pinecone/core-2020-05-10-deduplication huggingface dataset:
B-Oligomer of Pertussis Toxin Inhibits HIV-1 LTR-Driven Transcription through Suppression of NF-κB p65 Subunit Activity

AbstractThe binding subunit of pertussis toxin (PTX-B) has been shown recently to inhibit the entry and postentry events in HIV-1 replication in primary T lymphocytes and monocyte-derived macrophages. While the effect of PTX-B on HIV-1 entry was shown to involve CCR5 desensitization, the mechanism of postentry inhibition remained unclear. In T lymphocytes, PTX-B affected transcription or stability of Tat-stimulated HIV-1 mRNAs. In this study, we sought to identify the mechanism of postentry inhibition of HIV-1 replication by PTX-B in U-937 promonocytic cells. We demonstrate that in these cells PTX-B inhibits expression of luciferase reporter gene controlled by the HIV-1 LTR promoter. This effect is Tat-independent and is not restricted to the HIV-1 LTR promoter. Instead, PTX-B activity is mediated through suppression of the cellular transcription factor, NF-κB. PTX-B inhibits phosphorylation and nuclear translocation of the p65 subunit of NF-κB. This effect is independent of the cytoplasmic NF-κB inhibitor, IκBα, as PTX-B stimulates phosphorylation and subsequent degradation of this protein. The suppressive activity of PTX-B on NF-κB p65 phosphorylation and nuclear translocation is delayed, suggesting that PTX-B signaling might initiate synthesis and cytoplasmic accumulation of a p65 phosphorylation inhibitor
A Mechanism in Epstein–Barr Virus Oncogenesis: Inhibition of Transforming Growth Factor-β1-mediated Induction of MAPK/p21 by LMP1

AbstractEpstein-Barr virus (EBV)-infected, gastric epithelial cell line GT38 is resistant to TGF-β1-mediated growth inhibition and apoptosis, although TGF-β1 partially induces EBV reactivation in the cells. These findings indicate that abnormalities exist in these cells in the TGF-β1-mediated signaling pathway, influencing growth inhibition and apoptosis. In order to characterize the steps with abnormalities, we analyzed the TGF-β1/MAPK/p21 pathway in the cells. TGF-β1 activated MAPK (ERK 1/2) and p21 in the TGF-β1-susceptible cell line HSC-39 but not in GT38 cells. GT38 cells had higher constitutive levels of ERK 1/2 phosphorylation and p21 expression than did HSC-39 cells. U0126, a specific inhibitor of MEK, suppressed TGF-β1-mediated ERK 1/2 phosphorylation and p21 induction in HSC-39 cells and constitutive ERK 1/2 phosphorylation in GT38 cells. EBV latent membrane protein 1 (LMP1) induced constitutive ERK 1/2 phosphorylation and NF-κB activation in LMP1-transfected HSC-39 cells, which then became resistant to TGF-β1-mediated growth inhibition, TGF-β1-mediated ERK 1/2 phosphorylation, and p21 induction, and proliferated in low-serum medium. These results are consistent with the conclusion that the TGF-β1/MAPK/p21 pathway is required for TGF-β1-mediated growth inhibition, and that the resistance to TGF in GT38 cells is derived from constitutive MAPK phosphorylation induced by LMP1
Critical Residues in the CC′ Ridge of the Human Nectin1 Receptor V Domain Enable Herpes Simplex Virus Entry into the Cell and Act Synergistically with the Downstream Region

AbstractThe site on nectin1 receptor required for herpes simplex virus (HSV) entry into the cell was previously mapped to the 64–94 region, encompassing the predicted CC′C" region of the immunoglobulin V domain. Within it lies a minimal HSV entry site (residues 77–94). Here we transferred the 65–76 region (C strand and CC′ loop) and portions, or single amino acids, thereof to nectin2, a homolog nonfunctional for wt HSV-1 entry. Replacement of the seven- or of three-amino-acid-long stretches from nectin1 to nectin2 (amino acids 69–75, 69–71, or 72–75) transferred wt HSV-1 and BHV-1 entry activity and enhanced HSV-2, PrV, and HSV-HSV(U21) entry to levels observed with nectin1. Thus, the CC′ ridge is sufficient to mediate wt HSV entry at a reduced level and responsible for the wide virus range of the receptor. Altogether the HSV entry site appears to be composed of contiguous synergistic regions, 64–76 and 77–94, each independently capable of mediating virus entry at reduced efficiency
Evolution of Total and Integrated HIV-1 DNA and Change in DNA Sequences in Patients with Sustained Plasma Virus Suppression

AbstractBlood samples from patients with plasma HIV-1 RNA <20 copies/ml for more than 2 years were studied. Significant decreases in total and integrated HIV-1 DNA were observed during the first 15 months of suppressive therapy before the concentrations became stable. Clonal analysis of HIV-1 pol demonstrated that the proportions of resistance mutations in DNA sequences after 2 years were lower than those in baseline DNA and RNA sequences. The changes in the clonal composition of HIV-1 env populations in three patients with evidence of changes in HIV-1 pol populations indicated a shift from predominantly R5-like viruses to predominantly X4-like viruses in two patients and the persistence of predominantly X4-like viruses in the third. Our analyses indicate the reemergence of ancestral sequences from long-lived cells or the residual production of wild-type virus from anatomic sites with limited access to antiretroviral drugs and the preferential infection of cells expressing CXCR4
Human Papillomavirus Type 32 Does Not Display in Vitro Transforming Properties

AbstractHuman papillomavirus type 32 (HPV32) is one of the etiological agents of a benign oral condition, focal epithelial hyperplasia. However, the previously characterized properties of its E7 oncoprotein suggest a possible malignant nature for this virus. In this study we characterized the properties of HPV32 E6 and E7. Our data show that HPV32 E7, despite its high affinity for pRb, does not promote degradation of the cellular protein. In addition, HPV32 E6 does not prevent p53-mediated apoptosis and/or cell cycle arrest. Moreover, coexpression of HPV32 E6 and E7 in primary human fibroblasts or keratinocytes does not alter their proliferative state. Together, these data provide evidence of the benign nature of HPV32
CADA Inhibits Human Immunodeficiency Virus and Human Herpesvirus 7 Replication by Down-modulation of the Cellular CD4 Receptor

AbstractThe novel antiviral agent cyclotriazadisulfonamide (CADA) inhibited human immunodeficiency virus (HIV) (IC50, 0.3–3.2 μM) and human herpesvirus 7 (HHV-7) infection (IC50, 0.3–1.5 μM) in T-cell lines and PBMCs. When T-cells were pretreated with CADA for 24 h, they became markedly protected from viral infection. Flow cytometric analysis revealed a significant decrease in the expression of the CD4 glycoprotein, the primary receptor needed for entry of both viruses. Moreover, the antiviral activity of CADA correlated with its ability to down-modulate the CD4 receptor. CADA did not alter the expression of any other cellular receptor (or HIV coreceptor) examined. Time course experiments showed that CD4 down-modulation by CADA differs in mechanism from the effects of aurintricarboxylic acid, which binds directly to CD4, and phorbol myristate acetate, which activates protein kinase C. Further analysis of CD4 mRNA levels suggested that CADA was not involved in the regulation of CD4 expression at a transcriptional level, but very likely at (post) translational levels. This unique mechanism of action makes CADA an important lead in developing new drugs for treatment of AIDS, autoimmune diseases, and inflammatory disorders
Mechanism of Neutralization of Influenza Virus Infectivity by Antibodies

AbstractWe have determined the mechanism of neutralization of influenza virus infectivity by three antihemagglutinin monoclonal antibodies, the structures of which we have analyzed before as complexes with hemagglutinin. The antibodies differ in their sites of interaction with hemagglutinin and in their abilities to interfere in vitro with its two functions of receptor binding and membrane fusion. We demonstrate that despite these differences all three antibodies neutralize infectivity by preventing virus from binding to cells. Neutralization occurs at an average of one antibody bound per four hemagglutinins, a ratio sufficient to prevent the simultaneous receptor binding of hemagglutinins that is necessary to attach virus to cells
Murine Coronavirus-Induced Apoptosis in 17Cl-1 Cells Involves a Mitochondria-Mediated Pathway and Its Downstream Caspase-8 Activation and Bid Cleavage

AbstractMouse hepatitis virus (MHV) infection in murine 17Cl-1 cells results in apoptotic cell death. Inhibition of MHV-induced apoptosis by the pancaspase inhibitor Z-VAD-FMK promoted virus production late in infection, indicating that apoptosis could be a host response to limit the production of viral progeny. Activation of the mitochondria-mediated apoptotic pathway was indicated by the activation of caspase-9 and delay of apoptosis by Bcl-2 overexpression. Analyses of the subcellular distribution of cytochrome c, procaspase-9, and Apaf-1 suggested an aberrant apoptosome formation in the vicinity of the mitochondria, which could be a cell type-specific event. An increase in the amount of Fas (APO-1/CD95), caspase-8 activation, caspase-8-mediated Bid cleavage, and subsequent translocation of truncated Bid to mitochondria, all of which relate to the Fas-mediated pathway, also occurred in MHV-infected 17Cl-1 cells, whereas the formation of the death-inducing signaling complex, a direct indication of the activation of Fas-mediated pathway, was undetectable. Caspase-8 and Bid activation appeared to be downstream of mitochondria, because Bcl-2 overexpression suppressed both events, suggesting that infected 17Cl-1 cells might have activated a receptor-mediated “type II” signaling pathway, in which primary and low levels of receptor-mediated pathway activation lead to the activation of the mitochondria-mediated pathway. All our data indicate that a mitochondria-mediated pathway played a major regulatory role in apoptosis in MHV-infected 17Cl-1 cells
The Conserved Process of TCR/CD3 Complex Down-Modulation by SIV Nef Is Mediated by the Central Core, Not Endocytic Motifs

AbstractThe Nef protein of Simian immunodeficiency virus (SIV) associates with multiple T lymphocyte signaling proteins, including the T cell receptor (TCR) ζ chain. We demonstrate here that these interactions are conserved and highly specific. Nefs derived from genetically diverse strains of SIV (SIVmac239, SIVsmmPBj, and SIVsmmΔB670) all interacted with TCR ζ on two separate domains, referred to as SIV Nef interaction domains (SNIDs), as examined in both yeast two-hybrid and glutathione-S-transferase (GST) fusion protein pull-down assays. Multiple HIV-1 Nefs were examined and none interacted with TCR ζ. In contrast, HIV-2UC1 Nef, similar to SIV Nef, interacted with TCR ζ on two domains, although only the SIV Nefs potently reduced cell-surface expression of the TCR/CD3 complex in T cells. In addition, we examined the abilities of SIV, HIV-2, and HIV-1 Nefs to interact with the cytoplasmic domains of other signaling molecules including CD3ϵ, CD3γ, and FcϵRIγ, which also contain YxxL motifs, and determined that SIV and HIV-2 Nefs interacted only with TCR ζ, whereas HIV-1 Nef did not interact with any signal-transducing cytoplasmic domain examined. Last, to gain further insight into the mechanism by which Nef down-modulates the TCR/CD3 complex, we mutated or deleted regions on Nef involved in endocytosis, localization of Nef to the plasma membrane, interaction with cellular kinases, or that were conserved among multiple strains of SIV. Mutation of the myristoylation site and a conserved region surrounding a putative PKC phosphorylation site were the only mutations that abrogated Nef-mediated down-modulation of the TCR/CD3 complex. These findings demonstrate there is a spectrum of associations between SIV, HIV-2, and HIV-1 Nefs, and the TCR/CD3 complex, and suggest that down-modulation of the TCR/CD3 complex occurs via association with subsets of cellular proteins that are different from those involved in CD4 and CD28 down-modulation
Homotypic Cell–Cell Adhesion Induced by Human T Cell Leukemia Virus Type 1 Tax Protein in T Cell Lines

AbstractCell–cell adhesion is involved in the processes of cell growth, activation and migration, and inflammation. T cells infected with human T cell leukemia virus type 1 (HTLV-1) exhibit a high degree of homotypic cell–cell adhesion in vitro. In this study, we investigated the involvement of the viral protein Tax in such process. Expression of Tax in an interleukin (IL)-2-dependent mouse T cell line (CTLL-2) increased homotypic cell–cell adhesion; however, less cell adhesion was induced by Tax than that observed in HTLV-1-infected T cell lines. Moreover, Tax induced cell–cell adhesion in a human T cell line, in which the expression of Tax is inducible. Microscopic examination also revealed Tax-induced morphologic changes, including rounding of CTLL-2 cells, increased cell volume, and increased nucleus size. Taken together, our results suggest that Tax induces cell–cell adhesion and morphologic changes in HTLV-1-infected cells. Tax may thus play a role in persistent HTLV-1 infection and the pathogenesis of associated disease
PNA Targeting the PBS and A-Loop Sequences of HIV-1 Genome Destabilizes Packaged tRNA3Lys in the Virions and Inhibits HIV-1 Replication

AbstractDuring assembly of the HIV-1 virions, cellular tRNALys3 is packaged into the virion particles and is utilized as a primer for the initiation of reverse transcription. The 3′-terminal 18 nucleotides of the cellular tRNALys3 are complementary to nucleotides 183–201 of the viral RNA genome, referred to as the primer binding sequence (PBS). Additional sequences (A-Loop) upstream of the PBS are essential for tRNA primer selection. We report here that a PNA targeted to PBS and A-Loop sequence (PNAPBS) exhibits high specificity for its target sequence and prevents tRNALys3 priming on the viral genome. We also demonstrate that PNAPBS is able to invade the duplex region of the tRNALys3–viral RNA complex and destabilize the priming process, thereby inhibiting the in vitro initiation of reverse transcription. The endogenously packaged tRNALys3 bound to the PBS region of the viral RNA genome in the HIV-1 virion is efficiently competed out by PNAPBS, resulting in near complete inhibition of initiation of endogenous reverse transcription. Examination of the effect of PNAPBS on HIV-1 production in CEM cells infected with pseudotyped HIV-1 virions carrying luciferase reporter exhibited dramatic reduction of HIV-1 replication by nearly 99%. Analysis of the mechanism of PNAPBS-mediated inhibition indicated that PNAPBS interferes at the step of reverse transcription. These findings suggest the antiviral efficacy of PNAPBS in blocking the process of HIV-1 replication
Expression of Human CD81 in Transgenic Mice Does Not Confer Susceptibility to Hepatitis C Virus Infection

AbstractWe previously demonstrated that hepatitis C virus (HCV) binds to human CD81 through the E2 glycoprotein. Therefore, expression of the human CD81 molecule in transgenic mice was expected to provide a new tool to study HCV infection in vivo, as the chimpanzee is the only species currently available as a laboratory animal model that can be infected with HCV. We produced transgenic mice expressing the human CD81 protein in a wide variety of tissues. We confirmed binding of recombinant E2 glycoprotein to the liver tissue as well as to thymocytes and splenic lymphocytes in the transgenic mice. We inoculated chimpanzee plasma infected with HCV into these animals. None of these transgenic animals showed evidence of viral replication. Furthermore, human CD81 transgenic mice that lack expression of endogenous mouse CD81 were also resistant to HCV infection. We conclude that expression of human CD81 alone is insufficient to confer susceptibility to HCV infection in the mouse. The presence of additional possible factors for HCV infection is discussed
Purified Tomato spotted wilt virus Particles Support Both Genome Replication and Transcription in Vitro

AbstractPurified Tomato spotted wilt virus particles were shown to support either genome replication or transcription in vitro, depending on the conditions chosen. Transcriptional activity was observed only upon addition of rabbit reticulocyte lysate, indicating a dependence on translation. Under these conditions RNA molecules of subgenomic length were synthesized that hybridized to strand-specific probes for the N and NSs genes. Cloning of these transcripts demonstrated the presence of nonviral leader sequences at their 5′ ends, confirming the occurrence of genuine viral transcription initiation known as “cap snatching.” Sequence analyses revealed that both α- and β-globin mRNA, present in the reticulocyte lysate, as well as added Alfalfa mosaic virus (AMV) RNA sequences, were utilized as cap donors. Moreover, an artificially produced N mRNA containing an AMV-derived leader was shown to be used as cap donor, indicating that resnatching of viral mRNAs takes place in vitro
A Natural Recombinant between the Geminiviruses Tomato yellow leaf curl Sardinia virus and Tomato yellow leaf curl virus Exhibits a Novel Pathogenic Phenotype and Is Becoming Prevalent in Spanish Populations

AbstractThis work provides evidence of the significant contribution of recombination to the genetic diversification of emerging begomovirus populations. In southern Spain, Tomato yellow leaf curl Sardinia virus (TYLCSV) and Tomato yellow leaf curl virus (TYLCV) are distinct geminivirus species that coexist in the field and contribute to the tomato yellow leaf curl disease epidemic. A natural recombinant between TYLCSV and TYLCV has been detected and an infectious clone of a recombinant isolate (ES421/99) was obtained and characterized. Analysis of its genome showed that the recombination sites are located in the intergenic region in which a conserved stem-loop structure occurs and at the 3′-end of the replication enhancer protein open reading frame. ES421/99 exhibited a novel pathogenic phenotype that might provide it with a selective advantage over the parental genotypes. This agrees with results from field studies which revealed that the recombinant strain is becoming prevalent in the region in which it was detected
Substitution of Two Residues in the Measles Virus Nucleoprotein Results in an Impaired Self-Association

AbstractThe nucleoprotein (N) of measles virus encapsidates viral genomic RNA to form a helical nucleocapsid. Its strong self-association is a major hurdle in determining its high-resolution structure using X-ray crystallography. We report the bacterial expression, purification, and characterization of a variant N that has lost its ability to form nucleocapsid-like structures after substitution of two residues by polar residues. Using immunoprecipitation, circular dichroism, and limited proteolysis studies, we show that this nucleoprotein retains a folding similar to wild-type N. Furthermore, the variant N binds the phosphoprotein, indicating that it retains biochemical relevance. We also present evidence indicating that the N-terminus of N lies at the surface of the nucleocapsid. Beyond the identification of one region of N involved in self-association, our results should facilitate structural studies of N using X-ray crystallography
Sequence Diversity of the Capsid Gene and the Nonstructural Gene NS2B of Dengue-3 Virus in Vivo

AbstractPreviously, we studied the envelope (E) gene of dengue virus and reported that dengue-3 virus is present as a quasispecies. To investigate the extent of intrahost sequence variation of other dengue viral genes, we examined in this study the capsid (C) gene and the nonstructural gene, NS2B, derived directly from plasma dengue viruses from 18 confirmed dengue-3 patients. Using reverse transcription-PCR, multiple clones of a 360-nucleotide region covering the C gene and of a 404-nucleotide region covering the NS2B gene from each patient were completely sequenced and analyzed. Our findings of the intrahost sequence variation of the C and the NS2B genes (mean pairwise p-distance: 0.12 to 1.02%, and 0.16 to 1.20%, respectively) demonstrate the quasispecies structure of dengue virus in vivo. A linear relationship was found between the extent of sequence variation of the C and NS2B proteins, suggesting that intrahost sequence variation of dengue-3 virus is likely to reflect genetic drift. The extent of intrahost sequence variation observed is in the same range as that of acute human immunodeficiency virus or hepatitis C virus infection, indicating that the random mutation frequency of dengue virus is similar to that of other RNA viruses in vivo. Consistent with a previous report of the E gene, the observations of genome-defective clones in both the C and the NS2B genes (3.9 and 5.0% of the clones, respectively) suggest a higher frequency of defective viruses in vivo. These findings would add to our understanding of the evolution of dengue-3 virus
A Minimal Genome Simian Foamy Virus Type 1 Vector System with Efficient Gene Transfer

AbstractFoamy viruses have several inherent features for the opportunity to develop efficient and versatile vectors for gene therapy. We have constructed a series of vectors and helper plasmids based on simian foamy virus type 1 (SFV-1) to establish the minimum vector genome required for efficient gene transduction. To characterize the efficiency of gene transduction by these vectors, the green fluorescent protein (GFP) coding sequence is linked to the human cytomegalovirus immediate gene promoter. Several deletion analyses of SFV-1 vectors revealed that the minimum genome with efficient GFP transduction contained the 5′ untranslated region extending to the first 637 nucleotides of the gag gene, a 596 nucleotides of pol sequence from position 3137–3733, the 3′ pol region at position 5200–5693, the 3′ end polypurine tract, and the 3′ LTR. An additional 1131 nucleotides can be removed from the 3′ end LTR without affecting the efficiency of vector transduction. SFV-1 vector can therefore accommodate a minimum 8930 base-size heterologous DNA fragment. Furthermore, the efficiency of SFV-1 vector transduction was analyzed using different packaging plasmids. GFP transduction with packaging plasmid that contained the 5′ R-U5 region of the LTR was compared with helper plasmids that had deletions in this region except for 22 nucleotides (positions 21–41), the first 61, 77, or 140 nucleotides of the R of the LTR. Transduction efficiencies were significantly reduced with the deletion mutations implicating that for optimum SFV-1 vector productions a packaging construct that includes the 5′ R-U5 is required
Differential Effect of Nucleotide Substitutions in the 3′ Arm of the Influenza A Virus vRNA Promoter on Transcription/Replication by Avian and Human Polymerase Complexes Is Related to the Nature of PB2 Amino Acid 627

AbstractUsing a genetic system that allows the in vivo reconstitution of active ribonucleoproteins, the ability to ensure transcription/replication of a viral-like reporter RNA harboring the G3 → A3, U5 → C5, and C8 → U8 mutations (triple 3-5-8 mutations) in the 3′ arm of the promoter was examined with core proteins from human or avian strains of influenza A viruses. The efficiency of transcription/replication of the viral-like RNA with the triple 3-5-8 mutations in COS-1 cells was found to be slightly decreased as compared to the wild-type RNA when the polymerase was derived from a human virus. In contrast, it was found to be considerably increased when the polymerase was derived from an avian virus, in agreement with published observations using the avian A/FPV/Bratislava virus (G. Neumann and G. Hobom, 1995, J. Gen. Virol. 76, 1709–1717). This increase could be attributed to the compensation of the defect in transcription/replication activity in the COS-1 mammalian cell line due to the presence of a glutamic acid at PB2 residue 627, characteristic of avian strains of influenza viruses. Our results thus suggest that PB2 and/or cellular proteins interacting with PB2 could be involved in RNA conformational changes during the process of transcription/replication