pinecone/core-2020-05-10-deduplication huggingface dataset:
Analysis of Minimal Promoter Sequences for Plus-Strand Synthesis by the Cucumber necrosis virus RNA-Dependent RNA Polymerase

AbstractTombusviruses are small, plus-sense, single-stranded RNA viruses of plants. A partially purified RNA-dependent RNA polymerase (RdRp) preparation of Cucumber necrosis virus (CNV), which is capable of de novo initiation of complementary RNA synthesis from either plus-strand or minus-strand templates, was used to dissect minimal promoter sequences for tombusviruses and their defective interfering (DI) RNAs. In vitro RdRp assay revealed that the core plus-strand initiation promoter included only the 3′-terminal 11 nucleotides. A hypothetical promoter-like sequence, which has been termed consensus sequence by Wu and White (1998, J. Virol. 72, 9897–9905), is recognized less efficiently by the CNV RdRp than the core plus-strand initiation promoter. The CNV RdRp can efficiently recognize the core plus-strand initiation promoter for a satellite RNA associated with the distantly related Turnip crinkle virus, while artificial AU- or GC-rich 3′-terminal sequences make poor templates in the in vitro assays. Comparison of the “strength” of minimal plus-strand and minus-strand initiation promoters reveals that the latter is almost twice as efficient in promoting complementary RNA synthesis. Template competition experiments, however, suggest that the minimal plus-strand initiation promoter makes an RNA template more competitive than the minimal minus-strand initiation promoter. Taken together, these results demonstrate that promoter recognition by the tombusvirus RdRp requires only short sequences present at the 3′ end of templates
The Cytoskeleton and the Secretory Pathway Are Not Involved in Targeting the Cowpea Mosaic Virus Movement Protein to the Cell Periphery

AbstractThe movement protein (MP) of cowpea mosaic virus (CPMV) forms tubules on infected protoplasts and through plasmodesmata in infected plants. In protoplasts the MP fused to GFP (MP-GFP) was shown to localize in peripheral punctate structures and in long tubular structures extending from the protoplast surface. Using cytoskeletal assembly inhibitors (latrunculin B and oryzalin) and an inhibitor of the secretory pathway (brefeldin A), targeting of the MP to the peripheral punctate structures was demonstrated not to be dependent on an intact cytoskeleton or functional secretion pathway. Furthermore it was shown that a disrupted cytoskeleton had no effect on tubule formation but that the addition of brefeldin A severely inhibited tubule formation. The results presented in this paper suggest a role for a plasma membrane host factor in tubule formation of plant viral MPs
Identification and Characterization of a Novel Replicative Intermediate of Heron Hepatitis B Virus

AbstractWe have identified and characterized a novel intracellular DNA replicative intermediate that is synthesized by heron hepatitis B virus (HHBV) and not by other avian hepadnaviruses. The new DNA form is synthesized in all host cells tested. The HHBV nucleic acid template, and not HHBV proteins, is responsible for the formation of the new form. The new form is comprised of a full-length minus-strand DNA and an incomplete plus-strand DNA whose 5′ ends are mapped to DR2, predominantly. The 3′ ends of its plus-strand are located between nucleotides 946 and 1046. Genetic analysis indicates that the sequences responsible for the formation of the new form lie between nucleotides 910 and 1364. The endogenous polymerase activity of capsids isolated from cells converted the new form into RC DNA. Intracellular capsids containing the new form are secreted inefficiently as virions, in comparison to RC- and DL DNA-containing capsids. Our analysis suggests that the new form is an incomplete RC DNA molecule that is due to a specific block or pause in the synthesis of plus-strand DNA. Our analysis also suggests that capsids become competent for efficient secretion sometime after the synthesis of 1500 nucleotides of plus-strand DNA
Binding of Adenovirus to Its Receptors in Mouse Astrocytes Induces c-fos Proto-Oncogene and Apoptosis

AbstractWe have demonstrated that Ad.βGal, a broadly used adenoviral vector of serotype 5, binds and induces proto-oncogene c-fos expression in quiescent cultures of mouse brain astrocytes. As observed in Northern blots, the expression of this immediate early gene is induced by viral infection in a dose-dependent manner, peaking at a multiplicity of infection (m.o.i.) of 100. The expression of c-fos is transient, being maximal after 30 min and disappearing 2 h after infection. A previously reported method was used to study the presence of receptors for adenovirus in the cellular membrane of murine astrocytes. After absorption of the virus, rabbit antibodies and 125I-protein A were used to form a sandwich on the cellular surface, and 9000 adenovirus-specific receptors were demonstrated on each astrocytic cell. Binding was temperature dependent and reached a plateau after 60 min. The specificity of c-fos induction is demonstrated by its neutralization by anti-adenovirus-specific antibodies. Although clear apoptosis cannot be demonstrated in vitro by DNA laddering, maybe due to a lack of sensitivity of the method, a statistically significant increase in caspase-3 activity is demonstrated in astrocyte cultures infected at a m.o.i. of 100 by adenovirus. Furthermore, a perfect colocalization is shown in vivo between cells infected with the Ad.βGal vector and apoptotic astrocytes, as demonstrated by TdT-mediated dUTP nick end labeling (TUNEL) staining. The purpose of our study was to ascertain the potential for adenovirus as a gene therapy vector for neural disorders caused by astrocyte dysfunctions
Cloning, Expression, and Characterization of Avian Reovirus Guanylyltransferase

AbstractWe have cloned and sequenced the L3 genome segment of avian reovirus strain 1733, which specifies the viral guanylyltransferase protein, λC. The L3 gene is 3907 nucleotides long and encodes, in a single large open-reading frame, a polypeptide of 1285 amino acid residues, with a calculated Mr of 142.2 kDa. Expression of this gene in a baculovirus/insect cell system produced a recombinant protein that comigrated with reovirion λC and reacted with anti-reovirus polyclonal serum in a Western blot assay. Incubation of recombinant λC with GTP led to the formation GMP-λC complex via a phosphoamide linkage. Interestingly, a 42-kDa amino-terminal proteolytic fragment of recombinant λC protein also exhibited autoguanylylation activity, demonstrating both that this fragment is necessary and sufficient for autoguanylylation activity and that the 100-kDa complementary fragment is expendable for that activity. Comparison of the deduced amino acid sequence of protein λC with those of the mammalian and grass carp reovirus guanylyltransferases revealed that only two of eight lysine residues within the amino-terminal 42-kDa region are conserved. Interestingly, these two lysines match with the lysine residues in the mammalian reovirus capping enzyme proposed to be essential for autoguanylylation activity. Our alignment analysis also showed that the S-adenosyl-l-methionine-binding pocket previously detected in the mammalian reovirus capping enzyme is fully conserved in its avian and grass carp reovirus counterparts, suggesting that all three enzymes have methylase activity
Characterization of the Equilibrium between the Native and Fusion-Inactive Conformation of Rabies Virus Glycoprotein Indicates That the Fusion Complex Is Made of Several Trimers

AbstractRabies virus-induced membrane fusion is triggered at low pH and is mediated by the trimeric viral glycoprotein (G). G assumes three conformations: the native state (N) detected above pH 7; the activated state (A), which initiates the fusion process; and the fusion-inactive conformation (I) observed after prolonged incubation at low pH. Differently from other viral fusogenic glycoproteins, G in the I state recovers its native conformation when reincubated above pH 7. Here, we demonstrate that there is a thermodynamic equilibrium between the different states of G between pH 6 and pH 7.5. The study of this equilibrium at various pH values indicated that the conformational change toward I is induced by the protonation of at least three residues per trimer. Finally, studies on the mechanism leading to low pH induced fusion inactivation indicated that a large number of G molecules is required for stable hydrophobic interaction of the virus with the target membrane
Phylogenetic Analysis of 49 Newly Derived HIV-1 Group O Strains: High Viral Diversity but No Group M-like Subtype Structure

AbstractWe assess the genetic relationships between 49 HIV-1 group O strains from 24 and 25 patients living in Cameroon and France, respectively. Strains were sequenced in four genomic regions: gag (p24) and three env regions (C2-V3, gp41, and for 22 C2-gp41). In each of the genomic regions analyzed, the genetic diversity among the group O strains was higher than that exhibited by group M. We characterize three major group O phylogenetic clusters (O:A, O:B, and O:C) that comprised the same virus strains in each of the genomic regions analyzed. The majority of strains cluster in O:A, a cluster previously identified by analysis of pol and env sequences. Group O recombinants were also identified. Importantly, the distinction between these three major group O clades was weak compared to the strong clustering apparent in the global group M phylogenetic tree that led to the identification of subtypes. Thus, these clusters of group O viruses should not be considered as equivalent to the group M subtypes. This difference between the pattern of group O and the global group M diversity, both taking into account the pandemic status of the group M subtypes and the comparatively small number of group O-infected individuals (the majority being from Cameroon), indicates that the group O phylogeny primarily represents viral divergence in the Cameroon region, analogous to group M viral diversity present in the Democratic Republic of Congo
Yellow Fever Virus 17D Envelope and NS3 Proteins Are Major Targets of the Antiviral T Cell Response in Mice

AbstractThe yellow fever virus 17D vaccine strain is one of the most effective and safe vaccines available. The immune response after immunization is characterized by long-lasting high titers of neutralizing antibodies. Here, we have initiated a characterization of YFV-17D-specific cellular immune responses. This study makes three points. First, we have identified two CD8 T cell epitopes and one CD4 T cell epitope. An H-2Kb-restricted dominant epitope was mapped in the NS3 protein, whereas the viral envelope protein harbored an H-2Db-restricted subdominant epitope and the I-Ab-restricted CD4 T cell epitope. Second, illustrating the concept of immunodomination, we found that after abrogation of the dominant response in H-2Kb knockout mice, the frequencies of T cells recognizing the subdominant Db-restricted epitope increased dramatically. Finally, the H-2Db-restricted epitope lacks the canonical Asn anchor residue at position 5, indicating that epitopes may be missed by strict application of the H-2Db-binding motif. Identification of these T cell epitopes will facilitate studies on the cellular immunity against YFV-based expression or immunization vectors
Morphology of Marburg Virus NP–RNA

AbstractWhen Marburg virus (MBGV) nucleoprotein (NP) is expressed in insect cells, it binds to cellular RNA and forms NP–RNA complexes such as insect cell-expressed nucleoproteins from other nonsegmented negative-strand RNA viruses. Recombinant MBGV NP–RNA forms loose coils that resemble rabies virus N–RNA. MBGV NP monomers are rods that are spaced along the coil similar to the nucleoprotein monomers of the rabies virus N–RNA. High salt treatment induces tight coiling of the MBGV NP–RNA, again a characteristic observed for other nonsegmented negative-strand virus N–RNAs. Electron microscopy of fixed Marburg virus particles shows that the viral nucleocapsid has a smaller diameter than the free, recombinant NP–RNA. This difference in helical parameters could be caused by the interaction of other viral proteins with the NP–RNA. A similar but opposite phenomenon is observed for rhabdovirus nucleocapsids that are condensed by the viral matrix protein upon which they acquire a larger diameter. Finally, there appears to be an extensive and regular protein scaffold between the viral nucleocapsid and the membrane that seems not to exist in the other negative-strand RNA viruses
Human Immunodeficiency Virus Type-1 Activates Lytic Cycle Replication of Kaposi's Sarcoma-Associated Herpesvirus through Induction of KSHV Rta

AbstractHuman immunodeficiency virus type-1 (HIV-1) infection dramatically increases the risk of development of Kaposi's sarcoma (KS) in individuals infected with Kaposi's sarcoma-associated herpesvirus (KSHV). In a primary effusion lymphoma (PEL) tissue culture model system, HIV-1 replication potently induced the lytic replication of KSHV and led to the secretion of soluble factors capable of inducing lytic KSHV replication in bystander cells. Here we demonstrate that HIV induces KSHV lytic replication through activation of the KSHV Rta. HIV gene expression activated the KSHV Rta promoter following viral infection or after transfection of proviral DNA. Although HIV-1 Tat has previously been implicated as an activator of KSHV lytic replication, Tat alone was unable to activate lytic replication and failed to activate the Rta promoter. We conclude that HIV activates KSHV lytic replication by inducing the KSHV Rta promoter and that factors other than HIV-1 Tat are required to mediate this effect
Subcellular Localisation, Protein Interactions, and RNA Binding of Potato mop-top virus Triple Gene Block Proteins

AbstractSubcellular localisation, protein interactions, and RNA binding of the triple gene block proteins (TGBp) of Potato mop-top virus (PMTV) were studied. The 13-kDa (TGBp2) and 21-kDa (TGBp3) proteins with or without green fluorescent protein fused to their N-terminus, and the 51-kDa protein (TGBp1) were expressed individually from a recombinant Tobacco mosaic virus (TMV) vector. Fluorescent images and Western immunoblotting experiments of recombinant TMV-infected Nicotiana benthamiana cells suggested that TGBp2 and TGBp3 were associated with cellular endomembranes and that TGBp3 was associated with the cell wall, possibly located close to plasmodesmata. In Western blots, TGBp1 was detected in fractions containing the cell wall and those enriched for organelles and membranous structures. Self-interactions were demonstrated with all three proteins in yeast two-hybrid experiments, and a heterologous interaction was found between TGBp2 and TGBp3. No additional heterologous interactions were discovered between the different TGBp and none were detected in an in vitro binding assay. TGBp1 and TGBp2 but not TGBp3 were shown to bind ssRNA in a sequence nonspecific manner. The results support the model where TGBp2 and TGBp3 facilitate delivery and localisation of the ribonucleoprotein complex to the plasmodesmata. However, the process is facilitated by RNA–protein rather than protein:protein interactions between the TGBp1 in complex with viral RNA and membrane-localised TGBp2
Characterization of φ12, a Bacteriophage Related to φ6: Nucleotide Sequence of the Large Double-Stranded RNA

AbstractThe isolation of additional bacteriophages besides φ6 containing segmented double-stranded RNA genomes (dsRNA) has expanded the Cystoviridae family to nine members. Comparing the genomic sequences of these viruses has allowed evaluation of important genetic as well as structural motifs. These comparative studies are resulting in greater understanding of viral evolution and the role played by genetic and structural variation in the assembly mechanisms of the cystoviruses. In this regard, the large double-stranded RNA genomic segment of bacteriophage φ12 was copied as cDNA and its nucleotide sequence determined. This genome's organization is similar to that of the large segment of bacteriophages φ6, φ8, and φ13. In the amino acid sequence of the viral RNA-dependent RNA polymerase (P2), similarity was found to the comparable proteins of φ6, φ8, and φ13. Amino acid sequence similarity was also noted in the nucleotide triphosphate phosphorylase (P4) to the comparable proteins of φ8 and φ13
A Protein Phosphatase from Human T Cells Augments Tat Transactivation of the Human Immunodeficiency Virus Type 1 Long-Terminal Repeat

AbstractHIV-1 Tat protein regulates viral gene expression by modulating the activity and association of cellular transcription factors with RNA polymerase II (RNAPII). Possible mechanisms include Tat-associated protein kinase(s) and phosphatase(s) that regulate phosphorylation of the C-terminal domain (CTD) of the large subunit of RNAPII. Hypophosphorylated RNAPII (RNAPIIa) is recruited to promoters during formation of a preinitiation complex, whereas hyperphosphorylated RNAPII (RNAPIIo) is associated with the elongation complex. The role of phosphatases in maintaining the equilibrium between the two phosphorylated states of RNAPII, which is required for sustained transcriptional activation from the HIV-1 LTR, is not clear. In this study, we discuss the properties of a Tat-associated CTD phosphatase fractionated from Jurkat T cells. The Tat-associated protein phosphatase (TAPP) is related to the serine/threonine, type 1, protein phosphatase (PP1) family. TAPP dephosphorylates the hyperphosphorylated form of recombinant CTD specifically on serine 2, and augments Tat-mediated transcriptional transactivation of HIV-1 LTR in an in vitro transcription reaction. TAPP is associated with the transcription complex during the early initiation steps, and its release from the HIV-1 promoter coincides with the Tat-specific activation of CDK9. The results suggest a unique role of the Tat-associated phosphatase which regulates viral transcription by target-specific dephosphorylation of RNAPII during the early stages of elongation
Interaction between TGFβ Signaling Proteins and C/EBP Controls Basal and Tat-Mediated Transcription of HIV-1 LTR in Astrocytes

AbstractSignal transduction pathways induced by cytokines can modulate the level of HIV-1 gene transcription and replication in a variety of cells including those from the central nervous system. Here, we investigated the effect of TGFβ-1 signaling the factors, including Smads, on transcription of the viral LTR in human astrocytic cells. Ectopic expression of Smad-3 increased activity of the viral promoter, while its partner protein, Smad-4, caused a slight decrease in viral gene transcription. Further, Smad-4 was able to suppress transcriptional activation of the LTR by Smad-3 as well as by C/EBPβ, another activator of LTR transcription in these cells. Results from promoter deletion experiments identified the C/EBP-binding site, which is positioned between nucleotides −114 and −102 as one of the targets for Smad-mediated regulation of the LTR. Band-shift studies showed inhibition of C/EBP binding to its target DNA in protein extract from cells overexpressing Smad-3 and Smad-4. Results from GST pull-down assay and combined immunoprecipitation/Western blot of protein extracts from human astrocytes verified the association of Smad-3 and Smad-4 with C/EBPβ, suggesting that interaction of C/EBPβ with Smad-3 and Smad-4 may have a negative impact upon C/EBPβ-mediated activation of the LTR. Interestingly, Smad-4 showed no inhibitory effect on viral gene transcription in cells expressing Tat protein. However, in the presence of Smad-3, expression of Smad-4 exerted a negative effect on Tat-mediated activation of the LTR promoter. These observations pointed to the functional interplay between viral and cellular proteins in modulating LTR transcription
Protection by Intranasal Immunization of a nef-Deleted, Nonpathogenic SHIV against Intravaginal Challenge with a Heterologous Pathogenic SHIV

AbstractAn effective vaccine against sexual transmission of human immunodeficiency virus (HIV) should elicit both systemic and mucosal immune responses. In this study, to examine the possibility of using an attenuated virus for mucosal immunization, four female macaques were intranasally or intravenously administered with a chimeric simian-human immunodeficiency virus with a deleted nef gene (SHIV-dn). Although all the monkeys had anti-HIV-1 antibodies with neutralizing activity in the plasma, the intranasally immunized monkeys had much higher levels of HIV-1 Env-specific IgG and IgA antibodies in mucosal secretions compared with the intravenously immunized monkeys. Moreover, three of four intranasally immunized monkeys were completely protected from intravaginal challenge with a pathogenic virus, SHIV-89.6P, whereas only one intravenously immunized monkey was protected. Thus, intranasal immunization of an attenuated virus can induce the protective efficacy against intravaginal infection
Comparative Analysis of the Roles of Simian Immunodeficiency and Bovine Leukemia Virus Matrix Proteins in Gag Assembly in Insect Cells

AbstractThe role of the matrix (MA) domain of simian immunodeficiency virus (SIV) and bovine leukaemia virus (BLV) Gag in the assembly of virus-like particles (VLP) in insect cells has been investigated. Wild-type SIV and BLV Gag assembled to form discrete VLP structures typical of many retroviruses analysed by similar systems. When amino acids predicated by the three-dimensional structure to be at the interface of SIV MA monomers were deleted, VLP assembly was abolished consistent with a role for MA multimerization in assembly. When amino acids predicted to be in the analogous positions in BLV MA were mutated, however, VLP assembly was not affected. These data indicate that the models of assembly derived from one model retrovirus may not necessarily apply to more distantly related viruses despite the structural similarity present in equivalent Gag domains
Development of Feline Immunodeficiency Virus ORF-A (tat) Mutants: In Vitro and in Vivo Characterization

AbstractA functional ORF-A is essential for efficient feline immunodeficiency virus replication in lymphocytes. We have characterized a series of mutants of the Petaluma strain, derived from p34TF10 and having different combinations of stop codons and increasingly long deletions in ORF-A. Six clones proved fully replicative in fibroblastoid Crandell feline kidney cells and monocyte-derived macrophage cultures but failed to replicate in T cell lines and primary lymphoblasts. Cats inoculated with three selected mutants had considerably milder infections than controls given intact ORF-A virus. In vivo, the mutants maintained growth properties similar to those in vitro for at least 7 months, except that replication in lymphoid cells was strongly reduced but not ablated. One mutant underwent extensive ORF-A changes without, however, reverting to wild-type. Antiviral immune responses were feeble in all cats, suggesting that viral loads were too low to represent a sufficiently powerful antigenic stimulus