pinecone/core-2020-05-10-deduplication huggingface dataset:
The Role of the PKR-Inhibitory Genes, E3L and K3L, in Determining Vaccinia Virus Host Range

AbstractVaccinia virus encodes two regulators of the cellular antiviral response. The E3L gene is thought to act primarily by sequestering double-stranded RNA, whereas the K3L gene is thought to act as a competitive inhibitor of the double-stranded RNA-dependent protein kinase, PKR. The broad host range associated with vaccinia virus replication appears to be related to the presence of these genes. The E3L gene is required for replication in HeLa cells, but is not required for replication in BHK cells. On the contrary, the K3L gene is required for replication in BHK cells, but is dispensable for replication in HeLa cells. Our results suggest that these cell lines varied in the expression of endogenous activatable PKR and that replication of vaccinia virus in different cell lines led to altered levels of double-stranded RNA synthesis from the virus. Vaccinia virus was able to overcome these cellular variations by regulating PKR activity through the synthesis of either E3L or K3L. The results suggest that vaccinia virus has evolved a broad host range by maintaining both the E3L and the K3L genes
Chimeric Polypeptide of Thymidine Kinase and Thymidylate Kinase of Shrimp White Spot Syndrome Virus: Thymidine Kinase Activity of the Recombinant Protein Expressed in a Baculovirus/Insect Cell System

AbstractThe unique chimeric organization of the white spot syndrome virus (WSSV) tk-tmk gene encodes a protein which has significant homology to both cellular-type thymidine kinase (TK) and cellular-type thymidylate kinase (TMK), but the functional activity of this protein has not been demonstrated. Because TK is usually expressed only at very low levels in host cells, in this study, the coding region of WSSV tk-tmk was expressed in an insect/baculovirus expression system. The His-tagged recombinant WSSV TK-TMK was purified by affinity chromatography, and its enzyme activity was characterized by steady-state kinetics. The recombinant WSSV TK-TMK catalyzed the phosphorylation of thymidine to form thymidine monophosphate (TMP), but we found no evidence that it was able to catalyze the further phosphorylation of TMP to form thymidine diphosphate (or thymidine triphosphate). This TK activity is sensitive to feedback inhibition by thymidine triphosphate. In addition to thymidine, of the nine other substrates tested, including acyclovir, ganciclovir, and 5-(2-bromovinyl)-2′-deoxyuridine, only 2′-deoxyuridine and 5-bromo-2′-deoxyuridine could also serve as substrates. These data suggest that the enzymatic characteristics of the recombinant WSSV TK-TMK are similar to those of the eukaryotic cytosolic TKs. We also found that TK activity increased as infection advanced in the integument and gills of experimentally infected shrimp, suggesting its functional involvement during WSSV infection
Subdomain Specific Functions of the RNA Polymerase Region of Poliovirus 3CD Polypeptide

AbstractThe 3D polymerase domain of the poliovirus 3CD polypeptide plays a role in modulating its RNA binding and protein processing activities, even though the proteinase catalytic site and RNA binding determinants appear to reside within the 3Cpro portion of the molecule. In this study, we have generated recombinant 3CD polypeptides that contain chimeric 3D polymerase domains representing suballelic sequence exchanges between poliovirus type 1 (PV1) and coxsackievirus B3 (CVB3) to determine which portions of the 3D domain are responsible for influencing these activities. By utilizing these recombinant protein chimeras in protein processing and RNA binding studies in vitro, we have generated data suggesting the presence of separate subdomains within the polymerase domain of 3CD that may independently modulate its RNA binding and protein processing activities. In predicting where our sequence exchanges map by utilizing the previously published three-dimensional structure of the PV1 3D polymerase, we present evidence that sequences contained within the RNA recognition motif of the polymerase are critical for 3CD function in recognizing the 5′ RNA cloverleaf. Furthermore, our protein processing data indicate that at least some of the substrate recognition and processing determinants within the 3D domain of 3CD are separate and distinct from the RNA binding determinants in this domain
Avian Encephalomyelitis Virus Induces Apoptosis Via Major Structural Protein VP3

AbstractAvian encephalomyelitis virus (AEV) strain L2Z was investigated for its apoptotic activity in specific-pathogen-free chick embryo brain tissue. DNA fragmentation analysis and electron microscopy observation demonstrated that AEV could induce apoptosis in chick embryo brain tissues characterized by chromatin condensation, plasma membrane blebbing, cell shrinkage, and nucleosomal DNA fragmentation after 4 days postinfection. AEV structural protein genes VP1, VP2, and VP3 were transfected into Cos-7 and chick embryo brain (CEB) cells, respectively. The results showed that only VP3 protein was an apoptotic inducer, as demonstrated by DNA fragmentation analysis and TUNEL assay at 24 and 48 h posttransfection. Furthermore, expression of VP3 protein resulted in the activation of caspase-3-like proteases in both cells, which could be inhibited by a caspase-3-like protease-specific inhibitor Ac-DEVD-CHO peptide, suggesting that AEV VP3 protein induces apoptosis through a caspase-3-like protease pathway. In addition, VP3 protein localized to mitochondria in the Cos-7 and CEB cells at 24 h posttransfection observed by confocal microscopy, indicating that mitochondria may play an important role in VP3-induced apoptosis. Taken together, our results show that AEV could induce apoptosis in chick embryo brain tissue, structural protein VP3 could serve as an apoptotic inducer resulting in apoptosis in cell culture through a caspase-3-like protease pathway, which may be related to its localization to mitochondria
Surface Features of Potato Virus X from Fiber Diffraction

AbstractFiber diffraction patterns have been obtained from oriented sols of potato virus X. Orientation in the sols was greatly improved by a combination of centrifugation and exposure to very high magnetic fields. Diffraction patterns were also improved by using a very finely collimated synchrotron X-ray beam. The diffraction patterns show that there are 8.9 subunits in each turn of the viral helix and that intersecting sets of deep grooves mark the viral surface, with one set running almost longitudinally and the other following the simple viral helix
The Structure of P4 Procapsids Produced by Coexpression of Capsid and External Scaffolding Proteins

AbstractThe double-stranded DNA bacteriophage P4 has a T = 4 icosahedral arrangement of the gpN capsid protein derived from the P2 helper phage. The precursor procapsids in addition contain an external scaffold made up of the P4-encoded Sid protein. High yields of pure P4 procapsids have been obtained by coexpressing the gpN and Sid proteins from a chimeric plasmid. Biochemical measurements show that the ratio of gpN to Sid in the procapsids is 2:1, corresponding to 120 copies of Sid per procapsid particle. A reconstruction of the P4 procapsid, made from 213 particle images to an effective resolution of about 21 Å, greatly improves on the previously determined P4 procapsid structures. The structure shows a T = 4 capsid shell and a unique tandem arrangement of 120 copies of chilli-shaped Sid monomers, which form trimers and dimers on the procapsid surface
Role of Specific Cell-Mediated Cytotoxicity in Protecting Fish from Viral Infections

AbstractWe report the in vivo role of specific cytotoxic cells in protecting fish from acute viral infections. Specifically, we found that (1) there is an inverse relationship between cytotoxic activities and viral load and (2) adoptive transfer of immune leukocytes prevented viral infection. Crucian carp hematopoietic necrosis virus (CHNV), which has a virulence to ginbuna crucian carp, was recently found and identified in Japan. Specific cell-mediated cytotoxicity of ginbuna leukocytes against CHNV-infected syngeneic cells was induced as a result of intraperitoneal inoculation with CHNV. This cytotoxicity was not induced against either virus-infected allogeneic cells or eel rhabidovirus- (EVA) infected syngeneic cells. In these respects, the cytotoxic activity was similar to that of mammalian cytotoxic T-lymphocyte (CTL) activity. Viral titers of tissues from infected fish were remarkably reduced 8 days after infections, when specific cytotoxic activity reached a peak. This result suggested that specific cytotoxic cells were responsible for the early control of CHNV replication. On the other hand, CHNV-specific antibody was greatly increased when the virus was eliminated by cytotoxic activities. The effectiveness of the virus-specific cytotoxicity was evaluated using adoptive cell transfer. Recipients that received leukocytes from immune syngeneic donors escaped CHNV infection. These findings suggest that virus-specific cytotoxic cells have a role in controlling viral infections in a fish
Quasispecies, Error Catastrophe, and the Antiviral Activity of Ribavirin

AbstractRibavirin is the first synthetic, broad-spectrum antiviral nucleoside. Despite its more than 30 year history, the mechanism of action of this compound remains unclear and somewhat controversial. Recent data suggest the possibility that the activity of ribavirin against RNA viruses is a reflection of incorporation of ribavirin into the viral genome. Because ribavirin incorporation is not specific, this event leads to lethal mutagenesis of the virus population. The data supporting this new proposal for the mechanism of action of ribavirin are reviewed herein. In addition, we discuss briefly the challenges that remain for development of lethal mutagenesis as an effective antiviral strategy
The Equine Herpesvirus 1 UL34 Gene Product Is Involved in an Early Step in Virus Egress and Can Be Efficiently Replaced by a UL34-GFP Fusion Protein

AbstractThe structure and function of the equine herpesvirus type 1 (EHV-1) UL34 homologous protein were characterized. A UL34 protein-specific antiserum reacted with an Mr28,000 protein that could not be detected in purified extracellular virions. Confocal laser scanning microscopy demonstrated that UL34 reactivity mainly concentrated at the nuclear rim, which changed into a punctuate and filamentous pattern at late times after infection. These changes in UL34 distribution were especially prominent when analyzing the distribution of a GFP-UL34 fusion protein. A UL34-negative EHV-1 was generated by mutagenesis of a recently established BAC clone of EHV-1 strain RacH (pRacH). Release of extracellular infectious virus was severely impaired after infection of Rk13 cells with HΔ34. Electron microscopy revealed a virtual absence of virus particles in the cytoplasm of infected cells, whereas nucleocapsid formation and maturation within the nucleus appeared unaffected. A UL34-GFP fusion protein with GFP linked to the C-terminus of UL34 was able to complement for the UL34 deletion in trans, while a GFP-UL34-fusion protein with GFP linked to the N-terminus of UL34 was able to only partially restore virus growth. It was concluded that the EHV-1 UL34 product is essential for an early step in virus egress, i.e., release of capsids from infected-cell nuclei
Identification of the bZIP and Rta Homologues in the Genome of Rhesus Monkey Rhadinovirus

AbstractRhesus monkey rhadinovirus (RRV) is a γ2-herpesvirus identified from the peripheral blood mononuclear cells of rhesus macaques (Macaca mulatta). Serologic studies suggested that the infections of RRV are prevalent among rhesus monkeys. RRV can be efficiently propagated and grows to a high titer in cultured rhesus monkey fibroblasts, thus providing a valuable model to study the rhadinovirus replication. By comparative genomic studies, here we describe the identification of two potential transcriptional factors encoded by RRV, designated as R-Rta and R-bZIP. Initial functional characterization of these products suggested that R-Rta is a potent transcriptional activator and R-bZIP forms homodimers in vivo. Viral homologues of R-Rta and R-bZIP, previously identified from other rhadinoviruses, have been implicated in serving as molecular switches in lytic replication
Influenza A Virus Specific T Cell Immunity in Humans during Aging

AbstractTo study the decreasing responsiveness of the immune system during aging, influenza virus specific cellular immunity was investigated in a cohort of healthy blood donors between 18 and 70 years of age. The percentage of influenza A virus specific T cells was determined by flow cytometry and found not to change during aging. After stimulation with phorbol 12-myristate 13-acetate and ionomycin, an increase in the percentage of IFN-γ and IL-4 producing CD8+ T cells was observed during aging. In addition, the cytotoxic T lymphocyte (CTL) activity was investigated in two additional groups of five donors, 18–20 and 68–70 years of age. The lytic capacity of purified CD8+ T cells, after in vitro stimulation of peripheral blood mononuclear cells with influenza A virus, seemed lower in 68- to 70-year-old donors than in 18- to 20-year-old donors. Therefore we conclude that the reduced CTL activity in the elderly is not the result of a lower frequency of virus-specific T cells, but more likely the result of impaired antigen-specific proliferation or lower lytic capacity of these cells
Lyssavirus P Gene Characterisation Provides Insights into the Phylogeny of the Genus and Identifies Structural Similarities and Diversity within the Encoded Phosphoprotein

AbstractA comprehensive phylogenetic analysis of the Lyssavirus genus, employing P gene sequences from 128 isolates recovered globally, is presented. While confirming prior suggestions of the genetic distinctness of the Australian bat lyssaviruses, these data also revealed a clear division within the rabies virus clade (Genotype 1) between globally distributed viruses circulating predominantly in canid species (subgroup 1-1), and American strains harbored by both chiropteran and terrestrial hosts (subgroup 1-2). Nucleotide substitution patterns within the P locus suggested differential selection operating along the length of the open reading frame (ORF) between rabies viruses of these two subgroups. Comparison of the deduced primary sequences of the encoded phosphoproteins of all isolates provided insights into the product's structural organization. Two conserved (CD1,2) and two variable (VD1,2) domains were evident; high variation in the VD2 region was reflected by differences in hydropathic profiles. Only two of five serine residues reported to function as phosphate acceptors in the P protein of the rabies challenge virus standard (CVS) strain were absolutely conserved; similarly, out of four internal methionines reported to direct internal translation initiation of the CVS strain to produce N-terminally truncated P proteins, only Met20 was universally retained. In contrast, two sequence motifs, one believed to confer binding to the cytoplasmic dynein light chain LC8, and a lysine-rich sequence probably contributing to N protein binding, were conserved throughout the genus. Most rabies viruses of the carnivora (1-1) contain a potential C ORF in alternate frame to that of P, a feature limited or absent in most other isolates of the genus, an observation interpreted with consideration to the predicted course of lyssavirus evolution
Quasispecies Heterogeneity and Constraints on the Evolution of the 5′ Noncoding Region of Hepatitis C Virus (HCV): Relationship with HCV Resistance to Interferon-α Therapy

AbstractHepatitis C virus (HCV) polyprotein translation depends on direct internal entry of the 40S ribosomal subunit mediated by an internal ribosome entry segment (IRES) located in the 5′ noncoding (5′NC) region of the viral genome. HCV is genetically heterogeneous and is characterized by the existence of a quasispecies distribution of the virus population within a single infected individual. Cloning and sequencing strategies were used to characterize 5′NC quasispecies genetically. Similar to coding regions, the HCV 5′NC region was distributed as a quasispecies, but it appeared to be subjected to stronger conservatory constraints than other regions of the HCV genome, probably due to the need for structural (and functional) conservation of the IRES. Indeed, most of the quasispecies substitutions were in unpaired regions of the IRES or clustered such that base-pairing was maintained, whereas only 21% were expected to result in a loss of base-pairing. Quasispecies-related structural changes could be predicted in the core cruciform of IRES domain III composed of the RNA helices which extend from the four-way junction JIIIabc, mostly in minor variants, but sometimes in major ones. The results presented here suggest the simultaneous presence in infected patients of a mixture of genetically distinct but closely related IRES sequences that may have different structures. No significant genetic changes of 5′NC quasispecies were observed after interferon-α treatment, except in patients with mixed genotype infection who cleared one of the infecting strains during therapy, suggesting that the quasispecies distribution of IRES sequences does not play a role in HCV resistance to interferon-α therapy. In contrast, the overall quasispecies distribution of HCV genomes (including IRES sequences) might participate in regulation of hepatic and extrahepatic HCV replication
Functional Properties of the Predicted Helicase of Porcine Reproductive and Respiratory Syndrome Virus

AbstractPorcine reproductive and respiratory syndrome virus (PRRSV) is a member of the positive-strand RNA virus family Arteriviridae. Although considerable research has focused on this important pathogen, little is known about the function of most PRRSV proteins. To examine characteristics of putative nonstructural proteins (nsp) encoded in ORF1b, which have been identified by nucleotide similarity to domains of equine arteritis virus, defined genomic regions were cloned and expressed in the pRSET expression system. One region, nsp10, encoded a protein with a putative helicase domain and was further examined for functional helicase-like activities. PRRSV nsp10 was found to possess a thermolabile and pH-sensitive NTPase activity that was modulated by polynucleotides and to unwind dsRNA in a 5′ to 3′ polarity. These results provide the first evidence of the functional properties of PRRSV helicase and further support the finding that nidovirus helicases possess properties that distinguish them from other viral helicases
Binding Site Analysis of Human HBV Pol for Molecular Chaperonin, Hsp60

AbstractA previous study shows that Hsp60 not only interacts with, but also activates human hepatitis B virus polymerase, HBV Pol (S. G. Park and G. Jung, 2001, J. Virol. 75, 6962–6968). To provide a more detailed analysis of the relationship between the two proteins, (i) the binding sites on human HBV Pol for Hsp60 and (ii) the effect of pregenomic RNA on human HBV Pol-Hsp60 binding were analyzed. The binding sites on human HBV Pol were mapped with several deletion mutant proteins of the Pol expressed in insect cells by using recombinant baculovirus. Immunoprecipitation of each deletion mutant protein by M2 beads showed that binding of Hsp60 to human HBV Pol requires two minimal sites on human HBV Pol: amino acids 1 to 199 (TP) and amino acids 680 to 842 (RH). Human HBV Pol was also shown to bind to Hsp60 in HepG2 cells, the host cell line for human HBV. In addition, Hsp60 binding to the Pol was found to be dispensable to pregenomic RNA binding to human HBV Pol. Overall, this article infers that Hsp60 activates human HBV Pol through binding at the TP and RH domains of the Pol and the Pol binding to Hsp60 does not require pregenomic RNA
Effect of Proteolytic Processing at Two Distinct Sites on Shape and Aggregation of an Anchorless Fusion Protein of Human Respiratory Syncytial Virus and Fate of the Intervening Segment

AbstractWe have examined the consequences of cleaving the fusion glycoprotein (F) of human respiratory syncytial virus (HRSV) at two distinct furin-recognition sites. Purified anchorless F is a mixture of unaggregated cone-shaped molecules and rosettes of lollipop-shaped spikes. The unaggregated molecules contain a proportion of uncleaved F0 and an intermediate, FΔ1–109, cleaved only at site I, residues 106–109. Inhibition of cleavage at site I, by two amino acid changes (R108N/R109N), reduces the proportion of aggregated molecules with a concomitant increase in the amount of unprocessed F0. Inhibition of cleavage at site II, residues 131–136, by deletion of four amino acids (Δ131–134), abrogates aggregation of anchorless F and all molecules are seen as individual cone-shaped rods. In vitro cleavage of anchorless F, or mutant Δ131–134, with trypsin at 4, 20, or 37°C, under conditions in which cleavage at site II is complete in all molecules, leads to their aggregation in rosettes of lollipop-shaped spikes. Thus, cleavage at site II is required for the structural changes in anchorless F that lead to changes in shape and to aggregation. The segment between sites I and II, residues 110–136, is not associated with anchorless F in the supernatant of infected cell cultures, indicating that it is released from the processed protein when cleavage at sites I and II is completed
Antibodies Directed against an Epitope in the N-Terminal Region of the H4L Subunit of the Vaccinia Virus RNA Polymerase Inhibit Both Transcription Initiation and Transcription Termination, in Vitro

AbstractThe vaccinia virus virion RNA polymerase that is active in early gene transcription contains a unique subunit encoded by the H4L gene. Prior studies demonstrated that this protein is required both for early gene transcription initiation and for transcription termination. Polyclonal antibodies raised against H4L amino acids 1 to 256 prevent both initiation and termination of transcription, in vitro. Pretreatment of the anti-H4L antibody with a H4L fragment containing amino acids 1 to 99 prevents antibody inhibition of both steps, mapping the inhibitory antibody-binding site to this region. A combination of immunoprecipitation and competition studies of antibody binding to wild-type and site-specific mutations of H4L1–195 mapped the strong epitope to a site that includes Y18. H4L fragments containing an Y18A mutation exhibit diminished ability to block antibody inhibition of transcription initiation and termination. Antibodies inhibit preinitiation complex (PIC) formation but not the activity of preformed PICs, indicating that this region of H4L interacts with one or more factors during active PIC formation. Furthermore, isolated H4L1–195 directly inhibits PIC activity, supporting this model. Anti-H4L antibody inhibition of transcription termination is only observed in the absence of the essential termination cofactor NPH I. In contrast, antibody inhibition of PIC formation is unaffected by NPH I, demonstrating that the inhibitory antibody and NPH I can bind to H4L at the same time