pinecone/core-2020-05-10-deduplication huggingface dataset:
Interferon Inhibits Dengue Virus Infection by Preventing Translation of Viral RNA through a PKR-Independent Mechanism

AbstractPreviously, we demonstrated that pretreatment of cells with interferon (IFN) α + γ or β + γ inhibited dengue virus (DV) replication. In this study, experiments were performed to better define the mechanism by which IFN blocks the accumulation of dengue virus (DV) RNA. Pretreatment of human hepatoma cells with IFN β + γ did not significantly alter virus attachment, viral entry, or nucleocapsid penetration into the cytoplasm. The inhibitory effect of IFN was retained even when naked DV RNA was transfected directly into cells, confirming that steps associated with viral entry were not the primary target of IFN action. Biosynthetic labeling experiments revealed that IFN abolished the translation of infectious viral RNA that occurred prior to RNA replication. Subcellular fractionation experiments demonstrated that IFN did not significantly alter the ability of viral RNA to attach to ribosomes. The antiviral effect of IFN appeared independent of the IFN-induced, double-stranded RNA-activated protein kinase (PKR) and RNase L, as genetically deficient PKR− RNase L− cells that were infected by DV retained sensitivity to inhibition by IFN. We conclude that IFN prevents DV infection by inhibiting translation of the infectious viral RNA through a novel, PKR-independent mechanism
Identification and Analysis of a New Hepadnavirus in White Storks

AbstractWe identified, cloned, and functionally characterized a new avian hepadnavirus infecting storks (STHBV). STHBV has the largest DNA genome of all avian hepadnaviruses and, based on sequence and phylogenetic analysis, is most closely related to, but distinct from, heron hepatitis B virus (HHBV). Unique for STHBV among the other avian hepadnaviruses is a potential HNF1 binding site in the preS promoter. In common only with HHBV, STHBV has a myristylation signal on the S and not the preS protein, two C terminally located glycosylation sites on the precore/core proteins and lacks the phosphorylation site essential for the transcriptional transactivation activity of duck-HBV preS protein. The cloned STHBV genomes were competent in gene expression, replication, and viral particle secretion. STHBV infected primary duck hepatocytes very inefficiently suggesting a restricted host range, similar to other hepadnaviruses. This discovery of stork infections unravels novel evolutionary aspects of hepadnaviruses and provides new opportunities for hepadnavirus research
Studies on Functional Interaction between Brome Mosaic Virus Replicase Proteins during RNA Recombination, Using Combined Mutants in Vivo and in Vitro

AbstractTwo viral proteins, 1a and 2a, direct replication of brome mosaic bromovirus (BMV) RNAs as well as they participate in BMV RNA recombination. To study the relationship between replication and recombination, double BMV variants that carried mutations in 1a and 2a genes were tested. The observed effects revealed that the 1a helicase and 2a N-terminal or core domains were functionally linked during both processes in vivo. The use of a series of mutant BMV replicase (RdRp) preparations demonstrated in vitro the participation of the 1a and 2a domains in BMV RNA copying and in template switching during minus-strand synthesis. The observed effects support previous observations that the characteristics of homologous and nonhomologous recombination can be modified separately by mutations at different sites on BMV replicase proteins
The Crystal Structure of the Influenza Matrix Protein M1 at Neutral pH: M1–M1 Protein Interfaces Can Rotate in the Oligomeric Structures of M1

AbstractThe influenza matrix protein (M1) forms a protein layer under the viral membrane and is essential for viral stability and integrity. M1 mediates the encapsidation of the viral RNPs into the viral membrane by its membrane and RNP-binding activities. In order to understand the roles of M1–M1 protein interactions in forming the M1 layer, X-ray crystallographic studies of a M1 fragment (1–162) were carried out at neutral pH and compared with an acidic pH structure. At neutral pH the asymmetric unit was a stacked dimer of M1. A long molecular ribbon of neutral stacked dimers was formed by translation as dictated by the P1 space group. The elongated ribbon had a positively charged stripe on one side of the ribbon. A similar M1–M1 stacking interface was also found in the acidic asymmetric unit. However, within the acidic stacked dimer the molecules were not straight, but rotated in relation to each other by slightly changing the M1–M1 stacking interface. The acidic structure possessed an additional M1–M1 twofold interface. Protein docking confirmed that the M1–M1 stacking and M1–M1 twofold interfaces could be used to form a double ribbon of M1 molecules. By iterative repetition of the rotated relationship among the M1 molecules, a helix of M1 was generated. These studies suggest that M1 has the ability to form straight or bent elongated ribbons and helices. These oligomers are consistent with previous electron microscopic studies of M1, which demonstrated that isolated M1 formed elongated and flexible ribbons when isolated from what appeared to be a helical shell of M1 in the influenza virus
The Fusion Protein of Peste des Petits Ruminants Virus Mediates Biological Fusion in the Absence of Hemagglutinin–Neuraminidase Protein

AbstractTo study the process of membrane fusion in Morbilliviruses, the fusion (F) glycoproteins of Peste des petits ruminants virus (PPRV) and Rinderpest virus (RPV) were expressed transiently in mammalian cells. The recombinant F proteins were found to be localized at the surface of transfected cells. The fusion activity, as evident from cell fusion assays and lysis of chicken erythrocytes, documented that transiently expressed PPRV F glycoprotein induces cell fusion in the absence of homotypic hemagglutinin–neuraminidase (HN) attachment glycoprotein. The coexpression of homotypic HN increased the extent of fusion by twofold, while the efficiency of fusion was found to be substantially enhanced. In contrast, in RPV F-expressing cells, fusion was detected only when homotypic hemagglutinin (H) or heterotypic HN protein was coexpressed. This differs from the strict type-specific requirement for the attachment protein as in the fusion process of most of the paramyxoviruses. Further, we demonstrate by fluorescence transfer experiments that while PPRV F brings about both hemifusion and complete fusion on its own, RPV F induces only hemifusion while it brings about complete fusion in the presence of homotypic or heterotypic attachment protein
Hemagglutinin Residues of Recent Human A(H3N2) Influenza Viruses That Contribute to the Inability to Agglutinate Chicken Erythrocytes

AbstractTo identify the molecular determinants contributing to the inability of recent human influenza A(H3N2) viruses to agglutinate chicken erythrocytes, phenotypic revertants were selected upon passage in eggs or MDCK cells. The Leu194Ile or Val226Ile substitutions were detected in their hemagglutinin (HA) sequence concomitantly with the phenotypic reversion. Remarkably, as little as 3.5% of variants bearing a Val226Ile substitution was found to confer the ability to agglutinate chicken erythrocytes to the virus population. Hemadsorption assays following transient expression of mutated HA proteins showed that the successive Gln226 → Leu → Ile → Val changes observed on natural isolates resulted in a progressive loss of the ability of the HA to bind chicken erythrocytes. The Val226Ile change maintained the preference of the HA for SAα2,6Gal over SAα2,3Gal and enhanced binding of the HA to α2,6Gal receptors present on chicken erythrocytes. In contrast, simultaneous Ser193Arg and Leu194Ile substitutions that were found to confer the ability to agglutinate sheep erythrocytes increased the affinity of the HA for SAα2,3Gal
Differentiation-Dependent Redistribution of Heparan Sulfate in Epithelial Intestinal Caco-2 Cells Leads to Basolateral Entry of Cytomegalovirus

AbstractHuman cytomegalovirus (HCMV) causes a broad spectrum of clinical manifestations in immunocompromised patients, including infection of the gastrointestinal tract. To investigate the role of epithelial cells in the gastrointestinal HCMV disease, we used the intestinal epithelial cell line Caco-2, which is permissive for HCMV replication. In differentiated Caco-2 cells, we showed previously that HCMV infection proceeds preferentially from the basolateral membrane, suggesting that receptors for HCMV may be contained predominantly in the basolateral membrane (A. Esclatine et al., 2000, J. Virol. 74, 513–517). Therefore, we examined expression and localization in Caco-2 cells of heparan sulfate (HS) proteoglycan and annexin II, previously implicated in initial events of HCMV infection. We observed that annexin II is expressed in Caco-2 cells, but is not essential for entry of HCMV. We showed that, during the differentiation process, HS, initially present on the entire surface of the membrane of undifferentiated cells, ultimately became sequestered at the basolateral cell surface of fully differentiated cells. We established by biochemical assays that membrane-associated HS proteoglycan mediates both viral attachment to, and subsequent infection of, Caco-2 cells, regardless of the cell differentiation state. Thus, the redistribution of HS is implicated in the basolateral entry of HCMV into differentiated Caco-2 cells
Mutational Analysis of the Membrane Proximal Heptad Repeat of the Newcastle Disease Virus Fusion Protein

AbstractParamyxovirus fusion proteins have two heptad repeat domains, HR1 and HR2, that have been implicated in the fusion activity of the protein. Peptides from these two domains form a six-stranded, coiled-coil with the HR1 sequences forming a central trimer and three molecules of the HR2 helix located within the grooves in the central trimer (Baker et al., 1999, Mol. Cell 3, 309; Zhao et al. 2000, Proc. Natl. Acad. Sci. USA 97, 14172). Nonconservative mutations were made in the HR2 domain of the Newcastle disease virus fusion protein in residues that are likely to form contacts with the HR1 core trimer. These residues form the hydrophobic face of the helix and adjacent residues (“a” and “g” positions in the HR2 helical wheel structure). Mutant proteins were characterized for effects on synthesis, steady-state levels, proteolytic cleavage, and surface expression as well as fusion activity as measured by syncytia formation, content mixing, and lipid mixing. While all mutant proteins were transport competent and proteolytically cleaved, these mutations did variously affect fusion activity of the protein. Nonconservative mutations in the “g” position had no effect on fusion. In contrast, single changes in the middle “a” position of HR2 inhibited lipid mixing, content mixing, and syncytia formation. A single mutation in the more carboxyl-terminal “a” position had minimal effects on lipid mixing but did inhibit content mixing and syncytia formation. These results are consistent with the idea that the HR2 domain is involved in posttranslational interactions with HR1 that mediate the close approach of membranes. These results also suggest that the HR2 domain, particularly the carboxyl-terminal region, plays an additional role in fusion, a role related to content mixing and syncytia formation
Polyoma Virus: Old Findings and New Challenges

AbstractThe accidental discovery of the mouse polyoma virus nearly 50 years ago opened up an experimental system unique in opportunities for investigating virus–host interactions leading to the development of tumors. Extensive studies of the virus in tissue culture have provided a detailed understanding of its genetics and molecular biology. Knowledge of the virus as a transforming agent in culture can now be tested in the animal where multiple cell types are targets for tumorigenic conversion and where a variety of host factors, both immunological and nonimmunological, come into play. Studies in the animal using well-characterized wild-type and mutant virus strains have led to some unexpected findings. Some of these run counter to certain widely held beliefs in cancer biology. This minireview focuses on these surprising findings and the challenges they raise
Reassortant Analysis of Guinea Pig Virulence of Pichinde Virus Variants

AbstractThe new world arenavirus Pichinde (PIC) is the basis of an accepted small animal model for human Lassa fever. PIC (Munchique strain) variant P2 is attenuated in guinea pigs, whereas variant P18 is extremely virulent. Previous sequence analysis of the S segments of these two viruses indicated a small number of possible virulence markers in the glycoprotein precursor (GPC) and nucleoprotein (NP) genes. In order to determine the role of these S segment genes in guinea pig virulence in this system, we have generated reassortant viruses. When tested in outbred guinea pigs, the reassortant containing the S segment from the virulent parent P18 (S18L2) caused significantly higher morbidity than the reciprocal reassortant. This increased morbidity was associated with higher viral titers in serum and spleen. However, the S18L2 reassortant was not as fully virulent in this system as the P18 parent, indicating a role for L segment genes in virulence
Prolonged E55+ Retrovirus Expression in Aged Mice Is Associated with a Decline in the Anti-Virus Immune Response

AbstractE55+ murine leukemia retrovirus (E55+MuLV) infection of young and aged C57BL/6 (B6) mice was used to investigate the relationship between increased incidences of infection and decreased immune responsiveness of elderly individuals. Young mice decreased E55+MuLV burden to below detectable levels by 8 weeks postinfection (p.i.). In contrast, virus burden in aged mice did not reach undetectable levels until 20 weeks p.i. A significant T cell proliferative response to E55+MuLV was detected from 2 to 12 weeks p.i. in young mice, but was never observed in aged mice. Both age groups demonstrated significant E55+MuLV-specific T-cell-mediated cytotoxic responses at 3 and 4 weeks p.i. and virus neutralizing antibody titers at 2, 4, 8, and 12 weeks p.i. In both cases, responses were consistently higher in young mice (P < 0.04 and P < 0.02, respectively). These results demonstrate that the observed delay in E55+MuLV clearance by aged mice is associated with an age-related decrease in the immune response to the virus
Enhancement of the p300 HAT Activity by HIV-1 Tat on Chromatin DNA

AbstractHIV-1 Tat is able to form a ternary complex with P/CAF and p300 and increase the affinity for CDK9/P-TEFb CTD kinase complex. Our previous study demonstrated that Tat binds to p300/CBP in the minimal HAT domain (aa 1253–1790) and that the interaction results in a change of conformation on p300/CBP. Here, we show that the Tat–p300 interaction increases the HAT activity of p300 on histone H4 that is associated with nucleosomal DNA and not with free histones. Nucleosomal histone H4 was acetylated on lysines 8, 12, and 16. Acetylation of H4 was inhibited by Lys-coenzyme A (CoA), a selective inhibitor of p300 acetyltransferase activity. Unexpectedly, we also found that Tat could autoacetylate itself, which was specific to lysine residues 41 and 71. Peptides lacking these two lysines could not enhance the HAT activity of p300. Comparison of the sequences of Tat with other HIV-1 clades and HAT containing transcription factors indicated sequence identity in the acetyl-CoA binding motif A, KGXG. Furthermore, when utilizing an in vitro transcription assay, as well as a Tat mutant virus, we found that ectopic expression of only wild-type Tat in the presence of p300, and not a lysine 41 Tat mutant, could activate HIV-1 chromatin DNA, as evidenced by the absence of HIV-1 virion antigen. Therefore, transcription of integrated viral DNA in vivo requires the HAT activity of coactivators that are modulated by Tat to derepress the HIV-1 chromatin structure and aid in activated transcription
Truncation of the Human Adenovirus Type 5 L4 33-kDa Protein: Evidence for an Essential Role of the Carboxy-Terminus in the Viral Infectious Cycle

AbstractThe subgroup C human adenovirus L4 33-kDa protein is a nuclear phosphoprotein that plays a direct, but dispensable, role in virion assembly. The r-strand open reading frame (ORF) for this protein lies opposite to the 5′ end of the l-strand E2 early (E2E) transcription units. To facilitate studies of regulation of E2E transcription, we wished to construct a mutant virus in which the 33-kDa ORF was truncated to serve as a background into which specific E2E mutations could be introduced without also altering the 33-kDa protein. We constructed viral DNA (vDNA) containing within the 33-kDa ORF two tandem, premature stop codons that should prevent translation of the C-terminal 47 amino acids of the protein (Δ47). We report here the unanticipated lethality of such truncation of the L4 33-kDa protein. Viral DNA harboring the Δ47 mutations did not produce infectious virus when transfected into cultured cells. In contrast, infectious virus was recovered upon transfection of revertant vDNA, indicating that the Δ47 mutations were responsible for the observed phenotype. The Δ47 mutations did not affect E2E transcription or production of the E2 DNA-binding protein. Transfected Δ47 vDNA was replicated and directed the production of early and late viral proteins, including hexon protein in the trimer conformation. However, no virus particles of any kind were produced. We propose that truncation of the adenovirus 33-kDa protein results in a lethal, late block in the infectious cycle during the assembly of progeny virions and discuss the implications of this phenotype for the mechanism of virion assembly
The A17L Gene Product of Vaccinia Virus Is Exposed on the Surface of IMV

AbstractThe p21 membrane protein of vaccinia virus (VV), encoded by the A17L gene, has been reported to localize on the inner of the two membranes of the intracellular mature virus (IMV). It has also been shown that p21 acts as a membrane anchor for the externally located fusion protein p14 (A27L gene). Since p14 is located on the surface of IMVs, it is hard to envision that p21 should be located only on the inner membrane. Our results from (i) immunoelectron microscopy, (ii) biotinylation, and (iii) protease treatment of purified IMVs showed that the N-terminus of p21 is exposed on the surface of virus particles, while the C-terminus is embedded in the membrane. Mono-specific antibodies to the N-terminus of p21 neutralize infection of VV while antibodies to the C-terminal domain do not. We suggest that p21 molecules are located both in the inner and in the outer membrane of IMV
A Lethal Disease Model for Hantavirus Pulmonary Syndrome

AbstractHantaviruses are associated with two human diseases, hemorrhagic fever with renal syndrome (HFRS) and hantavirus pulmonary syndrome (HPS). Development of vaccines and therapies to prevent and treat HFRS and HPS have been hampered by the absence of a practical animal model. Here we report that Andes virus (ANDV), a South American hantavirus, is highly lethal in adult Syrian hamsters. The characteristics of the disease in hamsters, including the incubation period, symptoms of rapidly progressing respiratory distress, and pathologic findings of pulmonary edema and pleural effusion, closely resemble HPS in humans. This is the first report of a lethal disease model for hantaviruses that causes HPS
Solitary Human Endogenous Retroviruses-K LTRs Retain Transcriptional Activity in Vivo, the Mode of Which Is Different in Different Cell Types

AbstractSolitary long terminal repeats (LTRs) of human endogenous retroviruses (HERVs), tens of thousands of which are spread all over the genome, contain a variety of potential transcription regulatory elements. Information on transcriptional behavior of individual solitary LTRs, however, is limited. We studied the transcriptional activity of several individual HERV-K LTRs in a variety of tissues and cell lines. The RT-PCR technique targeted at specific amplification of the U3 or U5 regions of individual LTRs together with their unique genomic flanks was used to estimate the content of each region in the transcripts. An unequal abundance of the U3 and U5 regions in the transcripts of the same LTR in different cells and tumors was observed. Each LTR is transcribed differently in different cells or tissues, and transcriptional behavior of different LTRs was different in the same cell line or tissue. The transcriptional status of LTRs varies in response to mitogenic and stress factors and in tumor tissues compared to normal counterparts. The LTRs thus seem to be the subjects of specific transcription regulation. The data obtained indicate that an appreciable fraction of the LTRs retained regulatory potential throughout millions of years of evolution and thus may contribute to the overall transcription regulatory network
Display of Complete Life Cycle of Human Papillomavirus Type 16 in Cultured Placental Trophoblasts

AbstractHuman papillomavirus (HPV) infection is threefold more prevalent in spontaneous abortion specimens compared to elective abortions, preferentially targeting the placental trophoblasts in these specimens. Here, by using infectious center and Southern blot analysis, we demonstrate that the transfected HPV-16 genome de novo replicates in 3A trophoblasts in culture. Peak DNA replication occurred 9–24 days posttransfection, showing classic DNA forms I, II, and III and an 8-kb monomer band upon DpnI/BamHI digestion. Reverse transcription-polymerase chain reaction (RT-PCR) analysis of mRNA expression revealed that E6 and E2 were significantly expressed by day 9, coinciding with HPV-16 DNA replication. However, significant L1 expression was delayed until day 18. L1 protein expression on day 18, but not day 9, was also confirmed by Western blot analysis. The production of HPV-16 virions was demonstrated by three techniques: the appearance of HPV-16 infectious units coinciding with L1 expression, the neutralization of these infectious units with known neutralizing anti-HPV-16 antibodies, and the appearance of spliced E1∧E4 and E6∧E7 transcripts (RT-PCR) in normal keratinocyte rafts infected with these trophoblast-produced HPV-16 infectious units. These data suggest that HPV-16 is carrying out its complete life cycle in trophoblasts. Previously, HPVs were known to productively replicate only in differentiating keratinocytes of skin. These findings expand HPV biology, support the hypothesis of a possible link between HPV and some spontaneous abortions, and present a new technology for studying HPV