyzing the retroviral pro-pol sequences. Three OERV β families and nine OERV γ families were revealed. Novel open reading frames (ORF) in the amplified proviral fragment were found in one OERV β family and two OERV γ families. Hybrid OERV produced by putative recombination events were not detected. Quantitative analysis of the OERV sequences in the ovine genome revealed no relevant variations in the endogenous retroviral loads of different breeds. Expression analysis of different tissues from fetal and pregnant sheep detected mRNA from both gammaretrovirus families, showing ORF fragments. Thus, the release of retroviruses from sheep cells cannot be excluded.

scholarly journals Human APOBEC3G Prevents Emergence of Infectious Endogenous Retrovirus in Mice

2019 ◽  
Vol 93 (20) ◽  
Author(s):  
Rebecca S. Treger ◽  
Maria Tokuyama ◽  
Huiping Dong ◽  
Karen Salas-Briceno ◽  
Susan R. Ross ◽  
...  
Keyword(s):  
Ectopic Expression ◽  
Endogenous Retrovirus ◽  
Endogenous Retroviruses ◽  
Toll Like Receptor ◽  
Restriction Factors ◽  
Cytidine Deaminases ◽  
Endogenous Loci ◽  
Human Apobec3g

ABSTRACT Endogenous retroviruses (ERV) are found throughout vertebrate genomes, and failure to silence their activation can have deleterious consequences on the host. Mutation and subsequent disruption of ERV loci is therefore an indispensable component of the cell-intrinsic defenses that maintain the integrity of the host genome. Abundant in vitro and in silico evidence have revealed that APOBEC3 cytidine-deaminases, including human APOBEC3G (hA3G), can potently restrict retrotransposition; yet, in vivo data demonstrating such activity is lacking, since no replication-competent human ERV have been identified. In mice deficient for Toll-like receptor 7 (TLR7), transcribed ERV loci can recombine and generate infectious ERV. In this study, we show that ectopic expression of hA3G can prevent the emergence of replication-competent, infectious ERV in Tlr7−/− mice. Mice encode one copy of Apobec3 in their genome. ERV reactivation in Tlr7−/− mice was comparable in the presence or absence of Apobec3. In contrast, expression of a human APOBEC3G transgene abrogated emergence of infectious ERV in the Tlr7−/− background. No ERV RNA was detected in the plasma of hA3G+ Apobec3−/− Tlr7−/− mice, and infectious ERV virions could not be amplified through coculture with permissive cells. These data reveal that hA3G can potently restrict active ERV in vivo and suggest that expansion of the APOBEC3 locus in primates may have helped to provide for the continued restraint of ERV in the human genome. IMPORTANCE Although APOBEC3 proteins are known to be important antiviral restriction factors in both mice and humans, their roles in the restriction of endogenous retroviruses (ERV) have been limited to in vitro studies. Here, we report that human APOBEC3G expressed as a transgene in mice prevents the emergence of infectious ERV from endogenous loci. This study reveals that APOBEC3G can powerfully restrict active retrotransposons in vivo and demonstrates how transgenic mice can be used to investigate host mechanisms that inhibit retrotransposons and reinforce genomic integrity.

scholarly journals Human endogenous retrovirus transcription profiles of the kidney and kidney-derived cell lines

2011 ◽  
Vol 92 (10) ◽  
pp. 2356-2366 ◽  
Author(s):  
Sonja Haupt ◽  
Michele Tisdale ◽  
Michelle Vincendeau ◽  
Mary Anne Clements ◽  
David T. Gauthier ◽  
...  
Keyword(s):  
Cell Culture ◽  
Cell Line ◽  
Cell Lines ◽  
Kidney Tissue ◽  
Human Kidney ◽  
Endogenous Retrovirus ◽  
Endogenous Retroviruses ◽  
Human Endogenous Retrovirus ◽  
Tissue Samples ◽  
Transcription Pattern

The human genome comprises approximately 8–9 % of human endogenous retroviruses (HERVs) that are transcribed with tissue specificity. However, relatively few organs have been examined in detail for individual differences in HERV transcription pattern, nor have tissue-to-cell culture comparisons been frequently performed. Using an HERV-specific DNA microarray, a core HERV transcription profile was established for the human kidney comparing 10 tissue samples. This core represents HERV groups expressed uniformly or nearly so in non-tumour kidney tissue. The profiles obtained from non-tumour tissues were compared to 10 renal tumour tissues (renal cell carcinoma, RCC) derived from the same individuals and additionally, to 22 RCC cell lines. No RCC cell line or tumour-specific differences were observed, suggesting that HERV transcription is not altered in RCC. However, when comparing tissue transcription to cell line transcription, there were consistent differences. The differences were irrespective of cancer state and included cell lines derived from non-tumour kidney tissue, suggesting that a specific alteration of HERV transcription occurs when establishing cell lines. In contrast to previous publications, all known HERV-derived tumour antigens, including those identified in RCC, were expressed both in multiple RCC cell lines and several non-tumour tissue-derived cell lines, a result that contrasts with findings from patient samples. The results establish the core kidney transcription pattern of HERVs and reveal differences between cell culture lines and tissue samples.

scholarly journals The evolutionary history of a gammaretrovirus currently colonizing the mule deer genome is marked by extensive recombination

2021 ◽  
Author(s):  
Lei Yang ◽  
Raunaq Malhotra ◽  
Rayan Chikhi ◽  
Daniel Elleder ◽  
Theodora Kaiser ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Evolutionary Dynamics ◽  
De Novo ◽  
Mule Deer ◽  
Endogenous Retrovirus ◽  
Host Population ◽  
Endogenous Retroviruses ◽  
Genomic Diversity ◽  
Evolutionary Trajectory ◽  
History Of

AbstractBackgroundAll vertebrate genomes have been colonized by retroviruses along their evolutionary trajectory. Although it is clear that endogenous retroviruses (ERVs) can contribute important physiological functions to contemporary hosts, such benefits are attributed to long-term co-evolution of ERV and host. Newly colonized ERVs are thought unlikely to contribute to host genome evolution because germline infections are rare and because the host effectively silences them. The genomes of several outbred species including mule deer (Odocoileus hemionus) are currently being colonized by ERVs, which provides an opportunity to study ERV dynamics at a time when few are fixed.Here we investigate the history of cervid endogenous retrovirus (CrERV) acquisition and expansion in the mule deer genome to determine the potential impact of endogenizing retroviruses on host genomic diversity.MethodsA mule deer genome was de novo assembled from short and long insert mate pair reads. Scaffolds were further assembled using reference assisted chromosome assembly (RACA) to provide spatial orientation of CrERV insertion sites and to facilitate assembly of CrERV sequences. We applied phylogenetic and coalescent approaches to non-recombinant genomes to determine CrERV evolutionary history, augmenting ancestral divergence estimates with the prevalence of each CrERV locus in a population of mule deer. Recombination history was investigated on partial genome alignments.ResultsThe CrERV composition and diversity in the mule deer genome has recently measurably increased by horizontal acquisition of a new retroviruses lineage and because of recombination with existing CrERV. Resulting interlineage recombinants also endogenized and subsequently retrotransposed. CrERV loci are significantly closer to genes than expected if integration were random and gene proximity might explain the recent expansion by retrotransposition of one recombinant CrERV lineage.ConclusionsThere has been a burst of CrERV integrations during a recent retrovirus epizootic that increased genomic CrERV burden and has resulted in extensive insertional polymorphism in contemporary mule deer genomes. Recombination is a defining feature of CrERV evolutionary dynamics driven by this colonization, increasing CrERV burden and CrERV genetic diversity. These data support that retroviral colonization during an epizootic provides a burst of genomic diversity to the host population.

scholarly journals Discovery of a New Endogenous Type C Retrovirus (FcEV) in Cats: Evidence for RD-114 Being an FcEVGag-Pol/Baboon Endogenous Virus BaEVEnv Recombinant

1999 ◽  
Vol 73 (10) ◽  
pp. 7994-8002 ◽  
Author(s):  
Antoinette C. van der Kuyl ◽  
John T. Dekker ◽  
Jaap Goudsmit
Keyword(s):  
De Novo ◽  
Germ Line ◽  
Endogenous Retrovirus ◽  
Domestic Cat ◽  
Papio Cynocephalus ◽  
Endogenous Virus ◽  
Dna Library ◽  
Genomic Dna Library ◽  
Type C ◽  
Baboon Endogenous Virus

ABSTRACT Analysis of a cat genomic DNA library showed that cats harbor a previously unrecognized endogenous type C retrovirus, whoseenv gene has homology to the murine Fv-4resistance gene. This unique retrovirus, designated FcEV (Felis catus endogenous retrovirus), has a type C pol gene, closely related to the primate Papio cynocephalusendogenous virus (PcEV) pol, not overlapping theenv gene, unlike in other type C retroviruses, and is presumably present in a higher copy number than RD-114. Phylogenetic analysis of FcEV and RD-114 fragments amplified from cat species and comparison with baboon endogenous virus (BaEV) fragments from monkeys suggested that RD-114 does not represent the cat strain of BaEV but is actually a new recombinant between FcEV type C genes and theenv gene of BaEV. Although BaEV did appear to have infected an ancestor of the domestic cat lineage, it was a de novo recombinant that made its way into the cat germ line.

scholarly journals Study of Full-Length Porcine Endogenous Retrovirus Genomes with Envelope Gene Polymorphism in a Specific-Pathogen-Free Large White Swine Herd

2000 ◽  
Vol 74 (18) ◽  
pp. 8575-8581 ◽  
Author(s):  
Steffi Bösch ◽  
Claire Arnauld ◽  
André Jestin
Keyword(s):  
Endogenous Retrovirus ◽  
Amino Acid Sequences ◽  
Full Length ◽  
Endogenous Retroviruses ◽  
Envelope Gene ◽  
Specific Pathogen Free ◽  
Large White ◽  
Porcine Endogenous Retrovirus ◽  
Specific Pathogen

ABSTRACT Specific-pathogen-free (SPF) swine appear to be the most appropriate candidate for pig to human xenotransplantation. Still, the risk of endogenous retrovirus transmission represents a major obstacle, since two human-tropic porcine endogenous retroviruses (PERVs) had been characterized in vitro (P. Le Tissier, J. P. Stoye, Y. Takeuchi, C. Patience, and R. A. Weiss, Nature 389:681–682, 1997). Here we addressed the question of PERV distribution in a French Large White SPF pig herd in vivo. First, PCR screening for previously described PERV envelope genes envA, envB, and envC(D. E. Akiyoshi, M. Denaro, H. Zhu, J. L. Greenstein, P. Banerjee, and J. A. Fishman, J. Virol. 72:4503–4507, 1998; Le Tissier et al., op. cit.). demonstrated ubiquity of envAand envB sequences, whereas envC genes were absent in some animals. On this basis, selective out-breeding of pigs of remote origin might be a means to reduce proviral load in organ donors. Second, we investigated PERV genome carriage inenvC negative swine. Eleven distinct full-length PERV transcripts were isolated. The sequence of the complete envelope open reading frame was determined. The deduced amino acid sequences revealed the existence of four clones with functional and five clones with defective PERV PK-15 A- and B-like envelope sequences. The occurrence of easily detectable levels of PERV variants in different pig tissues in vivo heightens the need to assess PERV transmission in xenotransplantation animal models.

Oncoretroviral and Lentiviral Transduction of Donor T Cells to Facilitate Engraftment of Dog Leukocyte Antigen (DLA)-Haploidentical T-Cell-Depleted Marrow.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 1751-1751
Author(s):  
Dario Sangiolo ◽  
Marina Lesnikova ◽  
Alla Nikitine ◽  
Hans-Peter Kiem ◽  
Rainer Storb ◽  
...  
Keyword(s):  
Cell Culture ◽  
T Cells ◽  
T Cell ◽  
Transduction Efficiency ◽  
Endogenous Virus ◽  
Short Term ◽  
Donor T Cells ◽  
Allogeneic Stimulation ◽  
Short Term Culture

Abstract Several clinical studies of adoptive immunotherapy with genetically modified (GM) donor T cells infused after allogeneic hematopoietic cell transplantation (HCT) showed limited in vivo function of the transduced T cells. Factors that have hindered successful translation to clinical trials include insufficient preclinical data in large animal models and the need for prolonged cell culture - up to 2 to 3 weeks for optimal oncoretroviral (OR) vector transduction and selection of T cells. In preparation for in vivo studies of GM T cells to facilitate engraftment in the preclinical dog model of allogeneic HCT, we compared transduction protocols with OR and lentiviral (LV) vectors that aimed to decrease the duration of ex vivo T cell culture necessary for stable transduction while maintaining T cell alloreactivity. Vectors expressed enhanced yellow fluorescent protein (YFP) under a constitutive promoter. We compared vectors pseudotyped with viral glycoproteins (GP) including vesicular stomatitis virus (VSV)-G (LV only), feline endogenous virus (RD114), and chimeric RD114 envelope GP fused with murine leukemia virus-A cytoplasmic tail (RD114/TR). Although T cells transduced with LV vectors without prior mitogenic or allogeneic stimulation had 14% – 30% transduction efficiency of predominantly CD4+ cells, transgene expression was not sustained in CD8+ cells after allogeneic stimulation (n=3). In order to transduce T cells that could generate GM alloreactive cytotoxic T lymphocytes (CTL), freshly isolated T cells were stimulated with allogeneic dendritic cells (DC) for 4 days prior to transduction. VSV-G, RD114 or RD114/TR pseudotyped LV had primary transduction efficiency of 1.2 to 9% (n=5). Only cells that were transduced with RD114 or RD114/TR pseudotyped vectors maintained stable YFP expression after 2° allogeneic stimulation. Next, OR YFP vector pseudotyped with RD114 transduced 15 to 36% of DC allo-stimulated T cells (n=3). Both CD4+ and CD8+ cell populations were transduced (CD4+: CD8+ ratio 1.4:1) and the mean YFP fluorescence intensity was increased 0.6-log compared to LV vectors (p=0.01). We then evaluated T cells transduced with OR RD114 pseudotyped vector in vivo. To determine if short-term culture and transduction of T cells facilitated engraftment of CD3-depleted marrow in the DLA-haploidentical HCT model, donor T cells were collected on day −7 prior to HCT, cultured with recipient CD34+ derived DC, and on day −4 cells were transduced with RD114 pseudotyped YFP OR vector. To date, one dog was transplanted after 920cGy total body irradiation with 2x108 CD3+ donor cells/kg (1:1 CD4:CD8 ratio) 25% YFP expression and 2-log CD3-depleted marrow (4x108 TNC/kg). No post-grafting immunosuppression was given. Donor YFP transduced T cells were detected in the peripheral blood daily after HCT, and peaked on day +7. After engraftment on day +8, GVHD developed and the dog was euthanized on day +21 with all-donor chimerism. YFP+ T cells were detected in GVHD affected target organs. Previously, transduced donor CTL cultured for 4 weeks and transplanted with CD3-depleted marrow in this HCT model failed to engraft in all 5 dogs studied. These preliminary results support the hypothesis that short-term culture and transduction of donor T cells with RD114 pseudotyped OR vector maintain in vivo alloreactivity and facilitate engraftment of CD3-depleted marrow in MHC-mismatched recipients.

scholarly journals Human endogenous retrovirus HERV-K113 is capable of producing intact viral particles

2008 ◽  
Vol 89 (2) ◽  
pp. 567-572 ◽  
Author(s):  
Klaus Boller ◽  
Kurt Schönfeld ◽  
Stefanie Lischer ◽  
Nicole Fischer ◽  
Andreas Hoffmann ◽  
...  
Keyword(s):  
Germ Cell ◽  
Particle Production ◽  
Endogenous Retrovirus ◽  
Endogenous Retroviruses ◽  
Human Endogenous Retrovirus ◽  
Germ Cell Tumours ◽  
Typical Structure ◽  
Viral Particles ◽  
Baculovirus Expression Vector

Of all human endogenous retroviruses known today, HERV-K is the only one that has been shown to produce viral particles. While the first of the approximately 30 HERV-K sequences integrated into the human genome more than 40 million years ago, evidence is accumulating that HERV-K was active more recently, provirus HERV-K113 being the youngest sequence found. However, it is unclear which HERV-K sequences code for the viral particles that are produced by human germ-cell tumours or melanomas. Here, we show that the provirus HERV-K113, cloned into a baculovirus expression vector, is capable of producing intact particles of retroviral morphology, exhibiting the typical structure of those particles that were characterized in cell lines derived from human germ-cell tumours. Thus, the HERV-K113 sequence is a candidate for particle production in vivo and for an active human endogenous retrovirus of today.

scholarly journals pUL36 de-ubiquitinase activity augments both the initiation and progression of lytic virus infection in IFN–primed cells

2021 ◽  
Author(s):  
Jonas Mohnke ◽  
Irmgard Stark ◽  
Mara Fischer ◽  
Arnhild Grothey ◽  
Peter O’Hare ◽  
...  
Keyword(s):  
Cell Culture ◽  
Virus Infection ◽  
Virus Replication ◽  
De Novo ◽  
Virus Entry ◽  
Productive Infection ◽  
Virus Yield ◽  
Virus Particles ◽  
Hsv 1

AbstractThe conserved, structural HSV-1 tegument protein pUL36 is essential for both virus entry and assembly. While its N-terminal de-ubiquitinase (DUB) activity is dispensable for infection in cell culture, it is required for efficient virus spread in vivo by acting as a potent viral immune evasin. Here, we show that the pUL36 DUB activity was required to overcome interferon-(IFN)-mediated suppression of both plaque initiation and progression to productive infection. Immediately upon virus entry, incoming tegument-derived pUL36-DUB activity helped the virus to escape intrinsic antiviral resistance and efficiently initiate lytic virus replication in IFN-primed cells. Subsequently, de novo expressed pUL36-DUB augmented the efficiency of productive infection and virus yield. Interestingly, removal of IFN shortly after inoculation only resulted in a partial rescue of plaque formation, indicating that an IFN-induced defense mechanism eliminates invading virus particles unless counteracted by pUL36-DUB activity. Taken together, we demonstrated that the pUL36 DUB disarms IFN-induced antiviral responses at two levels, namely, to protect the infectivity of invading virus as well as to augment productive virus replication in IFN-primed cells.Author SummaryHSV-1 is an ubiquitous human pathogen that is responsible for common cold sores but may also cause life-threatening disease. pUL36 is an essential and conserved protein of infectious herpesvirus virions with a unique de-ubiquitinating (DUB) activity. The pUL36 DUB is dispensable for efficient virus infection in cell culture but represents an important viral immune evasin in vivo. Here, we showed that tegument-derived DUB activity delivered by the invading virus particles is required to overcome IFN-induced host resistance and to initiate efficient lytic infection. De novo expressed pUL36 DUB subsequently augments productive infection and virus yield. These data indicate that the pUL36 DUB antagonizes the activity of yet unidentified IFN-inducible E3 ligases to facilitate productive infection at multiple levels. Our findings underscore the therapeutic potential of targeting conserved herpesvirus DUBs to prevent or treat herpesvirus disease.

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