pinecone/core-2020-05-10-deduplication huggingface dataset:
Interferon Inhibits the Replication of HIV-1, SIV, and SHIV Chimeric Viruses by Distinct Mechanisms

AbstractInterferon (IFN) treatment of lentivirus-infected cells substantially reduces virus replicationin vitro. Although the replication of both HIV-1 and simian immunodeficiency virus (SIV) is inhibited, IFN blocks the replication of these viruses at different stages of the viral life cycle. We previously demonstrated that in HIV-1–infected cells, IFN blocks a late step in viral replication, leading to a decrease in viral protein stability and a deregulation of polyprotein processing. In contrast, in SIV-infected cells, IFN blocks an early step in viral replication, between virus binding and reverse transcription. Thus, the viral gene products targeted by IFN may be different for each of these viruses. To attempt to define which viral proteins are targeted by the IFN response, we examined the effects of IFN on the replication of two SIV/HIV-1 (SHIV) chimeric viruses, SHIV-4(vpu+) and SHIV-4(vpu−) in 174 × CEM cells. These viruses were grown from constructs in which the SIVmac239env,tat, andrevgenes have been replaced with those of HIV-1. The use of SHIV-4(vpu+) allowed us to examine whethervpu, which is unique to HIV-1, might contribute to the differential effects of IFN on HIV-1 and SIV replication. Surprisingly, we found that IFN inhibited SHIV replication differently than the replication of either HIV-1 or SIV. IFN treatment of SHIV-infected cells resulted in a decrease in the level of viral RNA expression but had no apparent effect on the integration of proviral DNA. Nuclear runoff transcription assays indicated that the reduction in SHIV RNA expression in IFN-treated cells was not due to alterations in RNA polymerase II-mediated transcription, suggesting that IFN may block SHIV replication by promoting the increased degradation of viral RNA. The presence or absence of thevpugene did not alter the effects of IFN on SHIV replication, indicating that Vpu is not responsible for the differential effect of IFN on HIV-1 and SIV replication. Thus the response of SHIVs to antiviral agents such as IFN may be unique from either HIV-1 or SIV. This may be an important consideration when using SHIVs to evaluate anti-HIV-1 therapies in animal models of AIDS
Role of Potassium in Human Immunodeficiency Virus Production and Cytopathic Effects

AbstractAcute infection of CD4+ lymphoid cells by human immunodeficiency virus type 1 (HIV-1) induces an increase in the intracellular concentration of potassium (K+). Media containing reduced or elevated concentrations of K+ were used to investigate the role of this ion in HIV-1 production and cytopathology. Incubation of CD4+ lymphoblastoid cells acutely infected by HIV-1 (strain LAI) in low K+ medium resulted in an approximately 50% decrease in HIV-1 production and markedly diminished HIV-1 induced cytopathic effects (CPE) relative to cells incubated in medium containing a normal K+ concentration (approximately 5 mM). Incubation of HIV-1 infected cells in media containing elevated concentrations of K+ (25 to 50 mM) increased HIV-1 production by two- to fivefold over the amount produced in cells incubated in normal K+ medium. Cells incubated in high K+ media also displayed enhanced HIV-1-induced cytopathology. The decrease in HIV-1 production by low K+ medium and increase by high K+ media could not be accounted for by effects on HIV-1 reverse transcription. However, low K+ medium inhibited HIV-1 protein synthesis and high K+ media increased HIV-1 protein synthesis. These results suggest that the HIV-1–induced increase in intracellular K+ concentration is required for efficient viral replication and to induce cytopathology
Inhibition of Cellular RNA Polymerase II Transcription by Delta Antigen of Hepatitis Delta Virus

AbstractHepatitis delta virus (HDV) contains a circular, viroid-like RNA and the hepatitis delta antigen (HDAg) protein. The viral RNA is replicated via RNA-dependent RNA synthesis, which is thought to be mediated by host DNA-dependent RNA polymerase II (pol II). The precise mechanism of HDV RNA replication using RNA as a template remains to be elucidated, although it is clear that HDAg is involved. We demonstrate here that both SP1-activated and basal pol II transcription are inhibited by HDAg. This inhibitory effect of HDAg was observedin vivoin transient cotransfection assays as well asin vitroin HeLa nuclear extracts with purified, recombinant HDAg. Thein vitroinhibition of pol II transcription could be reversed with excess HeLa nuclear extracts. Furthermore, HDAg specifically inhibited pol II-mediated transcription but not pol I- or pol III-mediated transcription. These results provide support for the model in which HDAg participates in a complex with host cell pol II transcription factors to mediate pol II-dependent HDV RNA replication, concomitantly inhibiting cellular pol II transcription
Mechanistic Independence of Nef and Cyclophilin A Enhancement of Human Immunodeficiency Virus Type 1 Infectivity

AbstractOptimal HIV-1 infectivity requires the presence of both the viral factor Nef and the cellular protein cyclophilin A (CyPA) during virion assembly. These two proteins are integral components of HIV-1 particles. Both CyPA and Nef facilitate a step in the viral life cycle occurring between penetration and reverse transcription, suggesting a common mechanism of action. Experiments were performed to test the potential interplay of Nef- and CyPA-mediated enhancement of HIV-1 infectivity. In single-cycle infection assays,nef-defective virions were partially resistant to cyclosporin A (CsA), a drug that inhibits the binding of CyPA to the HIV-1 Gag precursor and CyPA incorporation into virions. Genetic dissection of the relative contributions of Nef and the cyclophilin A-Gag interaction to HIV-1 infectivity demonstrated the independence of these two effects. Nef was not required for incorporation of CyPA into HIV-1 virions and vice-versa. Surprisingly, CyPA-deficient virions remained sensitive to inhibition by CsA, in a manner that depended strongly on the presence of a functionalnefgene. These results demonstrate that Nef and CyPA act independently to render HIV-1 particles fully infectious. They further suggest that in addition to blocking the CyPA-Gag interaction, CsA can also inhibit HIV-1 replication through a novel mechanism involving suppression of Nef-directed enhancement of virus infectivity
Identification of Glyceraldehyde-3-phosphate Dehydrogenase as a Cellular Protein that Binds to the Hepatitis B Virus Posttranscriptional Regulatory Element

AbstractThe hepatitis B virus posttranscriptional regulatory element (PRE) is an RNAcis-element that is required for high-level expression of viral surface gene transcripts and appears to function by activating mRNA export to the cytoplasm. We have previously shown that multiple fragments of the PRE bind to two cellular proteins of approximately 35 and 55 kDa in molecular mass and that this binding correlates with function. By a combination of column chromatographic techniques and SDS-polyacrylamide gel electrophoresis, we have been able to purify the smaller protein. Amino-terminal sequencing of the purified protein shows identity to glyceraldehyde-3-phosphate dehydrogenase (GAPDH), an RNA-binding glycolytic enzyme that has been implicated in the export of tRNA. Immunoprecipitation analysis reveals that GAPDH is indeed present in the protein-RNA complex resulting from incubation of crude nuclear extracts with a functional region of the PRE. Furthermore, binding of the cellular 35 kDa protein to the PRE fragment is blocked by NAPDH, as would be expected for RNA binding by GAPDH. Finally, purified commercial GAPDH also binds specifically to this RNA fragment. Therefore, GAPDH is one of the cellular proteins that binds to the PRE, and may be involved in the posttranscriptional regulation of hepatitis B virus gene expression
Deletions in the Conserved Amino-Terminal Basic Arm of Cucumber Mosaic Virus Coat Protein Disrupt Virion Assembly but Do Not Abolish Infectivity and Cell-to-Cell Movement

AbstractThe N-terminal basic arm of cucumber mosaic cucumovirus (CMV) coat protein (CP) contains a conserved arginine-rich motif, which is characteristic of RNA binding proteins of several plant and nonplant viruses. To identify regions of the CMV CP N-terminus that are essential for interacting with viral genomic RNA, a comprehensive set of mutations was engineered into biologically active clones of CMV RNA3 and the behavior of each variant with respect to infectivity, packaging and movement was examined. Biological assays conducted inChenopodium quinoa(local lesion host) andNicotiana benthamiana(systemic host) revealed that variants lacking either 12 N-proximal amino acids or a region containing four consecutive arginine residues of the CP N-terminus were competent for assembly into virions and remained infectious in plants. Interestingly, two other variants, lacking either 19 N-proximal amino acids or a domain containing a cluster of six arginines in the arginine-rich motif, were incompetent for virion assembly but retained the ability to move cell to cell. Taken together, these results indicate that a major portion of the N-terminal basic arm of CMV CP is dispensable for CP-RNA interactions and also establish that CMV can move cell to cell in a nonvirion form. The distinctive role played by the viral CP in movement and specifically, the extent to which the CP N-terminal basic arm is involved in the infection cycle of CMV are discussed
Mapping of a Neurovirulence Determinant within the Envelope Protein of a Polytropic Murine Retrovirus: Induction of Central Nervous System Disease by Low Levels of Virus

AbstractMurine leukemia virus (MuLV) clone Fr98 is a recombinant polytropic virus that causes neurological disease characterized by ataxia in susceptible mouse strains. The envelope gene of Fr98 has been previously shown to encode at least two separate neurovirulence determinants. In the present study, the determinant encoded within theEcoRI/AvrII fragment of the envelope gene was further defined. In these experiments, neurovirulence was associated with a change from a serine to an arginine at position 195 and a glycine to an alanine at position 198 within the envelope protein. Neurovirulent and nonvirulent virus clones, which differed only at these two amino acid residues, showed no difference in the type or location of cells infected. Furthermore, equivalent levels of viral p30 capsid protein were detected in the brains of mice infected with either the neurovirulent or nonvirulent virus clones. These results were consistent with the interpretation that the envelope protein of the neurovirulent virus differed from that of the nonvirulent virus by having a greater toxic effect on central nervous system function
A 47-Amino-Acid Fragment of SV40 T Antigen Represses Transcription from Human GSTα Promoters

AbstractSV40 T antigen downregulates the expression of an important detoxification enzyme, glutathioneS-transferase α (GSTα). We show here that the target of this repression is a 14-bp element common to the human GSTA1 and GSTA2 promoters. This element, which we have named TAGR, is also critical for high-level, constitutive expression from these promoters. The TAGR element does not appear to contain a binding site for any transcription factor known to be present in fibroblasts, although the TAGR element does resemble the binding site for the Ikaros transcription factor found in hematopoietic cells. We also have identified a 47-amino-acid fragment of T antigen that includes amino acids 83–100 and 119–147, which is sufficient to repress transcription from the GSTα promoter in transient transcription assays. Thus, GSTα repression does not require binding of T antigen to pRb, p300, or p53, since the domains of T antigen required for binding these cellular proteins are missing from this T antigen fragment. We show, however, that this fragment does bind to three cellular proteins with approximate molecular weights of 54, 59, and 94 kDa
Altered Tropism of an Ovine Adenovirus Carrying the Fiber Protein Cell Binding Domain of Human Adenovirus Type 5

AbstractOvine adenovirus OAV287 (OAV) is phylogenetically and serotypically distinct from human Ad5. OAV grows productively in CSL503 foetal ovine lung cells and abortively infects several human cell lines. OAV has a unique fiber and a penton protein that lacks a recognisable integrin-binding motif. It is not known whether a secondary receptor is required for infection. A hybrid virus was constructed in which the cell binding domain on the OAV fiber protein was exchanged for the equivalent region from human adenovirus type 5. The hybrid OAV grew to titres that were 1 to 2 log10lower than wild-type OAV in permissive ovine cells. Human Ad5 also infected CSL503 cells but failed to compete with OAV for receptor binding sites on those cells. However, the hybrid virus did compete with Ad5, consistent with its use of the Ad primary receptor. The hybrid virus was also neutralised by Ad5 antiserum whereas OAV was not. Human 293 kidney and LNCaP prostate cell lines that were not detectably infected by OAV were infected by the hybrid virus and other human prostate and breast cancer cell lines showed greatly enhanced infectivity. Thus, modification of the fiber cell binding domain was sufficient to profoundly alter the tropism of OAV, suggesting that the interaction between the primary receptor and the virus particle is the major factor controlling virus entry during infection
Temporal and Spatial Expression of the E5a Protein during the Differentiation-Dependent Life Cycle of Human Papillomavirus Type 31b

AbstractHuman papillomaviruses (HPVs) are epitheliotropic viruses, and their life cycle is intimately linked to the stratification and differentiation state of the host epithelial tissues. Defining a role for the E5 gene product in the differentiation-dependent viral life cycle has been difficult due to the lack of a suitable culture system. We used the organotypic (raft) culture system to investigate the spatial and temporal expression pattern of the E5 protein during the differentiation-dependent life cycle of HPV-31b. We report the generation of antisera specific to the HPV-31b E5a protein. The HPV-31b E5a protein was detected throughout the viral life cycle in raft cultures as determined by immunostaining analyses, and the protein was localized predominantly to the basal and granular layers. Expression of epidermal growth factor receptor or platelet-derived growth factor receptors, two proteins with which E5 has been shown to interact in cell culture, did not specifically colocalize with E5a expression. However, HPV-31b E5a expression did colocalize with the epithelial differentiation-specific marker filaggrin. The kinetics of E5a protein expression during the complete viral life cycle was analyzed by immunoblotting, and the highest level was found to be coincidental with the onset of virion morphogenesis
The Late-Expressed Region of the Temperate Coliphage 186 Genome

AbstractThe late-lytic region of the genome of bacteriophage 186 encodes the phage proteins that synthesize the complex viral particle and lyse the bacterial host. We report the completion of the DNA sequence of the late region and the assignment of 18 previously identified genes to open reading frames in the sequence. The 186 late region is similar to the late region of phage P2, sharing 26 genes of known function: the single gene for activation of late gene transcription, 6 genes for construction of DNA-containing heads, 16 for tail morphogenesis, and 3 for cell lysis. We identified two 186 late genes with unknown function; one is homologous to previously unrecognised genes in P2, HP1, and φCTX, and the other may modulate DNA packaging. The 186 late region, like the rest of the genome, lacks the lysogenic conversion genes that are carried by P2, allowing the 186 late region to be transcribed from only three late promoters rather than four. The relative absence of lysogenic conversion genes in 186 suggests that the two phages have evolved to use the lytic and lysogenic reproductive modes to different extents
Immunoprotective Determinants in Friend Murine Leukemia Virus Envelope Protein

AbstractSeveral immunological epitopes are known to be located within the Friend murine leukemia virus (F-MuLV) envelope protein, but their relative contributions to protection from Friend virus-induced disease are not known. To determine how expression of various immunological determinants affected protection, mice were immunized with recombinant vaccinia viruses expressing different portions of the F-MuLV envelope protein, and they were then challenged with a lethal dose of Friend virus complex. The disease parameters that were followed in the mice were early viremia, early splenomegaly, and late splenomegaly. Both the N-terminal and C-terminal portions of the F-MuLV gp70 were found to protect against late splenomegaly, the primary clinical sign associated with virus-induced erythroleukemia. However, neither region alone protected against early splenomegaly and early viremia, indicating poor immunological control over early virus replication and spread through the spleen and blood. In contrast, mice immunized with a vaccine expressing the entire F-MuLV envelope protein were protected against all three disease parameters. The results indicated that expression of multiple immunological determinants including both T-helper and B cell epitopes was necessary for full protection
An Anti-CD4 (CDR3-Loop) Monoclonal Antibody Inhibits Human Immunodeficiency Virus Type 1 Envelope Glycoprotein-Induced Apoptosis

AbstractInhibition of human immunodeficiency virus type 1 (HIV-1)-inducing programmed cell death (PCD) by anti-CD4 monoclonal antibodies (mAbs) was investigated using DNA intercalant YOPRO-1 assay. We found that 13B8.2, an mAb that binds the CDR3-like loop in domain 1 (D1) of CD4, protected infected CEM cell cultures against HIV-1-induced PCD. Protection was not observed using another anti-CD4 mAb (BL4) that binds D1-D2, suggesting that the mechanism involved in cell protection against HIV-1-induced PCD requires engagement of precise CD4 epitopes. Because 13B8.2 is known to inhibit syncytia formation and virus transcription, this mAb could inhibit HIV-1-induced PCD by (1) inhibiting virus gene expression, (2) preventing viral envelope-CD4 interaction, and/or (3) interfering with apoptotic signals. Our data indicated that the absence of enhanced PCD in infected cell cultures treated with 13B8.2 mAb probably was the result of inhibition of HIV-1 replication and virus spread. Moreover, 13B8.2 mAb was found to inhibit PCD mediated by membrane-expressed HIV-1 envelope glycoproteins. Finally, we found that 13B8.2 mAb displayed no protective interference with apoptotic signal induced by Fas, dexamethasone, and serum withdrawal
Heterologous Protection of Mice from a Lethal Human H1N1 Influenza A Virus Infection by H3N8 Equine Defective Interfering Virus: Comparison of Defective RNA Sequences Isolated from the DI Inoculum and Mouse Lung

AbstractWe have examined the RNAs involved in the heterologous protection of adult mice from otherwise lethal intranasal infection with mouse-adapted human A/WSN (H1N1) by defective interfering (DI) equine A/equine/Newmarket/7339/79 (H3N8: EQV) influenza virus, as well as the RNAs involved in the protection of WSN- or EQV-infected mice by their homologous DI viruses. The aim of this study was to describe the types of defective RNAs present in protected mice in order to guide the design of potentially protective DI RNAs. The interfering and mouse-protecting activity of DI virus was destroyed by prolonged UV irradiation (iDI virus) demonstrating that protection correlated with an active DI genome, and not viral antigen. Protected mice were all infected but suffered a lower degree of morbidity than those given iDI virus. The DI EQV inoculum contained defective segment 1–8 RNAs while DI WSN inoculum contained only defective segment 1–6 RNAs. However lungs of mice given EQV + DI EQV contained only defective segments 1–4 or 1–6 RNAs (mouse-to-mouse variation), while control mice given EQV or EQV + iDI EQV contained few very defective RNAs. Thus prevention of death was the result of quantitative and/or qualitative differences in defective RNAs administered to the mice. Only defective segments 1–3 RNAs were isolated from the lungs of mice given WSN + DI WSN, confirming the earlier report of Noble and Dimmock (1995). A detailed analysis showed that most defective RNAs isolated from the lungs of mice protected from a lethal WSN infection by DI EQV were EQV in origin. Thus, as no infectious EQV was present, these defective RNAs from the DI EQV inoculum must have been heterologously replicated in mouse lung by WSN. All defective segment 3–6 RNAs isolated were of EQV origin, indicating that they were replicated by WSN in preference to its own. Defective segments 1 and 2 were a mixture of EQV and WSN RNAs. Of 17 defective EQV segment 1–3 sequences from mouse lung, all but three differed in their primary central deletion from 20 defective RNAs isolated from the inoculum. No bias in the break points was evident. A number of minor deletions of 2 or more nts were also present in defective EQV and WSN RNAs in segments 1 and 2, but none in segment 3. Their 5′, but not 3′, breakpoints were heterogeneous, suggesting that defective RNAs were generated during positive strand synthesis. Two cloned EQV-defective segment 3 RNAs were chimeras containing a 30 nt insert from segment 1. Most defective RNAs possessed at least 178 nts from the 5′ end of vRNA. The amount of 5′ sequence present in those RNAs correlated with the segment of origin, suggesting that this was the minimum required for propagation of viral RNA in mouse lung and hence possibly for protection also
Transcription of Epstein–Barr Virus Latent Cycle Genes in Oral Hairy Leukoplakia

AbstractThe hairy leukoplakia lesion (HLP) is a unique example of a permissive infection with Epstein–Barr virus (EBV) in the tongue epithelium. HLP contains abundant replicating viral DNA and may be coinfected with multiple EBV strains. In this study, characterization of viral gene transcription within HLP biopsy specimens revealed that several genes, usually expressed in latently infected lymphocytes, are also transcribed in the HLP lesion. TheBamHI W and C promoters, (Wp and Cp) are consistently active in the HLP lesion, resulting in transcription and processing of mRNAs that encode the Epstein–Barr nuclear antigens (EBNAs) EBNA-LP, EBNA1, EBNA2, EBNA3B, and EBNA3C. The EBNA2 protein has been shown to activate expression of the EBV receptor, CD21. In HLP, CD21 transcription is also detected, usually in samples that contain transcripts for EBNA2. Transcripts encoding the LMP1 gene, the LMP2 gene, and rightward transcripts from theBamHI A fragment of the EBV genome are also detected in HLP. These gene products are invariably expressed in latently infected lymphocytes. This pattern of transcription suggests that genes characteristic of latent infection are also expressed in HLP. The activation of Wp and expression of EBNA2 and CD21 may contribute to the unique ability of the HLP lesion to permit superinfection and viral replication of multiple EBV strains