pinecone/core-2020-05-10-deduplication huggingface dataset:
HIV-1 Particle Release Mediated by Vpu Is Distinct from That Mediated by p6

AbstractVpu and the C-terminal peptide of Gag (p6) are both HIV-1-encoded proteins that augment the release of virus particles from cells. We examined the functional relationship between these proteins and their activities during particle release. Our results indicate that efficient HIV-1 particle release from HeLa and Jurkat cells depends on the presence of Vpu. However, Vpu is dispensable for efficient release from Cos cells. In contrast, p6 is required for efficient release from Cos cells but not from Jurkat or HeLa cells. These data suggest that Vpu and p6 have distinct activities in virus exit from different cell lines. Intracellular proteolytic processing of Gag precursor protein is more complete in Cos cells than in HeLa cells. However, this processing has little or no effect on Vpu- or p6-mediated particle release. p6 is required for incorporation of yet another virus protein (Vpr) into cells but our data suggest that Vpr plays no role in p6-dependent particle release. Vpu also facilitates the degradation of CD4 in virus producing cells but, in contrast to particle release, the ability of Vpu to facilitate the degradation of CD4 is not cell line-dependent
The Genome Organization and Affinities of an Australian Isolate of Carrot Mottle Umbravirus

AbstractThe genomic sequence of an Australian isolate of carrot mottle umbravirus (CMoV-A) was determined from cDNA generated from dsRNA. This provides the first data on the genome organization and phylogeny of an umbravirus. The 4201-nucleotide genome contains four major open reading frames (ORFs). Analysis suggests that ORF2 encodes an RNA-dependent RNA polymerase, that ORF4 encodes a movement protein, and that the virus has no coat protein gene. The functions of ORFs 1 and 3 remain unknown. ORF2 is probably translated following ribosomal frameshifting. ORFs 3 and 4 are probably translated from a subgenomic mRNA. Sequence comparisons showed CMoV-A to be closely related to pea enation mosaic RNA2 (PEMV-RNA2), but also to have affinities with theBromoviridae.These findings shed light on the relationships between the luteoviruses, PEMV, and the umbraviruses and on the relationships between the carmo-like viruses and theBromoviridae
The Effect of Regulatory Sequence Elements upon the Initiation of DNA Replication of the Minute Virus of Mice

AbstractThe minute virus of mice (MVM) genome is a linear single-stranded length of approximately 5000 nucleotides of DNA with unique terminal palindromic sequences at both ends. The left (3′) hairpin is used to prime the initiation of DNA synthesis on parental single-strand DNA while the right (5′) hairpin or stem-plus-arms structure can also prime the initiation of DNA synthesis during synthesis of dimer and higher oligomers as well as synthesis of progeny single strands. Previous studies have shown that if viral duplex DNA was input into anin vitroDNA replication system using extracts from uninfected HeLa cells, the 5′ end of the molecule was able to form a hairpin and initiate DNA synthesis by DNA polymerase δ (Cossonset al.(1996),Virology216, 258–264). In this study, the effect of the deletion of knowncis-acting genetic elements upon the initiation of DNA replication was studied using a series of MVM mutants with deletions within the 5′ terminal region. Mutants containing deletions of elements A (nucleotides 4489–4636), B (nucleotides 4636–4695), and either one or both of the 65-bp repeats (nucleotides 4720–4785 and 4785–4849) were used as template in thein vitroDNA replication system. When element A was deleted, the efficiency of initiation decreased significantly. Subsequent removal of element B, leaving just the two 65-bp repeats, restored levels of initiation back to those seen in the wild-type genome. In the absence of either A or B both 65-bp repeats were necessary for efficient initiation, and removal of one of these repeats caused a decrease in efficiency. Thus, element B appeared to have a negative regulatory effect (in the absence of element A), and element A appeared to have a positive regulatory effect, at least in the presence of element B. These data demonstrate, for the first time, a complex interaction between thesecis-acting regulatory elements which can function as both positive or negative regulators in the initiation of MVM DNA replication
Transcriptional and Translational Expression Kinetics of the Early Gene Encoding the BICP27 Protein of Bovine Herpesvirus Type 1

AbstractThe expression kinetics of an essentialtrans-regulatory protein, ICP27, from herpes simplex virus type 1 correspond to that of an immediate-early gene whose expression increases rapidly upon infection and then decreases as of 7 hr postinfection. In contrast, here we report that the bovine herpesvirus type 1 (BHV-1) homolog BICP27, a 50-kDa protein, is expressed as an early gene. Both the transcript and protein accumulated gradually reaching peak levels at approximately 12 hr postinfection, after which point steady state levels were maintained up to 24 hr. Thus the expression profiles of ICP27 and BICP27 are significantly different, suggesting that they may possess different functions
Vaccination with Herpes Simplex Virus Type 1 Glycoprotein K Impairs Clearance of Virus from the Trigeminal Ganglia Resulting in Chronic Infection

AbstractFollowing primary ocular infection, HSV-1 establishes a latent infection in the trigeminal ganglia with the complete absence of detectable infectious virus. Recently, we showed that vaccination of BALB/cJ with HSV-1 glycoprotein K (gK), but not other HSV-1 glycoproteins, significantly exacerbated the severity of HSV-1-induced ocular disease and herpetic dermatitis (H. Ghiasiet al., J. Virol.68, 2347–2354, 1994). We now report that prior vaccination with gK blocked viral clearance from trigeminal ganglia until at least Day 56 postinfection, resulting in a chronic infection. The significance of this novel finding with respect to potential harmful complications associated with the immune response to gK is discussed
Mapping Amino Acids of the Measles Virus Hemagglutinin Responsible for Receptor (CD46) Downregulation

AbstractWe compared the amino acid sequences of groups of receptor (CD46) downregulating and nondownregulating measles virus (MV) hemagglutinins (Hs) and identified seven group-specific differences as candidates for the mediation of the observed differential effects. Using site-directed mutagenesis, we mutated the chosen amino acids of the H of MV-strain WTF (WTF-H), a nondownregulating H, and introduced the corresponding amino acids of Edmonston-H (Edm-H), a downregulating H. We identified four amino acids, 211G, 243R, 451V, and 481Y, which influenced the downregulative function when introduced into WTF-H. The double mutation 451V and 481Y in WTF-H led to a degree of CD46 downregulation comparable to that of Edm-H. Conversely, introducing amino acids 451E and 481N into Edm-H resulted in a loss of the downregulative function. These results indicate that these amino acids play a decisive role in the H-CD46 interaction
RNA Splice Site Utilization by Simian Immunodeficiency Viruses Derived from Sooty Mangabey Monkeys

AbstractAlternative splicing of the full-length, primary transcript into numerous subgenomic mRNAs is one way that lentiviral gene expression is regulated. Because the behaviors of different viral isolates might reflect in part differences in splicing, we investigated the patterns of splice site utilization by simian immunodeficiency viruses (SIVs) originally isolated from sooty mangabey monkeys (Cercocebus atys). We used reverse transcription–polymerase chain reaction (RT–PCR), molecular cloning, and DNA sequencing approaches to characterize SIVdeltaB670, a pathogenic and neurovirulent isolate, and SIVsmmH4, a related molecular clone. The majority of randomly selected SIVdeltaB670 and SIVsmmH4 partial cDNAs containedtat, rev, nef,and long terminal repeat (LTR) intron splice donor and acceptor sites positioned as expected based on the proviral sequence of SIVsmmH4. Nearly all (87%) of the partial cDNAs analyzed contained a spliced LTR intron. A greater number of partial cDNAs derived from SIVdeltaB670–infected cells contained putative alternatively spliced introns in comparison to SIVsmmH4, including two previously undocumented splice junctions involving the LTR intron splice donor. These data provide the first comprehensive analysis of splice site utilization by an isolate of SIV in comparison to a related molecular clone and the first characterization of SIVsmm splice site utilization
A Murine and a Porcine Coronavirus Are Released from Opposite Surfaces of the Same Epithelial Cells

AbstractEpithelial cells are important target cells for coronavirus infection. Earlier we have shown that transmissible gastroenteritis coronavirus (TGEV) and mouse hepatitis coronavirus (MHV) are released from different sides of porcine and murine epithelial cells, respectively. To study the release of these viruses from the same cells, we constructed a porcine LLC-PK1 cell line stably expressing the recombinant MHV receptor cDNA (LMR cells). The MHV and TGEV receptor glycoproteins were shown by immunofluorescence to appear at the surface of the cells and to be functional so that the cells were susceptible to both MHV and TGEV infection. Both coronaviruses entered polarized LMR cells only through the apical surface. Remarkably, while the cells remained susceptible to TGEV for long periods, infectability by MHV decreased with time after plating of the cells onto filters. This was not due to a lack of expression of the MHV receptor, since this glycoprotein was still abundant on the apical surface of these cells. TGEV and MHV appeared to exit LMR cells from opposite sides. Whereas TGEV was released preferentially at the apical membrane, MHV was released preferentially at the basolateral surface. These results show that vesicles containing the two coronaviruses are targeted differently in LMR cells. We propose that the viruses are sorted at the Golgi complex into different transport vesicles that carry information directing them to one of the two surface domains. The apical release of TGEV and the basolateral release of MHV might be factors contributing to the difference in virus spread found between TGEV and MHV in their respective natural hosts, the former causing mainly a localized enteric infection, the latter spreading through the body to other organs
Adenovirus Serotype Evolution Is Driven by Illegitimate Recombination in the Hypervariable Regions of the Hexon Protein

AbstractThe origin of AIDS-associated adenoviruses (AV 43–AV 49) was investigated by examining evolutionary relationships among 18 serologically related subgenus D serotypes and 3 intermediates and determining the mutation rate of a single serotype, AV 48, among clinical isolates from AIDS patients over a 6-year period. Nucleotide sequence of conserved and seven hypervariable regions (HVRs) of the hexon protein, the pVI core protein signal peptide, and noncoding region between the two genes was determined. Among AV 48 isolates the base misincorporation rate was 3.2 per 10,000 bases over 6 years. A 6-bp deletion occurred in one isolate between short direct repeats in HVR 7. Among subgenus D serotypes mutation rates were extremely low in the pVI peptide, the 5′ hexon noncoding region, and first 187 bases of hexon protein. Small 2- and 3-bp deletions between short direct repeats in a polypurine stretch in the noncoding region occurred in 3 strains. Mutation increased with proximity to the HVRs. Within HVR 1, 2, 4, 5, and 7 variability consisted of extensive intrachromosomal illegitimate recombination, including deletions between short direct repeats, insertions and duplications in repetitive polypurine stretches, and numerous base substitutions. All serotypes and intermediates differed by at least one illegitimate recombination event, with one exception. We conclude that AV serotype evolution is driven by illegitimate recombination events (antigenic shift), concommitant with single base mutation (antigenic drift), and that the HVRs are “hot spots” for both. These events could be explained by slippage-misalignment of the AV DNA polymerase in repetitive polypurine stretches during single-strand DNA replication. This mutability in the surface regions of the major viral coat protein confers a distinct survival advantage to this family of viruses
NIa and NIb of Peanut Stripe Potyvirus Are Present in the Nucleus of Infected Cells, but Do Not Form Inclusions

AbstractWe investigated, by immunological and gene-fusion methods, whether the failure of peanut stripe potyvirus (PStV)-encoded nuclear inclusion proteins a (NIa) and b (NIb) to form nuclear inclusions is due to the lack of theirin vivoaccumulation or the inability of one or both proteins to be transported into the nucleus. NIa domains (NIa-VPg and NIa-proteinase), full-length NIb, and full-length cylindrical inclusion (CI) protein of PStV were cloned, expressed inEscherichia coli,and used for antisera production. Immunoblot analysis of accumulation of NIa, NIb, and CI in time course experiments revealed that they accumulated to similar levels in PStV-infectedNicotiana benthamiana.In immunocytochemical studies with electron microscopy, antiserum against NIa-VPg, NIa-Pro, and NIb specifically labeled NIa and NIb proteins throughout the nuclei of PStV-infected cells, in the absence of nuclear inclusions. Translational fusions were made between NIa and NIb to either the green fluorescence protein or the β-glucuronidase in vectors for transient gene expression or stable expression in transgenic plants, respectively. Fusion proteins containing NIa accumulated in the nucleus, whereas fusion proteins containing NIb accumulated in a punctate pattern in the cytoplasm. These data indicate that at least NIa possesses a nuclear localization signal
Intracellular Localization of the Herpes Simplex Virus Type-1 Origin Binding Protein, UL9

AbstractUL9 is the origin binding protein of herpes simplex virus type-1 (HSV-1). A UL9-specific monoclonal antibody (17B) whose epitope maps to the N-terminal 33 amino acids was used to study the localization of UL9 in infected and transfected cells. We demonstrate the colocalization of UL9 and the HSV-1 single-strand DNA binding protein (ICP8 or UL29) in replication compartments, sites of viral DNA synthesis. On the other hand, UL9 does not completely colocalize with ICP8 in prereplicative sites, structures observed under conditions that inhibit viral DNA polymerase. Cells transfected with various deletion or pyruvate kinase fusion constructs were analyzed by indirect immunofluorescence assay to define the nuclear localization signal (NLS) of UL9. Deletion analysis showed that the region required for nuclear localization lies within the C-terminal DNA binding domian (amino acids 535–851). Various regions of UL9 were tested in fusion constructs for their ability to direct the normally cytoplasmic chicken pyruvate kinase protein to the nucleus. A fusion construct containing the carboxy-terminal 107 residues (amino acids 745–851) localized efficiently to the nucleus, whereas a fusion construct containing the N-terminal 660 amino acids of UL9 was unable to do so. Mutations designed to alter a potential NLS sequence (793-KREFAGARFKLR-804) within the C-terminal 107 residues result in a mutant UL9 protein which fails to localize efficiently to the nucleus. These results suggest that the major NLS of UL9 maps within the C-terminal 107 amino acids
The Role of AV2 (“Precoat”) and Coat Protein in Viral Replication and Movement in Tomato Leaf Curl Geminivirus

AbstractWe analyzed various mutants of tomato leaf curl virus-India to investigate the role of ORFs AV3, AV2, and coat protein (CP) in viral replication, movement, and symptom development. The results of these studies indicate that ORF AV3 does not encode a protein. Plants inoculated with infectious DNA which contained deletions in AV2 developed very mild symptoms and accumulated only low levels of both single-stranded (ss) and double-stranded (ds) viral DNA, whereas inoculated protoplasts accumulated both ss and dsDNA to wild-type levels, showing that AV2 is required for efficient viral movement. However, both plants and protoplasts inoculated with substitution, frameshift, and other similar mutations in AV2 accumulated low levels of viral DNA. The low levels of accumulation of DNA of these mutants were apparently not due to a defect in AV2 synthesis. Mutations in the CP caused a marked decrease in ssDNA accumulation in plants and protoplasts while increasing dsDNA accumulation in protoplasts. Mutations in both AV2 and CP behaved like AV2 mutants in plants and like CP mutants in protoplasts. The results demonstrated that multiple functions provided by AV2, BV1, and BC1 are essential for viral movement, and that changes in A-component virion-sense mRNA structure or translation affect viral replication
Partial Characterization of a Sendai Virus Replication Promoter and the Rule of Six

AbstractWe have used a cDNA copy of a natural, internally deleted, Sendai virus defective interfering genome to study the effect of insertions and deletions (which maintain the hexamer genome length) on the ability of viral genomes to be amplified in a transfected cell system. The insertion of 18 nt at nt72(in the 5′ untranslated region of the N gene, just downstream of thele+region) was found to be lethal, whereas similar insertions further from the genome ends were well tolerated. Curiously, the insertion of 6 nt on either side of thele+/N junction (at nt47and nt67) was well tolerated, but the insertion of 12 nt at either site, or of 6 nt at both sites, largely ablated genome amplification. These results suggest that an element of this replication promoter is located downstream of nt67, in the 5′ untranslated region of the first gene. Remarkably, the addition of 6 nt by the insertion of 2, 3, or 4 nt at nt47plus the insertion of 4, 3, or 2 nt, respectively, at nt67was poorly tolerated, presumably because the hexamer phase of the intervening sequence was altered with respect to the N subunits of the template. These results suggest that the rule of six operates, at least in part, at the level of the initiation of antigenome synthesis
The V3 Domain of SIVmac251 gp120 Contains a Linear Neutralizing Epitope

AbstractAntisera to 21 synthetic peptides containing hydrophilic sequences of simian immunodeficiency virus strain mac251 (SIVmac251) gp120 and gp32 were tested for the ability to neutralize SIVmac251. Goat antisera raised to peptides SP-1 and SP-1V containing the carboxy-terminal portion of the V3 domain of SIVmac251 gp120 between amino acids 327 and 339 inhibited syncytium formation (90% inhibition at a 1/1024 dilution) and cell killing of CEMx174 cells by SIVmac251 (50% inhibition of cell killing at a dilution of 1/5832), SIVDeltaB670 (1/568), and SIVsmH4 (1/740). Neutralizing antibodies to SIVmac251, SIVDeltaB670, and SIVsmH4 could be adsorbed by peptides containing a neutralizing V3 sequence of SIVmac251 gp120 (GLVFHSQPIND, amino acids 329–339) but not by peptides lacking this sequence. This V3 neutralizing region corresponds to a homologous V3 neutralizing site within HIV-2 gp120 reported by Björlinget al.1991,Proc. Natl. Acad. Sci. USA88, 6082–6086, 1994,J. Immunol.152, 1952–1959). Antibodies in 20 of 31 sera obtained from rhesus macaques infected with SIVmac251 reacted with a peptide containing the entire V3 sequence of SIVmac251 gp120, whereas no sera contained antibodies reacting with the V3 neutralizing site between amino acids 329 and 339. Low levels of antibody-mediated recognition and subsequent lack of selective pressure against this linear V3 neutralizing site might in part explain why this region is not a dominant neutralizing site and also why sequences within V3 do not vary during the course of SIV infection
TheAmsacta mooreiEntomopoxvirus Spheroidin Gene Is Improperly Transcribed in Vertebrate Poxviruses

AbstractTheAmsacta mooreientomopoxvirus (AmEPV) spheroidin is the most highly expressed late viral gene product in infected insect cells. However, when a cassette containing the spheroidin gene and putative promoter was inserted into cowpox (CPV) or vaccinia viruses, only very low levels of spheroidin gene expression were observed. Primer extension analysis suggests much lower spheroidin gene transcript levels than seen either for the highly expressed CPV A-type inclusion gene or for the spheroidin gene within infected insect cells, indicating that in vertebrate cells, the spheroidin promoter functions poorly if at all. Examination of the spheroidin mRNA synthesized in recombinant CPV shows that the 5′ start site of the spheroidin transcript was also unexpectedly imprecise and upstream (approximately 31 bp) of the well-defined start site normally observed in AmEPV-infected insect cells. Sequencing of the 5′ terminus of the CPV recombinant spheroidin mRNA suggested that 5′ poly(A), a characteristic feature of late poxvirus mRNAs and spheroidin mRNA derived from insect cells, was absent, despite the presence of the typical vertebrate poxvirus late promoter consensus sequence, TAAATG. Our results indicate that insect and vertebrate poxvirus promoters may not be universally interchangeable and imply that there are regulatory features of gene expression unique to the infected insect cell environment
Mutational Analysis of a Neutralization Epitope on the Dengue Type 2 Virus (DEN2) Envelope Protein: Monoclonal Antibody Resistant DEN2/DEN4 Chimeras Exhibit Reduced Mouse Neurovirulence

AbstractThe antigenic site of dengue type 2 virus (DEN2)-neutralizing monoclonal antibody (mab) 3H5 was investigated by mutational analysis. Sequence comparisons indicated that much of the 12-amino-acid sequence extending from position 386 to 397 of the DEN2 envelope glycoprotein (E) previously thought to represent the DEN2-specific mab 3H5 binding site was also present in some dengue type 1, 3, or 4 virus strains. However, the region occupied by the Glu-Pro-Gly sequence at upstream positions 383 to 385 was completely conserved among DEN2 strains, but divergent in other serotype viruses, suggesting that this sequence might be part of the antigenic site of mab 3H5. We investigated this possibility by employing the previously constructed chimeric DEN2(PreM-E)/DEN4 cDNA clone to produce viable mutants bearing DEN2 PreM and E sequences that could be analyzed for binding to and neutralization by mab 3H5. We constructed 13 such DEN2 mutants that contained a single amino acid substitution in the region between positions 383 and 393 of DEN2 E. Each single substitution in the region spanning positions 386 through 393 of DEN2 yielded a virus that was as reactive with mab 3H5 as the parental chimeric virus. These results are consistent with the extent of sequence conservation in the region. In contrast, 5 of 6 mutants that sustained an amino acid substitution at position 383, 384, or 385 failed to react with mab 3H5 as detected by immunofluorescence assay and failed to be neutralized by the mab. Interestingly, each of the 5 mab-resistant DEN2 mutants also exhibited reduced mouse neurovirulence compared to parental chimeric DEN2 when inoculated intracerebrally. These observations suggest that the Glu-Pro-Gly sequence at positions 383–385 of the DEN2 E is a component of the site against which mab 3H5 is directed. In the recently determined three-dimensional structure of the related tick-borne encephalitis virus E, the Glu-Pro-Gly sequence would be located on the lateral surface of the immunoglobulin-like domain that is proposed to bind to the host cell receptor