pinecone/core-2020-05-10-deduplication huggingface dataset:
Tandem Placement of a Coronavirus Promoter Results in Enhanced mRNA Synthesis from the Downstream-Most Initiation Site

AbstractInsertion of the 17-nucleotide promoter region for the bovine coronavirus N gene as part of a 27-nucleotide cassette into the open reading frame of a cloned synthetic defective-interfering (DI) RNA resulted in synthesis of subDI RNA transcripts from the replicating DI RNA genome. Duplicating and triplicating the promoter sequence in tandem caused a progressive increase in the efficiency of subgenomic mRNA synthesis despite a concurrent decrease in the rate of DI RNA accumulation that was not specific to the promoter sequences being added. Although initiation of transcription (leader fusion) occurred at each of the three promoter sites in the tandem construct, almost all of the transcripts were found as a product of the most downstream (3′-most on the genome) promoter. These results show that enhancement of subgenomic mRNA synthesis is a property that can reside within sequence situated near the promoter. A possible role for the plus strand in the downstream promoter choice is suggested
Expression of Additional Genes in a Vector Derived from a Minimal RNA Virus

AbstractPrevious studies have shown that expression of the vesicular stomatitis virus (VSV) glycoprotein (G) from a Semliki Forest virus (SFV) RNA replicon results in the production of propagating infectious particles that we call minimal viruses. These minimal viruses consist of vesicles containing VSV G protein that bud from the plasma membrane and trap the infectious SFV G RNA, but they do not contain other viral structural proteins. The cell binding and membrane fusion activity of the VSV G protein allow minimal viruses to propagate in tissue culture cells. To determine if these minimal viruses could be used to express foreign genes, we added a second SFV promoter and a multiple cloning site downstream of the VSV G gene. We report here expression of three different proteins from this modified, minimal virus vector. Although expression of each foreign, unselected gene was lost rapidly from the vector upon passaging, it was possible after the initial transfection to derive stocks of infectious particles that could be used to infect multiple additional cultures and transfer protein expression efficiently. When cells were infected with these minimal viruses, host protein synthesis was shut off and the foreign protein and VSV G proteins were the major proteins expressed in the infected cells. Both were expressed at similar levels and accumulated to about 1–2% of total cell protein
Reduced Levels of α1(XI) Procollagen mRNA in SV40-Transformed Cells

AbstractWe have used mRNA differential display to search for cellular genes whose expression is modulated in SV40-transformed cells. We identified a gene, the α1 subunit of type XI procollagen (α1(XI)), whose mRNA level is reduced in most F111 rat cell lines that express either wild-type SV40 T antigen or an amino-terminal fragment of T antigen (T147D). α1(XI) mRNA expression is also reduced in rat embryo fibroblasts transformed by SV40. This phenomenon is not unique to rat cells, because α1(XI) mRNA expression is repressed in C3H10T1/2 mouse cells transformed by either T147D or wild-type SV40. Interestingly, α1(XI) mRNA levels are not reduced in F111 cells that express only the polyomavirus large T antigen, but are reduced in F111 cells transformed by polyoma virus (which expresses all three polyomavirus T antigens) and in F111 cells that express the adenovirus E1A proteins. Thus, repression of α1(XI) mRNA expression may be a common feature of transformation by DNA tumor viruses
The Attenuated V60 Strain of Channel Catfish Virus Possesses a Deletion in ORF50 Coding for a Potentially Secreted Glycoprotein

AbstractA wild-type strain of channel catfish virus was compared at the genomic level with the attenuated strain V60. In addition to several minor differences, restriction mapping revealed one major deletion (approximately 1200 bp) in ORF50 of the V60 strain. Cloning and sequencing of part of this ORF confirmed the presence of a 1164-bp deletion. It should result in a protein of 282 amino acids instead of 670. The predicted truncated protein lacks most of a threonine-rich, highly repetitive region in its central part. Since the protein encoded by ORF50 possesses a hydrophobic N-terminal leader sequence and no membrane anchor sequence, we suggest that it could be a secreted glycoprotein. This protein might beN-glycosylated (35 potential sites) and, given the repetitive arrangement of its residues (mainly threonines), also heavilyO-glycosylated like the mucin-type glycoproteins. The deletion observed in ORF50 of the V60 strain implies the loss of 24 potentialN-glycosylation sites and should considerably reduce the extent ofO-glycosylation
Chemical Cleavage of 5′-Linked Protein from Tobacco Ringspot Virus Genomic RNAs and Characterization of the Protein–RNA Linkage

AbstractEach of the two genomic RNAs of tobacco ringspot nepovirus is known to have a 5′-linked protein, the VPg. We report a simplified analysis of the covalent VPg-RNA connection that allowed us to identify the 5′ nucleotide residue of each genomic RNA and its phosphodiester link to a specific serine residue of the VPg, without resorting toin vivolabeling with32P,in vitroradioiodination, or separation of the two genomic RNAs. Unfractionated genomic RNA was incubated with an oligodeoxyribonucleotide specific for the 5′ region of either RNA 1 or RNA 2 and ribonuclease H. Reaction products were 3′-end-labeled and were fractionated by gel electrophoresis. The most highly labeled product derived from each genomic RNA was identified as a VPg-oligoribonucleotide (VPg-5′-oligo) by its sensitivity to proteinase. In a presumed β-elimination reaction that apparently was more rapid than phosphodiester cleavage, incubation in alkaline sodium bicarbonate released a rapidly migrating product, 5′-oligo. Phosphatase-treated 5′-oligo accepted 5′-label in a polynucleotide kinase-catalyzed reaction, and uridylate was identified as the 5′ terminal residue for both RNA 1 and RNA 2. Results from Edman degradation of the VPg suggest that the VPg is linked at serine 5 to the 5′ uridylate of each genomic RNA
Comparisons of the Genomiccis-Elements and Coding Regions in RNAβ Components of the Hordeiviruses Barley Stripe Mosaic Virus, Lychnis Ringspot Virus, and Poa Semilatent Virus

AbstractNucleotide sequences of the genomic RNAβ components of hordeiviruses poa semilatent virus (PSLV) and lychnis ringspot virus (LRSV) were determined. PSLV and LRSV closely resemble barley stripe mosaic virus (BSMV), type hordeivirus, in the gene arrangement of their RNAs β, comprising 5′-proximal βa (coat protein) gene and downstream triple gene block (TGB) coding for the βb, βc, and βd putative transport proteins. The βa, βb, βc, and βd proteins of the three hordeiviruses showed significant sequence similarity, with the respective proteins of PSLV and BSMV being closer to each other than to their counterparts of LSRV. Comparisons of the TGB-encoded proteins of hordeiviruses, potexviruses, carlaviruses, and furoviruses indicate that the first and second TGB genes belong to the monophyletic groups, whereas the third gene may have multiple ancestry. LRSV, PSLV, and BSMV showed remarkable variation in the 3′-untranslated regions of their genomic RNAs. Among the three hordeiviruses, LRSV has the shortest 3′-noncoding region that lacks tentative pseudoknot-forming elements conserved upstream of the 3′-tRNA-like structure in the BSMV and PSLV genomes. On the other hand, LRSV RNAβ, like that of BSMV, contained the internal poly(A) sequence that is absent from PSLV RNA
Identification of the Receptor-Binding Regions of pb5 Proteins of Bacteriophages T5 and BF23

AbstractThe receptor-binding protein pb5T5of bacteriophage T5, when expressed from theoadgene cloned in pVK88 under the control of the phage T7 promoter/polymerase system, has been shown to bind to its FhuA receptor on the surface ofE. coli,where it blocks FhuA for subsequent adsorption of T5 (Mondigleret al., FEMS Microbiol. Lett.,130, 293–300, 1995). In the present study the blocking assay has been applied to analyze the effects of several mutations withinoadon the FhuA-binding properties of corresponding pb5 derivatives. Three classes of mutations were tested: (i)oaddeletion derivatives, (ii) theoadmutation known to interfere with FhuA-binding of T5 (Heller and Bryniok,J. Virol.,49, 20–25, 1984), and (iii) linker-insertion mutations at a site very close to theoadmutation. Of the corresponding pb5 derivatives only one, a deletion derivative lacking the 153 C-terminal amino acids, was as active in the blocking assay as wild-type pb5T5. All other derivatives were inactive or almost inactive. Isolation and molecular characterization of phenotypic revertants of T5oadshowed that all revertants were true genotypic revertants of theoadmutation. Theoadmutation has been identified as a G to T exchange resulting in a substitution of Gly for Trp at position 166 of pb5T5. DNA sequencing of thehrsgene of bacteriophage BF23 and comparing the deduced amino acid sequence of pb5BF23with that of pb5T5revealed distinct regions of similarity and nonsimilarity. We propose that the receptor-binding region of pb5T5(pb5BF23) is formed by the region of nonsimilarity extending from amino acid position 89 (88) to position 305 (283)
Extensive Regions ofpolAre Required for Efficient Human Immunodeficiency Virus Polyprotein Processing and Particle Maturation

AbstractHuman Immunodeficiency type 1 particle maturation is dependent upon proteolytic cleavage of the gag and gag-pol precursors by thepol-encoded viral protease. We have investigated the importance of domains ofpolother than the protease for particle maturation and gag proteolytic processing. Truncations of the gag-pol polyprotein precursor of HIV-1 were created by deleting segments of the reverse transcriptase coding region or by introducing stop codons in the integrase region of an HIV-1 infectious molecular clone. In these mutants, the protease coding sequence was left intact. Particles produced by all of the mutants displayed abnormal morphologies and impaired proteolytic processing of gag. The severity of particle morphology abnormalities and of gag polyprotein processing impairment appeared to be affected both by the size and by the position of the deletions inpol,suggesting that the integrity of severalpoldomains within the gag-pol precursor is required for optimal protease activation and particle maturation. Additionally, cotransfection of a deletion mutant with wild-type provirus led to a marked reduction in the titer of infectious virus, suggesting that truncated gag-pol precursors can interfere with wild-type virus assembly and maturation
Virus-like Particles of Bovine Papillomavirus Type 4 in Prophylactic and Therapeutic Immunization

AbstractVirus-like particles were produced in insect cells containing either the L1 and L2 capsid proteins of bovine papillomavirus type 4 (BPV-4) or only the L1 protein. Both preparations of VLPs proved to be extremely effective prophylactic vaccines. Thirteen of 15 calves immunised with either L1–L2 VLPs or L1–VLPs were refractory to experimental challenge with high doses of BPV-4 and did not develop papillomas, while 9 of 10 control animals developed multiple oral papillomas. VLPs were not efficient as therapeutic vaccine in calves with established papillomas, although VLP-vaccinated animals appeared to undergo tumour regression more rapidly than nonvaccinated control animals. Antibody responses in VLP-vaccinated calves were associated with prevention of disease but not with regression of papillomas. Thus prophylactic VLP vaccination is effective in preventing disease in this model of mucosal papillomavirus infection. VLPs and native virus share at least some conformational epitopes, as shown by the cross-reactivity of their antibodies
Role of the Variable Domain in Modulating Potato Spindle Tuber Viroid Replication

AbstractPotato spindle tuber viroid (PSTVd) is believed to undergo a series of specific structural transitions during replication. The variable domain of PSTVd is known to contain sequences that are important for replication/accumulation as well as one of three “premelting regions” which control breakdown of the native structurein vitro.We have examined the structural and biological effects of five single and two double nucleotide substitutions within premelting region 3 in an effort to isolate temperature-sensitive mutations affecting PSTVd replication or pathogenesis. None of these mutants replicated as rapidly as the wild type, and a variety of spontaneous sequence changes were detected in their progeny. Higher temperatures were able to partially overcome the inhibition of replication associated with a more stable secondary structure, but no well-defined temperature-sensitive PSTVd mutants were identified. Selective pressures arising from the interaction of assay temperature and structural stabilityin vivoappear capable of moving PSTVd populations between peaks of relatively high fitness. Depending on the exact nature and location of the mutation, selection may occur at the level of either the plus or the minus strand
Aphid Transmission and Systemic Plant Infection Determinants of Barley Yellow Dwarf Luteovirus-PAV are Contained in the Coat Protein Readthrough Domain and 17-kDa Protein, Respectively

AbstractProteins encoded by open reading frames (ORF) 3, 4, and 5 of the barley yellow dwarf luteovirus genome are translated from a single subgenomic RNA. The structural proteins are encoded by ORF 3 (coat protein) and ORF 5 (readthrough domain) and contain undefined domains that regulate the movement of virus through aphid vectors. The biological function of the nonstructural 17-kDa protein encoded by ORF 4 is unknown. A complementation method was employed to test the ability of barley yellow dwarf virions carrying mutations within the readthrough domain and the 17-kDa protein to be transmitted by aphids and to cause systemic infections in plants. We show that the readthrough domain is required for aphid transmission; however, it is not required for virus to be taken up by aphid hindgut cells and released into the hemocoel. The circulative pathway of luteoviruses in aphid vectors requires that virus be actively transported from the hemolymph into the salivary system. Thus, it appears that the readthrough domain is required for transport of virus through membranes of the aphid salivary glands. Furthermore, the readthrough domain was not required for systemic infection of plants, but did influence the accumulation of virus in infected plants. The 17-kDa protein is required for the systemic infection of plants
Identification and Characterization of a Bovine Herpesvirus-1 (BHV-1) Glycoprotein gL Which Is Required for Proper Antigenicity, Processing, and Transport of BHV-1 Glycoprotein gH

AbstractDNA sequence analysis of the bovine herpesvirus-1 (BHV-1) genome revealed the presence of an open reading frame named UL1 which exhibited limited homology to glycoprotein gL of herpes simplex virus-1 (S. K. Khattar, S. van Drunen Littel-van den Hurk, L. A. Babiuk, and S. K. Tikoo,Virology213, 28–37). To identify the BHV-1 UL1 protein, rabbit antisera were prepared against two synthetic peptides that were predicted by computer analysis to encompass antigenic epitopes. Sera against both peptides immunoprecipitated a 16- to 17-kDa protein fromin vitrotranslatedin vitrotranscribed mRNA, BHV-1-infected MDBK cells, and purified virions. Enzymatic deglycosylation and lectin binding assays confirmed that the BHV-1 UL1 protein contains only O-linked oligosaccharides and was named glycoprotein gL. Sera against UL22 protein immunoprecipitated a protein of 108 kDa from BHV-1-infected MDBK cells and purified virions, which was modified only by N-linked oligosaccharides and was named glycoprotein gH. Glycoprotein gL expressed by recombinant vaccinia virus was properly processed and secreted into the medium. In contrast glycoprotein gH expressed by recombinant vaccinia virus was found to be retained in the rough endoplasmic reticulum. However, gH coexpressed with gL by recombinant vaccinia viruses was properly processed and transported to the cell surface, suggesting that complex formation between gH and gL is necessary for the proper processing and transport of gH but not gL. In addition gH–gL complex formation is also required for induction of neutralizing antibody response and anchoring of gL to the plasma membrane
Catalytic Activities of the Human T-Cell Leukemia Virus Type II Integrase

AbstractDespite the widespread nature of HTLV-II in New World populations and intravenous drug users, the enzymatic activities of thepolgenes have not been reported. To ascertain the activity of the HTLV-IIG12integrase (IN), the coding region was isolated and the encoded protein was purified, using nickel-affinity chromatography, to greater than 90% homogeneity. HTLV-IIG12IN proved active on HTLV-IIG12and HIV-1 integration and disintegration substrates. Distinct differences in requirements for enzyme concentration for 3′-processing, strand-transfer, and disintegration reactions were observed. Catalysis of integration reactions occurred in the presence of either Mn2+or Mg2+, although strand-transfer activity preferred Mn2+. In comparison, HTLV-IIG12IN catalyzed disintegration reactions with almost 10-fold less protein, was not selective for Mn2+or Mg2+, and tolerated higher NaCl concentrations than integration. HTLV-IIG12IN was unable to catalyze the “splicing” reaction, which suggests that this may not be an activity ubiquitous to all retroviral integrases
Site-Specific Spontaneous Deletions in Three Genome Regions of a TemperateStreptococcus thermophilusPhage

AbstractSite-specific spontaneous deletions were observed with high frequency in three regions of the genome of the temperateStreptococcus thermophilusphage φSFi21. Deletion sizes were 750 bp (type 1), 2.7 kb (type 2), and 1 kb (type 3). Combinations of types 1 and 3 and 2 and 3 were observed. The mutants grew lytically although with reduced burst sizes. Type 2 mutants lost the capacity to lysogenize host cells. Upon serial passage, the deletion mutants overgrew the wild-type phage. No direct or inverted DNA repeats were associated with type 1 or 2 deletion sites. Several independent phage isolates showed deletions at identical nucleotide positions, suggesting a site-specific recombination system. Sequencing of anXbaI restriction fragment covering the type 1 deletion predicted a single long open reading frame (ORF) showing a high degree of amino acid similarity with two proteins from bacteriophage P1 implicated in its immunity control (KilA, Ant). Type 1 deletion leads to a loss of the conserved C-terminal part of this ORF
Defining the SOS Operon of Coliphage 186

AbstractWe have sequenced the LexA-controlled operon of coliphage 186 that carries thetumgene, whose product is necessary for UV induction of the 186 prophage. The operon consists oforf95andorf97,and we have identifiedorf95as thetumgene. The major translation products fromorf95result from internal initiations and modulate Tum activity. Tum is the product of the full-length Orf95 protein. The second gene of the operon,orf97,is of unknown function but, while it has little effect on prophage induction, its presence in the cell totally blocks infection of that cell by 186
TheEscherichia coliRetrons Ec67 and Ec86 Replace DNA between thecosSite and a Transcription Terminator of a 186-Related Prophage

AbstractRetrons are unusual, reverse transcriptase-encoding elements found in bacteria. Although there are a number of indications that retrons are mobile elements, their transposition has not been observed. TheEscherichia coliretrons Ec67 and Ec86 are different retrons inserted at the same site and we have further characterized this site in search of clues to the mechanism of retron transposition. We confirm, by extending previous sequence analysis, that Ec67 and Ec86 are inserted into prophages related to coliphage 186. Comparison with the recently published sequence of the 186 96–2% region indicates that the retrons have replaced ∼180 bp of DNA between the phage cohesive end site (cos) and the transcription terminator of a phage DNA-packaging gene. These features—DNA replacement at the insertion site and the location of retron junctions near transcription terminators or DNA cleavage sites—are shared with other retrons and suggest ways in which retron transposition might have occurred
Analysis of the Contribution of CTL Epitopes in the Immunobiology of Morbillivirus Infection

AbstractIn Balb/c (H-2d) mice, the nucleoprotein (NP) of measles virus (MV) induces a MHC class I restricted-CTL response to a single 9-amino-acid epitope (aa 281–289). This Ld-restricted epitope is also present in the NP of the closely related canine distemper virus (CDV). To investigate whether this epitope is immunologically effective when it is present within the primary sequence of a nonviral protein, we have incorporated the 281–289 motif into the human CD36 protein. When cells are infected with vaccinia virus (VV) recombinants expressing this protein, CD36NP, the MV epitope is correctly processed and the cells are lysed by MVNP-specific CTLs.In vivo,VV-CD36NP induced CTLs which protected mice from a lethal dose of CDV, but did not block virus replication. The MVNP contains four other potential Ld-restricted motifs. To investigate if these could be utilized in the absence of the dominant epitope, a mutant NP was produced in which one of the anchor residues in the aa 281–289 motif was mutated. Cells infected with a VV recombinant expressing this protein (VV-NP F289S) were only poorly lysed by MVNP-specific CTLs. Similarly, immunization of Balb/c mice with VV-NP F289S induced a lower level of CTL activity compared to the VV-NP, but the activity was now directed to three other epitopes. When mice were vaccinated with VV-NP F289S they were only partially protected from a lethal CDV challenge. The significance of these results for MV vaccine development is discussed
Poliovirus Replicons That Express the Gag or the Envelope Surface Protein of Simian Immunodeficiency Virus SIVsmmPBj14

AbstractPoliovirus genomes encoding the completegagorenvsurface gene of the simian immunodeficiency virus SIVsmmPBj14 (SIV-PBj14) were constructed. Thein vitro-transcribed RNA from these genomes, referred to as replicons, have the capacity for self-replication when transfected into tissue culture cells. Serial passage of the replicons containing the SIV-PBj14gagor SIV-PBj14env(SU) genes with a recombinant vaccinia virus, VV-P1, which provides P1in trans,resulted in the encapsidation of these replicons. Infection of cells with the encapsidated replicons that encodegag,referred to as vIC-SIV-PBj14 Gag, resulted in the production of a 55-kDa protein that was released from the infected cells. Using a sucrose density-gradient analysis, the protein was found to sediment at a density consistent with that of a virus-like particle. Infection of cells with a replicon that encodes theenvSU gene, referred to as vIC-SIV-PBj14 SU, resulted in the production of two SIV-PBj14 envelope-related intracellular proteins. One of these proteins had a molecular mass consistent with that of the unglycosylated SIV-PBj14 SU protein (63 kDa); the second protein had a higher molecular mass (>160 kDa). Characterization of this larger protein revealed that it was glycosylated and possibly represented a dimer of the SU protein. A pulse–chase analysis of cells infected with vIC-SIV-PBj14 SU demonstrated that a 110- to 130-kDa protein was released, which is consistent with the molecular mass of the SIV-PBj14 SU protein. The results of these studies demonstrate that poliovirus replicons can be used to express foreign proteins, including glycoproteins, which retain many of the physical features of the native protein