pinecone/core-2020-05-10-deduplication huggingface dataset:
The Genomes of Three of Four Novel HPV Types, Defined by Differences of Their L1 Genes, Show High Conservation of the E7 Gene and the URR

AbstractThe DNA genomes of four new human papillomaviruses, HPV 75, HPV 76, HPV 77, and HPV 80, have been cloned, sequenced, and characterized. HPV 75, HPV 76 (both HPV 49-related), and HPV 77 (HPV 29-related) were isolated from benign cutaneous warts and HPV 80 (HPV 15-related) from histologically normal skin. HPV 77 has also been demonstrated in dysplastic warts and squamous cell carcinomas of the skin. The sequence data presented in this study led to a proposed modification of the definition of a new HPV type. The high degree of DNA sequence similarity between the E7 ORF of HPV 77 and HPV 29 (97.7%), as opposed to the E6 (82.8%) and L1 (85.3%) ORFs, might suggest conservation of a specific function or a possible recombinational event. Only the E6 and L1 ORFs of HPV 75 and HPV 76 have a similarity lower than 90%, whereas the DNA sequences of their upstream regulatory regions (URRs) share a similarity of 93%. The E7, E1, and E4 ORFs, as well as the URR of HPV 15 and HPV 80, share sequence similarities higher than 90%. Such a divergence in the similarity between different segments of the virus genomes of closely related HPV types has not been noted to date. A detailed comparative sequence analysis was performed. HPV 75, HPV 76, and HPV 80 revealed features characteristic of truly cutaneous HPV types, whereas HPV 77 shared several characteristics with the mucosal HPV types, some of which may have functional consequences
Identification and Characterization of a Protein Kinase-Interacting Protein Encoded by theAutographa californicaNuclear Polyhedrosis Virus

AbstractWe have used a yeast two-hybrid system to identify a baculoviral gene encoding a protein kinase-interacting protein (PKIP). Thepkipgene is located at 15.8–16.2 m.u (map units) and represents ORF 24 in the sequence of978944of theAutographa californicanuclear polyhedrosis virus. PKIP is a 19.2-kDa protein and appears to stimulate the activity of the viral protein kinase-1in vitro.Northern blotting analysis revealed thatpkipis a late gene. Attempts to plaque purify apkip−virus were unsuccessful
Rice Dwarf Phytoreovirus Segment S11 Encodes a Nucleic Acid Binding Protein

AbstractThe function of rice dwarf virus segment 11 and the corresponding segments of other phytoreoviruses is not yet determined. The amino acid sequence of Pns11, encoded by segment 11, contains a putative zinc finger and five flanking basic regions at the C-terminus. The full-length Pns11 protein and three truncated derivatives, which lack the N-terminus, the zinc-finger, or the C-terminal five basic regions were expressed inEscherichia coliand their nucleic acid binding properties were studied. Pns11 interacts with single- and double-stranded forms of DNA and RNA in a sequence-nonspecific manner. The truncated derivative which contains both the zinc-finger and the C-terminal basic regions has the same binding properties as the full-length Pns11. However, removal of either of these domains prevents binding activity. The binding activity of Pns11 was drastically reduced when the blots were treated with a high concentration of EDTA. Moreover, Pns11 extracted from infected rice also binds to single-stranded RNA. These data suggest that RDV Pns11 binding activity is structure-dependent and it may play an important role in virus replication and/or genome assortment
Nonstructural Protein-2 and the Replication of Canine Parvovirus

AbstractThe nonstructural protein-2 (NS2) of canine parvovirus (CPV) is produced from the left-hand open reading frame of the viral genome and contains 87 amino-terminal amino acids in common with nonstructural protein 1 (NS1) joined to 78 amino acids from an alternative open reading frame. In the minute virus of mice parvovirus NS2 plays a role in controlling capsid protein assembly and translation in a host-specific manner. The predicted NS2 of CPV is divergent from the proteins of the rodent parvoviruses, and the protein and its functions have not been described. We characterized the large and the small splices of CPV using reverse transcriptase–PCR. NS2 was identified using anti-peptide antibodies against the predicted C-terminal sequence and also by expressing the protein from a plasmid vector. The protein could be detected at low levels in the nucleus and the cytoplasm of a proportion of CPV-infected cells, as well as in cells transfected with the expression plasmid. Virus genomes were prepared with mutations in the splice donor or acceptor sites of the NS2-specific intron or with three different termination codons in the NS2-unique exon. Both splice donor and acceptor mutations resulted in the use of previously cryptic splice sites, and the virus containing the splice donor mutation replicated inefficiently. However, the other four mutant viruses were all viable and replicated efficiently in cat and dog cells, and two mutant viruses that were tested appeared to assemble their capsids in the same manner as did the wildtype. After inoculation of dogs an NS2 mutant virus with a termination codon in the NS2-unique exon replicated to titers similar to those seen for wildtype CPV in several tissues examined
Regulation of the Bacteriophage MugemOperon

AbstractThegemoperon of bacteriophage Mu, responsible for the complex phenomenon of phage conversion, is included in the so called “semiessential early” region of phage DNA. Unlike the other early genes of the phage which are transcribed from the pepromoter, expression of thegemoperon is driven by its own promoter, which escapes the control of the repressor. In fact, the transcript corresponding togemwas detected in immune lysogens by using a combined reverse transcription and a subsequent amplification of the resulting cDNA. The transcription initiation site from pgemwas determined by primer extension mapping experiments and localized at 8217 bp from the left end of phage DNA. Two elements which could perform the negative control ofgemwere also identified. The first is a phage product, GemB, which presumably interferes withgemexpression at a posttranscriptional level, whereas the second is a structural element, an inverted repeat immediately downstream of pgem, which acts as a terminator for the transcripts starting from pe. These transcripts could regulategemexpression by interfering with the initiation of transcription from pgem
Chimeras Containing Influenza NS1 and HIV-1 Rev Protein Sequences: Mechanism of Their Inhibition of Nuclear Export of Rev Protein–RNA Complexes

AbstractNuclear RNA export mediated by the HIV-1 Rev protein is inhibited by chimeric proteins in which the wild-type Rev protein is covalently linked to amino acid sequences of the NS1 protein of influenza A virus (NS1A protein), a protein that inhibits nuclear RNA export. These chimeric molecules function not only incisbut also intrans:they inhibit nuclear RNA export mediated by Rev protein molecules that are not covalently linked to the NS1A protein sequence. Here we show that inhibition occurs with a NS1-Rev chimera in which the 78 amino-terminal amino acids of the NS1A protein comprising its entire RNA-binding domain is deleted, thereby establishing that this carboxyl portion of the NS1A protein can function as an independent effector domain. The mechanism by which this NS1-Rev chimera inhibits Rev function intranswas determined. The Rev sequence in this chimera oligomerizes with Rev molecules intrans,and the resulting mixed oligomers are retained in the nucleus because the nuclear retention activity of the NS1 effector domain is dominant over the nuclear transport activity of the Rev effector domain. Binding of the FG-containing nucleoporin-like Rab protein to this NS1-Rev chimera, as measured in yeast two-hybrid assays, is much stronger than that to the Rev protein itself, yet nuclear export does not occur in the presence of the chimera. Unexpectedly, the introduction of specific mutations into the NS1A portion of this NS1-Rev chimera not only restores Rev-mediated nuclear export of RNA but also eliminates detectable Rab binding, indicating that this nuclear export can occur without detectable Rab binding. A different NS1-Rev chimera, one in which the NS1A protein is full-length but contains a mutated RNA-binding domain, effectively inhibits Rev-mediated nuclear export of RNA without blocking the nuclear export of the Rev protein, indicating that nuclear export of the carrier Rev protein can be uncoupled from nuclear export of its passenger RNA
Interaction between the Herpes Simplex Virus Type 1 Origin-Binding and DNA Polymerase Accessory Proteins

AbstractInteractions between the herpes simplex virus type 1 (HSV-1) origin (ori)-binding protein (UL9) and two other components of the functional DNA replication complex have been observed. However, to date, no interaction between UL9 and a component of the DNA polymerase holoenzyme has been demonstrated. In this report, we demonstrate that UL9 and the DNA polymerase accessory protein (UL42) can form a stable complexin vitroas determined by coimmunoprecipitation with specific antibodies to each protein and by affinity chromatography using glutathioneS-transferase (GST) fusion proteins. Complex formation does not require the presence of other viral proteins and occurs in the presence of ethidium bromide, indicating that UL9–UL42 interaction is DNA independent. Affinity beads charged with increasing concentrations of GST-42 fusion protein up to 5 μM bound increasing amounts of UL9 expressed byin vitrotranscription/translation in rabbit reticulocyte lysates. Binding of N- and C-terminal portions of UL9 to GST affinity matrices revealed that the N-terminal 533 amino acids were sufficient for binding to GST-42, albeit at approximately a four- to six-fold reduced affinity compared to the full-length protein. No binding of a polypeptide containing the remainder of the UL9 C-terminal residues was observed. Thus the ori-binding protein, UL9, can physically associate with at least one member of each of the complexes (helicase/primase, DNA polymerase holoenzyme, single-stranded DNA-binding protein) required for origin-dependent DNA replication. These specific interactions provide a means by which the ordered assembly of HSV-1 DNA replication proteins at origins of replication can occur in the infected cell for initiation of viral DNA synthesis
One Amino Acid Change on the Capsid Surface of Poliovirus Sabin 1 Allows the Establishment of Persistent Infections in HEp-2c Cell Cultures

AbstractPoliovirus mutants (PVpi) selected during the persistent infection of human neuroblastoma cells can establish secondary persistent infections in nonneural HEp-2c cells (I. Pelletier, T. Couderc, S. Borzakian, E. Wyckoff, R. Crainic, E. Ehrenfeld, and F. Colbère-Garapin, 1991,Virology,180, 729–737). Previous results from our laboratory have also shown that, in the genome of PVpi S11 derived from the Sabin 1 strain, the genomic region involved in this phenotype contains 11 missense mutations which map exclusively to the genes encoding the capsid proteins VP1 and VP2. We report here the identification of precise viral determinants able to confer the capacity to establish persistent infections in HEp-2c cell cultures to the lytic Sabin 1 strain. We used a strategy based on the observation that PVpi, after a few months of persistent infection in HEp-2c cells, tend to regain a more lytic phenotype in uninfected HEp-2c cell cultures. We constructed mutant viruses carrying only a few mutations potentially involved in the phenotype of persistence. Two mutations were identified, one corresponding to the substitution His>Tyr of amino acid 142 of VP2 and another corresponding to the substitution Val>Ile of amino acid 160 of VP1. Mutants carrying one or the other of the two determinants established persistent infections in HEp-2c cell cultures in about 20% of the infections. Higher frequencies were obtained with the mutant carrying both determinants (30%), and with PVpi S11 (63%), indicating that the effects of several determinants can be cumulative. The two determinants are localized on the capsid surface in a region known to be involved in the interactions between poliovirus and its cell receptor and in fact, we demonstrate here that in the case of the two persistent mutants, these interactions are modified
Two Amino Acid Substitutions in the Type 3 Poliovirus Capsid Contribute to the Establishment of Persistent Infection in HEp-2c Cells by Modifying Virus–Receptor Interactions

AbstractAfter 2.5 months of persistent infection in human neuroblastoma cells by the type 3 poliovirus (PV3) wild-type Leon strain, a mutant (PVpi), L2-2, capable of establishing a persistent infection in nonneural HEp-2c cells was isolated. Sequence analysis of the viral capsid protein genes revealed the presence of seven missense mutations, three of which were also present in a second PVpi, suggesting that they could be important determinants of the persistent phenotype. When the three mutations were introduced into the lytic Leon strain separately, in pairs or all together, all but one of the viruses was capable of establishing a persistent infection. However, aside from the triple mutant, only one mutant virus, bearing a Leu at position VP213in the capsid interior and an Asn at position VP1290on the capsid surface, was capable of establishing persistent infections in more than 30% of the cultures. When present together, these two determinants affect the early steps of the virus cycle including cell binding and the receptor-mediated conformational changes believed to be necessary for viral penetration and uncoating. In fact, this persistent double mutant appears to undergo a novel capsid transition when in contact with the human PV receptor, altering from the native virion which sediments at 160S to a form which sediments at about 147S. We propose that this modification could be the mechanism by which PV3 is able to establish persistent infections in HEp-2c cell cultures
Attenuation of Japanese Encephalitis Virus by Selection of Its Mouse Brain Membrane Receptor Preparation Escape Variants

AbstractSix variants of Japanese encephalitis (JE) virus strain P3 were selected for resistance to binding to mouse brain membrane receptor preparations (MRP). All but one of these MRP escape (MRPR) variants were significantly attenuated in mice for both neuroinvasiveness (>200-fold) and neurovirulence (>500-fold) compared to their parent virus. Attenuated mouse brain MRPRvariants could be detected in the sera of mice following either intracerebral (i.c.) or intraperitoneal inoculation, whereas virus was detected only in brains of mice following ic inoculation. Immunization of mice with MRPRs induced neutralizing antibodies and protected mice against challenge with wild-type JE virus. A common amino acid mutation was found in the envelope (E) protein gene of all attenuated mouse brain MRPRvariants at residue E-306 compared to P3 virus grown in mosquito C6-36 cells or plaque purified and amplified in monkey kidney Vero cells. This amino acid is putatively responsible for attenuation due to alteration in binding of JE virus to its cell receptor in mouse brain. The methodology developed in this study has general applicability to the attenuation of virulence of viruses and to the identification of agents that will block amino acids in a viral attachment protein(s) that interacts with cell receptors
Genetic Complementation among Three Panels of Mouse Hepatitis Virus Gene 1 Mutants

AbstractTemperature-sensitive (ts) mutant viruses have been useful for the study of replication processes in many viral systems. To determine how our panel of MHV-JHM-derived RNA−ts mutants (Robbet al.,1979) is genetically related to other panels of MHV RNA−ts mutants, we tested our mutants for complementation with representatives from two different sets of MHV-A59 ts mutants (Koolenet al.,1983; Schaadet al.,1990). These three ts mutant panels together comprise eight genetically distinct complementation groups. Considerable genetic similarity was observed among the three mutant panels. Only three complementation classes are unique to their particular mutant panel, and genetically equivalent mutants were not observed within the other two mutant panels. There are two overlapping complementation groups between the mutant sets derived from MHV-A59 and four overlapping complementation classes between the MHV-JHM panel and the MHV-A59 panels. Two complementation groups had representative mutants in all three mutant panels. One of these latter complementation classes demonstrated nonreciprocal complementation patterns consistent with intragenic complementation
Studies of the Binding Properties of Influenza Hemagglutinin Receptor-Site Mutants

AbstractSite-specific mutations have been made in the influenza hemagglutinin (HA) receptor binding site to assess the contribution of individual amino acid residues to receptor recognition. Screening of mutant HAs, expressed using recombinant vaccinia virus-infected cells, for their abilities to bind human erythrocytes indicated that substitutions involving conserved residues Y98F, H183F, and L194A severely restricted binding and that the substitution W153A prevented cell surface expression of HA. Mutation of residues E190 and S228 that are in positions to form hydrogen bonds with the 9-OH of sialic acid appeared to increase erythrocyte binding slightly, as did the substitution G225R. Substitutions of other residues that are directly or indirectly involved in receptor binding, S136T, S136A, Y195F, G225D, and L226P, had intermediate effects on binding between these two extremes. Estimates of changes in receptor binding specificity based on inhibition of binding to erythrocytes by nonimmune horse sera indicated that mutants G225R and L226P, unlike wild-type HA, were not inhibited; Y195F and G225D mutants were, like wild type, inhibited; and erythrocyte binding by mutants S136A, S136T, E190A, and S228G was only partially inhibited. Viruses containing mutant HAs Y98F, S136T, G225D, and S228G that cover the range of erythrocyte binding properties observed were also constructed by transfection. All four transfectant viruses replicated in MDCK cells and embryonated hens' eggs as efficiently as wild-type X-31 virus, although the Y98F mutant virus was unable to agglutinate erythrocytes. Mutant MDCK cells that have reduced levels of cell surface sialic acids were susceptible to infection by S136T, G225D, and S228G transfectant viruses and by wild type but not by the Y98F transfectant virus
Evolution ofStreptococcus thermophilusBacteriophage Genomes by Modular Exchanges Followed by Point Mutations and Small Deletions and Insertions

AbstractComparative sequence analysis of 40% of the genomes from two prototypeStreptococcus thermophilusbacteriophages (lytic group I phage φSfi19 and thecossite containing temperate phage φSfi21) suggested two processes in the evolution of their genomes. In a first evolutionarily distant phase the basic genome structure was apparently constituted by modular exchanges. Over the 17-kb-long DNA segment analyzed in the present report, we observed clusters of genes with similarity to genes fromLeuconostoc oenosphage L10,Lactococcus lactisphage BK5-T, andStreptococcus pneumoniaephage Dp-1. A chimeric protein was predicted for orf 1291 which showed similarity to both phage BK5-T and phage Dp-1 proteins. The very large orf 1626 gene product showed similarity to two adjacent genes from theLactobacillus delbrueckiiphage LL-H and further phage proteins (Lactococcus lactis, Bacillus subtilis). The similarities were localized to distinct parts of this apparently multifunctional protein. The putative φSfi19 lysin showed similarity to both lysins of phages and cellular enzymes. In a second, evolutionarily more recent, phase theS. thermophilusphage genomes apparently diversified by point mutations and small deletions/insertions. Over the investigated 17-kb DNA region φSfi19 differed from φSfi21 by 10% base pair changes, the majority of which were point mutations (mainly at the third codon position), while a third of the base pair differences were contributed by small deletions/insertions. The base pair changes were unevenly distributed: Over theLeuconostocphage-related DNA the change rate was high, while over theLactococcusandS. pneumoniaephage-related DNA the change rate was low. We speculate that the degree of base pair change could provide relative time scales for the modular exchange reactions observed inS. thermophilusphages
Comparison of the Lysogeny Modules from the TemperateStreptococcus thermophilusBacteriophages TP-J34 and Sfi21: Implications for the Modular Theory of Phage Evolution

AbstractA 7.6-kb DNA segment covering the putative lysogeny module of thepac-site-containing temperateStreptococcus thermophilusbacteriophage TP-J34 was sequenced. Sequence alignment with the lysogeny module from thecos-site-containingS. thermophilusbacteriophage φSfi21 revealed areas of high sequence conservation (e.g., over theintgene), interspersed with regions of low or no sequence similarity (e.g., over thecrogene). Four of the six sharp transition zones from high to low sequence conservation were found within open reading frames coding for the CI repressor, the Anti-repressor, the Immunity protein, and a protein of unknown function. The transition points in thecIandantgenes appear to separate gene segments coding for distinct functional domains of these proteins. In addition, these two transition points were located at or near the deletion sites observed in spontaneous phage φSfi21 deletion mutants, thus suggesting these transition points as recombinational hotspots. Furthermore, the sequence at the transition point in thecIgene resembles the attachment site of the phage, suggesting the involvement of the phage integrase in at least some of the exchange reactions. Contrary to the initial formulation of the modular theory of phage evolution the unit of the evolutionary exchange in streptococcal phages is not a group of functional genes, but can be as small as a single gene. Exchange reactions can also occur within genes, possibly between gene segments encoding distinct protein domains
Differential Stability of Baculovirus Late Transcription Complexes during Initiation and Elongation

AbstractAnin vitrosystem for baculovirus late transcription was developed that allows comparison of conditions that affect transcription initiation and elongation. A series of synthetic promoters was constructed based on the baculovirus late p6.9 promoter. The modified promoters were designed with a cytidine-free region downstream of the late promoter in order to yield paused transcripts of defined lengths in the absence of CTP. Transcription was found to be more efficient from a supercoiled template than from a linear template for this promoter. The stalled transcription complex remained competent and could be elongated in the presence of a full set of nucleotides. This made it possible to separately test the effects of heat treatment and inhibition by sarkosyl and heparin on initiation and elongation. Elongation complexes were more resistent than initiation complexes to each of these treatments. Furthermore a 1–2 mM MgCl2concentration is critical for optimal initiation, but elongation can proceed in the presence of MgCl2concentrations as high as 20 mM