Characterization of the RNA-binding domain in the Dendrolimus punctatus cytoplasmic polyhedrosis virus nonstructural protein p44

Dendrolimus punctatus cytoplasmic polyhedrosis virus (DpCPV-1) belongs to the Cypovirus genus in the Reoviridae family. The ORF of genome segment 8 (S8) of DpCPV-1 was cloned into vector pMAL-c2X and used to express a 44kDa protein (p44) in E. coli, which was detected by Western blotting. The gel mobility shift assays showed that p44 had ssRNA-binding activity. Competitive assay indicated that this protein only bind to ssRNA and could not interact with DNA and dsRNA. The binding of p44 to ssRNA is sequence non-specific. To identify the domain(s) important for RNA binding of the protein, a number of deletions were made. These truncated proteins were expressed in E. coli and purified. The affinity of each truncated protein towards ssRNA was then assayed by electrophoretic mobility shift assays and northwestern blot. The results indicated that glutamic acid-rich domain in the central region of p44 from residues 104 to 201 was the ssRNA-binding domain.     

Molecular characterization of segments 7-10 of Dendrolimus punctatus cytoplasmic polyhedrosis virus provides the complete genome

The nucleotide sequences of genomic segments S7-S10 from Dendrolimus punctatus cypovirus strain Hunan (DpCPV-Hn) have been determined. This provides the complete genome sequences of DpCPV-Hn. Each segment of S7-S10 possess a single segment each. Homology searches showed that the nucleotide sequences and the deduced amino acid sequences of DpCPV S7-10 had high level of identities with those of Bombyx mori cypovirus (BmCPV) S7-10, respectively. While the amino acid sequences of the proteins encoded by DpCPV S7 and S8 have low identities with those of the proteins encoded by type 14 Lymantria dispar cypovirus S7 and S8, respectively. DpCPV S7 encodes viral structural protein VP5, S8 and S9 encode viral non-structural proteins, and S10 encodes polyhedrin gene, according to the function of the genome segments of BmCPV. There are glutamic-acid-rich and proline-rich domains in the central region of DpCPV S8 encoded protein. A nuclear localization signal was found in the protein encoded by DpCPV S9. Phylogenetic analysis of RNA-dependent RNA polymerases from nine viruses of the family Reoviridae and polyhedrin from eight viruses of the genus Cypovirus indicate that DpCPV is a type 1 cypovirus, more closely related to BmCPV than to other cypovirus species. These results also support the classification of CPV groups based on the electrophoretic migration of genomic dsRNA.     

The complete nucleotide sequence of the type 5 <Emphasis Type="Italic">Helicoverpa armigera</Emphasis> cytoplasmic polyhedrosis virus genome

The S1–6, S8, and S9 segments of the type 5 Helicoverpa armigera cytoplasmic polyhedrosis virus (HaCPV-5, Chinese strain) were cloned and sequenced, completing the HaCPV-5 genome. We found that each HaCPV-5 segment exhibits the conserved terminal sequences AGUU and UUGC located at the 5′ and 3′ ends, respectively. We also analyzed the translation initiation codon of the HaCPV-5 genome and compared it with the available cypovirus sequences in GenBank. We postulated that the conserved purine at the −3 position in relation to the AUG codon is probably the most important nucleotide for efficient translation initiation in cypovirus. Although the nucleotide sequences of the HaCPV-5 segments S1–10 exhibit no significant similarity to other viruses, blast searches did reveal some similarities between predicted HaCPV-5 amino acid sequences and those of other viruses. GenBank accession numbers: EF634320–EF634325, DQ178179, DQ178180.     

Molecular characterization of the genome of duck enteritis virus

The genomic sequence of a strain of duck enteritis virus (DEV) was determined and analyzed in this study. The size of its genome is 158,091 bp in length and the genome is predicted to encode 78 putative proteins and resembles the members of the Alphaherpesvirinae in genomic organization and gene composition. The genome of the virus is composed of a unique long (UL) region, a unique short (US) region, a unique short internal repeat (IRS) region and a unique short terminal repeat (TRS) region. Its genomic arrangement pattern (UL-IRS-US-TRS) corresponds to D-type herpesvirus and is consistent with the members of Varicellovirus and Iltovirus genera. Sequence analysis reveals that the genome of the virus contains 67 genes having homologs in most members of the Alphaherpesvirinae. Out of these genes, one gene has a homolog in cercopithecine herpesvirus 8 which is a virus of Betaherpesvirinae, and 5 genes have homologs in avian herpesviruses. Furthermore, the genome possesses three unique genes without homologs in any other herpesviruses. Like most members of the Alphaherpesvirinae, the genes in the UL region of its genome are well conserved, whereas the gene arrangement of IRS-US is similar to that of Marek's disease virus and equine herpesviruses 1. Therefore, our data based on the genomic analysis suggest that DEV represents an osculant taxonomic entity within the Alphaherpesvirinae.     

Complete nucleotide sequence of segment 5 of epizootic haemorrhagic disease virus; the outer capsid protein VP5 is homologous to the VP5 protein of bluetongue virus

The complete nucleotide sequence of a cDNA clone representing the segment 5 RNA of epizootic haemorrhagic disease virus (EHDV) United States serotype 1 was determined. The 5' and 3' termini of the RNA are complementary and are capable of forming secondary structures. The comparison of the predicted amino acid sequence of the encoded outer capsid protein (VP5) with the sequences of VP5 from four serotypes of bluetongue virus, the prototype orbivirus, revealed that the protein shares 59% to 62% homologies with various BTV serotypes, including a single conserved glycine residue at the amino terminus. The sequence has been submitted to the Genebank databox (X55782).     

Molecular characterization of genome segment 2 encoding RNA dependent RNA polymerase of Antheraea mylitta cytoplasmic polyhedrosis virus

Genome segment 2 (S2) from Antheraea mylitta cypovirus (AmCPV) was converted into cDNA, cloned and sequenced. S2 consisted of 3798 nucleotides with a long ORF encoding a 1116 amino acid long protein (123 kDa). BLAST and phylogenetic analysis showed 29% sequence identity and close relatedness of AmCPV S2 with RNA dependent RNA polymerase (RdRp) of other insect cypoviruses, suggesting a common origin of all insect cypoviruses. The ORF of S2 was expressed as 123 kDa soluble His-tagged fusion protein in insect cells via baculovirus recombinants which exhibited RdRp activity in an in vitro RNA polymerase assay without any intrinsic terminal transferase activity. Maximum activity was observed at 37 °C at pH 6.0 in the presence of 3 mM MgCl_2. Site directed mutagenesis confirmed the importance of the conserved GDD motif. This is the first report of functional characterization of a cypoviral RdRp which may lead to the development of anti-viral agents.     

Isolation and characterization of the Mason-Pfizer monkey virus p12 protein

The Mason-Pfizer monkey virus (M-PMV) Gag protein, precursor to the structural proteins of the infectious virion, assembles into immature capsid-like particles when expressed at high levels in bacterial cells. Similar capsid-like particles can be obtained by in vitro assembly using a high concentration of isolated Gag. M-PMV Gag contains a p12 protein that has no corresponding analogues in most other retroviruses and has been suggested to contain an internal scaffold domain (ISD). We have expressed and purified p12 and the N- and C-terminal halves (Np12 and Cp12) that are predicted to be structurally independent domains. The behavior of these proteins was analyzed using chemical cross-linking, CD spectroscopy, and electron microscopy. The N-terminal half of p12 is largely alpha-helical although the C-terminal portion lacks any apparent ordered structure. Both p12 and Np12 form high-order oligomers in vitro and when expressed in E. coli produce organized structures that are visible by electron microscopy. Interestingly, Cp12, as well as the whole protein, can form dimers in the presence of SDS. The data show that both domains of p12 contribute to its ability to multimerize with much of this potential residing in its N-terminal part, most probably within the leucine zipper-like (LZL) sequence.     

A 2a/1b full-length p7 inter-genotypic chimeric genome of hepatitis C virus is infectious in vitro

The p7 protein of hepatitis C virus (HCV) functions as an ion channel in planar lipid bilayers, and its function is vital for the virus life cycle. In this study, we replaced either the entire or partial p7 of genotype 2a (strain JFH1), an HCV strain that replicates and produces virus progeny in vitro, with the corresponding regions of the p7 protein from genotype 1b (Australian isolate, HCV-A). Compared to wild type, the chimeric viruses reached their peak of infectivity with a delay but they produced a comparable titer to the wild type virus and the progeny viruses were able to infect naive permissive cells. Amantadine treatment of wild type and chimeric viruses reduced the virus titers by about 50% and 45%, respectively. Therefore, in this study, for the first time, we demonstrated that genotype 2a (JFH1 strain) genome encoding a full-length genotype 1b p7 gene produces infectious particles in vitro. These chimeric viruses are valuable instruments for comparative studies of the p7 proteins.     

Rapid genome sequencing and characterization of novel avian-origin influenza A H7N9 virus directly from clinical sample by semiconductor sequencing

BackgroundRecent outbreaks of severe pneumonia or acute respiratory distress syndrome have attracted much public interest. Rapid and accurate diagnosis of the causative agent is key for an adequate response to suspected outbreaks.ObjectivesWe report a case that highlights the potential of semiconductor sequencing to rapidly determine the novel virus genome sequences.Study designWe have developed a method for rapid de novo assembly of the novel influenza A H7N9 virus genome directly from the tracheal aspirate of a patient using semiconductor sequencer without culture and prior sequence information. Further, characteristic amino acids were analyzed and phylogenetic analysis were done for key genes of the influenza A virus.ResultsDeep sequencing yielded 435,239 reads assigned to H7N9 viruses, with an average length of 172 bp, accounting for 18.6% of total reads (2,339,680). Complete genome of the virus was obtained by de novo assembly method within 2 days. Genomic average depth of coverage of the Ion Torrent PGM was up to 5679 fold. Selected characteristic amino acids were observed, and phylogenetic analyses showed that the novel H7 virus was genetically close to 2011 duck H7N3 viruses in Zhejiang. The novel N9 sequences were most closely related to gene sequences of N9 derived from ducks H11N9 in 2011 in Jiangxi and H2N9 sequences from Hong Kong in 2010, in China, and therefore they may share a common ancestor.ConclusionsThe sequence-independent semiconductor sequencing is a powerful tool to investigate outbreak of a novel pathogen.     

A novel surface molecule homologous to the p58/p50 family of receptors is selectively expressed on a subset of human natural killer cells and induces both triggering of cell functions and proliferation

Human natural killer (NK) cells express inhibitory (p58) or activatory (p50) receptors for HLA-C alleles. Here, we describe a novel member of the p58/p50 family that is expressed by a subset of NK cells in about one third of donors. This molecule, termed p50.3, mediates NK cell triggering as revealed by the induction of intracellular free calcium mobilization, cytokine release and cytotoxicity. In addition, anti-p50.3 monoclonal antibody (mAb) induced a selective, strong proliferation of p50.3⁺ NK cells in peripheral blood lymphocytes. Although p50.3 molecules do not appear to display an obvious HLA class I specificity, they are usually coexpressed with known inhibitory receptors for HLA class I alleles. mAb-mediated cross-linking of these receptors leads to inhibition of the anti-p50.3 mAb-induced NK cell activation and proliferation. Surface p50.3 molecules are glycoproteins of ∼ 55–58 kDa which, upon deglycosylation, display a relative molecular mass of 36 kDa, similar to that of deglycosylated (activatory) p50 receptors. Analysis of the two-dimensional peptide maps of the 50.3 molecules revealed a high homology with the other HLA-C-specific p58/p50 receptors. The use of a set of oligodeoxynucleotide primers, previously shown to amplify the activatory (p50) forms of HLA-C-specific receptors, consistently amplified in p50.3⁺ clones a cDNA sequence termed KKA3. This sequence belongs to the p58/p50 multigene family, that encodes for a transmembrane protein specifically stained by anti-p50.3 mAb in cell transfectants. Similar to p50 molecules, the KKA3-encoded molecules are characterized by two extracellular immunoglobulin-like domains, by the presence of a lysine in the transmembrane region and a short (39 amino acids) cytoplasmic tail which does not contain immune receptor tyrosine-based activation motifs (ITAM)-like sequences.     

Molecular characterization of the genes coding for glycoprotein and L protein of lymphocytic choriomeningitis virus strain MX

Lymphocytic choriomeningitis virus (LCMV) is the prototype Arenavirus with ambisense coding strategy. We have previously described a new MX strain LCMV and determined the primary structure of the genes coding for the nucleoprotein and RING finger Z protein. In this report, we describe amplification and sequencing of the entire coding sequences of additional MX genes, the glycoprotein precursor (GPC) and L protein. The obtained MX GPC cDNA sequence was 1,615 nucleotides long and contained an ORF, which encodes the GPC precursor of 498 amino acids. MX L polymerase cDNA sequence was 6,668 nucleotides long and predicted ORF encodes the L polymerase of 2,209 amino acids. Nucleotide and deduced amino acid sequences were compared with the known GPC and L sequences and the comparison revealed that both genes shared the highest amino acid identity with Armstrong strain. Phylogenetic analysis confirmed that MX represents a separate LCMV strain. The GPC and L genes products contained several characteristic conserved regions. On the other hand, we have observed numerous differences in predicted protein sequences, which distinguish MX LCMV from other LCMV strains and might be of potential biological significance.     

Expression of Epstein-Barr virus BZLF1 immediate-early protein induces p53 degradation independent of MDM2, leading to repression of p53-mediated transcription

The Epstein-Barr virus (EBV) lytic program elicits ATM-dependent DNA damage response, resulting in phosphorylation of p53 at N-terminus, which prevents interaction with MDM2. Nevertheless, p53-downstream signaling is blocked. We found here that during the lytic infection p53 was actively degraded in a proteasome-dependent manner even with a reduced level of MDM2. BZLF1 protein enhanced the ubiquitination of p53 in SaOS-2 cells. The degradation of p53 was observed even in the presence of Nutlin-3, an inhibitor of p53-MDM2 interaction, and also in mouse embryo fibroblasts lacking mdm2 gene, indicating that the BZLF1 protein-induced degradation of p53 was independent of MDM2. Furthermore, Nutlin-3 increased the level of p53 in the latent phase of EBV infection but not in the lytic phase. Although p53 level is regulated by MDM2 in the latent phase, it might be mediated by the BZLF1 protein-associated E3 ubiquitin ligase in the lytic phase for efficient viral propagation.     

Association of Epstein-Barr virus infection with p53 protein accumulation but not bcl-2 protein in nasopharyngeal carcinoma

AIMS: The aim of this study was to investigate the association of Epstein-Barr virus (EBV) infection with status of p53 protein expression in nasopharyngeal carcinoma (NPC). The expression of EBV gene and gene product, p53 protein and bcl-2 protein in NPC was histopathologically studied. METHODS AND RESULTS: In-situ hybridization using oligonucleotide probe to EBV-encoded small RNAs (EBERs) and immunohistochemistry using monoclonal antibodies against EBV latent membrane protein 1 (LMP1), p53 protein and bcl-2 proteins were performed in 56 primary NPCs. EBERs were detected in 46 (82%) cases and LMP1 in 17 (30%) cases. While 30 of 32 (94%) cases in differentiated nonkeratinizing carcinoma (NKC, WHO type 2) and 16 of 17 (94%) cases in undifferentiated carcinoma (UC, WHO type 3) showed EBERs expression, neither five cases of keratinizing squamous cell carcinoma (KSCC, WHO type 1) nor two cases of adenocarcinoma showed EBERs. bcl-2 protein was detected in 50 (89%) cases, but its expression did not depend on expression of LMP1. p53 protein was detected in 31 (55%) cases, and there was a correlation between expression of EBERs and p53 protein (P < 0.05) but not between LMP1 and p53 protein. CONCLUSION: In this study, close association of NKC and UC but not KSCC with the latent infection with EBV was demonstrated. The induction of bcl-2 protein by LMP1, as shown in vitro, was not demonstrated. The association between overexpression of p53 protein and the presence of EBV suggests that some EBV-encoded protein, which may be different from LMP1, may play a role for nuclear accumulation of p53 protein.     

Sendai virus particle production: Basic requirements and role of the SYWST motif present in HN cytoplasmic tail

Sendai virus (SeV) HN protein is dispensable for virus particle production. HN incorporation into virions strictly depends on a cytoplasmic domain SYWST motif. HNAFYKD, with SYWST replaced with the analogous sequence of measles virus (MeV) H (AFYKD), is not incorporated in virus particles produced by LLCMK2 cells, although it is normally expressed at the plasma membrane. Unlike HNSYWST, HNAFYKD is not internalized to late endosomes, raising the possibility that HN internalization is required for uptake into virus particles. Various mosaic MeV-H containing increasing amounts of the SeV-HN all failed to be taken up in SeV virions. However, when co-expressed with HNAFYKD these MeV-H chimera induced HNAFYKD uptake into virions showing that internalization is not a prerequisite for HN uptake into particles. We propose that HN incorporation in virus particles requires first neutralization by HN of a putative inhibitor of infectious particle formation.     

Ⅲ期鼻咽癌p53蛋白表达与生物学行为及预后的关系及其与p53基因突变、潜伏膜蛋白-1表达的相关研究

目的：探讨Ⅲ期鼻咽分化型非角化性鳞癌中P53蛋白的表达与生物学行为及预后的关系,以及P53蛋白表达与P53基因突变和潜伏膜蛋白（LMP）－1蛋白表达的关系。方法：应用免疫组织化学EnVison法和聚合酶链反应－单链构象多态性分析（PCR－SSCP）检测58Ⅲ例鼻咽分化型非角化性鳞癌标本。结果：58份Ⅲ期鼻咽分化型非角化性鳞癌中,P53蛋白总阳性率为65．5％（3858）,生存期在5年以下的患者阳性率为82．1％（32／39）,5年以上患者31．6％（6／19）,两组间P53蛋白表达差异有显著性意义（P＜0．05）,P53蛋白表达在有预底侵袭组为74．4％（29／39）,无颅底侵袭组为47．4％（919）,两组间差异有显著性意义（P＜0．05）,PCR－SSCP检测15例P53蛋白阳性的病例,P53基因5－8外显子突变率为0（0／15）,LMP－1蛋白免疫组织化学总阳性率为72．4％（42／58）,与P53蛋白表达呈正相关关系（r=0.504)。结论：本组Ⅲ期鼻咽分化型非角化性鳞癌患者中P53蛋白表达与P53基因突变无相关关系。与LMP－1蛋白的表达相关,P53蛋白的表达阳性率随着患者生存期的延长而降低,有颅底侵袭组P53蛋白表达阳性率高于无颅底侵袭组。     

Genetic and functional heterogeneity of the hepatitis C virus p7 ion channel during natural chronic infection

The present study describes natural genetic heterogeneity of hepatitis C virus (HCV) p7 protein, the ion channel that plays a critical role in assembly and release of HCV, within 299 variants isolated from serum specimens of 27 chronically infected patients, 12 of whom with human immunodeficiency virus (HIV) co-infection. Liver fibrosis stage was inversely correlated with p7 synonymous substitutions (dS) (p = 0.033), and indices of p7 genetic diversity were significantly higher in HIV-negative subjects compared to HIV-positive subjects (dS, p = 0.005; non-synonymous substitutions (dN), p = 0.002; dN/dS ratio, p = 0.024; amino acid distances, p = 0.007). Six p7 genes with naturally occurring unique amino acid variations were selected for in vitro study. The variants demonstrated diversified functional heterogeneity in vitro, with one variant from a subject with severe liver disease displaying hyperactive ion channel function, as well as other variants presenting altered pH-activated channel gating activities.     

Downregulation of human immunodeficiency virus type 1 Gag expression by a gp41 cytoplasmic domain fusion protein

The cytoplasmic domain of human immunodeficiency virus type 1 (HIV-1) envelope (Env) transmembrane protein gp41 interacts with the viral matrix MA protein, which facilitates incorporation of the trimeric Env complex into the virus. It is thus feasible to design an anti-HIV strategy targeting this interaction. We herein describe that Gag expression can be downregulated by a cytoplasmic domain fusion protein of the Env transmembrane protein, beta-galactosidase (beta-gal)/706-856, which contains the cytoplasmic tail of gp41 fused at the C terminus of Escherichia coli beta-gal. This mediator depleted intracellular Gag molecules in a dose-dependent manner. Sucrose gradient ultracentrifugation and confocal microscopy revealed that Gag and beta-gal/706-856 had stable interactions and formed aggregated complexes in perinuclear, intracellular sites. Pulse-chase and cycloheximide chase analyses demonstrated that this mediator enhanced unmyristylated Gag degradation. The results demonstrate a novel mode of HIV-1 Gag downregulation by directing Gag to an intracellular site via the interaction of Gag with a gp41 cytoplasmic domain fusion protein.