pinecone/core-2020-05-10-deduplication huggingface dataset:
Evolutionary Relationships among Putative RNA-Dependent RNA Polymerases Encoded by a Mitochondrial Virus-like RNA in the Dutch Elm Disease Fungus,Ophiostoma novo-ulmi,by Other Viruses and Virus-like RNAs and by theArabidopsisMitochondrial Genome

AbstractThe nucleotide sequence (2617 nucleotides) of virus-like double-stranded (ds) RNA 3a in a diseased isolate, Log1/3-8d2(Ld), of the ascomycete fungusOphiostoma novo-ulmihas been determined. One strand of the dsRNA contains an open reading frame (ORF) with the potential to encode a protein of 718 amino acids, and the complementary strand contains two smaller ORFs with the potential to encode proteins of 178 and 182 amino acids, respectively. The large ORF contains 12 UGA codons which code for tryptophan in ascomycete mitochondria and has a codon bias typical of mitochondrial genes, consistent with the localization of Ld dsRNAs within the mitochondria. The amino acid sequence contains motifs characteristic of RNA-dependent RNA polymerases (RdRps). This putative RdRp was shown to be related to putative RdRps of mitochondrial dsRNAs of another ascomycete and a basidiomycete fungus and also to a putative RdRp encoded by the mitochondrial genome ofArabidopsis thaliana.In multiple sequence alignments, the fungal mitochondrial dsRNA-encoded RdRp-like proteins formed a cluster, ancestrally related to the RdRps of the yeast 20S and 23S RNA replicons and of the positive-stranded RNA bacteriophages of the Leviviridae family, but distinct from RdRps of other families and genera of fungal RNA viruses and related plant and animal RNA viruses. Northern blot analysis with RNA 3a strand-specific probes indicated that nucleic acid extracts of Ld contain more single-stranded (positive-stranded) RNA than dsRNA, consistent with an evolutionary relationship between RNA 3a and positive-stranded RNA phages
Proteolytic Processing of Rubella Virus Nonstructural Proteins

AbstractThe genomic RNA of rubella virus contains two long open reading frames (ORF), a 5′-proximal ORF that codes for the nonstructural proteins and a 3′-proximal ORF that encodes the structural proteins. The cDNA encoding the nonstructural protein ORF of the wild-type M33 strain of rubella virus has been obtained and sequenced. Comparison between the nonstructural proteins of the M33 and Therien strains of rubella virus revealed a 98% homology in nucleotide sequence and 98.1% in deduced amino acid sequence. To examine the processing of rubella virus nonstructural protein, the complete nonstructural protein ORF was expressed in BHK cells using a pSFV expression vector. Three nonstructural protein products (p200, p150, and p90) with molecular weights of 200, 150, and 90 kDa were identified using antisera raised against synthetic peptides corresponding to regions of the nonstructural proteins. p200 is the polyprotein precursor, while p150 and p90 are the cleavage products. Site-directed mutagenesis of the Cys-1151 residue (one of the catalytic dyad residues of the viral protease) and of the Gly-1300 residue (the viral protease cleavage site) abrogated protease activity and p200 precursor cleavage, respectively. Coexpression of mutant constructs in BHK cells indicated that rubella virus protease can function both in cis and in trans
Mouse Adenovirus Type-1 Replication Is Restricted to Vascular Endothelium in the CNS of Susceptible Strains of Mice

AbstractPrevious studies have shown that mouse adenovirus type-1 (MAV-1) caused a fatal hemorrhagic encephalitis in certain strains of mice. C57Bl/6 mice exhibited 100% mortality when given as little 103plaque-forming units (PFU) of MAV, in contrast to BALB/c mice which were resistant to as many as 106PFU. Susceptible animals died with a flaccid paralysis on the 3rd or 4th day after inoculation. The brains and spinal cords of these animals displayed numerous petechial hemorrhages that were found in virtually all areas of the brain, but were more numerous in white matter. In this paper, immunohistochemistry and electron microscopy were used to identify the viral target of replication within the CNS of susceptible mice. These studies showed that the CNS vascular endothelial cell was the primary site of viral replication within the CNS of mice infected with MAV-1. Characterization of cytokine mRNA levels and disease course in immunodeficient mice revealed that the host immune response played little, if any, role in the pathogenesis of MAV-1 disease in susceptible mice and was not responsible for the resistance of BALB/c mice. These results support the conclusion that disease course and outcome in susceptible and resistant strains of mice were determined primarily by the ability of the virus to replicate within the CNS vascular endothelium
The 105-kDa Polyprotein of Southern Bean Mosaic Virus Is Translated by Scanning Ribosomes

AbstractThe cowpea strain of southern bean mosaic virus (SBMV-C) is a positive-sense RNA virus. Three open reading frames (ORF1, ORF2, and ORF3) are expressed from the genomic RNA. The ORF1 and ORF2 initiation codons are located at nucleotide (nt) positions 49 and 570, respectively. ORF1 is expressed by a 5′ end-dependent scanning mechanism, but it is not known how ribosomes gain access to the ORF2 initiation codon. In experiments described here, it was demonstrated that the translation of ORF2 was sensitive to cap analog in a cell-free extract.In vitroandin vivostudies showed that the addition of one or more AUG codons between the 5′ end of the SBMV-C RNA and the ORF2 initiation codon reduced ORF2 expression and that elimination of the ORF1 initiation codon increased ORF2 expression. Altering the sequence context of the ORF1 initiation codon to one more favorable for translation initiation also reduced ORF2 expressionin vivo.Nucleotide deletions and insertions between SBMV-C nt 218–520 did not abolish ORF2 expression. In most cases, these mutations resulted in reduced expression of both ORF1 and ORF2. These results are consistent with translation of ORF2 by leaky scanning
Critical Point Mutations for Hepatitis C Virus NS3 Proteinase

AbstractThe hepatitis C virus NS3 proteinase plays an essential role in processing of HCV nonstructural precursor polyprotein. To detect its processing activity, we developed a simpletrans-cleavage assay. Two recombinant plasmids expressing the NS3 proteinase region and a chimeric substrate polyprotein containing the NS5A/5B cleavage site between maltose binding protein and protein A were co-introduced intoEscherichia colicells. The proteinase processed the substrate at the single site during their polyprotein expression. Deletion analysis indicated that the functionally minimal domain of the NS3 proteinase was composed of 146 amino acids, 1059 to 1204. We isolated several cDNA clones encoding the functional domain of the NS3 proteinase from the sera of patients chronically infected with HCV and determined their proteinase activity by thistrans-cleavage assay. Both active and inactive clones existed in the same patients. Comparative sequence analyses of these clones suggested that certain point mutations seemed to be related to the loss of proteolytic activity. This was confirmed by back mutation experiments. Among the critical mutations, Pro-1168 to Thr and Arg-1135 to Gly were intriguing. These amino acids, which are situated near the oxyanion hole, seem to be essential for maintaining the conformation of the active center of the NS3 proteinase
Shared Antigenic Epitopes on the V3 Loop of HIV-1 gp120 and Proteins on Activated Human T Cells

AbstractProliferation of HIV-1 in the infected host is characterized by a progressive loss of CD4+T lymphocytes and consequent dysregulation of the immune system. Both direct and indirect mechanisms have been proposed. We show here that proteins with molecular weights 35, 48, and 110 kDa on stimulated primary human T cells are recognized by neutralizing antibodies against the V3 loop of HIV-1 gp120. Recognition is specific since it can be blocked by a recombinant HIV-1 gp120. Furthermore, these V3 monoclonal antibodies, as well as sera from AIDS patients that recognized these V3-like proteins, induced killing of HIV-1-infected as well as uninfected T cells. This killing was also inhibited by HIV-1 gp120 V3 peptides. These results indicate that the V3 loop shares epitopes with proteins on stimulated T cells. This may be an additional autoimmune mechanism contributing to CD4+T cell disappearance in AIDS. V3 antibodies have been proposed as potential prophylactic agents. However, if such vaccines were based on certain epitopes, they might induce cross-reacting immune responses with cellular proteins. Vaccine candidates should be evaluated for such potential effects
Suppression of Antigen-Specific T Cell Proliferation by Measles Virus Infection: Role of a Soluble Factor in Suppression

AbstractMeasles virus infection causes a profound immunosuppression. The basis for this immunosuppression is not known. This immunosuppression could be due to virus acting directly on lymphoid cells, the production of an immunosuppressive viral product, or a lymphoid product. We have developed an antigen-specific T cell system to study measles virus–T-cell interactions. We demonstrate that as few as five infectious viral particles added to 1000 T cells results in profound inhibition of antigen-specific T cell proliferation. Supernates taken from measles virus-infected T cells suppress the proliferation of uninfected T cells. Measles-virus-infected HeLa or Vero cells do not produce the factor. The antiproliferative effects of the supernates cannot be attributed to infectious virus, IL-10 or TGF-β. The soluble factor appears to be larger than 100 kDa, yet retains antiproliferative activity following trypsin digestion with a size less than 10 kDa. Loss of activity is seen following heat treatment at 56°C. The factor is lymphoid cell specific and exhibits cytokine-like behavior yet appears not to be a known cytokine. This soluble factor may be responsible for the overt clinical immunosuppression seen in man and a previously undescribed cytokine induced by measles virus infection of human lymphocytes
Infectious Bursal Disease Virus Changes the Potassium Current Properties of Chicken Embryo Fibroblasts

AbstractInfectious bursal disease virus (IBDV) is the causative agent of an economically significant poultry disease. IBDV infection leads to apoptosis in chicken embryos and cell cultures. Since changes in cellular ion fluxes during apoptosis have been reported, we investigated the membrane ion currents of chicken embryo fibroblasts (CEFs) inoculated with the Cu-1 strain of IBDV using the patch-clamp recording technique. Incubation of CEFs with IBDV led to marked changes in their K+outward current properties, with respect to both the kinetics of activation and inactivation and the Ca2+dependence of the activation. The changes occurred in a time-dependent manner and were complete after 8 h. UV-treated noninfectious virions induced the same K+current changes as live IBDV. When CEFs were inoculated with IBDV after pretreatment with a neutralizing antibody, about 30% of the cells showed a normal K+current, whereas the rest exhibited K+current properties identical to or closely resembling those of IBDV-infected cells. Incubation of CEFs with culture supernatant from IBDV-infected cells from which the virus particles were removed had no influence on the K+current. Our data strongly suggest that the K+current changes induced by IBDV are not due to virus replication, but are the result of attachment and/or membrane penetration. Possibly, the altered K+current may delay the apoptotic process in CEFs after IBDV infection
Characterization of the Thermosensitive ts453 Reovirus Mutant: Increased dsRNA Binding of ς3 Protein Correlates with Interferon Resistance

AbstractThe mutation harbored by the reovirus ts453 thermosensitive mutant has been assigned to the S4 gene encoding the major outer capsid protein ς3. Previous gene sequencing has identified a nonconservative amino acid substitution located near the zinc finger of ς3 protein in the mutant. Coexpression in COS cells of the ς3 protein presenting this amino acid substitution (N16K), together with the other major capsid protein μ1, has also revealed an altered interaction between the two proteins; this altered interaction prevents the ς3-dependent cleavage of μ1 to μ1C. This could explain the lack of outer capsid assembly observed during ts453 virus infection at nonpermissive temperature. In the present study, we pursued the characterization of this mutant ς3 protein. Although the N16K mutation is located close to the zinc finger region, it did not affect the ability of the protein to bind zinc. In contrast, this mutation, as well as mutations within the zinc finger motif itself, can increase the binding of the protein to double-stranded RNA (dsRNA). It also appears that the N16K mutant protein is more efficiently transported to the nucleus than the wild-type protein, an observation consistent with the postulated role of dsRNA binding in ς3 nuclear presence. The lack of association with μ1, and/or the increased dsRNA-binding activity of ς3, could be responsible for a partial resistance of the ts453 virus to interferon treatment and this could have important consequences in the context of protein synthesis regulation during natural reovirus infection
Functional Modules Important for Activated Expression of Early Genes of Herpes Simplex Virus Type 1 Are Clustered Upstream of the TATA Box

AbstractFunctional analysis of two promoters controlling early herpes simplex virus type 1 (HSV-1) transcripts encoding the UL37 and UL50 (dUTPase) proteins are described in this report. Transcripts expressed under the control of these promoters were found to be expressed early regardless of the position of the transcription unit within the viral genome. Despite this,wtdUTPase mRNA was 6–10 times more abundant than the UL37 transcript both inwtand recombinant viruses. This same difference in transcript abundance was seen when a reporter gene (β-galactosidase) was controlled by the two promoters in recombinant viruses in the heterologous glycoprotein C (gC) locus. Thus, both the kinetics and relative abundance of UL50 and UL37 transcripts are a direct function of their respective promoter regulatory elements. Characterization of mutated UL37 and UL50 promoters in recombinant viruses showed that the functional modules important for expression from these promoters are concentrated upstream of the transcription start site; however the extent and composition of these modules in terms of thecis-acting elements they contain was different for each. For the UL37 promoter, both a HiNF-P factor binding site (−53 to −58 bp) and the TATA homology (−22 to −27) were required for any detectable expression, while an Sp1 binding site at −123 augmented this but was not absolutely required. In contrast, the only functional elements crucial for expression from the UL50 promoter were the TATA box (−25 to −31) and an Sp1 binding site at −117 bp relative to the cap site. Despite differences in detail, when the functional architecture of these two early promoters were compared to the extensively characterized HSV-1 thymidine kinase (UL23) promoter, class-specific similarities are clearly apparent
The Structural Gene Module inStreptococcus thermophilusBacteriophage φSfi11 Shows a Hierarchy of Relatedness to Siphoviridae from a Wide Range of Bacterial Hosts

AbstractThe structural gene cluster and the lysis module from lytic group IIStreptococcus thermophilusbacteriophage φSfi11 was compared to the corresponding region from other Siphoviridae. The analysis revealed a hierarchy of relatedness. φSfi11 differed from the temperateS. thermophilusbacteriophage φO1205 by about 10% at the nucleotide level. The majority of the changes were point mutations, mainly at the third base position. Only a single gene (orf 695) differed substantially between the two phages. Over the putative minor tail and lysis genes, φSfi11 and the lytic group IS. thermophilusφSfi19 shared regions with variable degrees of similarity. Orf 1291 from φSfi19 was replaced by four genes in φSfi11, two of which (orf 1000 and orf 695) showed a complicated pattern of similarity and nonsimilarity compared with φSfi19. The predicted orf 695 gp resembles the receptor-recognizing protein of T-even coliphages in its organization, but not its sequence. No sequence similarity was detected between φSfi11 and φSfi19 in the region covering the major head and tail genes. Comparison of the structural gene map of φSfi11 with that of Siphoviridae from gram-positive and -negative bacterial hosts revealed a common genomic organization. Sequence similarity was only found between φSfi11 and Siphoviridae from gram-positive hosts and correlated with the evolutionary distance between the bacterial hosts. Our data are compatible with the hypothesis that the structural gene operon from Siphoviridae of the low G+C group of gram-positive bacteria is derived from a common ancestor
Characterization of Cucumber Mosaic Virus

AbstractTo ascertain the importance of amino-terminal proximal capsid protein (CP) sequences in cell-to-cell movement, virion formation, and stabilization, two CP mutants of cucumber mosaic virus (CMV) were generated by deletion of sequences encoding CP amino acids 15–40 (ΔSal-Nru) or 26–40 (ΔSac-Nru). Wildtype CMV and CMV containing ΔSac-Nru could infect systemically four host species, although symptoms induced by the two viruses usually were different. CMV containing ΔSal-Nru could only infectNicotiana benthamianaandN. clevelandiisystemically, but only slowly, suggesting phloem-independent long-distance movement. A variant mutant designated ΔSal-Nru* could systemically infectN. tabacumas well as the above twoNicotianaspecies, rapidly, but could not systemically infectCucurbita pepo.Virus particles could not be detected in plants infected by ΔSal-Nru, while ΔSal-Nru* and ΔSac-Nru formed particles of lower stabilities than for wildtype virus. The CPs of ΔSal-Nru and ΔSal-Nru* could bind RNAin vitro,although less strongly than ΔSac-Nru or wildtype CMV. These data indicate that amino-terminal proximal sequences of the CMV CP interact with viral RNA and are required for the formation of stable virions. Moreover, while the CP is necessary for cell-to-cell movement, the ability to form virions is not a prerequisite for cell-to-cell movement
Transfer RNA Mimicry in a New Group of Positive-Strand RNA Plant Viruses, the Furoviruses: Differential Aminoacylation between the RNA Components of One Genome

AbstractRecent sequencing of the genomes of several furoviruses—fungus-transmitted rod-shaped positive-strand plant viruses—has suggested the presence of tRNA-like structures (TLSs) at the 3′ ends of the genomic RNAs. We show here that the genomic RNAs of soil-borne wheat mosaic virus (SBWMV), beet soil-borne virus (BSBV), potato mop-top virus (PMTV), peanut clump virus (PCV), and Indian peanut clump virus (IPCV) all possess functional TLSs that are capable of high-efficiency valylation. While the SBWMV, BSBV, and PMTV TLSs are similar to those found in tymoviruses, the PCV and IPCV TLSs harbor an insertion of about 40 nucleotides between the two halves of the TLS. The valylated SBWMV and BSBV RNAs formed tight complexes with wheat germ EF-1α · GTP (Kd= 2 to 11 nM), whereas valylated PMTV, PCV, and IPCV RNAs bound EF-1α · GTP weakly (Kd≥ 50 nM). The TLS of PCV RNA2 differs from PCV RNA1 in lacking the major valine identity nucleotide in the anticodon and consequently is capable of only very inefficient valylation. This is the first case of differential aminoacylation between the RNA components of one genome
The Interaction of Neuraminidase and Hemagglutinin Mutations in Influenza Virus in Resistance to 4-Guanidino-Neu5Ac2en

AbstractWe have previously described a 4-guanidino-Neu5Ac2en (zanamivir)-resistant neuraminidase (NA) variant G70C4-G, with an active site mutation Glu 119 to Gly. This variant has been found to also harbor a hemagglutinin (HA) mutation in the receptor binding site, Ser 186 to Phe. Examination of early passages of the G70C4-G virus revealed that this HA mutation had arisen by the first passage. From a subsequent passage two transient variants were isolated which had each acquired a different second HA mutation, Ser 165 to Asn and Lys 222 to Thr. Both were highly drug resistant and drug dependent and their ability to adsorb to and penetrate cells was decreased. Comparison of drug sensitivities between the variant, with the additional HA mutation at Ser 165, and viruses with either mutation alone revealed that these two HA mutations acted synergistically to increase resistance. To determine the contribution to resistance of each of the NA and HA mutations in G70C4-G, the NA mutation was separated from the HA mutation by reassorting. The NA mutation and the HA mutation each conferred low-level resistance to zanamivir, while the two mutations interacted synergistically in the double mutant to give higher resistancein vitro.Infectivity was not adversely affected in the double mutant and while there was a small decrease in sensitivity to zanamivir in the mouse model, there was no detectable resistance to zanamivir in the ferret model
Characterization of Toscana Virus-Defective Interfering Particles Generatedin Vivo

AbstractToscana (TOS) virus stocks strongly interfering with standard virus replication were obtained by sequential passages of virus in suckling mouse brain. Characterization of viral RNAs in these stocks showed the presence of a heterogeneous population of defective RNA molecules derived from the L genomic segment, in both nucleocapsid (NC) and messenger RNAs, suggesting that these molecules could be replicated, assembled, and transcribed. Subgenomic RNAs from the L segment but not from the S or M segments were found in cells infected with these stocks. Defective RNA molecules interfered with virus replication and retained 5′ and 3′ genomic termini. Nucleotide sequence analysis of some cloned defective interfering (DI) RNAs revealed they contained one or more internal deletions reducing their length to 7–13% of the full-length L segment. An identical sequence motif, of variable length, was found at both terminal sites of the RNA junction on standard L sequences. This motif was retained only in one copy in the subgenomic RNA. These results are consistent with the generation of TOS virus DI particlesin vivoand suggest that the defective genomic RNAs could be generated by polymerase jumping from a sequence to an identical one spatially closed because of the RNA structure
The Maastricht Strain and England Strain of Rat Cytomegalovirus Represent Different Betaherpesvirus Species Rather Than Strains

AbstractThe major immediate early (MIE) locus of the Maastricht strain of rat cytomegalovirus (RCMV) was found to comprise five exons of which the first is noncoding. The first three exons are spliced to either exon 4, generating IE1, or exon 5, generating IE2. An additional splicing event unique to RCMV (Maastricht) was identified in exon 5, resulting in a 466-bp deletion. IE1 transcripts were detected exclusively during the IE phase of infectionin vitro,whereas IE2 transcripts were detected during both the IE and late phase of infection. The similarities between amino acid sequences derived from the MIE gene of RCMV (Maastricht) and murine cytomegalovirus are low (22 and 37% for IE1 and IE2, respectively). Surprisingly, the similarities between the MIE proteins of RCMV (Maastricht) and the England strain of RCMV are also low (23 and 32% for IE1 and IE2, respectively). This suggests that these RCMV strains represent different betaherpesvirus species rather than strains. This is underscored by the difference between both viruses in genome size as well as growth characteristics. The existence of two different RCMV-like species might have important implications for the use of these viruses as models for human cytomegalovirus