pinecone/core-2020-05-10-deduplication huggingface dataset:
Suppression of Apoptotic Cell Death by Hepatitis C Virus Core Protein

AbstractWe have previously demonstrated the role of hepatitis C virus (HCV) core protein in the transcriptional regulation of cellular and unrelated viral promoters. Furthermore, the core protein in cooperation with H-ras oncogene transforms primary rat embryo fibroblast cells to the tumorigenic phenotype. In the present study, the functional role of HCV core protein was investigated to determine its potential to inhibit the onset of apoptotic cell death. Expression of HCV core protein inhibited cisplatin mediated apoptosis in human cervical epithelial cells, and apoptosis induced by the overexpression of c-myc in Chinese hamster ovarian cells. Results from these studies suggest that the core protein may have a biological implication in the pathogenesis of HCV infection
Effects of Internal Cleavages and Mutations in the C-Terminal Region of NIa Protease of Turnip Mosaic Potyvirus on the Catalytic Activity

AbstractThe nuclear inclusion protein a (NIa) of turnip mosaic potyvirus is a protease processing the viral polyprotein into functional proteins. It has been shown that the NIa C-terminal 27-kDa protease cleaves itself between Ser-223 and Gly-224 to generate a 25-kDa protein lacking the C-terminal 20 amino acids. We have found a second internal cleavage near the C-terminus resulting in the degradation of the 25-kDa protein into a 24-kDa protein. Substitution of the active site Asp-81 or Cys-151 with Asn or Ser, respectively, prevented the second cleavage, suggesting that the internal cleavage is also due to the proteolytic activity of the NIa protease. This second internal cleavage was found to occur between Thr-207 and Ser-208, eliminating the C-terminal 36 amino acids from the 27-kDa protease. The proteolytic activity of the 24-kDa protein was not detected at all when it was measured using a nonapeptide containing the cleavage site between 6K1and CI as a substrate, suggesting that the C-terminal region between residues 208 and 223 contains essential amino acids for the processing of 6K1–CI polyprotein. The deletion analyses of the C-terminal region revealed that at least 217 amino acids from the N-terminus are required for the catalytic activity of the NIa protease. The point mutation of Trp-212 to Ser, Gly-213 to Ser, or Ile-217 to Asp drastically abolished the catalytic activity, demonstrating that Trp-212, Gly-213, and Ile-217 are important for the processing of 6K1–CI polyprotein
A Single Nucleotide Substitution Converts Potato Spindle Tuber Viroid (PSTVd) from a Noninfectious to an Infectious RNA for Nicotiana tabacum

AbstractMechanical inoculation ofNicotiana tabacumwith the PSTVd isolate KF 440-2 from the host plant tomato resulted in thede novoemergence, replication, and accumulation of a new “tobacco variant,” designated PSTVd NT. It produces no symptoms in tobacco but, like PSTV KF 440-2, severe ones in tomato. The sequence analysis of PSTVd NT revealed a single nucleotide substitution from C → U at position 259. Autonomous viroid replication was also induced in tobacco by genomic integration of oligomeric cDNA copies of PSTVd KF 440-2. Although these cDNAs contained the original tomato-specific C259, the circular PSTVd RNA subsequently accumulating in tobacco also exhibited the C259→ U259substitution. In the secondary structure of PSTVd, nucleotide 259 is part of an internal loop analogous to loop E of eukaryotic 5S rRNA and presumed to be the only bulged extrahelical nucleotide of this loop. The C259in PSTVd KF 440-2 and in practically all other isolates and the U259in PSTVd NT of the loop E-like structure might be involved in protein binding and in viroid processing. The new variant PSTVd NT is genetically stable in both tobacco and tomato
Mapping of Host Range Restriction of the Rakkyo Strain of Tobacco Mosaic Virus inNicotiana tabacumcv. Bright Yellow

AbstractThe rakkyo strain (TMV-R) and the common strain (TMV-U1) of tobacco mosaic virus exhibit distinct host range differences. TMV-R infects rakkyo plants, a monocot host that TMV-U1 is unable to infect. However, TMV-R causes only latent infection inNicotiana tabacumcv. Bright Yellow (BY) in inoculated leaves, whereas TMV-U1 infects BY systemically and induces mosaic symptoms. Complete nucleotide sequencing of the TMV-R genomic RNA revealed amino acid changes in the 130K/180K replicase proteins, the 30K protein, and the coat protein and nucleotide changes in the 5′ and 3′ noncoding regions compared to TMV-U1. To identify viral components involved in determination of differences in host range, we have mapped determinants for the differential infection phenotype in BY plants by constructing chimeric viruses between the two strains in the present study. Examination of the infection phenotypes of the 14 constructed chimeric viruses in BY showed that determinants defining the differential infection phenotype in BY reside in the 130K/180K replicase proteins and the 3′ noncoding region. Cognate combination of the 130K/180K replicase proteins and the 3′ noncoding region of TMV-U1 origin is required to produce systemic infection in BY plants
Preliminaryin VitroGrowth Cycle and Transmission Studies of HIV-1 in an Autologous Primary Cell Assay of Blood-Derived Macrophages and Peripheral Blood Mononuclear Cells

AbstractRecent interest focused on the dynamics of HIV-1 replication in primary monocytes/macrophages and T-lymphocytes of the immune system, as well as the standardization of virological and immunologicalin vitroassays with primary isolates, provided the impetus for these studies. These types of studies have never been performed as they would occurin vivo,i.e., where the envelope of the virus and cell membranes of the two cell types of the same host origin. Therefore, the biological and physicochemical properties of an uncloned, primary dual-tropic isolate HIV-1ADAduring the initial lag, log, and stationary phases of viral replication were studied in an autologous donor cell assay in peripheral blood mononuclear cells (PBMC) and blood monocyte-derived macrophages (MDM). Similar total numbers (109virus particles/ml) were produced by both cell types during the stationary period. On a per cell per day basis, during peak stationary periods, 0.92 × 103virions/day for MDMs and 5.31 × 103virions/day for PBMCs were produced. Interestingly, virus replicating from MDMs during the log-growth phase demonstrated the greatest infectious fraction which was 3 logs greater than virus replicating in PBMCs. Despite constant virus particle production in MDMs, the infectious fraction was found to fall 3 to 4 logs over a 10-day period. Due to an infectious fraction less than 1 (0.053 infectious unit/cell/24 hr), virus spread in PBMCs during the rapid log phase could only have occurred by cell-to-cell contact, whereas in MDMs with an infectious fraction of about one infectious particle (∼1/cell/24 hr), cell-free transmission could account for the observed results. Most of the MDMs (>90%) became productively infected, whereas only 5–10% of the total PBMCs were found replicating virus. The period of peak stationary virus production (i.e., stationary phase) was at minimum 4 to 5 times longer in MDMs than PBMCs. Whereas the majority of p24, RT, and gp120 found to be associated with MDM-derived virions, no increased dissociation of these components was observed in PBMC-derived virions. The virion-associated gp120 was 3 to 4 times more stable on both PBMC- and MDM-derived virus (>96 hr) and present at 10–25 times the concentration per virion than that observed for a T-cell-line-adapted laboratory strain of HIV-1 replicating in T-cell lines. Thesein vitroresults suggest that important differences exist between MDMs and PBMCs with regard to the viral dynamics of infection and replication which should provide for a qualitative and quantitative basis to estimate virus replication on a per-cell basis for other known cellular targets of HIV-1. Studying the multiple biophysicochemical characteristics and viral replication dynamics as described herein provides an autologousin vitromodel of additional quantifiable parameters for analysis and understanding of virus/host factor(s) and/or antivirals which influence them
Role of the V2, V3, and CD4-Binding Domains of GP120 in Curdlan Sulfate Neutralization Sensitivity of HIV-1 during Infection of T Lymphocytes

AbstractA sulfated polysaccharide, curdlan sulfate (CRDS) with 1,3-β-D-glucan as a main chain, inhibits HIV-1 infection of human peripheral blood lymphocytes (PBLs) by binding to the V3 region of gp120. We previously showed that T cell (T)-tropic HIV-1 isolates are over 10-fold more sensitive to neutralization by CRDS than macrophage (MT)-tropic viruses, which posseses a relatively less charged amino acid composition in the V3 sequence. To analyze the interaction of CRDS with V3 and its association with neutralization sensitivity of HIV-1 isolates, we examined the effect of CRDS on the binding of neutralizing antibodies to monomeric and oligomeric gp120 mutants of T- and MT-tropic HIV-1 clones in which the V3 loop was either deleted or substituted by V3 of another isolate. Our results showed that the presence and the amino acid composition of the V3 loop appears to determine the extent of interaction of CRDS with the V2 and CD4-binding regions on native gp120 monomers; however, the positive charge of V3 has less effect on this interaction on oligomeric gp120. Furthermore, our results established that only the CRDS-induced masking of V3 on oligomeric gp120 appears to be associated with the anti-HIV-1 activity of CRDSin vitro.Our findings underline the usefulnes of CRDS for understanding the structural constraints on gp120 that drive the transition from MT- to T-tropic isolatesin vivoand enable the virus to use multiple fusion cofactors
Tobamovirus Cross Protection Using a Potexvirus Vector

AbstractCross protection is the ability of one virus to prevent or delay infection by a related challenge virus. To examine this phenomena, a potato X potexvirus (PVX) vector (Chapmanet al.,1992,Plant J.2, 549) was used to systemically express the tobacco mosaic tobamovirus (TMV) coat protein (CP) open reading frame inNicotiana benthamiana.PVX constructs induce mild mosaic symptoms inN. benthamiana,whereas TMV infection results in rapid systemic necrosis and plant death. Healthy plants or plants preinfected with the unmodified PVX vector succumbed to necrosis within 1 week of TMV challenge inoculation. However, plants preinfected with PVX vectors expressing the TMV CP or RNA coding sequence displayed a 1- to 2-week delay in the appearance of TMV-induced necrosis along with reduced accumulations of TMV. Symptom delay and reductions in the accumulation of TMV were more pronounced in plants protected with the vector expressing the TMV CP than with the vector expressing a nontranslatable CP sequence. Protection was overcome more quickly using a 10-fold higher concentration of challenge inoculum and was ineffective against TMV RNA or a TMV construct expressing a distantly related tobamovirus CP. These findings demonstrate that both RNA and protein are involved in this cross protection phenomenon, but that CP is the main contributor to protection. Taken together, these studies indicate that virus vectors can be used to simulate both cross protection and transgene-derived coat protein-mediated protection, thus providing a new method to further investigate the mechanisms behind each
The UL16 Gene Product of Herpes Simplex Virus 1 Is a Virion Protein That Colocalizes with Intranuclear Capsid Proteins

AbstractThe UL16 gene of herpes simplex virus maps within the intron of the UL15 gene. This report shows the following: (i) A polyclonal antiserum directed against a bacterial fusion protein containing glutathioneS-transferase fused to the C-terminus of the UL16 gene reacted with an apparentMr40,000 protein in HSV-1 infected cell lysates. (ii) The protein encoded by UL16 was dependent on viral DNA synthesis for accumulation to detectable levels. (iii) In immunofluorescence studies, the polyclonal UL16/GST-specific antiserum was shown to stain the nucleus of infected cells at 18 hr after infection in areas containing high concentrations of HSV capsid proteins. These nuclear compartments have been described previously as viral assemblons (Wardet al., J. Virol.70, 4623–4631, 1996) and are distinct from compartments containing replicating DNA. Localization within assemblons argues for a role of UL16 encoded protein in capsid assembly or maturation. (iv) At 22 hr after infection, UL16-specific immunofluorescence was present in both the nucleus and the cytoplasm. (v) Consistent with the change in localization at late times after infection, the UL16 protein was found to be a component of purified virions
The Equine Herpesvirus 1 IR6 Protein Influences Virus Growth at Elevated Temperature and Is a Major Determinant of Virulence

AbstractThe diploid IR6 gene (ORF 67) of equine herpesvirus type 1 (EHV-1) is absent in the modified live EHV-1 vaccine strain RacH and is present in a mutated form in the avirulent EHV-1 strains RacM24 and RacM36, such that the IR6 protein fails to form the typical rod-like structures observed for wild-type EHV-1 RacL11. To assess the role of the IR6 protein in EHV-1 replication and virulence, two recombinant RacH viruses, HIR6-1 and HIR6-2, that harbor a single copy of the wild-type IR6 gene were engineered and characterized. It was shown that: (i) HIR6-1 or HIR6-2 virus encoded for an IR6 protein that was capable of forming the rod-like structures typical of cells infected with the wild-type virulent virus strain RacL11. (ii) Whereas the avirulent EHV-1 strains RacH and RacM36 are temperature-sensitive (in that virus replication at 40° versus that at 37° was reduced by as much as 7,500-fold), the HIR6-1 and HIR6-2 viruses, like RacL11 virus, were capable of significant replication at the elevated temperature. (iii) Electron microscopic analyses revealed that cells infected with the HIR6-1 or HIR6-2 virus, like those infected with virulent RacL11 virus, produced and released comparable numbers of virus particles at both 37 and 40°. In cells infected with the RacH virus at 40°, however, release of extracellular particles was inhibited by greater than 90% and relatively few of the particles were enveloped. (iv) Infections of BALB/cA mice revealed that both the HIR6-1 and HIR6-2 viruses, unlike the parent RacH virus, were as virulent as the wild-type RacL11 strain as judged by the criteria of body weight loss, development of clinical signs of EHV-1 infection, virus titers in the lung, and ability to cause viremia. These findings and those of our recent studies indicate that the IR6 protein is a major determinant of EHV-1 virulence and that the IR6 protein may play a role in virus maturation and/or egress
TheEnv-like Open Reading Frame of the Baculovirus-Integrated Retrotransposon TED Encodes a Retrovirus-like Envelope Protein

AbstractTED is a 7.5-kbp member of the gypsy family of retrotransposons that was first identified by its integration within the baculovirus DNA genome. This lepidopteran (moth) transposon contains three retrovirus-like genes, including functionalgagandpolthat yield reverse transcriptase-containing virus-like particles. To identify and characterize the product(s) of the thirdenv-like open reading frame, TED ORF3 was expressed in homologous lepidopteran cells by using a baculovirus vector, vENV. Immunoblots and immunoprecipitations with antiserum raised against a bacterial ORF3-fusion protein detected two ORF3-encoded proteins, p68envand gp75env. On the basis of selective incorporation of [3H]mannose and inhibition of modification by tunicamycin which blocks N-linked glycosylation, gp75envis a glycoprotein derived from core precursor p68env. As predicted by the presence of a transmembrane domain near the carboxyl terminus, both p68envand gp75envwere associated with heavy membranes of vENV-infected cells. Thus, TED ORF3 encodes a membrane glycoprotein with properties characteristic of retroviralenvproteins. These data are consistent with the hypothesis that TED is an invertebrate retrovirus. Moreover, TED integration within the baculovirus genome provides an example of retroelement-mediated acquisition of host genes that may contribute to virus evolution
Characterization of an Envelope Mutant of HIV-1 That Interferes with Viral Infectivity

AbstractA mutant human immunodeficiency virus (HIV-1) provirus encoding an envelope (Env) protein with a truncated transmembrane protein cytoplasmic domain was defective for replication. Coexpression of the mutant with a wild-type (wt) HIV-1 provirus potently inhibited the production of infectious virus. The maximum inhibitory effect was reached when the ratio of mutant to wt proviral DNA was 2:1. This transdominant defect in infectivity conferred by the mutant Env did not appear to involve the late steps of virus replication, since the synthesis, precursor processing, and intracellular transport of the Env proteins were not blocked; nor did it prevent the incorporation of the envelope proteins into virions or the subsequent release of the virus. Although the mutant Env protein still retained syncytia-forming ability, the truncated protein was unable to mediate cell-to-cell transmission of the virus. Moreover, coexpression with the mutant effectively inhibited the ability of the wt Env to mediate cell-to-cell transmission. The mutant Env protein formed a complex with the wt protein when they were coexpressed, producing heterooligomeric structures which appeared to be severely defective in an early, post-CD4 binding step of the virus life cycle despite the inclusion of wt Env in the complexes
Reduced Precore Transcription and Enhanced Core-Pregenome Transcription of Hepatitis B Virus DNA after Replacement of the Precore-Core Promoter with Sequences Associated with e Antigen-Seronegative Persistent Infections

AbstractHepatitis B virus variants harboring nucleotide alterations in the preC-C promoter have been detected in fulminant hepatitis B as well as in HBeAg-seronegative persistent infection. However, it has not been demonstrated that variants with nucleotide alterations in the preC-C promoter cause various disease states. We replaced the preC-C promoter region of a wild-type genome with the most frequent naturally occurring mutated form and introduced it into HepG2 cells. The mutant with coexisting A1762T and G1764A substitutions produced less than one-fifth of the wild-type level of HBeAg. Conversely, the mutant generated 2.4 times more core particle antigen and showed a high-replicator phenotype. RNase protection and quantitative 5′ RACE showed a 16- to 32-fold reduction of preC transcripts and a 4-fold induction of C transcripts of the mutant compared to wild-type. The preC transcript of the mutant had a more heterogeneous 5′ end than that of the wild-type. However, the mutations did not alter the initiation sites of C transcription. When the promoter region was cloned into CAT plasmids, the mutations had dual effects on preC and C promoter activities, decreasing and increasing them, respectively. These results suggest that these mutations are responsible for the reduced HBeAg production as well as the enhanced replication and core production. Analysis of revertants with either single point mutation showed that T at 1762 is critical for the mutant phenotype
Molecular Studies on Bromovirus Capsid Protein I. Characterization of Cell-to-Cell Movement-Defective RNA3 Variants of Brome Mosaic Virus

AbstractTo evaluate the extent to which brome mosaic virus (BMV) coat protein (CP) gene is involved in the process of cell-to-cell movement,Chenopodium quinoaplants were coinoculated with BMV wild-type RNAs 1 and 2 and a RNA3 variant containing either the β-glucuronidase (GUS) gene in place of CP (B3/CP-GUS), to be subjected to GUS analysis, or a deletion in the CP gene to be analyzed by fluorescencein situhybridization (FISH). Irrespective of time postinoculation, GUS expressed from the subgenomic mRNA of B3/CP-GUS was restricted to initially infected, single epidermal cells. The defective cell-to-cell movement exhibited by B3/CP-GUS was not complementedin transwhen transcripts of B3ΔMP, a RNA3 variant capable of synthesizing functional wt CP but not movement protein (MP), were added to the inoculum. Application of FISH, a technique versatile in discriminating subliminal infections from efficient cell-to-cell spread in nonpermissive and permissive hosts, respectively, to leaves inoculated with BMV RNA3 variants defective in CP synthesis, confirmed that the resulting infections were subliminal. These data provide direct evidence for the requirement of an encapsidation-competent CP to be expressed in conjunction with a functional MP for efficient cell-to-cell spread of BMV
Molecular Studies on Bromovirus Capsid Protein II. Functional Analysis of the Amino-Terminal Arginine-Rich Motif and Its Role in Encapsidation, Movement, and Pathology

AbstractThe N-terminal region of the brome mosaic bromovirus (BMV) coat protein (CP) contains an arginine-rich motif that is conserved among plant and nonplant viruses and implicated in binding the RNA during encapsidation. To elucidate the functional significance of this conserved motif in the BMV CP, a series of deletions encompassing the arginine-rich motif was introduced into a biologically active clone of BMV RNA3, and their effect on replication, encapsidation, and infection in plants was examined. Analysis of infection phenotypes elicited onChenopodium quinoarevealed the importance of the first 19 N-proximal amino acids of BMV CP in encapsidation and pathogenicity. Inoculation ofC. quinoawith three viable variants of BMV RNA3 lacking the first 11, 14, and 18 N-terminal amino acids of the CP resulted in the development of necrotic local lesions and restricted the spread of infection to inoculated leaves. Progeny analysis from symptomatic leaves revealed that, in each case, virus accumulation was severely affected by the introduced mutations and each truncated CP differed in its ability to package genomic RNA. In contrast to these observations inC. quinoa,none of the CP variants was able to establish either local or systemic infections in barley plants. The intrinsic role played by the N-terminal arginine-rich motif of BMV CP in packaging viral RNAs and the interactions between the host and the truncated CPs in modulating symptom expression and movement are discussed