pinecone/core-2020-05-10-deduplication huggingface dataset:
HIV-1 Evolves into a Nonsyncytium-Inducing Virus upon Prolonged Culture in Vitro

AbstractHIV-1 LAI is a syncytium-inducing (SI) virus with a broad host cell range. We previously isolated a LAI variant that improved replication in the SupT1 T cell line due to mutations within the C1 and C4 constant regions of the Env protein. We now report that this variant exhibits a severely restricted host cell range, as replication in other T cell lines and primary cells was abolished. Several Env-mediated functions were analyzed to provide a mechanistic explanation for this selective adaptation. The change in host cell tropism was not caused by a switch to a SupT1-specific coreceptor. Biosynthesis of the variant Env glycoprotein was not improved in SupT1 cells, and in fact a small defect in intracellular Env processing was observed. SupT1 infection assays did not reveal an improved Env function either, and a dramatic loss of infectivity was measured with other cell types. The Env-mutated HIV-1 reached an approximately fivefold higher level of virus production in SupT1 cells at the peak of infection. Unlike the LAI virus, the variant did not trigger the formation of syncytia. Our combined results suggest that the HIV-1 variant allows the infected host cell to survive longer, thus producing more viral progeny. The intricate virus-cell interaction results in a balance between optimal virus replication and host cell survival, causing a cytopathic SI isolate to evolve toward a nonsyncytium-inducing (NSI) phenotype in cell culture. These findings may help explain the absence of SI variants in the initial phase of HIV-1 infection, and the results dispute the notion that HIV-1 evolution should always go from the NSI to SI phenotype
Resistance to Pseudorabies Virus Infection in Transgenic Mice Expressing the Chimeric Transgene That Represses the Immediate-Early Gene Transcription

AbstractA chimeric gene encoding a fusion protein consisting of the DNA-binding domain of the immediate-early (IE) protein of pseudorabies virus (PRV) and a tail-truncated VP16 of herpes simplex virus 1, lacking the transcription activation domain, has been shown to repress transcription of the PRV IE gene, resulting in the inhibition of PRV growth in vitro. To assess the antiviral potential of the fusion protein in vivo, transgenic mice containing the chimeric gene under the control of the virus- and interferon-inducible Mx 1 promoter were generated. A transgenic mouse line showed marked resistance to PRV infection when the mice were challenged intranasally with PRV. Inhibition of PRV replication was also observed in monolayers of embryonic cells prepared from the transgenic mice. In the cells infected with PRV, transcription of the PRV IE gene was repressed. The present results indicate that the chimeric gene is able to exert a significant antiviral effect against PRV infection in vivo
Characterization of Human Herpesvirus-8 K8.1A/B Glycoproteins by Monoclonal Antibodies

AbstractHuman herpesvirus-8 K8.1 gene encodes for two immunogenic class I glycoproteins, K8.1A and B, originating from spliced messages [(1998) Virology 243, 208–217]. The 228-amino-acid-long K8.1A open reading frame (ORF) contains four N-glycosylation sites and the 167-amino-acid-long K8.1B ORF contains three N-glycosylation sites, sharing similar amino- and carboxyl-termini with ORF K8.1A but with an in-frame deletion [(1998) Virology 249, 140–149]. To characterize the K8.1A and B glycoproteins in the infected body cavity-based B cell lymphoma (BCBL-1) cells and in the virion envelopes, monoclonal antibodies (MAbs) recognizing only K8.1A protein or both K8.1A and B proteins were generated. These antibodies reacted with the infected cell membranes and virion envelopes. Stable COS-1 transformant cells expressed the K8.1A and B proteins independently on the plasma membranes. MAbs recognized multiple proteins with molecular weights ranging from 23 to 72 kDa from the BCBL-1 cells and COS-1 cells and the 72 to 68 kDa molecular-weight proteins from the virion particles. The K8.1A is the predominant protein affinity purified from the infected BCBL-1 cells. Digestion with glycosidases show that these proteins contain both N- and O-linked sugars, suggesting that the multiple proteins recognized by the MAbs represent the precursor and product forms of K8.1A and B proteins, and the 72 to 68 kDa molecular-weight proteins represent the virion particle-associated mature forms of these glycoproteins
Nematode Transmission of Tobacco Rattle Virus Serves as a Bottleneck to Clear the Virus Population from Defective Interfering RNAs

AbstractDI7 is a defective interfering RNA derived from RNA 2 of tobacco rattle tobravirus (TRV) isolate PpK20. Tobacco was transformed with DI7 cDNA fused to the CaMV 35S promoter. Upon infection of the transgenic plants with TRV isolate PpK20 or the serologically unrelated isolate PaY4, the transgenic DI7 RNA started to accumulate at high levels and strongly interfered with accumulation of wild-type (wt) RNA 2. When DI7 transgenic plants infected with isolate PpK20 were used as source plants in nematode-transmission experiments, the vector Paratrichodorus pachydermus efficiently transmitted virus to healthy bait plants. However, the nematodes transmitted only the wt virus present in the transgenic source plants, whereas virus particles containing the abundant, accumulated DI7 RNA were excluded from transmission. Evidence is presented that wt RNA 2 and DI7 RNA are encapsidated in cis by their encoded CPs, which are known to be functional and nonfunctional in transmission, respectively. This mechanism would result in defective interfering RNAs, which rapidly arise after mechanical transmission of the virus in the laboratory, being eliminated from tobraviruses under natural field conditions. Also this mechanism which acts with nematode transmitted virus isolates contrasts with that of vector-transmission of defective potyviruses and luteoviruses by wt helper viruses
Isolation and Characterization of APSE-1, a Bacteriophage Infecting the Secondary Endosymbiont of Acyrthosiphon pisum

AbstractA bacteriophage infecting the secondary endosymbiont of the pea aphid Acyrthosiphon pisum was isolated and characterized. The phage was tentatively named bacteriophage APSE-1, for bacteriophage 1 of the A. pisum secondary endosymbiont. The APSE-1 phage particles morphologically resembled those of species of the Podoviridae. The complete nucleotide sequence of the bacteriophage APSE-1 genome was elucidated, and its genomic organization was deduced. The genome consists of a circularly permuted and terminally redundant double-stranded DNA molecule of 36524 bp. Fifty-four open reading frames, putatively encoding proteins with molecular masses of more than 8 kDa, were distinguished. ORF24 was identified as the gene coding for the major head protein by N-terminal amino acid sequencing of the protein. Comparison of APSE-1 sequences with bacteriophage-derived sequences present in databases revealed the putative function of 24 products, including the lysis proteins, scaffolding protein, transfer proteins, and DNA polymerase. This is the first report of a phage infecting an endosymbiont of an arthropod
A2 Cro, the Lysogenic Cycle Repressor, Specifically Binds to the Genetic Switch Region of Lactobacillus casei Bacteriophage A2

AbstractLysogenic induction of temperate bacteriophage A2 of Lactobacillus casei is controlled by the action of its cI and cro products at the phage operator region. Three 20-bp inverted repeated DNA segments (subsites O1, O2, and O3) and the two divergent (PL and PR) promoters were mapped within the 153-bp operator region. The A2-encoded Cro product is shown to be the functional homolog of λ Cro. The binding of Cro to the three operator subsites is noncooperative and yields two discrete protein–DNA complexes of retarded migration in mobility shift assays. The Kapp value for the Cro–PL–PR DNA complex was estimated to be 6 nM. Cro shows a slightly higher affinity for O3 than for O1 and O2 subsites. The O3 subsite overlaps the −35 hexamer of the PL promoter, which directs cI expression. A Cro mutant protein, devoid of the last 12 residues (Cro*), allowed the assignment of the DNA-binding domain to the NH2 end of Cro. The C end enhances its affinity for the DNA and probably stabilizes bending induced by Cro
Faba Bean Necrotic Yellows Virus (Genus Nanovirus) Requires a Helper Factor for Its Aphid Transmission

AbstractPurified faba bean necrotic yellows virus (FBNYV; genus Nanovirus) alone is not transmissible by its aphid vector, Acyrthosiphon pisum, regardless of whether it is acquired from artificial diets or directly microinjected into the aphid's hemocoel. The purified virus contains all of the genetic information required for its infection cycle as it readily replicated in cowpea protoplasts and systemically infected Vicia faba seedlings that were biolistically inoculated using gold particles coated with intact virions or viral DNA. The bombarded plants not only developed the typical disease syndrome, thus indicating that FBNYV is the sole causal agent of the disease, but also served as a source from which the virus was readily acquired and transmitted by A. pisum. The defect of the purified virus in aphid transmissibility suggests that FBNYV requires a helper factor (HF) for its vector transmission that is either nonfunctional or absent in purified virus suspensions. The requirement for an HF was confirmed in complementation experiments using two distinct isolates of the virus. These experiments revealed that aphids transmitted the purified virus isolate from artificial diets only when they had fed previously on plants infected with the other FBNYV isolate. Also, microinjected FBNYV, which persisted to the same extent in A. pisum as naturally acquired virus, was transmissible when aphids had acquired the HF from infected plants. This suggests that one of the functions of the HF in the transmission process is to facilitate virus transport across the hemocoel–salivary gland interface
A Carboxy-Terminally Truncated Form of the Vpr Protein of Human Immunodeficiency Virus Type 1 Retards Cell Proliferation Independently of G2 Arrest of the Cell Cycle

AbstractVpr, one of the accessory gene products of HIV-1, is a 96-residue protein with several functions. It is involved in import of the HIV-1 preintegration complex into the nucleus of nondividing cells, in cellular differentiation, inducing cell cycle arrest at the G2/M phase, in immune suppression, and in enhancement of replication of the virus. We found recently that Vpr interferes with the proliferation of mouse NIH3T3 fibroblasts but fails to arrest these cells in the G2 phase. Thus, it seems possible that Vpr might retard cell proliferation via a novel pathway that is distinct from G2 arrest. To elucidate the mechanism by which Vpr induces the retardation of cell growth, we developed a panel of expression vectors that encoded Vpr molecules with deletions of specific putative domains, namely, the first α-helical domain, the second α-helical domain, a leucine zipper-like domain, and an arginine-rich carboxy-terminal domain. These vectors were introduced into HeLa cells since expression of Vpr can induce G2 arrest in such cells. A carboxy-terminally truncated form of Vpr, C81, which failed to induce G2 arrest, led to the G1 arrest and retained the ability to prevent cell proliferation. All the other mutant proteins had completely lost the capacity to induce G2 arrest and to suppress growth. Substitutions of Ile/Leu for Pro at positions 60, 67, 74, and 81 within the leucine zipper-like domain of Vpr or of C81 revealed that Ile60, Leu67, and Ile74 play an important role in the C81-induced suppression of growth, while Ile74 and Ile81 were found to be indispensable for Vpr-induced G2 arrest. Collectively, our results strongly suggest that Vpr can retard cell proliferation independently of G2 arrest of the cell cycle
Analysis of the RNA Binding Specificity of the Human Tap Protein, a Constitutive Transport Element-Specific Nuclear RNA Export Factor

AbstractThe human Tap protein has been proposed to mediate Mason Pfizer monkey virus constitutive transport element (CTE)-dependent nuclear RNA export and may also play a role in global mRNA export. Here, we have used in vivo assays, in both yeast and human cells, together with in vitro assays, to further characterize the RNA binding properties of Tap, which has been proposed to contain a novel leucine-rich RNA binding motif. Using the yeast three hybrid assay, we selected RNA molecules that retain Tap binding activity from a pool of randomized CTE sequences. The recovered RNA sequences differed only minimally from the wild-type CTE yet all displayed lower affinity for Tap both in vivo and in vitro. Analysis of the RNA export activity of the recovered CTE variants revealed that Tap affinity was highly predictive of CTE biological activity. Together, these observations provide additional evidence supporting the identification of Tap as the direct cofactor for CTE function and demonstrate that RNA binding by Tap is highly sequence specific
Regulation of Bacteriophage λ Development by Guanosine 5′-Diphosphate-3′-diphosphate

AbstractOn infection of its host, Escherichia coli, bacteriophage λ can follow one of two alternative developmental pathways: lytic or lysogenic. Here we demonstrate that the “lysis-versus-lysogenization” decision is influenced by guanosine tetraphosphate (ppGpp), a nucleotide that is synthesized in E. coli cells in response to amino acid or carbon source starvation. We found that the efficiency of lysogenization is the highest at ppGpp concentrations somewhat higher than the basal level; too low and too high levels of ppGpp result in less efficient lysogenization. Maintenance of the already integrated λ prophage and phage lytic development were not significantly influenced in the host lacking ppGpp. We found that the level of HflB/FtsH protease, responsible for degradation of the CII protein, an activator of “lysogenic” promoters, depends on ppGpp concentration. The highest levels of HflB/FtsH was found in bacteria lacking ppGpp and in cells bearing increased concentrations of this nucleotide. Using lacZ fusions, we investigated the influence of ppGpp on activities of λ promoters important at the stage of the lysis-versus-lysogenization decision. We found that each promoter is regulated differentially in response to the abundance of ppGpp. Moreover, our results suggest that the cAMP level may influence ppGpp concentration in cells. The mechanism of the ppGpp-mediated control of λ development at the stage of the lysis-versus-lysogenization decision may be explained on the basis of differential influence of guanosine tetraphosphate on activities of pL, pR, pE, pI, and paQ promoters and by dependence of HflB/FtsH protease level on ppGpp concentration
Fatal Immunopathogenesis by SIV/HIV-1 (SHIV) Containing a Variant Form of the HIV-1sf33 env Gene in Juvenile and Newborn Rhesus Macaques

AbstractSIV/HIV-1 (SHIV) chimeric clones, constructed by substituting portions of the pathogenic molecular clone SIVmac239 with counterpart portions from HIV-1 clones, provide a means to analyze functions of selected HIV-1 genes in vivo in nonhuman primates. Our studies focused on SHIVsf33, which contains the vpu, tat, rev, and env genes of the cytopathic, T-cell line tropic clone HIV-1sf33 (subtype-B); this clone has a premature stop codon in the vpu gene. In three juvenile macaques inoculated intravenously with SHIVsf33, low-level persistent infection was established; no disease was observed for a period of >2 years. However, at ∼16 months p.i., one of four SHIVsf33-infected juvenile macaques exhibited an increase in virus load, depletion of CD4+ T cells in peripheral blood and lymph nodes, and other symptoms of simian AIDS (SAIDS). Virus recovered from this animal in the symptomatic stage was designated SHIVsf33a (A, adapted); this virus displayed multiple amino acid sequence changes throughout the HIV-1 env gene compared with the input SHIVsf33 clone. Additionally, a mutation in all clones from SHIVsf33a restored the open reading frame for the vpu gene. In vitro evaluations in tissue-culture systems revealed that SHIVsf33a replicated to higher levels and exhibited greater cytopathicity than SHIVsf33. Furthermore cloned env genes for SHIVsf33a were more fusogenic in a cell-fusion assay compared with the env gene of the SHIVsf33. Intravenous inoculation of SHIVsf33a into juvenile and newborn macaques resulted in a rapid decline in CD4+ T cells to very low levels and development of a fatal AIDS-like disease. A cell-free preparation of this pathogenic chimeric virus also established persistent infection when applied to oral mucosal membranes of juvenile macaques and produced a fatal AIDS-like disease. These studies on pathogenic SHIVsf33a establish the basis for further investigations on the role of the HIV-1 env gene in virus adaptation and in mechanism(s) of immunodeficiency in primates; moreover, the chimeric virus SHIVsf33a can play a role in elucidating mucosal membrane transmission and development of antiviral vaccines in newborns as well as juvenile and adult macaques
Defective and Wild-Type Human T-Cell Leukemia Virus Type I Proviruses: Characterization of Gene Products and trans-Interactions between Proviruses

AbstractDefective provirus genomes of human T-cell leukemia virus type I are frequently detected in lymphocytes from infected individuals and in infected cell lines. One type of defective provirus contains internal deletions spanning gag, pol, and env genes but retains portions of open reading frames for trans-regulatory proteins. The deleted proviruses could potentially contribute to viral pathology by producing novel gene products that directly affect cell metabolism or that modulate expression of resident, wild-type proviruses. Virus gene products and the control of their expression were examined in cells transfected with defined molecular clones of wild-type and defective proviruses. Internally deleted provirus clones, which are unable to produce functional Tax and Rex proteins, were transcriptionally inactive in transfected cells. Ectopic expression of p40Tax activated transcription of the deleted provirus, resulting in the accumulation of a two-exon mRNA that yields a truncated form of Rex (p21Rex). Although this two-exon mRNA also has a potential initiation codon in the tax frame, a truncated form of Tax was not detected by immunoblotting or in transactivation assays. When complemented with p40Tax and p27Rex, cells transfected with deleted proviruses accumulated an unspliced mRNA that could potentially encode gag-pX fusion proteins. Although expression of deleted proviruses was dependent on trans-acting factors produced from intact proviruses, gene products from defective proviruses did not significantly affect expression of a cotransfected, full-length provirus
Proteolytic Processing in Infectious Bursal Disease Virus: Identification of the Polyprotein Cleavage Sites by Site-Directed Mutagenesis

AbstractThe infectious bursal disease virus (IBDV), a member of the Birnaviridae family, is the causative agent of an immune depressive disease that affects domesticated and wild avian species. The expression strategy of IBDV includes the synthesis of a 110-kDa polyprotein containing the capsid precursor polypeptides. The polyprotein is autocatalitically processed rendering three polypeptides: NH2-VPX-VP4-VP3-COOH. We have carried out a systematic analysis, using a series of plasmids encoding polyproteins containing either deletions or single amino acid substitutions, to identify the processing sites. The results obtained showed the existence of two sites, 511LAA513 and 754MAA756, that are essential for the processing of the VPX–VP4 and VP4–VP3 precursors, respectively. These sequences are highly conserved among IBDV strains form serotypes 1 and 2. A secondary VPX–VP4 processing site was detected in a 19-amino acid stretch located upstream of the 511LAA513 site. Analyses using versions of the 754MAA756 VP4–VP3 processing site containing conservative and nonconservative amino acid substitutions demonstrated that the specificity of the cleavage is dictated by the conserved AA dipeptide
Minor Displacements in the Insertion Site Provoke Major Differences in the Induction of Antibody Responses by Chimeric Parvovirus-like Particles

AbstractAn antigen-delivery system based on hybrid virus-like particles (VLPs) formed by the self-assembly of the capsid VP2 protein of canine parvovirus (CPV) and expressing foreign peptides was investigated. In this report, we have studied the effects of inserting the poliovirus C3:B epitope in the four loops and the C terminus of the CPV VP2 on the particle structure and immunogenicity. Epitope insertions in the four loops allowed the recovery of capsids in all of the mutants. However, only insertions of the C3:B epitope in VP2 residue 225 of the loop 2 were able to elicit a significant anti-peptide antibody response, but not poliovirus-neutralizing antibodies, probably because residue 225 is located in an small depression of the surface. To fine modulate the insertion site in loop 2, a cassette-mutagenesis was carried out to insert the epitope in adjacent positions 226, 227, and 228. The epitope C3:B inserted into these positions was well recognized by the specific monoclonal antibody C3 by immunoelectron microscopy. BALB/c mice immunized with these chimeric C3:B CPV:VLPs were able to elicit an strong neutralizing antibody response (>3 log10 units) against poliovirus type 1 (Mahoney strain). Therefore, minor displacements in the insertion place cause dramatic changes in the accessibility of the epitope and the induction of antibody responses
Diarrhea Induction by Rotavirus NSP4 in the Homologous Mouse Model System

AbstractComparison of the NSP4 amino acid sequences from 31 strains of mammalian rotaviruses revealed the presence of four distinct NSP4 alleles; i.e., the Wa, KUN, AU-1, and EW alleles. The EW allele consists only of NSP4s from murine rotavirus strains and is divergent from other NSP4 alleles from the evolutionary perspective. There have been conflicting reports regarding the enterotoxigenic activity of NSP4 in the mouse model system; heterologous simian and porcine rotavirus NSP4s function as an enterotoxin in mice, while a homologous EC NSP4 does not play a dominant role as an enterotoxin in the cystic fibrosis conductance regulator knockout mice. To further examine the enterotoxigenic activity of NSP4, we expressed in Escherichia coli a recombinant protein consisting of glutathione S-transferase and amino acid residues 86–175 of the EW NSP4. We found that this fusion protein caused diarrhea in the majority (8/14) of 5- to 6-day-old CD1 mice. This study confirmed and extended that group A rotavirus NSP4s were able to induce diarrhea in neonatal mice and had an enterotoxigenic activity