pinecone/core-2020-05-10-deduplication huggingface dataset:
Isolation of Sooty Mangabey Simian T-Cell Leukemia Virus Type I [STLV-I(sm)] and Characterization of a Mangabey T-Cell Line Coinfected with STLV-I(sm) and Simian Immunodeficiency Virus SIVsmmPBj14

AbstractIt has been postulated that dual infections of humans with human immunodeficiency virus (HIV) and human T-cell leukemia/lymphotropic virus (HTLV) may potentiate disease progression. Counterparts of both of these pathogenic human retroviruses have been identified in various simian species indigenous to Asia and Africa, including sooty mangabey monkeys (Cercocebus atys). Using peripheral blood mononuclear cells (PBMC) from a mangabey naturally infected with both SIV and STLV-I, T-cell lines were established and maintained continuously for more than 3 years; these cell lines harbored only a newly identified mangabey STLV-I(sm) or both STLV-I(sm) and the acutely lethal variant SIVsmmPBj14. The dually infected cell line (FEd-P14) was established byde novoinfection of mangabey PBMC with SIVsmmPBj14. This cell line was characterized by multiple assays which showed that structural proteins encoded by both viruses were produced in large quantities, but that the predominant viral glycoprotein on the cell surface was the STLV-I(sm) Env. Unusual interactions of the two retroviral glycoproteins were suggested by the formation of syncytia between Raji and the FEd-P14 cells, but not between Raji and simian cells infected with only one retrovirus or human cells infected with HTLV-I. The STLV-I(sm) strain obtained from the sooty mangabey was transmitted to normal macaque and mangabey PBMC and was shown to be unique by sequencing of the entireenvgene. STLV-I(sm) from this African species was more closely related to “cosmopolitan” HTLV-I strains than to the prototypic STLV-I from an Asian pig-tailed macaque.In vitroandin vivostudies of STLV-I(sm) and SIVsmm, both isolated from a naturally infected mangabey monkey, may provide insight into disease induction and manifestations associated with coinfection by their human counterparts
Comparison of the Role of 5′ Terminal Sequences of Alfalfa Mosaic Virus RNAs 1, 2, and 3 in Viral RNA Replication

AbstractThe 5′ untranslated regions (UTRs) of the genomic RNAs 1, 2, and 3 of alfalfa mosaic virus (AMV) are 100, 54, and 345 nucleotides (nt) long, respectively, and lack extensive sequence similarity to each other. RNA 3 encodes the movement protein P3 and the coat protein and can be replicated in transgenic tobacco plants expressing the replicase proteins P1 and P2 (P12 plants). 5′Cis-acting sequences involved in RNA 3 replication have been shown to be confined to the 5′ UTR. When the 5′ UTR of RNA 3 was replaced by the 5′ UTRs of RNAs 1 or 2, the recombinant RNA was not infectious to P12 plants. Also, when the P3 gene in RNA 3 was put under the control of a subgenomic promoter and the 5′ UTR of this RNA was replaced by 5′ terminal RNA 1 sequences of 103 to 860 nt long or RNA 2 sequences of 57 to 612 nt long, no accumulation of the hybrid RNAs was observed. Deletion of the 5′ 22 nucleotides of RNA 3 resulted in the accumulation of a major progeny that lacked the 5′ 79 nt. However, when the 5′ 22 nucleotides of RNA 3 were replaced by the complete 5′ UTR of RNA 1 or 5′ sequences of RNAs 1, 2, or 3 with a length of 5 to 15 nt, accumulation of the full-length mutant RNAs was observed. The effect of mutations in the 5′ viral sequences of 5 to 15 nt was analyzed. It is concluded that although elements within nucleotides 80–345 of the 5′ UTR of RNA 3 are sufficient for replication, a specific sequence of 3 to 5 nt is required to target the replicase to an initiation site corresponding to the 5′ end of the RNA
Intracisternal A-Type Particles Express Their Proteinase in a Separate Reading Frame by Translational Frameshifting, Similar to D-Type Retroviruses

AbstractIntracisternal A-type particles (IAP) are defective endogenous retroviruses that accumulate in the endoplasmic reticulum of rodent cells. IAP genomes share extensive sequence homologies with D-type retroviruses, but were presumed to express the viral proteinase (PR) as part of thegagopen reading frame (ORF) while D-type retroviruses express PR in a separate ORF. Here we show that expression of the murine IAP element MIA14 yields three major translation products, corresponding to the Gag, Gag-PR, and Gag-PR-Pol polyproteins. Sequence analysis revealed that MIA14 PR is encoded in its own reading frame, separate fromgagandpol.Frameshifting occurred with an efficiency of approximately 25% between thegagandproORFs and 35% betweenproandpol.The region containing the putativegag-proframeshift signal consists of a heptanucleotide slippery sequence (A6C) and a stem–loop structure probably forming a pseudoknot. Deletion of this structure element almost completely abolished frameshifting. Insertion of an additional base next to the frameshift signal placedgagandproin the same ORF and resulted in predominant formation of Gag-PR and Gag-PR-Pol polyproteins which were not processed followingin vitrotranslation. Expression of a similar construct in tissue culture cells, on the other hand, led to efficient intracellular processing of the mutant polyproteins
A Single Sequence Change Destabilizes the Influenza Virus Neuraminidase Tetramer

AbstractA single change (E119G) in the influenza A virus N9 neuraminidase (NA) results in resistance of the enzyme to the NA inhibitor 4-Guanidino-Neu5Ac2en (4-GuDANA). This change causes a salt link between Glu119, which sits in a pocket in the bottom of the active site of the enzyme, and the 4-guanidinium moiety of the inhibitor to be lost. NA “heads” of the resistant enzyme produced only a few small crystals under conditions in which the wild-type enzyme readily formed large crystals. These small crystals were of sufficient quality to yield X-ray crystallographic data which confirmed the E119G change and demonstrated the presence of electron density representing either a strong structural–water molecule or an anionic species in place of the glutamate carboxylate. NA heads of the resistant enzyme also have greatly reduced NA activity per milligram of total protein. We have now found that the mutant NA heads consist predominantly of monomers with a few dimers and tetramers, as determined by electron microscopic analysis of the protein. The low level of enzymatic activity as well as the small number of crystals obtained were probably from the few tetramers remaining intact in the preparation. The purified wild-type and 4-GuDANA-resistant enzymes were treated with the homobifunctional NHS-ester cross linker, DTSSP. SDS–PAGE analysis of the treated enzymes clearly revealed cross-linked dimers of the wild-type enzyme. In contrast, only a small proportion of the 4-GuDANA-resistant neuraminidase was cross-linked. An examination of the known X-ray crystallographic structure of the wild-type NA reveals a salt bridge between Glu119 and Arg156 of the same monomer. Arg156 is a conserved amino acid that is situated at the interface between monomers, and a salt link between this amino acid and Glu119 may contribute to the stability of enzyme tetramers. It is suggested that the E119G alteration in the 4-GuDANA-resistant NA leads to the abrogation of this interaction and thus to the instability of the NA tetramers
The UL13 Protein Kinase and the Infected Cell Type Are Determinants of Posttranslational Modification of ICP0

AbstractThe herpes simplex virus infected-cell protein 0 (ICP0) acts as a promiscuous transactivator of genes introduced into eukaryotic cells by transfection or infection. The protein is highly posttranslationally modified by phosphorylation and nucleotidylylation. We have examined the electrophoretic mobility and phosphorylation of ICP0 in Vero and rabbit skin cells infected with wild-type virus or viruses from which the UL13 gene (ΔUL13) encoding a protein kinase or the α22/US1.5 genes (Δα22/ΔUS1.5) encoding putative transcriptional factors has been deleted. We report the following: (i) The accumulation of ICP0 and the electrophoretic mobility of ICP0 were dependent on the nature of the infected cell type and the presence of UL13. ICP0 encoded by wild-type virus accumulated to maximum levels earlier in infected Vero cells and its electrophoretic mobility was slower than that made in rabbit skin cells. In both Vero and rabbit skin cells infected with the ΔUL13 virus, the prevailing ICP0 form migrated faster than that accumulating in the corresponding cells infected with wild-type virus. (ii) The alteration in electrophoretic mobility of ICP0 made in cells infected with ΔUL13 virus was due to the absence of the UL13 protein and not to failure of posttranslational modification of Δα22/ΔUS1.5 proteins inasmuch as the mobility of ICP0 in cells infected with Δα22/ΔUS1.5 virus could not be differentiated from that of wild-type infected cells. (iii) ICP0 is extensively phosphorylated in infected cells even in the absence of UL13 protein. ICP0 is, however, a substrate for the UL13 kinase inasmuch as ICP0 was phosphorylated in mixtures of immune complexes of ICP0 and UL13. Complexes containing ICP0 only or infected cell lysate proteins reacting with preimmune serum from the rabbit immunized with UL13 protein failed to phosphorylate ICP0. (iv) In the absence of UL13, ICP22 is overproduced—an imbalance attributed to UL13. Thus, ICP22 regulates both the utilization of splice acceptor sites and the longevity of ICP0 mRNA (K. L. Carter and B. Roizman, 1996,Proc. Natl. Acad. Sci. USA93, 12535–12540); UL13 is involved in the posttranslational modification of ICP0 and is required for both posttranslational processing and control of abundance of ICP22
The HIV-1 Matrix Domain of Gag Is Required for Vpu Responsiveness during Particle Release

AbstractHIV-1 viral protein U (Vpu) facilitates virus particle release. To determine whether Gag is sufficient for generation of a target for Vpu-mediated particle release, we expressed HIV-1 Gag protein in the absence of the other viral genes. The resulting particles were still Vpu responsive. Mutational analysis of Gag indicated that the matrix domain (MA) is required for Vpu responsiveness. However, additional mutations in other domains of Gag, which affect the formation of stable virus particles, also abrogate Vpu responsiveness on total Gag release. Coexpression of the wild-typegaggene and agagmutant lacking the MA domain renders the MA−mutant Vpu responsive. This indicates that Gag molecules lacking MA are still incorporated into particles through association with wild-type Gag molecules and that the resulting composite particles are sufficient for Vpu-mediated exit
Petunia Vein-Clearing Virus: A Plant Pararetrovirus with the Core Sequences for an Integrase Function

AbstractPetunia vein-clearing virus (PVCV) is a plant pararetrovirus that has some features of retrotransposons. It encapsidates dsDNA and has isometric particles and inclusion bodies similar to those of caulimoviruses. The PVCV genome of 7205 bp has two large ORFs in the transcribed strand and a methionine tRNA primer-binding site in its 663-bp intergenic region. The N-terminal position of the large protein (126 kDa) encoded by ORF I has similarity to the movement protein of caulimoviruses. Toward the C-terminus of this same polyprotein are the two distinctive sequence elements [HHCC and DD(35)E] of the integrase function of retroviruses and retrotransposons. ORF II of PVCV encodes a protein of 125 kDa with domains for an RNA-binding element, common to thegaggene of retroelements, followed by consensus sequences for an acid protease, reverse transcriptase, and ribonuclease H. Hence, thegagequivalent (capsid protein) andpolgene of PVCV are part of the same polyprotein. Phylogenetic comparison of the reverse transcriptase of PVCV with that of various other retroelements grouped PVCV between caulimoviruses and the Ty3/gypsyretrotransposons, suggesting that PVCV is a divergent member of the caulimoviruses
The Structure and Coding Organization of the Genomic Termini of Kaposi's Sarcoma-Associated Herpesvirus (Human Herpesvirus 8)

AbstractKaposi's sarcoma-associated herpesvirus (KSHV) is a novel human herpesvirus closely linked to two AIDS-related neoplasms. We have prepared DNA from KSHV virions produced in cell culture and have examined the structure of the viral genomic termini. As in the related simian herpesvirus H. saimiri (HVS), the central unique region of KSHV DNA is bounded by tandemly repeated units of noncoding, GC-rich DNA. The KSHV repeats are 803 bp in length and are 85% G+C. Each molecule harbors 35–45 such repeats, but the repeats are not arrayed uniformly and symmetrically at each end. Rather, different molecules appear to contain different numbers of repeats at each end, with the sum total of repeated DNA per genome being relatively fixed, since the full genome is uniformly 165–170 kb. Thus, molecules with many repeats at one end will have fewer at the other. Because the unique viral genes bordering the left-hand repeats of the HVS genome play key roles in oncogenesis, we also examined the coding organization of the corresponding region of KSHV. No homologs of the HVS transforming genes were identified in this region of KSHV; rather, this region bears a novel gene encoding a putative transmembrane protein that appears to be upregulated during the early phase of lytic viral replication
Defects in Concatemer Processing of Bacteriophage T7 DNA Deleted in the M-Hairpin Region

AbstractThe intracellular replicating form of T7 DNA is a concatemer in which linear genomes are joined head to tail by sharing 160-bp terminally repeated sequences. A unique hairpin (M-hairpin) end generated on the left side of the TR was proposed to be responsible for the duplication of the concatemer junction for efficient packaging. We characterized the defects caused by loss of the M-hairpin by constructing a recombinant T7 (T7Δm) deleted in themregion. Initially, the intracellular growth rate of progeny phage was normal in T7Δminfection. However, the titer of progeny phage was eventually reduced by two- to threefold and lysis was significantly delayed. The restriction fragment, LEΔ160, generated simultaneously with the double-strand cleavage at the onset of packaging reaction was found more or less at the same intensity in both T7+and T7Δminfection at the beginning but preferentially in T7Δminfection during the later phase of infection. These observations suggest that the DNA packaging of T7 proceeds on the intact concatemer junctions during the early stage of infection while the duplication of the concatemer junction by the M-hairpin seemed to be important during the later phase, presumably due to reduced replication. While the generation of the M-hairpin involves DNA replication, the loss ofmdid not reduce DNA synthesis, suggesting that the role of the M-hairpin as an origin of replication is minimal
Rescue of a Viral Gene from VERO Cells Latently Infected with Influenza Virus B/Lee/40

AbstractBy growing VERO cells infected with 5 PFU/cell of influenza virus B/Lee/40, a latently infected culture was readily established (L/V cells). The cells continued to multiply stably, excreting a small amount of virus in the beginning, which sharply declined according to cell division to undetectable level by day 9. However, nucleotide sequences for all the 8 genes of B/Lee/40 as well as their mRNAs were amplified from L/V cells on day 50 or later by RT-PCR. Moreover, from the 95-day-old L/V cells, a persisting NP gene of B/Lee/40 was rescued into infectious virus particles upon superinfection with homotypic influenza virus B/Yamagata/1/73
Strain-Specific Expression of Spliced MMTV RNAs Containing thesuperantigenGene

AbstractThe transmission of milk-borne or exogenous mouse mammary tumor virus (MMTV) requires infection of B cells in the gut-associated lymphoid tissue and expression of the superantigen (Sag) protein at the B-cell surface. Presentation of Sag at the B-cell surface is required for the transmission of MMTV to T cells and subsequent infection of the target mammary gland tissue. Because several different promoters have been reported for MMTVsagmRNA expression, we investigated whether the detection of splicedsagRNAs was dependent upon the cell type infected or the particular MMTV strain examined. In this study, we detected expression of splicedsagRNA from the standard promoter and from an internal U3 promoter in B-cell lines expressing endogenousMtv-6by RT-PCR, although expression from the standard promoter appeared to be at least 10-fold higher than that observed from the internal U3 promoter.SagRNA originating from exogenous C3H MMTV was not observed from either of the U3 promoters in any cell type examined. However, spliced mRNAs containing the exogenous C3H MMTV, endogenousMtv-8,or endogenousMtv-17 saggenes could be detected from a previously described promoter in theenvelopecoding region regardless of the cell type infected. Becausesag-specific RNAs can be initiated independently of the LTR promoters, there may be selection for independent control of MMTVsagand structural gene expression
Human Immunodeficiency Virus Type-1 mRNA Splicing Pattern in Infected Persons Is Determined by the Proportion of Newly Infected Cells

AbstractPlasma viremia during HIV-1 infection is regulated by a dynamic balance between viral replication and removal of infected cells and cell-free virus. Administration of novel potent antiretroviral drugs provides an opportunity to study the consequences of perturbing this equilibrium by blockingde novoinfections. In this study, we examined the expression of differentially spliced forms of HIV-1 mRNA, unspliced (US) and multiply spliced (MS), in peripheral blood mononuclear cells (PBMCs) of patients treated with HIV protease inhibitors or combination therapy. In all nine patients studied, a significant reduction in the MS/US mRNA ratio was observed after 1 week of treatment, suggesting that the majority of HIV MS mRNA in the steady-state situation prior to therapy was expressed by cells which had been infected during the previous couple of days. This idea was supported by a detailed analysis of serial PBMC specimens collected from two of the patients during the first hours and days after initiation of therapy. In both cases, a substantial decrease in MS mRNA expression was evident already after 48 hr, whereas the expression of US mRNA at this time was virtually unaffected. These data indicate that the HIV mRNA splicing patternin vivois mainly determined by the relative proportion of newly infected cells and suggest that examination of this pattern could be useful in evaluating the potency of antiretroviral therapies and in studying dynamics of HIV-1 infection
Activation of the IFN-Inducible Enzyme RNase L Causes Apoptosis of Animal Cells

AbstractThe interferon (IFN)-induced enzyme RNase L produced by a recombinant vaccinia virus (VV) causes death of mammalian cells with morphological and biochemical characteristics of apoptosis. Coexpression of 2-5A-synthetase enhances apoptosis induced by RNase L. Activation of endogenous RNase L by infection with a VV ts mutant (ts22) or with wild-type virus in the presence of the antipoxvirus drug isatin-β-thiosemicarbazone, a treatment known to significantly increase the amount of double-stranded RNA late during infection, also causes pronounced apoptosis of infected cells. The effects observed with recombinant virus-derived RNase L or with the endogenous enzyme are specific, since apoptosis also occurs in cells derived from mice lacking the IFN-induced protein kinase (PKR). The apoptosis antagonist Bcl-2 prevents induction of cell death by RNase L activation. Apoptosis of mammalian cells by RNase L activation could be a mechanism mediating anticellular actions of IFN
Activation of Bcl-2 Expression in Human Endothelial Cells Chronically Expressing the Human T-Cell Lymphotropic Virus Type I

AbstractProgrammed cell death (PCD) characteristically involves chromatin condensation, membrane blebbing, and DNA oligonucleosomal fragmentation. These events, collectively referred to as apoptosis, represent an active cell suicide mechanism that eliminates cellular threats including potentially cancerous or virus-infected cells. Various types of programmed cell death can be blocked by the proto-oncogene Bcl-2. Levels of this protein are consistently low or undetectable in human endothelial cells (EC), which are important for immunoregulation through their interactions with circulating lymphocytes and are potential targets for infection by virus-bearing T-cells. Accumulating evidence suggests that EC may be infectedin vivoto play an important role in HTLV-I-associated neuromyelopathy. In the present study, we report the establishment and characterization of human endothelial cell lines stably transfected with an HTLV-I-derived molecular clone. We observed constitutive expression of HTLV-I genes coinciding with activated Bcl-2 expression. Transient transfection of EC with the viral transactivator Tax and a reporter construct Bcl-2 promoter-CAT did not result in a significant increase in CAT activity and suggests that, in EC, expression of a second viral protein might be required for Bcl-2 activation. Further, Tax-induced apoptosis in rat fibroblasts has been shown to be blocked by Bcl-2 expression. Thus, HTLV-I-mediated induction of Bcl-2 expression in EC may provide protection against viral-induced apoptosis or extend cellular survival and create a reservoir for viral gene expression
Maintenance of an Unusual Polypurine Tract in HIV-2: Stability to Passage in Culture

AbstractA stretch of purine residues, the polypurine tract (PPT), is found in all retroviruses and is used to initiate plus-strand DNA synthesis. While the PPT of most lentiviruses is a homogeneous sequence of purine residues, the PPT of some isolates of the human and simian immunodeficiency viruses is interrupted with a single pyrimidine residue. The ROD strain of human immunodeficiency virus type 2 (HIV-2) has such a pyrimidine-containing variant PPT. Virus generated from an infectious molecular clone, pROD10, was used to infect two CD4-positive T-cell lines, H9 and CEM. The sequence of the PPT was determined after two passages. From both cell lines, the variant PPT was retained, demonstrating that the presence of a pyrimidine in the PPT was fully functional and that there was no strong selection for an all-purine PPT
Completion of the Lassa Fever Virus Sequence and Identification of a RING Finger Open Reading Frame at the L RNA 5′ End

AbstractLassa (LAS) fever virus is a highly pathogenic arenavirus with large (L) and small (S) RNA genomic segments. The 5′ end of the LAS L segment is described here, thereby completing the sequence of the most virulent arenavirus analyzed to date. In keeping with the ambisense gene structure of the arenaviruses, the LAS L RNA encodes a 250-kDa protein and an 11-kDa protein in opposite senses with respect to each other. The 11-kDa protein, defined previously in arenaviruses lymphocytic choriomeningitis (LCM), Tacaribe (TAC), and Pichinde (PIC), contains a RING type of zinc-binding structure. Expression of the 11-kDa protein in LAS virus-infected cells has been confirmed by binding to peptide-specific antibody
Mutagenesis of a cAMP Response Element within the Latency-Associated Transcript Promoter of HSV-1 Reduces Adrenergic Reactivation

AbstractMutagenesis of a cyclic AMP response element (CRE) within the LAT promoter of HSV-1 reduces the ability of LAT expression to be induced in transient assays, but has only a minimal impact on reactivation of the virus inin vitrosystems. Here we show that a CRE mutation results in a significant reduction of adrenergically induced reactivationin vivoin the rabbit eye model. Spontaneous reactivation frequencies were also reduced. In addition, we demonstrate that this mutation has no effect on the amount of LAT expressed during latency when compared with the parent, 17syn+, and the rescuant. These results indicate a greater effect of CRE on induced reactivationin vivothan inin vitrosystems, but also suggest that the CRE in the LAT promoter is not autonomous in conducting the reactivation signal