pinecone/core-2020-05-10-deduplication huggingface dataset:
The CD4-Mediated Immune Response Is Critical in Determining the Outcome of Infection Using Theiler's Viruses with VP1 Capsid Protein Point Mutations

AbstractDaniel's strain of Theiler's virus (DA) induces a chronic demyelinating disease in the central nervous system (CNS) of susceptible SJL mice, which serves as an excellent model of multiple sclerosis. We previously demonstrated that point mutations near a putative virus receptor-binding site [VP1 99 (Gly to Ser) or 100 (Gly to Asp)] totally attenuate the ability of DA to persist and induce demyelination in SJL mice. The current studies demonstrate that class II-restricted CD4+ T cells play a major role in clearing VP1 mutant DA viruses from the CNS to prevent demyelination. Infection of SJL CD4(−/−) mice with DA-VP1-99(Ser) or DA-VP1-100(Asp) resulted in virus persistence and prominent demyelination in the spinal cord. In contrast, infection of SJL CD8(−/−) mice with DA-VP1-99(Ser) or DA-VP1-100 did not result in virus persistence or demyelination. In addition, no virus-specific cytotoxicity was observed in CNS-infiltrating lymphocytes following infection of SJL mice with VP1 mutant viruses. The mutant DA-VP1-99(Ser) and DA-VP1(100) viruses were in fact neurovirulent when compared to the wild-type DA virus, as they induced an overwhelming encephalitis and early lethality (2 to 4 days postinfection) in mice deficient in the IFN-α/β receptor. Therefore, the nondemyelinating phenotype observed with DA-VP1-99(Ser) and DA-VP1-100(Asp) viruses is dependent in part on the CD4-mediated host immune response
Spacing Constraints on Reinitiation of Paramyxovirus Transcription: The Gene End U Tract Acts as a Spacer to Separate Gene End from Gene Start Sites

AbstractThe paramyxovirus gene end U tracts are thought to serve as templates for the addition of a 3′ polyA tail to viral mRNAs. The goal of the work described here was to determine the function in transcription of the naturally occurring variability in length of the gene end U tracts of the paramyxovirus simian virus 5 (SV5). An anchored RT–PCR assay was developed to test the hypothesis that the variable U tracts template the addition of variable lengths of polyA tails to mRNAs. The results showed that although the SV5 NP, M, and SH genes encode U tracts of seven, four, and six U residues, respectively, their mRNAs contain similar polyA tails of ∼250–290 bases. These results indicate that the variable gene end U tracts are functionally equivalent in directing polyadenylation. A reverse genetics system based on a dicistronic minigenome containing the SH–HN gene junction was used to test the hypothesis that the variable U tracks affect the efficiency of transcription termination. Minigenome templates containing an SH gene end with a long U tract of six residues (U6) directed efficient transcription termination and reinitiation at the downstream HN start site with no nucleotide preference for the downstream intergenic region. Surprisingly, truncating the SH gene end U tract to four residues (U4) did not affect SH termination but, rather, reduced downstream HN reinitiation to 20–30% of wild-type levels. Efficient HN reinitiation could be restored to mutant U4 templates in either of two ways: by increasing the U-tract length from four to six residues or by increasing the length of the intergenic region. Efficient HN reinitiation required a minimum of six bases between the last nucleotide in SH and the first nucleotide in HN. We propose that for some paramyxoviruses, the gene end U tract serves a previously unrecognized role as a spacer region between the gene end and gene start sites
Mutational Analysis of Two Structural Genes of the Temperate Lactococcal Bacteriophage TP901-1 Involved in Tail Length Determination and Baseplate Assembly

AbstractTwo putative structural genes, orf tmp (tape measure protein) and orf bpp (baseplate protein), of the temperate lactococcal phage TP901-1 were examined by introduction of specific mutations in the prophage strain Lactococcus lactic ssp. cremoris 901-1. The adsorption efficiencies of the mutated phages to the indicator strain L. lactic ssp. cremoris 3107 were determined and electron micrographs were obtained. Specific mutations in orf tmp resulted in the production of mostly phage head structures without tails and a few wild-type looking phages. Furthermore, construction of an inframe deletion or duplication of 29% in orf tmp was shown to shorten or lengthen the phage tail by approximately 30%, respectively. The orf tmp is proposed to function as a tape measure protein, TMP, important for assembly of the TP901-1 phage tail and involved in tail length determination. Specific mutations in orf bpp produced phages which were unable to adsorb to the indicator strain and electron microscopy revealed particles lacking the baseplate structure. The orf bpp is proposed to encode a highly immunogenic structural baseplate protein, BPP, important for assembly of the baseplate. Finally, an assembly pathway of the TP901-1 tail and baseplate structure is presented
Comparative Genomics of the Late Gene Cluster from Lactobacillus Phages

AbstractThree prophage sequences were identified in the Lactobacillus johnsoni strain NCC533. Prophage Lj965 predicted a gene map very similar to those of pac-site Streptococcus thermophilus phages over its DNA packaging and head and tail morphogenesis modules. Sequence similarity linked the putative DNA packaging and head morphogenesis genes at the protein level. Prophage Lj965/S. thermophilus phage Sfi11/Lactococcus lactis phage TP901-1 on one hand and Lactobacillus delbrueckii phage LL-H/Lactobacillus plantarum phage phig1e/Listeria monocytogenes phage A118 on the other hand defined two sublines of structural gene clusters in pac-site Siphoviridae from low-GC Gram-positive bacteria. Bacillus subtilis phage SPP1 linked both sublines. The putative major head and tail proteins from Lj965 shared weak sequence similarity with phages from Gram-negative bacteria. A clearly independent line of structural genes in Siphoviridae from low-GC Gram-positive bacteria is defined by temperate cos-site phages including Lactobacillus gasseri phage adh, which also shared sequence similarity with phage D3 infecting a Gram-negative bacterium. A phylogenetic tree analysis demonstrated that the ClpP-like protein identified in four cos-site Siphoviridae from Lactobacillus, Lactococcus, Streptococcus, and Pseudomonas showed graded sequence relationships. The tree suggested that the ClpP-like proteins from the phages were not acquired by horizontal gene transfer from their corresponding bacterial hosts
Broad-Range Bacteriophage Resistance in Streptococcus thermophilus by Insertional Mutagenesis

AbstractStreptococcus thermophilus is a lactic acid bacterium used in industrial milk fermentation. To obtain phage-resistant starters, S. thermophilus strain Sfi1 was submitted to mutagenesis with the thermolabile insertional vector pG+host9:ISS1 followed by a challenge with the lytic S. thermophilus phage Sfi19. Vector insertions into four distinct sites led to a phage-resistance phenotype. Three mutants were characterized further. They were protected against the homologous challenging phage and 14 heterologous phages. All three mutants adsorbed phages. No intracellular phage DNA synthesis was observed in mutants R7 and R71, while mutant R24 showed a delayed and diminished phage DNA synthesis compared to the parental Sfi1 strain. In mutant R7 a short deletion occurred next to the insertion site which removed the upstream sequences and the 15 initial codons from orf 394, encoding a likely transmembrane protein. Analogy with other phage systems suggests an involvement of this protein in the phage DNA injection process. In mutant R24 the vector was inserted into orf 269 predicting an oxido-reductase. When the vector sequence was removed via homologous recombination across the duplicated insertion elements, mutant R24 returned to the phage susceptibility of the parental strain. This observation suggested that inactivation of orf 269 was not crucial for the resistance phenotype. A gene encoding a likely restriction subunit of a type I restriction-modification system was located directly downstream of the insertion site in mutant R24. hsdM and hsdS genes encoding the modification and specificity subunits of a type I R-M system and biological evidence for an active R-M system were detected in strain Sfi1, suggesting involvement of a type I R-M system in the resistance phenotype of R24
Characterization of a β-1,3-Glucanase Encoded by Chlorella Virus PBCV-1

AbstractSequence analysis of the 330-kb chlorella virus PBCV-1 genome revealed an open-reading frame, A94L, that encodes a protein with significant amino acid identity to Glycoside Hydrolase Family 16 β-1,3-glucanases. The a94l gene was cloned and the protein was expressed as a GST-A94L fusion protein in Escherichia coli. The recombinant A94L protein hydrolyzed the β-1,3-glucose polymer laminarin and had slightly less hydrolytic activity on β-1,3-1,4-glucose polymers, lichenan and barley β-glucan. The recombinant enzyme had the highest activity at 65°C and pH 8. We predicted that the a94l-encoded β-1,3-glucanase is involved in degrading the host cell wall either during virus release and/or is packaged in the virion particle and involved in virus entry. Therefore, we expected a94l to be expressed late in virus infection. However, contrary to expectations, both the a94l mRNA and the A94L protein appeared 15 min after PBCV-1 infection and disappeared 60- and 120-min p.i. postinfection, respectively, indicating that a94l is an early gene. Twenty-seven of 42 chlorella viruses contained the a94l gene. To our knowledge, this is the first report of a virus-encoded β-1,3-glucanase
Characterization of Φ13, a Bacteriophage Related to Φ6 and Containing Three dsRNA Genomic Segments

AbstractThe three dsRNA genomic segments of bacteriophage Φ13 were copied as cDNA and the nucleotide sequences were determined. The organization of the genome is similar to that of Φ6, and there is significant similarity in the amino acid sequences of the proteins of the polymerase complex and one of the membrane proteins, P6. There is little or no similarity in the nucleotide sequences. Several features of the viral proteins differ markedly from those of Φ6. Although both phages are covered by a lipid-containing membrane, the protein compositions are different. The host attachment protein consists of two peptides rather than one and the phage attaches directly to the LPS of the host rather than to a Type IV pilus. Despite the differences in the structure of the membranes, the two viruses can successfully exchange the genes for host attachment proteins and thereby change their host specificities
Approximately 150 Nucleotides from the 5′ End of an Influenza A Segment 1 Defective Virion RNA Are Needed for Genome Stability during Passage of Defective Virus in Infected Cells

AbstractDefective influenza A virus RNAs analyzed in two studies so far possess at least 80–90 nucleotides from the 5′ end of the virion RNA segment and more typically around 200 nucleotides, whereas the 3′ sequence could be as short as 25 nucleotides (P. A. Jennings et al., Cell 34, 619–627; 1983; S. D. Duhaut and N. J. Dimmock, Virology 247, 241–253, 1998). To determine the biological significance of the highly conserved 5′ sequence, we constructed plasmids that expressed a naturally occurring defective segment 1 RNA from A/equine/Newmarket/7339/79 (EQV, H3N8) or modified RNAs with lesser amounts of the 5′ end. These had terminal 5′ sequences of 220 nucleotides (POLI-220), 150 nucleotides (POLI-150), 80 nucleotides (POLI-80), and 30 nucleotides (POLI-30). Their remaining sequence came from the 3′ end of virion RNA, and all were exactly 445 nucleotides in length. After transfection with one of the RNA-expressing POLI plasmids and plasmids encoding PB1, PB2, PA, and NP proteins, Vero cells were infected with a helper influenza virus of one of three different subtypes (the parental H3N8, an H2N2, or an H1N1 virus). Progeny infectious and presumptive progeny defective virus in the resulting tissue culture fluids were then passaged serially to new cultures up to 10 times. We found that POLI-220 and POLI-150 RNAs proved stable on passage and POLI-80 RNA was detected intermittently, while POLI-30 was not detected beyond passage three. Data were essentially reproducible with the three helper viruses and in two cell lines. It thus appears that the terminal 5′ 150 nucleotides are necessary for influenza virion RNA molecules to be replicated and packaged consistently in cell culture. The possible functional significance of the 5′ sequence is discussed
Human Cytomegalovirus Immediate-Early Gene 2 Expression Leads to JCV Replication in Nonpermissive Cells via Transcriptional Activation of JCV T Antigen

AbstractHuman papovavirus JCV is the causative agent of the demyelinating brain disease progressive multifocal leukoencephalopathy (PML) that typically develops as a complication of impaired immunocompetence. JCV displays a strong tropism for glial cells which is correlated by glial-specific transcriptional regulation of viral gene expression. In a previous report HCMV was shown to overcome the restricted cell specificity of JCV by inducing DNA replication of a PML-derived JCV strain in human fibroblasts which are nonpermissive for the replication of JCV alone. Here we show that productive JCV replication is induced by HCMV in human glioblastoma cells. Both in fibroblasts and in glioblastoma cells, the HCMV immediate-early transactivator 2 (IE2) is sufficient to mediate JCV replication. Furthermore, IE2 induces DNA replication of several structurally different brain- or kidney-derived JCV variants. IE2-induced JCV DNA replication is accompanied by the induction of JCV T antigen expression due to stimulation of the JCV early promoter. Our results indicate that stimulation of JCV early gene expression by HCMV-IE2 is sufficient to overcome the restricted cell specificity of JCV
Induction of Circular Episomes during Rescue and Replication of Adeno-Associated Virus in Experimental Models of Virus Latency

AbstractThe synthesis of linear duplex replicative structures (monomers, head-to-head, and tail-to-tail dimers) is an important hallmark of the productive phase of the adeno-associated virus (AAV) life cycle. These structures are generated by a strand-displacement replication mechanism and believed to be a reservoir for single-stranded DNA genomes. During the course of studies with recombinant versions of AAV (rAAV), we discovered the assembly of circular duplex provirus derivatives in latently infected cell lines under conditions permissive for replication (i.e., helper virus dependent). These novel structures were cloned by bacterial trapping revealing a markedly homogeneous structure that included a single copy of the rAAV genome joined head-to-tail about the inverted terminal repeats (ITR). Restriction and sequence analysis of the point of circularization revealed a so-called “TRT” domain, consisting of a single ITR hairpin palindrome flanked by 5′ and 3′ D sequence elements. The circular conformation was additionally characterized by Southern blotting and confirmed by purification on an ethidium bromide–CsCl gradient where the buoyant density was consistent with circular supercoiled DNA. These findings suggest that AAV replication is accompanied by the assembly of circular duplex structures
Coevolution of Host and Virus: Cellular Localization of Virus in Myxoma Virus Infection of Resistant and Susceptible European Rabbits

AbstractThe coevolution of myxoma virus and the wild European rabbit in Australia and the development of resistance to myxomatosis in wild rabbits have been well described. However, the mechanism of resistance to myxomatosis in wild rabbits is not understood. To determine the basis of resistance, the pathogenesis of the virulent standard laboratory strain (SLS) and the attenuated Uriarra (Ur) strain of myxoma virus were examined in Australian wild rabbits that have been naturally selected in the field for resistance to myxomatosis and in laboratory rabbits which have never been selected for resistance. Virus was localized in tissue sections by immunofluorescence. In all cases virus antigen was initally present in dendritic cells of the dermis before localizing predominantly to the epidermis by Day 6. Antigen-containing cells were detected in the lymph nodes by 24 h after inoculation. Virus replication occurred predominantly in T lymphocytes of the paracortex but SLS also replicated in germinal centers. SLS replication induced loss of most lymphocytes from the lymph nodes of susceptible rabbits. Apoptosis of lymphocytes within the lymph nodes was a major feature of all infections. These apoptotic cells did not contain detectable viral antigen but were often adjacent to infected cells. Ongoing apoptosis of lymphocytes within lymph nodes was also a feature of the recovery phase when very few or no virus-infected cells could be detected. Differences between virulent and attenuated viruses in the wild and laboratory rabbits were predominantly in the degree of tissue pathology in the draining lymph node and distal lymph node and in the type of inflammatory responses, particularly in the skin. SLS infection of laboratory rabbits was associated with a very mild inflammatory response, often distant from the site of virus replication and comprised predominantly of neutrophils. In contrast, Ur-infected rabbits and SLS-infected wild rabbits had an intense inflammatory response adjacent to the site of virus replication and this was comprised predominantly of mononuclear cells. Both the initial infection of dendritic cells and the ongoing destruction of lymphocytes provide obvious mechanisms for the suppression of the immune response by myxoma virus
Analysis of in Vitro Activities of Herpes Simplex Virus Type 1 UL42 Mutant Proteins: Correlation with in Vivo Function

AbstractThe DNA polymerase (pol) catalytic subunit of herpes simplex virus type 1, encoded by UL30, and its accessory factor, UL42 protein, are both essential for the replication of the virus. Because the stable interaction between UL42 and pol renders the pol fully processive for replicative DNA synthesis, disruption of this interaction represents a potential goal in the development of novel antiviral compounds. To better compare the effects of mutations in UL42 protein on its known in vitro functions, mutations were expressed as glutathione-S-transferase (GST)-fusions and the fusion proteins used in affinity chromatography. In this report, we demonstrate the relationship between the abilities of mutant UL42 fusion proteins to bind pol and to stimulate pol activity in vitro, and the abilities of nonfusion mutant proteins to function in viral replication. The pol stimulation assay using GST fusion proteins was found to be a more accurate and sensitive measure of the ability of the UL42 protein to function in vitro than the pol binding assay using the fusion proteins linked to a solid matrix. We also found an excellent correlation between the ability of purified GST fusion proteins to stimulate pol activity in vitro and the ability of full-length nonfusion UL42 mutant genes to support DNA replication in infected cells. Our results demonstrate that two noncontiguous stretches of amino acids, from 137 to 142 and from 274 to 282, are essential for UL42 function in vivo and in vitro. Although mutant d241–261 exhibited close to wild-type abilities to stimulate pol activity in vitro, it was not capable of complementing the replication of a UL42 null mutant virus. The region of UL42 protein within or close to 241–261 may serve to hinge the essential regions within the N- and C-terminal portions of the protein which are thought to interdigitate. It is hypothesized that reduction in the length of the hinge region could alter the ability of UL42, and/or its complex with pol, to function with one or more of the other proteins present in the DNA replisome within infected cells
Varicella-Zoster Virus gE Escape Mutant VZV-MSP Exhibits an Accelerated Cell-to-Cell Spread Phenotype in both Infected Cell Cultures and SCID-hu Mice

AbstractVaricella-zoster virus is considered to have one of the most stable genomes of all human herpesviruses. In 1998, we reported the unanticipated discovery of a wild-type virus that had lost an immunodominant B-cell epitope on the gE ectodomain (VZV-MSP); the gE escape mutant virus exhibited an unusual pattern of egress. Further studies have now documented a markedly enhanced cell-to-cell spread by the mutant virus in cell culture. This property was investigated by laser scanning confocal microscopy combined with a software program that allows the measurement of pixel intensity of the fluorescent signal. For this new application of imaging technology, the VZV immediate early protein 62 (IE 62) was selected as the fluoresceinated marker. By 48 h postinfection, the number of IE 62-positive pixels in the VZV-MSP-infected culture was nearly fourfold greater than the number of pixels in a culture infected with a low-passage laboratory strain. Titrations by infectious center assays supported the above image analysis data. Confirmatory studies in the SCID-hu mouse documented that VZV-MSP spread more rapidly than other VZV strains in human fetal skin implants. Generally, the cytopathology and vesicle formation produced by other strains at 21 days postinfection were demonstrable with VZV-MSP at 14 days. To assess whether additional genes were contributing to the unusual VZV-MSP phenotype, ∼20 kb of the VZV-MSP genome was sequenced, including ORFs 31 (gB), 37 (gH), 47, 60 (gL), 61, 62 (IE 62), 66, 67 (gI), and 68 (gE). Except for a few polymorphisms, as well as the previously discovered mutation within gE, the nucleotide sequences within most open reading frames were identical to the prototype VZV-Dumas strain. In short, VZV-MSP represents a novel variant virus with a distinguishable phenotype demonstrable in both infected cell cultures and SCID-hu mice
Human p32: A Coactivator for Epstein–Barr Virus Nuclear Antigen-1-Mediated Transcriptional Activation and Possible Role in Viral Latent Cycle DNA Replication

AbstractThe Epstein–Barr virus (EBV) nuclear antigen-1 (EBNA-1) is required for the maintenance of the viral chromosome in latently infected, proliferating cells and plays a role in latent cycle DNA replication. EBNA-1 also functions as a positive and negative regulator of EBV gene expression. We have investigated the interaction of EBNA-1 with p32, a host mitochondrial protein that associates with EBNA-1 in EBV-positive Burkitt's lymphoma cells. Using a chromatin immunoprecipitation assay, we found that a fraction of p32 localizes to the viral latent cycle origin of DNA replication oriP in vivo. p32 binds EBNA-1 independently of other proteins or DNA. EBNA-1 variants lacking one of two p32 binding elements did not interact stably with p32 in cultured cells and were defective for both transcriptional activation of a reporter gene linked to oriP FR and replication and/or maintenance of a plasmid bearing oriP. These results support a role for p32 in transcriptional activation by EBNA-1 and suggest that p32 plays a role in EBV latent cycle DNA replication