pinecone/core-2020-05-10-deduplication huggingface dataset:
Dual Interaction of a Geminivirus Replication Accessory Factor with a Viral Replication Protein and a Plant Cell Cycle Regulator

AbstractGeminiviruses replicate their small, single-stranded DNA genomes through double-stranded DNA intermediates in plant nuclei using host replication machinery. Like most dicot-infecting geminiviruses, tomato golden mosaic virus encodes a protein, AL3 or C3, that greatly enhances viral DNA accumulation through an unknown mechanism. Earlier studies showed that AL3 forms oligomers and interacts with the viral replication initiator AL1. Experiments reported here established that AL3 also interacts with a plant homolog of the mammalian tumor suppressor protein, retinoblastoma (pRb). Analysis of truncated AL3 proteins indicated that pRb and AL1 bind to similar regions of AL3, whereas AL3 oligomerization is dependent on a different region of the protein. Analysis of truncated AL1 proteins located the AL3-binding domain between AL1 amino acids 101 and 180 to a region that also includes the AL1 oligomerization domain and the catalytic site for initiation of viral DNA replication. Interestingly, the AL3-binding domain was fully contiguous with the domain that mediates AL1/pRb interactions. The potential significance of AL3/pRb binding and the coincidence of the domains responsible for AL3, AL1, and pRb interactions are discussed
Enhanced Cellular Immune Response and Reduced CD8+ Lymphocyte Apoptosis in Acutely SIV-Infected Rhesus Macaques after Short-Term Antiretroviral Treatment

AbstractLosing the decisive virus-specific functions of both CD4+ and CD8+ T lymphocytes in the first weeks after immunodeficiency virus infection ultimately leads to AIDS. The SIV/rhesus monkey model for AIDS was used to demonstrate that a 4-week chemotherapeutic reduction of viral load during acute SIV infection of macaques allowed the development of a competent immune response able to control virus replication after discontinuation of treatment in two of five monkeys. Increasing SIV-specific CD4+ T-helper-cell proliferation was found in all macaques several weeks after treatment, independent of their viral load. However, only macaques with low viral loads showed persistent T-cell reactivity of lymph node cells. In contrast to animals with higher viral loads, T-helper-cell counts and memory T-helper cells did not decline in the two macaques controlling viral replication. Lymphocyte apoptosis was consistently low in all treated macaques. In contrast, high CD8+ lymphocyte death but only slightly increased CD4+ lymphocyte apoptosis were observed during the first weeks after infection in untreated control animals, indicating that early apoptotic death of virus-specific CTL could be an important factor for disease development. Antiretroviral treatment early after infection obviously retained virus-specific and competent T lymphocytes, whereby a virus-specific immune response could develop in two animals able to control the viral replication after cessation of treatment
Epitopes on the Dengue 1 Virus Envelope Protein Recognized by Neutralizing IgM Monoclonal Antibodies

AbstractThree of 41 IgM monoclonal antibodies derived from dengue 1 virus immunized mice neutralized dengue 1 infection in vitro. All three neutralizing monoclonal antibodies reacted with spatially related epitopes on the E protein of dengue 1 which were also recognized by antibodies in sera from dengue patients. Two neutralization-resistant populations of dengue 1 virus, D1-M10 and D1-M17, were selected by sequential passage of virus in C6/36 cells in the presence of neutralizing IgM monoclonal antibodies M10 and M17, respectively. Single nucleotide changes occurred in the E protein gene of each of these virus populations resulting in single amino acid substitutions at E279 (Phe–Ser) in D1-M10 and at E293 (Thr–Ile) in D1-M17. Both neutralization-resistant populations of virus were more sensitive to elevated temperature than was the wild-type dengue 1 virus and the infectivity and haemagglutinating ability of the neutralization-resistant populations decreased more slowly than that of wild-type virus when exposed to pH in the range 5.8 to 7.0. These are the first epitopes involved in neutralization to have been identified in dengue 1 virus and the first outside domain III of the E protein on any dengue virus
Variation in Liposome Binding among Enteroviruses

AbstractLiposome-binding properties of native virions and in vitro generated 135S particles of eight enteroviruses were studied. The temperature required for the structural transition from the native 160S virion to a 135S particle was virus-specific, ranging from +38°C to more than +50°C. While the 135S particles of poliovirus 1/Mahoney (PV1) and coxsackievirus A21 (CAV21) were capable of binding to liposomes, the other viruses showed minimal binding. Both of the viruses that bound to liposomes as 135S particles also bound as native virions. In addition, PV3/Sabin bound to liposomes as native virions but not as 135S particles, and the flotation patterns were different from those of PV1 and CAV21. The nonbinding viruses included coxsackieviruses A7, A9, A16, and B5, and enterovirus 68. The results follow the new classification of enteroviruses, as CAV21 is a member of the human enterovirus C species, which is genetically close to the poliovirus species
A Novel Model for the Study of the Therapy of Flavivirus Infections Using the Modoc Virus

AbstractThe murine Flavivirus Modoc replicates well in Vero cells and appears to be as equally sensitive as both yellow fever and dengue fever virus to a selection of antiviral agents. Infection of SCID mice, by either the intracerebral, intraperitoneal, or intranasal route, results in 100% mortality. Immunocompetent mice and hamsters proved to be susceptible to the virus only when inoculated via the intranasal or intracerebral route. Animals ultimately die of (histologically proven) encephalitis with features similar to Flavivirus encephalitis in man. Viral RNA was detected in the brain, spleen, and salivary glands of infected SCID mice and the brain, lung, kidney, and salivary glands of infected hamsters. In SCID mice, the interferon inducer poly IC protected against Modoc virus-induced morbidity and mortality and this protection was associated with a reduction in infectious virus content and viral RNA load. Infected hamsters shed the virus in the urine. This allows daily monitoring of (inhibition of) viral replication, by means of a noninvasive method and in the same animal. The Modoc virus model appears attractive for the study of chemoprophylactic or chemotherapeutic strategies against Flavivirus infections
Cellular Basis of Potato Spindle Tuber Viroid Systemic Movement

AbstractViroids are small, nontranslatable pathogenic RNAs that replicate autonomously and traffic systemically in their host plants. We have used in situ hybridization to analyze the trafficking pattern of Potato spindle tuber viroid (PSTVd) in tomato and Nicotiana benthamiana. When PSTVd was inoculated onto the stem of a plant, it replicated and trafficked to sink, but not source, leaves. PSTVd was absent from shoot apical meristems. In the flowers of infected plants, PSTVd was present in the sepals, but was absent in the petals, stamens, and ovary. The replicative form of PSTVd was detected in the phloem. Our data demonstrate that (i) PSTVd traffics long distance in the phloem and this trafficking is likely sustained by replication of the viroid in the phloem, and (ii) PSTVd trafficking is governed by plant developmental and cellular factors. The dependency of PSTVd and other viroids on cellular mechanisms for RNA trafficking makes them excellent tools to study such mechanisms
The Equine Herpesvirus 1 Immediate-Early Protein Interacts with EAP, a Nucleolar-Ribosomal Protein

AbstractThe equine herpesvirus 1 (EHV-1) immediate-early (IE) phosphoprotein is essential for the activation of transcription from viral early and late promoters and regulates transcription from its own promoter. The IE protein of 1487 amino acids contains a serine-rich tract (SRT) between residues 181 and 220. Deletion of the SRT decreased transactivation activity of the IE protein. Previous results from investigation of the ICP4 protein, the IE homolog of herpes simplex virus 1 (HSV-1), revealed that a domain containing a serine-rich tract interacts with EAP (Epstein–Barr virus-encoded small nuclear RNA-associated protein), a 15-kDa nucleolar-ribosomal protein (R. Leopardi, and B. Roizman, Proc. Natl. Acad. Sci. USA 93, 4572–4576, 1996). DNA binding assays revealed that (i) glutathione S-transferase (GST)-EAP disrupted the binding of HSV-1 ICP4 to its cognate DNA in a dose-dependent manner, (ii) GST-EAP interacted with the EHV-1 IE protein, but did not disrupt its binding to its cognate site in viral DNA. GST-pulldown assays indicated that the SRT of the IE protein is required for physical interaction with EAP. The IE protein and EAP colocalized in the cytoplasm of the infected equine ETCC cells at late times of the infection cycle. This latter finding may be important in EHV-1 gene regulation since late viral gene expression is greatly influenced by the EICP0 trans-activator protein whose function is antagonized by the IE protein
The Sequence and Antiapoptotic Functional Domains of the Human Cytomegalovirus UL37 Exon 1 Immediate Early Protein Are Conserved in Multiple Primary Strains

The human cytomegalovirus UL37 exon 1 gene encodes the immediate early protein pUL37x1 that has antiapoptotic and regulatory activities. Deletion mutagenesis analysis of the open reading frame of UL37x1 identified two domains that are necessary and sufficient for its antiapoptotic activity. These domains are confined within the segments between amino acids 5 to 34, and 118 to 147, respectively. The first domain provides the targeting of the protein to mitochondria. Direct PCR sequencing of UL37 exon 1 amplified from 26 primary strains of human cytomegalovirus demonstrated that the promoter, polyadenylation signal, and the two segments of pUL37x1 required for its antiapoptotic function were invariant in all sequenced strains and identical to those in AD169 pUL37x1. In total, UL37 exon 1 varies between 0.0 and 1.6% at the nucleotide level from strain AD169. Only 11 amino acids were found to vary in one or more viral strains, and these variations occurred only in the domains of pUL37x1 dispensable for its antiapoptotic function. We infer from this remarkable conservation of pUL37x1 in primary strains that this protein and, probably, its antiapoptotic function are required for productive replication of human cytomegalovirus in humans
Combined Results from Solution Studies on Intact Influenza Virus M1 Protein and from a New Crystal Form of Its N-Terminal Domain Show That M1 Is an Elongated Monomer

AbstractThe amino-terminal domain of influenza A virus matrix protein (residues 1–164) was crystallized at pH 7 into a new crystal form in space group P1. This packing of the protein implies that M1(1–164) was monomeric in solution when it crystallized. Otherwise, the structure of the M1 fragment in the pH 7 crystals was the same as the monomers in crystals formed at pH 4 where crystal packing resulted in dimer formation [B. Sha and M. Luo, 1997, Nature Struct. Biol. 4, 239–244]. Analysis of intact M1 protein, the N-terminal domain, and the remaining C-terminal fragment (residues 165–252) in solution also showed that the N-terminal domain was monomeric with the same dimensions as determined from the crystal structure. Intact M1 protein was also monomeric but with an elongated shape due to the presence of the C-terminal part. Circular dichroism showed that the C-terminal part of M1 contained helical structure. A model for soluble M1 is presented, based on the assumption that the C-terminal domain is spherical, in which the N- and C-terminal domains are connected by a linker sequence which is available for proteolytic attack
Association of Bovine Papillomavirus Type 1 with Microtubules

AbstractTransport of BPV-1 virus from the cell membrane to the nucleus was studied in vitro in CV-1 cells. At reduced temperature (4°C), BPV-1 binding to CV-1 cells was unaffected but there was no transport of virions across the cytosol. Electron microscopy showed BPV-1 virions in association with microtubules in the cytoplasm, a finding confirmed by co-immunoprecipitation of L1 protein and tubulin. Internalization of virus was unimpaired in cells treated with the microtubule-depolymerizing drug nocodazole but virions were retained in cytoplasmic vesicles and not transported to the nucleus. We conclude that a microtubule transport mechanism in CV-1 cells moves intact BPV-1 virions from the cell surface to the nuclear membrane
Replication of Porcine Circovirus Type 1 Requires Two Proteins Encoded by the Viral rep Gene

AbstractThe rep gene of porcine circovirus type 1 (PCV1) is indispensable for replication of viral DNA. Truncation or introduction of point mutations into four conserved sequence motifs led to inactivation of Rep as replication initiator. Transcription of rep starts at nucleotide 767 ± 10 bp. An intron (nucleotides 1176 to 1558) is removed by splicing. This leads to synthesis of a truncated protein, which was termed Rep′ (19.2 kDa). Because of a frameshift, the last 48 amino acids of Rep′ deviate from the C-terminus of the 35.6-kDa full-length Rep protein. The presence of full-length and spliced rep transcripts was demonstrated in PCV1-infected cells as well as in cells transfected with a plasmid carrying the rep gene by real-time PCR. In contrast to other viruses replicating via a rolling circle, Rep protein alone cannot promote replication: Rep and Rep′ together comprise the functional replication initiator factor of PCV1
Enhanced Expression of the Early Retrotransposon in C3H Mouse-Derived Myeloid Leukemia Cells

AbstractCells of acute myeloid leukemia (AML) from C3H/He mice express an increased amount of RNA for an endogenous retrovirus-like retrotransposon, intracisternal A-particle element. We analyzed the transcription of other mouse retrotransposons in C3H-derived tumor cells and found that all the AML lines from different mice overexpress early-transposon (ETn) RNA. In contrast, only faint levels of ETn were detected in the cells from other tumors, including hepatoma and lymphoma. The polyadenylation sites of the ETn RNA in the AML cells varied. We also determined the binding site for the nuclear extract of the AML cells in the long terminal repeat sequence of ETn. The overexpression of ETn as a common phenotype of AML cells suggests that myeloid cells with this phenotype are the origin of all the AML cells or that the phenotype is acquired during leukemogenesis
Hepatitis C Virus Structural Proteins Reside in the Endoplasmic Reticulum as Well as in the Intermediate Compartment/cis-Golgi Complex Region of Stably Transfected Cells

AbstractThe intracellular localization of hepatitis C virus structural proteins was analyzed by confocal immunofluorescence microscopy, cell fractionation, and immunoelectron microscopy in stably transfected cells that do not overexpress the viral proteins. The results strongly suggest that at steady state the structural proteins reside not only in the endoplasmic reticulum but also in the intermediate compartment and cis-Golgi complex region. By analogy with other viral systems, this finding raises the possibility that the intermediate compartment and cis-Golgi complex play a role in the assembly and budding of hepatitis C virus
Canine Parvovirus Capsid Assembly and Differences in Mammalian and Insect Cells

AbstractWe examined the assembly processes of the capsid proteins of canine parvovirus (CPV) in mammalian and insect cells. In CPV-infected cells empty capsids assembled within 15 min, and then continued to form over the following 1 h, while full (DNA-containing) capsids were detected only after 60 min, and those accumulated slowly over several hours. In cells expressing VP1 and VP2 or only VP2, empty capsid formation was also efficient, but was slightly slower than that in infected cells. Small amounts of trimer forms of VP2 were detected in cells expressing wild type capsid proteins, but were not seen for mutants containing changes that prevented capsid assembly. CPV capsids accumulated in the cell nucleus, but mutant VP1 and VP2 proteins that did not assemble became distributed throughout the nucleus and the cytoplasm, irrespective of whether they were expressed as VP1 and VP2, or as VP2 only. Urea or pH treatment of empty capsids released dimer, trimer, or pentamer capsid protein combinations, while treatment of full capsids consistently released trimer and, in some cases, pentamer forms. When wild type or assembly-defective VP2 genes were expressed from recombinant baculoviruses in insect cells, most of the protein was recovered as noncapsid aggregates, and only a small proportion assembled into capsids. Both the assembled capsids and the noncapsid aggregates were seen primarily in the cytoplasm of the insect cells. The VP2 expressed in insect cells that was recovered in aggregates had an isoelectric point of about pH 6.3, while that recovered from assembled capsids had a pI of about 5.2, similar to that seen for the VP2 of capsids recovered from mammalian cells
The Structure of Isometric Capsids of Bacteriophage T4

AbstractThe three-dimensional structure of DNA-filled, bacteriophage T4 isometric capsids has been determined by means of cryoelectron microscopy and image reconstruction techniques. The packing geometry of protein subunits on the capsid surface was confirmed to be that of the triangulation class T = 13. The reconstruction clearly shows pentamers, attributed to capsid protein gp24*, surrounded by hexamers of the major capsid protein, gp23*. Positions of the accessory proteins, Hoc and Soc, are also clearly delineated in the surface lattice. The Hoc protein is the most prominent surface feature and appears as an extended molecule with a rounded base from which a thin neck and a globular head protrude. One Hoc molecule associates with each hexamer. Nearly continuous “ridges” are formed at the periphery of the gp23* hexamers by an association of 12 Soc molecules; however, Soc is absent along the boundaries between the hexamers and the pentamers. The duplex DNA genome forms a highly condensed series of concentric layers, spaced about 2.36 nm apart, that follow the general contour of the inner wall of the protein capsid
Vesicular Stomatitis Virus Glycoprotein Containing the Entire Green Fluorescent Protein on Its Cytoplasmic Domain Is Incorporated Efficiently into Virus Particles

AbstractThe envelope glycoprotein (G) of vesicular stomatitis virus (VSV) contains a short cytoplasmic domain of 29 amino acids. To determine whether VSV particle assembly could accommodate a G protein with a large cytoplasmic domain, we constructed a gene called G/GFP encoding the VSV G protein with the 27-kDa green fluorescent protein linked to its cytoplasmic domain. This gene was inserted into the infectious clone of VSV and we recovered a recombinant virus expressing G/GFP from this extra gene. This VSV-G/GFP virus grew to titers equivalent to that of wild-type virus and was stable upon passaging. The G/GFP protein formed mixed trimers containing an average of two wild-type G proteins and one G/GFP protein. This heterotrimeric protein was expressed on the cell surface, and was incorporated into virus particles with almost the same efficiency as wild-type VSV G protein. These results indicate that there is substantial space available between the viral membrane and the nucleocapsid that can accommodate such a large cytoplasmic domain. The green fluorescent virus particles were readily visualized by fluorescence microscopy and had a normal morphology by electron microscopy. To determine whether virus assembly could occur efficiently when all G proteins contained the GFP cytoplasmic domain, a VSV recombinant in which the G gene was completely replaced by the VSV-G/GFP gene was recovered. This virus rapidly lost expression of the GFP protein sequence through introduction of a stop codon within the sequence encoding the G cytoplasmic domain, indicating strong selection against homotrimeric G protein bearing such a large cytoplasmic domain
Characterization of the Three HERV-H Proviruses with an Open Envelope Reading Frame Encompassing the Immunosuppressive Domain and Evolutionary History in Primates

AbstractThe HERV-H family is one of the largest human endogenous retrovirus families, with approximately 1000 elements. Using a direct coupled in vitro transcription/translation approach (PTT for protein truncation test) and an extended series of primers on human genomic DNA, on monochromosomal hybrids and on a BAC library, we could demonstrate that there are only three envelopes with a large open reading frame encompassing the immunosuppressive (ISU) domain, corresponding to 62-, 60-, and 59-kDa potential translational products. The associated proviruses, HERV-H/env62, HERV-H/env60, and HERV-H/env59 were sequenced together with their flanking DNA and mapped by FISH, and their entry times within the primate lineage were determined. Analysis of the LTR sequences revealed numerous recombinational and/or homogenization events in the course of evolution, with divergences between 5′ and 3′ LTRs higher than expected for a simple time-dependent genetic drift. PTT analyses further revealed that the three large envelopes in humans are prematurely stopped in the majority of primates, and sequencing of the largest envelope gene, from HERV-H/env62, in five human individuals revealed two polymorphic sites. The results are consistent with the absence of a strong selective pressure for the conservation of a functional envelope gene of possible benefit for the host, but do not exclude somatic effects possibly associated with the immunosuppressive domain carried by these genes
Structure of the Maize Streak Virus Geminate Particle

AbstractThe Geminiviridae is an extensive family of plant viruses responsible for economically devastating diseases in crops worldwide. Geminiviruses package circular, single-stranded DNA (ssDNA) genomes. The characteristic twinned or “geminate” particles, which consist of two joined, incomplete T = 1 icosahedra, are unique among viruses. We have determined the first structure of a geminivirus particle, the Nigerian strain of Maize streak virus (MSV-N), using cryo-electron microscopy and three-dimensional image reconstruction methods. The particle, of dimensions 220 × 380 Å, has an overall 52-point-group symmetry, in which each half particle “head” consists of the coat protein (CP) arranged with quasi-icosahedral symmetry. We have modeled the MSV-N CP as an eight-stranded, antiparallel β-barrel motif (a structural motif common to all known ssDNA viruses) with an N-terminal α-helix. This has produced a model of the geminate particle in which 110 copies of the CP nicely fit into the reconstructed density map. The reconstructed density map and MSV-N pseudo-atomic model demonstrate that the geminate particle has a stable, defined structure
Bovine Herpesvirus 1 Glycoprotein G Is Required for Prevention of Apoptosis and Efficient Viral Growth in Rabbit Kidney Cells

AbstractIn rabbit kidney (RK13) cells, gG-negative BHV-1 exhibited significant defects in plaque formation and growth compared to that of gG-positive BHV-1. RK13 cells infected with gG-negative BHV-1 exhibited a distinctive CPE and contained a larger number of cells stained with trypan blue dye compared to those infected with gG-positive strains, suggesting that gG-negative BHV-1 inflicted more damage to the infected cells than gG-positive BHV-1. Apoptotic cell death was induced in RK13 cells infected with gG-negative BHV-1 within 8 h. In contrast, the onset of apoptosis in gG-positive BHV-1-infected RK13 cells was around 12–16 h postinfection. In the presence of caspase inhibitor Z-Asp-CH2-DCB, multiplication of gG-negative minus BHV-1 was significantly increased. These results demonstrate that BHV-1 gG is involved in stabilizing the cell structure, postponing apoptotic process, and efficient BHV-1 replication in infected RK13 cells