pinecone/core-2020-05-10-deduplication huggingface dataset:
Nucleotide Sequences within the U5 Region of the Viral RNA Genome Are the Major Determinants for an Human Immunodeficiency Virus Type 1 to Maintain a Primer Binding Site Complementary to tRNAHis

AbstractThe initiation of reverse transcription of the human immunodeficiency virus type 1 (HIV-1) genome requires cellular tRNALys,3as a primer and occurs at a site in the viral RNA genome, designated as the primer binding site (PBS), which is complementary to the 3′-terminal 18 nucleotides of tRNALys,3. We previously described an HIV-1 virus [designated as HXB2(His-AC)], which contained a sequence within the U5 region complementary to the anticodon region of tRNAHisin addition to a PBS complementary to the 3′-terminal 18 nucleotides of the tRNAHis. That virus maintained a PBS complementary to tRNAHisafter extendedin vitroculture (Wakefieldet al., J. Virol.70, 966–975, 1996). In the present study, we report that subcloning a 200-base-pair DNA fragment encompassing the U5 and PBS regions from an integrated provirus of HXB2(His-AC) back into the wild-type genome (pHXB2) resulted in an infectious virus, designated as HXB2(His-AC-gac), which again stably maintained a PBS complementary to tRNAHis. DNA sequence analysis of the 200-base-pair region revealed only three nucleotide changes from HXB2(His-AC): a T-to-G change at nucleotide 174, a G-to-A change at nucleotide 181, and a T-to-C change at nucleotide 200. The new mutant virus replicated in CD4+Sup T1 cells similarly to the wild-type virus. Comparison of the nucleotide sequence of nucleocapsid gene of the wild-type and HXB2 (His-AC-gac) virus revealed no differences. Although we found numerous mutations in the reverse transcriptase gene in proviral clones derived from HXB2 (His-AC-gac), no common mutations were found among the 13 clones examined. Comparison of the virion-associated tRNAs of HXB2(His-AC-gac) with those of the wild type revealed that both viruses incorporated a similar subset of cellular tRNAs, with tRNALys,3being the predominant tRNA found within virions. There was no selective enrichment for tRNAHiswithin virions of HXB2(His-AC-gac) virus which selectively use tRNAHisto initiate reverse transcription. The results of these studies suggest that the U5 and PBS regions in the viral RNA genome are important determinants for HXB2(His-AC) viruses in the selective use of tRNAHisto initiate reverse transcription
Generation of a Novel Poliovirus with a Requirement of Hepatitis C Virus Protease NS3 Activity

AbstractHepatitis C virus (HCV) is the major etiologic agent of non-A, non-B hepatitis. One of the difficulties in developing anti-HCV drugs is the lack of an efficient HCV cultivation system. We have generated an artificial surrogate virus suitable for testing the antiviral effects of drugs affecting HCV protease NS3, an enzyme believed to be essential for HCV proliferation. The surrogate virus genome is composed of most of the poliovirus genome and HCV protease NS3 and an NS3-specific cleavage site. The activity of HCV protease NS3 is required for proliferation of this chimeric virus. The antiviral efficacy of HCV protease inhibitors can, therefore, be evaluated by examining the effects of the drugs on the surrogate virus proliferation
A Neutralization Site of DA Strain of Theiler's Murine Encephalomyelitis Virus Important for Disease Phenotype

AbstractDA strain of TMEV induces a chronic, persistent, demyelinating disease in SJL/J weanling mice, while inoculation with GDVII strain of TMEV induces an acute, lethal neurovirulent disease. We show that three amino acids in the DA EF loop—DAVP2 141 Lys, 143 Gly, and 173 Thr—are part of a neutralization site of DA monoclonal antibody (mAb), DAmAb1. DA virus with a mutation of VP2 143 from Gly to Asp, like wild-type virus, persists 6 weeks postinfection (PI) and produces white matter disease. DA virus with a mutation of VP2 141 from Lys to Asn persists but does not induce significant white matter disease. DA virus with a mutation of DA VP2 173 from Thr to Phe fails to persist or to induce significant white matter disease. The diversity and complexity of the mutant virus-induced disease phenotype presumably reflects the varied effects of the mutated amino acid residues on the three-dimensional structure of the viral capsid. The localization of DA VP2 141 and VP2 173 near the putative receptor binding region of the virus suggest that a disruption of interactions between the virus and its receptor is important in the late demyelinating disease and for virus neutralization
Kinetics of Duck Hepatitis B Virus Infection Following Low Dose Virus Inoculation: One Virus DNA Genome Is Infectious in Neonatal Ducks

AbstractUsing pooled serum from congenitally duck hepatitis B virus (DHBV)-infected ducks as inoculum, we examined the effect of virus dose on the incubation period of infection and on the patterns of spread of virus infection in the liver. The pooled serum inoculum contained 9.5 × 109DHBV genomes per milliliter and had an infectivity titre (ID50) in newly hatched ducks of 1.5 × 1010per milliliter with a 95% confidence interval of 3.0 × 109to 6.3 × 1010ID50/ml, indicating the equivalence between one DHBV genome and one infectious unit within the limits of the assays. The incubation period of infection was inversely related to the dose of inoculum and the onset of viraemia ranged from Day 6 with the highest dose to Day 14 or 29 with the lowest dose inoculum. To study the spread of virus infection from a low percentage of initially infected cells we inoculated newly hatched ducks intravenously with sufficient DHBV (1.5 × 103ID50) to infect only ∼0.0001% of total liver cells. DHBV infection first reached detectable levels on Day 4 postinoculation (p.i.) and was detected in ∼0.035% of hepatocytes, most of which occurred as single cells or pairs of cells, indicating that a number of rounds of infection had occurred with the spread of virus both to adjoining cells, i.e., by cell-to-cell spread, and to cells located in other parts of the liver lobule. Despite some bird-to-bird variation in timing, the percentage of infected hepatocytes increased exponentially with a mean doubling time of 16 hr from Day 4 to Day 14 p.i., by which time replication was seen in >95% of hepatocytes. This rapid dissemination from a small number of infected hepatocytes suggests that, in neonatal ducks, there are no major delays in virus replication within the liver, that any innate and adaptive defence mechanisms operating during the first 10 to 14 days of infection are insufficient to contain virus spread, and that even a small number of infected hepatocytes produce enough progeny to rapidly infect the remaining hepatocytes
Epstein–Barr Nuclear Antigen-3 and -4 Interact with RBP-2N, a Major Isoform of RBP-Jκ in B Lymphocytes

AbstractThe Epstein–Barr nuclear antigen (EBNA)-3 and EBNA-4 proteins are thought to act as transcriptional transactivators. The yeast two-hybrid system and coimmunoprecipitation were used to demonstrate that EBNA-3 and -4 associate with the DNA-binding protein RBP-2N, an isoform of RBP-Jκ. A comparison between EBNA-3, EBNA-4, and EBNA-6 binding to RBP-2N indicated that EBNA-3 enhanced β-galactosidase activity 4-fold more than EBNA-6 and 30-fold more than EBNA-4. Assay of RBP-2N deletion mutants demonstrated that EBNA-3 binds to regions of RBP-2N which are distinct from those to which EBNA-2 and -6 interact, whereas EBNA-4 binds to the same region of RBP-2N as EBNA-2 and -6 (amino acids 159–331 of RBP-2N). Interaction of both A- and B-type EBNA-3 with RBP-2N was also demonstrated by immunoprecipitation. RT-PCR analysis of a panel of B cell lymphomas and lymphoblastoid cell lines demonstrated that higher levels of RBP-2N were expressed, in comparison to RBP-Jκ, indicating that RBP-2N is a major isoform expressed in B cells. These results suggest that all the EBNA-3 family proteins lead to transcriptional regulation via interaction with RBP-2N
Characterization of Cucumber Mosaic Virus II. Identification of Movement Protein Sequences That Influence Its Accumulation and Systemic Infection in Tobacco

AbstractTobacco plants infected by the Sny strain of cucumber mosaic virus (CMV) showed chronic symptoms rather than cycles of acute disease followed by no symptoms, as seen for many strains such as Fny-CMV. The Sny-CMV 3a movement protein (MP) accumulated at 10 to 50 times the level of the Fny-CMV MP in the first few systemically infected leaves showing disease symptoms. The increased production of movement protein was not associated with an increase in synthesis of viral RNA and/or capsid protein. The correlation of high levels of accumulated MP and chronic infection in tobacco mapped to the 3a gene of Sny-CMV. Sequence analysis of the 3a gene of Sny-CMV showed that there were three nucleotide changes that altered amino acid sequences within the MP. Analysis of the kinetics of infection and level of MP accumulation for various CMV RNA 3 chimeric constructs and site-directed mutants of RNA 3 showed that chronic infection and high MP accumulation were associated with nucleotide sequence changes at two positions within codons 51 and 240 of the MP gene. These changes in the MP of Fny-CMV resulted in an altered subcellular distribution of the 3a protein, as also was observed for the Sny-CMV 3a protein. In both cases, considerably more 3a protein was associated with a fraction containing membranes. The potential relationship between membrane association and chronic infection is discussed
Central Nervous System Expression of HIV-1 Gp120 Activates the Hypothalamic-Pituitary-Adrenal Axis: Evidence for Involvement of NMDA Receptors and Nitric Oxide Synthase

AbstractThe impact of HIV-1 expression in the brain on the development of AIDS is unknown. In the present study, we examined the hypothalamic-pituitary-adrenal (HPA) axis in a transgenic model in which expression of the HIV-1 envelope glycoprotein gp120 induced central nervous system (CNS) damage similar to that seen in HIV-1-infected patients. Compared with nontransgenic littermates, gp120 transgenic mice showed significant increases in plasma corticosterone and adrenocorticotrophic hormone (ACTH) levels and pituitary ACTH content. To determine whether this activation of the HPA axis could be mediated by ACTH secretagogues, the effect of recombinant gp120 on the release of these factors from hypothalamic slices was investigatedin vitro.Recombinant gp120 induced release of the ACTH secretagogue arginine vasopressin from nontransgenic hypothalamic slices in a calcium-dependent fashion. This effect was inhibited by antagonists ofN-methyl-D-aspartate (NMDA) receptors or of nitric oxide synthase (NOS), suggesting a role for NMDA receptor stimulation and NOS activity. Further evidence for a role of free radicals was obtained from bigenic mice coexpressing gp120 and the free radical scavenger human copper/zinc superoxide dismutase which showed normal corticosterone levels. This might relate to superoxide dismutase-mediated scavenging of superoxides generated by NOS. These findings demonstrate that CNS expression of a viral envelope protein can activate the HPA axis and thereby alter peripheral levels of immunomodulatory hormones
Cellular Proteins Bind to Multiple Sites of the Leader Region of Cauliflower Mosaic Virus 35S RNA

AbstractUV crosslinking assays were performed to characterize interactions between the leader of the cauliflower mosaic virus (CaMV) 35S RNA and cellular, cytoplasmic proteins. From turnip, a host for CaMV, three different proteins, p35, p49, and p100, interacted with multiple binding sites within the leader. p35 binds to RNA nonspecifically and p49 binds with low specificity, whereas p100 interacts specifically with viral sequences. The expression of the proteins is not induced upon virus infection, as there is no difference in the protein pattern between healthy and infected cell extracts. In a cellular fractionation, p35 and p100 remain in the high-speed supernatant whereas p49 cosediments with polysomes. A possible involvement of these proteins in the translation of the CaMV 35S RNA is discussed
The GlycosylatedgagProtein of MuLV Is a Determinant of Neuroinvasiveness: Analysis of Second Site Revertants of a Mutant MuLV Lacking Expression of This Protein

AbstractNeuroinvasiveness is a property of all neurovirulent murine retroviruses, although the factors which facilitate infection of the CNS are not understood. We previously showed that mutant MuLV which lack expression of an accessory protein, glycosylatedgag,had lost neurovirulence, indicating that this protein may be involved in promoting CNS infection. The mutations were located in the “Kozak” consensus sequence of the initiation codon for this protein. Here it is shown that shortly after inoculation of mice with one of these mutant viruses, revertants emerged which had regained expression of glycosylatedgagand had also regained the neuroinvasiveness and neurovirulence exhibited by the wild-type virus. The phenotypic revertants retained the mutations in the “Kozak” consensus sequence but exhibited a G → A mutation 12 codons downstream from the mutated start site, creating a new initiation codon and a glycosylatedgagprotein, which was truncated at its N-terminus. Using antibodies specific for glycosylatedgagit is shown that the frequency of splenic infectious centers expressing revertant virus increased progressively during the 2 months following inoculation of mutant virus until ≥50% of the virus-producing cells in the spleen expressed revertant virus. In contrast, although phenotypic revertants were detectable at low frequency after cell-free passagein vitroinM. dunnifibroblasts, there was no evidence for selection. These results indicate that glycosylatedgagfacilitates virus spread within the spleen and to extra-splenic sites, such as the CNS, and suggest that the protein may function through its interaction with the host
Characterization of Regulatory Functions of the HSV-1 Immediate-Early Protein ICP22

AbstractPrevious work has shown that the 68-kDa immediate-early protein of herpes simplex virus type 1 (HSV-1), also known as ICP22, is involved in the control of viral gene expression, although the precise mechanism remains to be elucidated. In order to study the function(s) of this protein, we constructed expression vectors containing the coding sequence of the ICP22 gene placed under the control of the SV40 or HCMV promoter. After cell transfection, ICP22 synthesis was studied by immunoblotting, using a specific antiserum. In transient expression experiments in COS cells in which the ICP22 vector was under the control of the SV40 promoter, we found that ICP22 was able to inhibit chloramphenicol acetyltransferase (CAT) expression under the control of either the α22 (IE4) promoter or other immediate-early promoters, such as α4 (IE3), α0 (IE1), and α27 (IE2). CAT expression under the control of the α4 (IE3) promoter was inhibited in these cells by expression of ICP22 under the control of the HCMV promoter; it was also inhibited in RAT-1 cells by ICP22 expressed under the control of the SV40 or HCMV promoter. In contrast, CAT expression directed by the SV40 or HCMV promoters was only weakly or not inhibited by the ICP22 vectors. We also constructed an expression vector for UL13, a gene whose product is implicated in the phosphorylation of ICP22. Although CAT expression under the control of the α4 (IE3) promoter was also negatively regulated by the UL13 gene product, the effects of the ICP22 (directed by the SV40 or HCMV promoter) and UL13 vectors were not synergistic; furthermore, at a particular molar ratio of the two vectors, inhibition of CAT activity was partially reversed. The results in the present work suggest that ICP22 can negatively regulate the expression of immediate-early viral genes and that its phosphorylation by UL13 protein kinase might be involved in the modulation of its function
Vaccinia VirusG4LGene Encodes a Second Glutaredoxin

AbstractVaccinia virus (VV) was previously shown to encode a functional glutaredoxin, the product of theo2lgene, which is synthesized late in infection, after the onset of DNA replication. Here we report that an open reading frame in the VV genome designated asg4lencodes a protein that has sequence similarity to glutaredoxins and possesses thioltransferase and dehydroascorbate reductase activities. G4L protein in infected cells can be detected as early as 4 hr after infection and is constitutively expressed up to 24 hr postinfection. A protein homologous to G4L and retaining the predicted glutaredoxin active center is encoded by the recently sequenced Molluscum Contagiosum virus (MCV), whereas O2L protein is not conserved, suggesting that the glutaredoxin activity of G4L may be involved in replication of all poxviruses
Novel Variation in the N Protein of Avian Infectious Bronchitis Virus

AbstractThe nucleocapsid protein of coronaviruses has been considered highly conserved, showing greater than 94% conservation within strains of a given species. We determined the nucleotide sequence of the N gene and the 3′ untranslated region (UTR) of eight naturally occurring strains of IBV which differed in pathogenicity and tissue tropism. In pairwise comparisons, the deduced amino acid sequences of N of five strains Vic S, N1/62, N9/74, N2/75, and V5/90 (group I) shared 92.3–98.8% identity. The three strains N1/88, Q3/88, and V18/91 (group II) shared 85.8–89.2% identity with each other, but only 60.0–63.3% identity with viruses of group I. Amino acid substitutions, deletions, and insertions occurred throughout the N protein and involved regions previously identified as being conserved. Despite the considerable variation observed between the two virus groups, all N proteins contained a high proportion of basic residues, 80% of which were conserved in position. In addition, all strains contained approximately 30 serine residues of which 10 were conserved, the majority occurring between positions 168 and 194. As for all other coronaviruses, the region between positions 92 and 103 was highly conserved. Hence, a large number of amino acid changes can be tolerated within the N protein without affecting its integrity or functioning. The 3′ UTR immediately downstream from the N gene was highly heterogeneous with extensive deletions occurring in the group II strains
Distinct Quasi-Species in the Blood and the Brain of an HIV-2-Infected Individual

AbstractSequences of the HIV-2 envelope C2–C3 region were obtained after direct PCR amplification of proviral DNA from the brain and peripheral blood mononuclear cells of an HIV-2-infected AIDS patient. Tissue-specific sequences confirmed previous observations that HIV-2 is indeed present in the central nervous system of infected individuals. Distinct but related quasi-species were present in these two different tissues of the same individual. Residues at position 18 and 19 of the V3 loop and overall charge of the loop suggest that the brain virus was NSI/macrophage tropic; whereas the sequences from the two blood samples were indicative of a SI/T-cell tropic virus. This is the first description of these two genotypes in the same HIV-2-infected individual. Analysis of more samples from different compartments would help to better understand tissue-specific factors in quasi-species evolutionin vivo
Replication of Primary HIV-1 Isolates Is Inhibited in PM1 Cells Expressing sCD4-KDEL

AbstractExpression of a soluble CD4 molecule (sCD4-KDEL) containing a specific retention signal for the endoplasmic reticulum was shown previously to block propagation of the HIV-1MNprototype strain in a transformed T cell line. However, the virus present in HIV-1-infected individuals is more closely represented by primary HIV-1 isolates which, unlike the HIV-1MNstrain, have not been adapted to growth in cell lines. To determine if sCD4-KDEL could block replication of primary isolates we used the PM1 cell line that has been shown to propagate primary isolates without adaptation. Here we show that the replication of four primary HIV-1 isolates was strongly inhibited in PM1 cells that expressed sCD4-KDEL under control of the HIV-1 LTR. Infection with primary HIV-1 isolates induced sCD4-KDEL expression driven by the LTR, HIV-1 spread was dramatically reduced, and reverse transcriptase activity in the cell culture supernatants was greatly diminished. sCD4-KDEL, therefore, represents a potent inhibitor of HIV-1 replication for gene therapy-based approaches for the treatment of AIDS
Surprising Function of the Three Influenza Viral Polymerase Proteins: Selective Protection of Viral mRNAs against the Cap-Snatching Reaction Catalyzed by the Same Polymerase Proteins

AbstractInfluenza virus, a negative strand RNA virus, cannibalizes host cell, capped RNA polymerase II transcripts in the nucleus via a process termed “cap-snatching.” The viral transcriptase enzyme, which is composed of a complex of the three viral polymerase (P) proteins, contains a cap-dependent endonuclease that cleaves capped cellular RNAs in the nucleus 10–13 nucleotides from their 5′ ends. The resulting capped RNA fragments are required as primers for the initiation of viral mRNA synthesis. In the 18 years since the discovery of “cap-snatching” it has not been determined how the viral transcriptase exhibits selectivity and “snatches” caps from cellular, but not viral, mRNAs. Here we elucidate the surprising mechanism of this selectivity: the complex of the same three viral P proteins that catalyzes “cap-snatching” is also responsible for selectivity protecting the 5′ ends of viral, but not cellular, mRNAs from “cap-snatching.” The viral P protein complex is able to acquire these two very different functions because this complex lacks any detectable activity unless it binds to one or more specific RNA sequences. Here we demonstrate that the viral P protein complex binds to the common sequence in all the viral mRNAs that is immediately 3′ to the 5′ sequence that is “snatched” from host cell RNAs. This binding activates the cap-binding activity of the P protein complex, thereby enhancing its binding to the capped viral mRNA. We show that these P protein complexes protect the 5′ ends of viral mRNAs from endonucleolytic cleavage by the viral transcriptase, whereas the 5′ ends of nonviral mRNAs are not protected
Fiber Genes of Adenoviruses with Tropism for the Eye and the Genital Tract

AbstractWe have characterized the fibergenes of adenovirus type 19p (Ad19p), Ad19a, and Ad37 by sequencing. The fiber genes of Ad19a and Ad37 are identical and only five amino acids differ comparing Ad19a/Ad37 with Ad19p. Based on the translated sequences we calculated the isoelectrical points (Ips) and found that the fiber knobs of Ad19p, Ad19a, and Ad37 together with Ad8 display the highest Ips of all so far characterized. Two regions within the fiber knob with unusually basic characteristics have been identified. Sequence alignments revealed that the corresponding regions in other fiber knobs are highly antigenic in pepscan analysis and of importance for hemagglutination. Only two positions differ in the knobs comparing Ad19a/Ad37 with Ad19p. Hence, either of these or both amino acid residues should be expected to be responsible for the observed differences in hemagglutination between Ad19p and Ad19a/Ad37. Moreover, we have found two amino acids (Ala227and Lys252) that are unique in their respective position in Ad19p, Ad19a, Ad37, and Ad8. Three amino acids (Lys236, Lys240, and Asn251) are unique in their respective position in Ad19a and Ad37, that manifest a tropism for the genital tract. All five amino acids colocalize within one of the two basic regions