pinecone/core-2020-05-10-deduplication huggingface dataset:
Gene 61.3 of Bacteriophage T4 Is the spackle Gene

AbstractThe bacteriophage T4 e gene encodes lysozyme (e-lysozyme), which releases progeny phage after normal infection of Escherichia coli cells. A mutation in the spackle gene suppresses the defect in e-lysozyme (Emrich, 1968). The spackle gene was mapped between genes 41 and 61, but its precise location has not previously been determined. In the current study, we constructed an amber mutant of gene 61.3, amST14, by site-directed mutagenesis. The gene 61.3 mutant shares phenotypes with spackle mutants: The amST14 mutant forms large plaques with sharp edges and exhibits truncated lysis inhibition, and furthermore, the mutation can suppress the defect in e-lysozyme activity. In addition, cloned gene 61.3 can rescue (by homologous recombination) as well as complement the S12 mutation in the spackle gene. These results strongly suggest that gene 61.3 is the spackle gene. Indeed, the S12 mutant has one base deletion of five in a consecutive A tract in the gene 61.3 coding region, substituting an unrelated 6-amino acid sequence for the 9 C-terminal amino acids in the gene 61.3 protein. The gene 61.3 protein is predicted to localize in the periplasmic space after cleavage of a signal sequence
Comparative Sequence Analysis of the DNA Packaging, Head, and Tail Morphogenesis Modules in the Temperate cos-Site Streptococcus thermophilus Bacteriophage Sfi21

AbstractThe temperate Streptococcus thermophilus bacteriophage Sfi21 possesses 15-nucleotide-long cohesive ends with a 3′ overhang that reconstitutes a cos-site with twofold hyphenated rotational symmetry. Over the DNA packaging, head and tail morphogenesis modules, the Sfi21 sequence predicts a gene map that is strikingly similar to that of lambdoid coliphages in the absence of any sequence similarity. A nearly one to one gene correlation was found with the phage lambda genes Nu1 to H, except for gene B-to-E complex, where the Sfi21 map resembled that of coliphage HK97. The similarity between Sfi21 and HK97 was striking: both major head proteins showed an N-terminal coiled-coil structure, the mature major head proteins started at amino acid positions 105 and 104, respectively, and both major head genes were preceded by genes encoding a possible protease and portal protein. The purported Sfi21 protease is the first viral member of the ClpP protease family. The prediction of Sfi21 gene functions by reference to the gene map of intensively investigated coliphages was experimentally confirmed for the major head and tail gene. Phage Sfi21 shows nucleotide sequence similarity with Lactococcus phage BK5-T and a lactococcal prophage and amino acid sequence similarity with the Lactobacillus phage A2 and the Staphylococcus phage PVL. PVL is a missing link that connects the portal proteins from Sfi21 and HK97 with respect to sequence similarity. These observations and database searches, which demonstrate sequence similarity between proteins of phage from gram-positive bacteria, proteobacteria, and Archaea, constrain models of phage evolution
The Feline Immunodeficiency Virus vif Gene Is Required for Productive Infection of Feline Peripheral Blood Mononuclear Cells and Monocyte-Derived Macrophages

AbstractThe role of the feline immunodeficiency virus (FIV) vif gene in establishing productive infection in feline peripheral blood mononuclear cells (PBMCs) and monocyte-derived macrophages (MDMs) was examined in cell culture systems. A 375-bp deletion was introduced into the vif gene of the wild-type FIV-pPPR infectious molecular clone to produce Vif deletion mutant FIV-pPPRΔvif. This mutant FIV proviral construct expressed FIV proteins p24gag and gp100env in transfected Crandell feline kidney cells as measured by immunoprecipitation and Western blot analysis as well as immunocytochemical analysis; these cultures produced very low levels of virus by cocultivation of transfected cells with PBMCs and K-258 cells, as measured by production of p24gag. Replication kinetics of wild-type and vif-deleted virus were compared in PBMCs and monocyte-derived macrophages (MDMs) by infection with cell-free virus preparations. Similar to findings with other lentiviruses, the vif gene was found to be essential for establishment of productive FIV infection in both PBMCs and MDMs. This study indicates that vif is essential for productive FIV infection of host target cells in vitro and that FIV-pPPRΔvif may be an excellent candidate viral mutant for attenuated virus vaccine studies
Extensive Sequence Divergence and Phylogenetic Relationships between the Fusogenic and Nonfusogenic Orthoreoviruses: A Species Proposal

AbstractThe orthoreoviruses can be divided into subgroups based on either their restricted host range or the unusual ability of certain members of this group of nonenveloped viruses to induce cell–cell fusion from within. Phylogenetic relationships cannot be inferred based on these biological properties because fusogenic reoviruses are present in both the avian and mammalian subgroups. To address this issue, the complete nucleotide sequences of the three S-class genome segments encoding the major ς-class core, outer capsid, and nonstructural proteins of four fusogenic reoviruses were determined and used to establish the phylogeny of the orthoreoviruses. The viruses analysed included two strains of avian reovirus and the only known fusogenic mammalian reoviruses, Nelson Bay virus and baboon reovirus. Comparative sequence analysis of these fusogenic reoviruses and the prototypical nonfusogenic mammalian reoviruses indicated a highly diverged genus with both conserved and unique sequence-predicted structural motifs in the major ς-class proteins. Phylogenetic analysis provided the basis for the first taxonomic subdivision of the orthoreoviruses into species classes based on inferred evolutionary relationships. It is proposed that the orthoreoviruses consist of at least four species that separate into three clades. The nonfusogenic mammalian reovirus species represent a single clade, and the fusogenic reoviruses separate into two distinct clades. The first clade of fusogenic reoviruses contains the avian reovirus- and Nelson Bay virus-type species, with the second clade being occupied by the single baboon reovirus isolate that represents a fourth orthoreovirus species
Virus-Specific Lymphokine Production Differs Quantitatively but Not Qualitatively in Acute and Chronic Hepatitis B Infection

AbstractCytokines that are secreted as a response to viral antigen not only have direct antiviral properties but also crucially influence immune reactions determining the outcome of infection. As an advantageous alternative to the study of cytokines present in the supernatants of antigen-specific T cell clones and lines, we have used ELISPOT assays to determine the number of interferon-γ (IFN-γ)- and IL4-producing cells generated by peripheral blood mononuclear cells from patients with acute hepatitis B (AHB) and chronic hepatitis B (CHB) infection in response to HBcAg in a short-term culture (48 h). In response to HBcAg IFN-γ was predominantly produced. In contrast to the results obtained in acute hepatitis B, the typical lymphokine pattern in CHB was characterized by a weak or absent antigen-specific IFN-γ production. A predominance of IL-4-producing cells was not observed in either AHB or CHB. A significant number of IFN-γ-producing cells was usually detectable during phases of viral elimination and the quality of the lymphokine response seemed to be epitope independent. Comparison of the results obtained in proliferation assays and ELISPOT assays clearly shows that lymphokine production upon stimulation with viral protein is totally independent of T cell proliferation and more sensitively reflects antiviral reactivity
Type I Interferons and IRF-1 Play a Critical Role in the Control of a Gammaherpesvirus Infection

AbstractThe murine gammaherpesvirus 68 (MHV-68) is an ideal model system for the study of interactions between gammaherpesviruses and their hosts. Intranasal infection of mice with MHV-68 results in replication of the virus in the lung epithelium followed by latent infection of B cells. Resolution of productive MHV-68 infection depends on the adaptive immune system, but little is known about the role of innate immune mechanisms and the early interaction between the host and the virus. In this report, we have used mice that are deficient in components of the early defence system, the common type I interferon (IFN) receptor (IFN R), the transcriptional activator IRF-1, and the inducible nitric oxide synthase, to investigate the contribution of these mechanisms to control of MHV-68 infection. We show that while wild-type mice are highly resistant to infection with MHV-68, mice unresponsive to type I IFNs (IFN-α/β R−/− ) are highly susceptible to the virus. At high multiplicities of infection (m.o.i.; 4 × 106 PFU), 80–90% of IFN-α/β R−/− mice succumb to infection, and at low m.o.i. (4 × 103 PFU), 50% mortality rates occur. Both high and low doses of virus lead to 100- to 1000-fold higher lung virus titres in IFN-α/β R−/− mice than are found in wild-type mice and result in systemic dissemination of the virus. Latently infected cells are detectable in the spleens of IFN-α/β R−/− mice earlier than in wild-type mice, and the numbers of latently infected cells are 10-fold higher in the IFN-α/β R−/− mice during the acute phase of infection. We find IRF-1 has a critical role in protection from fatal disease, whereas inducible nitric oxide synthase does not appear to be important. The results indicate that innate immune mechanisms are critical for the early control of MHV-68 and may play a role in the establishment of latency
Respiratory Syncytial Virus Strain A2 Is Resistant to the Antiviral Effects of Type I Interferons and Human MxA

AbstractRespiratory syncytial virus (RSV) belongs to Paramyxoviridae family of enveloped negative-strand RNA viruses and causes severe bronchiolitis and pneumonia in children younger than 2 years of age. As members of Paramyxoviridae family, RSV and parainfluenza type 3 (PIV3) have similar modes of infection and replication. A variety of negative-strand RNA virus infections, including that of PIV3, are inhibited by human MxA protein, a type I interferon (IFN)-inducible GTPase. We tested whether the MxA protein, induced either by type I human IFNs or by stable transfection of human MxA gene in human (U-87) or simian (Vero) cells, confers resistance to these cells against infection by RSV strain A2. RSV infection was resistant to antiviral effects induced by 0–10,000 U/ml type I IFNs (IFN-α or -β) in both human lung epithelial, A549, and fibroblast, MRC-5 cells. RSV virus yield was reduced only by 10- to 20-fold, and viral protein synthesis was not significantly affected under conditions of IFN treatment where PIV3 yield was reduced by 1000- to 10,000-fold. Human or simian cell lines constitutively expressing MxA were protected against infection by PIV3 but not by RSV. Our results indicate that RSV A2 is resistant to the antiviral effects of MxA, even though RSV and PIV3 have similar replication strategies. In IFN-treated coinfected cultures, IFN-resistant RSV A2 did not prevent the IFN-mediated inhibition of PIV3 multiplication. Hence the resistance of RSV A2 to type I IFNs does not appear to be due to soluble factors released into the medium or a disruption in the cellular antiviral machinery brought about by RSV A2 infection
The Complete Genome Sequence of PM2, the First Lipid-Containing Bacterial Virus To Be Isolated

AbstractBacteriophage PM2 was isolated from the Pacific Ocean off the coast of Chile in the late 1960s. It was a new virus type, later classified as Corticoviridae, and also the first bacterial virus for which it was demonstrated that lipids are part of the virion structure. Here we report the determination and analysis of the 10,079-bp circular dsDNA genome sequence. Noteworthy discoveries are the replication initiation system, which is related to the rolling circle mechanism described for phages such as φX174 and P2, and a 1.2-kb sequence that is similar to the maintenance region of a plasmid found in a marine Pseudoalteromonas sp. strain A28
Purification and Protein Composition of PM2, the First Lipid-Containing Bacterial Virus To Be Isolated

AbstractThe marine, icosahedral bacteriophage PM2 was isolated in the late 1960s. It was the first phage for which lipids were firmly demonstrated to be part of the virion structure and it has been classified as the type organism of the Corticoviridae family. The host, Pseudoalteromonas espejiana BAL-31, belongs to a common group of marine bacteria. We developed a purification method producing virions with specific infectivity approximately as high as that of the lipid-containing phages PRD1 and φ6. The sensitivity of the virus to normally used purification media such as those containing sucrose is demonstrated. We also present an alternative host, a pseudoalteromonad, that allows enhanced purification of the virus under reduced salt conditions. We show, using N-terminal amino acid sequencing and comparison with the genomic sequence, that there are at least eight structural proteins in the infectious virus
Endosomal/Lysosomal Retention and Degradation of Major Histocompatibility Complex Class I Molecules Is Induced by Myxoma Virus

AbstractThe highly immunosuppressive leporipoxvirus myxoma, previously was shown to promote the loss of cell surface class I major histocompatibility complex (MHC I) molecules. Here, we show that myxoma virus induces the loss of both cell surface and intracellular post-Golgi, β2-microglobulin-associated MHC I. Myxoma-induced loss of these MHC I molecules is abrogated by vacuolar ATPase inhibitors, NH4Cl, and leupeptin. Furthermore, immunofluorescence microscopic studies reveal that in myxoma-infected cells, β2-microglobulin-associated MHC I accumulates in Lamp-1+ vesicular structures, suggesting that myxoma virus targets MHC I for degradation in late endosomes and/or lysosomes. These events are regulated by early gene product or products because they occur unabated in cells infected with myxoma virus in the presence of cytosine arabinoside, an inhibitor of DNA synthesis. Studies with baby green monkey kidney cells transfected with wild-type and tail-less forms of a mouse MHC I molecule, H-2Ld, indicate that the MHC I cytoplasmic tail is required for myxoma-induced localization in Lamp-1+ organelles. Myxoma-induced endocytosis and degradation of MHC I may provide the virus with a means of dispensing with cell surface MHC I molecules that were loaded with peptides derived from viral proteins synthesized early in infection
Acidic pH Enhancement of the Fusion of Newcastle Disease Virus with Cultured Cells

AbstractFusion of the lentogenic strain “Clone 30” of Newcastle disease virus (NDV) with the cell line COS-7 has been studied. Fusion was monitored using the octadecylrhodamine B chloride dequenching assay [Hoekstra, D., de Boer, T., Klappe, K. and Wilschut, J. (1984). Biochemistry 23, 5675–5681]. In the present work, fusion of NDV with COS-7 cells was found to occur in a time- and temperature-dependent fashion. Significant dequenching of the probe occurred at temperatures higher than 28°C. A 20-fold excess of unlabeled virus inhibited fusion by about 53% compared with the control, whereas 62% inhibition of fusion was obtained after digestion of viral glycoproteins with trypsin. The data are discussed in terms of the nonfusion transfer of the probe. In addition, preincubation of cells with 50 mM ammonium chloride or 0.1% sodium azide prevented NDV from fusing with COS-7 cells by about 30% in comparison with the control. The cytopathic effect of NDV infection in cell culture in the presence of ammonium chloride was reduced compared with control. Moreover, viral preincubation at pH 5 yielded a mild inhibition of fusogenic activity. Our results suggest that NDV may use the endocytic pathway as a complementary way of entering cells by direct fusion with the plasma membrane
Phosphorylation of Tobacco Mosaic Virus Movement Protein Abolishes Its Translation Repressing Ability

AbstractPreviously we showed that the ribonucleoprotein complexes (RNPs) of the TMV 30-kDa movement protein (MP) with TMV RNA are nontranslatable in vitro and noninfectious to protoplasts, but are infectious to intact plants. It has been suggested that MP–TMV RNA complexes could be converted into the translatable and replicatable form in planta in the course of passage through plasmodesmata (Karpova et al., 1997, Virology 230, 11–21). The role of TMV MP phosphorylation was investigated in terms of its capacity to modulate the translation-repressing ability of the MP. Phosphorylation of the TMV MP, either before or after RNP complex formation, caused a conversion of nontranslatable MP–RNA complexes into a form that was translatable in vitro and infectious to protoplasts and plants
Restoration of a Stem-Loop Structure Required for Potato Virus X RNA Accumulation Indicates Selection for a Mismatch and a GNRA Tetraloop

AbstractThe 5′ region of potato virus X (PVX) RNA contains a stem-loop structure, stem-loop 1 (SL1), that is required for efficient plus-strand RNA accumulation. To determine how changes to individual elements in SL1 are accommodated by the virus, we inoculated PVX transcripts containing modifications in the terminal tetraloop (TL), stem C (SC), and stem D (SD) regions ontoNicotiana benthamianaplants and analyzed progeny RNAs over a series of passages. Several progeny RNAs isolated from plants inoculated with the TL mutants containing changes to the first nucleotide of the GAAA motif or deletion of the entire TL sequence were found to contain multiple A insertions within the terminal loop region. The wild-type TL motif, GAAA, was recovered for all TL mutants by the second passage, suggesting that the sequence and potential structure of this element are crucial for PVX infection. Revertant RNAs isolated from plants inoculated with mutants in SD and the central region of SC indicated that increased stem length is tolerated. Restoration of SD length to the 4 bp typical of the wild-type PVX RNA was accompanied by A insertion into loop C. Mutants with a conversion of the C55–C78 mismatch to a G–C pair, relocation of this mismatch within the central region of SC, or deletion of C55–C78 were unable to infect protoplasts and plants. In contrast, the mutant with a conversion of the C55–C78 mismatch to an A–C mismatch, which exhibited low levels of PVX plus-strand RNA in protoplasts, was able to infect plants and quickly reverted to the wild-type C–C mismatch. These data indicate that important sequence and secondary structural elements within SL1 are required for efficient viral infection and that multiple A insertions within the TL and loop C regions, potentially by polymerase stuttering, accompany restoration of SL1 structure
A New Avian Hepadnavirus Infecting Snow Geese (Anser caerulescens) Produces a Significant Fraction of Virions Containing Single-Stranded DNA

AbstractWe describe the identification and functional analysis of an evolutionary distinct new avian hepadnavirus. Infection of snow geese (Anser caerulescens) with a duck hepatitis B virus (DHBV)-related virus, designated SGHBV, was demonstrated by detection of envelope proteins in sera with anti-DHBV preS and S antibodies. Comparative sequence analysis of the PCR-amplified SGHBV genomes revealed unique SGHBV sequence features compared with other avian hepadnaviruses. Unlike DHBV, SGHBV shows an open reading frame in an analogous position to orthohepadnavirus X genes. Four of five cloned genomes were competent in replication, gene expression, and virus particle secretion in chicken hepatoma cells. Primary duck hepatocytes were permissive for infection with SGHBV, suggesting a similar or identical host range. SGHBV was found to secrete a significant fraction of virion-like particles containing single-stranded viral DNA. This was observed both in cell culture medium of SGHBV DNA-transfected LMH cells and in viremic sera of several birds, suggesting that it is a stable trait of SGHBV. Taken together, SGHBV has several unique features that expand the knowledge of the functional and evolutionary diversity of hepadnaviruses and offers new experimental opportunities for studies on the life cycle of hepadnaviruses
High Levels of IL-4 and IL-10 mRNA and Low Levels of IL-2, IL-9 and IFN-γ mRNA in MuLV-Induced Lymphomas

AbstractThe expression of cytokines may influence the development of lymphoma in retrovirally infected animals in at least two ways: (1) cytokines in the tumor environment may stimulate the proliferation of tumor cells and/or (2) cytokines in the tumor environment may diminish the cell-mediated antitumor immune response. To evaluate these possibilities, a semiquantitative RT–PCR approach was utilized to permit a broad screening of cytokine mRNAs in a large number of tissue samples. Examination of MuLV-induced end-stage lymphomas revealed the absence of mRNA for cytokines known to stimulate the proliferation of T cells (i.e., IL-2, IL-9), the absence of mRNA for cytokines known to enhance cell-mediated antitumor immune responses (i.e., IL-2, IFNγ), and the presence of mRNA for cytokines known to diminish such responses (i.e., IL-4, IL-10). Similar patterns of cytokine mRNA expression were detected in tumor-derived cell lines. Spleen and thymus from animals collected longitudinally during infection and from age-matched uninfected mice also demonstrated a similar pattern, except that IFNγ mRNA was readily detectable. These findings do not support the hypothesis that the developing tumor depends on cytokines to provide proliferative signals. The findings suggest that cytokines in the immediate environment of the lymphoma support tumor development by acting to diminish an effective antitumor immune response
Truncation of the Human Immunodeficiency Virus-Type-2 Envelope Glycoprotein Allows Efficient Pseudotyping of Murine Leukemia Virus Retroviral Vector Particles

AbstractThe incorporation of human immunodeficiency virus-type-2 (HIV-2) envelope glycoprotein into murine leukemia virus (MuLV) particles was studied in a transient transfection packaging cell system. We observed that wild-type HIV-2 envelope protein or a frameshift mutant with 187 unrelated carboxyl-terminal residues did not allow the formation of infectious retroviral particles. In view of recent findings that an HIV-1 envelope protein variant with a shortened cytoplasmic domain was incorporated into MuLV particles, we constructed carboxyl-terminal truncations of the HIV-2 envelope protein. An envelope variant with 18 cytoplasmic amino acids formed only very few viral pseudotypes. The further removal of an additional 11 amino acids allowed the efficient pseudotyping of MuLV particles. As with the HIV-1 envelope protein, an HIV-2 envelope variant with 7 cytoplasmic amino acids was incorporated into functional MuLV particles. The pseudotyped vectors obtained are able to infect human CD4/CXCR4-expressing cells. Cell lines expressing human CD4 and other coreceptors could not be infected. This retroviral vector will prove useful for the study of HIV infection events mediated by the HIV-2 envelope glycoproteins, as well as for the targeting of CD4+ cells in the context of gene therapy of AIDS