pinecone/core-2020-05-10-deduplication huggingface dataset:
The Structural Protein E of the Archaeal Virus φCh1: Evidence for Processing in Natrialba magadii during Virus Maturation

AbstractφCh1 is a lysogenic virus for the haloalkalophilic archaeon Natrialba magadii. The virus morphology resembles other members of Myoviridae infecting Halobacterium species. The gene of the major capsid protein E of virus φCh1 was cloned and the DNA sequence was determined. Gene E was mapped to a 3.2-kbp ClaI fragment, localized to the 5′-end of the φCh1 genome. The complete nucleotide sequence of this region was determined and the identity of gene E was confirmed by comparing the experimentally determined N-terminal amino acid sequence of the purified protein to the translated DNA sequence of its open reading frame. We present evidence that the gene E product is proteolytically cleaved between Lys16 and Asn17 to yield the 305 residue polypeptides found in the mature viral capsid. Processing of the protein itself during virus development was determined by 2D gel electrophoresis using protein E-specific antibodies. Sequence similarity studies revealed an 80% identity to capsid protein Hp32 of φH, infecting Halobacterium salinarum. RT-PCR analysis as well as Western blot studies revealed gene E as a late gene. Transcripts and proteins could be detected shortly before onset of lysis of the lysogenic strain N. magadii L11
Use of Conventional or Replicating Nucleic Acid-Based Vaccines and Recombinant Semliki Forest Virus-Derived Particles for the Induction of Immune Responses Against Hepatitis C Virus Core and E2 Antigens

AbstractReplicating and nonreplicating nucleic acid-based vaccines as well as Semliki Forest-recombinant Viruses (rSFVs) were evaluated for the development of a vaccine against hepatitis C virus (HCV). Replicating SFV-DNA vaccines (pSFV) and rSFVs expressing HCV core or E2 antigens were compared with classical CMV-driven plasmids (pCMV) in single or bimodal vaccine protocols. In vitro experiments indicated that all vaccine vectors produced the HCV antigens but to different levels depending on the antigen expressed. Both replicating and nonreplicating core-expressing plasmids induced, upon injection in mice, specific comparable CTL responses ranging from 10 to 50% lysis (E:T ratio 100:1). Comparison of different injection modes (intramuscular versus intraepidermal) and the use of descalating doses of DNA (1–100 μg) did not show an increased efficacy of the core–SFV plasmid compared with the CMV-driven one. Surprisingly, rSFVs yielded either no detectable anticore CTL or very low anti-E2 antibody titers following either single or bimodal administration together with CMV-expressing counterparts. Prime-boost experiments revealed, in all cases, the superiority of DNA-based only vaccines. The anti-E2 antibody response was evaluated using three different assays which indicated that all generated anti-E2 antibodies were targeted at similar determinants. This study emphasizes the potential of DNA-based vaccines for induction of anti-HCV immune responses and reveals an unexpected and limited benefit of SFV-based vaccinal approaches in the case of HCV core and E2
A Novel Type D Simian Retrovirus Naturally Infecting the Indian Hanuman Langur (Semnopithecus entellus)

AbstractAs a simian species, the langurs are not known to harbor simian retroviruses, except for one report on a simian Type D endogenous retrovirus from the spectacled langur (Trachypithecus obscurus) from Malaysia. The present report describes for the first time natural infection of the common Hanuman langur (Semnopithecus entellus) from India by a novel simian retrovirus (SRV). The new SRV is phylogenetically related to but distinct from the three molecularly characterized serotypes, SRV 1–3, of the five known serotypes of SRVs, based on sequence analyses from the 3′orf and env regions of the viral genome. The novel SRV isolated from the Indian Hanuman langur is provisionally named SRV-6
Differential Expression of Intracisternal A-Particle Transcripts in Immunogenic versus Tumorigenic S49 Murine Lymphoma Cells

AbstractTumorigenic S49 mouse lymphoma cells (T-25) were compared to their nontumorigenic (immunogenic) substrate-adherent descendants (T-25-Adh), using the differential display technique. A 784-bp fragment with 92% sequence homology to the intracisternal A-particle (IAP) element family was isolated from the latter cells. IAP sequences are endogenous, noninfectious retroviral elements that can undergo transpositions and act as mutagens. Expression of IAP transcripts (as detected by the isolated fragment) was 5- to 10-fold higher in T-25-Adh cells than in T-25 cells. IAP RT-PCR cDNA clones derived from the immunogenic T-25-Adh cells, but not from T-25 cells, contain two distinctive motifs: (i) a motif characteristic of IAP elements expressed in lymphoid cells (lymphocyte specific, LS); (ii) a nonapeptide sequence known to stimulate cytotoxic T lymphocytes in a leukemia cell line expressing IAP sequences. In addition, expression of transcripts containing these motifs is enhanced in the immunogenic cells as opposed to the tumorigenic cells. Furthermore, one of the IAP elements (belonging to the LS1 subfamily) is specifically hypomethylated in the DNA of the immunogenic cells. The above-mentioned relationship was strengthened when tumorigenic revertants derived from T-25-Adh cells, as well as independently selected tumorigenic and immunogenic S49 sublines, were studied. In all cases, enhanced immunogenicity was linked to the up-regulation of specific IAP elements. No transpositions of LS1 elements were observed among the different sublines studied. These findings suggest that, in the S49 lymphoma, selectively expressed IAP retroviral elements may function in a tumor suppressive capacity by affecting the immunogenic potential of these cells
Cucumber Mosaic Virus Mutants with Altered Physical Properties and Defective in Aphid Vector Transmission

AbstractTwo mutant strains of cucumber mosaic virus (CMV) were investigated with respect to virion stability and molecular determinants of aphid vector transmission. The mutant 2A1-MT-60x, derived from the mechanically passaged wild type 2A1-AT, is poorly transmissible by the aphid Aphis gossypii and not transmissible by the aphid Myzus persicae, whereas the wild type virus is transmissible by both aphid species. The mutant phenotype was shown to be conferred by a single encoded amino acid change of alanine to threonine at position 162 of the coat protein (CP). Modifying the mutant CP gene to encode the wild type sequence (alanine) at position 162 restored aphid transmission. To test for a correspondence between changes in the physical stability of virions and defects in aphid transmission, a urea disruption assay was developed. Virions of aphid-transmissible strains 2A1-AT and CMV-Fny were stable with treatments of up to between 3 and 4 M urea. In this assay mutant viruses 2A1-MT-60x and CMV-M were less stable, as they were completely disrupted at urea concentrations of 2 and 1 M urea, respectively. The mutant 2A1-MT-60x also accumulated at a reduced level in infected squash relative to the wild type virus. These studies suggest that a primary factor in the loss of aphid transmissibility of some strains of CMV is a reduction in virion stability
Activation of the Lck Tyrosine Protein Kinase by the Herpesvirus Saimiri Tip Protein Involves Two Binding Interactions

AbstractThe Tip protein of Herpesvirus saimiri strain 484C binds to and activates the Lck tyrosine protein kinase. Two sequences in the Tip protein were previously shown to be involved in binding to Lck. A proline-rich region, residues 132–141, binds to the SH3 domain of the Lck protein. We show here that the other Lck-binding domain, residues 104–113, binds to the carboxyl-terminal half of Lck and that this binding does not require the Lck SH3 domain. Mutated Tip containing only one functional Lck-binding domain can bind stably to Lck, although not as strongly as wild-type Tip. Interaction of Tip with Lck through either Lck-binding domain increases the activity of Lck in vivo. Simultaneous binding of both domains is required for maximal activation of Lck. The transient expression of Tip in T cells was found to stimulate both Stat3-dependent and NF-AT-dependent transcription. Mutant forms of Tip lacking one or the other of the two Lck-binding domains retained the ability to stimulate Stat3-dependent transcription. Tip lacking the proline-rich Lck-binding domain exhibited almost wild-type activity in this assay. In contrast, ablation of either Lck-binding domain abolished the ability of Tip to stimulate NF-AT-dependent transcription. Full biological activity of Tip, therefore, appears to require both Lck-binding domains
Dissimilar Immunogenicities of Human Papillomavirus E7 and Adenovirus E1A Proteins Influence Primary Tumor Development

AbstractAlthough human papillomaviruses (HPV) and adenoviruses (Ad) both transform cells by expressing functionally related oncogenes (Ad-E1A/E1B; HPV-E7/E6), only HPV are oncogenic in humans. Prior studies have shown that HPV-transformed cells are resistant to NK cell lysis and E7- and E6-specific CTL are inefficiently generated in women with HPV-induced cervical cancer. Therefore, we postulated that the dissimilar oncogenicities of Ad and HPV may be caused by a protective NK and T cell response that is triggered by transformed cells expressing E1A, but not by E7. To test this hypothesis, mice that were either immunologically intact, lacked T cells, or lacked both NK and T cells were challenged with Ad serotype 5 (Ad5)-E1A- or HPV16-E7-transfected tumor cells. E7-expressing tumor cells were resistant to NK cell lysis in vitro and failed to elicit a measurable anti-tumor NK or T cell response in vivo. The concomitant expression of E6 did not change this phenotype. In contrast, E1A-expressing tumor cells were sensitive to NK lysis in vitro and triggered a protective NK and T cell immune response in vivo. These data suggest differences in the capacities of E1A or E7 oncoproteins to trigger protective anti-tumor immune responses may contribute to the dissimilar oncogenicities of Ad and HPV in humans
Molecular Characterization of Guinea Pig-Adapted Variants of Ebola Virus

AbstractSerial passage of initially nonlethal Ebola virus (EBOV) in outbred guinea pigs resulted in the selection of variants with high pathogenicity. Nucleotide sequence analysis of the complete genome of the guinea pig-adapted variant 8mc revealed that it differed from wild-type virus by eight mutations. No mutations were identified in nontranscribed regions, including leader, trailer, and intragenic sequences. Among noncoding regions the only base change was found in the VP30 gene. Two silent base changes were found in the open reading frame (ORF) encoding NP protein. Nucleotide changes resulting in single-amino-acid exchanges were identified in both NP and L genes. Three other mutations found in VP24 caused amino acid substitutions, which are responsible for larger structural changes of this protein, as indicated by an alteration in electrophoretic mobility. A highly pathogenic EBOV variant K5 from another passaging series showed an amino acid substitution at nearly the same location in the VP24 gene, suggesting the importance of this protein in the adaptation process. In addition, sequence variability of the GP gene was found when plaque-purified clones of EBOV-8mc were analyzed. Three of five viral clones showed insertion of one uridine residue at the GP gene-editing site, which led to a significant change in the expression of virus glycoproteins. This observation suggests that the editing site is a hot spot for insertion and deletion of nucleotides, not only at the level of transcription but also of genome replication. Irrespective of the number of uridine residues at the editing site, all plaque-purified clones of EBOV variant 8mc resembled each other in their pathogenicity for guinea pigs, indicating either the absence or only supportive role of mutations in the GP gene on the adaptation process
Structure of Simian Virus 40 DNA Replicated by Herpes Simplex Virus Type 1

AbstractReplicating herpes simplex virus type 1 (HSV-1) DNA is known to form large branched structures. The aim of this study was to define whether HSV-1-specific DNA elements in cis play a critical role in formation of this structure. We did this by investigating the structure of heterologous simian virus 40 (SV40) DNA, which is replicated in HSV-infected cells by SV40 large T-antigen and defined HSV-encoded replication factors (e.g., DNA polymerase, single-stranded DNA-binding protein, and helicase-primase). During this process, extrachromosomal concatemeric DNA replication products are formed, indicating a herpesvirus-specific replication mode. In this study, we found that the replicating SV40 DNA consisted of a complex branched structure indistinguishable from that of replicating HSV DNA. Thus, no HSV-specific DNA element is necessary in cis for the formation of the large branched structure during HSV DNA replication. The trans-acting HSV DNA replication proteins seem to be sufficient to generate these complex structures. Moreover, replicating SV40 DNA showed a high frequency of homologous recombination events, which is typical for HSV DNA replication. However, in contrast to HSV origin-bearing amplicon plasmids, SV40 plasmids bearing the HSV cleavage-packaging signal were not efficiently processed to linear 150-kb DNA packaged into HSV capsids. This indicates that initiation of DNA synthesis on HSV-ori determines some, yet undefined, property of replicating HSV DNA, which is crucial for regular processing of the replication intermediates to daughter genomes
The Gamma-2-Herpesvirus Bovine Herpesvirus 4 Causes Apoptotic Infection in Permissive Cell Lines

AbstractIncreasing evidence suggests that regulation of apoptosis in infected cells is associated with several viral infections. The gammaherpesvirus bovine herpesvirus 4 (BHV-4) has been shown to harbor genes with antiapoptotic potentialities. However, here we have demonstrated that productive infection of adherent, permissive cell lines by BHV-4 resulted in a cytopathic effect characterized by induction of apoptosis. This phenomenon was confirmed using different techniques to detect apoptosis and using different virus strains and cell targets. Apoptosis induced by BHV-4 was inhibited by (1) treatment with doses of heparin, which completely inhibited virus attachment and infectivity; (2) UV treatment, which completely abrogated infectivity; and (3) treatment with a dose of phosphonoacetic acid, which blocked virus replication. Virus-induced apoptosis was associated with a down-regulation of Bcl-2 expression and was reduced by Z-VAD-FMK, but not by Z-DEVD-FMK (caspase-3-specific) caspase inhibitors. Inhibition of apoptosis by Z-VAD-FMK treatment during infection did not modify virus yield. Therefore, despite the presence of antiapoptotic genes in its genoma, BHV-4 could complete its cycle of productive infection while inducing apoptosis of infected cells. This finding might have implications for the pathobiology of BHV-4 and other gammaherpesviruses in vivo
Nitric Oxide Inhibits Marek's Disease Virus Replication but Is Not the Single Decisive Factor in Interferon-γ-Mediated Viral Inhibition

AbstractThe purpose of this study was to determine to what extent nitric oxide (NO) may play a role in the antiviral-mediated effect of chicken IFN-γ against the Marek's disease virus (MDV) RB-1B. NO-generating compounds S-nitroso-N-acetylpenicillamine (SNAP) and 3-morpholino-sydononimine (SIN-1) strongly inhibited RB-1B replication in chicken embryo fibroblasts (85%) in a dose-dependent manner. The addition of superoxide dismutase (SOD) did not alter the inhibitory effect of SIN-1, which is also known to generate superoxide anions. IFN-γ-stimulated embryo fibroblasts almost totally suppressed viral replication and were high NO producers. Nevertheless, addition of NG-monomethyl-l-arginine (l-NMMA), a competitive inhibitor of NO synthase, inhibited NO production without preventing the dramatic viral suppression. IFN-γ-stimulated chicken bone-marrow macrophages were good NO producers and demonstrated a specific cell dose-related inhibiting effect on RB-1B replication in bystander fibroblasts (around 60% at 106 macrophages). Adding l-NMMA together with oxygen scavengers such as SOD or d-mannitol restored viral replication almost completely. In conclusion, NO alone is a powerful inhibitor of MDV replication in chicken fibroblasts. Nevertheless, NO is not responsible for the direct inhibitory effect of the IFN-γ treatment of fibroblasts and is only partially involved in the inhibitory effect of IFN-γ-stimulated macrophages, which is also mediated by reactive oxygen intermediates
Partial Purification and Characterization of Cucumber necrosis virus and Tomato bushy stunt virus RNA-Dependent RNA Polymerases: Similarities and Differences in Template Usage between Tombusvirus and Carmovirus RNA-Dependent RNA Polymerases

AbstractTombusviruses are small, plus-sense, single-stranded RNA viruses of plants. RNA-dependent RNA polymerases (RdRp) of two tombusviruses, Tomato bushy stunt virus (TBSV) and Cucumber necrosis virus (CNV), have been partially purified from infected Nicotiana benthamiana plants. The obtained RdRp complexes are capable of de novo initiation of complementary RNA synthesis using either plus- or minus-strand templates derived from tombusvirus defective interfering (DI) RNAs. In addition to template-sized products, shorter than full-length products were also generated efficiently apparently because of internal initiation of RNA synthesis by the tombusvirus RdRp. This property could be important for the formation of DI RNAs that are observed in tombusvirus infections. The tombusvirus RdRp is also able to use heterologous RNAs derived from satellite RNAs associated with Turnip crinkle virus (TCV) as templates. Generation of full-length, complementary RNA by the tombusvirus RdRp suggests that it can correctly and efficiently recognize the heterologous TCV-specific promoters. Reduced generation of a 3′-terminal extension product in the preceding assay suggests that the previously characterized replication enhancer present in sat-RNA C (Nagy et al., 1999, EMBO J. 18, 5653–5665) does not stimulate tombusvirus RdRp activity. Taken together, these results suggest that template usage by the tombusvirus and carmovirus RdRps are similar, but not identical
Influenza A Virus Neuraminidase: Regions of the Protein Potentially Involved in Virus–Host Interactions

AbstractPhylogenetically informative amino acid positions (PIPs) were identified in influenza A neuraminidases of subtypes N1 and N2. Neuraminidase evolves in a lineage-specific way as the virus adapts to a new host or changes to evade the host's immune system. Thus, many PIPs undoubtedly identify positions involved in virus–host interactions. Phylogenetically important regions (PIRs) are defined as several PIPs near one another. There are 15 PIRs on N1 and 12 on N2, seven of which are shared between the two subtypes. Many PIRs are coincident with antigenic or glycosylation sites. Other PIRs may represent additional antigenic sites or may be involved in other aspects of virus–host biology
Identification and Genomic Mapping of the ORF3 and VPg Proteins in Feline Calicivirus Virions

AbstractTwo minor proteins with molecular masses of 8.5 and 15.5 kDa were identified in feline calicivirus (FCV) virions. Direct sequence analysis showed that the N-terminal sequence of the 8.5-kDa protein was identical to that of the predicted protein encoded by open reading frame 3 (ORF3) of the FCV genome. The N-terminal sequence of the 15.5-kDa protein corresponded to amino acids 961–980 of the FCV ORF1 polyprotein and mapped to the genomic location of the calicivirus VPg. Antisera raised against recombinant ORF3 protein or the N-terminal 20 amino acids of the putative VPg reacted with the corresponding proteins present in both a Western blot analysis of purified FCV virions and an immunofluorescence assay of FCV-infected cells. A comparative analysis of radioactivity incorporated into virion proteins during in vivo labeling experiments indicated that the ORF3 protein is likely present in one or two copies per virion. The mobility of the ORF3 protein present in virions was similar to that of the ORF3 protein found in FCV-infected cells or expressed in bacteria. Direct N- and C-terminal sequence analysis of the purified ORF3 protein obtained by expression in bacteria demonstrated the presence of intact, uncleaved termini, suggesting that the observed difference between the calculated and the apparent masses in SDS–PAGE was not due to proteolytic processing of the protein
Structural Determinants in Adenovirus 12 E1A Involved in the Interaction with C-Terminal Binding Protein 1

AbstractThe interaction between the C-terminal binding protein 1 (CtBP-1) and purified Ad12 E1A protein has been examined through the use of a combination of biophysical techniques. A fragment equivalent to the 77 C-terminal amino acids of Ad12 E1A (Ad12 77-a.a. E1A) was generated by limited proteolysis of Ad12 266-a.a. E1A at Phe187 and/or Tyr189 using chymotrypsin. The impact of deletion of the 189 N-terminal amino acids from E1A on the equilibrium dissociation constant Kd for binding to CtBP was assessed using ELISA in vitro binding assays and intrinsic fluorescence spectroscopy. Values of Kd of 4.0 and 38 nM were determined for full-length and truncated forms of E1A, respectively. Circular dichroism spectroscopic studies revealed that the conformation adopted by these polypeptides is dependent on the surrounding environment, which is predominately randomly folded when free in solution, but adopting a more ordered α-helical secondary structure in the presence of trifluoroethanol. Using nuclear magnetic resonance (NMR) spectroscopy to examine the interaction between Ad E1A and CtBP it was observed that the chemical shift positions of individual backbone amide nitrogen atoms were well resolved in 15N-1H-HSQC NMR spectra performed on samples of isotopically 15N-labeled Ad12 77-a.a. E1A. In the presence of CtBP, signals of backbone amide nitrogen atoms displayed increased linewidth consistent with an increase in molecular mass upon binding CtBP. In addition, some signals that have been attributed to Val254/256 and Leu259, and reside within the binding site for CtBP on E1A, are shifted in the 15N- and/or 1H-dimensions, defining specific contacts between E1A and CtBP. These data suggest that structural determinants in the C-terminal PXDLS binding motif in the rest of exon 2 and in exon 1 all contribute to optimizing the conformation of the binding site on Ad12 E1A for CtBP. However, no interaction was observed between CtBP and truncated Ad12 E1A, which no longer contained the C-terminal binding motif
Transcription of Epstein–Barr Virus-Encoded Nuclear Antigen 1 Promoter Qp Is Repressed by Transforming Growth Factor-β via Smad4 Binding Element in Human BL Cells

AbstractIn Epstein–Barr virus (EBV)-infected BL cells, the oncogenic EBV-encoded nuclear antigen 1 (EBNA 1) gene is directed from the latent promoter Qp. Yeast one-hybrid screen analysis using the −50 to −37 sequence of Qp as the bait was carried out to identify transcriptional factors that may control Qp activity. Results showed that Smad4 binds the −50 to −37 sequence of Qp, indicating that this promoter is potentially regulated by TGF-β. The association of Smad4 with Qp was further confirmed by supershift of EMSA complexes using Smad4-specific antibody. The transfection of a Qp reporter construct in two EBV(+) BL cell lines, Rael and WW2, showed that Qp activity is repressed in response to the TGF-β treatment. This repression involves the interaction of a Smad3/Smad4 complex and the transcriptional repressor TGIF, as determined by cotransfection assay and coimmunoprecipitation analysis. Results suggest that TGF-β may transcriptionally repress Qp through the Smad4-binding site in human BL cells