pinecone/core-2020-05-10-deduplication huggingface dataset:
Genes and Regulatory Sites of the “Host-Takeover Module” in the Terminal Redundancy ofBacillus subtilisBacteriophage SPO1

AbstractEarly in infection ofBacillus subtilisby bacteriophage SPO1, the synthesis of most host-specific macromolecules is replaced by the corresponding phage-specific biosyntheses. It is believed that this subversion of the host biosynthetic machinery is accomplished primarily by a cluster of early genes in the SPO1 terminal redundancy. Here we analyze the nucleotide sequence of this 11.5-kb “host-takover module,” which appears to be designed for particularly efficient expression. Promoters, ribosome-binding sites, and codon usage statistics all show characteristics known to be associated with efficient function inB. subtilis.The promoters and ribosome-binding sites have additional conserved features which are not characteristic of their host counterparts and which may be important for competition with host genes for the cellular biosynthetic machinery. The module includes 24 genes, tightly packed into 12 operons driven by the previously identified early promoters PE1 to PE12. The genes are smaller than average, with half of them having fewer than 100 codons. Most of their inferred products show little similarity to known proteins, although zinc finger, trans-membrane, and RNA polymerase-binding domains were identified. Transcription–termination and RNase III cleavage sites were found at appropriate locations
Varicella-Zoster Virus ORF61 Deletion Mutants Replicate in Cell Culture, but a Mutant with Stop Codons in ORF61 Reverts to Wild-Type Virus

AbstractVaricella-zoster virus (VZV) ORF61 encodes a phosphoprotein that transactivates VZV promoters. Transfection of cells with cosmid DNAs, including a cosmid with a large deletion in ORF61, resulted in a VZV ORF61 deletion mutant that was impaired for growthin vitroand could be partially complemented by growth in neuroblastoma or osteosarcoma cell lines. Cells infected with the VZV ORF61 deletion mutant expressed normal levels of an immediate-early VZV protein, but had reduced levels of a late protein and showed abnormal syncytia. Carboxy terminal truncation mutants of VZV ORF61 protein have a transrepressing phenotype and inhibit the infectivity of cotransfected wild-type viral DNA. Transfection of cells with cosmid DNAs, including a cosmid with stop codons that should result in an ORF61 truncation mutant expressing a transrepressing protein that retains the RING finger domain, resulted in a viral genome which reverted back to the wild-type sequence. BAL-31 exonuclease was used to produce deletions at the site of the stop codons in ORF61 of the cosmid, resulting in loss of the RING finger domain. Transfection of tissue culture cells with the ORF61 BAL-31 deletion mutants and other cosmid DNAs yielded viable viruses. Thus, while deletion mutants lacking the RING finger domain of ORF61 replicate in cell culture, a mutant with stop codons that retains this domain could not be propagated and reverted to wild-type virus
Proteolytic Mapping of the Coronavirus Infectious Bronchitis Virus 1b Polyprotein: Evidence for the Presence of Four Cleavage Sites of the 3C-like Proteinase and Identification of Two Novel Cleavage Products

AbstractWe have previously reported that the 3C-like proteinase of the coronavirus infectious bronchitis virus (IBV) is responsible for processing of the 1a and 1a/1b polyproteins to three mature products of 24, 10, and 100 kDa (Liuet al.,1994, 1997; Ng and Liu, 1998). The C-terminal cleavage site of the 100-kDa protein was defined to be the Q891(1b)-S892(1b)dipeptide bond encoded by nucleotides 15,129 to 15,134 (Liu and Brown, 1995). In this report, other cleavage sites of the 3C-like proteinase in the polyprotein encoded by the ORF 1b region were mapped by coexpression, deletion, and site-directed mutagenesis studies. Using two ORF 1b-specific antisera, V58 and V17, three more Q-S(G) dipeptide bonds, encoded by nucleotides 16,929 to 16,934, 18,492 to 18,497, and 19,506 to 19,511, respectively, were demonstrated to be the cleavage sites of the 3C-like proteinase. Cleavage at these four positions would result in the release of four mature products with molecular masses of approximately 68, 58, 39, and 35 kDa. Among them, the 39- and 35-kDa proteins were specifically identified in IBV-infected cells. Taken together with the 100-kDa protein previously identified, these results suggest that the ORF 1b region of IBV mRNA1 may be able to encode five mature products
Monoclonal Antibody Mapping of the Envelope Glycoprotein of the Dengue 2 Virus, Jamaica

AbstractAlthough dengue (DEN) virus is the etiologic agent of dengue fever, the most prevalent vector-borne viral disease in the world, precise information on the antigenic structure of the dengue virion is limited. We have prepared a set of murine monoclonal antibodies (MAbs) specific for the envelope (E) glycoprotein of DEN 2 virus and used these antibodies in a comprehensive biological and biochemical analysis to identify 16 epitopes. Following domain nomenclature developed for the related flavivirus, tick-borne encephalitis, three functional domains were identified. Five epitopes associated with domain A were arranged in three spatially independent regions. These A-domain epitopes were destroyed by reduction, and antibodies reactive with these epitopes were able to block virus hemagglutination, neutralize virus infectivity, and block virus-mediated cell membrane fusion. Domain-A epitopes were present on the full-length E glycoprotein, a 45-kDa tryptic peptide representing its first 400 amino acids (aa) and a 22-kDa tryptic peptide representing at least aa 1–120. Four epitopes mapped into domain B, as determined by their partial resistance to reduction and the localization of these epitopes on a 9-kDa tryptic or chymotryptic peptide fragment (aa 300–400). One domain-B-reactive MAb was also capable of binding to a DEN 2 synthetic peptide corresponding to aa 333–351 of the E glycoprotein, confirming the location of this domain. Domain-B epitopes elicited MAbs that were potent neutralizers of virus infectivity and blocked hemagglutination, but they did not block virus-mediated cell-membrane fusion. Domains A and B were spatially associated. As with tick-borne encephalitis virus, determination of domain C was more problematic; however, at least four epitopes had biochemical characteristics consistent with C-domain epitopes
Mutations in the Exo III Motif of the Herpes Simplex Virus DNA Polymerase Gene Can Confer Altered Drug Sensitivities

AbstractTwo herpes simplex virus mutants containing mutated residues within the conserved Exo III motif of the polymerase gene were previously shown to be defective in 3′–5′ exonuclease activity and exhibited extremely high mutation frequencies. In this study, we have shown that these mutants also exhibited higher resistance to phosphonoacetic acid and sensitivity to aphidicolin and all nucleoside analogs tested, including acyclovir and gancicolvir, compared to wild-type virus. Marker transfer experiments and sequencing analyses demonstrated that these altered phenotypes were the result of mutations within the Exo III motif. The data indicate that, aside from leading to exonuclease deficiency, mutations in the Exo III motif may also affect interaction of nucleoside triphosphates with the catalytic sites of polymerase activity
Characterization of Human Monoclonal Antibodies Specific to the Hepatitis C Virus Glycoprotein E2 within VitroBinding Neutralization Properties

AbstractBoth linear and conformational determinants of hepatitis C virus (HCV) are believed to be involved in viral neutralization. After immortalization of B cells from HCV chronically infected patients with Epstein-Barr virus, we obtained two polyclonal lymphoblastoid cell lines (LCL) secreting human monoclonal antibodies (HMabs). One clone was derived from a patient infected with a genotype 4 isolate while the second was isolated from a genotype 1b-infected patient. Immunoprecipitation studies, Western blot, and immunofluorescence analysis, peptide scanning, and ELISA studies indicated that the HMabs (1) recognized conformation-dependent determinant(s), (2) were capable of recognizing genotype 1a and 1b derived antigens, and (3) were able to precipitate noncovalently associated E1E2 complexes believed to exist on the surface of virion particles. The HMab derived from the genotype 4-infected patient was in addition shown to neutralize thein vitrobinding of recombinant E2 protein onto susceptible cells suggesting a potential forin vivoneutralization. These data indicate that anti-E2 antibodies directed at conserved conformational-dependent determinant(s) exist in chronic HCV infection
The Polyvalent Staphylococcal Phage φ812:Its Host-Range Mutants and Related Phages

AbstractNinety-five percent of 782 culture collection strains, as well as hospital strains ofStaphylococcus aureussubsp.aureusof different provenance and 43% of 89 culture collection strains of different coagulase-negative species of the genusStaphylococcus,were found to be sensitive to the polyvalent phage φ812or to at least one of its host-range mutants or to the polyvalent phagesSK311, ϕ131,andU16.Thus sensitivity to the polyvalent staphylococcal phages seems to be one of the common features ofS. aureussubsp.aureusstrains. The adsorption kinetics and one-step growth characteristics of the phages φ812andSK311were estimated. Restriction genomic maps of the phages φ812(146.5 kb) andSK311(141.1 kb) were constructed by use of the restriction endonucleasesAvaII,PstI,KpnI,SacI,SmaI, andXhoI. The host-range mutations of the phage φ812were localized on this map. Comparison of restriction patterns of the phages φ812andSK311with those of the polyvalent phagesU16and ϕ131suggests that all these phages are closely related. Their genomes differ from each other mostly by some deletions, insertions (1–3 kb), or inversions. Evidence was given that the phage φ812together withSK311,ϕ131,andU16belongs in the phage species Twort, the description of which is substantially supplemented with the data on the phage φ812reported in this paper
Three Closely Related Herpesviruses Are Associated with Fibropapillomatosis in Marine Turtles

AbstractGreen turtle fibropapillomatosis is a neoplastic disease of increasingly significant threat to the survivability of this species. Degenerate PCR primers that target highly conserved regions of genes encoding herpesvirus DNA polymerases were used to amplify a DNA sequence from fibropapillomas and fibromas from Hawaiian and Florida green turtles. All of the tumors tested (n= 23) were found to harbor viral DNA, whereas no viral DNA was detected in skin biopsies from tumor-negative turtles. The tissue distribution of the green turtle herpesvirus appears to be generally limited to tumors where viral DNA was found to accumulate at approximately two to five copies per cell and is occasionally detected, only by PCR, in some tissues normally associated with tumor development. In addition, herpesviral DNA was detected in fibropapillomas from two loggerhead and four olive ridley turtles. Nucleotide sequencing of a 483-bp fragment of the turtle herpesvirus DNA polymerase gene determined that the Florida green turtle and loggerhead turtle sequences are identical and differ from the Hawaiian green turtle sequence by five nucleotide changes, which results in two amino acid substitutions. The olive ridley sequence differs from the Florida and Hawaiian green turtle sequences by 15 and 16 nucleotide changes, respectively, resulting in four amino acid substitutions, three of which are unique to the olive ridley sequence. Our data suggest that these closely related turtle herpesviruses are intimately involved in the genesis of fibropapillomatosis
Pleiotropic Effects of HIV-1 Protein R (Vpr) on Morphogenesis and Cell Survival in Fission Yeast and Antagonism by Pentoxifylline

AbstractExpression of HIV-1 Vpr causes cell cycle G2 arrest, changes in cell shape, and cell death over a large evolutionary distance ranging from human to yeast cells. As a step toward understanding these highly conserved Vpr functions, we have examined the effect of Vpr on cytoskeletal elements and the viability of fission yeast. We demonstrate that the changes in cell morphology induced by Vpr in fission yeast are caused by several underlying cellular abnormalities, including increased biosynthesis of chitin in the cell wall, disruption of the actin cytoskeleton, and altered polarity for cell growth. The extent of these cellular alterations and cell survival correlates with the level ofvprexpression. Accompanying cell death, Vpr induces aberrant nuclear morphologies in fission yeast which are similar to those found during the apoptosis induced by Vpr in mammalian cells. The Vpr-induced cytopathic effects and cell death can be suppressed by treatment with pentoxifylline, a compound that inhibits HIV-1 viral replication and suppresses Vpr-induced cell cycle G2 arrest in human and fission yeast cells. The results presented here suggest that pentoxifylline suppresses the effects of Vpr by blocking interactions of Vpr with cellular proteins. Given that pentoxifylline has potential therapeutic value in blocking the effects of Vpr in HIV-infected patients, understanding the molecular mechanisms by which pentoxifylline antagonizes Vpr may have general implications for HIV therapy
Evidence That the RNA Methylation and Poly(A) Polymerase Stimulatory Activities of Vaccinia Virus Protein VP39 Do Not Impinge upon One Another

AbstractVaccinia protein VP39 has two RNA modifying activities. In monomeric form, it acts as an mRNA cap-specific 2′-O-methyltransferase, specifically modifying the ribose moiety of the first transcribed nucleotide of m7G-capped mRNA. In association with VP55, the catalytic subunit of the vaccinia poly(A) polymerase, VP39 facilitates the rapid elongation of poly(A) tails that are already greater than ∼35 nt in length. Introducing new assays, we provide evidence that substrates for each of VP39's two activities do not detectably modulate the converse reaction and that VP39's 2′-O-methyltransferase activity is not significantly affected by its association with VP55. In an electrophoretic mobility shift assay, VP39 interacted with a short (5 nucleotide) RNA only when the latter was m7G-capped. Complexes with longer (22 nucleotide) RNAs were more stable (i.e., cap-independent) but were further stabilized by the presence of an m7G cap. An additional complex was observed at elevated RNA:protein molar ratios, indicating the presence of two RNA binding sites per VP39 molecule. Interaction at one of these sites was stabilized by the cap structure. Additional experiments indicated that RNA molecules undergoing poly(A) tail elongation by the VP55-VP39 heterodimer are not favored as cap-methylation substrates
A Baculovirus Mutant Defective in PKIP, a Protein Which Interacts with a Virus-Encoded Protein Kinase

AbstractWe have found that a temperature-sensitive mutant of the baculovirus AcMNPV, tsB97, is defective in PKIP, the product of ORF24 which was previously found to interact with and stimulate the activity of a virus-encoded protein kinase, PK-1. The mutant lacks the ability to form plaques and occlusion bodies at the nonpermissive temperature. The mutant displays several properties which suggest a defect in the latter half of the late phase of infection; these properties include a delay in the shutoff of host protein synthesis, the presence of aberrant electron-dense bodies associated with the virogenic stroma, and the production of few, if any, progeny budded virus. A study of the expression of selected late genes showed no difference in the timing or level of transcription or translation of most late genes. However, elevated levels of the late 6.9K protein, a protamine-like protein, were observed in mutant-infected cells at 24 h postinfection, suggesting a defect in the regulation of this protein. Two polypeptides, 40 and 6 kDa, exhibited considerably higher levels of steady-state phosphorylation in wt-infected cells versus tsB97-infected cells at 24 h p.i. and could be candidates for PK-1/PKIP-mediated phosphorylation. The tsB97 mutant also displayed a severe defect in very late gene transcription which accounts for its inability to form occlusion bodies. The effect of PKIP on very late gene transcription may be a secondary effect of the block in the late phase of infection. PKIP showed no ability to transactivate expression from a very late promoter in transient expression assays
Full Genome Sequences of Human Immunodeficiency Virus Type 1 Subtypes G and A/G Intersubtype Recombinants

AbstractMultiple genetic subtypes and intersubtype recombinant strains have been identified among isolates of HIV-1. Thegreatest diversity of strains has been recovered from Central Africa, where mixtures of subtypes and recombinant forms have been recovered. However, many of the HIV-1 subtypes and recombinants have been characterized by partial rather than full-length genome sequencing. Here we report the first two virtually full-length genome sequences from HIV-1 subtype G, isolated in Sweden and Finland but originating in Congo and Kenya, and from two Djibouti isolates sharing the A/G recombinant structure of Nigerian isolate, IbNG. By comparison with reference sequences of other subtypes, it appears that the subtype G strains are largely nonrecombinant, while the Djibouti strains show alternating segments from subtypes A and G. In the cytoplasmic domain of the gp41 protein of the Djibouti viruses the E, G, and IbNG strains form a single cluster, separate from subtype A, clouding the subtype origin of these particular segments. Within the resolution of current technology, the structure of the Djibouti strains is identical to that of IbNG, establishing for the first time the geographic spread of this recombinant in Africa. The geographic spread of the IbNG-like strains suggests that, like the subtype E recombinants, these should be given a specific name to facilitate future identification and tracking; the name “IbNG subtype” is proposed
The Acidic Domain of pUL37x1 and gpUL37 Plays a Key Role in Transactivation of HCMV DNA Replication Gene Promoter Constructions

AbstractTransient complementation of human cytomegalovirus (HCMV)oriLyt DNA replication in permissive human diploid cells expressing replication genes under native promoters requires its UL36-38 gene products. Two of the immediate early (IE) proteins encoded by this locus, pUL37x1 and, to a lesser extent, gpUL37, activated expression of HCMV early gene promoter constructions. The other IE protein encoded by the UL36-38 locus, pUL36, and the early product, pUL38, did not transactivate the HCMV early promoter constructions under similar conditions. The acidic domain, common to both pUL37x1 and gpUL37, is required for activation of HCMV early promoter constructions. Conversely, gpUL37 sequences downstream of amino acid 199 are not required for transactivation of viral early promoters. Taken together, these results suggest that the requirement for UL36-38 products for HCMV DNA replication results, at least in part, from the requirement of the transactivation of HCMV early DNA replication promoters by pUL37x1 and, to a lesser extent, by gpUL37 and that the acidic domain is critical for this activity
Recombinant Dengue Virus Type 1 NS3 Protein Exhibits Specific Viral RNA Binding and NTPase Activity Regulated by the NS5 Protein

AbstractThe full-length dengue virus NS3 protein has been successfully expressed as a 94-kDa GST fusion protein inEscherichia coli.Treatment of the purified fusion protein with thrombin released a 68-kDa protein which is the expected molecular mass for the DEN1 NS3 protein. The identity of this protein was confirmed by Western blotting using dengue virus antisera. Two related activities of the recombinant NS3 protein were characterized, which were the binding of the protein to the 3′-noncoding region of the dengue virus RNA genome and NTPase activity. We demonstrated using a band shift assay that the DEN1 NS3 protein could form a complex with the stem-loop structure in the 3′-noncoding region (3′-NCR), although sites outside the stem-loop may also participate in binding. Using various unlabeled homopolymeric and heteropolymeric RNAs as competitors for binding, it was further shown that the DEN1 NS3 protein exhibits preferential binding to a 94-nt RNA transcript from the 3′-NCR of the dengue virus. The NTPase activity of the recombinant DEN1 NS3 protein was characterized using a thin-layer chromatography assay. We found that the DEN1 NS3 protein possesses some aspects of NTPase activity, which are distinct from those found in other flaviviruses. Although the NS3 protein was able to utilize all four ribonucleoside triphosphates as its substrates, the NS3 protein showed a distinct preference for purine triphosphates (i.e., ATP and GTP). The addition of poly(U) did not stimulate NTPase activity in DEN1 NS3 protein, which contrasts with the reports for other flaviviral NS3 proteins. However, NTPase activity was specifically stimulated by the viral NS5 protein, which was manifested by a more than twofold increase in the rate of ATP hydrolysis and a 25% increase in the yield of ADP at the end of a 120-min reaction. These data suggest that the NTPase activity of the NS3 protein may be regulated by the viral NS5 protein during virus replication
Impaired Activation and Binding of the Erythropoietin Receptor by a Mutant gp55 of Friend Spleen Focus-Forming Virus, Which Has a Cytoplasmic Domain

AbstractA murine erythroleukemogenic retrovirus, Friend spleen focus-forming virus, encodes an envelope protein-like membrane glycoprotein (gp55) in its defectiveenvgene which is responsible for activation of the erythropoietin receptor (EpoR) and the abnormally rapid proliferation of erythroid precursor cells. The S34 mutant gp55, which possesses an additional cytoplasmic domain, is nonpathogenic and its processing to the cell surface is severely reduced compared to that of the wild-type gp55. In this study, we found that the S34 mutant gp55 neither binds to nor activates the EpoR. The S34 mutant gp55 formed disulfide-bonded homodimers in the rough endoplasmic reticulum (RER) membrane much less efficiently than the wild-type gp55, which is consistent with the proposal that homodimer formation is a prerequisite for gp55 to be exported from the RER. We found that the wild-type gp55 that is bound to EpoR in the RER consists of a large number of monomers and a small number of dimers, suggesting that monomers of the S34 mutant gp55 have lost the ability to bind to the EpoR. The 1-bp insertion present in the wild-type gp55 gene, causing a loss of the cytoplasmic domain, is essential for pathogenicity in that it renders the encoded protein capable of both binding to the EpoR and transport to the cell surface