pinecone/core-2020-05-10-deduplication huggingface dataset:
Interaction with Simian Hck Tyrosine Kinase Reveals Convergent Evolution of the Nef Protein from Simian and Human Immunodeficiency Viruses Despite Differential Molecular Surface Usage

AbstractSimian and human immunodeficiency virus type 1 (SIV and HIV-1) Nef proteins are thought to use different molecular surfaces to mediate the protein–protein interactions required for their otherwise similar functions. This genetically separable function suggests convergent evolution of primate lentiviruses and/or structural differences between human and nonhuman primate cellular target proteins. However, such comparative molecular analyses have not been undertaken so far using the respective natural host-derived cellular targets. We cloned simian Src family kinase Hck and analyzed structurally and biochemically its interaction with SIV Nef
Leporipoxvirus Cu-Zn Superoxide Dismutase Homologs Inhibit Cellular Superoxide Dismutase, but Are Not Essential for Virus Replication or Virulence

AbstractVertebrate poxviruses encode homologs of cellular cupro-zinc superoxide dismutases (Cu-Zn SOD). In this study we have examined the molecular genetic properties of two Cu-Zn SOD homologs encoded by the Shope fibroma virus (SFV) and myxoma virus. These Leporipoxvirus proteins should be catalytically inactive as judged by the point mutations which alter a key catalytic arginine and restructure the predicted Cu-binding domain. This prediction was confirmed using in situ gel assays and recombinant proteins produced both in bacteria and in mammalian cells. Western blot analysis showed that these proteins are produced in abundance late in infection and can, upon exposure to oxidizing conditions, form disulfide cross-linked dimers. They are also virion components and not essential for growth in culture or virulence. Leporipoxvirus Cu-Zn SOD homologs affected two phenotypes. First, deletion of the myxoma M131R gene caused the mutant virus to grow better (∼10-fold) in culture than does the wild-type parent. Second, expression of either native or recombinant Leporipoxvirus proteins is accompanied by a decline in cellular Cu-Zn SOD activity. We concluded that these gene products can somehow modulate the activity of host Cu-Zn SODs, but what advantage is thus gained by the virus remains to be established
Identification of Two Nuclear Import Signals in the α-Gene Product ICP22 of Herpes Simplex Virus 1

AbstractThe herpes simplex virus 1 (HSV-1) infected cell protein 22 (ICP22) is a multifunctional viral regulator that localizes in the nucleus of infected cells. ICP22 is required for optimal virus replication in certain cell types and is subject to extensive posttranslational modification. To map the signals in ICP22 which mediate its efficient nuclear localization, we investigated the nuclear import of fusion proteins comprising various fragments of ICP22 fused to green fluorescent protein (GFP) or β-galactosidase (β-Gal). These data demonstrated that ICP22 contains two independent regions with nuclear localization signal (NLS) activity. NLS1 maps to ICP22 amino acid position 16–31 and closely resembles the classical bipartite NLS of the type originally identified in nucleoplasmin. In contrast, NLS2 maps to ICP22 amino acid position 118–131 and contains multiple critical basic residues. Furthermore, fusion of both NLSs to chimeric glutathione-S-transferase (GST)–GFP protein and subsequent cytoplasmic microinjection of the respective transport substrates allowed us to monitor nuclear import in real-time. These data demonstrated that both ICP22-derived NLSs mediated efficient nuclear import with identical kinetics, resulting in complete nuclear accumulation of the chimeric transport cargoes at approximately 30 min postinjection. Finally, our data provide new insights into the domain structure of the multifunctional α-gene product ICP22 of HSV-1
Sequence-Specific Binding of Poly(ADP-Ribose) Polymerase-1 to the Human T Cell Leukemia Virus Type-I Tax Responsive Element

AbstractWe have previously identified poly(ADP-ribose) polymerase-1 (PARP-1) as a coactivator for the human T cell leukemia virus type I (HTLV-I) transcription activator Tax. While PARP-1 is believed to contribute to DNA repair, PARP-1 has been described as a coactivator for other transcription factors. Recent evidence suggests that PARP-1 forms complexes on cellular promoters, so we investigated PARP-1 complexes on the HTLV-I Tax responsive elements (TxREs) using an end-blocked DNA binding assay. We observed sequence-specific binding of PARP-1 to the TxREs. The DNA binding domain of PARP-1 was fused to the transcriptional activation domain of VP16, and this fusion protein activated the HTLV-I promoter in a TxRE-dependent manner. Internal, sequence-specific binding of PARP-1 to DNA provides a mechanism for transcriptional regulation of the HTLV-I promoter. The mechanism of PARP-1 function in the HTLV-I system may have common mechanistic steps with other cellular promoters, including the formation of active complexes on the promoter
Genetic Diversity of the M RNA Segment among Crimean-Congo Hemorrhagic Fever Virus Isolates in China

AbstractThe complete nucleotide sequences of the medium (M) segment of seven Chinese isolates of Crimean-Congo hemorrhagic fever (CCHF) virus were determined. The M-segment RNA of CCHF virus comprises 5356–5377 nucleotides depending on the isolate and encodes a protein comprising 1689–1697 amino acids in a viral complementary sense. Phylogenetic analysis of the M segment showed that the Chinese CCHF virus isolates were clustered into three groups, one of which was more closely related to a Nigerian isolate. Pairwise comparison of a precursor protein showed that amino-terminal regions comprising 250 amino acids were extraordinary heterogeneous, with a 22.4% identity in amino acids being observed between the most distantly related isolates. Since all the viruses were isolated from 1966 to 1988 within a restricted area in the Xinjiang Autonomous Region in western China, the results indicate that a multisource virus population is endemic in this region
Sequence Analysis of the Genome of Porcine Lymphotropic Herpesvirus 1 and Gene Expression during Posttransplant Lymphoproliferative Disease of Pigs

AbstractThe porcine lymphotropic herpesvirus 1 (PLHV-1), the first gammaherpesvirus of pigs, has been detected at a high prevalence in healthy pig populations. A porcine gammaherpesvirus has also been detected at high copy numbers in animals suffering from posttransplant lymphoproliferative disease (PTLD). While human PTLD is a EBV-associated complication following clinical transplantation, porcine PTLD is a disease recently described in pigs undergoing experimental allogeneic hematopoietic stem cell transplantation. Here we demonstrate that PLHV-1 and the virus present in porcine PTLD are indistinguishable, and present the characterization of 73 kbp of the genome of PLHV-1. We identified homologs of cellular genes, including a putative G protein-coupled receptor (GCR) as well as a viral homolog of the bcl-2 oncogene (v-bcl-2) and show significant transcription of these genes as well as of several other PLHV-1 genes in lymph nodes of a PTLD-affected pig. These data indicate that PLHV-1 is active during PTLD and may be involved in the etiology of this lymphoproliferative disease
Communication between S1N330 and a Region in S2 of Murine Coronavirus Spike Protein Is Important for Virus Entry into Cells Expressing CEACAM1b Receptor

AbstractThe soluble receptor-resistant (srr) mutants, srr7 and srr11, isolated from a murine coronavirus, mouse hepatitis virus (MHV) JHMV, have an amino acid mutation at positions 1114 (Leu to Phe) and 65 (Leu to His), respectively, in the spike (S) protein. These mutants failed to efficiently infect BHK cells expressing CEACAM1b (BHK-R2), due to their low entry into this cell line, although they infected cells expressing CEACAM1a (BHK-R1) in a manner similar to that of wild-type (wt) JHMV cl-2 (Matsuyama and Taguchi, Virology 273, 80–89, 2000). Following the repeated passage of these mutants through BHK-R2 cells, viruses were no longer isolated from srr11-infected cells, while two distinct mutants, srr7A and srr7B, were obtained from srr7-infected cells. Srr7A and srr7B grew 2 log10 higher than srr7 and induced fusion in BHK-R2 cells, being similar to wt virus. In addition to the amino acid change at position 1114 that stemmed from parental srr7, srr7A and srr7B had mutations around position 280, corresponding to the third region of the S1N330 receptor-binding site (S1N330-III) common to all MHV strains examined thus far. Srr7A and srr7B S proteins showed high fusogenicity in both BHK-R1 and BHK-R2 cells, like the wt virus, while srr7Aa and srr7Ba S proteins, which had mutations in S1N330-III but not at amino acid 1114, exhibited profoundly reduced fusion activity in these cell lines. These findings suggest that communication between S1N330-III and the amino acid at position 1114 is important for efficient fusion activity in BHK-R2 cells. S1N330-III is a possible region in the S1 involved in viral entry into cells
Potential Multiple Endonuclease Functions and a Ribonuclease H Encoded in Retroposon Genomes

AbstractAmong the retroposons, the source of the endonuclease activity is known to be variable and can be provided as either a retroviral-like integrase or a protein similar to the cellular apurinic–apyrimidinic endonuclease. It has also been reported that other retroposon and retrointron sequences have limited similarity to various eubacterial endonucleases. We investigated whether any retroposon genomes possibly encode multiple endonuclease functions. Amino acid alignments were generated and analyzed for the presence of the characterized ordered-series-of-motifs (OSM) representative of four different endonuclease functions. The results indicate that SLACS, CZAR, CRE1, CRE2, and some Trypanosoma brucei retroposon sequences encode multiple putative endonuclease functions. Interestingly, one of the endonuclease functions is embedded within the potential ribonuclease H sequence found in SLACS, CZAR, CRE1, CRE2, and R2BM retroposons
In the Virion, the 11-Amino-Acid Peptide Cofactor pVIc Is Covalently Linked to the Adenovirus Proteinase

AbstractPreviously, the adenovirus proteinase (AVP) had been shown to be stimulated by an 11-amino-acid cofactor pVIc; the crystal structure of an AVP–pVIc complex formed in vitro reveals a disulfide bond between AVP and pVIc. However, that disulfide bond was recently shown not to be required for maximal stimulation of enzyme activity by pVIc in vitro. Is the disulfide bond physiologically relevant or is it an artifact that arose in the crystallization of the complex? Here we show that a disulfide bond between AVP and pVIc is physiologically relevant, because in the virus particle AVP is linked to pVIc via a disulfide bond. This is also the first experimental proof that AVP interacts in vivo with one of its cofactors, all of which were discovered and characterized in vitro. A rationale as to why this apparently unnecessary disulfide bond between AVP and pVIc forms in the virus particle is presented
Simian Immunodeficiency Virus Encephalitis: Analysis of Envelope Sequences from Individual Brain Multinucleated Giant Cells and Tissue Samples

AbstractSimian immunodeficiency virus (SIV)-infected macaques develop an encephalitis (SIVE) that is pathologically virtually indistinguishable from that associated with HIV infection, with multinucleated giant cells (MNGCs) being the principal histopathological manifestation. To dissect SIV variants responsible for MNGC development, we examined the relationships between env sequences transcribed in individual MNGCs and those from genomic DNA of brain and spleen tissues. The brain-specific variant found in all brain clones was dominant among the clones from MNGCs, suggesting a role in the formation of giant cells. Furthermore, two additional minor groups of sequences were present in MNGCs. One group consisted of sequences closely related to those from spleen, indicating recent and probably multiple episodes of neuroinvasion. The second group represented clones similar or identical to the initial inoculum. The survival of archival sequences and their activation presumably by the fusion of productively and quiescently infected macrophages/microglia identify the central nervous system as a possible anatomical reservoir for latent infection
Identification of the Subgenomic mRNAs That Encode 6-kDa Movement Protein and Hsp70 Homolog of Beet Yellows Virus

AbstractA tandem arrangement of the genes encoding the ∼6-kDa hydrophobic protein (p6) and Hsp70 homolog (Hsp70h) is conserved among the members of the Closterovirus genus. It was not known, however, if these movement proteins are expressed from one or two subgenomic (sg) RNAs. Here we employ RNA ligase-mediated RACE to show that the Beet yellows virus (BYV), a prototype Closterovius, produces separate sgRNAs encoding p6 and Hsp70h. This result is further supported by generation of the recombinant BYV in which the truncated variants of these sgRNAs are resolved by Northern analysis. The 5′-termini of the p6 and Hsp70h sgRNAs are localized to BYV nucleotides G-9402 and A-9467, respectively. Each of the sgRNAs was generated in vitro and found to direct the expected product upon translation in wheat germ extract. Inactivation of the first start codons in these sgRNAs abolished translation of the each product. The polyclonal antibodies raised to synthetic C-terminal peptides of p6 and Hsp70h specifically recognized corresponding translation products, as well as p6 and Hsp70h produced in BYV-infected plants. Taken together with the previous work, our data demonstrate that expression of the BYV genome involves the formation of as many as seven sgRNAs
Stability of Rice yellow mottle virus and Cellular Compartmentalization during the Infection Process in Oryza sativa (L.)

AbstractRice yellow mottle virus (RYMV) is icosahedral in morphology and known to swell in vitro, but the biological function of swollen particles remains unknown. Anion-exchange chromatography was used to identify three markedly stable forms of RYMV particles from infected plants: (1) an unstable swollen form lacking Ca2+ and dependent upon basic pH; (2) a more stable transitional form lacking Ca2+ but dependent upon acidic pH; and (3) a pH-independent, stable, compact form containing Ca2+. Particle stability increased over the time course of infection in rice plants: transitional and swollen forms were abundant during early infection (2 weeks postinfection), whereas compact forms increased during later stages of infection. Electron microscopy of infected tissue revealed virus particles in vacuoles of xylem parenchyma and mesophyll cells early in the time course of infection and suggested that vacuoles and other vesicles were the major storage compartments for virus particles. We propose a model in which virus maturation is associated with the virus accumulation in vacuoles. In this acidic compartment, virus particles may bind Ca2+ to produce a highly stable, compact form of the virus. The localization of subcellular RYMV isoforms in infected cells and the corresponding biological properties of the virus are discussed
Involvement of Integrin αvβ3 in the Pathogenesis of Human Immunodeficiency Virus Type 1 Infection in Monocytes

AbstractAttachment of HIV to macrophages is a critical early event in the establishment of infection. In the present study, we demonstrate the involvement of integrin αvβ3 (vitronectin receptor) in HIV infection of peripheral blood monocyte-derived macrophages. Culturing monocytes in the presence of M-CSF for 3 days upregulated expression of the αv-containing integrins, αvβ3 and αvβ5. The increase in αvβ3 expression was accompanied by increased HIV-1 replication by monocytes. Immunoblot analysis showed that purified HIV-gp120 protein interacted with CD4 and αvβ3 in immunoprecipitation experiments. Neutralizing antibodies against the αvβ3 integrin interfered with the coprecipitation of αvβ3 with an anti-gp120 antibody and substantially inhibited HIV infection of monocytes. Neutralizing antibodies against αvβ5 or β1 integrins did not significantly affect HIV infection. These results indicate that HIV infection of primary monocytes requires differentiation of these cells and may involve αvβ3 interaction with the HIV-1 envelope protein gp120 for productive infection
Interleukin 17 Modulates the Immune Response to Vaccinia Virus Infection

AbstractInterleukin 17 (IL-17) is a newly identified cytokine that has a homolog in herpesvirus saimiri. We inserted murine IL-17 into vaccinia virus to study the role of IL-17 in viral infection. Vaccinia virus expressing IL-17 (vv-IL17) and its parental control virus (vv-pRB) grew to similar titers in vitro; however, vv-IL17 was more virulent in mice with a threefold lower LD50 than for vv-pRB, and mean time to death of 2.8 days versus 4.5 days. Mice infected with vv-IL17 had higher titers of virus in the ovaries (P < 0.02) and showed a decrease in NK cell cytotoxicity (P < 0.02) on day 3 after infection. No significant difference was found in CTL activity. In addition, a significant decrease in IgG2a (P < 0.01) and increases in IgG1, IgG3, and IgA (P < 0.03) vaccinia virus-specific antibody titers were observed in mice infected with vv-IL17 versus vv-pRB, suggesting a Th-2-like response to infection. These data indicate that IL-17 modulates the immune response during virus infection
Complete Genomic Sequence of Bacteriophage ul36: Demonstration of Phage Heterogeneity within the P335 Quasi-Species of Lactococcal Phages

AbstractThe complete genomic sequence of the Lactococcus lactis virulent phage ul36 belonging to P335 lactococcal phage species was determined and analyzed. The genomic sequence of this lactococcal phage contained 36,798 bp with an overall G+C content of 35.8 mol %. Fifty-nine open reading frames (ORFs) of more than 40 codons were found. N-terminal sequencing of phage structural proteins as well as bioinformatic analysis led to the attribution of a function to 24 ORFs (41%). A lysogeny module was found within the genome of this virulent phage. The putative integrase gene seems to be the product of a horizontal transfer because it is more closely related to Streptococcus pyogenes phages than it is to L. lactis phages. Comparative genome analysis with six complete genomes of temperate P335-like phages confirmed the heterogeneity among phages of P335 species. A dUTPase gene is the only conserved gene among all P335 phages analyzed as well as the phage BK5-T. A genetic relationship between P335 phages and the phage-type of the BK5-T species was established. Thus, we proposed that phage BK5-T be included within the P335 species and thereby reducing the number of lactococcal phage species to 11
The Novel Early Region 3 Protein E3/49K Is Specifically Expressed by Adenoviruses of Subgenus D: Implications for Epidemic Keratoconjunctivitis and Adenovirus Evolution

AbstractThe early transcription unit 3 (E3) of adenoviruses (Ads) encodes immunomodulatory functions. We previously described a novel gene of 49K within the E3 region of Ad19a, an Ad of subgenus D that is similar to Ad8 and Ad37 causes epidemic keratoconjunctivitis (EKC). Interestingly, 49K was reported not to be present in Ad9 and Ad17, other subgenus D Ads not causing EKC. Therefore, we investigated whether 49K is selectively expressed in EKC-causing Ads. Using specific DNA probes, we detect 49K-homologous genes in all subgenus D Ads tested. Moreover, 49K-specific antibodies recognize a high molecular weight protein in cells infected with all subgenus D serotypes irrespective of their ability to cause EKC. Sequencing of several 49K genes reveals a high homology without a distinct feature recognizable for those of EKC-associated Ad strains. Thus, E3/49K is a subgenus D specific E3 protein whose expression does not correlate with the EKC-causing phenotype and thus may rather be implicated in illnesses commonly caused by this subgenus. Interestingly, the 49K sequences of Ad19a and Ad37 are identical. To estimate the extent of the sequence identity between these two viruses, we initially sequenced the right ITR and the hexon. This analysis revealed that the right ITR of Ad19a is identical to Ad37, while the hexon sequence is Ad19p-like. This suggested that the region of identity is much larger and that Ad19a arose by recombination of Ad37 with an Ad19p-like Ad. Further sequencing mapped the crossover within the DNA binding protein. Thus, Ad19a contains a large sequence block (∼13 kb), from the 100K gene to the right ITR, identical to Ad37. The implications of these findings in light of the temporal appearance of the EKC-causing Ad strains are discussed
Temporal Acceleration of the Human Papillomavirus Life Cycle by Adeno-Associated Virus (AAV) Type 2 Superinfection in Natural Host Tissue

AbstractEpidemiologically, certain human papillomaviruses are positively associated with cervical cancer, while adeno-associated viruses (AAV-2) are negatively associated with this same cancer. Both HPV and AAV productively replicate in differentiating keratinocytes of the skin and interact with each other. However, AAV has a relatively fast life cycle, generating infectious progeny by the third to fourth day of an organotypic epithelial raft culture. In contrast, HPV is slow, generating infectious progeny only after 10–12 days. As earlier studies indicated that these two skin-tropic virus types significantly affect each other's life cycle, we investigated if the temporal kinetics of the slow HPV life cycle was affected by the fast AAV in raft cultures. Here it is shown that the presence of AAV-2 at a variety of multiplicities of infection (m.o.i.) resulted in early onset HPV-31b DNA replication. Using plasmids which each expressed only one of the four rep proteins, an enhancement affect was seen for all four rep proteins of AAV, with Rep40 having the highest activity. Furthermore, AAV (m.o.i. of 5) also resulted in a temporally accelerated production of HPV infectious units, seen as early as Day 4, with high levels of viral progeny being produced by Day 6.5. Like earlier studies at Day 12, histological differences were seen at Day 6.5 between AAV-infected and mock-infected HPV/rafts. These data suggest that under specific conditions the AAV rep trans-factors can positively regulate HPV gene expression in addition to the usual negative regulation that has been consistently observed by the rep proteins. These data also suggest that AAV has a significant effect upon the temporal kinetics of the HPV life cycle in natural host tissue. However, it is unclear if or how this AAV-induced fast HPV life cycle mechanistically correlates with lower rates of HPV-associated cervical disease
Evaluation of Accuracy and Precision of Adenovirus Absorptivity at 260 nm under Conditions of Complete DNA Disruption

AbstractA simple, accurate, and precise method to determine adenovirus particle concentration using 260-nm absorbance was developed as an enhancement to the method of Maizel et al. (1968, Virology 36, 115–125). This modified method ensures complete disruption of virus particles and viral DNA prior to absorbance measurements, therefore eliminating absorbance measurement errors due to hyperchromic shift and thus providing an extinction coefficient at 260 nm that is directly related to protein concentration as measured by the method of Lowry et al. (1951, J. Biol. Chem. 193, 265–275). Application of this modified method will reduce interlaboratory variability in determining adenovirus particle concentrations, as current practices reflected in the literature utilize varying sample preparation procedures and calculation methods which cause underestimation of adenovirus concentration by almost twofold. The sample pretreatment conditions used in this modified method entail incubation in 1% sodium dodecyl sulfate at 100°C for 4 min and result in an adenovirus 260-nm absorptivity of 1.8 × 1012 viral particles per milliliter per absorbance unit in a 1-cm-pathlength cell