pinecone/core-2020-05-10-deduplication huggingface dataset:
IPNV VP5, a Novel Anti-apoptosis Gene of the Bcl-2 Family, Regulates Mcl-1 and Viral Protein Expression

AbstractVP5, a 5′-terminal, small open reading frame in segment A of the aquatic birnavirus (infectious pancreatic necrosis virus, IPNV) genome, encodes a 17-kDa nonstructural protein. We previously reported apoptosis induced by IPNV in a fish cell line. In the present study, we cloned and identified VP5 and tested its function. Comparisons of the amino acid sequence of VP5 with well-known Bcl-2 family member proteins showed that the VP5 protein contains Bcl-2 homology (BH) domains BH1, BH2, BH3, and BH4 but without the transmembrane region. VP5-stable clones enhanced viability, prevented membrane blebbing, delayed DNA internucleosomal cleavage, and decreased virus titer during IPNV infection but, when deleted, BH domains 1 and 2 could lose the preventable ability. In addition, VP5 was demonstrated to be able to enhance or assist in maintaining the functional half-life of survival factor Mcl-1 and regulate specific viral protein expression during the early replication cycle. Finally, we found that VP5 was capable of enhancing cell viability when cells were exposed to UV irradiation. In summary, these results suggest that the aquatic birnavirus may utilize a notable strategy via VP5 to regulate the host apoptosis-off system for enhancing progeny production
Influence of Calcium on the Early Steps of Rotavirus Infection

AbstractThe structure of rotaviruses and many steps of their replication cycle depend on the concentration of calcium in the microenvironment. In this work, to learn about the role of calcium during the early steps of the infection, we characterized the effect of increasing the calcium concentration in the medium on the infectivity of rotaviruses. We found that a fivefold increase in the calcium concentration of the cell culture medium results in an increased viral titer in all rotavirus strains tested. The effect of this divalent ion seems to be mainly on the viral particle and not on the surface of the cell. Analysis of the intrinsic fluorescence spectra of purified triple-layered particles revealed that changes in the environment of tryptophan residues occurred as calcium concentration increased, suggesting that conformational changes in the viral particle might be responsible for the effect of this ion on the viral infectivity
Characterization of Complex B Cell Epitopes on Woodchuck Hepatitis Virus Surface Antigens by Using Plasmids Encoding Chimeric Proteins and DNA Immunization

AbstractThe conformational nature of the B cell epitopes on the hepadnavirus surface antigens makes its characterization difficult. Here, a new approach by DNA vaccination with plasmids expressing chimeric hepadnavirus surface antigens was explored to determine B cell epitopes on the surface antigens of woodchuck hepatitis virus (WHsAg). A series of chimeric genes consisting of complementary fragments of WHsAg and hepatitis B virus surface antigens (HBsAg) was constructed. These plasmids expressed the following: (i) middle chimeric surface antigens (MCSAgs), including pre-S2 region and small surface antigens; (ii) small chimeric surface antigens (CSAgs); (iii) a mutated WHsAg with two amino acid substitutions, the Leu 136 to Thr and Ala 140 to Asp, within the central immunogenic region. The mutated region from amino acid 135 to 143 within WHsAg mimics the second loop of the HBsAg a-determinant. MCSAgs and CSAgs were expressed in transiently transfected mammalian cells and were reactive to anti-HBsAg and anti-WHsAg, as shown by indirect immunofluorescence staining and ELISA. Vaccination with plasmids encoding MCSAgs induced strong antibody responses to the pre-S2 region. Anti-pre-S2 antibodies were directed to a linear, immunodominant region within the amino-terminal region of the pre-S2 region and were able to precipitate serum WHsAg. Vaccinations with the plasmids expressing the CSAgs led to the conclusion that an extended region aa 116–169 of WHsAg, analogous to the HBsAg a-determinant, was sufficient for the induction of anti-WHsAg antibodies. The mutated WHsAg with the second loop of the HBsAg a-determinant efficiently induced anti-WHsAg antibodies, but also a low titer of anti-HBsAg. Thus, multiple B cell epitopes of a linear and conformational nature are present on WHsAg. We presented an efficient and broadly applicable strategy for analysis of complex immunogenic determinants of natural or mutated viral antigens
A Single Glycosylation Site Within the Receptor-Binding Domain of the Avian Sarcoma/Leukosis Virus Glycoprotein Is Critical for Receptor Binding

AbstractRetroviral envelope proteins are heavily glycosylated. In some cases, glycosylation has been shown to be important for folding, protein stability, immune evasion, or receptor usage. The receptor-binding subunit (SU or gp85) of the envelope protein (EnvA) of the avian sarcoma/leukosis virus, subtype A (ASLV-A), contains 11 potential N-linked glycosylation sites (NXS/T). To address the importance of N-linked glycosylation for the function of EnvA, we prepared a series of EnvA proteins lacking one or more of these carbohydrate addition sites. Using site-directed mutagenesis, we mutated the S or T in each NXS/T glycosylation sequon to A. We also prepared EnvAs bearing selected double and triple mutations. We examined each mutant EnvA for its ability to be expressed at the cell surface, proteolytically processed into gp85 and gp37, incorporated into MLV pseudotyped virions, and to support infection of cells expressing the ASLV-A receptor, Tva. Eight single mutations were well tolerated, and, in general, EnvA was able to tolerate double mutations of these glycosylation sites. Triple mutations were more variable in their effects. Of the three glycosylation sites important for EnvA function, two are important for folding (EnvA production and processing were severely impaired). For the third, although EnvA processing was impaired, significant amounts of processed EnvA were expressed at the cell surface and incorporated into virions. Nonetheless, this mutant EnvA, EnvAΔNg10, was unable to support infection. Further examination of EnvAΔNg10 revealed that it was unable to bind Tva and was severely impaired for binding to a monoclonal antibody which inhibits receptor binding. This work has therefore identified a single N-linked glycosylation site in the SU domain of EnvA that is critical for binding between EnvA and its receptor, Tva
Respiratory Syncytial Virus with the Fusion Protein as Its only Viral Glycoprotein Is Less Dependent on Cellular Glycosaminoglycans for Attachment than Complete Virus

AbstractCell surface glycosaminoglycans (GAGs) are responsible for the majority of respiratory syncytial virus (RSV) attachment to cultured cells leading to infection. The viral glycoprotein G binds to GAGs and was thought to be the viral attachment protein, but more recently virus lacking the G protein was shown to be infectious in cell culture. We have compared the GAG dependence of a recombinant, green fluorescent protein-expressing virus containing the F protein as its only viral glycoprotein (rgRSV-F) to isogenic complete virus containing all three viral glycoproteins (rgRSV-SGF). Attachment and infection by each virus was found to be largely dependent on cell surface heparan sulfate (HS) based on the finding that both activities were inhibited by preincubation of virus with soluble HS, by removal of HS from target cells by enzymatic treatment or mutation, or by pretreatment of the target cells with basic fibroblast growth factor (bFGF), which binds HS. These results, coupled with the previous finding that SH is not involved in virion binding (S. Techaarpornkul, N. Barretto, and M. Peeples, 2001, J. Virol. 75, 6825–6834), suggest that, in the context of the virion, both the G and F proteins bind to HS. Interestingly, both rgRSV-F and rgRSV-SGF retained significant binding activity and infectivity despite these treatments, suggesting an alternate productive attachment and infection pathway. This property of GAG independence was particularly apparent for rgRSV-F virions, which retained nearly half of its attachment and infection activities in most of these experiments. Comparison of the attachment and infection activities of rgRSV-SGF and rgRSV-F virions with a Chinese hamster ovary cell line and a derivative thereof that is defective in GAG synthesis indicated that approximately 50% of rgRSV-SGF attachment is due to G protein–GAG binding, 25% to F protein–GAG binding, and 25% to an independent pathway. This alternative pathway presumably is mediated by the sole remaining viral surface protein, F, although the formal possibility exists that some other virion-associated protein is involved
Reassortment and Interspecies Transmission of North American H6N2 Influenza Viruses

AbstractH6N2 influenza viruses were isolated from California chickens in 2000 and 2001. Here we report the characterization of these H6N2 viruses, one of the few descriptions of non-H5, non-H7 subtype influenza viruses in this host. The H6N2 viruses were nonpathogenic in experimentally infected chickens and could be divided into three genotypes. All three genotypes of virus had similar surface glycoproteins and all contained an 18 amino acid deletion in the neuraminidase, a characteristic of other chicken influenza viruses. Differences were apparent, however, in the complement of replicative protein genes between the genotypes. The presence of multiple H6N2 genotypes suggests that independent transmission and/or reassortment events may have taken place between aquatic bird and chicken influenza viruses
All Four Sendai Virus C Proteins Bind Stat1, but only the Larger Forms also Induce Its Mono-ubiquitination and Degradation

AbstractSendai virus infection strongly induces interferon (IFN) production and has recently been shown to interdict the subsequent IFN signaling through the Jak/Stat pathway. This anti-IFN activity of SeV is due to its “C” proteins, a nested set of four proteins (C′, C, Y1, Y2) that carry out a nested set of functions in countering the innate immune response. We previously reported that all four C proteins interact with Stat1 to prevent IFN signaling through the Jak/Stat pathway. Nevertheless, only the longer C proteins reduced Stat1 levels and prevented IFN from inducing an antiviral (VSV) state, or apoptosis, in IFN-competent murine cells. Here, we investigate the mechanism by which the various C proteins differentially affect the host antiviral defenses. All four C proteins were found to physically associate with Stat1 during cell culture infections, and in vitro in the absence of other viral gene products (as evidenced by co-immunoprecipitation). In addition, the inability of a null mutant (CF170S) to bind Stat1 suggests that this interaction is physiologically relevant. We have also shown that the proteasomal inhibitor MG132 can prevent the C protein-induced dismantling of the antiviral (VSV) state in murine cells; thus, the turnover of Stat1 correlates with the C protein-mediated counteraction of the antiviral (VSV) state. The C protein-induced instability of Stat1 was accompanied by a clear increase in the level of mono-ubiquinated Stat1, an unexpected hallmark of protein degradation. Finally, we show that a rSeV with mutant C proteins but wild-type Y proteins (CΔ10–15, that does not counteract the endogenous antiviral (VSV) state of MEFs even though their C proteins bind Stat1 and prevent its activity) is also unable to decrease bulk Stat1 levels or to increase the level of ubiquinated Stat1
The Genome of Camelpox Virus

AbstractCamelpox virus (CMLV), a member of the Orthopoxvirus genus in the Poxviridae, is the etiologic agent of a disease of camels. Here we report the CMLV genomic sequence with analysis. The 205,719-bp CMLV genome contains 211 putative genes and consists of a central region bound by identical inverted terminal repeats of approximately 7 kb. A high degree of similarity in gene order, gene content, and amino acid composition in the region located between CMLV017 and CMLV184 (average 96% amino acid identity to vaccinia virus (VACV)) indicates a close structural and functional relationship between CMLV and other known orthopoxviruses (OPVs). Notably, CMLV contains a unique region of approximately 3 kb, which encodes three ORFs (CMLV185, CMLV186, CMLV187) absent in other OPVs. These ORFs are most similar to B22R homologues found in other chordopoxvirus genera. Among OPVs, CMLV is the most closely related to variola virus (VARV), sharing all genes involved in basic replicative functions and the majority of genes involved in other host-related functions. Differences between CMLV and VARV include deletion and disruption of a large number of genes. Twenty-seven CMLV ORFs are absent in VARV, including seven full-length homologues of NMDA-like receptor, phospholipase D, Schlafen, MT-4 virulence, kelch, VACV C8L, and cowpox (CPXV) B21R proteins. Thirty-eight CMLV ORFs, some of which are fragments of larger genes, differ in size from corresponding VARV ORFs by more than 10% (amino acids). Genome structure and phylogenetic analysis of DNA sequences for all ORFs indicate that CMLV is clearly distinct from VARV and VACV and, as it has been suggested for VARV, it may have originated from a CPXV virus-like ancestor
Comparison of Vaccine Strategies Using Recombinant env–gag–pol MVA with or without an Oligomeric Env Protein Boost in the SHIV Rhesus Macaque Model

AbstractRhesus macaques were immunized with a replication-deficient vaccinia virus (MVA) expressing human immunodeficiency virus type 1 89.6 envelope (env) and SIV gagpol (MVA/SHIV89.6) with or without a protein boost consisting of soluble 89.6 env (gp140). Immunization with MVA/SHIV89.6 alone elicited binding antibodies in all animals and neutralizing antibodies in 5 of 15 animals. Both types of antibodies were enhanced by protein boosting. In addition, CD8 cells exhibiting CM9 tetramer binding were detected in the subset of animals that were Mamu-A*01 positive. Animals were challenged intravenously with either SHIV-89.6 (Study 1) or the more pathogenic derivative SHIV-89.6P (Study 2). In Study 1, all control and vaccinated animals except one became infected. However, the levels of viremia were as follows: controls > rMVA alone > rMVA + protein. The differences were statistically significant between immunized and control groups but not between the two immunized groups. In Study 2, all animals became infected; however, the vaccinated group exhibited a 5-fold reduction in peak viremia and a 10-fold reduction in the postacute phase viremia in comparison to the controls. All of the controls required euthanasia by 10 months after challenge. A relationship between vaccine-induced antibody titers and reduction in virus burden was observed in both studies. Thus, immunization with MVA/SHIV89.6 alone or with a protein boost stimulated both arms of the immune system and resulted in significant control of viremia and delayed progression to disease after challenge with SHIV-89.6P
Differential Dependence of the Infectivity of HIV-1 Group O Isolates on the Cellular Protein Cyclophilin A

AbstractThe cellular protein Cyclophilin A (Cyp A) is packaged into human immunodeficiency virus type 1 (HIV-1) particles through a specific interaction with the capsid domain of the Gag polyprotein. Inhibition of Cyp A incorporation by mutagenesis or cyclosporin treatment severely affects infectivity of all HIV-1 M subtypes tested. In contrast, the closely related lentiviruses HIV-2 and simian immunodeficiency virus (SIV) do not package Cyp A and are not inhibited by cyclosporin. For the HIV-1 group O isolate MVP5180, it was found that Cyp A incorporation and Cyp A dependence of infectivity did not correlate. This virus incorporates Cyp A but is not sensitive to treatment with cyclosporin A. For a more detailed study concerning the relationship between Cyp A incorporation and Cyp A dependence, we have analyzed five group O isolates for their ability to incorporate Cyp A and their sensitivity to cyclosporin treatment. All group O viruses incorporated Cyp A in comparable amounts as the M-group HIV-1 strain NL4-3. Furthermore, Cyp A incorporation was inhibited by cyclosporin in all cases. However, while isolate MVP 5180 was confirmed to replicate independent of Cyp A, three of the other four isolates were sensitive to cyclosporin treatment. Sequence analysis of the Cyp A binding regions revealed that the proline-rich motif, which is responsible for Cyp A incorporation, was conserved in all four isolates, while some sequence variations were detected in other positions close to this region. These results suggest that Cyp A dependence of replication is influenced by regions outside the Cyp-binding loop and may aid in determination of Cyp A function in HIV-1 replication
Apoptosis Induced in an Early Step of African Swine Fever Virus Entry into Vero Cells Does Not Require Virus Replication

AbstractPermissive Vero cells develop apoptosis, as characterized by DNA fragmentation, caspases activation, cytosolic release of mitochondrial cytochrome c, and flow cytometric analysis of DNA content, upon infection with African swine fever virus (ASFV). To determine the step in virus replication that triggers apoptosis, we used UV-inactivated virus, inhibitors of protein and nucleic acid synthesis, and lysosomotropic drugs that block virus uncoating. ASFV-induced apoptosis was accompanied by caspase-3 activation, which was detected even in the presence of either cytosine arabinoside or cycloheximide, indicating that viral DNA replication and protein synthesis were not required to activate the apoptotic process. The activation of caspase-3 was released from chloroquine inhibition 2 h after virus absorption, while the infection with UV-inactivated ASFV did not induce the activation of the caspase cascade. We conclude that ASFV induces apoptosis in the infected cell by an intracellular pathway probably triggered during the process of virus uncoating
Characterization of Two Kinds of Subgenomic RNAs Produced by Citrus Leaf Blotch Virus

AbstractCitrus leaf blotch virus (CLBV) has a single-stranded, positive-sense, genomic RNA (gRNA) organized in three ORFs, which encode a polyprotein involved in replication (RP), a potential movement protein (MP), and coat protein (CP). Northern blot hybridization of total, virion, or double-stranded RNA with probes of different gRNA regions revealed that CLBV produces two 3′-coterminal and two 5′-coterminal subgenomic RNAs (sgRNAs). The 3′-coterminal sgRNAs contain the MP (3′MP sgRNA) and CP (3′CP sgRNA) genes and untranslated regions (UTRs) of 123 and 284 nt, respectively, at their 5′ end. These sgRNAs start with a hexanucleotide which is also present at the 5′ terminus of the gRNA. The 5′-coterminal sgRNAs have 6795 and 5798 nt, colinear with the gRNA, and contain ORF1 and most MP gene (5′RPMP sgRNA) and most ORF1 (5′RP sgRNA), respectively. Their 3′ termini map 35 and 40 nt upstream of the transcription initiation of the 3′CP and 3′MP sgRNAs, respectively, next to a potential promoter element. Our results suggest that, as in alphaviruses, CLBV internal genes are expressed via 3′-coterminal sgRNAs transcribed from the minus gRNA strand. The 5′-coterminal sgRNAs may result from early termination of the gRNA during the plus-strand synthesis
Bovine Papillomavirus Type 1 E6-Induced Sensitization to Apoptosis Is Distinct from Its Transforming Activity

AbstractThe bovine papillomavirus type 1 (BPV-1) E6 oncoprotein induces tumorigenic transformation of murine C127 cells and stimulates transcription when targeted to a promoter. We have previously shown that C127 cells expressing BPV-1 E6 exhibited increased tumor necrosis factor α (TNF)-mediated apoptosis. To understand the mechanisms by which BPV-1 E6 sensitizes cells to apoptosis and to investigate the relevance of E6-enhanced apoptosis to its other biological activities, we analyzed a BPV-1 E6 mutant (491, with four amino acids deleted at the C-terminus) for its ability to sensitize C127 cells to apoptosis. The result was then compared with the E6 mutant's ability to transform cells, to activate transcription, and to associate with known cellular binding proteins. Our data indicated that the transcriptional activation function of BPV-1 E6 correlated with sensitization of cells to TNF-mediated apoptosis. Moreover, functions required for BPV-1 E6-mediated sensitization of cells to apoptosis are distinct from those required for transformation. A potential role of paxillin in E6 sensitization of cells to apoptosis is implicated. These results thus indicate that sensitization of cells to TNF-induced apoptosis represents a novel function of BPV-1 E6
In Vivo Suppression of Precore mRNA Synthesis Is Associated with Mutations in the Hepatitis B Virus Core Promoter

AbstractWe have examined the in vivo effect of hepatitis B virus (HBV) core promoter mutations on the expression of precore mRNA and pregenomic RNA transcripts in the liver of 24 patients with chronic HBV infection, applying a novel transcript-specific RT-PCR assay. The double A1762T/G1764A mutation in the basic core promoter was detected in 11 cases. This mutation was in all cases associated with absence or low levels of precore mRNA transcripts without significantly affecting the levels of total core promoter-directed transcription in the liver of infected patients. Precore mRNA synthesis was suppressed by the A1762T/G1764A mutation regardless of the presence of the precore stop codon mutation G1896A, suggesting that in addition to downregulating an immunomodulatory protein this double basic core promoter mutation may also confer a replication advantage to the virus. Additional mutations detected in the core promoter may also contribute to the observed changes in precore mRNA levels. Our in vivo study shows therefore that the double A1762T/G1764A mutation is associated with the specific suppression of precore mRNA synthesis directed by the HBV core promoter
Analysis of the Genomic Sequence of a Human Metapneumovirus

AbstractWe recently described the isolation of a novel paramyxovirus from children with respiratory tract disease in The Netherlands. Based on biological properties and limited sequence information the virus was provisionally classified as the first nonavian member of the Metapneumovirus genus and named human metapneumovirus (hMPV). This report describes the analysis of the sequences of all hMPV open reading frames (ORFs) and intergenic sequences as well as partial sequences of the genomic termini. The overall percentage of amino acid sequence identity between APV and hMPV N, P, M, F, M2-1, M2-2, and L ORFs was 56 to 88%. Some nucleotide sequence identity was also found between the noncoding regions of the APV and hMPV genomes. Although no discernible amino acid sequence identity was found between two of the ORFs of hMPV and ORFs of other paramyxoviruses, the amino acid content, hydrophilicity profiles, and location of these ORFs in the viral genome suggest that they represent SH and G proteins. The high percentage of sequence identity between APV and hMPV, their similar genomic organization (3′-N-P-M-F-M2-SH-G-L-5′), and phylogenetic analyses provide evidence for the proposed classification of hMPV as the first mammalian metapneumovirus